From f11a698a026ead806c33b7676ee700b3c09c2176 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 21 Jun 2019 10:33:19 -0700
Subject: [PATCH 001/207] new directory test

---
 atomate/csld/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 atomate/csld/__init__.py

diff --git a/atomate/csld/__init__.py b/atomate/csld/__init__.py
new file mode 100644
index 000000000..e69de29bb

From 0b1d39d4d315d6e05cea7ff1dd66e41955eb2b07 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 21 Jun 2019 10:40:18 -0700
Subject: [PATCH 002/207] new directory test

---
 atomate/csld/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/atomate/csld/__init__.py b/atomate/csld/__init__.py
index e69de29bb..ed0f110e2 100644
--- a/atomate/csld/__init__.py
+++ b/atomate/csld/__init__.py
@@ -0,0 +1 @@
+print('hello')
\ No newline at end of file

From 5027e10c6dbf9561266c0d372ac9a62c18fa346f Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 21 Jun 2019 10:46:09 -0700
Subject: [PATCH 003/207] new directory test

---
 atomate/csld/__init__.py            | 1 -
 atomate/vasp/workflows/base/csld.py | 0
 2 files changed, 1 deletion(-)
 delete mode 100644 atomate/csld/__init__.py
 create mode 100644 atomate/vasp/workflows/base/csld.py

diff --git a/atomate/csld/__init__.py b/atomate/csld/__init__.py
deleted file mode 100644
index ed0f110e2..000000000
--- a/atomate/csld/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-print('hello')
\ No newline at end of file
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
new file mode 100644
index 000000000..e69de29bb

From f60db1eaf41b6edc626e2acdbb8431b6c5b58869 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Mon, 24 Jun 2019 17:30:36 -0700
Subject: [PATCH 004/207] new directory test

---
 .../vasp/workflows/base/CSLD_sc_enumerator.py | 105 ++++++++++++++++++
 1 file changed, 105 insertions(+)
 create mode 100644 atomate/vasp/workflows/base/CSLD_sc_enumerator.py

diff --git a/atomate/vasp/workflows/base/CSLD_sc_enumerator.py b/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
new file mode 100644
index 000000000..5f9121050
--- /dev/null
+++ b/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
@@ -0,0 +1,105 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+
+import numpy as np
+
+"""
+This module defines a script that generates perturbed supercells from a supercell structure
+"""
+
+class CSLDPerturbedSupercellEnumerator:
+    """
+    Uses a supercell Structure, a transformation matrix, a min/max displacement,
+    number of displacement values, and number of supercells per displacement
+    to generate a list of randomly perturbed supercells from a given supercell.
+    """
+
+    def __init__(self, original_supercell,
+                 transformation_matrix,
+                 min_displacement,
+                 max_displacement,
+                 num_displacements,
+                 scs_per_displacement):
+
+        self.supercell = original_supercell
+        self.trans_mat = transformation_matrix
+        self.min_disp = min_displacement
+        self.max_disp = max_displacement
+        self.num_disps = num_displacements
+        self.scs_per_disp = scs_per_displacement
+        self.perturbed_supercells = []
+
+
+    def random_displacements(self, natom, rmax, rmin=None, dim=3):
+        #*** Adapted from csld.util.mathtool
+
+        # Generate matrix of size (natom, 3) where each row is a Gaussian random vector
+        # If 'rmax'=None, then all vectors will have magnitude 'rmin'.
+        # Else, magnitudes are uniformly distributed between 'rmin' and 'rmax'.
+
+        dx = np.random.normal(size=(natom, dim)) #Gaussian sampled displacements. Matrix size: (natom, 3)
+        dx_norms = np.linalg.norm(dx, axis=1)
+        veclen = np.full(natom, rmax) if rmax is None else np.random.uniform(rmin, rmax, natom)
+
+        if not 0 in dx_norms:
+            return dx * (veclen / dx_norms)[:, None]
+        else:
+            self.random_displacements(natom, rmax, rmin, dim)
+
+
+    def perturb_supercell(self, structure, disp):
+        # *** Adapted from CSLD's 'polaron_main' file
+
+        na = structure.num_sites
+        disp = float(disp)
+        if isinstance(disp, float):
+            # from csld.util.mathtool import random_displacements
+            dr = self.random_displacements(na, disp) #generate random displacements
+
+            # Perturb structure with the random displacements
+            for i in range(len(structure._sites)):
+                structure.translate_sites([i], dr[i], frac_coords=False, to_unit_cell=True)
+        else:
+            print('displacement entered is not a float.')
+
+
+    def generate_transformations(self):
+        for disp_val in range(self.num_disps):
+            for cell in range(self.scs_per_disp):
+                sc = self.original_supercell.copy()
+                self.perturb_supercell(sc, self.max_disp)
+                self.perturbed_supercells += [sc]
+
+
+####################################
+# BELOW IS FOR DEBUGGING PURPOSES #
+####################################
+def main():
+    print('test')
+    natom = 10
+    dim = 3
+    rmin = 0
+    rmax = 0.1
+    dx = np.random.normal(size=(natom, dim))  # Gaussian sampled displacements. Matrix size: (natom, 3)
+    print(dx.shape)
+    veclen = np.full(natom, rmin) if rmax is None else np.random.uniform(rmin, rmax, natom)  # vector of length natom
+    dx *= (veclen / np.linalg.norm(dx, axis=1))[:, None]
+    test = (veclen / np.linalg.norm(dx, axis=1))[:, None]
+    print(test.shape)
+
+    x = np.array([[1, 1, 1],
+                  [1, 1, 1],
+                  [1, 1, 1],
+                  [1, 1, 1]])
+    y = np.array([[1],
+                  [2],
+                  [3],
+                  [4]])
+    print(x*y)
+
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From ab7e06ca255ed0305500e7f6d119d29c790517cf Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 25 Jun 2019 13:25:12 -0700
Subject: [PATCH 005/207] Confirmed supercell volume compares with Pymatgen's
 volume Added functionality for constraining supercell to a min number of
 atoms on top of the X times NN distances.

---
 atomate/vasp/workflows/base/csld.py | 194 ++++++++++++++++++++++++++++
 1 file changed, 194 insertions(+)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index e69de29bb..b651e8f02 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -0,0 +1,194 @@
+#!/usr/bin/env python3
+
+import math
+
+import numpy as np
+
+from pymatgen.ext.matproj import MPRester
+from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
+from pymatgen.transformations.standard_transformations import SupercellTransformation
+
+"""
+This module defines the Compressed Sensing Lattice Dynamics (CSLD) workflow.
+"""
+
+def gen_scaling_matrix(structure=None, max_atoms=np.Inf, min_atoms=-np.Inf, length_cutoff=5):
+    """
+    Returns the transformation matrix of a Pymatgen structure into a suitable supercell for CSLD
+
+    Args:
+        structure (Structure): input structure.
+        max_atoms (int): maximum number of atoms allowed in the supercell
+        min_atoms (int): minimum number of atoms allowed in the supercell
+        length_cutoff (int): number of multiples of the unit cell nearest neighbor distance to
+            force all directions of the supercell to be at least as large
+
+    Returns:
+        Transformation matrix (numpy array)
+    """
+
+    if not structure:
+        print('No structure was passed into gen_scaling_matrix()')
+    else:
+
+        # -------- Store relevant structure data ----------
+        latVecs = structure.lattice.matrix #lattice vectors
+        bondLengths = get_max_bond_lengths(structure) #dictionary of bond lengths
+        bondMatrix = structure.distance_matrix #NxN matrix of bond distances (diagonal is 0)
+        print(bondMatrix)
+        print(structure.sites)
+        np.fill_diagonal(bondMatrix, np.Inf)
+        nnDist = np.amin(bondMatrix) #nearest neighbor bond length
+        print("nn Dist: " + str(nnDist))
+
+        # --------- Transform lattice vectors -------------
+        SCnotFound = True  # boolean indicator for whether a sufficiently large supercell has been created
+        hard_threshold = nnDist * length_cutoff
+        print("hard_threshold: " + str(hard_threshold))
+        target_threshold = hard_threshold  # target_threshold is used as the desired CUBE side lengths of
+                                            # the supercell (SC)
+        # note: if it is not possible to get a cubic SC, the real SC dimensions will be less
+        #      than the target
+        while SCnotFound:
+            print('---------------------------------------------------------')
+            print('target threshold: ' + str(target_threshold))
+            target_supercell = np.eye(3, 3) * target_threshold
+
+            T = np.linalg.inv(latVecs) @ target_supercell
+            # T = target_supercell @ np.linalg.inv(latVecs)
+            T = np.around(T)
+            print("proposed sc.txt:")
+            print(T)
+
+            print("\nSupercell dimensions:")
+            scBases = latVecs @ T
+            print(scBases)
+            print("Supercell volume:")
+            vol = np.cross(scBases[0],scBases[1]).T @ scBases[2]
+            print(vol)
+
+            # -------------------- Check how many nearest neighbors the supercell allows ---------------------------
+            def proj(b, a):
+                # Returns vector projection of b onto a
+                return (b.T @ (a / np.linalg.norm(a))) * (a / np.linalg.norm(a))
+
+            scBasesNorms = [np.linalg.norm(scBases[0]), np.linalg.norm(scBases[1]), np.linalg.norm(scBases[2])]
+            maxNorm = max(scBasesNorms)
+            maxIndex = scBasesNorms.index(maxNorm)
+            idx = list(range(3))
+            idx.remove(maxIndex)
+            a = scBases[maxIndex]
+            b = scBases[idx[0]]
+            c = scBases[idx[1]]
+            projb_a = proj(b, a)
+            projc_a = proj(c, a)
+
+            if np.linalg.norm(projb_a) > np.linalg.norm(projc_a):
+                length = np.linalg.norm(a - projb_a)
+            else:
+                length = np.linalg.norm(a - projc_a)
+            width = math.sqrt(np.linalg.norm(b) ** 2 - np.linalg.norm(projb_a) ** 2)
+            ab_normal = np.cross(a, b)  # get normal direction from AB plane
+            height = np.linalg.norm(proj(c, ab_normal))  # project c onto AB plane normal
+
+            cubeSide = min([length, width, height])
+            print('smallest dimension of proposed SC: ' + str(cubeSide))
+
+            superstructure = SupercellTransformation(T).apply_transformation(structure)
+            num_at = superstructure.num_sites
+            if cubeSide >= hard_threshold and num_at >= min_atoms and num_at <= max_atoms:
+                print(T)
+                print("FINISHED")
+                return T
+            else:
+                # Increase threshold until
+                target_threshold += 1
+
+
+def parallelipipedVol(a=[1, 0, 0], b=[0, 1, 0], c=[0, 0, 1]):
+    vol = np.cross(a,b).T @ c
+    return vol
+
+def main():
+    mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
+    structure = mpr.get_structure_by_material_id('mp-7814')
+    print('structure loaded')
+
+    T = gen_scaling_matrix(structure, length_cutoff=4, min_atoms=150)
+    #***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
+
+    print('~~~~~~~~~~~~~~~~~~~~~~~~~')
+    print("FINISHED2")
+    # print(T)
+
+    # Pymatgen version
+    superstructure = SupercellTransformation(T).apply_transformation(structure)
+    print(superstructure.lattice)
+    print(superstructure.volume)
+    print(parallelipipedVol(superstructure.lattice.matrix[0],
+                            superstructure.lattice.matrix[1],
+                            superstructure.lattice.matrix[2]))
+    print(superstructure.num_sites)
+    superstructure.to(fmt='poscar', filename='POSCAR-scTest')
+
+    # Find Primitive
+    # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    # sga = SpacegroupAnalyzer(superstructure)
+    # print(sga.find_primitive().lattice)
+
+    # # CSLD version
+    # # *** Can't call CSLD Structure member functions because structure scraped is a Pymatgen Structure ***
+    # from csld.structure import Structure as CSLDStructure
+    # from csld.lattice import Lattice as CSLDLattice
+    # from csld.coord_utils import supercell_latticepoints
+    #
+    # def generate_supercell(CSLDStructure, scaling_matrix, scref=None):
+    #     """
+    #     Create a supercell.
+    #
+    #     Args:
+    #         scaling_matrix: A scaling matrix for transforming the lattice
+    #             vectors. Has to be all integers. Several options are possible:
+    #
+    #             a. A full 3x3 scaling matrix defining the linear combination
+    #                the old lattice vectors. E.g., [[2,1,0],[0,3,0],[0,0,
+    #                1]] generates a new structure with lattice vectors a' =
+    #                2a + b, b' = 3b, c' = c where a, b, and c are the lattice
+    #                vectors of the original structure.
+    #             b. An sequence of three scaling factors. E.g., [2, 1, 1]
+    #                specifies that the supercell should have dimensions 2a x b x
+    #                c.
+    #             c. A number, which simply scales all lattice vectors by the
+    #                same factor.
+    #     """
+    #     scmat = np.array(scaling_matrix, np.int16)
+    #     if scmat.shape != (3, 3):
+    #         scmat= np.array(scmat* np.eye(3), np.int16)
+    #     n_cell=int(round(np.linalg.det(scmat)))
+    #     old_lattice = CSLDStructure._lattice
+    #     new_lattice = CSLDLattice(np.dot(scmat, old_lattice.matrix))
+    #     tvects = supercell_latticepoints(scmat)
+    #     inv=np.linalg.inv(scmat)
+    #     if scref is None:
+    #         sc_ref= supercell_latticepoints(scmat)
+    #     else:
+    #         sc_ref= scref
+    #     return CSLDStructure(CSLDLattice(np.dot(scmat, CSLDStructure._lattice.matrix)),
+    #        [s.species_and_occu for s in CSLDStructure for _ in range(n_cell)],
+    #        (CSLDStructure.frac_coords[:,None,:]+sc_ref[None,:,:]).reshape((-1,3)).dot(inv),
+    #        coords_are_cartesian=False, to_unit_cell=True,
+    #        site_properties_T=[s.properties for s in CSLDStructure for _ in range(n_cell)],
+    #        intensive_properties=CSLDStructure.intensive_properties,extensive_properties=
+    #                        {k:v*CSLDStructure.n_cell for k,v in CSLDStructure.extensive_properties.items()})
+    #
+    # # csld_structure = csld.structure.Structure(structure.lattice, structure.species, structure.lattice.get_fractional_coords())
+    # csld_supercell = SupercellStructure.from_scmat(csld_structure, T)
+    # print("here:")
+    # print(csld_supercell)
+
+if __name__ == '__main__':
+    main()
+
+
+
+

From 278b535329a6aa7e80c61432fe043e995c8cc83f Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 25 Jun 2019 14:49:39 -0700
Subject: [PATCH 006/207] Added handling for transformation matrices with zero
 columns/rows (i.e. materials with extremely high/low angles)

---
 atomate/vasp/workflows/base/csld.py | 81 ++++++++++++++++++++++++-----
 1 file changed, 69 insertions(+), 12 deletions(-)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index b651e8f02..1c2d26a09 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -7,11 +7,19 @@
 from pymatgen.ext.matproj import MPRester
 from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
 from pymatgen.transformations.standard_transformations import SupercellTransformation
+from csld.structure import SupercellStructure
 
 """
 This module defines the Compressed Sensing Lattice Dynamics (CSLD) workflow.
+
+V3 added rounding of entries away from 0 if there are zero rows or columns in the transformation matrix.
 """
 
+
+def round_away_from_zero(x):
+    aX = abs(x)
+    return math.ceil(aX)*(aX/x) if x is not 0 else 0
+
 def gen_scaling_matrix(structure=None, max_atoms=np.Inf, min_atoms=-np.Inf, length_cutoff=5):
     """
     Returns the transformation matrix of a Pymatgen structure into a suitable supercell for CSLD
@@ -35,8 +43,8 @@ def gen_scaling_matrix(structure=None, max_atoms=np.Inf, min_atoms=-np.Inf, leng
         latVecs = structure.lattice.matrix #lattice vectors
         bondLengths = get_max_bond_lengths(structure) #dictionary of bond lengths
         bondMatrix = structure.distance_matrix #NxN matrix of bond distances (diagonal is 0)
-        print(bondMatrix)
-        print(structure.sites)
+        # print(bondMatrix)
+        # print(structure.sites)
         np.fill_diagonal(bondMatrix, np.Inf)
         nnDist = np.amin(bondMatrix) #nearest neighbor bond length
         print("nn Dist: " + str(nnDist))
@@ -56,7 +64,37 @@ def gen_scaling_matrix(structure=None, max_atoms=np.Inf, min_atoms=-np.Inf, leng
 
             T = np.linalg.inv(latVecs) @ target_supercell
             # T = target_supercell @ np.linalg.inv(latVecs)
-            T = np.around(T)
+            print('T before rounding:')
+            print(T)
+            print('T after rounding:')
+            T_rounded = np.around(T)
+            print(T_rounded)
+
+
+            # Zero columns or rows make T singular, so make them non-singular
+            if (~T_rounded.any(axis=1)).any(): #Check for zero rows
+                zero_row_idxs = np.where(~T_rounded.any(axis=1))[0]
+                for zero_row_idx in zero_row_idxs:
+                    # print(zero_row_idx)
+                    zero_row = T[zero_row_idx, :]
+                    # print('zero row:' + str(zero_row))
+                    col_idx_to_fix = np.where(np.absolute(zero_row) == np.amax(np.absolute(zero_row)))[0]
+                    # print('amax:')
+                    # print(np.amax(np.absolute(zero_row)))
+                    # print('col idx to fix:')
+                    # print(col_idx_to_fix)
+                    for j in col_idx_to_fix:
+                        T_rounded[zero_row_idx, j] = round_away_from_zero(T[zero_row_idx, j])
+            if (~T_rounded.any(axis=1)).any(): #Check for zero columns
+                zero_col_idxs = np.where(~T_rounded.any(axis=1))[0]
+                for zero_col_idx in zero_col_idxs:
+                    zero_col = T[:, zero_col_idx]
+                    row_idx_to_fix = np.where(np.absolute(zero_col) == np.amax(np.absolute(zero_col)))[0]
+                    for i in row_idx_to_fix:
+                        T_rounded[i, zero_col_idx] = round_away_from_zero(T[i, zero_col_idx])
+
+
+            T = T_rounded
             print("proposed sc.txt:")
             print(T)
 
@@ -109,12 +147,27 @@ def parallelipipedVol(a=[1, 0, 0], b=[0, 1, 0], c=[0, 0, 1]):
     vol = np.cross(a,b).T @ c
     return vol
 
+
 def main():
     mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
-    structure = mpr.get_structure_by_material_id('mp-7814')
+    # structure = mpr.get_structure_by_material_id('mp-7814') #passed
+    structure = mpr.get_structure_by_material_id('mp-1101039') #passed
+    # structure = mpr.get_structure_by_material_id('mp-20012')
+
     print('structure loaded')
+    print(structure.num_sites)
+    # print('structure')
+    # print(structure)
+    # structure.to(fmt='poscar', filename='POSCAR-tlbise2-scraped')
+
+    # # Find Primitive
+    # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    # sga = SpacegroupAnalyzer(structure)
+    # # print(sga.find_primitive().lattice)
+    # sga.find_primitive().to(fmt='poscar', filename='POSCAR-tlbise2-scraped-prim')
+
 
-    T = gen_scaling_matrix(structure, length_cutoff=4, min_atoms=150)
+    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150)
     #***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
 
     print('~~~~~~~~~~~~~~~~~~~~~~~~~')
@@ -124,17 +177,21 @@ def main():
     # Pymatgen version
     superstructure = SupercellTransformation(T).apply_transformation(structure)
     print(superstructure.lattice)
-    print(superstructure.volume)
-    print(parallelipipedVol(superstructure.lattice.matrix[0],
-                            superstructure.lattice.matrix[1],
-                            superstructure.lattice.matrix[2]))
+    # print(superstructure.volume)
+    # print(parallelipipedVol(superstructure.lattice.matrix[0],
+    #                         superstructure.lattice.matrix[1],
+    #                         superstructure.lattice.matrix[2]))
     print(superstructure.num_sites)
-    superstructure.to(fmt='poscar', filename='POSCAR-scTest')
 
-    # Find Primitive
+    # # Find Primitive
     # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
     # sga = SpacegroupAnalyzer(superstructure)
-    # print(sga.find_primitive().lattice)
+    # # print(sga.find_primitive().lattice)
+    # sga.find_primitive().to(fmt='poscar', filename='POSCAR-scTest-prim')
+
+    superstructure.to(fmt='poscar', filename='POSCAR-scTest')
+
+
 
     # # CSLD version
     # # *** Can't call CSLD Structure member functions because structure scraped is a Pymatgen Structure ***

From 678b2b690c9947bc55b38bf6f4fbff7c7304ff4c Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 25 Jun 2019 15:04:06 -0700
Subject: [PATCH 007/207] Handling for max_atoms

---
 atomate/vasp/workflows/base/csld.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 1c2d26a09..f440a9212 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -7,7 +7,6 @@
 from pymatgen.ext.matproj import MPRester
 from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
 from pymatgen.transformations.standard_transformations import SupercellTransformation
-from csld.structure import SupercellStructure
 
 """
 This module defines the Compressed Sensing Lattice Dynamics (CSLD) workflow.
@@ -132,8 +131,10 @@ def proj(b, a):
             cubeSide = min([length, width, height])
             print('smallest dimension of proposed SC: ' + str(cubeSide))
 
+            # Get number of atoms
             superstructure = SupercellTransformation(T).apply_transformation(structure)
             num_at = superstructure.num_sites
+
             if cubeSide >= hard_threshold and num_at >= min_atoms and num_at <= max_atoms:
                 print(T)
                 print("FINISHED")
@@ -141,6 +142,11 @@ def proj(b, a):
             else:
                 # Increase threshold until
                 target_threshold += 1
+                if num_at > max_atoms:
+                    raise AttributeError('While trying to solve for the supercell, the max'
+                                         'number of atoms was exceeded. Try lowering the number'
+                                         'of nearest neighbor distances.')
+                    return
 
 
 def parallelipipedVol(a=[1, 0, 0], b=[0, 1, 0], c=[0, 0, 1]):
@@ -167,7 +173,7 @@ def main():
     # sga.find_primitive().to(fmt='poscar', filename='POSCAR-tlbise2-scraped-prim')
 
 
-    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150)
+    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150, max_atoms=1)
     #***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
 
     print('~~~~~~~~~~~~~~~~~~~~~~~~~')

From 01b1dbfd63c6789834515be469dc3ff9fe4cf7e8 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 25 Jun 2019 16:32:00 -0700
Subject: [PATCH 008/207] IO for ShengBTE CONTROL file V1 (needs testing)

---
 atomate/vasp/workflows/base/sbte_IO.py | 100 +++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 atomate/vasp/workflows/base/sbte_IO.py

diff --git a/atomate/vasp/workflows/base/sbte_IO.py b/atomate/vasp/workflows/base/sbte_IO.py
new file mode 100644
index 000000000..9a4d505bd
--- /dev/null
+++ b/atomate/vasp/workflows/base/sbte_IO.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python3
+
+import f90nml
+"""
+This module defines IO ShengBTE for making CONTROL file (i.e. a class that can read/write the ‘control’ file, f90ml)
+
+TO-DO: Test this thing
+"""
+
+class ShengBTE_CONTROL_IO:
+
+    """
+
+        Args:
+            nelements (int): number of elements in the material
+            natoms (int): number of atoms in the cell
+            ngrid (3 length list of ints): q-point mesh
+            ***norientations (int):
+            ***lfactor (float):
+            lattvec1 (3 length list of floats): first lattice vector
+            lattvec2 (3 length list of floats): second lattice vector
+            lattvec3 (3 length list of floats): third lattice vector
+            elements (comma-separated list of strings): list of elements present
+            types (natoms length list of ints): atom types listed in the same order as in 'elements' (first atom should be '1')
+            positions (natoms x 3 matrix): atomic positions of each atom
+            scell (3 length list of ints): dimensions of supercell input
+            ***temperature (int): temperature in Kelvin?
+            scalebroad (float): Gaussian broadening of allowable energies that can scatter a phonon to a certain state
+                (higher broadening = more scattering allowed. Too high is unphysical. For complex
+                materials, make 'scalebroad' smaller since there will be more scattering candidates
+                for any given phonon.
+            ***onlyharmonic (bool): Whether to only consider harmonic scattering (2-phonon?)
+            ***isotopes (bool): Whether to consider scattering from isotopic disorder.
+            ***nonanalytic (bool): Used for Born effective charge and dielectric constant.
+            nanowires (bool): Whether the structure input is a nanowire.
+
+        Returns:
+            IO reader/writer for ShengBTE's CONTROL file, composed of FORTRAN namelists
+    """
+
+    def __init__(self, nelements=None, natoms=None, elements=None, types=None, positions=None, ngrid=[25, 25, 25],
+                 lfactor=0.1, lattvec1=[1, 0, 0], lattvec2=[0, 1, 0], lattvec3=[0, 0, 1], scell=[5, 5, 5],
+                 temperature=500,  scalebroad=0.5, onlyharmonic=False, isotopes=False, nonanalytic=True,
+                 nanowires=False, norientations=0):
+
+        self.nelements = nelements
+        self.natoms = natoms
+        self.ngrid = ngrid
+        self.norientations = norientations
+        self.lfactor = lfactor
+        self.lattvec1 = lattvec1
+        self.lattvec2 = lattvec2
+        self.lattvec3 = lattvec3
+        self.elements = elements
+        self.types = types
+        self.positions = positions
+        self.scell = scell
+        self.temperature = temperature
+        self.scalebroad = scalebroad
+        self.onlyharmonic = onlyharmonic
+        self.isotopes = isotopes
+        self.nonanalytic = nonanalytic
+        self.nanowires = nanowires
+
+
+    def read_CONTROL(self, filename):
+        nml = f90nml.read(filename)
+        return nml
+
+    def write_CONTROL(self):
+        with open('CONTROL.nml', 'w') as control_file:
+            nml = {'allocations':
+                       {'nelements': self.nelements,
+                        'natoms': self.natoms,
+                        'ngrid': self.ngrid,
+                        'norientations': self.norientations},
+                   'crystal':
+                       {'lfactor': self.lfactor,
+                        'lattvec(:,1)': self.lattvec1,
+                        'lattvec(:,2)': self.lattvec2,
+                        'lattvec(:,3)': self.lattvec3,
+                        'elements': self.elements,
+                        'types': self.types,
+                        'scell': self.scell},
+                   'parameters':
+                       {'T': self.temperature,
+                        'scalebroad': self.scalebroad},
+                   'flags':
+                       {'onlyharmonic': self.onlyharmonic,
+                        'isotopes': self.isotopes,
+                        'nonanalytic': self.nonanalytic,
+                        'nanowires': self.nanowires}}
+
+            #add positions to the dict
+            num_atoms, _ = self.positions.shape
+            for at in range(num_atoms):
+                at_position = 'positions(:,' + str(at+1) + ')'
+                nml['crystal'][at_position] = self.positions[at, :]
+
+            f90nml.write(nml, control_file, force=True) #force=True overwrites an existing file

From 38ce381c769b5023fc4a654ed885865884784667 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 25 Jun 2019 17:12:02 -0700
Subject: [PATCH 009/207] V1, needs testing with csld_main

---
 .../workflows/base/scrape_forces_from_DB.py   | 85 +++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 atomate/vasp/workflows/base/scrape_forces_from_DB.py

diff --git a/atomate/vasp/workflows/base/scrape_forces_from_DB.py b/atomate/vasp/workflows/base/scrape_forces_from_DB.py
new file mode 100644
index 000000000..90178a709
--- /dev/null
+++ b/atomate/vasp/workflows/base/scrape_forces_from_DB.py
@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+
+
+import numpy as np
+from pymongo import MongoClient
+
+
+# MongoDB database settings/details
+host = "brmyvxghlvvkgkx-mongodb.services.clever-cloud.com"
+port = 27017
+database_name = "brmyvxghlvvkgkx"
+username = "usxrmfzwh9ed1plwi027"
+password = "JJGXekEfnNYtXQSBYHv8"
+
+# Connect to the database
+db = MongoClient(host, port)[database_name]
+db.authenticate(username, password)
+tasks = db.tasks #connects to the 'tasks' collection
+
+"""
+This module defines IO ShengBTE for making CONTROL file (i.e. a class that can read/write the ‘control’ file, f90ml)
+
+TO-DO: Test this thing with csld_main
+"""
+
+def scrape_forces_to_txt(task_id):
+    # Input a Firetask task_id (int)
+    # Output a .txt with all the atomic forces
+
+    forces_list = tasks.find_one({'task_id': task_id})['calcs_reversed'][0]['output']['ionic_steps'][0]['forces']
+    # print(forces_list)
+    # print(len(forces_list))
+
+    num_atoms = len(forces_list)
+    forces = np.empty((num_atoms,3))
+    for atom in range(num_atoms):
+        forces[atom,:] = forces_list[atom][:]
+    # print(forces)
+    np.savetxt('forces.txt', forces, fmt='%.6f')
+
+
+def main():
+    scrape_forces_to_txt(2)
+
+
+if __name__ == '__main__':
+    main()
+
+# def get_structure_from_task_id(task_id):
+#     # Input a Firetask task_id (int)
+#     # Return the corresponding Pymatgen structure (Structure)
+#     try:
+#         return Structure.from_dict(tasks.find_one({"task_id": task_id})["input"]["structure"])
+#     except:
+#         print("No structure with task id '{}' was found.".format(task_id))
+#
+#
+#
+# def get_structures_from_formulaV2(formula, task_label=None):
+#     # Required:
+#     #   Input a Pymatgen 'pretty formula' (String)
+#     # Optional:
+#     #   Input a 'task_label' or substring of a 'task_label' (String)
+#     # Return the corresponding Pymatgen Structures (list)
+#
+#     structs = []
+#     try:
+#         query = {"formula_pretty": formula}
+#         if task_label is not None and isinstance(task_label, str):
+#             # query["$and"] += [{"task_label": task_label}]
+#             query["task_label"] = {"$regex": task_label}
+#         dicts = list(tasks.find(query, ["input.structure"]))
+#
+#         # dicts = list(tasks.find({"$and": [{"formula_pretty": formula},
+#         #                                   {"task_label": task_label}]},
+#         #                                 ["input.structure"]))
+#         for dict in dicts:
+#             struct = Structure.from_dict(dict["input"]["structure"])
+#             structs += [struct]
+#         return structs
+#     except:
+#         if isinstance(formula, str):
+#             print("No structures with the formula '{}' found.".format(formula))
+#         else:
+#             print("Entered formula is not a string.")

From 74fb2b09fe5c32e7783e4d2e59a2f23f48cfcfbb Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 26 Jun 2019 11:54:05 -0700
Subject: [PATCH 010/207] Revised script and tested for reading, updating, and
 writing namelist files from a Python dict.

---
 atomate/vasp/workflows/base/sbte_IO.py | 91 ++++++++++++--------------
 1 file changed, 41 insertions(+), 50 deletions(-)

diff --git a/atomate/vasp/workflows/base/sbte_IO.py b/atomate/vasp/workflows/base/sbte_IO.py
index 9a4d505bd..a86b09246 100644
--- a/atomate/vasp/workflows/base/sbte_IO.py
+++ b/atomate/vasp/workflows/base/sbte_IO.py
@@ -38,63 +38,54 @@ class ShengBTE_CONTROL_IO:
             IO reader/writer for ShengBTE's CONTROL file, composed of FORTRAN namelists
     """
 
-    def __init__(self, nelements=None, natoms=None, elements=None, types=None, positions=None, ngrid=[25, 25, 25],
-                 lfactor=0.1, lattvec1=[1, 0, 0], lattvec2=[0, 1, 0], lattvec3=[0, 0, 1], scell=[5, 5, 5],
-                 temperature=500,  scalebroad=0.5, onlyharmonic=False, isotopes=False, nonanalytic=True,
-                 nanowires=False, norientations=0):
-
-        self.nelements = nelements
-        self.natoms = natoms
-        self.ngrid = ngrid
-        self.norientations = norientations
-        self.lfactor = lfactor
-        self.lattvec1 = lattvec1
-        self.lattvec2 = lattvec2
-        self.lattvec3 = lattvec3
-        self.elements = elements
-        self.types = types
-        self.positions = positions
-        self.scell = scell
-        self.temperature = temperature
-        self.scalebroad = scalebroad
-        self.onlyharmonic = onlyharmonic
-        self.isotopes = isotopes
-        self.nonanalytic = nonanalytic
-        self.nanowires = nanowires
-
-
     def read_CONTROL(self, filename):
         nml = f90nml.read(filename)
         return nml
 
-    def write_CONTROL(self):
-        with open('CONTROL.nml', 'w') as control_file:
+    def write_CONTROL_from_dict(self, dict, filename='CONTROL'):
+        with open(filename, 'w') as control_file:
             nml = {'allocations':
-                       {'nelements': self.nelements,
-                        'natoms': self.natoms,
-                        'ngrid': self.ngrid,
-                        'norientations': self.norientations},
+                       {'nelements': dict.get('allocations', None).get('nelements', None),
+                        'natoms': dict.get('allocations', None).get('natoms', None),
+                        'ngrid': dict.get('allocations', [25, 25, 25]).get('ngrid', [25, 25, 25]),
+                        'norientations': dict.get('allocations', 0).get('norientations', 0)},
                    'crystal':
-                       {'lfactor': self.lfactor,
-                        'lattvec(:,1)': self.lattvec1,
-                        'lattvec(:,2)': self.lattvec2,
-                        'lattvec(:,3)': self.lattvec3,
-                        'elements': self.elements,
-                        'types': self.types,
-                        'scell': self.scell},
+                       {'lfactor': dict.get('crystal', 0.1).get('lfactor', 0.1),
+                        # 'lattvec(:,1)': dict.get('crystal', None).get('lattvec(:,1)', None),
+                        # 'lattvec(:,2)': dict.get('crystal', None).get('lattvec(:,2)', None),
+                        # 'lattvec(:,3)': dict.get('crystal', None).get('lattvec(:,3)', None),
+                        'lattvec': dict.get('crystal', None).get('lattvec', None),
+                        'positions': dict.get('crystal', None).get('positions', None),
+                        'elements': dict.get('crystal', None).get('elements', None),
+                        'types': dict.get('crystal', None).get('types', None),
+                        'scell': dict.get('crystal', [5, 5, 5]).get('scell', [5, 5, 5])},
                    'parameters':
-                       {'T': self.temperature,
-                        'scalebroad': self.scalebroad},
+                       {'T': dict.get('parameters', 500).get('T', 500),
+                        'scalebroad': dict.get('parameters', 0.5).get('scalebroad', 0.5)},
                    'flags':
-                       {'onlyharmonic': self.onlyharmonic,
-                        'isotopes': self.isotopes,
-                        'nonanalytic': self.nonanalytic,
-                        'nanowires': self.nanowires}}
-
-            #add positions to the dict
-            num_atoms, _ = self.positions.shape
-            for at in range(num_atoms):
-                at_position = 'positions(:,' + str(at+1) + ')'
-                nml['crystal'][at_position] = self.positions[at, :]
+                       {'onlyharmonic': dict.get('flags', False).get('onlyharmonic', False),
+                        'isotopes': dict.get('flags', False).get('isotopes', False),
+                        'nonanalytic': dict.get('flags', True).get('nonanalytic', True),
+                        'nanowires': dict.get('flags', False).get('nanowires', False)}}
 
             f90nml.write(nml, control_file, force=True) #force=True overwrites an existing file
+
+
+def main():
+    # Read the CONTROL file into a Fortran namelist object
+    sbte_io = ShengBTE_CONTROL_IO()
+    namelist = sbte_io.read_CONTROL('CONTROL')
+    print(namelist)
+    print('---------------------')
+
+    # Convert the namelist object to a dict for easy access of contents
+    dict = namelist.todict()
+    print(dict)
+    print(dict['allocations']['nelements'])
+
+    # Write the dict back into a namelist file
+    sbte_io.write_CONTROL_from_dict(dict, filename='CONTROL_test')
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 9aaa03defae21b955a8297ba7a97ad53a0010230 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 26 Jun 2019 14:26:09 -0700
Subject: [PATCH 011/207] fixed some bugs and added a working test case in
 main(). Imports csld_sc_gen

---
 .../vasp/workflows/base/CSLD_sc_enumerator.py | 152 ++++++++++++------
 .../base/{csld.py => csld_sc_gen.py}          |   2 +-
 2 files changed, 108 insertions(+), 46 deletions(-)
 rename atomate/vasp/workflows/base/{csld.py => csld_sc_gen.py} (99%)

diff --git a/atomate/vasp/workflows/base/CSLD_sc_enumerator.py b/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
index 5f9121050..b37f9ad54 100644
--- a/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
+++ b/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-import os
-import sys
-
 import numpy as np
 
 """
@@ -14,25 +11,47 @@ class CSLDPerturbedSupercellEnumerator:
     Uses a supercell Structure, a transformation matrix, a min/max displacement,
     number of displacement values, and number of supercells per displacement
     to generate a list of randomly perturbed supercells from a given supercell.
+
+        Args:
+            original_supercell (Structure): supercell to displace, typically already relaxed
+            max_displacement_val (float): maximum displacement value for perturbing the supercell (in Angstroms)
+            min_displacement_val (float): minimum displacement value for perturbing the supercell (in Angstroms)
+            num_displacements (int): number of unique displacement values to try, bounded by
+                min_displacement and max_displacement. This argument is ignored if min_displacement
+                is not passed as an argument.
+            scs_per_displacement_val (int): number of perturbed supercells to generate for each unique
+                displacement value.
+
+            floor_displacement (Optional float): If None (default), then for a given perturbed supercell, all atoms will
+                move the same distance from their original locations. If float, then for a given perturbed supercell,
+                the distances that atoms move will be uniformly distributed from a minimum value of 'floor_displacement'
+                to the displacement value 'displacement_val'.
+
     """
 
     def __init__(self, original_supercell,
-                 transformation_matrix,
-                 min_displacement,
-                 max_displacement,
+                 max_displacement_val,
+                 min_displacement_val,
                  num_displacements,
-                 scs_per_displacement):
+                 scs_per_displacement_val,
+                 floor_displacement=None):
 
-        self.supercell = original_supercell
-        self.trans_mat = transformation_matrix
-        self.min_disp = min_displacement
-        self.max_disp = max_displacement
+        self.original_supercell = original_supercell
+        self.max_disp_val = max_displacement_val
+        self.min_disp_val = min_displacement_val
         self.num_disps = num_displacements
-        self.scs_per_disp = scs_per_displacement
-        self.perturbed_supercells = []
+        self.scs_per_disp_val = scs_per_displacement_val
 
+        if floor_displacement is not None:
+            self.floor_disp = float(floor_displacement)
+        else:
+            self.floor_disp = None
 
-    def random_displacements(self, natom, rmax, rmin=None, dim=3):
+        self.disp_vals = np.linspace(min_displacement_val, max_displacement_val, num=num_displacements)
+        self.perturbed_supercells = self.generate_transformations()
+
+
+    def random_displacements(self, natom, rmax, rmin, dim=3):
         #*** Adapted from csld.util.mathtool
 
         # Generate matrix of size (natom, 3) where each row is a Gaussian random vector
@@ -41,7 +60,7 @@ def random_displacements(self, natom, rmax, rmin=None, dim=3):
 
         dx = np.random.normal(size=(natom, dim)) #Gaussian sampled displacements. Matrix size: (natom, 3)
         dx_norms = np.linalg.norm(dx, axis=1)
-        veclen = np.full(natom, rmax) if rmax is None else np.random.uniform(rmin, rmax, natom)
+        veclen = np.full(natom, rmax) if rmin is None else np.random.uniform(rmin, rmax, natom)
 
         if not 0 in dx_norms:
             return dx * (veclen / dx_norms)[:, None]
@@ -49,56 +68,99 @@ def random_displacements(self, natom, rmax, rmin=None, dim=3):
             self.random_displacements(natom, rmax, rmin, dim)
 
 
-    def perturb_supercell(self, structure, disp):
+    def perturb_supercell(self, structure, max_disp, floor_disp):
         # *** Adapted from CSLD's 'polaron_main' file
 
         na = structure.num_sites
-        disp = float(disp)
-        if isinstance(disp, float):
+        max_disp = float(max_disp)
+        if isinstance(max_disp, float):
             # from csld.util.mathtool import random_displacements
-            dr = self.random_displacements(na, disp) #generate random displacements
+            dr = self.random_displacements(na, max_disp, floor_disp) #generate random displacements
 
             # Perturb structure with the random displacements
             for i in range(len(structure._sites)):
                 structure.translate_sites([i], dr[i], frac_coords=False, to_unit_cell=True)
+            return structure
         else:
             print('displacement entered is not a float.')
 
 
     def generate_transformations(self):
-        for disp_val in range(self.num_disps):
-            for cell in range(self.scs_per_disp):
+        perturbed_supercells = []
+        for disp_val in self.disp_vals:
+            for cell in range(self.scs_per_disp_val):
                 sc = self.original_supercell.copy()
-                self.perturb_supercell(sc, self.max_disp)
-                self.perturbed_supercells += [sc]
+                sc = self.perturb_supercell(sc, disp_val, self.floor_disp)
+                perturbed_supercells += [sc]
+        return perturbed_supercells
 
 
 ####################################
 # BELOW IS FOR DEBUGGING PURPOSES #
 ####################################
 def main():
-    print('test')
-    natom = 10
-    dim = 3
-    rmin = 0
-    rmax = 0.1
-    dx = np.random.normal(size=(natom, dim))  # Gaussian sampled displacements. Matrix size: (natom, 3)
-    print(dx.shape)
-    veclen = np.full(natom, rmin) if rmax is None else np.random.uniform(rmin, rmax, natom)  # vector of length natom
-    dx *= (veclen / np.linalg.norm(dx, axis=1))[:, None]
-    test = (veclen / np.linalg.norm(dx, axis=1))[:, None]
-    print(test.shape)
-
-    x = np.array([[1, 1, 1],
-                  [1, 1, 1],
-                  [1, 1, 1],
-                  [1, 1, 1]])
-    y = np.array([[1],
-                  [2],
-                  [3],
-                  [4]])
-    print(x*y)
-
+    # print('test')
+    # natom = 10
+    # dim = 3
+    # rmin = 0
+    # rmax = 0.1
+    # dx = np.random.normal(size=(natom, dim))  # Gaussian sampled displacements. Matrix size: (natom, 3)
+    # print(dx.shape)
+    # veclen = np.full(natom, rmin) if rmax is None else np.random.uniform(rmin, rmax, natom)  # vector of length natom
+    # dx *= (veclen / np.linalg.norm(dx, axis=1))[:, None]
+    # test = (veclen / np.linalg.norm(dx, axis=1))[:, None]
+    # print(test.shape)
+    #
+    # x = np.array([[1, 1, 1],
+    #               [1, 1, 1],
+    #               [1, 1, 1],
+    #               [1, 1, 1]])
+    # y = np.array([[1],
+    #               [2],
+    #               [3],
+    #               [4]])
+    # print(x*y)
+
+    from atomate.vasp.workflows.base.csld_sc_gen import gen_scaling_matrix
+
+    from pymatgen.ext.matproj import MPRester
+    from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
+    from pymatgen.transformations.standard_transformations import SupercellTransformation
+
+    mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
+    # structure = mpr.get_structure_by_material_id('mp-7814') #passed
+    structure = mpr.get_structure_by_material_id('mp-1101039')  # passed
+    # structure = mpr.get_structure_by_material_id('mp-20012')
+
+    print('structure loaded')
+    print(structure.num_sites)
+    # print('structure')
+    # print(structure)
+    # structure.to(fmt='poscar', filename='POSCAR-tlbise2-scraped')
+
+    # # Find Primitive
+    # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    # sga = SpacegroupAnalyzer(structure)
+    # # print(sga.find_primitive().lattice)
+    # sga.find_primitive().to(fmt='poscar', filename='POSCAR-tlbise2-scraped-prim')
+
+    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150, max_atoms=1000)
+    # ***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
+
+    print('~~~~~~~~~~~~~~~~~~~~~~~~~')
+    print("FINISHED2")
+    # print(T)
+
+    # Pymatgen version
+    superstructure = SupercellTransformation(T).apply_transformation(structure)
+
+    enum = CSLDPerturbedSupercellEnumerator(superstructure,
+                                            max_displacement_val=0.05,
+                                            min_displacement_val=0.01,
+                                            num_displacements=2,
+                                            scs_per_displacement_val=1)
+    print('perturbed supercells list:')
+    print(enum.perturbed_supercells)
 
 
 if __name__ == '__main__':
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld_sc_gen.py
similarity index 99%
rename from atomate/vasp/workflows/base/csld.py
rename to atomate/vasp/workflows/base/csld_sc_gen.py
index f440a9212..6fa54d80e 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld_sc_gen.py
@@ -173,7 +173,7 @@ def main():
     # sga.find_primitive().to(fmt='poscar', filename='POSCAR-tlbise2-scraped-prim')
 
 
-    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150, max_atoms=1)
+    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150, max_atoms=1000)
     #***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
 
     print('~~~~~~~~~~~~~~~~~~~~~~~~~')

From de011a9a8a2fe17016b4f4190593057c785600c7 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 26 Jun 2019 16:35:09 -0700
Subject: [PATCH 012/207] Made a custom IO writer from a dict to a string to a
 file since f90nml was not writing files in format that was readable by
 ShengBTE.

---
 atomate/vasp/workflows/base/sbte_IO.py | 145 ++++++++++++++++++++-----
 1 file changed, 117 insertions(+), 28 deletions(-)

diff --git a/atomate/vasp/workflows/base/sbte_IO.py b/atomate/vasp/workflows/base/sbte_IO.py
index a86b09246..ffd465645 100644
--- a/atomate/vasp/workflows/base/sbte_IO.py
+++ b/atomate/vasp/workflows/base/sbte_IO.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import f90nml
+import numpy as np
 """
 This module defines IO ShengBTE for making CONTROL file (i.e. a class that can read/write the ‘control’ file, f90ml)
 
@@ -10,7 +11,6 @@
 class ShengBTE_CONTROL_IO:
 
     """
-
         Args:
             nelements (int): number of elements in the material
             natoms (int): number of atoms in the cell
@@ -42,33 +42,120 @@ def read_CONTROL(self, filename):
         nml = f90nml.read(filename)
         return nml
 
-    def write_CONTROL_from_dict(self, dict, filename='CONTROL'):
+
+
+    def file_writer_helper_func(self, dict, filename):
+        nelements = str(dict['allocations']['nelements'])
+        natoms = str(dict['allocations']['natoms'])
+        ngrid = dict['allocations']['ngrid']
+        norientations = str(dict['allocations']['norientations'])
+
+        lfactor = str(dict['crystal']['lfactor'])
+        lattvec1 = dict['crystal']['lattvec'][0]
+        lattvec2 = dict['crystal']['lattvec'][1]
+        lattvec3 = dict['crystal']['lattvec'][2]
+        elements = dict['crystal']['elements'] #string or list of strings, needs to be parsed
+        types = dict['crystal']['types'] #list of ints, needs to be parsed
+        positions = np.asarray(dict['crystal']['positions']) #numpy array, needs to be parsed
+        num_sites, _ = positions.shape
+        scell = dict['crystal']['scell'] #list of ints, needs to be parsed
+
+        temperature = str(int(dict['parameters']['T']))
+        scalebroad = str(dict['parameters']['scalebroad'])
+
+        onlyharmonic = dict['flags']['onlyharmonic']
+        isotopes = dict['flags']['isotopes']
+        nonanalytic = dict['flags']['nonanalytic']
+        nanowires = dict['flags']['nanowires']
+
+        def boolean_to_string(boolean):
+            if boolean is True:
+                return '.TRUE.'
+            else:
+                return '.FALSE.'
+
+        indent = '        '
+        types_string ='types='
+        positions_string = ''
+        for line in range(num_sites):
+            if line != num_sites-1:
+                types_string += str(types[line])+' '
+            else:
+                types_string += str(types[line])+',\n'
+            positions_string += 'positions(:,' + str(line+1) + ')=' + str(positions[line,0]) + '  ' \
+                                + str(positions[line,1]) + '  ' + str(positions[line,2]) + ',\n' + indent
+
+        full_string = '&allocations\n'+indent+'nelements='+nelements+',\n'
+        full_string += indent+'natoms='+natoms+',\n'
+        full_string += indent+'ngrid(:)='+str(ngrid[0])+' '+str(ngrid[1])+' '+str(ngrid[2])+'\n'
+        full_string += indent+'norientations='+norientations+'\n'
+        full_string += '&end\n&crystal\n'
+        full_string += indent+'lfactor='+lfactor+',\n'
+        full_string += indent+'lattvec(:,1)='+str(lattvec1[0])+'  '+str(lattvec1[1])+'  '+str(lattvec1[2])+',\n'
+        full_string += indent+'lattvec(:,2)='+str(lattvec2[0])+'  '+str(lattvec2[1])+'  '+str(lattvec2[2])+',\n'
+        full_string += indent+'lattvec(:,3)='+str(lattvec3[0])+'  '+str(lattvec3[1])+'  '+str(lattvec3[2])+',\n'
+        full_string += indent+'elements='
+        if isinstance(elements, list):
+            for i in range(len(elements)):
+                full_string += '\"'+elements[i]+str('\"')
+                if i != (len(elements)-1):
+                    full_string += ' '
+                else:
+                    full_string += '\n'
+        else:
+            full_string += '\"'+elements+str('\"\n')
+        full_string += indent+types_string
+        full_string += indent+positions_string
+        full_string += 'scell(:)='+str(scell[0])+' '+str(scell[1])+' '+str(scell[2])+'\n'
+        full_string += '&end\n&parameters\n'
+        full_string += indent+'T='+temperature+'\n'
+        full_string += indent+'scalebroad='+scalebroad+'\n'
+        full_string += '&end\n&flags\n'
+        full_string += indent+'isotopes='+boolean_to_string(isotopes)+'\n'
+        full_string += indent+'onlyharmonic='+boolean_to_string(onlyharmonic)+'\n'
+        full_string += indent+'nonanalytic='+boolean_to_string(nonanalytic)+'\n'
+        full_string += indent+'nanowires='+boolean_to_string(nanowires)+'\n'
+        full_string += '&end'
+
+        file = open(filename, 'w+')
+        file.write(full_string)
+        file.close()
+
+
+    def write_CONTROL_from_dict(self, dict, filename='CONTROL', overwrite=True):
         with open(filename, 'w') as control_file:
-            nml = {'allocations':
-                       {'nelements': dict.get('allocations', None).get('nelements', None),
-                        'natoms': dict.get('allocations', None).get('natoms', None),
-                        'ngrid': dict.get('allocations', [25, 25, 25]).get('ngrid', [25, 25, 25]),
-                        'norientations': dict.get('allocations', 0).get('norientations', 0)},
-                   'crystal':
-                       {'lfactor': dict.get('crystal', 0.1).get('lfactor', 0.1),
-                        # 'lattvec(:,1)': dict.get('crystal', None).get('lattvec(:,1)', None),
-                        # 'lattvec(:,2)': dict.get('crystal', None).get('lattvec(:,2)', None),
-                        # 'lattvec(:,3)': dict.get('crystal', None).get('lattvec(:,3)', None),
-                        'lattvec': dict.get('crystal', None).get('lattvec', None),
-                        'positions': dict.get('crystal', None).get('positions', None),
-                        'elements': dict.get('crystal', None).get('elements', None),
-                        'types': dict.get('crystal', None).get('types', None),
-                        'scell': dict.get('crystal', [5, 5, 5]).get('scell', [5, 5, 5])},
-                   'parameters':
-                       {'T': dict.get('parameters', 500).get('T', 500),
-                        'scalebroad': dict.get('parameters', 0.5).get('scalebroad', 0.5)},
-                   'flags':
-                       {'onlyharmonic': dict.get('flags', False).get('onlyharmonic', False),
-                        'isotopes': dict.get('flags', False).get('isotopes', False),
-                        'nonanalytic': dict.get('flags', True).get('nonanalytic', True),
-                        'nanowires': dict.get('flags', False).get('nanowires', False)}}
-
-            f90nml.write(nml, control_file, force=True) #force=True overwrites an existing file
+            new_dict = {'allocations':
+                               {'nelements': dict.get('allocations', None).get('nelements', None),
+                                'natoms': dict.get('allocations', None).get('natoms', None),
+                                'ngrid': dict.get('allocations', [25, 25, 25]).get('ngrid', [25, 25, 25]),
+                                'norientations': dict.get('allocations', 0).get('norientations', 0)},
+                        'crystal':
+                               {'lfactor': dict.get('crystal', 0.1).get('lfactor', 0.1),
+                                # 'lattvec(:,1)': dict.get('crystal', None).get('lattvec(:,1)', None),
+                                # 'lattvec(:,2)': dict.get('crystal', None).get('lattvec(:,2)', None),
+                                # 'lattvec(:,3)': dict.get('crystal', None).get('lattvec(:,3)', None),
+                                'lattvec': dict.get('crystal', None).get('lattvec', None),
+                                'elements': dict.get('crystal', None).get('elements', None),
+                                'types': dict.get('crystal', None).get('types', None),
+                                'positions': dict.get('crystal', None).get('positions', None),
+                                'scell': dict.get('crystal', [5, 5, 5]).get('scell', [5, 5, 5])},
+                        'parameters':
+                               {'T': dict.get('parameters', 300).get('t', 300),
+                                'scalebroad': dict.get('parameters', 0.5).get('scalebroad', 0.5)},
+                        'flags':
+                               {'onlyharmonic': dict.get('flags', False).get('onlyharmonic', False),
+                                'isotopes': dict.get('flags', False).get('isotopes', False),
+                                'nonanalytic': dict.get('flags', True).get('nonanalytic', True),
+                                'nanowires': dict.get('flags', False).get('nanowires', False)}}
+
+            # nml = f90nml.namelist.Namelist(new_dict) #convert dict to namelist object
+            # nml.false_repr = '.FALSE.'
+            # nml.true_repr = '.TRUE.'
+            # nml.index_spacing = False
+            # nml.uppercase = False
+            # nml.indent = '        '
+            # f90nml.write(nml, control_file, force=overwrite, sort=False) #force=True overwrites an existing file
+            self.file_writer_helper_func(new_dict, filename=filename)
 
 
 def main():
@@ -82,9 +169,11 @@ def main():
     dict = namelist.todict()
     print(dict)
     print(dict['allocations']['nelements'])
+    print(dict['crystal']['lattvec'])
+    print(dict['crystal']['lattvec'][0])
 
     # Write the dict back into a namelist file
-    sbte_io.write_CONTROL_from_dict(dict, filename='CONTROL_test')
+    sbte_io.write_CONTROL_from_dict(dict, filename='CONTROL_test2')
 
 
 if __name__ == '__main__':

From 2692be06e7d5d09e18d1405b417ea41b5388f205 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 10 Jul 2019 16:50:10 -0700
Subject: [PATCH 013/207] CSLD workflow first try

---
 atomate/vasp/firetasks/parse_outputs.py | 271 ++++++++++++++++++++++++
 atomate/vasp/workflows/base/csld.py     | 158 ++++++++++++++
 2 files changed, 429 insertions(+)
 create mode 100644 atomate/vasp/workflows/base/csld.py

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 0b4935abc..9a9281fd1 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1754,6 +1754,277 @@ def split_abc(var, var_name):
         coll = vaspdb.db["polarization_tasks"]
         coll.insert_one(polarization_dict)
 
+@explicit_serialize
+class PerformCSLDMinimization(FiretaskBase):
+    """
+    Used to aggregate atomic forces of perturbed supercells in compressed
+    sensing lattice dynamics (CSLD) workflow and generate interatomic force
+    constants.
+
+    Required parameters:
+        db_file (str): path to the db file that holds your tasks
+        collection and that you want to hold the magnetic_orderings
+        collection
+        wf_uuid (str): auto-generated from get_wf_magnetic_orderings,
+        used to make it easier to retrieve task docs
+        parent_structure (Structure): material that CSLD is being run on
+        forces_paths (list of str): paths to directories containing 'force.txt'
+            files
+        csld_settings (ConfigParser): settings for running CSLD
+        csld_options (dict): options for running CSLD
+    # Optional parameters:
+    #     to_db (bool): if True, the data will be inserted into
+    #     dedicated collection in database, otherwise, will be dumped
+    #     to a .json file.
+    """
+
+    required_params = ["db_file", "wf_uuid", "parent_structure", "forces_paths",
+                       # "csld_settings", "csld_options",
+
+                       "trans_mat", "supercell_structure",
+                       "disps"]
+
+    def set_params(self, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
+        from configparser import ConfigParser
+        supercell_folder = self["parent_structure"].composition.reduced_formula + \
+                           "_supercell_iter" + str(iteration_number)
+        os.mkdir(supercell_folder)
+        np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
+                   delimiter=" ")
+        self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
+
+        disp_folders = []
+        csld_traindat_disp_folders = ''
+        for disp in self["disps"]:
+            disp_folder = supercell_folder+'/disp'+str(disp)
+            disp_folders += [disp_folder]
+            csld_traindat_disp_folders += ' ' + str(disp_folder)
+            os.mkdir(disp_folder)
+
+            # Parameters for conducting CSLD
+            csld_traindat_string = supercell_folder + '/SPOSCAR'
+            csld_traindat_string += csld_traindat_disp_folders
+
+            csld_settings = ConfigParser()
+            csld_settings['convergence_info'] = {
+                'iteration': 0,
+                'settings_tried': {}
+            }
+            csld_settings['structure'] = {
+                'prim': 'POSCAR',
+                'sym_tol': '1e-3',
+                'epsilon_inf': None,  # check how it reads 3x3 matrix
+                'born_charge': None  # check reading n_atom*9 numbers
+            }
+            csld_settings['model'] = {
+                'model_type': 'LD',
+                'cluster_in': 'clusters.out',
+                'cluster_out': 'clusters.out',
+                'symC_in': 'Cmat.mtx',
+                'symC_out': 'Cmat.mtx',
+                'max_order': max_order, #3,  # this should be variable
+                'fractional_distance': False,
+                'cluster_diameter': cluster_diam, #'11 6.5 5.0', #this should be variable
+                'cluster_filter': lambda cls: ((cls.order_uniq <= 2)
+                                               or (cls.bond_counts(2.9) >= 2))
+                                              and cls.is_small_in(
+                    supercell_folder + "/sc.txt")
+                # rewrote how it reads the trans_mat
+            }
+            csld_settings['training'] = {
+                'interface': 'VASP',
+                'corr_type': 'f',
+                'corr_in': 'Amat.mtx',
+                'corr_out': 'Amat.mtx',
+                'fval_in': 'fval.txt',
+                'fval_out': 'fval.txt',
+                'traindat1': csld_traindat_string
+                # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
+                # Rewrote how it reads forces
+            }
+            csld_settings['fitting'] = {
+                'solution_in': 'solution_all',
+                'solution_out': 'solution_all',
+                'nsubset': 5,
+                'holdsize': 0.1,
+                ## 1 FPC 2 FPC sparse 3 split 4 sparse split
+                ## 5 split+ right preconditioning 6 sparse split + r preconditioning
+                ## 101 Bayesian CS
+                'method': 5,
+
+                # For weight of L1 or L2 regularization
+                'mulist': '1E-5 1E-7 1E-9 1E-11',
+                'maxIter': 300,
+                'tolerance': 1E-6,
+                'subsetsize': 0.85,
+                'lambda': 0.5,
+                'uscale_list': '0.03',
+                'submodel1': submodel1, #'anh 0 1 2 3',  # this should be variable
+            }
+            csld_settings['phonon'] = {
+                'qpoint_fractional': False,
+                # 'Auto' or something like "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
+                'wavevector': "[[25,  [0,0,0],'\Gamma', [0,0.5,0.5], 'X'],"
+                              " [25, [1,0.5,0.5], 'X', [0.75,0.375,0.375], "
+                              "'K', [0,0,0], '\Gamma', [0.5, 0.5, 0.5], 'L']]",
+                'unit': 'meV',  # THz, meV, eV, cm
+
+                # number of grid points
+                'dos_grid': '15 15 15',
+
+                # number of points in DOS
+                'nE_dos': 500,
+
+                ## 0 (Gaussian), 1 (Lorentzian), -1 (tetrahedron method)
+                'ismear': -1,
+
+                ## width in THz of Gaussian/Lorentzian smearing
+                'epsilon': 0.05,
+                'pdos': True,
+
+                'thermal_T_range': '50 800 50',
+                'thermal_out': 'thermal_out.txt'
+            }
+            csld_settings['export_potential'] = {
+                'export_shengbte': export_sbte, #'5 5 5 2 3'  # 5x5x5 supercell
+                # 2 and 3 orders to be considered
+                # should be variable?
+            }
+            csld_settings['prediction'] = {
+                'interface': 'VASP',
+                'corr_type': 'f',
+                'corr_in': 'Amat_pred.mtx',
+                'corr_out': 'Amat_pred.mtx',
+                'fval_in': 'fval_pred.txt',
+                'fval_out': 'fval_pred.txt',
+                'traindat0': 'fcc222/POSCAR fcc222/traj*'
+            }
+            # set default values
+            csld_settings['DEFAULT'] = {
+                "qpoint_fractional": False,
+                "true_v_fit": 'true_fit.txt',
+                'epsilon': '0.05',
+                "bcs_reweight": 'True',
+                "bcs_penalty": 'arctan',
+                "bcs_jcutoff": '1E-8'}
+
+            csld_options = {}
+            csld_options['pdfout'] = 'plots.pdf'
+            csld_options['ldff_step'] = 0
+            csld_options['phonon_step'] = 1
+            csld_options['phonon'] = False
+            csld_options['save_pot_step'] = 0  # WHAT DOES THIS NEED TO BE?
+            csld_options['pot'] = False
+
+            self["csld_settings"] = csld_settings
+            self["csld_options"] = csld_options
+
+    def run_task(self, fw_spec):
+
+        iter = 0
+        not_converged = True
+        maxIter = 10
+        convergence_info_dict = self["csld_settings"]["convergence_info"]
+        summaries = []
+
+        #FILL THESE IN FURTHER
+        cluster_diam_settings = ['11 6.5 5.0']
+        max_order_settings = [3]
+        submodel1_settings = ['anh 0 1 2 3']
+        export_sbte_settings = ['5 5 5 2 3']
+
+        while not_converged or iter < maxIter:
+            self.set_params(iter,
+                            cluster_diam_settings[iter],
+                            max_order_settings[iter],
+                            submodel1_settings[iter],
+                            export_sbte_settings[iter])
+
+            uuid = self["wf_uuid"]
+            db_file = env_chk(self.get("db_file"), fw_spec)
+
+            mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+            tasks = mmdb["tasks"]
+            formula = self["parent_structure"].formula
+            formula_pretty = self["parent_structure"].composition.reduced_formula
+            task_label = 'static'
+            supercells_dicts = list(tasks.find({"wf_meta.wf_uuid": uuid,
+                                                "task_label": {"$regex": task_label},
+                                                "formula_pretty": formula_pretty},
+                                                ['task_id', 'output.forces']))
+            #list of dicts where each dict contatins a task_id and a list of forces
+            #   for each supercell
+
+            supercells_forces = []
+            supercells_task_ids = []
+            for supercell_dict in supercells_dicts:
+                #List of np.ndarrays where each np.ndarray is a matrix of forces
+                #  for a perturbed supercell
+                supercells_forces += [np.asarray(supercell_dict['output']['forces'])]
+
+                #List of task ids for each perturbed supercell
+                supercells_task_ids += [supercell_dict['task_id']]
+
+            supercell_idx = 0
+            for supercell_forces in supercells_forces:
+                path = self["forces_paths"][supercell_idx]
+                np.savetxt(path + "/force.txt", supercell_forces, fmt='%.6f')
+
+            #Perform csld minimization now
+            import scripts.csld_main_rees as csld_main
+            rel_err, freq_matrix = csld_main.main(self["csld_options"],
+                                                  self["csld_settings"])
+            freq_matrix = np.asarray(freq_matrix)
+            imaginary_idx = freq_matrix < 0
+            imaginary_freqs = freq_matrix[imaginary_idx]
+            num_imaginary_bands = np.any(imaginary_idx, axis=1)
+            most_imaginary_freq = np.amin(imaginary_freqs)
+            # For imaginary frequencies, w^2 is negative
+            # code handles it as w = sign(sqrt(abs(w^2)), w^2)
+
+            if num_imaginary_bands == 0:
+                not_converged = False
+
+            #Save to DB
+            summary = {
+                "formula": formula,
+                "formula_pretty": formula_pretty,
+                "parent_structure": self["parent_structure"].as_dict(),
+                "wf_meta": {"wf_uuid": uuid},
+
+                #<store relevant CSLD settings>
+                "iteration": iter,
+                "cluster_diam": self["csld_settings"]["model"]["cluster_diameter"],
+                "max_order": self["csld_settings"]["model"]["max_order"],
+                "submodel1": self["csld_settings"]["fitting"]["submodel1"],
+                "export_potential": self["csld_settings"]["export_potential"]["export_shengbte"],
+
+                "cross_val_error": rel_err,
+                "num_imaginary_modes": num_imaginary_bands, #number or percent?
+                "most_imaginary_freq": most_imaginary_freq
+            }
+            latest_settings = {str(convergence_info_dict["iteration"]):
+                                   {self["csld_settings"]["model"]["max_order"],
+                                    self["csld_settings"]["fitting"]["submodel1"],
+                                    self["csld_settings"]["export_potential"][
+                                        "export_shengbte"]}}
+            convergence_info_dict["iteration"] += 1
+            convergence_info_dict["settings_tried"].update(latest_settings)
+
+            if fw_spec.get("tags", None):
+                summary["tags"] = fw_spec["tags"]
+
+            summaries.append(summary)
+
+        mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
+        mmdb.collection.insert(summaries)
+
+        if iter < maxIter:
+            logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
+        else:
+            logger.info("Compressed Sensing Lattice Dynamics calculation failed."
+                        "Max iterations was reached.")
+
 
 # the following definitions for backward compatibility
 class VaspToDbTask(VaspToDb):
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
new file mode 100644
index 000000000..23df7e6b5
--- /dev/null
+++ b/atomate/vasp/workflows/base/csld.py
@@ -0,0 +1,158 @@
+# coding: utf-8
+
+import os
+
+import numpy as np
+from uuid import uuid4
+from pymatgen.alchemy.materials import TransformedStructure
+from pymatgen.transformations.advanced_transformations import (
+    CubicSupercellTransformation,
+    PerturbSitesTransformation
+)
+from fireworks import Workflow, Firework
+from atomate.utils.utils import get_logger
+from atomate.vasp.config import VASP_CMD, DB_FILE, ADD_WF_METADATA #                what is this?
+from atomate.vasp.fireworks.core import StaticFW
+from atomate.vasp.firetasks.parse_outputs import PerformCSLDMinimization
+
+from pymatgen.io.vasp.sets import MPStaticSet
+
+# NEW THINGS TO INSTALL?
+from configparser import ConfigParser
+from scripts import csld_main_rees #csld>scripts
+
+logger = get_logger(__name__)
+
+__author__ = "Rees Chang"
+__email__ = "rc564@cornell.edu"
+__date__ = "July 2019"
+
+__csld_wf_version__ = 1.0
+
+class CompressedSensingLatticeDynamicsWF:
+    def __init__(
+            self,
+            parent_structure,
+            min_atoms=-np.Inf,
+            max_atoms=np.Inf,
+            num_nn_dists=5,
+            max_displacement=0.1,
+            min_displacement=0.01,
+            num_displacements=10,
+            supercells_per_displacement_distance=1,
+            min_random_distance=None,
+            #csld input params here
+    ):
+        """
+        This workflow will use compressed sensing lattice dynamics (CSLD)
+        (doi: 10.1103/PhysRevLett.113.185501) to generate interatomic force
+        constants from an input structure and output a summary to a database.
+
+        A summary of the workflow is as follows:
+            1. Transform the input structure into a supercell
+            2. Transform the supercell into a list of supercells with all atoms
+                randomly perturbed from their original sites
+            3. Run static VASP calculations on each perturbed supercell to
+                calculate atomic forces.
+            4. Aggregate the forces and conduct the CSLD minimization algorithm
+                to compute interatomic force constants.
+            5. Output the interatomic force constants to the database.
+
+        Args:
+            parent_structure (Structure):
+            min_atoms (int):
+            max_atoms (int):
+            num_nn_dists (int or float):
+            max_displacement (float)
+        """
+        self.uuid = str(uuid4())
+        self.wf_meta = {
+            "wf_uuid": self.uuid,
+            "wf_name": self.__class__.__name__,
+        }
+
+    # Create supercell
+        self.parent_structure = parent_structure
+        self.min_atoms = min_atoms
+        self.max_atoms = max_atoms
+        self.num_nn_dists = num_nn_dists
+        supercell_transform = CubicSupercellTransformation(
+            self.min_atoms,
+            self.max_atoms,
+            self.num_nn_dists,
+        )
+        # supercell (Structure)
+        self.supercell = supercell_transform.apply_transformation(self.parent_structure)
+        self.trans_mat = supercell_transform.trans_mat
+
+    # Generate randomly perturbed supercells
+        perturbed_supercells_transform = PerturbSitesTransformation(
+            max_displacement,
+            min_displacement,
+            num_displacements,
+            supercells_per_displacement_distance,
+            min_random_distance
+        )
+        # list of perturbed supercell structures (list)
+        self.perturbed_supercells = perturbed_supercells_transform.apply_transformation(self.supercell)
+        # list of (non-unique) displacement values used in the perturbation (np.ndarray)
+        self.disps = np.repeat(perturbed_supercells_transform.disps,
+                               supercells_per_displacement_distance)
+
+
+    def get_wf(
+            self,
+            c=None
+    ):
+        fws = []
+        c = c or {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
+
+        def _add_metadata(structure):
+            """
+            Add metadata for easy querying from the database later.
+            """
+            return TransformedStructure(
+                structure, other_parameters={"wf_meta": self.wf_meta}
+            )
+
+        user_incar_settings = {"NSW": 0, "LCHARG": False, "IBRION": -1}
+        user_incar_settings.update(c.get("user_incar_settings", {}))
+
+        for idx, perturbed_supercell in enumerate(self.perturbed_supercells):
+            # Run static calculations on the perturbed supercells to compute forces on each atom
+            name = "perturbed supercell, idx: {}, disp_val: {},".format(idx, self.disps[idx])
+
+
+            vis = MPStaticSet(perturbed_supercell,
+                              user_incar_settings,
+                              reciprocal_density=1)  #@ALEX is this right/ok
+                                                    # how to run vasp_gam instead of vasp_std?
+            fws.append(StaticFW(
+                perturbed_supercell,
+                vasp_input_set=vis,
+                vasp_cmd=c["VASP_CMD"],
+                db_file=c["DB_FILE"],
+                name=name + " static"
+            ))
+
+        # Collect force constants from the DB and output on cluster
+        fw_collect_force_constants = Firework(
+            PerformCSLDMinimization(
+                db_file=c["DB_FILE"], # wot
+                wf_uuid=self.uuid,
+                csld_settings=self.csld_settings,
+                csld_options=self.csld_options,
+                forces_paths=self.disp_folders,
+                trans_mat=self.trans_mat,
+                supercell_structure=self.supercell,
+                disps=self.disps
+            )
+        )
+
+        # Add a firework here to check for imaginary modes
+
+
+        formula = self.parent_structure.composition.reduced_formula
+        wf_name = "{} - compressed sensing lattice dynamics".format(formula)
+        wf = Workflow(fws, name=wf_name)
+        return wf
\ No newline at end of file

From d50ef73052947a7401de28b65c90349339d54a42 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 10 Jul 2019 16:57:35 -0700
Subject: [PATCH 014/207] quick change

---
 atomate/vasp/firetasks/parse_outputs.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 9a9281fd1..1fa15b2c2 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1933,6 +1933,9 @@ def run_task(self, fw_spec):
         submodel1_settings = ['anh 0 1 2 3']
         export_sbte_settings = ['5 5 5 2 3']
 
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+        tasks = mmdb["tasks"]
         while not_converged or iter < maxIter:
             self.set_params(iter,
                             cluster_diam_settings[iter],
@@ -1941,10 +1944,7 @@ def run_task(self, fw_spec):
                             export_sbte_settings[iter])
 
             uuid = self["wf_uuid"]
-            db_file = env_chk(self.get("db_file"), fw_spec)
 
-            mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-            tasks = mmdb["tasks"]
             formula = self["parent_structure"].formula
             formula_pretty = self["parent_structure"].composition.reduced_formula
             task_label = 'static'

From 51117924aea92d5fcf0d4a4441a61dc699e5cf45 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 11 Jul 2019 14:04:18 -0700
Subject: [PATCH 015/207] Debugging stuff. First version that was launched on
 cori

---
 atomate/vasp/firetasks/parse_outputs.py | 13 ++--
 atomate/vasp/workflows/base/csld.py     | 79 +++++++++++++++++++------
 2 files changed, 66 insertions(+), 26 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 1fa15b2c2..632e9417a 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1755,7 +1755,7 @@ def split_abc(var, var_name):
         coll.insert_one(polarization_dict)
 
 @explicit_serialize
-class PerformCSLDMinimization(FiretaskBase):
+class CSLDForceConstantsToDB(FiretaskBase):
     """
     Used to aggregate atomic forces of perturbed supercells in compressed
     sensing lattice dynamics (CSLD) workflow and generate interatomic force
@@ -1768,8 +1768,6 @@ class PerformCSLDMinimization(FiretaskBase):
         wf_uuid (str): auto-generated from get_wf_magnetic_orderings,
         used to make it easier to retrieve task docs
         parent_structure (Structure): material that CSLD is being run on
-        forces_paths (list of str): paths to directories containing 'force.txt'
-            files
         csld_settings (ConfigParser): settings for running CSLD
         csld_options (dict): options for running CSLD
     # Optional parameters:
@@ -1778,7 +1776,7 @@ class PerformCSLDMinimization(FiretaskBase):
     #     to a .json file.
     """
 
-    required_params = ["db_file", "wf_uuid", "parent_structure", "forces_paths",
+    required_params = ["db_file", "wf_uuid", "parent_structure",
                        # "csld_settings", "csld_options",
 
                        "trans_mat", "supercell_structure",
@@ -1913,21 +1911,22 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             csld_options['ldff_step'] = 0
             csld_options['phonon_step'] = 1
             csld_options['phonon'] = False
-            csld_options['save_pot_step'] = 0  # WHAT DOES THIS NEED TO BE?
+            csld_options['save_pot_step'] = 1  # usual default is 0
             csld_options['pot'] = False
 
             self["csld_settings"] = csld_settings
             self["csld_options"] = csld_options
+            self["forces_paths"] = disp_folders
 
     def run_task(self, fw_spec):
 
         iter = 0
         not_converged = True
-        maxIter = 10
+        maxIter = 1
         convergence_info_dict = self["csld_settings"]["convergence_info"]
         summaries = []
 
-        #FILL THESE IN FURTHER
+        #<FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
         cluster_diam_settings = ['11 6.5 5.0']
         max_order_settings = [3]
         submodel1_settings = ['anh 0 1 2 3']
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 23df7e6b5..e53003aaa 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -13,13 +13,16 @@
 from atomate.utils.utils import get_logger
 from atomate.vasp.config import VASP_CMD, DB_FILE, ADD_WF_METADATA #                what is this?
 from atomate.vasp.fireworks.core import StaticFW
-from atomate.vasp.firetasks.parse_outputs import PerformCSLDMinimization
+from atomate.vasp.firetasks.parse_outputs import CSLDForceConstantsToDB
+from atomate.vasp.powerups import (
+    add_additional_fields_to_taskdocs
+)
 
 from pymatgen.io.vasp.sets import MPStaticSet
 
 # NEW THINGS TO INSTALL?
-from configparser import ConfigParser
-from scripts import csld_main_rees #csld>scripts
+# from configparser import ConfigParser
+# from scripts import csld_main_rees #csld>scripts
 
 logger = get_logger(__name__)
 
@@ -68,7 +71,7 @@ def __init__(
         self.uuid = str(uuid4())
         self.wf_meta = {
             "wf_uuid": self.uuid,
-            "wf_name": self.__class__.__name__,
+            "wf_name": self.__class__.__name__, #"CompressedSensingLatticeDynamicsWF"
         }
 
     # Create supercell
@@ -115,18 +118,24 @@ def _add_metadata(structure):
                 structure, other_parameters={"wf_meta": self.wf_meta}
             )
 
-        user_incar_settings = {"NSW": 0, "LCHARG": False, "IBRION": -1}
+        user_incar_settings = {"ADDGRID": True, #Fast Fourier Transform grid
+                               "LCHARG": False,
+                               "ENCUT": 700,
+                               "EDIFF": 1e-7, #may need to tune this
+                               "PREC": 'Accurate',
+                               "LAECHG": False,
+                               "LREAL": False,
+                               "LASPH": True}
         user_incar_settings.update(c.get("user_incar_settings", {}))
 
         for idx, perturbed_supercell in enumerate(self.perturbed_supercells):
             # Run static calculations on the perturbed supercells to compute forces on each atom
-            name = "perturbed supercell, idx: {}, disp_val: {},".format(idx, self.disps[idx])
+            name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(idx, self.disps[idx])
 
 
             vis = MPStaticSet(perturbed_supercell,
-                              user_incar_settings,
-                              reciprocal_density=1)  #@ALEX is this right/ok
-                                                    # how to run vasp_gam instead of vasp_std?
+                              user_incar_settings=user_incar_settings)
+
             fws.append(StaticFW(
                 perturbed_supercell,
                 vasp_input_set=vis,
@@ -135,24 +144,56 @@ def _add_metadata(structure):
                 name=name + " static"
             ))
 
+        print('DISPS')
+        print(self.disps)
         # Collect force constants from the DB and output on cluster
-        fw_collect_force_constants = Firework(
-            PerformCSLDMinimization(
+        csld_fw = Firework(
+            CSLDForceConstantsToDB(
                 db_file=c["DB_FILE"], # wot
                 wf_uuid=self.uuid,
-                csld_settings=self.csld_settings,
-                csld_options=self.csld_options,
-                forces_paths=self.disp_folders,
+                name='CSLDForceConstantsToDB',
+                parent_structure=self.parent_structure,
                 trans_mat=self.trans_mat,
                 supercell_structure=self.supercell,
                 disps=self.disps
-            )
+            ),
+            name="Compressed Sensing Lattice Dynamics",
+            parents=fws[-len(self.perturbed_supercells):]
         )
-
-        # Add a firework here to check for imaginary modes
-
+        fws.append(csld_fw)
 
         formula = self.parent_structure.composition.reduced_formula
         wf_name = "{} - compressed sensing lattice dynamics".format(formula)
         wf = Workflow(fws, name=wf_name)
-        return wf
\ No newline at end of file
+
+        wf = add_additional_fields_to_taskdocs(wf,
+                                               {"wf_meta": self.wf_meta},
+                                               task_name_constraint="VaspToDb"
+                                               #may need to change this to "CSLDForceConstantsToDB"?
+                                               )
+        #tag =   #insert anything relevant to every firework in the workflow
+        # wf = add_tags(wf, [tag, <insert whatever string you'd like>])
+        return wf
+
+
+if __name__ == "__main__":
+
+    from fireworks import LaunchPad
+    from pymatgen.ext.matproj import MPRester
+
+    #get a structure
+    mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
+    structure = mpr.get_structure_by_material_id('mp-149')
+
+    csld_class = CompressedSensingLatticeDynamicsWF(structure)
+    # print(csld_class.disps)
+    # print(len(csld_class.disps))
+
+    wf = csld_class.get_wf()
+
+    print(wf)
+
+    lpad = LaunchPad.auto_load()
+    lpad.add_wf(wf)
+
+    #how did lpad know which database to put the wf?

From 88bfa6803cf7b8e990672d6c0b3c3afa10f7bfeb Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Mon, 15 Jul 2019 17:03:52 -0700
Subject: [PATCH 016/207] first pass local debugging

---
 atomate/vasp/firetasks/parse_outputs.py | 257 +++++++++++++-----------
 1 file changed, 136 insertions(+), 121 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 632e9417a..f3afa8327 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1,5 +1,6 @@
 import json
 import os
+import shutil
 import re
 from collections import defaultdict
 from datetime import datetime
@@ -1756,6 +1757,8 @@ def split_abc(var, var_name):
 
 @explicit_serialize
 class CSLDForceConstantsToDB(FiretaskBase):
+    #TODO: Update this class once a public version of CSLD is released
+    #TODO: Update this class once Junsoo has fixed the cluster generation
     """
     Used to aggregate atomic forces of perturbed supercells in compressed
     sensing lattice dynamics (CSLD) workflow and generate interatomic force
@@ -1786,7 +1789,12 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
         from configparser import ConfigParser
         supercell_folder = self["parent_structure"].composition.reduced_formula + \
                            "_supercell_iter" + str(iteration_number)
+
+        # Remove supercell_folder if it already exists, then make a new one
+        if os.path.exists(supercell_folder) and os.path.isdir(supercell_folder):
+            shutil.rmtree(supercell_folder)
         os.mkdir(supercell_folder)
+
         np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
                    delimiter=" ")
         self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
@@ -1799,131 +1807,135 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             csld_traindat_disp_folders += ' ' + str(disp_folder)
             os.mkdir(disp_folder)
 
-            # Parameters for conducting CSLD
-            csld_traindat_string = supercell_folder + '/SPOSCAR'
-            csld_traindat_string += csld_traindat_disp_folders
+        self['convergence_info'] = {
+            'iteration': 0,
+            'settings_tried': {}
+        }
 
-            csld_settings = ConfigParser()
-            csld_settings['convergence_info'] = {
-                'iteration': 0,
-                'settings_tried': {}
-            }
-            csld_settings['structure'] = {
-                'prim': 'POSCAR',
-                'sym_tol': '1e-3',
-                'epsilon_inf': None,  # check how it reads 3x3 matrix
-                'born_charge': None  # check reading n_atom*9 numbers
-            }
-            csld_settings['model'] = {
-                'model_type': 'LD',
-                'cluster_in': 'clusters.out',
-                'cluster_out': 'clusters.out',
-                'symC_in': 'Cmat.mtx',
-                'symC_out': 'Cmat.mtx',
-                'max_order': max_order, #3,  # this should be variable
-                'fractional_distance': False,
-                'cluster_diameter': cluster_diam, #'11 6.5 5.0', #this should be variable
-                'cluster_filter': lambda cls: ((cls.order_uniq <= 2)
-                                               or (cls.bond_counts(2.9) >= 2))
-                                              and cls.is_small_in(
-                    supercell_folder + "/sc.txt")
-                # rewrote how it reads the trans_mat
-            }
-            csld_settings['training'] = {
-                'interface': 'VASP',
-                'corr_type': 'f',
-                'corr_in': 'Amat.mtx',
-                'corr_out': 'Amat.mtx',
-                'fval_in': 'fval.txt',
-                'fval_out': 'fval.txt',
-                'traindat1': csld_traindat_string
-                # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
-                # Rewrote how it reads forces
-            }
-            csld_settings['fitting'] = {
-                'solution_in': 'solution_all',
-                'solution_out': 'solution_all',
-                'nsubset': 5,
-                'holdsize': 0.1,
-                ## 1 FPC 2 FPC sparse 3 split 4 sparse split
-                ## 5 split+ right preconditioning 6 sparse split + r preconditioning
-                ## 101 Bayesian CS
-                'method': 5,
-
-                # For weight of L1 or L2 regularization
-                'mulist': '1E-5 1E-7 1E-9 1E-11',
-                'maxIter': 300,
-                'tolerance': 1E-6,
-                'subsetsize': 0.85,
-                'lambda': 0.5,
-                'uscale_list': '0.03',
-                'submodel1': submodel1, #'anh 0 1 2 3',  # this should be variable
-            }
-            csld_settings['phonon'] = {
-                'qpoint_fractional': False,
-                # 'Auto' or something like "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
-                'wavevector': "[[25,  [0,0,0],'\Gamma', [0,0.5,0.5], 'X'],"
-                              " [25, [1,0.5,0.5], 'X', [0.75,0.375,0.375], "
-                              "'K', [0,0,0], '\Gamma', [0.5, 0.5, 0.5], 'L']]",
-                'unit': 'meV',  # THz, meV, eV, cm
+        # Parameters for conducting CSLD
+        csld_traindat_string = supercell_folder + '/SPOSCAR'
+        csld_traindat_string += csld_traindat_disp_folders
+
+        csld_settings = ConfigParser()
+        csld_settings['convergence_info'] = {
+            'iteration': 0,
+            'settings_tried': {}
+        }
+        csld_settings['structure'] = {
+            'prim': 'POSCAR',
+            'sym_tol': '1e-3',
+            # 'epsilon_inf': None,  # check how it reads 3x3 matrix
+            # 'born_charge': None  # check reading n_atom*9 numbers
+        }
+        csld_settings['model'] = {
+            'model_type': 'LD',
+            'cluster_in': 'clusters.out',
+            'cluster_out': 'clusters.out',
+            'symC_in': 'Cmat.mtx',
+            'symC_out': 'Cmat.mtx',
+            'max_order': max_order, #3,  # this should be variable
+            'fractional_distance': False,
+            'cluster_diameter': cluster_diam, #'11 6.5 5.0', #this should be variable
+            'cluster_filter': lambda cls: ((cls.order_uniq <= 2)
+                                           or (cls.bond_counts(2.9) >= 2))
+                                          and cls.is_small_in(
+                supercell_folder + "/sc.txt")
+            # rewrote how it reads the trans_mat
+        }
+        csld_settings['training'] = {
+            'interface': 'VASP',
+            'corr_type': 'f',
+            'corr_in': 'Amat.mtx',
+            'corr_out': 'Amat.mtx',
+            'fval_in': 'fval.txt',
+            'fval_out': 'fval.txt',
+            'traindat1': csld_traindat_string
+            # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
+            # Rewrote how it reads forces
+        }
+        csld_settings['fitting'] = {
+            'solution_in': 'solution_all',
+            'solution_out': 'solution_all',
+            'nsubset': 5,
+            'holdsize': 0.1,
+            ## 1 FPC 2 FPC sparse 3 split 4 sparse split
+            ## 5 split+ right preconditioning 6 sparse split + r preconditioning
+            ## 101 Bayesian CS
+            'method': 5,
+
+            # For weight of L1 or L2 regularization
+            'mulist': '1E-5 1E-7 1E-9 1E-11',
+            'maxIter': 300,
+            'tolerance': 1E-6,
+            'subsetsize': 0.85,
+            'lambda': 0.5,
+            'uscale_list': '0.03',
+            'submodel1': submodel1, #'anh 0 1 2 3',  # this should be variable
+        }
+        csld_settings['phonon'] = {
+            'qpoint_fractional': False,
+            # 'Auto' or something like "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
+            'wavevector': "[[25,  [0,0,0],'\Gamma', [0,0.5,0.5], 'X'],"
+                          " [25, [1,0.5,0.5], 'X', [0.75,0.375,0.375], "
+                          "'K', [0,0,0], '\Gamma', [0.5, 0.5, 0.5], 'L']]",
+            'unit': 'meV',  # THz, meV, eV, cm
 
-                # number of grid points
-                'dos_grid': '15 15 15',
+            # number of grid points
+            'dos_grid': '15 15 15',
 
-                # number of points in DOS
-                'nE_dos': 500,
+            # number of points in DOS
+            'nE_dos': 500,
 
-                ## 0 (Gaussian), 1 (Lorentzian), -1 (tetrahedron method)
-                'ismear': -1,
+            ## 0 (Gaussian), 1 (Lorentzian), -1 (tetrahedron method)
+            'ismear': -1,
 
-                ## width in THz of Gaussian/Lorentzian smearing
-                'epsilon': 0.05,
-                'pdos': True,
+            ## width in THz of Gaussian/Lorentzian smearing
+            'epsilon': 0.05,
+            'pdos': True,
 
-                'thermal_T_range': '50 800 50',
-                'thermal_out': 'thermal_out.txt'
-            }
-            csld_settings['export_potential'] = {
-                'export_shengbte': export_sbte, #'5 5 5 2 3'  # 5x5x5 supercell
-                # 2 and 3 orders to be considered
-                # should be variable?
-            }
-            csld_settings['prediction'] = {
-                'interface': 'VASP',
-                'corr_type': 'f',
-                'corr_in': 'Amat_pred.mtx',
-                'corr_out': 'Amat_pred.mtx',
-                'fval_in': 'fval_pred.txt',
-                'fval_out': 'fval_pred.txt',
-                'traindat0': 'fcc222/POSCAR fcc222/traj*'
-            }
-            # set default values
-            csld_settings['DEFAULT'] = {
-                "qpoint_fractional": False,
-                "true_v_fit": 'true_fit.txt',
-                'epsilon': '0.05',
-                "bcs_reweight": 'True',
-                "bcs_penalty": 'arctan',
-                "bcs_jcutoff": '1E-8'}
-
-            csld_options = {}
-            csld_options['pdfout'] = 'plots.pdf'
-            csld_options['ldff_step'] = 0
-            csld_options['phonon_step'] = 1
-            csld_options['phonon'] = False
-            csld_options['save_pot_step'] = 1  # usual default is 0
-            csld_options['pot'] = False
-
-            self["csld_settings"] = csld_settings
-            self["csld_options"] = csld_options
-            self["forces_paths"] = disp_folders
+            'thermal_T_range': '50 800 50',
+            'thermal_out': 'thermal_out.txt'
+        }
+        csld_settings['export_potential'] = {
+            'export_shengbte': export_sbte, #'5 5 5 2 3'  # 5x5x5 supercell
+            # 2 and 3 orders to be considered
+            # should be variable?
+        }
+        csld_settings['prediction'] = {
+            'interface': 'VASP',
+            'corr_type': 'f',
+            'corr_in': 'Amat_pred.mtx',
+            'corr_out': 'Amat_pred.mtx',
+            'fval_in': 'fval_pred.txt',
+            'fval_out': 'fval_pred.txt',
+            'traindat0': 'fcc222/POSCAR fcc222/traj*'
+        }
+        # set default values
+        csld_settings['DEFAULT'] = {
+            "qpoint_fractional": False,
+            "true_v_fit": 'true_fit.txt',
+            'epsilon': '0.05',
+            "bcs_reweight": 'True',
+            "bcs_penalty": 'arctan',
+            "bcs_jcutoff": '1E-8'}
+
+        csld_options = {}
+        csld_options['pdfout'] = 'plots.pdf'
+        csld_options['ldff_step'] = 0
+        csld_options['phonon_step'] = 1
+        csld_options['phonon'] = False
+        csld_options['save_pot_step'] = 1  # usual default is 0
+        csld_options['pot'] = False
+
+        self["csld_settings"] = csld_settings
+        self["csld_options"] = csld_options
+        self["forces_paths"] = disp_folders
 
     def run_task(self, fw_spec):
 
         iter = 0
         not_converged = True
         maxIter = 1
-        convergence_info_dict = self["csld_settings"]["convergence_info"]
         summaries = []
 
         #<FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
@@ -1947,7 +1959,7 @@ def run_task(self, fw_spec):
             formula = self["parent_structure"].formula
             formula_pretty = self["parent_structure"].composition.reduced_formula
             task_label = 'static'
-            supercells_dicts = list(tasks.find({"wf_meta.wf_uuid": uuid,
+            supercells_dicts = list(tasks.find({"wf_meta.wf_uuid": uuid, #<insert
                                                 "task_label": {"$regex": task_label},
                                                 "formula_pretty": formula_pretty},
                                                 ['task_id', 'output.forces']))
@@ -1986,6 +1998,7 @@ def run_task(self, fw_spec):
 
             #Save to DB
             summary = {
+                "date": datetime.now(),
                 "formula": formula,
                 "formula_pretty": formula_pretty,
                 "parent_structure": self["parent_structure"].as_dict(),
@@ -1998,22 +2011,23 @@ def run_task(self, fw_spec):
                 "submodel1": self["csld_settings"]["fitting"]["submodel1"],
                 "export_potential": self["csld_settings"]["export_potential"]["export_shengbte"],
 
-                "cross_val_error": rel_err,
-                "num_imaginary_modes": num_imaginary_bands, #number or percent?
-                "most_imaginary_freq": most_imaginary_freq
+                "cross_val_error": float(rel_err),
+                "num_imaginary_modes": int(num_imaginary_bands), #number or percent?
+                "most_imaginary_freq": float(most_imaginary_freq)
             }
-            latest_settings = {str(convergence_info_dict["iteration"]):
+            latest_settings = {str(self["convergence_info"]["iteration"]):
                                    {self["csld_settings"]["model"]["max_order"],
                                     self["csld_settings"]["fitting"]["submodel1"],
                                     self["csld_settings"]["export_potential"][
                                         "export_shengbte"]}}
-            convergence_info_dict["iteration"] += 1
-            convergence_info_dict["settings_tried"].update(latest_settings)
+            self["convergence_info"]["iteration"] += 1
+            self["convergence_info"]["settings_tried"].update(latest_settings)
 
             if fw_spec.get("tags", None):
                 summary["tags"] = fw_spec["tags"]
 
             summaries.append(summary)
+            iter = self['convergence_info']['iteration']
 
         mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
         mmdb.collection.insert(summaries)
@@ -2022,7 +2036,8 @@ def run_task(self, fw_spec):
             logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
         else:
             logger.info("Compressed Sensing Lattice Dynamics calculation failed."
-                        "Max iterations was reached.")
+                        "Max iterations of CSLD trials (each with different "
+                        "settings) was reached.")
 
 
 # the following definitions for backward compatibility

From d8dedfb0681e81840b687470c03107bd86a0ff3f Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 16 Jul 2019 10:23:39 -0700
Subject: [PATCH 017/207] Fixed workflow generation script and added perturbed
 supercells as a required param (for putting poscars inside displacement
 folders)

---
 atomate/vasp/firetasks/parse_outputs.py | 17 +++---
 atomate/vasp/workflows/base/csld.py     | 80 +++++++++++++++++--------
 2 files changed, 64 insertions(+), 33 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index f3afa8327..e852bc492 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1780,8 +1780,7 @@ class CSLDForceConstantsToDB(FiretaskBase):
     """
 
     required_params = ["db_file", "wf_uuid", "parent_structure",
-                       # "csld_settings", "csld_options",
-
+                        "perturbed_supercells",
                        "trans_mat", "supercell_structure",
                        "disps"]
 
@@ -1798,14 +1797,17 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
         np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
                    delimiter=" ")
         self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
+        self["parent_structure"].to("poscar", filename=supercell_folder + "POSCAR")
 
         disp_folders = []
         csld_traindat_disp_folders = ''
-        for disp in self["disps"]:
+        for idx, disp in enumerate(self["disps"]):
             disp_folder = supercell_folder+'/disp'+str(disp)
             disp_folders += [disp_folder]
             csld_traindat_disp_folders += ' ' + str(disp_folder)
             os.mkdir(disp_folder)
+            self["perturbed_supercells"][idx].to("poscar",
+                                                 filename=disp_folder + "/POSCAR")
 
         self['convergence_info'] = {
             'iteration': 0,
@@ -1822,7 +1824,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'settings_tried': {}
         }
         csld_settings['structure'] = {
-            'prim': 'POSCAR',
+            'prim': supercell_folder + 'POSCAR',
             'sym_tol': '1e-3',
             # 'epsilon_inf': None,  # check how it reads 3x3 matrix
             # 'born_charge': None  # check reading n_atom*9 numbers
@@ -1836,10 +1838,9 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'max_order': max_order, #3,  # this should be variable
             'fractional_distance': False,
             'cluster_diameter': cluster_diam, #'11 6.5 5.0', #this should be variable
-            'cluster_filter': lambda cls: ((cls.order_uniq <= 2)
-                                           or (cls.bond_counts(2.9) >= 2))
-                                          and cls.is_small_in(
-                supercell_folder + "/sc.txt")
+            'cluster_filter': r"lambda cls: ((cls.order_uniq <= 2) or "
+                              r"(cls.bond_counts(2.9) >= 2)) and "
+                              r"cls.is_small_in('" +supercell_folder+ "/sc.txt')"
             # rewrote how it reads the trans_mat
         }
         csld_settings['training'] = {
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index e53003aaa..6acbd1b3d 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -12,13 +12,13 @@
 from fireworks import Workflow, Firework
 from atomate.utils.utils import get_logger
 from atomate.vasp.config import VASP_CMD, DB_FILE, ADD_WF_METADATA #                what is this?
-from atomate.vasp.fireworks.core import StaticFW
+from atomate.vasp.fireworks.core import StaticFW, OptimizeFW
 from atomate.vasp.firetasks.parse_outputs import CSLDForceConstantsToDB
 from atomate.vasp.powerups import (
     add_additional_fields_to_taskdocs
 )
 
-from pymatgen.io.vasp.sets import MPStaticSet
+from pymatgen.io.vasp.sets import MPStaticSet, MPRelaxSet
 
 # NEW THINGS TO INSTALL?
 # from configparser import ConfigParser
@@ -118,27 +118,46 @@ def _add_metadata(structure):
                 structure, other_parameters={"wf_meta": self.wf_meta}
             )
 
-        user_incar_settings = {"ADDGRID": True, #Fast Fourier Transform grid
-                               "LCHARG": False,
-                               "ENCUT": 700,
-                               "EDIFF": 1e-7, #may need to tune this
-                               "PREC": 'Accurate',
-                               "LAECHG": False,
-                               "LREAL": False,
-                               "LASPH": True}
-        user_incar_settings.update(c.get("user_incar_settings", {}))
+        #TODO: Move this relaxation section elsewhere
+        # relax_user_incar_settings = {"EDIFF": 1e-8,
+        #                              "EDIFFG": -1e-5,
+        #                              }
+        # relax_vis = MPRelaxSet(self.parent_structure,
+        #                        user_incar_settings=relax_user_incar_settings)
+        # # relax
+        # fws.append(
+        #     OptimizeFW(
+        #         self.parent_structure,
+        #         vasp_input_set=relax_vis,
+        #         vasp_cmd=c["VASP_CMD"],
+        #         db_file=c["DB_FILE"],
+        #         max_force_threshold=0.05, #idk, should i change this?
+        #         half_kpts_first_relax=False, #idk what this is
+        #         name="{} - CSLD relax parent".format(self.parent_structure.composition.reduced_formula),
+        #     )
+        # )
+        #####################
+
+        static_user_incar_settings = {"ADDGRID": True,
+                                      # Fast Fourier Transform grid
+                                      "LCHARG": False,
+                                      "ENCUT": 700,
+                                      "EDIFF": 1e-7,  # may need to tune this
+                                      "PREC": 'Accurate',
+                                      "LAECHG": False,
+                                      "LREAL": False,
+                                      "LASPH": True}
+        static_user_incar_settings.update(c.get("user_incar_settings", {}))
 
         for idx, perturbed_supercell in enumerate(self.perturbed_supercells):
             # Run static calculations on the perturbed supercells to compute forces on each atom
             name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(idx, self.disps[idx])
 
-
-            vis = MPStaticSet(perturbed_supercell,
-                              user_incar_settings=user_incar_settings)
-
+            static_vis = MPStaticSet(perturbed_supercell,
+                                     user_incar_settings=static_user_incar_settings)
             fws.append(StaticFW(
                 perturbed_supercell,
-                vasp_input_set=vis,
+                vasp_input_set=static_vis,
                 vasp_cmd=c["VASP_CMD"],
                 db_file=c["DB_FILE"],
                 name=name + " static"
@@ -155,6 +174,7 @@ def _add_metadata(structure):
                 parent_structure=self.parent_structure,
                 trans_mat=self.trans_mat,
                 supercell_structure=self.supercell,
+                perturbed_supercells=self.perturbed_supercells,
                 disps=self.disps
             ),
             name="Compressed Sensing Lattice Dynamics",
@@ -176,24 +196,34 @@ def _add_metadata(structure):
         return wf
 
 
+# SCRIPT FOR CREATING THE WORKFLOW AND ADDING IT TO THE DATABASE
 if __name__ == "__main__":
 
     from fireworks import LaunchPad
     from pymatgen.ext.matproj import MPRester
+    from atomate.vasp.powerups import add_tags, set_execution_options
 
     #get a structure
     mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
     structure = mpr.get_structure_by_material_id('mp-149')
 
     csld_class = CompressedSensingLatticeDynamicsWF(structure)
-    # print(csld_class.disps)
-    # print(len(csld_class.disps))
+    print("uuid")
+    print(csld_class.uuid)
 
     wf = csld_class.get_wf()
-
-    print(wf)
-
-    lpad = LaunchPad.auto_load()
-    lpad.add_wf(wf)
-
-    #how did lpad know which database to put the wf?
+    print("trans mat")
+    print(csld_class.trans_mat)
+
+    # wf = add_tags(wf, ['csld', 'v1', 'rees'])
+    # wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
+    # print(wf)
+    #
+    # lpad = LaunchPad.auto_load()
+    # lpad.add_wf(wf)
+
+    # [[4.  0. - 2.]
+    #  [-1.  4. - 1.]
+    # [0.
+    # 0.
+    # 4.]]

From e19c32a5a756165e7f2d7f194c2b9c7ce160a486 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 16 Jul 2019 11:49:19 -0700
Subject: [PATCH 018/207] Workflow now runs without errors but with garbage
 results

---
 atomate/vasp/firetasks/parse_outputs.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index e852bc492..1da28890c 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1968,19 +1968,25 @@ def run_task(self, fw_spec):
             #   for each supercell
 
             supercells_forces = []
-            supercells_task_ids = []
+            # supercells_task_ids = []
+            supercells_task_labels = []
             for supercell_dict in supercells_dicts:
                 #List of np.ndarrays where each np.ndarray is a matrix of forces
                 #  for a perturbed supercell
                 supercells_forces += [np.asarray(supercell_dict['output']['forces'])]
 
-                #List of task ids for each perturbed supercell
-                supercells_task_ids += [supercell_dict['task_id']]
+                # #List of task ids for each perturbed supercell
+                # supercells_task_ids += [supercell_dict['task_id']]
 
-            supercell_idx = 0
-            for supercell_forces in supercells_forces:
+                supercells_task_labels += [supercell_dict['task_label']]
+
+            supercells_zip = sorted(zip(supercells_task_labels, supercells_forces), key=lambda pair: pair[0])
+                                                        #sort by task labels
+            supercells_forces = [supercells_forces for (supercells_task_labels, supercells_forces) in supercells_zip]
+
+            for supercell_idx, supercell_force in enumerate(supercells_forces):
                 path = self["forces_paths"][supercell_idx]
-                np.savetxt(path + "/force.txt", supercell_forces, fmt='%.6f')
+                np.savetxt(path + "/force.txt", supercell_force, fmt='%.6f')
 
             #Perform csld minimization now
             import scripts.csld_main_rees as csld_main

From 32c4a048557c1c2e713426fc333416db6a851a3e Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 17 Jul 2019 10:25:25 -0700
Subject: [PATCH 019/207] IT WORKS LETS GOOOOOO

---
 atomate/vasp/firetasks/parse_outputs.py | 31 +++++++++++++++----------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 1da28890c..c0976d43e 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1797,7 +1797,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
         np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
                    delimiter=" ")
         self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
-        self["parent_structure"].to("poscar", filename=supercell_folder + "POSCAR")
+        self["parent_structure"].to("poscar", filename=supercell_folder + "/POSCAR")
 
         disp_folders = []
         csld_traindat_disp_folders = ''
@@ -1819,12 +1819,8 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
         csld_traindat_string += csld_traindat_disp_folders
 
         csld_settings = ConfigParser()
-        csld_settings['convergence_info'] = {
-            'iteration': 0,
-            'settings_tried': {}
-        }
         csld_settings['structure'] = {
-            'prim': supercell_folder + 'POSCAR',
+            'prim': supercell_folder + '/POSCAR', #original structure poscar
             'sym_tol': '1e-3',
             # 'epsilon_inf': None,  # check how it reads 3x3 matrix
             # 'born_charge': None  # check reading n_atom*9 numbers
@@ -1850,7 +1846,8 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'corr_out': 'Amat.mtx',
             'fval_in': 'fval.txt',
             'fval_out': 'fval.txt',
-            'traindat1': csld_traindat_string
+            'traindat1': csld_traindat_string #directories of unperturbed followed
+                                                #by perturbed supercell poscars
             # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
             # Rewrote how it reads forces
         }
@@ -1948,7 +1945,7 @@ def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
         tasks = mmdb["tasks"]
-        while not_converged or iter < maxIter:
+        while not_converged and iter < maxIter:
             self.set_params(iter,
                             cluster_diam_settings[iter],
                             max_order_settings[iter],
@@ -1963,7 +1960,9 @@ def run_task(self, fw_spec):
             supercells_dicts = list(tasks.find({"wf_meta.wf_uuid": uuid, #<insert
                                                 "task_label": {"$regex": task_label},
                                                 "formula_pretty": formula_pretty},
-                                                ['task_id', 'output.forces']))
+                                                ['task_id',
+                                                 'task_label',
+                                                 'output.forces']))
             #list of dicts where each dict contatins a task_id and a list of forces
             #   for each supercell
 
@@ -1995,8 +1994,15 @@ def run_task(self, fw_spec):
             freq_matrix = np.asarray(freq_matrix)
             imaginary_idx = freq_matrix < 0
             imaginary_freqs = freq_matrix[imaginary_idx]
-            num_imaginary_bands = np.any(imaginary_idx, axis=1)
-            most_imaginary_freq = np.amin(imaginary_freqs)
+            print('IMAGINARY FREQUENCIES:')
+            print(imaginary_freqs)
+            num_imaginary_bands = np.sum(np.any(imaginary_idx, axis=1))
+            print('NUMBER OF IMAGINARY BANDS:')
+            print(num_imaginary_bands)
+            if np.any(imaginary_freqs):
+                most_imaginary_freq = np.amin(imaginary_freqs)
+            else:
+                most_imaginary_freq = 0
             # For imaginary frequencies, w^2 is negative
             # code handles it as w = sign(sqrt(abs(w^2)), w^2)
 
@@ -2034,12 +2040,13 @@ def run_task(self, fw_spec):
                 summary["tags"] = fw_spec["tags"]
 
             summaries.append(summary)
+
             iter = self['convergence_info']['iteration']
 
         mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
         mmdb.collection.insert(summaries)
 
-        if iter < maxIter:
+        if iter <= maxIter:
             logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
         else:
             logger.info("Compressed Sensing Lattice Dynamics calculation failed."

From bfd0b247e73f0dba544106d22372f07ac458551f Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 17 Jul 2019 10:47:30 -0700
Subject: [PATCH 020/207] Added conventional standard primitive structure from
 pymatgen sga

---
 atomate/vasp/workflows/base/csld.py | 33 +++++++++++++++++++++++------
 1 file changed, 26 insertions(+), 7 deletions(-)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 6acbd1b3d..b050279f7 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -4,6 +4,8 @@
 
 import numpy as np
 from uuid import uuid4
+
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.transformations.advanced_transformations import (
     CubicSupercellTransformation,
@@ -36,6 +38,7 @@ class CompressedSensingLatticeDynamicsWF:
     def __init__(
             self,
             parent_structure,
+            symprec=0.1,
             min_atoms=-np.Inf,
             max_atoms=np.Inf,
             num_nn_dists=5,
@@ -75,7 +78,9 @@ def __init__(
         }
 
     # Create supercell
-        self.parent_structure = parent_structure
+        sga = SpacegroupAnalyzer(parent_structure, symprec=symprec)
+        self.parent_structure = sga.get_primitive_standard_structure()
+
         self.min_atoms = min_atoms
         self.max_atoms = max_atoms
         self.num_nn_dists = num_nn_dists
@@ -102,7 +107,6 @@ def __init__(
         self.disps = np.repeat(perturbed_supercells_transform.disps,
                                supercells_per_displacement_distance)
 
-
     def get_wf(
             self,
             c=None
@@ -207,18 +211,33 @@ def _add_metadata(structure):
     mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
     structure = mpr.get_structure_by_material_id('mp-149')
 
-    csld_class = CompressedSensingLatticeDynamicsWF(structure)
+    # prim_structure = structure.get_primitive_structure() #this method is bad
+
+    # CONVENTIONAL PRIMITIVE CELL WITH SYMMETRIZATION
+    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    sga = SpacegroupAnalyzer(structure, symprec=0.1)
+    prim = sga.get_primitive_standard_structure()
+    prim.to("poscar", filename="POSCAR-pmg_prim_si")
+
+    # CSLD'S POLARON MAIN-GENERATED PRIMITIVE CELL
+    # from pymatgen.core.structure import Structure
+    # prim = Structure.from_file('POSCAR_csld_primitivized')
+
+    csld_class = CompressedSensingLatticeDynamicsWF(prim, max_displacement=0.05,
+                                                    min_displacement=0.01,
+                                                    num_displacements=5)
     print("uuid")
     print(csld_class.uuid)
 
     wf = csld_class.get_wf()
     print("trans mat")
     print(csld_class.trans_mat)
+    csld_class.supercell.to("poscar", filename="POSCAR-csld_super_si")
+
+    wf = add_tags(wf, ['csld', 'v1', 'rees', 'sga primitizer'])
+    wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
+    print(wf)
 
-    # wf = add_tags(wf, ['csld', 'v1', 'rees'])
-    # wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
-    # print(wf)
-    #
     # lpad = LaunchPad.auto_load()
     # lpad.add_wf(wf)
 

From 827f2cdff29548f1c5c903833048eaccb05c1797 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 19 Jul 2019 13:39:26 -0700
Subject: [PATCH 021/207] Added random search for csld parameters and shengbte
 stuff

---
 atomate/vasp/firetasks/parse_outputs.py |  1 +
 atomate/vasp/workflows/base/csld.py     | 53 +++++++++++++------------
 2 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index c0976d43e..6cb02e24b 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1782,6 +1782,7 @@ class CSLDForceConstantsToDB(FiretaskBase):
     required_params = ["db_file", "wf_uuid", "parent_structure",
                         "perturbed_supercells",
                        "trans_mat", "supercell_structure",
+                       "supercell_smallest_dim",
                        "disps"]
 
     def set_params(self, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index b050279f7..c457b2401 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -92,6 +92,7 @@ def __init__(
         # supercell (Structure)
         self.supercell = supercell_transform.apply_transformation(self.parent_structure)
         self.trans_mat = supercell_transform.trans_mat
+        self.supercell_smallest_dim = supercell_transform.smallest_dim
 
     # Generate randomly perturbed supercells
         perturbed_supercells_transform = PerturbSitesTransformation(
@@ -178,6 +179,7 @@ def _add_metadata(structure):
                 parent_structure=self.parent_structure,
                 trans_mat=self.trans_mat,
                 supercell_structure=self.supercell,
+                supercell_smallest_dim=self.supercell_smallest_dim,
                 perturbed_supercells=self.perturbed_supercells,
                 disps=self.disps
             ),
@@ -208,41 +210,42 @@ def _add_metadata(structure):
     from atomate.vasp.powerups import add_tags, set_execution_options
 
     #get a structure
-    mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
-    structure = mpr.get_structure_by_material_id('mp-149')
-
-    # prim_structure = structure.get_primitive_structure() #this method is bad
-
-    # CONVENTIONAL PRIMITIVE CELL WITH SYMMETRIZATION
+    # mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
+    # # structure = mpr.get_structure_by_material_id('mp-149') #Si
+    # structure = mpr.get_structure_by_material_id('mp-1101039')
+    # test_trans_mat = np.linalg.inv(structure.lattice.matrix) @ (np.eye(3,3) * 20)
+    # print(test_trans_mat)
+    # print(np.linalg.det(test_trans_mat))
+    # structure_test = structure * test_trans_mat
+    # structure_test.to("poscar", filename="POSCAR-noninteger_trans_test")
+
+    # # CONVENTIONAL PRIMITIVE CELL WITH SYMMETRIZATION
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    sga = SpacegroupAnalyzer(structure, symprec=0.1)
-    prim = sga.get_primitive_standard_structure()
-    prim.to("poscar", filename="POSCAR-pmg_prim_si")
+    # sga = SpacegroupAnalyzer(structure, symprec=0.1)
+    # prim = sga.get_primitive_standard_structure()
 
     # CSLD'S POLARON MAIN-GENERATED PRIMITIVE CELL
-    # from pymatgen.core.structure import Structure
+    from pymatgen.core.structure import Structure
     # prim = Structure.from_file('POSCAR_csld_primitivized')
 
-    csld_class = CompressedSensingLatticeDynamicsWF(prim, max_displacement=0.05,
-                                                    min_displacement=0.01,
-                                                    num_displacements=5)
+    prim = Structure.from_file('POSCAR-well_relaxed_InSb_csld_primitivized')
+    # sga = SpacegroupAnalyzer(prim, symprec=0.1)
+    # prim2 = sga.get_primitive_standard_structure()
+    # prim2.to("poscar", 'POSCAR-InSb-standard')
+
+    csld_class = CompressedSensingLatticeDynamicsWF(prim)
     print("uuid")
     print(csld_class.uuid)
 
     wf = csld_class.get_wf()
     print("trans mat")
     print(csld_class.trans_mat)
-    csld_class.supercell.to("poscar", filename="POSCAR-csld_super_si")
-
-    wf = add_tags(wf, ['csld', 'v1', 'rees', 'sga primitizer'])
-    wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
-    print(wf)
-
+    print(csld_class.supercell_smallest_dim)
+    csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_InSb_standard")
+    #
+    # wf = add_tags(wf, ['csld', 'v1', 'rees', 'InSb', 'first_try'])
+    # wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
+    # print(wf)
+    #
     # lpad = LaunchPad.auto_load()
     # lpad.add_wf(wf)
-
-    # [[4.  0. - 2.]
-    #  [-1.  4. - 1.]
-    # [0.
-    # 0.
-    # 4.]]

From 002e8558c05d184402a10aea31f9b7e74df13da3 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Mon, 22 Jul 2019 17:29:24 -0700
Subject: [PATCH 022/207] accounted for CSLD github and added csld random
 search

---
 atomate/vasp/firetasks/parse_outputs.py | 265 ++++++++++++++++++------
 atomate/vasp/workflows/base/csld.py     |  91 +++++++-
 2 files changed, 279 insertions(+), 77 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 6cb02e24b..9a7568372 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1785,9 +1785,64 @@ class CSLDForceConstantsToDB(FiretaskBase):
                        "supercell_smallest_dim",
                        "disps"]
 
-    def set_params(self, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
+    def random_search(self, maxIter):
+        """
+        -pair potential is roughly 12 Angstroms, so supercell should be safely
+        larger than that (at least 20 in each direction) so you don't get artifacts
+        from periodic boundary conditions (i.e. atoms being double-counted in the
+        pair potential)
+        -"most likely" at least 4 nearest neighbor distances is ok
+        -
+        -150+ atom-supercell
+        -for low symmetry, more atoms = finer displacement linspace (0.02 - 0.05 in
+        steps of 0.01 or 0.005)
+        -9-12 lattice parameters for pair cutoffs, triplets usually a little more than half of pairs
+        - -1 meV phonon mode is
+    	-change cutoff diameter (easiest, probably increase)
+    	-either increase supercells or relax primitive cell better (check total drift)
+
+    	CSLD CHECKS: IF FITTING IS BAD...
+        Option 1.
+        Play with cluster diameters
+            -random search? bayesopt?
+            -if tried some max number trials and still bad, pick the best one and move to Option 2
+
+        Option 2.
+        Include higher displacement supercells
+            1. If Natom>5, generate supercells at large displacements (>0.1 angstroms)
+            2. Fit up to 3rd order only with supercells perturbed <0.1 angstroms
+                -If good, run SBTE
+                -If bad, then fit including supercells >0.1 angstroms
+                    -If good, run SBTE
+                    -If bad, redo step 2 with 4th order
+        :return:
+        """
+        import random
+
+        if maxIter % 2 != 0 or maxIter <= 0:
+            raise AttributeError('maxIter must be even.')
+
+        cluster_diam_settings = []
+        for _ in range(maxIter):
+            pair_diam = random.uniform(10, 14) #self["supercell_smallest_dim"])
+            triplet_diam = random.uniform(pair_diam * 0.4, pair_diam)
+            quadruplet_diam = random.uniform(triplet_diam * 0.6, triplet_diam)
+
+            cluster_diam_settings += [
+                str(pair_diam) + ' ' + str(triplet_diam) + ' ' + str(
+                    quadruplet_diam)]
+
+        max_order_settings = [3] * int(maxIter / 2) + [4] * int(maxIter / 2)
+        submodel1_settings = ['anh 0 1 2 3'] * int(maxIter / 2) + \
+                             ['anh 0 1 2 3 4'] * int(maxIter / 2)
+
+        return cluster_diam_settings, max_order_settings, submodel1_settings
+
+    def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
+                   export_sbte):
         from configparser import ConfigParser
-        supercell_folder = self["parent_structure"].composition.reduced_formula + \
+        supercell_folder = self[
+                               "parent_structure"].composition.reduced_formula + \
                            "_supercell_iter" + str(iteration_number)
 
         # Remove supercell_folder if it already exists, then make a new one
@@ -1795,33 +1850,46 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             shutil.rmtree(supercell_folder)
         os.mkdir(supercell_folder)
 
+        # Save transformation matrix, supercell POSCAR, and parent structure
+        #   POSCAR to file
         np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
                    delimiter=" ")
-        self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
-        self["parent_structure"].to("poscar", filename=supercell_folder + "/POSCAR")
+        self["supercell_structure"].to("poscar",
+                                       filename=supercell_folder + "/SPOSCAR")
+        self["parent_structure"].to("poscar",
+                                    filename=supercell_folder + "/POSCAR")
 
+        # Create folders for perturbed supercell POSCARS and force.txt's
         disp_folders = []
         csld_traindat_disp_folders = ''
         for idx, disp in enumerate(self["disps"]):
-            disp_folder = supercell_folder+'/disp'+str(disp)
-            disp_folders += [disp_folder]
-            csld_traindat_disp_folders += ' ' + str(disp_folder)
+            disp_folder = supercell_folder + '/disp' + str(disp)
+            disp_folders += [disp_folder]  # list of folder paths
+            csld_traindat_disp_folders += ' ' + str(
+                disp_folder)  # Create string for CSLD input
+            if os.path.exists(disp_folder) and os.path.isdir(disp_folder):
+                shutil.rmtree(disp_folder)
             os.mkdir(disp_folder)
             self["perturbed_supercells"][idx].to("poscar",
                                                  filename=disp_folder + "/POSCAR")
 
+        # Store information related to convergence of CSLD
         self['convergence_info'] = {
             'iteration': 0,
-            'settings_tried': {}
+            'settings_tried': [],
+            'cross_val_errors': [],
+            'most_imaginary_freqs': [],
+            'imaginary_freqs_sum': []
         }
 
-        # Parameters for conducting CSLD
+        # training>traindat1 setting for CSLD input
         csld_traindat_string = supercell_folder + '/SPOSCAR'
         csld_traindat_string += csld_traindat_disp_folders
 
+        # Create ConfigParser of all CSLD input settings
         csld_settings = ConfigParser()
         csld_settings['structure'] = {
-            'prim': supercell_folder + '/POSCAR', #original structure poscar
+            'prim': supercell_folder + '/POSCAR',  # original structure poscar
             'sym_tol': '1e-3',
             # 'epsilon_inf': None,  # check how it reads 3x3 matrix
             # 'born_charge': None  # check reading n_atom*9 numbers
@@ -1832,12 +1900,13 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'cluster_out': 'clusters.out',
             'symC_in': 'Cmat.mtx',
             'symC_out': 'Cmat.mtx',
-            'max_order': max_order, #3,  # this should be variable
+            'max_order': max_order,  # 3,  # this should be variable
             'fractional_distance': False,
-            'cluster_diameter': cluster_diam, #'11 6.5 5.0', #this should be variable
+            'cluster_diameter': cluster_diam,
+            # '11 6.5 5.0', #this should be variable
             'cluster_filter': r"lambda cls: ((cls.order_uniq <= 2) or "
                               r"(cls.bond_counts(2.9) >= 2)) and "
-                              r"cls.is_small_in('" +supercell_folder+ "/sc.txt')"
+                              r"cls.is_small_in('" + supercell_folder + "/sc.txt')"
             # rewrote how it reads the trans_mat
         }
         csld_settings['training'] = {
@@ -1847,8 +1916,9 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'corr_out': 'Amat.mtx',
             'fval_in': 'fval.txt',
             'fval_out': 'fval.txt',
-            'traindat1': csld_traindat_string #directories of unperturbed followed
-                                                #by perturbed supercell poscars
+            'traindat1': csld_traindat_string
+            # directories of unperturbed followed
+            # by perturbed supercell poscars
             # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
             # Rewrote how it reads forces
         }
@@ -1863,13 +1933,13 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'method': 5,
 
             # For weight of L1 or L2 regularization
-            'mulist': '1E-5 1E-7 1E-9 1E-11',
+            'mulist': '1E-5 1E-6 1E-7 1E-9',
             'maxIter': 300,
             'tolerance': 1E-6,
             'subsetsize': 0.85,
             'lambda': 0.5,
             'uscale_list': '0.03',
-            'submodel1': submodel1, #'anh 0 1 2 3',  # this should be variable
+            'submodel1': submodel1,  # 'anh 0 1 2 3',  # this should be variable
         }
         csld_settings['phonon'] = {
             'qpoint_fractional': False,
@@ -1896,7 +1966,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             'thermal_out': 'thermal_out.txt'
         }
         csld_settings['export_potential'] = {
-            'export_shengbte': export_sbte, #'5 5 5 2 3'  # 5x5x5 supercell
+            'export_shengbte': export_sbte,  # '5 5 5 2 3'  # 5x5x5 supercell
             # 2 and 3 orders to be considered
             # should be variable?
         }
@@ -1919,98 +1989,136 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
             "bcs_jcutoff": '1E-8'}
 
         csld_options = {}
-        csld_options['pdfout'] = 'plots.pdf'
+        csld_options['pdfout'] = 'plots.pdf'  # Name of pdf to output results
         csld_options['ldff_step'] = 0
         csld_options['phonon_step'] = 1
         csld_options['phonon'] = False
-        csld_options['save_pot_step'] = 1  # usual default is 0
+        csld_options[
+            'save_pot_step'] = 1  # usual default is 0. 1 means output to ShengBTE format.
         csld_options['pot'] = False
 
+        # set default values
+        csld_options['log_level'] = 1
+        csld_options['symm_step'] = 2
+        csld_options['symm_prim'] = True
+        csld_options['clus_step'] = 3
+        csld_options['symC_step'] = 3
+        csld_options['train_step'] = 3
+        csld_options['fit_step'] = 3
+        csld_options['pred_step'] = 0
+        csld_options['refit'] = False
+        csld_options['cont'] = False
+        csld_options['predict'] = False
+
         self["csld_settings"] = csld_settings
         self["csld_options"] = csld_options
-        self["forces_paths"] = disp_folders
+        self["forces_paths"] = disp_folders  # Paths to perturbed supercell folders
 
     def run_task(self, fw_spec):
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+        tasks = mmdb["tasks"]
 
         iter = 0
         not_converged = True
-        maxIter = 1
+        maxIter = 2
         summaries = []
 
-        #<FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
-        cluster_diam_settings = ['11 6.5 5.0']
-        max_order_settings = [3]
-        submodel1_settings = ['anh 0 1 2 3']
-        export_sbte_settings = ['5 5 5 2 3']
+        # <FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
+        # cluster_diam_settings = ['11 6.5 5.0']
+        # max_order_settings = [3]
+        # submodel1_settings = ['anh 0 1 2 3']
+        # export_sbte_settings = ['5 5 5 2 3']
+
+        cluster_diam_settings, max_order_settings, submodel1_settings = self.random_search(
+            maxIter)
+        print('cluster_diam')
+        print(cluster_diam_settings)
+        print('max order')
+        print(max_order_settings)
+        print('submodel')
+        print(submodel1_settings)
+        export_sbte_settings = ['5 5 5 2 3'] * maxIter
 
-        db_file = env_chk(self.get("db_file"), fw_spec)
-        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        tasks = mmdb["tasks"]
         while not_converged and iter < maxIter:
             self.set_params(iter,
                             cluster_diam_settings[iter],
                             max_order_settings[iter],
                             submodel1_settings[iter],
                             export_sbte_settings[iter])
+            self["csld_options"]["pdfout"] = 'plots' + str(iter) + '.pdf'
 
             uuid = self["wf_uuid"]
 
             formula = self["parent_structure"].formula
-            formula_pretty = self["parent_structure"].composition.reduced_formula
+            formula_pretty = self[
+                "parent_structure"].composition.reduced_formula
             task_label = 'static'
-            supercells_dicts = list(tasks.find({"wf_meta.wf_uuid": uuid, #<insert
-                                                "task_label": {"$regex": task_label},
-                                                "formula_pretty": formula_pretty},
-                                                ['task_id',
-                                                 'task_label',
-                                                 'output.forces']))
-            #list of dicts where each dict contatins a task_id and a list of forces
+            supercells_dicts = list(
+                tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
+                            "task_label": {"$regex": task_label},
+                            "formula_pretty": formula_pretty},
+                           ['task_id',
+                            'task_label',
+                            'output.forces']))
+            # list of dicts where each dict contatins a task_id and a list of forces
             #   for each supercell
 
             supercells_forces = []
             # supercells_task_ids = []
             supercells_task_labels = []
             for supercell_dict in supercells_dicts:
-                #List of np.ndarrays where each np.ndarray is a matrix of forces
+                # List of np.ndarrays where each np.ndarray is a matrix of forces
                 #  for a perturbed supercell
-                supercells_forces += [np.asarray(supercell_dict['output']['forces'])]
+                supercells_forces += [
+                    np.asarray(supercell_dict['output']['forces'])]
 
                 # #List of task ids for each perturbed supercell
                 # supercells_task_ids += [supercell_dict['task_id']]
 
                 supercells_task_labels += [supercell_dict['task_label']]
 
-            supercells_zip = sorted(zip(supercells_task_labels, supercells_forces), key=lambda pair: pair[0])
-                                                        #sort by task labels
-            supercells_forces = [supercells_forces for (supercells_task_labels, supercells_forces) in supercells_zip]
+            supercells_zip = sorted(
+                zip(supercells_task_labels, supercells_forces),
+                key=lambda pair: pair[0])
+            # sort by task labels
+            supercells_forces = [supercells_forces for
+                                 (supercells_task_labels, supercells_forces) in
+                                 supercells_zip]
 
+            # Create force.txt files for perturbed supercells
             for supercell_idx, supercell_force in enumerate(supercells_forces):
                 path = self["forces_paths"][supercell_idx]
                 np.savetxt(path + "/force.txt", supercell_force, fmt='%.6f')
 
-            #Perform csld minimization now
-            import scripts.csld_main_rees as csld_main
-            rel_err, freq_matrix = csld_main.main(self["csld_options"],
-                                                  self["csld_settings"])
+            # Perform csld minimization now
+            # import scripts.csld_main_rees as csld_main
+            from atomate.vasp.workflows.base.csld import csld_main
+            rel_err, freq_matrix = csld_main(self["csld_options"],
+                                             self["csld_settings"])
+            # rel_err = 0.01
+            # freq_matrix = [[1, -1, 1],
+            #                [-1, 1, 1]] #(nbands, nkpoints)
+
             freq_matrix = np.asarray(freq_matrix)
-            imaginary_idx = freq_matrix < 0
+            imaginary_idx = freq_matrix < -0.01  # UPDATE THIS NUMBER TO HAVE SOME CUSHION
             imaginary_freqs = freq_matrix[imaginary_idx]
-            print('IMAGINARY FREQUENCIES:')
+            print('IMAGINARY FREQUENCIES')
             print(imaginary_freqs)
             num_imaginary_bands = np.sum(np.any(imaginary_idx, axis=1))
-            print('NUMBER OF IMAGINARY BANDS:')
             print(num_imaginary_bands)
             if np.any(imaginary_freqs):
                 most_imaginary_freq = np.amin(imaginary_freqs)
             else:
                 most_imaginary_freq = 0
+            print(most_imaginary_freq)
             # For imaginary frequencies, w^2 is negative
             # code handles it as w = sign(sqrt(abs(w^2)), w^2)
 
             if num_imaginary_bands == 0:
                 not_converged = False
 
-            #Save to DB
+            # Save to DB
             summary = {
                 "date": datetime.now(),
                 "formula": formula,
@@ -2018,24 +2126,34 @@ def run_task(self, fw_spec):
                 "parent_structure": self["parent_structure"].as_dict(),
                 "wf_meta": {"wf_uuid": uuid},
 
-                #<store relevant CSLD settings>
+                # <store relevant CSLD settings>
                 "iteration": iter,
-                "cluster_diam": self["csld_settings"]["model"]["cluster_diameter"],
+                "cluster_diam": self["csld_settings"]["model"][
+                    "cluster_diameter"],
                 "max_order": self["csld_settings"]["model"]["max_order"],
                 "submodel1": self["csld_settings"]["fitting"]["submodel1"],
-                "export_potential": self["csld_settings"]["export_potential"]["export_shengbte"],
+                "export_potential": self["csld_settings"]["export_potential"][
+                    "export_shengbte"],
 
                 "cross_val_error": float(rel_err),
-                "num_imaginary_modes": int(num_imaginary_bands), #number or percent?
-                "most_imaginary_freq": float(most_imaginary_freq)
+                "num_imaginary_modes": int(num_imaginary_bands),
+                # number or percent?
+                "most_imaginary_freq": float(most_imaginary_freq),
+                "imaginary_freq_sum": float(sum(imaginary_freqs))
             }
             latest_settings = {str(self["convergence_info"]["iteration"]):
                                    {self["csld_settings"]["model"]["max_order"],
-                                    self["csld_settings"]["fitting"]["submodel1"],
+                                    self["csld_settings"]["fitting"][
+                                        "submodel1"],
                                     self["csld_settings"]["export_potential"][
                                         "export_shengbte"]}}
             self["convergence_info"]["iteration"] += 1
-            self["convergence_info"]["settings_tried"].update(latest_settings)
+            self["convergence_info"]["settings_tried"] += [latest_settings]
+            self["convergence_info"]["cross_val_errors"] += [rel_err]
+            self["convergence_info"]["most_imaginary_freqs"] += [
+                most_imaginary_freq]
+            self["convergence_info"]["imaginary_freqs_sum"] += [
+                sum(imaginary_freqs)]
 
             if fw_spec.get("tags", None):
                 summary["tags"] = fw_spec["tags"]
@@ -2044,15 +2162,30 @@ def run_task(self, fw_spec):
 
             iter = self['convergence_info']['iteration']
 
-        mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
-        mmdb.collection.insert(summaries)
-
-        if iter <= maxIter:
-            logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
+        # mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
+        # mmdb.collection.insert(summaries)
+        mmdb.compressed_sensing_lattice_dynamics.insert(summaries)
+
+        best_idx = self["convergence_info"]["cross_val_errors"].index(
+            min(self["convergence_info"]["cross_val_errors"]))
+        print("The lowest error was {} percent.".format(
+            min(self["convergence_info"]["cross_val_errors"])))
+        print("The corresponding settings were: {}".format(
+            self["convergence_info"]["settings_tried"][best_idx]))
+
+        if not_converged is False:
+            #     logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
+            #     from fireworks.core.firework import Firework
+            #     shengbte_fw = Firework('<shengbte firetask>, {fw_spec: dict of info to pass to next firework}')
+            #           <mpirun -n 32 ./ShengBTE 2>BTE.err >BTE.out>
+            #     return FWAction(additions=shengbte_fw)
+            raise NotImplementedError("Implement ShengBTE firework")
         else:
-            logger.info("Compressed Sensing Lattice Dynamics calculation failed."
-                        "Max iterations of CSLD trials (each with different "
-                        "settings) was reached.")
+            #     logger.info("Compressed Sensing Lattice Dynamics calculation failed."
+            #                 "Max iterations was reached.")
+            raise TimeoutError(
+                "The workflow was unable to find a solution to CSLD"
+                " for this material.")
 
 
 # the following definitions for backward compatibility
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index c457b2401..993cbb129 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -228,12 +228,12 @@ def _add_metadata(structure):
     from pymatgen.core.structure import Structure
     # prim = Structure.from_file('POSCAR_csld_primitivized')
 
-    prim = Structure.from_file('POSCAR-well_relaxed_InSb_csld_primitivized')
-    # sga = SpacegroupAnalyzer(prim, symprec=0.1)
-    # prim2 = sga.get_primitive_standard_structure()
-    # prim2.to("poscar", 'POSCAR-InSb-standard')
+    prim = Structure.from_file('POSCAR-well_relaxed_Sr8Sb4Au4')
 
-    csld_class = CompressedSensingLatticeDynamicsWF(prim)
+    csld_class = CompressedSensingLatticeDynamicsWF(prim,
+                                                    num_nn_dists=5,
+                                                    num_displacements=10,
+                                                    supercells_per_displacement_distance=1)
     print("uuid")
     print(csld_class.uuid)
 
@@ -241,11 +241,80 @@ def _add_metadata(structure):
     print("trans mat")
     print(csld_class.trans_mat)
     print(csld_class.supercell_smallest_dim)
-    csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_InSb_standard")
-    #
-    # wf = add_tags(wf, ['csld', 'v1', 'rees', 'InSb', 'first_try'])
-    # wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
-    # print(wf)
-    #
+    print(csld_class.supercell.num_sites)
+    csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Sr8Sb4Au4")
+
+    wf = add_tags(wf, ['csld', 'v1', 'rees', 'Sr8Sb4Au4', '10disps_1each'])
+    wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
+    print(wf)
+
     # lpad = LaunchPad.auto_load()
     # lpad.add_wf(wf)
+
+# uuid
+# 0ff0d430-b43f-4cb5-ac8b-55c465b7867c
+# DISPS
+# [0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1 ]
+# trans mat
+# [[-3.  3.  3.]
+#  [ 3. -3.  3.]
+#  [ 3.  3. -3.]]
+# 23.745154105620003
+# 432
+
+#################custom csld_main below##################
+def csld_main(options, settings):
+    """
+    Runs CSLD minimization.
+
+    Changes from original version:
+        - Made 'prim' an argument in 'phonon_step()'
+        - Moved execution files to this main() function to be called from
+          atomate
+        - Rewrote 'add_common_parameter' in 'common_main' to treat 'options' as
+          a dictionary instead of ArgumentParser
+    """
+    import matplotlib
+    matplotlib.use('Agg')
+    from matplotlib.backends.backend_pdf import PdfPages
+    import atexit
+    import csld
+    from csld.symmetry_structure import SymmetrizedStructure
+
+    from csld.lattice_dynamics import init_ld_model
+
+    from csld.common_main import upon_exit, \
+        init_training, fit_data, phonon_step, \
+        save_pot, predict
+
+    freq_matrix = None #Rees
+    pdfout = PdfPages(
+        options['pdfout'].strip()) if options['pdfout'].strip() else None
+    atexit.register(upon_exit, pdfout)
+
+    prim = SymmetrizedStructure.init_structure(settings['structure'],
+                                               options['symm_step'],
+                                               options['symm_prim'],
+                                               options['log_level'])
+    model = init_ld_model(prim, settings['model'], settings[
+        'LDFF'] if 'LDFF' in settings.sections() else {}, options['clus_step'],
+                          options['symC_step'], options['ldff_step'])
+    Amat, fval = init_training(model, settings['training'], options['train_step'])
+    ibest, solutions, rel_err = fit_data(model, Amat, fval, settings['fitting'],
+                                options['fit_step'], pdfout)
+    if settings.has_section('phonon'):
+        phonon, freq_matrix = phonon_step(model, solutions, settings['phonon'],
+                             options['phonon_step'], pdfout, prim)
+    if settings.has_section('export_potential'):
+        save_pot(model, solutions[ibest], settings['export_potential'],
+                 options['save_pot_step'], phonon)
+    if settings.has_section('prediction'):
+        predict(model, solutions, settings['prediction'], options['pred_step'])
+
+    #OUTPUT
+    # freq_matrix is (nbands, nkpoints) = frequencies. Check for negative entries
+    # rel_err is cross validation error in percent
+    return rel_err, freq_matrix #also want to return force constants
+
+
+

From 123f034497b6e5be06e973149ee9713b592529f9 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 23 Jul 2019 14:28:19 -0700
Subject: [PATCH 023/207] Added dynamic fireworks for possible error handling
 (i.e. larger displacement values)

---
 atomate/vasp/firetasks/parse_outputs.py | 153 ++++++++++++++++++------
 atomate/vasp/workflows/base/csld.py     |   5 +-
 2 files changed, 119 insertions(+), 39 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 9a7568372..99a902b45 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -8,9 +8,15 @@
 import numpy as np
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 from fireworks.utilities.fw_serializers import DATETIME_HANDLER
+<<<<<<< HEAD
 from monty.json import MontyEncoder, jsanitize
 from monty.os.path import zpath
 from pydash.objects import get, has
+=======
+from fireworks import Firework
+
+from pymatgen import Structure
+>>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 from pymatgen.analysis.elasticity.elastic import ElasticTensor, ElasticTensorExpansion
 from pymatgen.analysis.elasticity.strain import Deformation, Strain
 from pymatgen.analysis.elasticity.stress import Stress
@@ -29,12 +35,26 @@
 from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer
 from pymatgen.io.vasp.sets import get_vasprun_outcar
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+<<<<<<< HEAD
+=======
+from pymatgen.analysis.ferroelectricity.polarization import Polarization, get_total_ionic_dipole, \
+    EnergyTrend
+from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering, magnetic_deformation
+from pymatgen.command_line.bader_caller import bader_analysis_from_path
+from pymatgen.transformations.advanced_transformations import PerturbSitesTransformation
+from pymatgen.io.vasp.sets import MPStaticSet
+>>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 
 from atomate.common.firetasks.glue_tasks import get_calc_loc
 from atomate.utils.utils import env_chk, get_logger, get_meta_from_structure
 from atomate.vasp.config import DEFUSE_UNSUCCESSFUL, STORE_VOLUMETRIC_DATA
 from atomate.vasp.database import VaspCalcDb
+<<<<<<< HEAD
 from atomate.vasp.drones import BADER_EXE_EXISTS, VaspDrone
+=======
+from atomate.vasp.drones import VaspDrone
+from atomate.vasp.fireworks.core import StaticFW
+>>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 
 __author__ = "Anubhav Jain, Kiran Mathew, Shyam Dwaraknath"
 __email__ = "ajain@lbl.gov, kmathew@lbl.gov, shyamd@lbl.gov"
@@ -1779,11 +1799,16 @@ class CSLDForceConstantsToDB(FiretaskBase):
     #     to a .json file.
     """
 
-    required_params = ["db_file", "wf_uuid", "parent_structure",
-                        "perturbed_supercells",
-                       "trans_mat", "supercell_structure",
-                       "supercell_smallest_dim",
-                       "disps"]
+    logger = get_logger(__name__)
+
+    required_params = ["db_file",
+        "wf_uuid", "parent_structure",
+        "perturbed_supercells",
+        "trans_mat", "supercell_structure",
+        "supercell_smallest_dim",
+        "disps", "first_pass"]
+
+    optional_params = ["static_user_incar_settings", "env_vars"]
 
     def random_search(self, maxIter):
         """
@@ -1838,11 +1863,9 @@ def random_search(self, maxIter):
 
         return cluster_diam_settings, max_order_settings, submodel1_settings
 
-    def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
-                   export_sbte):
+    def set_params(self, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
         from configparser import ConfigParser
-        supercell_folder = self[
-                               "parent_structure"].composition.reduced_formula + \
+        supercell_folder = self["parent_structure"].composition.reduced_formula + \
                            "_supercell_iter" + str(iteration_number)
 
         # Remove supercell_folder if it already exists, then make a new one
@@ -1854,19 +1877,16 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
         #   POSCAR to file
         np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
                    delimiter=" ")
-        self["supercell_structure"].to("poscar",
-                                       filename=supercell_folder + "/SPOSCAR")
-        self["parent_structure"].to("poscar",
-                                    filename=supercell_folder + "/POSCAR")
+        self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
+        self["parent_structure"].to("poscar", filename=supercell_folder + "/POSCAR")
 
         # Create folders for perturbed supercell POSCARS and force.txt's
         disp_folders = []
         csld_traindat_disp_folders = ''
         for idx, disp in enumerate(self["disps"]):
             disp_folder = supercell_folder + '/disp' + str(disp)
-            disp_folders += [disp_folder]  # list of folder paths
-            csld_traindat_disp_folders += ' ' + str(
-                disp_folder)  # Create string for CSLD input
+            disp_folders += [disp_folder] # list of folder paths
+            csld_traindat_disp_folders += ' ' + str(disp_folder) # Create string for CSLD input
             if os.path.exists(disp_folder) and os.path.isdir(disp_folder):
                 shutil.rmtree(disp_folder)
             os.mkdir(disp_folder)
@@ -1889,7 +1909,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
         # Create ConfigParser of all CSLD input settings
         csld_settings = ConfigParser()
         csld_settings['structure'] = {
-            'prim': supercell_folder + '/POSCAR',  # original structure poscar
+            'prim': supercell_folder + '/POSCAR', # original structure poscar
             'sym_tol': '1e-3',
             # 'epsilon_inf': None,  # check how it reads 3x3 matrix
             # 'born_charge': None  # check reading n_atom*9 numbers
@@ -1900,10 +1920,9 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
             'cluster_out': 'clusters.out',
             'symC_in': 'Cmat.mtx',
             'symC_out': 'Cmat.mtx',
-            'max_order': max_order,  # 3,  # this should be variable
+            'max_order': max_order, # 3,  # this should be variable
             'fractional_distance': False,
-            'cluster_diameter': cluster_diam,
-            # '11 6.5 5.0', #this should be variable
+            'cluster_diameter': cluster_diam, # '11 6.5 5.0', #this should be variable
             'cluster_filter': r"lambda cls: ((cls.order_uniq <= 2) or "
                               r"(cls.bond_counts(2.9) >= 2)) and "
                               r"cls.is_small_in('" + supercell_folder + "/sc.txt')"
@@ -1916,8 +1935,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
             'corr_out': 'Amat.mtx',
             'fval_in': 'fval.txt',
             'fval_out': 'fval.txt',
-            'traindat1': csld_traindat_string
-            # directories of unperturbed followed
+            'traindat1': csld_traindat_string # directories of unperturbed followed
             # by perturbed supercell poscars
             # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
             # Rewrote how it reads forces
@@ -1939,7 +1957,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
             'subsetsize': 0.85,
             'lambda': 0.5,
             'uscale_list': '0.03',
-            'submodel1': submodel1,  # 'anh 0 1 2 3',  # this should be variable
+            'submodel1': submodel1, # 'anh 0 1 2 3',  # this should be variable
         }
         csld_settings['phonon'] = {
             'qpoint_fractional': False,
@@ -1966,7 +1984,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
             'thermal_out': 'thermal_out.txt'
         }
         csld_settings['export_potential'] = {
-            'export_shengbte': export_sbte,  # '5 5 5 2 3'  # 5x5x5 supercell
+            'export_shengbte': export_sbte, # '5 5 5 2 3'  # 5x5x5 supercell
             # 2 and 3 orders to be considered
             # should be variable?
         }
@@ -1993,8 +2011,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1,
         csld_options['ldff_step'] = 0
         csld_options['phonon_step'] = 1
         csld_options['phonon'] = False
-        csld_options[
-            'save_pot_step'] = 1  # usual default is 0. 1 means output to ShengBTE format.
+        csld_options['save_pot_step'] = 1  # usual default is 0. 1 means output to ShengBTE format.
         csld_options['pot'] = False
 
         # set default values
@@ -2025,20 +2042,25 @@ def run_task(self, fw_spec):
         summaries = []
 
         # <FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
-        # cluster_diam_settings = ['11 6.5 5.0']
-        # max_order_settings = [3]
-        # submodel1_settings = ['anh 0 1 2 3']
-        # export_sbte_settings = ['5 5 5 2 3']
-
-        cluster_diam_settings, max_order_settings, submodel1_settings = self.random_search(
-            maxIter)
+        cluster_diam_settings = ['11 6.5 5.0',
+                                 '9 6.5 5.0']
+        max_order_settings = [3] * len(cluster_diam_settings)
+        submodel1_settings = ['anh 0 1 2 3'] * len(cluster_diam_settings)
+        export_sbte_settings = ['5 5 5 2 3'] * len(cluster_diam_settings)
+        if self["first_pass"] is False:
+            max_order_settings += [4] * len(cluster_diam_settings)
+            cluster_diam_settings += cluster_diam_settings
+            submodel1_settings += submodel1_settings
+            export_sbte_settings += export_sbte_settings
+
+        # cluster_diam_settings, max_order_settings, submodel1_settings = self.random_search(maxIter)
+        # export_sbte_settings = ['5 5 5 2 3'] * maxIter
         print('cluster_diam')
         print(cluster_diam_settings)
         print('max order')
         print(max_order_settings)
         print('submodel')
         print(submodel1_settings)
-        export_sbte_settings = ['5 5 5 2 3'] * maxIter
 
         while not_converged and iter < maxIter:
             self.set_params(iter,
@@ -2101,7 +2123,7 @@ def run_task(self, fw_spec):
             #                [-1, 1, 1]] #(nbands, nkpoints)
 
             freq_matrix = np.asarray(freq_matrix)
-            imaginary_idx = freq_matrix < -0.01  # UPDATE THIS NUMBER TO HAVE SOME CUSHION
+            imaginary_idx = freq_matrix < -1  # UPDATE THIS NUMBER TO HAVE SOME CUSHION
             imaginary_freqs = freq_matrix[imaginary_idx]
             print('IMAGINARY FREQUENCIES')
             print(imaginary_freqs)
@@ -2183,9 +2205,64 @@ def run_task(self, fw_spec):
         else:
             #     logger.info("Compressed Sensing Lattice Dynamics calculation failed."
             #                 "Max iterations was reached.")
-            raise TimeoutError(
-                "The workflow was unable to find a solution to CSLD"
-                " for this material.")
+            if self["parent_structure"].num_sites > 5 and self["first_pass"]:
+                #     logger.info("Compressed Sensing Lattice Dynamics calculation failed."
+                #                 " Max iterations was reached. Creating larger displacements"
+                #                 " and trying again,")
+                print('placeholder')
+                new_fws = []
+
+                # Create new perturbed supercells
+                more_perturbed_supercells_transform = PerturbSitesTransformation(
+                    max_displacement=0.2,
+                    min_displacement=0.12,
+                    num_displacements=5,
+                    structures_per_displacement_distance=1,
+                    min_random_distance=None
+                )
+                more_perturbed_supercells = more_perturbed_supercells_transform.apply_transformation(self["supercell_structure"])
+                more_disps = more_perturbed_supercells_transform.disps
+
+                # Create new static FWs
+                for idx, more_perturbed_supercell in enumerate(more_perturbed_supercells):
+                    name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(idx+len(self["perturbed_supercells"]),
+                                                                                    more_disps)
+                    static_vis = MPStaticSet(more_perturbed_supercell,
+                                             user_incar_settings=self["static_user_incar_settings"])
+
+                    new_fws.append(StaticFW(
+                        more_perturbed_supercell,
+                        vasp_input_set=static_vis,
+                        vasp_cmd=self["env_vars"]["VASP_CMD"],
+                        db_file=self["env_vars"]["DB_FILE"],
+                        name=name + " static"
+                    ))
+
+                # Create new CSLD FW
+                new_csld_fw = Firework(
+                    CSLDForceConstantsToDB(
+                        db_file=self["env_vars"]["DB_FILE"],
+                        wf_uuid=self["wf_uuid"],
+                        name='CSLDForceConstantsToDB',
+                        parent_structure=self["parent_structure"],
+                        trans_mat=self["trans_mat"],
+                        supercell_structure=self["supercell_structure"],
+                        supercell_smallest_dim=self["supercell_smallest_dim"],
+                        perturbed_supercells=self["perturbed_supercells"]+more_perturbed_supercells,
+                        disps=self["disps"]+more_disps,
+                        first_pass=False
+                    ),
+                    name="Compressed Sensing Lattice Dynamics",
+                    parents=new_fws[-len(more_perturbed_supercells):]
+                )
+                new_fws.append(new_csld_fw)
+
+                # Dynamically add new fireworks to the workflow
+                return FWAction(additions=new_fws)
+
+            else:
+                raise TimeoutError("The workflow was unable to find a solution to CSLD"
+                    " for this material.")
 
 
 # the following definitions for backward compatibility
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 993cbb129..5a4e1890c 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -181,7 +181,10 @@ def _add_metadata(structure):
                 supercell_structure=self.supercell,
                 supercell_smallest_dim=self.supercell_smallest_dim,
                 perturbed_supercells=self.perturbed_supercells,
-                disps=self.disps
+                disps=self.disps,
+                first_pass=True,
+                static_user_incar_settings=static_user_incar_settings,
+                env_vars=c
             ),
             name="Compressed Sensing Lattice Dynamics",
             parents=fws[-len(self.perturbed_supercells):]

From fa59f5c711f29d9c8aa8f9bd808e36af06797cc6 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 26 Jul 2019 14:20:58 -0700
Subject: [PATCH 024/207] Added fw_spec updates to all dynamically added
 fireworks and wrote a ShengBTE firetask

---
 atomate/vasp/firetasks/parse_outputs.py | 162 +++++++++++++++++++++---
 atomate/vasp/workflows/base/csld.py     |  13 +-
 2 files changed, 155 insertions(+), 20 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 99a902b45..cbd49b086 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -53,8 +53,11 @@
 from atomate.vasp.drones import BADER_EXE_EXISTS, VaspDrone
 =======
 from atomate.vasp.drones import VaspDrone
+<<<<<<< HEAD
 from atomate.vasp.fireworks.core import StaticFW
 >>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
+=======
+>>>>>>> fd3cc888 (Added fw_spec updates to all dynamically added fireworks and wrote a ShengBTE firetask)
 
 __author__ = "Anubhav Jain, Kiran Mathew, Shyam Dwaraknath"
 __email__ = "ajain@lbl.gov, kmathew@lbl.gov, shyamd@lbl.gov"
@@ -2184,9 +2187,9 @@ def run_task(self, fw_spec):
 
             iter = self['convergence_info']['iteration']
 
-        # mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
-        # mmdb.collection.insert(summaries)
-        mmdb.compressed_sensing_lattice_dynamics.insert(summaries)
+        mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
+        mmdb.collection.insert(summaries)
+        # mmdb.compressed_sensing_lattice_dynamics.insert(summaries)
 
         best_idx = self["convergence_info"]["cross_val_errors"].index(
             min(self["convergence_info"]["cross_val_errors"]))
@@ -2198,18 +2201,28 @@ def run_task(self, fw_spec):
         if not_converged is False:
             #     logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
             #     from fireworks.core.firework import Firework
-            #     shengbte_fw = Firework('<shengbte firetask>, {fw_spec: dict of info to pass to next firework}')
-            #           <mpirun -n 32 ./ShengBTE 2>BTE.err >BTE.out>
-            #     return FWAction(additions=shengbte_fw)
-            raise NotImplementedError("Implement ShengBTE firework")
+            shengbte_fw = Firework(
+                ShengBTEToDB(
+                    parent_structure=self["parent_structure"],
+                    shengbte_cmd=">>shengbte_cmd<<",
+                    db_file=self["db_file"],
+                    wf_uuid=self["wf_uuid"]
+                )
+            )
+            shengbte_fw.spec["_fworker"] = fw_spec["_fworker"]
+            CSLD_path = self.get("path", os.getcwd())
+            shengbte_fw.spec["successful_CSLD_path"] = CSLD_path
+            if fw_spec.get("tags", None):
+                shengbte_fw.spec["tags"] = fw_spec["tags"]
+            return FWAction(additions=shengbte_fw)
+            # raise NotImplementedError("Implement ShengBTE firework")
         else:
-            #     logger.info("Compressed Sensing Lattice Dynamics calculation failed."
-            #                 "Max iterations was reached.")
+            logger.info("Compressed Sensing Lattice Dynamics calculation failed."
+                        "Max iterations was reached.")
             if self["parent_structure"].num_sites > 5 and self["first_pass"]:
-                #     logger.info("Compressed Sensing Lattice Dynamics calculation failed."
-                #                 " Max iterations was reached. Creating larger displacements"
-                #                 " and trying again,")
-                print('placeholder')
+                logger.info("Compressed Sensing Lattice Dynamics calculation failed."
+                            " Max iterations was reached. Creating larger displacements"
+                            " and trying again,")
                 new_fws = []
 
                 # Create new perturbed supercells
@@ -2230,13 +2243,18 @@ def run_task(self, fw_spec):
                     static_vis = MPStaticSet(more_perturbed_supercell,
                                              user_incar_settings=self["static_user_incar_settings"])
 
-                    new_fws.append(StaticFW(
+                    from atomate.vasp.fireworks.core import StaticFW
+                    new_static_fw = StaticFW(
                         more_perturbed_supercell,
                         vasp_input_set=static_vis,
                         vasp_cmd=self["env_vars"]["VASP_CMD"],
                         db_file=self["env_vars"]["DB_FILE"],
                         name=name + " static"
-                    ))
+                    )
+                    new_static_fw.spec["_fworker"] = fw_spec["_fworker"]
+                    if fw_spec.get("tags", None):
+                        new_static_fw.spec["tags"] = fw_spec["tags"]
+                    new_fws.append(new_static_fw)
 
                 # Create new CSLD FW
                 new_csld_fw = Firework(
@@ -2255,6 +2273,9 @@ def run_task(self, fw_spec):
                     name="Compressed Sensing Lattice Dynamics",
                     parents=new_fws[-len(more_perturbed_supercells):]
                 )
+                new_csld_fw.spec["_fworker"] = fw_spec["_fworker"]
+                if fw_spec.get("tags", None):
+                    new_csld_fw.spec["tags"] = fw_spec["tags"]
                 new_fws.append(new_csld_fw)
 
                 # Dynamically add new fireworks to the workflow
@@ -2264,6 +2285,117 @@ def run_task(self, fw_spec):
                 raise TimeoutError("The workflow was unable to find a solution to CSLD"
                     " for this material.")
 
+@explicit_serialize
+class ShengBTEToDB(FiretaskBase):
+    """
+    Run ShengBTE
+
+    Required parameters:
+        db_file (str): path to the db file that holds your tasks
+        collection and that you want to hold the magnetic_orderings
+        collection
+        wf_uuid (str): auto-generated from get_wf_magnetic_orderings,
+        used to make it easier to retrieve task docs
+        parent_structure (Structure): material that CSLD is being run on
+        csld_settings (ConfigParser): settings for running CSLD
+        csld_options (dict): options for running CSLD
+    # Optional parameters:
+    #     to_db (bool): if True, the data will be inserted into
+    #     dedicated collection in database, otherwise, will be dumped
+    #     to a .json file.
+    """
+
+    required_params = ["parent_structure", "shengbte_cmd", "db_file",
+                       "wf_uuid"]
+
+    def run_task(self, fw_spec):
+        from atomate.utils.utils import env_chk
+        import subprocess
+        from pymatgen.io.vasp.inputs import Kpoints
+        import six
+        import shlex
+
+        # Generate CONTROL file
+        from pymatgen.io.shengbte import Control
+        qpts = Kpoints.automatic_density(self["parent_structure"], 50000)
+        unique_elements = [
+            str(self["parent_structure"].types_of_specie[i])
+            for i in range(len(self["parent_structure"].types_of_specie))
+        ]
+        nonunique_elements_list = [
+            str(self["parent_structure"].species[i])
+            for i in range(len(self["parent_structure"].species))
+        ]
+        element_to_number = {ele: idx + 1 for (idx, ele) in
+                             enumerate(unique_elements)}
+        shengbte_control_dict = {
+            'nelements': self["parent_structure"].ntypesp,
+            'natoms': self["parent_structure"].num_sites,
+            'ngrid': qpts.qpts[0], #[25, 25, 25],  # NEED TO GENERATE THIS BY DENSITY
+            'norientations': 0,
+
+            'lfactor': 0.1,  # 0.1 nm = 1 Ang
+            'lattvec': self["parent_structure"].lattice.matrix.tolist(),
+            'elements': unique_elements,
+            'types': [element_to_number[ele] for ele in
+                      nonunique_elements_list],
+            'positions': [
+                self["parent_structure"].sites[i]._frac_coords.tolist()
+                for i in range(self["parent_structure"].num_sites)
+            ],
+            'scell': [5, 5, 5],
+            't': 300,
+            'scalebroad': 0.5,
+            'nonanalytic': False,
+            'isotopes': False,
+        }
+        io = Control.from_dict(shengbte_control_dict)
+        io.to_file() #writes CONTROL file to current directory
+
+        # Copy force constants from previous CSLD firework
+        force_constants_path = fw_spec["successful_CSLD_path"]
+        shutil.copy(force_constants_path+"/FORCE_CONSTANTS_2ND", os.getcwd())
+        shutil.copy(force_constants_path+"/FORCE_CONSTANTS_3RD", os.getcwd())
+
+        # Set up/run ShengBTE
+        shengbte_cmd = env_chk(self["shengbte_cmd"], fw_spec)
+        if isinstance(shengbte_cmd, six.string_types):
+            shengbte_cmd = os.path.expandvars(shengbte_cmd)
+            shengbte_cmd = shlex.split(shengbte_cmd)
+        shengbte_cmd = list(shengbte_cmd)
+        logger.info("Running command: {}".format(shengbte_cmd))
+        return_code = subprocess.call(shengbte_cmd) #call() waits for the process to finish
+        logger.info("Command {} finished running with returncode: {}".format(shengbte_cmd, return_code))
+
+        try:
+            flattened_kappa = np.loadtxt('BTE.kappa_tensor')[1][1:] #xx, xy, xz, yx, yy, yz, zx, zy, zz
+
+            # Save to DB
+            db_file = env_chk(self.get("db_file"), fw_spec)
+            mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+            tasks = mmdb["tasks"]
+            summary = {
+                "date": datetime.now(),
+                "parent_structure": self["parent_structure"].as_dict(),
+                "wf_meta": {"wf_uuid": self["wf_uuid"]},
+                "kappa_xx": flattened_kappa[0],
+                "kappa_xy": flattened_kappa[1],
+                "kappa_xz": flattened_kappa[2],
+                "kappa_yx": flattened_kappa[3],
+                "kappa_yy": flattened_kappa[4],
+                "kappa_yz": flattened_kappa[5],
+                "kappa_zx": flattened_kappa[6],
+                "kappa_zy": flattened_kappa[7],
+                "kappa_zz": flattened_kappa[8]
+            }
+            if fw_spec.get("tags", None):
+                summary["tags"] = fw_spec["tags"]
+
+            mmdb.collection = mmdb.db["sheng_bte"]
+            mmdb.collection.insert(summary)
+        except:
+            raise FileNotFoundError('BTE.kappa_tensor was not output from ShengBTE.')
+
 
 # the following definitions for backward compatibility
 class VaspToDbTask(VaspToDb):
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 5a4e1890c..0c8252a43 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -175,7 +175,6 @@ def _add_metadata(structure):
             CSLDForceConstantsToDB(
                 db_file=c["DB_FILE"], # wot
                 wf_uuid=self.uuid,
-                name='CSLDForceConstantsToDB',
                 parent_structure=self.parent_structure,
                 trans_mat=self.trans_mat,
                 supercell_structure=self.supercell,
@@ -210,7 +209,7 @@ def _add_metadata(structure):
 
     from fireworks import LaunchPad
     from pymatgen.ext.matproj import MPRester
-    from atomate.vasp.powerups import add_tags, set_execution_options
+    from atomate.vasp.powerups import add_tags, set_execution_options, add_modify_incar
 
     #get a structure
     # mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
@@ -247,12 +246,16 @@ def _add_metadata(structure):
     print(csld_class.supercell.num_sites)
     csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Sr8Sb4Au4")
 
-    wf = add_tags(wf, ['csld', 'v1', 'rees', 'Sr8Sb4Au4', '10disps_1each'])
+    wf = add_tags(wf, ['csld', 'v1', 'rees', 'Sr8Sb4Au4', '10disps_1each', '8nodes',
+                       'encut 500', 'ispin 1'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
+    wf = add_modify_incar(wf,
+                          modify_incar_params={'incar_update': {'ENCUT': 500,
+                                                                'ISPIN': 1}})
     print(wf)
 
-    # lpad = LaunchPad.auto_load()
-    # lpad.add_wf(wf)
+    lpad = LaunchPad.auto_load()
+    lpad.add_wf(wf)
 
 # uuid
 # 0ff0d430-b43f-4cb5-ac8b-55c465b7867c

From 706c9a2ed72916b65de68a36307bc6699a5577ea Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 26 Jul 2019 14:40:04 -0700
Subject: [PATCH 025/207] Added optional temperature ranges for shengbte

---
 atomate/vasp/firetasks/parse_outputs.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index cbd49b086..e3d0ac52e 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1811,7 +1811,7 @@ class CSLDForceConstantsToDB(FiretaskBase):
         "supercell_smallest_dim",
         "disps", "first_pass"]
 
-    optional_params = ["static_user_incar_settings", "env_vars"]
+    optional_params = ["static_user_incar_settings", "env_vars", "shengbte_temps"]
 
     def random_search(self, maxIter):
         """
@@ -2206,7 +2206,10 @@ def run_task(self, fw_spec):
                     parent_structure=self["parent_structure"],
                     shengbte_cmd=">>shengbte_cmd<<",
                     db_file=self["db_file"],
-                    wf_uuid=self["wf_uuid"]
+                    wf_uuid=self["wf_uuid"],
+                    t_max=self["shengbte_temps"]["t_max"],
+                    t_min=self["shengbte_temps"]["t_min"],
+                    t_step=self["shengbte_temps"]["t_step"]
                 )
             )
             shengbte_fw.spec["_fworker"] = fw_spec["_fworker"]
@@ -2307,6 +2310,7 @@ class ShengBTEToDB(FiretaskBase):
 
     required_params = ["parent_structure", "shengbte_cmd", "db_file",
                        "wf_uuid"]
+    optional_params = ["t_max", "t_min", "t_step"]
 
     def run_task(self, fw_spec):
         from atomate.utils.utils import env_chk
@@ -2349,6 +2353,10 @@ def run_task(self, fw_spec):
             'nonanalytic': False,
             'isotopes': False,
         }
+        if self["shengbte_tmax"] and self["shengbte_tmin"] and self["shengbte_tstep"]:
+            shengbte_control_dict['t_min'] = self["t_min"]
+            shengbte_control_dict['t_max'] = self["t_max"]
+            shengbte_control_dict['t_step'] = self["t_step"]
         io = Control.from_dict(shengbte_control_dict)
         io.to_file() #writes CONTROL file to current directory
 

From 63bcd4bf25cabb8842ae15f84dceac74d2741579 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 26 Jul 2019 14:40:26 -0700
Subject: [PATCH 026/207] Added optional temperature ranges for shengbte

---
 atomate/vasp/workflows/base/csld.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 0c8252a43..c6b12db2a 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -47,7 +47,10 @@ def __init__(
             num_displacements=10,
             supercells_per_displacement_distance=1,
             min_random_distance=None,
-            #csld input params here
+            shengbte_tmin=None,
+            shengbte_tmax=None,
+            shengbte_tstep=None
+            #csld input params here?
     ):
         """
         This workflow will use compressed sensing lattice dynamics (CSLD)
@@ -108,6 +111,10 @@ def __init__(
         self.disps = np.repeat(perturbed_supercells_transform.disps,
                                supercells_per_displacement_distance)
 
+        self.shengbte_tmax = shengbte_tmax
+        self.shengbte_tmin = shengbte_tmin
+        self.shengbte_tstep = shengbte_tstep
+
     def get_wf(
             self,
             c=None
@@ -183,7 +190,10 @@ def _add_metadata(structure):
                 disps=self.disps,
                 first_pass=True,
                 static_user_incar_settings=static_user_incar_settings,
-                env_vars=c
+                env_vars=c,
+                shengbte_temps={'t_max': self.shengbte_tmax,
+                                't_min': self.shengbte_tmin,
+                                't_step': self.shengbte_tstep}
             ),
             name="Compressed Sensing Lattice Dynamics",
             parents=fws[-len(self.perturbed_supercells):]

From d5852e6831107158c29b6035f08a34e7a6f7a977 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 26 Jul 2019 15:55:28 -0700
Subject: [PATCH 027/207] Edited shengbte t_range option and created a CSLD
 preset workflow

---
 atomate/vasp/firetasks/parse_outputs.py | 58 ++++++++++++-------------
 atomate/vasp/workflows/base/csld.py     | 15 ++-----
 atomate/vasp/workflows/presets/core.py  | 41 +++++++++++++++++
 3 files changed, 73 insertions(+), 41 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index e3d0ac52e..817b54fa8 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1811,7 +1811,7 @@ class CSLDForceConstantsToDB(FiretaskBase):
         "supercell_smallest_dim",
         "disps", "first_pass"]
 
-    optional_params = ["static_user_incar_settings", "env_vars", "shengbte_temps"]
+    optional_params = ["static_user_incar_settings", "env_vars", "shengbte_t_range"]
 
     def random_search(self, maxIter):
         """
@@ -2207,9 +2207,7 @@ def run_task(self, fw_spec):
                     shengbte_cmd=">>shengbte_cmd<<",
                     db_file=self["db_file"],
                     wf_uuid=self["wf_uuid"],
-                    t_max=self["shengbte_temps"]["t_max"],
-                    t_min=self["shengbte_temps"]["t_min"],
-                    t_step=self["shengbte_temps"]["t_step"]
+                    t_range=self["shengbte_t_range"]
                 )
             )
             shengbte_fw.spec["_fworker"] = fw_spec["_fworker"]
@@ -2310,7 +2308,7 @@ class ShengBTEToDB(FiretaskBase):
 
     required_params = ["parent_structure", "shengbte_cmd", "db_file",
                        "wf_uuid"]
-    optional_params = ["t_max", "t_min", "t_step"]
+    optional_params = ["t_range"] #boolean for multiple temperatures
 
     def run_task(self, fw_spec):
         from atomate.utils.utils import env_chk
@@ -2353,10 +2351,10 @@ def run_task(self, fw_spec):
             'nonanalytic': False,
             'isotopes': False,
         }
-        if self["shengbte_tmax"] and self["shengbte_tmin"] and self["shengbte_tstep"]:
-            shengbte_control_dict['t_min'] = self["t_min"]
-            shengbte_control_dict['t_max'] = self["t_max"]
-            shengbte_control_dict['t_step'] = self["t_step"]
+        if self["t_range"]:
+            shengbte_control_dict['t_min'] = 100
+            shengbte_control_dict['t_max'] = 1000
+            shengbte_control_dict['t_step'] = 100
         io = Control.from_dict(shengbte_control_dict)
         io.to_file() #writes CONTROL file to current directory
 
@@ -2376,31 +2374,31 @@ def run_task(self, fw_spec):
         logger.info("Command {} finished running with returncode: {}".format(shengbte_cmd, return_code))
 
         try:
-            flattened_kappa = np.loadtxt('BTE.kappa_tensor')[1][1:] #xx, xy, xz, yx, yy, yz, zx, zy, zz
-
-            # Save to DB
             db_file = env_chk(self.get("db_file"), fw_spec)
             mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-            tasks = mmdb["tasks"]
-            summary = {
-                "date": datetime.now(),
-                "parent_structure": self["parent_structure"].as_dict(),
-                "wf_meta": {"wf_uuid": self["wf_uuid"]},
-                "kappa_xx": flattened_kappa[0],
-                "kappa_xy": flattened_kappa[1],
-                "kappa_xz": flattened_kappa[2],
-                "kappa_yx": flattened_kappa[3],
-                "kappa_yy": flattened_kappa[4],
-                "kappa_yz": flattened_kappa[5],
-                "kappa_zx": flattened_kappa[6],
-                "kappa_zy": flattened_kappa[7],
-                "kappa_zz": flattened_kappa[8]
-            }
-            if fw_spec.get("tags", None):
-                summary["tags"] = fw_spec["tags"]
+            if self["t_range"]:
+                temps = np.linspace(100, 1000, 10)
+            else:
+                temps = 300
+
+            # Save to DB
+            summaries = []
+            for temp in temps:
+                # xx, xy, xz, yx, yy, yz, zx, zy, zz
+                flattened_kappa = list(np.loadtxt('t'+str(temp)+'K/BTE.kappa_tensor')[1][1:])
+                summary = {
+                    "date": datetime.now(),
+                    "temperature": temp,
+                    "parent_structure": self["parent_structure"].as_dict(),
+                    "wf_meta": {"wf_uuid": self["wf_uuid"]},
+                    "flattened_kappa": flattened_kappa
+                }
+                if fw_spec.get("tags", None):
+                    summary["tags"] = fw_spec["tags"]
+                summaries.append(summary)
 
             mmdb.collection = mmdb.db["sheng_bte"]
-            mmdb.collection.insert(summary)
+            mmdb.collection.insert(summaries)
         except:
             raise FileNotFoundError('BTE.kappa_tensor was not output from ShengBTE.')
 
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index c6b12db2a..ee25558a9 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -47,9 +47,7 @@ def __init__(
             num_displacements=10,
             supercells_per_displacement_distance=1,
             min_random_distance=None,
-            shengbte_tmin=None,
-            shengbte_tmax=None,
-            shengbte_tstep=None
+            shengbte_t_range=False #whether to calculate 100-1000K or just 300K
             #csld input params here?
     ):
         """
@@ -111,10 +109,7 @@ def __init__(
         self.disps = np.repeat(perturbed_supercells_transform.disps,
                                supercells_per_displacement_distance)
 
-        self.shengbte_tmax = shengbte_tmax
-        self.shengbte_tmin = shengbte_tmin
-        self.shengbte_tstep = shengbte_tstep
-
+        self.shengbte_t_range = shengbte_t_range
     def get_wf(
             self,
             c=None
@@ -154,7 +149,7 @@ def _add_metadata(structure):
                                       # Fast Fourier Transform grid
                                       "LCHARG": False,
                                       "ENCUT": 700,
-                                      "EDIFF": 1e-7,  # may need to tune this
+                                      "EDIFF": 1e-8,  # may need to tune this
                                       "PREC": 'Accurate',
                                       "LAECHG": False,
                                       "LREAL": False,
@@ -191,9 +186,7 @@ def _add_metadata(structure):
                 first_pass=True,
                 static_user_incar_settings=static_user_incar_settings,
                 env_vars=c,
-                shengbte_temps={'t_max': self.shengbte_tmax,
-                                't_min': self.shengbte_tmin,
-                                't_step': self.shengbte_tstep}
+                shengbte_t_range=self.shengbte_t_range
             ),
             name="Compressed Sensing Lattice Dynamics",
             parents=fws[-len(self.perturbed_supercells):]
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index d9634307e..3f9622b7e 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -826,3 +826,44 @@ def wf_nudged_elastic_band(structures, parent, c=None):
         )
 
     return wf
+
+
+def wf_lattice_thermal_conductivity(structure, c=None):
+    """
+    Lattice thermal conductivity workflow from the given structure and config
+    dict.
+
+    Args:
+        structure (Structure): input structure
+        c (dict): workflow config dict
+
+    Returns:
+        Workflow
+    """
+    from atomate.vasp.workflows.base.csld import CompressedSensingLatticeDynamicsWF
+    c = c or {}
+    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
+    db_file = c.get("DB_FILE", DB_FILE)
+
+    optimize = {"LAECHG": False, 'ENCUT': 700,
+                'ADDGRID': True, 'EDIFFG': -5e-4,
+                'PREC': 'Accurate', "LREAL": False,
+                'EDIFF': 1e-8, "ISMEAR": 0,
+                'LCHARG': False, 'LASPH': True}
+    vis_relax = MPRelaxSet(structure, user_incar_settings=optimize)
+    wf = get_wf(structure, "optimize_only.yaml", vis=vis_relax,
+                      params=[{"vasp_cmd": vasp_cmd, "db_file": db_file,
+                               "name": "phonon structure optimization"}])
+    wf_csld = CompressedSensingLatticeDynamicsWF(structure,
+                                                 num_nn_dists=5,
+                                                 num_displacements=10,
+                                                 supercells_per_displacement_distance=1).get_wf()
+
+    wf.append(wf_csld, wf.leaf_fw_ids)
+    wf = add_common_powerups(wf, c)
+
+    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
+        wf = add_wf_metadata(wf, structure)
+
+    return wf
+

From e403133967c3bf729c19ae513f3d3cd0b38a5cb5 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 26 Jul 2019 16:07:07 -0700
Subject: [PATCH 028/207] Minor edits

---
 atomate/vasp/firetasks/parse_outputs.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 817b54fa8..f2d5e74dc 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -2289,7 +2289,7 @@ def run_task(self, fw_spec):
 @explicit_serialize
 class ShengBTEToDB(FiretaskBase):
     """
-    Run ShengBTE
+    Run ShengBTE and output the lattice thermal conductivity matrix to database.
 
     Required parameters:
         db_file (str): path to the db file that holds your tasks
@@ -2385,13 +2385,13 @@ def run_task(self, fw_spec):
             summaries = []
             for temp in temps:
                 # xx, xy, xz, yx, yy, yz, zx, zy, zz
-                flattened_kappa = list(np.loadtxt('t'+str(temp)+'K/BTE.kappa_tensor')[1][1:])
+                flattened_kappa = list(np.loadtxt('T'+str(int(temp))+'K/BTE.kappa_tensor')[1][1:])
                 summary = {
                     "date": datetime.now(),
                     "temperature": temp,
                     "parent_structure": self["parent_structure"].as_dict(),
                     "wf_meta": {"wf_uuid": self["wf_uuid"]},
-                    "flattened_kappa": flattened_kappa
+                    str(temp)+" K": {"flattened_kappa": flattened_kappa}
                 }
                 if fw_spec.get("tags", None):
                     summary["tags"] = fw_spec["tags"]

From fdbde4b904789c7f9c1cb56ea4291eacc2a6b913 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Mon, 29 Jul 2019 17:16:45 -0700
Subject: [PATCH 029/207] Added documentation and cleaned up comments

---
 atomate/vasp/firetasks/parse_outputs.py | 99 ++++++++++++++-----------
 atomate/vasp/workflows/base/csld.py     | 19 -----
 2 files changed, 54 insertions(+), 64 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index f2d5e74dc..7e3ea5ce4 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1784,22 +1784,41 @@ class CSLDForceConstantsToDB(FiretaskBase):
     #TODO: Update this class once Junsoo has fixed the cluster generation
     """
     Used to aggregate atomic forces of perturbed supercells in compressed
-    sensing lattice dynamics (CSLD) workflow and generate interatomic force
-    constants.
+    sensing lattice dynamics (CSLD) workflow and generate/write interatomic
+    force constants up to 3rd order to file. The workflow uses a CSLD software
+    implemented by Zhou et al which can be found at https://github.com/LLNL/csld.
 
     Required parameters:
         db_file (str): path to the db file that holds your tasks
-        collection and that you want to hold the magnetic_orderings
-        collection
-        wf_uuid (str): auto-generated from get_wf_magnetic_orderings,
-        used to make it easier to retrieve task docs
-        parent_structure (Structure): material that CSLD is being run on
-        csld_settings (ConfigParser): settings for running CSLD
-        csld_options (dict): options for running CSLD
-    # Optional parameters:
-    #     to_db (bool): if True, the data will be inserted into
-    #     dedicated collection in database, otherwise, will be dumped
-    #     to a .json file.
+            collection specifying the database that the perturbed supercell
+            forces are stored and that CSLD results should be stored to
+        wf_uuid (str): auto-generated from CompressedSensingLatticeDynamicsWF,
+            used to make it easier to retrieve task docs
+        parent_structure (Structure): input (usually primitive) structure on
+            which CSLD is being done
+        perturbed_supercells (list of Structures): list of perturbed supercell
+            structures auto-generated from CompressedSensingLatticeDynamicsWF
+        trans_mat (3x3 np.ndarray): supercell transformation matrix auto-
+            generated from CompressedSensingLatticeDynamicsWF
+        supercell_structure (Structure): supercell structure of parent_structure,
+            auto-generated from CompressedSensingLatticeDynamicsWF
+        supercell_smallest_dim (float): length of shortest direction of the
+            supercell lattice, auto-generated from
+            CompressedSensingLatticeDynamicsWF
+        disps (list of floats): displacement values corresponding to
+            perturbed_supercells, auto-generated from
+            CompressedSensingLatticeDynamicsWF
+        first_pass (boolean): indicator of whether this firetask has already
+            been attempted or if it is automatically running a second time
+            with larger perturbations
+        static_user_incar_settings (dict): incar settings used in static calculations
+            in CompressedSensingLatticeDynamicsWF
+        env_vars (dict): environmental variables used in static calculations in
+            CompressedSensingLatticeDynamicsWF
+    Optional parameters:
+        shengbte_t_range (boolean): If True, pass to the ShengBTEToDB firetask
+            that lattice thermal conductivity should be calculated for 100 K to
+            1000 K in steps of 100 K. If False, only calculate at 300 K.
     """
 
     logger = get_logger(__name__)
@@ -1809,9 +1828,10 @@ class CSLDForceConstantsToDB(FiretaskBase):
         "perturbed_supercells",
         "trans_mat", "supercell_structure",
         "supercell_smallest_dim",
-        "disps", "first_pass"]
+        "disps", "first_pass",
+        "static_user_incar_settings", "env_vars"]
 
-    optional_params = ["static_user_incar_settings", "env_vars", "shengbte_t_range"]
+    optional_params = ["shengbte_t_range"]
 
     def random_search(self, maxIter):
         """
@@ -1843,7 +1863,6 @@ def random_search(self, maxIter):
                 -If bad, then fit including supercells >0.1 angstroms
                     -If good, run SBTE
                     -If bad, redo step 2 with 4th order
-        :return:
         """
         import random
 
@@ -1852,8 +1871,8 @@ def random_search(self, maxIter):
 
         cluster_diam_settings = []
         for _ in range(maxIter):
-            pair_diam = random.uniform(10, 14) #self["supercell_smallest_dim"])
-            triplet_diam = random.uniform(pair_diam * 0.4, pair_diam)
+            pair_diam = random.uniform(8, 12) #self["supercell_smallest_dim"])
+            triplet_diam = random.uniform(5.5, 7)
             quadruplet_diam = random.uniform(triplet_diam * 0.6, triplet_diam)
 
             cluster_diam_settings += [
@@ -2044,6 +2063,7 @@ def run_task(self, fw_spec):
         maxIter = 2
         summaries = []
 
+        #Set list of parameter settings to try (i.e. grid search settings)
         # <FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
         cluster_diam_settings = ['11 6.5 5.0',
                                  '9 6.5 5.0']
@@ -2056,6 +2076,7 @@ def run_task(self, fw_spec):
             submodel1_settings += submodel1_settings
             export_sbte_settings += export_sbte_settings
 
+        ##Generate list of parameter settings to try from random search
         # cluster_diam_settings, max_order_settings, submodel1_settings = self.random_search(maxIter)
         # export_sbte_settings = ['5 5 5 2 3'] * maxIter
         print('cluster_diam')
@@ -2090,7 +2111,6 @@ def run_task(self, fw_spec):
             #   for each supercell
 
             supercells_forces = []
-            # supercells_task_ids = []
             supercells_task_labels = []
             for supercell_dict in supercells_dicts:
                 # List of np.ndarrays where each np.ndarray is a matrix of forces
@@ -2098,9 +2118,6 @@ def run_task(self, fw_spec):
                 supercells_forces += [
                     np.asarray(supercell_dict['output']['forces'])]
 
-                # #List of task ids for each perturbed supercell
-                # supercells_task_ids += [supercell_dict['task_id']]
-
                 supercells_task_labels += [supercell_dict['task_label']]
 
             supercells_zip = sorted(
@@ -2121,12 +2138,9 @@ def run_task(self, fw_spec):
             from atomate.vasp.workflows.base.csld import csld_main
             rel_err, freq_matrix = csld_main(self["csld_options"],
                                              self["csld_settings"])
-            # rel_err = 0.01
-            # freq_matrix = [[1, -1, 1],
-            #                [-1, 1, 1]] #(nbands, nkpoints)
 
             freq_matrix = np.asarray(freq_matrix)
-            imaginary_idx = freq_matrix < -1  # UPDATE THIS NUMBER TO HAVE SOME CUSHION
+            imaginary_idx = freq_matrix < -1
             imaginary_freqs = freq_matrix[imaginary_idx]
             print('IMAGINARY FREQUENCIES')
             print(imaginary_freqs)
@@ -2137,8 +2151,8 @@ def run_task(self, fw_spec):
             else:
                 most_imaginary_freq = 0
             print(most_imaginary_freq)
-            # For imaginary frequencies, w^2 is negative
-            # code handles it as w = sign(sqrt(abs(w^2)), w^2)
+            # For imaginary frequencies, w^2 is negative.
+            # Code handles it as w = sign(sqrt(abs(w^2)), w^2)
 
             if num_imaginary_bands == 0:
                 not_converged = False
@@ -2151,7 +2165,7 @@ def run_task(self, fw_spec):
                 "parent_structure": self["parent_structure"].as_dict(),
                 "wf_meta": {"wf_uuid": uuid},
 
-                # <store relevant CSLD settings>
+                # Store relevant CSLD settings
                 "iteration": iter,
                 "cluster_diam": self["csld_settings"]["model"][
                     "cluster_diameter"],
@@ -2162,7 +2176,6 @@ def run_task(self, fw_spec):
 
                 "cross_val_error": float(rel_err),
                 "num_imaginary_modes": int(num_imaginary_bands),
-                # number or percent?
                 "most_imaginary_freq": float(most_imaginary_freq),
                 "imaginary_freq_sum": float(sum(imaginary_freqs))
             }
@@ -2189,7 +2202,6 @@ def run_task(self, fw_spec):
 
         mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
         mmdb.collection.insert(summaries)
-        # mmdb.compressed_sensing_lattice_dynamics.insert(summaries)
 
         best_idx = self["convergence_info"]["cross_val_errors"].index(
             min(self["convergence_info"]["cross_val_errors"]))
@@ -2199,8 +2211,7 @@ def run_task(self, fw_spec):
             self["convergence_info"]["settings_tried"][best_idx]))
 
         if not_converged is False:
-            #     logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
-            #     from fireworks.core.firework import Firework
+            logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
             shengbte_fw = Firework(
                 ShengBTEToDB(
                     parent_structure=self["parent_structure"],
@@ -2216,7 +2227,6 @@ def run_task(self, fw_spec):
             if fw_spec.get("tags", None):
                 shengbte_fw.spec["tags"] = fw_spec["tags"]
             return FWAction(additions=shengbte_fw)
-            # raise NotImplementedError("Implement ShengBTE firework")
         else:
             logger.info("Compressed Sensing Lattice Dynamics calculation failed."
                         "Max iterations was reached.")
@@ -2288,22 +2298,21 @@ def run_task(self, fw_spec):
 
 @explicit_serialize
 class ShengBTEToDB(FiretaskBase):
+    #TODO: Test this firetask
     """
     Run ShengBTE and output the lattice thermal conductivity matrix to database.
 
     Required parameters:
+        parent_structure (Structure): material that ShengBTE is being run on
         db_file (str): path to the db file that holds your tasks
-        collection and that you want to hold the magnetic_orderings
-        collection
-        wf_uuid (str): auto-generated from get_wf_magnetic_orderings,
-        used to make it easier to retrieve task docs
-        parent_structure (Structure): material that CSLD is being run on
-        csld_settings (ConfigParser): settings for running CSLD
-        csld_options (dict): options for running CSLD
-    # Optional parameters:
-    #     to_db (bool): if True, the data will be inserted into
-    #     dedicated collection in database, otherwise, will be dumped
-    #     to a .json file.
+            collection specifying the database that ShengBTE results should be
+            stored to
+        shengbte_cmd (str): should be set to "<<shengbte_cmd>>"
+        wf_uuid (str): passed from the CSLDForceConstantsToDB firetask,
+            used for storing task docs
+    Optional parameters:
+        t_range (bool): If True, run lattice thermal conductivity calculations
+            at 100 K through 1000 K at steps of 100 K.
     """
 
     required_params = ["parent_structure", "shengbte_cmd", "db_file",
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index ee25558a9..bba886f21 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -125,25 +125,6 @@ def _add_metadata(structure):
                 structure, other_parameters={"wf_meta": self.wf_meta}
             )
 
-        #TODO: Move this relaxation section elsewhere
-        # relax_user_incar_settings = {"EDIFF": 1e-8,
-        #                              "EDIFFG": -1e-5,
-        #                              }
-        # relax_vis = MPRelaxSet(self.parent_structure,
-        #                        user_incar_settings=relax_user_incar_settings)
-        # # relax
-        # fws.append(
-        #     OptimizeFW(
-        #         self.parent_structure,
-        #         vasp_input_set=relax_vis,
-        #         vasp_cmd=c["VASP_CMD"],
-        #         db_file=c["DB_FILE"],
-        #         max_force_threshold=0.05, #idk, should i change this?
-        #         half_kpts_first_relax=False, #idk what this is
-        #         name="{} - CSLD relax parent".format(self.parent_structure.composition.reduced_formula),
-        #     )
-        # )
-        #####################
 
         static_user_incar_settings = {"ADDGRID": True,
                                       # Fast Fourier Transform grid

From efdfcbd6acf5830a8956d1c21cc01d95e67c06e9 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 31 Jul 2019 10:36:58 -0700
Subject: [PATCH 030/207] Updated to reflect changes in
 PerturbSitesTransformation and CSLD

---
 atomate/vasp/firetasks/parse_outputs.py |  8 ++++----
 atomate/vasp/workflows/base/csld.py     | 17 ++++++++++-------
 atomate/vasp/workflows/presets/core.py  |  2 ++
 3 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 7e3ea5ce4..488aec335 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -2238,9 +2238,9 @@ def run_task(self, fw_spec):
 
                 # Create new perturbed supercells
                 more_perturbed_supercells_transform = PerturbSitesTransformation(
-                    max_displacement=0.2,
-                    min_displacement=0.12,
-                    num_displacements=5,
+                    max_disp=0.2,
+                    min_disp=0.12,
+                    num_disps=5,
                     structures_per_displacement_distance=1,
                     min_random_distance=None
                 )
@@ -2342,7 +2342,7 @@ def run_task(self, fw_spec):
         shengbte_control_dict = {
             'nelements': self["parent_structure"].ntypesp,
             'natoms': self["parent_structure"].num_sites,
-            'ngrid': qpts.qpts[0], #[25, 25, 25],  # NEED TO GENERATE THIS BY DENSITY
+            'ngrid': qpts.kpts[0], #[25, 25, 25],  # NEED TO GENERATE THIS BY DENSITY
             'norientations': 0,
 
             'lfactor': 0.1,  # 0.1 nm = 1 Ang
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index bba886f21..215ebdcd9 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -104,7 +104,8 @@ def __init__(
             min_random_distance
         )
         # list of perturbed supercell structures (list)
-        self.perturbed_supercells = perturbed_supercells_transform.apply_transformation(self.supercell)
+        self.perturbed_supercells = [d['structure'] for d in
+                                     perturbed_supercells_transform.apply_transformation(self.supercell)]
         # list of (non-unique) displacement values used in the perturbation (np.ndarray)
         self.disps = np.repeat(perturbed_supercells_transform.disps,
                                supercells_per_displacement_distance)
@@ -233,9 +234,9 @@ def _add_metadata(structure):
     wf = add_tags(wf, ['csld', 'v1', 'rees', 'Sr8Sb4Au4', '10disps_1each', '8nodes',
                        'encut 500', 'ispin 1'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
-    wf = add_modify_incar(wf,
-                          modify_incar_params={'incar_update': {'ENCUT': 500,
-                                                                'ISPIN': 1}})
+    # wf = add_modify_incar(wf,
+    #                       modify_incar_params={'incar_update': {'ENCUT': 500,
+    #                                                             'ISPIN': 1}})
     print(wf)
 
     lpad = LaunchPad.auto_load()
@@ -274,8 +275,10 @@ def csld_main(options, settings):
     from csld.lattice_dynamics import init_ld_model
 
     from csld.common_main import upon_exit, \
-        init_training, fit_data, phonon_step, \
-        save_pot, predict
+        init_training
+    from csld.csld_main_functions import phonon_step, \
+        save_pot, predict, fit_data
+
 
     freq_matrix = None #Rees
     pdfout = PdfPages(
@@ -294,7 +297,7 @@ def csld_main(options, settings):
                                 options['fit_step'], pdfout)
     if settings.has_section('phonon'):
         phonon, freq_matrix = phonon_step(model, solutions, settings['phonon'],
-                             options['phonon_step'], pdfout, prim)
+                             options['phonon_step'], pdfout, prim, return_eigen=True)
     if settings.has_section('export_potential'):
         save_pot(model, solutions[ibest], settings['export_potential'],
                  options['save_pot_step'], phonon)
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 3f9622b7e..9b722147b 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -845,6 +845,8 @@ def wf_lattice_thermal_conductivity(structure, c=None):
     vasp_cmd = c.get("VASP_CMD", VASP_CMD)
     db_file = c.get("DB_FILE", DB_FILE)
 
+    ## DFPT AT GAMMA POINT
+
     optimize = {"LAECHG": False, 'ENCUT': 700,
                 'ADDGRID': True, 'EDIFFG': -5e-4,
                 'PREC': 'Accurate', "LREAL": False,

From f71b330c48c8207aa63dbfc465c1f2a1401a9d73 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 31 Jul 2019 11:11:05 -0700
Subject: [PATCH 031/207] Preset runs smoothly. Waiting on Si test run scraped
 from MP

---
 atomate/vasp/workflows/presets/core.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 9b722147b..6e91dcb62 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -861,9 +861,13 @@ def wf_lattice_thermal_conductivity(structure, c=None):
                                                  num_displacements=10,
                                                  supercells_per_displacement_distance=1).get_wf()
 
-    wf.append(wf_csld, wf.leaf_fw_ids)
+    wf.append_wf(wf_csld, wf.leaf_fw_ids)
     wf = add_common_powerups(wf, c)
 
+    formula = structure.composition.reduced_formula
+    wf_name = "{} - lattice thermal conductivity preset".format(formula)
+    wf.name = wf_name
+
     if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
         wf = add_wf_metadata(wf, structure)
 

From 9fa3175e0a4a69ceab80089044e1405058682e1d Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 1 Aug 2019 13:44:00 -0700
Subject: [PATCH 032/207] - Updated workflow to reflect changes in
 PerturbStructureTransformation and diagonal CubicSupercellTransformation

---
 atomate/vasp/workflows/base/csld.py | 88 +++++++++++++++++++----------
 1 file changed, 59 insertions(+), 29 deletions(-)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 215ebdcd9..f5aba8d41 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -7,9 +7,10 @@
 
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.alchemy.materials import TransformedStructure
+from pymatgen.transformations.standard_transformations import \
+    PerturbStructureTransformation
 from pymatgen.transformations.advanced_transformations import (
-    CubicSupercellTransformation,
-    PerturbSitesTransformation
+    CubicSupercellTransformation
 )
 from fireworks import Workflow, Firework
 from atomate.utils.utils import get_logger
@@ -42,13 +43,13 @@ def __init__(
             min_atoms=-np.Inf,
             max_atoms=np.Inf,
             num_nn_dists=5,
+            force_diagonal_transformation=True,
             max_displacement=0.1,
             min_displacement=0.01,
             num_displacements=10,
-            supercells_per_displacement_distance=1,
             min_random_distance=None,
-            shengbte_t_range=False #whether to calculate 100-1000K or just 300K
-            #csld input params here?
+            supercells_per_displacement_distance=1,
+            shengbte_t_range=False
     ):
         """
         This workflow will use compressed sensing lattice dynamics (CSLD)
@@ -66,11 +67,39 @@ def __init__(
             5. Output the interatomic force constants to the database.
 
         Args:
-            parent_structure (Structure):
-            min_atoms (int):
-            max_atoms (int):
-            num_nn_dists (int or float):
-            max_displacement (float)
+            parent_structure (Structure): Structure to primitize and conduct
+                CSLD on
+            symprec (float): symmetry precision parameter for
+                SpacegroupAnalyzer's 'get_primitive_standard_structure()'
+                function
+            min_atoms (int): Minimum number of atoms to constrain the supercell
+            max_atoms (int): Maximum number of atoms to constrain the supercell
+            num_nn_dists (int or float): Number of nearest neighbor distances
+                that the shortest direction of the supercell must be as long as
+            force_diagonal_transformation (bool): If True, the supercell
+                transformation will be constrained to have a diagonal
+                transformation matrix. If False, the supercell transformation
+                will not be constrained to be diagonal (resulting in a more
+                cubic supercell).
+            max_displacement (float): Maximum displacement distance for
+                perturbing the supercell structure (Angstroms)
+            min_displacement (float): Minimum displacement distance for
+                perturbing the supercell structure (Angstroms)
+            num_displacements (int): Number of unique displacement distances to
+                generate uniformly between 'min_displacement' and
+                'max_displacement'
+            min_random_distance (Optional float): If None (default), then all
+                atoms in the supercell will move the same distance from their
+                original locations. If float, then for a given supercell, the
+                distances that atoms move will be uniformly distributed from a
+                minimum distance of 'min_random_distance' to one of the
+                displacement distances uniformly sampled between
+                'min_displacement' and 'max_displacement'.
+            supercells_per_displacement_distance (int): number of supercells to
+                generate for each unique displacement distance.
+            shengbte_t_range (bool): If False (default), calculate the lattice
+                thermal conductivity with ShengBTE at 300 K. If True, do the
+                calculation from 100-1000 K with 100 K steps (much slower).
         """
         self.uuid = str(uuid4())
         self.wf_meta = {
@@ -89,28 +118,29 @@ def __init__(
             self.min_atoms,
             self.max_atoms,
             self.num_nn_dists,
+            force_diagonal_transformation=force_diagonal_transformation
         )
         # supercell (Structure)
         self.supercell = supercell_transform.apply_transformation(self.parent_structure)
         self.trans_mat = supercell_transform.trans_mat
         self.supercell_smallest_dim = supercell_transform.smallest_dim
 
-    # Generate randomly perturbed supercells
-        perturbed_supercells_transform = PerturbSitesTransformation(
-            max_displacement,
-            min_displacement,
-            num_displacements,
-            supercells_per_displacement_distance,
-            min_random_distance
-        )
-        # list of perturbed supercell structures (list)
-        self.perturbed_supercells = [d['structure'] for d in
-                                     perturbed_supercells_transform.apply_transformation(self.supercell)]
+    # Generate list of perturbed supercells
         # list of (non-unique) displacement values used in the perturbation (np.ndarray)
-        self.disps = np.repeat(perturbed_supercells_transform.disps,
-                               supercells_per_displacement_distance)
+        self.disps = np.repeat(
+            np.linspace(min_displacement, max_displacement, num_displacements),
+            supercells_per_displacement_distance
+        )
+        self.min_random_distance = min_random_distance
+        self.perturbed_supercells = [] # list of perturbed supercell structures
+        for amplitude in self.disps:
+            perturb_structure_transformer = PerturbStructureTransformation(amplitude,
+                                                                           self.min_random_distance)
+            perturbed_supercell = perturb_structure_transformer.apply_transformation(self.supercell)
+            self.perturbed_supercells += [perturbed_supercell]
 
         self.shengbte_t_range = shengbte_t_range
+
     def get_wf(
             self,
             c=None
@@ -215,12 +245,13 @@ def _add_metadata(structure):
     from pymatgen.core.structure import Structure
     # prim = Structure.from_file('POSCAR_csld_primitivized')
 
-    prim = Structure.from_file('POSCAR-well_relaxed_Sr8Sb4Au4')
+    prim = Structure.from_file('POSCAR-well_relaxed_Si')
 
     csld_class = CompressedSensingLatticeDynamicsWF(prim,
                                                     num_nn_dists=5,
                                                     num_displacements=10,
-                                                    supercells_per_displacement_distance=1)
+                                                    supercells_per_displacement_distance=1,
+                                                    )
     print("uuid")
     print(csld_class.uuid)
 
@@ -229,15 +260,14 @@ def _add_metadata(structure):
     print(csld_class.trans_mat)
     print(csld_class.supercell_smallest_dim)
     print(csld_class.supercell.num_sites)
-    csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Sr8Sb4Au4")
+    csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Si")
 
-    wf = add_tags(wf, ['csld', 'v1', 'rees', 'Sr8Sb4Au4', '10disps_1each', '8nodes',
-                       'encut 500', 'ispin 1'])
+    wf = add_tags(wf, ['csld', 'v1', 'rees', 'pre-relaxed si'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
     # wf = add_modify_incar(wf,
     #                       modify_incar_params={'incar_update': {'ENCUT': 500,
     #                                                             'ISPIN': 1}})
-    print(wf)
+    # print(wf)
 
     lpad = LaunchPad.auto_load()
     lpad.add_wf(wf)

From a893c2d5cd819303b5a1efad39ad165577485540 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 1 Aug 2019 14:55:52 -0700
Subject: [PATCH 033/207] -Added a new csld analysis file to atomate

parse_outputs:
- Made export_sbte be the diagonal of the trans_mat rather than 5,5,5
- Added supercell structure and trans_mat to the CSLD firework DB summary
- Passed trans_mat into the sbte firetask

csld:
- Minor edits
---
 atomate/vasp/analysis/csld.py           | 58 +++++++++++++++++++++++++
 atomate/vasp/firetasks/parse_outputs.py | 35 +++++++++------
 atomate/vasp/workflows/base/csld.py     | 42 ++++++++++--------
 3 files changed, 104 insertions(+), 31 deletions(-)
 create mode 100644 atomate/vasp/analysis/csld.py

diff --git a/atomate/vasp/analysis/csld.py b/atomate/vasp/analysis/csld.py
new file mode 100644
index 000000000..8f624bce7
--- /dev/null
+++ b/atomate/vasp/analysis/csld.py
@@ -0,0 +1,58 @@
+# coding: utf-8
+
+from __future__ import division, print_function, unicode_literals, absolute_import
+
+import numpy as np
+
+from pymatgen.transformations.standard_transformations import PerturbStructureTransformation
+
+__author__ = 'Rees Chang'
+__email__ = 'rc564@cornell.edu'
+
+
+def generate_perturbed_supercells(supercell,
+                                  min_displacement=0.01, max_displacement=0.1,
+                                  num_displacements=10,
+                                  supercells_per_displacement_distance=1,
+                                  min_random_distance=None):
+    """
+    Generate a list of supercells with perturbed atomic sites.
+
+    Args:
+        supercell (Structure): original structure whose atomic sites are to be
+            perturbed
+        max_displacement (float): maximum displacement distance for
+            perturbing the structure (Angstroms)
+        min_displacement (float): minimum displacement distance for
+            perturbing the structure (Angstroms)
+        num_displacements (int): number of unique displacement distances to
+            try, uniformly distributed between 'min_displacement' and
+            'max_displacement'.
+        structures_per_displacement_distance (int): number of perturbed
+            structures to generate for each unique displacement distance.
+        min_random_distance (Optional float): If None (default), then for a
+            given perturbed structure, all atoms will move the same distance
+            from their original locations. If float, then for a given
+            perturbed structure, the distances that atoms move will be
+            uniformly distributed from a minimum distance of
+            'min_random_distance' to one of the displacement distances
+            uniformly sampled between 'min_displacement' and
+            'max_displacement'.
+    Returns:
+        (List of randomly displaced structures (List of Structures),
+         List of corresponding displacements)
+    """
+    displacements = np.repeat(
+        np.linspace(min_displacement, max_displacement, num_displacements),
+        supercells_per_displacement_distance
+    )
+    # self.min_random_distance = min_random_distance
+    perturbed_supercells = []  # list of perturbed supercell structures
+    for displacement in displacements:
+        perturb_structure_transformer = PerturbStructureTransformation(
+            displacement,
+            min_random_distance)
+        perturbed_supercell = perturb_structure_transformer.apply_transformation(
+            supercell)
+        perturbed_supercells += [perturbed_supercell]
+    return perturbed_supercells, displacements
diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 488aec335..d8ccfed71 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -41,7 +41,7 @@
     EnergyTrend
 from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering, magnetic_deformation
 from pymatgen.command_line.bader_caller import bader_analysis_from_path
-from pymatgen.transformations.advanced_transformations import PerturbSitesTransformation
+from pymatgen.transformations.standard_transformations import PerturbStructureTransformation
 from pymatgen.io.vasp.sets import MPStaticSet
 >>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 
@@ -2069,7 +2069,10 @@ def run_task(self, fw_spec):
                                  '9 6.5 5.0']
         max_order_settings = [3] * len(cluster_diam_settings)
         submodel1_settings = ['anh 0 1 2 3'] * len(cluster_diam_settings)
-        export_sbte_settings = ['5 5 5 2 3'] * len(cluster_diam_settings)
+        export_sbte_string = str(self["trans_mat"][0][0]) + ' ' + \
+                             str(self["trans_mat"])[1][1] + ' ' + \
+                             str(self["trans_mat"])[2][2] + ' 2 3'
+        export_sbte_settings = [export_sbte_string] * len(cluster_diam_settings)
         if self["first_pass"] is False:
             max_order_settings += [4] * len(cluster_diam_settings)
             cluster_diam_settings += cluster_diam_settings
@@ -2163,6 +2166,8 @@ def run_task(self, fw_spec):
                 "formula": formula,
                 "formula_pretty": formula_pretty,
                 "parent_structure": self["parent_structure"].as_dict(),
+                "supercell_structure": self["supercell_structure"].as_dict(),
+                "supercell_transformation_matrix": self["trans_mat"].tolist(),
                 "wf_meta": {"wf_uuid": uuid},
 
                 # Store relevant CSLD settings
@@ -2174,11 +2179,13 @@ def run_task(self, fw_spec):
                 "export_potential": self["csld_settings"]["export_potential"][
                     "export_shengbte"],
 
+                # Store CSLD results
                 "cross_val_error": float(rel_err),
                 "num_imaginary_modes": int(num_imaginary_bands),
                 "most_imaginary_freq": float(most_imaginary_freq),
                 "imaginary_freq_sum": float(sum(imaginary_freqs))
             }
+
             latest_settings = {str(self["convergence_info"]["iteration"]):
                                    {self["csld_settings"]["model"]["max_order"],
                                     self["csld_settings"]["fitting"][
@@ -2218,7 +2225,8 @@ def run_task(self, fw_spec):
                     shengbte_cmd=">>shengbte_cmd<<",
                     db_file=self["db_file"],
                     wf_uuid=self["wf_uuid"],
-                    t_range=self["shengbte_t_range"]
+                    t_range=self["shengbte_t_range"],
+                    trans_mat=self["trans_mat"]
                 )
             )
             shengbte_fw.spec["_fworker"] = fw_spec["_fworker"]
@@ -2237,15 +2245,12 @@ def run_task(self, fw_spec):
                 new_fws = []
 
                 # Create new perturbed supercells
-                more_perturbed_supercells_transform = PerturbSitesTransformation(
-                    max_disp=0.2,
-                    min_disp=0.12,
-                    num_disps=5,
-                    structures_per_displacement_distance=1,
-                    min_random_distance=None
-                )
-                more_perturbed_supercells = more_perturbed_supercells_transform.apply_transformation(self["supercell_structure"])
-                more_disps = more_perturbed_supercells_transform.disps
+                from atomate.vasp.analysis.csld import generate_perturbed_supercells
+                more_perturbed_supercells, more_disps = generate_perturbed_supercells(self["supercell_structure"],
+                                                                                      min_displacement=0.12,
+                                                                                      max_displacement=0.2,
+                                                                                      num_displacements=5,
+                                                                                      )
 
                 # Create new static FWs
                 for idx, more_perturbed_supercell in enumerate(more_perturbed_supercells):
@@ -2316,7 +2321,7 @@ class ShengBTEToDB(FiretaskBase):
     """
 
     required_params = ["parent_structure", "shengbte_cmd", "db_file",
-                       "wf_uuid"]
+                       "wf_uuid", "trans_mat"]
     optional_params = ["t_range"] #boolean for multiple temperatures
 
     def run_task(self, fw_spec):
@@ -2354,7 +2359,9 @@ def run_task(self, fw_spec):
                 self["parent_structure"].sites[i]._frac_coords.tolist()
                 for i in range(self["parent_structure"].num_sites)
             ],
-            'scell': [5, 5, 5],
+            'scell': [self["trans_mat"][0][0],
+                      self["trans_mat"][1][1],
+                      self["trans_mat"][2][2]],
             't': 300,
             'scalebroad': 0.5,
             'nonanalytic': False,
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index f5aba8d41..d64d64071 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -20,6 +20,7 @@
 from atomate.vasp.powerups import (
     add_additional_fields_to_taskdocs
 )
+from atomate.vasp.analysis.csld import generate_perturbed_supercells
 
 from pymatgen.io.vasp.sets import MPStaticSet, MPRelaxSet
 
@@ -39,6 +40,7 @@ class CompressedSensingLatticeDynamicsWF:
     def __init__(
             self,
             parent_structure,
+            symmetrize=False,
             symprec=0.1,
             min_atoms=-np.Inf,
             max_atoms=np.Inf,
@@ -67,8 +69,14 @@ def __init__(
             5. Output the interatomic force constants to the database.
 
         Args:
-            parent_structure (Structure): Structure to primitize and conduct
-                CSLD on
+            parent_structure (Structure): Structure to conduct CSLD on
+            symmetrize (bool): If True, the parent_structure will be primitized
+                before running CSLD. Else, the parent_structure will be used
+                for CSLD as is.
+            tight_relaxation (bool): If True, run a tight relaxation step on the
+                parent_structure. Else, do not. TODO: IMPLEMENT
+            dfpt_check (bool): If True, run a DFPT calculation at the gamma
+                point to check for dynamic instabilities. TODO: IMPLEMENT
             symprec (float): symmetry precision parameter for
                 SpacegroupAnalyzer's 'get_primitive_standard_structure()'
                 function
@@ -108,8 +116,10 @@ def __init__(
         }
 
     # Create supercell
-        sga = SpacegroupAnalyzer(parent_structure, symprec=symprec)
-        self.parent_structure = sga.get_primitive_standard_structure()
+        self.parent_structure = parent_structure
+        if symmetrize:
+            sga = SpacegroupAnalyzer(parent_structure, symprec=symprec)
+            self.parent_structure = sga.get_primitive_standard_structure()
 
         self.min_atoms = min_atoms
         self.max_atoms = max_atoms
@@ -126,18 +136,16 @@ def __init__(
         self.supercell_smallest_dim = supercell_transform.smallest_dim
 
     # Generate list of perturbed supercells
-        # list of (non-unique) displacement values used in the perturbation (np.ndarray)
-        self.disps = np.repeat(
-            np.linspace(min_displacement, max_displacement, num_displacements),
-            supercells_per_displacement_distance
-        )
-        self.min_random_distance = min_random_distance
-        self.perturbed_supercells = [] # list of perturbed supercell structures
-        for amplitude in self.disps:
-            perturb_structure_transformer = PerturbStructureTransformation(amplitude,
-                                                                           self.min_random_distance)
-            perturbed_supercell = perturb_structure_transformer.apply_transformation(self.supercell)
-            self.perturbed_supercells += [perturbed_supercell]
+        # self.perturbed_supercells: list of perturbed supercells (list of Structures)
+        # self.disps: list of (non-unique) displacement values used in the perturbation (np.array)
+        self.perturbed_supercells, self.disps = generate_perturbed_supercells(
+            self.supercell,
+            min_displacement=min_displacement,
+            max_displacement=max_displacement,
+            num_displacements=num_displacements,
+            supercells_per_displacement_distance=supercells_per_displacement_distance,
+            min_random_distance=min_random_distance
+            )
 
         self.shengbte_t_range = shengbte_t_range
 
@@ -262,7 +270,7 @@ def _add_metadata(structure):
     print(csld_class.supercell.num_sites)
     csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Si")
 
-    wf = add_tags(wf, ['csld', 'v1', 'rees', 'pre-relaxed si'])
+    wf = add_tags(wf, ['csld', 'v1', 'rees', 'pre-relaxed si', 'diagonal supercell'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
     # wf = add_modify_incar(wf,
     #                       modify_incar_params={'incar_update': {'ENCUT': 500,

From bc5098d59ec51bcceeb61cf22ca1d7fa2a9cac55 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 1 Aug 2019 15:42:49 -0700
Subject: [PATCH 034/207] -Only pass successful static calculations into the
 CSLD firework

---
 atomate/vasp/firetasks/parse_outputs.py | 32 ++++++++++++++-----------
 atomate/vasp/workflows/base/csld.py     | 12 +++++++---
 2 files changed, 27 insertions(+), 17 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index d8ccfed71..fc9dddcca 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -41,7 +41,6 @@
     EnergyTrend
 from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering, magnetic_deformation
 from pymatgen.command_line.bader_caller import bader_analysis_from_path
-from pymatgen.transformations.standard_transformations import PerturbStructureTransformation
 from pymatgen.io.vasp.sets import MPStaticSet
 >>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 
@@ -1885,7 +1884,7 @@ def random_search(self, maxIter):
 
         return cluster_diam_settings, max_order_settings, submodel1_settings
 
-    def set_params(self, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
+    def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
         from configparser import ConfigParser
         supercell_folder = self["parent_structure"].composition.reduced_formula + \
                            "_supercell_iter" + str(iteration_number)
@@ -1905,7 +1904,7 @@ def set_params(self, iteration_number, cluster_diam, max_order, submodel1, expor
         # Create folders for perturbed supercell POSCARS and force.txt's
         disp_folders = []
         csld_traindat_disp_folders = ''
-        for idx, disp in enumerate(self["disps"]):
+        for idx, disp in enumerate(disps):
             disp_folder = supercell_folder + '/disp' + str(disp)
             disp_folders += [disp_folder] # list of folder paths
             csld_traindat_disp_folders += ' ' + str(disp_folder) # Create string for CSLD input
@@ -2090,15 +2089,7 @@ def run_task(self, fw_spec):
         print(submodel1_settings)
 
         while not_converged and iter < maxIter:
-            self.set_params(iter,
-                            cluster_diam_settings[iter],
-                            max_order_settings[iter],
-                            submodel1_settings[iter],
-                            export_sbte_settings[iter])
-            self["csld_options"]["pdfout"] = 'plots' + str(iter) + '.pdf'
-
             uuid = self["wf_uuid"]
-
             formula = self["parent_structure"].formula
             formula_pretty = self[
                 "parent_structure"].composition.reduced_formula
@@ -2106,15 +2097,18 @@ def run_task(self, fw_spec):
             supercells_dicts = list(
                 tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
                             "task_label": {"$regex": task_label},
-                            "formula_pretty": formula_pretty},
+                            "formula_pretty": formula_pretty,
+                            "state": 'successful'},
                            ['task_id',
                             'task_label',
-                            'output.forces']))
+                            'output.forces',
+                            'displacement_value']))
             # list of dicts where each dict contatins a task_id and a list of forces
             #   for each supercell
 
             supercells_forces = []
             supercells_task_labels = []
+            successful_disps = [] #displacement values of successful static calcs
             for supercell_dict in supercells_dicts:
                 # List of np.ndarrays where each np.ndarray is a matrix of forces
                 #  for a perturbed supercell
@@ -2122,6 +2116,7 @@ def run_task(self, fw_spec):
                     np.asarray(supercell_dict['output']['forces'])]
 
                 supercells_task_labels += [supercell_dict['task_label']]
+                successful_disps += supercell_dict['displacement_value']
 
             supercells_zip = sorted(
                 zip(supercells_task_labels, supercells_forces),
@@ -2131,6 +2126,14 @@ def run_task(self, fw_spec):
                                  (supercells_task_labels, supercells_forces) in
                                  supercells_zip]
 
+            self.set_params(iter,
+                            successful_disps,
+                            cluster_diam_settings[iter],
+                            max_order_settings[iter],
+                            submodel1_settings[iter],
+                            export_sbte_settings[iter])
+            self["csld_options"]["pdfout"] = 'plots' + str(iter) + '.pdf'
+
             # Create force.txt files for perturbed supercells
             for supercell_idx, supercell_force in enumerate(supercells_forces):
                 path = self["forces_paths"][supercell_idx]
@@ -2268,6 +2271,7 @@ def run_task(self, fw_spec):
                         name=name + " static"
                     )
                     new_static_fw.spec["_fworker"] = fw_spec["_fworker"]
+                    new_static_fw.spec["displacement_value"] = more_disps[idx]
                     if fw_spec.get("tags", None):
                         new_static_fw.spec["tags"] = fw_spec["tags"]
                     new_fws.append(new_static_fw)
@@ -2283,7 +2287,7 @@ def run_task(self, fw_spec):
                         supercell_structure=self["supercell_structure"],
                         supercell_smallest_dim=self["supercell_smallest_dim"],
                         perturbed_supercells=self["perturbed_supercells"]+more_perturbed_supercells,
-                        disps=self["disps"]+more_disps,
+                        disps=successful_disps+more_disps,
                         first_pass=False
                     ),
                     name="Compressed Sensing Lattice Dynamics",
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index d64d64071..9cd5a0e37 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -182,13 +182,15 @@ def _add_metadata(structure):
 
             static_vis = MPStaticSet(perturbed_supercell,
                                      user_incar_settings=static_user_incar_settings)
-            fws.append(StaticFW(
+            static_fw = StaticFW(
                 perturbed_supercell,
                 vasp_input_set=static_vis,
                 vasp_cmd=c["VASP_CMD"],
                 db_file=c["DB_FILE"],
                 name=name + " static"
-            ))
+            )
+            static_fw.spec["displacement_value"] = self.disps[idx]
+            fws.append(static_fw)
 
         print('DISPS')
         print(self.disps)
@@ -256,9 +258,11 @@ def _add_metadata(structure):
     prim = Structure.from_file('POSCAR-well_relaxed_Si')
 
     csld_class = CompressedSensingLatticeDynamicsWF(prim,
+                                                    symmetrize=False,
                                                     num_nn_dists=5,
                                                     num_displacements=10,
                                                     supercells_per_displacement_distance=1,
+                                                    force_diagonal_transformation=True
                                                     )
     print("uuid")
     print(csld_class.uuid)
@@ -270,7 +274,9 @@ def _add_metadata(structure):
     print(csld_class.supercell.num_sites)
     csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Si")
 
-    wf = add_tags(wf, ['csld', 'v1', 'rees', 'pre-relaxed si', 'diagonal supercell'])
+    wf = add_tags(wf, ['csld', 'v1', 'rees',
+                       'pre-relaxed si', 'diagonal supercell',
+                       'not symmetrized'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
     # wf = add_modify_incar(wf,
     #                       modify_incar_params={'incar_update': {'ENCUT': 500,

From bd22677248baae994c5f479a79ebc92664d3fa3c Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Mon, 5 Aug 2019 15:46:57 -0700
Subject: [PATCH 035/207] Working workflow

---
 atomate/vasp/firetasks/parse_outputs.py | 58 ++++++++++++++++---------
 atomate/vasp/workflows/base/csld.py     | 36 ++++++++++-----
 requirements-optional.txt               |  4 ++
 3 files changed, 67 insertions(+), 31 deletions(-)
 create mode 100644 requirements-optional.txt

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index fc9dddcca..5b9c30bdf 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1828,9 +1828,10 @@ class CSLDForceConstantsToDB(FiretaskBase):
         "trans_mat", "supercell_structure",
         "supercell_smallest_dim",
         "disps", "first_pass",
-        "static_user_incar_settings", "env_vars"]
+        "static_user_incar_settings", "env_vars",
+        "shengbte_t_range", "shengbte_fworker"]
 
-    optional_params = ["shengbte_t_range"]
+    optional_params = []
 
     def random_search(self, maxIter):
         """
@@ -1983,9 +1984,10 @@ def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1
         csld_settings['phonon'] = {
             'qpoint_fractional': False,
             # 'Auto' or something like "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
-            'wavevector': "[[25,  [0,0,0],'\Gamma', [0,0.5,0.5], 'X'],"
-                          " [25, [1,0.5,0.5], 'X', [0.75,0.375,0.375], "
-                          "'K', [0,0,0], '\Gamma', [0.5, 0.5, 0.5], 'L']]",
+            'wavevector': 'Auto',
+            # "[[25,  [0,0,0],'\Gamma', [0,0.5,0.5], 'X'],"
+            #               " [25, [1,0.5,0.5], 'X', [0.75,0.375,0.375], "
+            #               "'K', [0,0,0], '\Gamma', [0.5, 0.5, 0.5], 'L']]",
             'unit': 'meV',  # THz, meV, eV, cm
 
             # number of grid points
@@ -2055,7 +2057,8 @@ def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1
     def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        tasks = mmdb["tasks"]
+        # tasks = mmdb["tasks"]
+        tasks = mmdb.collection
 
         iter = 0
         not_converged = True
@@ -2069,8 +2072,8 @@ def run_task(self, fw_spec):
         max_order_settings = [3] * len(cluster_diam_settings)
         submodel1_settings = ['anh 0 1 2 3'] * len(cluster_diam_settings)
         export_sbte_string = str(self["trans_mat"][0][0]) + ' ' + \
-                             str(self["trans_mat"])[1][1] + ' ' + \
-                             str(self["trans_mat"])[2][2] + ' 2 3'
+                             str(self["trans_mat"][1][1]) + ' ' + \
+                             str(self["trans_mat"][2][2]) + ' 2 3'
         export_sbte_settings = [export_sbte_string] * len(cluster_diam_settings)
         if self["first_pass"] is False:
             max_order_settings += [4] * len(cluster_diam_settings)
@@ -2101,8 +2104,7 @@ def run_task(self, fw_spec):
                             "state": 'successful'},
                            ['task_id',
                             'task_label',
-                            'output.forces',
-                            'displacement_value']))
+                            'output.forces']))
             # list of dicts where each dict contatins a task_id and a list of forces
             #   for each supercell
 
@@ -2112,11 +2114,15 @@ def run_task(self, fw_spec):
             for supercell_dict in supercells_dicts:
                 # List of np.ndarrays where each np.ndarray is a matrix of forces
                 #  for a perturbed supercell
+                print('SUPERCELL_DICT')
+                print(supercell_dict)
                 supercells_forces += [
                     np.asarray(supercell_dict['output']['forces'])]
 
                 supercells_task_labels += [supercell_dict['task_label']]
-                successful_disps += supercell_dict['displacement_value']
+
+                successful_disp = re.search('disp_val: (\d+.\d+)', supercell_dict['task_label'])
+                successful_disps += [successful_disp.group(1)]
 
             supercells_zip = sorted(
                 zip(supercells_task_labels, supercells_forces),
@@ -2170,7 +2176,7 @@ def run_task(self, fw_spec):
                 "formula_pretty": formula_pretty,
                 "parent_structure": self["parent_structure"].as_dict(),
                 "supercell_structure": self["supercell_structure"].as_dict(),
-                "supercell_transformation_matrix": self["trans_mat"].tolist(),
+                "supercell_transformation_matrix": self["trans_mat"],
                 "wf_meta": {"wf_uuid": uuid},
 
                 # Store relevant CSLD settings
@@ -2195,7 +2201,7 @@ def run_task(self, fw_spec):
                                         "submodel1"],
                                     self["csld_settings"]["export_potential"][
                                         "export_shengbte"]}}
-            self["convergence_info"]["iteration"] += 1
+            self["convergence_info"]["iteration"] = iter
             self["convergence_info"]["settings_tried"] += [latest_settings]
             self["convergence_info"]["cross_val_errors"] += [rel_err]
             self["convergence_info"]["most_imaginary_freqs"] += [
@@ -2208,7 +2214,7 @@ def run_task(self, fw_spec):
 
             summaries.append(summary)
 
-            iter = self['convergence_info']['iteration']
+            iter += 1
 
         mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
         mmdb.collection.insert(summaries)
@@ -2230,9 +2236,13 @@ def run_task(self, fw_spec):
                     wf_uuid=self["wf_uuid"],
                     t_range=self["shengbte_t_range"],
                     trans_mat=self["trans_mat"]
-                )
+                ),
+                name="ShengBTE for Lattice Thermal Conductivity"
             )
-            shengbte_fw.spec["_fworker"] = fw_spec["_fworker"]
+            if isinstance(self["shengbte_fworker"], str):
+                shengbte_fw.spec["_fworker"] = self["shengbte_fworker"]
+            else:
+                shengbte_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
             CSLD_path = self.get("path", os.getcwd())
             shengbte_fw.spec["successful_CSLD_path"] = CSLD_path
             if fw_spec.get("tags", None):
@@ -2293,7 +2303,7 @@ def run_task(self, fw_spec):
                     name="Compressed Sensing Lattice Dynamics",
                     parents=new_fws[-len(more_perturbed_supercells):]
                 )
-                new_csld_fw.spec["_fworker"] = fw_spec["_fworker"]
+                new_csld_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
                 if fw_spec.get("tags", None):
                     new_csld_fw.spec["tags"] = fw_spec["tags"]
                 new_fws.append(new_csld_fw)
@@ -2390,8 +2400,15 @@ def run_task(self, fw_spec):
             shengbte_cmd = shlex.split(shengbte_cmd)
         shengbte_cmd = list(shengbte_cmd)
         logger.info("Running command: {}".format(shengbte_cmd))
-        return_code = subprocess.call(shengbte_cmd) #call() waits for the process to finish
+        # return_code = subprocess.call(shengbte_cmd) #call() waits for the process to finish
+
+        with open("shengbte.out", 'w') as f_std, \
+                open("shengbte_err.txt", "w", buffering=1) as f_err:
+            # use line buffering for stderr
+            return_code = subprocess.call(shengbte_cmd, stdout=f_std, stderr=f_err)
         logger.info("Command {} finished running with returncode: {}".format(shengbte_cmd, return_code))
+        if return_code==1:
+            raise RuntimeError("Running ShengBTE failed")
 
         try:
             db_file = env_chk(self.get("db_file"), fw_spec)
@@ -2399,13 +2416,14 @@ def run_task(self, fw_spec):
             if self["t_range"]:
                 temps = np.linspace(100, 1000, 10)
             else:
-                temps = 300
+                temps = [300]
 
             # Save to DB
             summaries = []
             for temp in temps:
                 # xx, xy, xz, yx, yy, yz, zx, zy, zz
-                flattened_kappa = list(np.loadtxt('T'+str(int(temp))+'K/BTE.kappa_tensor')[1][1:])
+                flattened_kappa = np.loadtxt('T'+str(int(temp))+'K/BTE.kappa_tensor')[1][1:]
+                flattened_kappa = flattened_kappa.reshape((3, 3)).tolist()
                 summary = {
                     "date": datetime.now(),
                     "temperature": temp,
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 9cd5a0e37..4160175e6 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -51,7 +51,8 @@ def __init__(
             num_displacements=10,
             min_random_distance=None,
             supercells_per_displacement_distance=1,
-            shengbte_t_range=False
+            shengbte_t_range=False,
+            shengbte_fworker=None
     ):
         """
         This workflow will use compressed sensing lattice dynamics (CSLD)
@@ -108,7 +109,14 @@ def __init__(
             shengbte_t_range (bool): If False (default), calculate the lattice
                 thermal conductivity with ShengBTE at 300 K. If True, do the
                 calculation from 100-1000 K with 100 K steps (much slower).
+            shengbte_fworker (None or str): If None, the ShengBTE firework's
+                fworker will be set to all the previous fireworks' fworker. If
+                str, the ShengBTE firework's fworker will be set to
+                shengbte_fworker.
         """
+        # if force_diagonal_transformation is True and num_nn_dists==5:
+        #     num_nn_dists = 6
+
         self.uuid = str(uuid4())
         self.wf_meta = {
             "wf_uuid": self.uuid,
@@ -132,7 +140,7 @@ def __init__(
         )
         # supercell (Structure)
         self.supercell = supercell_transform.apply_transformation(self.parent_structure)
-        self.trans_mat = supercell_transform.trans_mat
+        self.trans_mat = supercell_transform.trans_mat.tolist()
         self.supercell_smallest_dim = supercell_transform.smallest_dim
 
     # Generate list of perturbed supercells
@@ -148,6 +156,7 @@ def __init__(
             )
 
         self.shengbte_t_range = shengbte_t_range
+        self.shengbte_fworker = shengbte_fworker
 
     def get_wf(
             self,
@@ -208,7 +217,8 @@ def _add_metadata(structure):
                 first_pass=True,
                 static_user_incar_settings=static_user_incar_settings,
                 env_vars=c,
-                shengbte_t_range=self.shengbte_t_range
+                shengbte_t_range=self.shengbte_t_range,
+                shengbte_fworker=self.shengbte_fworker
             ),
             name="Compressed Sensing Lattice Dynamics",
             parents=fws[-len(self.perturbed_supercells):]
@@ -255,11 +265,13 @@ def _add_metadata(structure):
     from pymatgen.core.structure import Structure
     # prim = Structure.from_file('POSCAR_csld_primitivized')
 
-    prim = Structure.from_file('POSCAR-well_relaxed_Si')
+    prim = Structure.from_file('POSCAR-Si555')
+    # prim = Structure.from_file('POSCAR-Mg3Sb2_save')
+    # print(prim)
 
     csld_class = CompressedSensingLatticeDynamicsWF(prim,
                                                     symmetrize=False,
-                                                    num_nn_dists=5,
+                                                    num_nn_dists=6,
                                                     num_displacements=10,
                                                     supercells_per_displacement_distance=1,
                                                     force_diagonal_transformation=True
@@ -270,21 +282,23 @@ def _add_metadata(structure):
     wf = csld_class.get_wf()
     print("trans mat")
     print(csld_class.trans_mat)
+    print(type(csld_class.trans_mat))
     print(csld_class.supercell_smallest_dim)
     print(csld_class.supercell.num_sites)
     csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Si")
+    # csld_class.supercell.to("poscar", filename="SPOSCAR-Mg3Sb2")
 
     wf = add_tags(wf, ['csld', 'v1', 'rees',
                        'pre-relaxed si', 'diagonal supercell',
-                       'not symmetrized'])
+                       'not symmetrized', '555'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
-    # wf = add_modify_incar(wf,
-    #                       modify_incar_params={'incar_update': {'ENCUT': 500,
-    #                                                             'ISPIN': 1}})
+    wf = add_modify_incar(wf,
+                          modify_incar_params={'incar_update': {'ENCUT': 500,
+                                                                'ISPIN': 1}})
     # print(wf)
 
-    lpad = LaunchPad.auto_load()
-    lpad.add_wf(wf)
+    # lpad = LaunchPad.auto_load()
+    # lpad.add_wf(wf)
 
 # uuid
 # 0ff0d430-b43f-4cb5-ac8b-55c465b7867c
diff --git a/requirements-optional.txt b/requirements-optional.txt
new file mode 100644
index 000000000..a46c4ef70
--- /dev/null
+++ b/requirements-optional.txt
@@ -0,0 +1,4 @@
+nose==1.3.7
+coverage==4.5.3
+coveralls==1.7.0
+f90nml==1.1.2
\ No newline at end of file

From da7435ddafb0d86a42ee6156d478c85c6c80b69b Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 6 Aug 2019 14:31:56 -0700
Subject: [PATCH 036/207] Updated doc strings and comments for CSLD firetasks
 and moved code outside the grid search loop

---
 atomate/vasp/firetasks/parse_outputs.py | 195 +++++++++++++++---------
 atomate/vasp/workflows/base/csld.py     |  58 ++-----
 2 files changed, 141 insertions(+), 112 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 5b9c30bdf..973e7000c 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1817,7 +1817,12 @@ class CSLDForceConstantsToDB(FiretaskBase):
     Optional parameters:
         shengbte_t_range (boolean): If True, pass to the ShengBTEToDB firetask
             that lattice thermal conductivity should be calculated for 100 K to
-            1000 K in steps of 100 K. If False, only calculate at 300 K.
+            1000 K in steps of 100 K. If False (default), only calculate at
+            300 K.
+        shengbte_fworker (str): If None (default), set the ShengBTE fworker to
+            the previous f_worker. Else, set it to the specified fworker
+            (allowing the user to run ShengBTE with different Fireworks
+            configurations than used to run the VASP static calculations).
     """
 
     logger = get_logger(__name__)
@@ -1829,9 +1834,9 @@ class CSLDForceConstantsToDB(FiretaskBase):
         "supercell_smallest_dim",
         "disps", "first_pass",
         "static_user_incar_settings", "env_vars",
-        "shengbte_t_range", "shengbte_fworker"]
+        ]
 
-    optional_params = []
+    optional_params = ["shengbte_t_range", "shengbte_fworker"]
 
     def random_search(self, maxIter):
         """
@@ -1885,7 +1890,40 @@ def random_search(self, maxIter):
 
         return cluster_diam_settings, max_order_settings, submodel1_settings
 
-    def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1, export_sbte):
+    def set_params(self, iteration_number, disps,
+                   cluster_diam, max_order, submodel1, export_sbte):
+        """
+        This function deals with creating all the files, directories, and input
+        parameters necessary for running CSLD.
+
+        Specifically, it will save the transformation matrix (sc.txt) and parent
+        structure (POSCAR) in the current directory, create a folder for the current
+        iteration (e.g. Si_supercell_iter0) with subdirectories (e.g. disp0.010)
+        for each perturbed supercell. POSCARs of each perturbed supercell is written
+        inside the corresponding subdirectory. Next, all of CSLD's input parameters
+        are automatically generated in a format readable by CSLD and then saved to
+        the class' dictionary.
+
+        Args:
+            disps (list of floats): list of displacement distances for perturbed
+                supercells that ran successfully
+            iteration_number (int): current iteration (0-indexed) of the CSLD
+                grid or random search
+            cluster_diam (str): Space-separated string containing the spherical
+                length cutoffs for pair, triplet, and quadruplet interactions
+                 for CSLD (e.g. '11 6.5 5.0')
+            max_order (int): Max order of interatomic force constants to
+                consider (up to 6th order)
+            submodel1 (str): Anharmonicity orders to consider (e.g.
+                'anh 0 1 2 3')
+            export_sbte (str): Space-separated parameters for exporting CSLD's
+                interatomic force constants into a format readable by ShengBTE.
+                The first 3 numbers are the size of the supercell for which
+                interatomic force constants are exported. The next numbers are
+                the force constant orders to consider. E.g. To output 2nd and
+                3rd order force constants for a 5x5x5 supercell, the
+                corresponding string must be '5 5 5 2 3'.
+        """
         from configparser import ConfigParser
         supercell_folder = self["parent_structure"].composition.reduced_formula + \
                            "_supercell_iter" + str(iteration_number)
@@ -1902,7 +1940,7 @@ def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1
         self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
         self["parent_structure"].to("poscar", filename=supercell_folder + "/POSCAR")
 
-        # Create folders for perturbed supercell POSCARS and force.txt's
+        # Create folders for perturbed supercell POSCARS and force.txt's (e.g. "Si_supercell_iter0/disp0.010")
         disp_folders = []
         csld_traindat_disp_folders = ''
         for idx, disp in enumerate(disps):
@@ -1915,15 +1953,6 @@ def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1
             self["perturbed_supercells"][idx].to("poscar",
                                                  filename=disp_folder + "/POSCAR")
 
-        # Store information related to convergence of CSLD
-        self['convergence_info'] = {
-            'iteration': 0,
-            'settings_tried': [],
-            'cross_val_errors': [],
-            'most_imaginary_freqs': [],
-            'imaginary_freqs_sum': []
-        }
-
         # training>traindat1 setting for CSLD input
         csld_traindat_string = supercell_folder + '/SPOSCAR'
         csld_traindat_string += csld_traindat_disp_folders
@@ -2055,18 +2084,29 @@ def set_params(self, disps, iteration_number, cluster_diam, max_order, submodel1
         self["forces_paths"] = disp_folders  # Paths to perturbed supercell folders
 
     def run_task(self, fw_spec):
+        # Connect to the database
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
         # tasks = mmdb["tasks"]
         tasks = mmdb.collection
 
+        # Store information related to convergence of CSLD
         iter = 0
         not_converged = True
         maxIter = 2
         summaries = []
+        self['convergence_info'] = {
+            'iteration': iter,
+            'settings_tried': [],
+            'cross_val_errors': [],
+            'most_imaginary_freqs': [],
+            'imaginary_freqs_sum': []
+        }
 
-        #Set list of parameter settings to try (i.e. grid search settings)
-        # <FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN ORDER>
+        # Set list of parameter settings to try (i.e. grid search settings)
+        # TODO: FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN THE ORDER YOU WANT
+        #  TO TRY THEM. (May want to generate this with a grid search, depending
+        #  on what settings seem to work on many materials)
         cluster_diam_settings = ['11 6.5 5.0',
                                  '9 6.5 5.0']
         max_order_settings = [3] * len(cluster_diam_settings)
@@ -2076,14 +2116,14 @@ def run_task(self, fw_spec):
                              str(self["trans_mat"][2][2]) + ' 2 3'
         export_sbte_settings = [export_sbte_string] * len(cluster_diam_settings)
         if self["first_pass"] is False:
+            # If we are running CSLD a second time (i.e. with larger displaced
+            #  supercells, then duplicate all the settings to try with 4th order
+            #  instead of 3rd order anharmonicity
             max_order_settings += [4] * len(cluster_diam_settings)
             cluster_diam_settings += cluster_diam_settings
             submodel1_settings += submodel1_settings
             export_sbte_settings += export_sbte_settings
 
-        ##Generate list of parameter settings to try from random search
-        # cluster_diam_settings, max_order_settings, submodel1_settings = self.random_search(maxIter)
-        # export_sbte_settings = ['5 5 5 2 3'] * maxIter
         print('cluster_diam')
         print(cluster_diam_settings)
         print('max order')
@@ -2091,47 +2131,51 @@ def run_task(self, fw_spec):
         print('submodel')
         print(submodel1_settings)
 
+        uuid = self["wf_uuid"]
+        formula = self["parent_structure"].formula
+        formula_pretty = self[
+            "parent_structure"].composition.reduced_formula
+        task_label = 'static'
+        supercells_dicts = list(
+            tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
+                        "task_label": {"$regex": task_label},
+                        "formula_pretty": formula_pretty,
+                        "state": 'successful'},
+                       ['task_id',
+                        'task_label',
+                        'output.forces']))
+        # list of dicts where each dict contains a task_id and a list of forces
+        #   for each supercell
+
+        supercells_forces = []
+        supercells_task_labels = []
+        successful_disps = [] #displacement values of successful static calcs
+        for supercell_dict in supercells_dicts:
+            # List of np.ndarrays where each np.ndarray is a matrix of forces
+            #  for a perturbed supercell
+            supercells_forces += [
+                np.asarray(supercell_dict['output']['forces'])]
+
+            # Supercell task labels
+            # e.g. 'InSb-perturbed supercell, idx: 0, disp_val: 0.010, static'
+            supercells_task_labels += [supercell_dict['task_label']]
+
+            # Store list of displacement values whose corresponding perturbed supercells successfully ran
+            successful_disp = re.search('disp_val: (\d+.\d+)', supercell_dict['task_label'])
+            successful_disps += [successful_disp.group(1)]
+
+        # Sort the forces by their task label so CSLD correctly matches forces
+        # with their corresponding perturbed supercell
+        supercells_zip = sorted(
+            zip(supercells_task_labels, supercells_forces),
+            key=lambda pair: pair[0])
+        supercells_forces = [supercells_forces for
+                             (supercells_task_labels, supercells_forces) in
+                             supercells_zip]
+
+        # Iterate over CSLD settings until real solutions are found or max
+        # iterations is reached.
         while not_converged and iter < maxIter:
-            uuid = self["wf_uuid"]
-            formula = self["parent_structure"].formula
-            formula_pretty = self[
-                "parent_structure"].composition.reduced_formula
-            task_label = 'static'
-            supercells_dicts = list(
-                tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
-                            "task_label": {"$regex": task_label},
-                            "formula_pretty": formula_pretty,
-                            "state": 'successful'},
-                           ['task_id',
-                            'task_label',
-                            'output.forces']))
-            # list of dicts where each dict contatins a task_id and a list of forces
-            #   for each supercell
-
-            supercells_forces = []
-            supercells_task_labels = []
-            successful_disps = [] #displacement values of successful static calcs
-            for supercell_dict in supercells_dicts:
-                # List of np.ndarrays where each np.ndarray is a matrix of forces
-                #  for a perturbed supercell
-                print('SUPERCELL_DICT')
-                print(supercell_dict)
-                supercells_forces += [
-                    np.asarray(supercell_dict['output']['forces'])]
-
-                supercells_task_labels += [supercell_dict['task_label']]
-
-                successful_disp = re.search('disp_val: (\d+.\d+)', supercell_dict['task_label'])
-                successful_disps += [successful_disp.group(1)]
-
-            supercells_zip = sorted(
-                zip(supercells_task_labels, supercells_forces),
-                key=lambda pair: pair[0])
-            # sort by task labels
-            supercells_forces = [supercells_forces for
-                                 (supercells_task_labels, supercells_forces) in
-                                 supercells_zip]
-
             self.set_params(iter,
                             successful_disps,
                             cluster_diam_settings[iter],
@@ -2152,6 +2196,14 @@ def run_task(self, fw_spec):
                                              self["csld_settings"])
 
             freq_matrix = np.asarray(freq_matrix)
+
+            # CHECK FOR IMAGINARY PHONON MODES
+            # For imaginary frequencies, w^2 is negative.
+            # CSLD handles these as w = sign(sqrt(abs(w^2)), w^2).
+            # i.e. if w < 0, it is imaginary.
+            # Here, we consider phonon frequencies < -1 meV to be imaginary
+            #  (numerical noise can sometimes make frequencies slightly negative,
+            #   so we ignore these)
             imaginary_idx = freq_matrix < -1
             imaginary_freqs = freq_matrix[imaginary_idx]
             print('IMAGINARY FREQUENCIES')
@@ -2163,8 +2215,6 @@ def run_task(self, fw_spec):
             else:
                 most_imaginary_freq = 0
             print(most_imaginary_freq)
-            # For imaginary frequencies, w^2 is negative.
-            # Code handles it as w = sign(sqrt(abs(w^2)), w^2)
 
             if num_imaginary_bands == 0:
                 not_converged = False
@@ -2195,6 +2245,9 @@ def run_task(self, fw_spec):
                 "imaginary_freq_sum": float(sum(imaginary_freqs))
             }
 
+            # Store latest CSLD input settings tried
+            # TODO: If desired, store this information in a database to keep
+            #   track of what settings work and what doesn't for different materials
             latest_settings = {str(self["convergence_info"]["iteration"]):
                                    {self["csld_settings"]["model"]["max_order"],
                                     self["csld_settings"]["fitting"][
@@ -2216,9 +2269,12 @@ def run_task(self, fw_spec):
 
             iter += 1
 
+        # Store the summaries in a "compressed_sensing_lattice_dynamics"
+        #  collection of the database (if it does not exist, it will be created)
         mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
         mmdb.collection.insert(summaries)
 
+        # Output lowest validation error and corresponding CSLD input settings
         best_idx = self["convergence_info"]["cross_val_errors"].index(
             min(self["convergence_info"]["cross_val_errors"]))
         print("The lowest error was {} percent.".format(
@@ -2227,6 +2283,7 @@ def run_task(self, fw_spec):
             self["convergence_info"]["settings_tried"][best_idx]))
 
         if not_converged is False:
+        # If CSLD converged to 0 imaginary frequencies, create the ShengBTE FW
             logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
             shengbte_fw = Firework(
                 ShengBTEToDB(
@@ -2234,7 +2291,7 @@ def run_task(self, fw_spec):
                     shengbte_cmd=">>shengbte_cmd<<",
                     db_file=self["db_file"],
                     wf_uuid=self["wf_uuid"],
-                    t_range=self["shengbte_t_range"],
+                    t_range=self.get("shengbte_t_range", False),
                     trans_mat=self["trans_mat"]
                 ),
                 name="ShengBTE for Lattice Thermal Conductivity"
@@ -2254,7 +2311,7 @@ def run_task(self, fw_spec):
             if self["parent_structure"].num_sites > 5 and self["first_pass"]:
                 logger.info("Compressed Sensing Lattice Dynamics calculation failed."
                             " Max iterations was reached. Creating larger displacements"
-                            " and trying again,")
+                            " and trying again.")
                 new_fws = []
 
                 # Create new perturbed supercells
@@ -2336,7 +2393,7 @@ class ShengBTEToDB(FiretaskBase):
 
     required_params = ["parent_structure", "shengbte_cmd", "db_file",
                        "wf_uuid", "trans_mat"]
-    optional_params = ["t_range"] #boolean for multiple temperatures
+    optional_params = ["t_range"]
 
     def run_task(self, fw_spec):
         from atomate.utils.utils import env_chk
@@ -2345,7 +2402,7 @@ def run_task(self, fw_spec):
         import six
         import shlex
 
-        # Generate CONTROL file
+        # Generate CONTROL file (a FORTRAN input file for ShengBTE)
         from pymatgen.io.shengbte import Control
         qpts = Kpoints.automatic_density(self["parent_structure"], 50000)
         unique_elements = [
@@ -2393,24 +2450,24 @@ def run_task(self, fw_spec):
         shutil.copy(force_constants_path+"/FORCE_CONSTANTS_2ND", os.getcwd())
         shutil.copy(force_constants_path+"/FORCE_CONSTANTS_3RD", os.getcwd())
 
-        # Set up/run ShengBTE
+        # Run ShengBTE
         shengbte_cmd = env_chk(self["shengbte_cmd"], fw_spec)
         if isinstance(shengbte_cmd, six.string_types):
             shengbte_cmd = os.path.expandvars(shengbte_cmd)
             shengbte_cmd = shlex.split(shengbte_cmd)
         shengbte_cmd = list(shengbte_cmd)
         logger.info("Running command: {}".format(shengbte_cmd))
-        # return_code = subprocess.call(shengbte_cmd) #call() waits for the process to finish
-
         with open("shengbte.out", 'w') as f_std, \
                 open("shengbte_err.txt", "w", buffering=1) as f_err:
             # use line buffering for stderr
             return_code = subprocess.call(shengbte_cmd, stdout=f_std, stderr=f_err)
         logger.info("Command {} finished running with returncode: {}".format(shengbte_cmd, return_code))
         if return_code==1:
-            raise RuntimeError("Running ShengBTE failed")
+            raise RuntimeError("Running ShengBTE failed. Check 'shengbte_err.txt'"
+                               " in the launch_dir for details.")
 
         try:
+            # Store lattice thermal conductivity matrix in the database
             db_file = env_chk(self.get("db_file"), fw_spec)
             mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
             if self["t_range"]:
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 4160175e6..40d73dc96 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -114,8 +114,8 @@ def __init__(
                 str, the ShengBTE firework's fworker will be set to
                 shengbte_fworker.
         """
-        # if force_diagonal_transformation is True and num_nn_dists==5:
-        #     num_nn_dists = 6
+        if force_diagonal_transformation is True and num_nn_dists==5:
+            num_nn_dists = 6
 
         self.uuid = str(uuid4())
         self.wf_meta = {
@@ -138,8 +138,10 @@ def __init__(
             self.num_nn_dists,
             force_diagonal_transformation=force_diagonal_transformation
         )
+
         # supercell (Structure)
         self.supercell = supercell_transform.apply_transformation(self.parent_structure)
+        self.nn_dist = supercell_transform.nn_dist
         self.trans_mat = supercell_transform.trans_mat.tolist()
         self.supercell_smallest_dim = supercell_transform.smallest_dim
 
@@ -243,31 +245,11 @@ def _add_metadata(structure):
 if __name__ == "__main__":
 
     from fireworks import LaunchPad
-    from pymatgen.ext.matproj import MPRester
     from atomate.vasp.powerups import add_tags, set_execution_options, add_modify_incar
-
-    #get a structure
-    # mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
-    # # structure = mpr.get_structure_by_material_id('mp-149') #Si
-    # structure = mpr.get_structure_by_material_id('mp-1101039')
-    # test_trans_mat = np.linalg.inv(structure.lattice.matrix) @ (np.eye(3,3) * 20)
-    # print(test_trans_mat)
-    # print(np.linalg.det(test_trans_mat))
-    # structure_test = structure * test_trans_mat
-    # structure_test.to("poscar", filename="POSCAR-noninteger_trans_test")
-
-    # # CONVENTIONAL PRIMITIVE CELL WITH SYMMETRIZATION
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    # sga = SpacegroupAnalyzer(structure, symprec=0.1)
-    # prim = sga.get_primitive_standard_structure()
-
-    # CSLD'S POLARON MAIN-GENERATED PRIMITIVE CELL
     from pymatgen.core.structure import Structure
-    # prim = Structure.from_file('POSCAR_csld_primitivized')
 
-    prim = Structure.from_file('POSCAR-Si555')
-    # prim = Structure.from_file('POSCAR-Mg3Sb2_save')
-    # print(prim)
+    prim = Structure.from_file('POSCAR-well_relaxed_InSb_csld_primitivized')
 
     csld_class = CompressedSensingLatticeDynamicsWF(prim,
                                                     symmetrize=False,
@@ -282,35 +264,25 @@ def _add_metadata(structure):
     wf = csld_class.get_wf()
     print("trans mat")
     print(csld_class.trans_mat)
-    print(type(csld_class.trans_mat))
+    print("nn dist")
+    print(csld_class.nn_dist)
+    print("supercell shortest direction (Angstroms)")
     print(csld_class.supercell_smallest_dim)
+    print("supercell number of atoms")
     print(csld_class.supercell.num_sites)
-    csld_class.supercell.to("poscar", filename="SPOSCAR-csld_super_Si")
-    # csld_class.supercell.to("poscar", filename="SPOSCAR-Mg3Sb2")
+    csld_class.supercell.to("poscar", filename="SPOSCAR-InSb_diagonal")
 
     wf = add_tags(wf, ['csld', 'v1', 'rees',
-                       'pre-relaxed si', 'diagonal supercell',
-                       'not symmetrized', '555'])
+                       'pre-relaxed insb', 'diagonal supercell',
+                       'not symmetrized'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
-    wf = add_modify_incar(wf,
-                          modify_incar_params={'incar_update': {'ENCUT': 500,
-                                                                'ISPIN': 1}})
-    # print(wf)
+    # wf = add_modify_incar(wf,
+    #                       modify_incar_params={'incar_update': {'ENCUT': 500,
+    #                                                             'ISPIN': 1}})
 
     # lpad = LaunchPad.auto_load()
     # lpad.add_wf(wf)
 
-# uuid
-# 0ff0d430-b43f-4cb5-ac8b-55c465b7867c
-# DISPS
-# [0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1 ]
-# trans mat
-# [[-3.  3.  3.]
-#  [ 3. -3.  3.]
-#  [ 3.  3. -3.]]
-# 23.745154105620003
-# 432
-
 #################custom csld_main below##################
 def csld_main(options, settings):
     """

From 623f0e7909680d6b0437c7adb807f9343892b347 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 6 Aug 2019 14:49:41 -0700
Subject: [PATCH 037/207] Updated trans_mat doc string

---
 atomate/vasp/firetasks/parse_outputs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 973e7000c..89c96315c 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1797,7 +1797,7 @@ class CSLDForceConstantsToDB(FiretaskBase):
             which CSLD is being done
         perturbed_supercells (list of Structures): list of perturbed supercell
             structures auto-generated from CompressedSensingLatticeDynamicsWF
-        trans_mat (3x3 np.ndarray): supercell transformation matrix auto-
+        trans_mat (3x3 nested list): supercell transformation matrix auto-
             generated from CompressedSensingLatticeDynamicsWF
         supercell_structure (Structure): supercell structure of parent_structure,
             auto-generated from CompressedSensingLatticeDynamicsWF

From 6731adab0de2ef81f8cf268671859421d7345660 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Tue, 6 Aug 2019 14:53:51 -0700
Subject: [PATCH 038/207] docstring

---
 atomate/vasp/firetasks/parse_outputs.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 89c96315c..f4eaff023 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1779,13 +1779,13 @@ def split_abc(var, var_name):
 
 @explicit_serialize
 class CSLDForceConstantsToDB(FiretaskBase):
-    #TODO: Update this class once a public version of CSLD is released
-    #TODO: Update this class once Junsoo has fixed the cluster generation
+    #TODO: Update this class once Fei's CSLD is modified correctly
     """
     Used to aggregate atomic forces of perturbed supercells in compressed
     sensing lattice dynamics (CSLD) workflow and generate/write interatomic
     force constants up to 3rd order to file. The workflow uses a CSLD software
-    implemented by Zhou et al which can be found at https://github.com/LLNL/csld.
+    implemented by Zhou et al (https://github.com/LLNL/csld) and modified for
+    use in atomate (Aug 6, 2019: https://github.com/rees-c/csld).
 
     Required parameters:
         db_file (str): path to the db file that holds your tasks

From 3b6860fe40c1de5bfc9c546e728cf7ad321ba116 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 10:55:54 -0700
Subject: [PATCH 039/207] Cleaned up code (made functions for CSLD firetask,
 adhered to PEP guidelines, etc.)

---
 atomate/vasp/firetasks/parse_outputs.py | 855 ++++++++++++------------
 atomate/vasp/workflows/base/csld.py     | 335 ++++------
 2 files changed, 584 insertions(+), 606 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index f4eaff023..25cbb8137 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -3,9 +3,20 @@
 import shutil
 import re
 from collections import defaultdict
+from copy import deepcopy
 from datetime import datetime
 
 import numpy as np
+<<<<<<< HEAD
+=======
+
+from monty.json import MontyEncoder, jsanitize
+from pydash.objects import has, get
+
+from atomate.vasp.analysis.csld import default_csld_options, \
+    default_csld_settings
+from atomate.vasp.config import DEFUSE_UNSUCCESSFUL
+>>>>>>> 816883c7 (Cleaned up code (made functions for CSLD firetask, adhered to PEP guidelines, etc.))
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 from fireworks.utilities.fw_serializers import DATETIME_HANDLER
 <<<<<<< HEAD
@@ -1779,7 +1790,6 @@ def split_abc(var, var_name):
 
 @explicit_serialize
 class CSLDForceConstantsToDB(FiretaskBase):
-    #TODO: Update this class once Fei's CSLD is modified correctly
     """
     Used to aggregate atomic forces of perturbed supercells in compressed
     sensing lattice dynamics (CSLD) workflow and generate/write interatomic
@@ -1787,6 +1797,10 @@ class CSLDForceConstantsToDB(FiretaskBase):
     implemented by Zhou et al (https://github.com/LLNL/csld) and modified for
     use in atomate (Aug 6, 2019: https://github.com/rees-c/csld).
 
+    TODO: Update this class once Fei's CSLD is modified correctly
+    TODO: Add to the summary inside 'run_CSLD()' as needed
+    TODO: Rename this class to something more accurate
+
     Required parameters:
         db_file (str): path to the db file that holds your tasks
             collection specifying the database that the perturbed supercell
@@ -1799,7 +1813,7 @@ class CSLDForceConstantsToDB(FiretaskBase):
             structures auto-generated from CompressedSensingLatticeDynamicsWF
         trans_mat (3x3 nested list): supercell transformation matrix auto-
             generated from CompressedSensingLatticeDynamicsWF
-        supercell_structure (Structure): supercell structure of parent_structure,
+        supercell_structure (Structure): supercell structure of parent_structure
             auto-generated from CompressedSensingLatticeDynamicsWF
         supercell_smallest_dim (float): length of shortest direction of the
             supercell lattice, auto-generated from
@@ -1807,15 +1821,24 @@ class CSLDForceConstantsToDB(FiretaskBase):
         disps (list of floats): displacement values corresponding to
             perturbed_supercells, auto-generated from
             CompressedSensingLatticeDynamicsWF
+        force_diagonal_transformation (bool): Whether the transformation matrix
+            used to generate the supercell was diagonal (True) or not (False)
         first_pass (boolean): indicator of whether this firetask has already
             been attempted or if it is automatically running a second time
             with larger perturbations
-        static_user_incar_settings (dict): incar settings used in static calculations
-            in CompressedSensingLatticeDynamicsWF
+        static_user_incar_settings (dict): incar settings used in static
+            calculations in CompressedSensingLatticeDynamicsWF
         env_vars (dict): environmental variables used in static calculations in
             CompressedSensingLatticeDynamicsWF
+
     Optional parameters:
-        shengbte_t_range (boolean): If True, pass to the ShengBTEToDB firetask
+        dynamic_static_calcs (bool): If True, dynamically create more static
+            perturbed supercell calculations with larger displacements if CSLD
+            fails. Default: False.
+        do_shengbte (bool): If True, dynamically create a ShengBTE firework
+            for computing lattice thermal conductivity if CSLD yields a good
+            solution. Default: False.
+        shengbte_t_range (bool): If True, pass to the ShengBTEToDB firetask
             that lattice thermal conductivity should be calculated for 100 K to
             1000 K in steps of 100 K. If False (default), only calculate at
             300 K.
@@ -1827,55 +1850,40 @@ class CSLDForceConstantsToDB(FiretaskBase):
 
     logger = get_logger(__name__)
 
-    required_params = ["db_file",
-        "wf_uuid", "parent_structure",
-        "perturbed_supercells",
-        "trans_mat", "supercell_structure",
-        "supercell_smallest_dim",
-        "disps", "first_pass",
-        "static_user_incar_settings", "env_vars",
+    required_params = [
+        "db_file", "wf_uuid", "parent_structure",
+        "perturbed_supercells", "trans_mat", "supercell_structure",
+        "supercell_smallest_dim", "disps", "force_diagonal_transformation",
+        "first_pass", "static_user_incar_settings", "env_vars"
         ]
 
-    optional_params = ["shengbte_t_range", "shengbte_fworker"]
+    optional_params = [
+        "dynamic_static_calcs", "do_shengbte", "shengbte_t_range",
+        "shengbte_fworker"
+        ]
 
-    def random_search(self, maxIter):
+    @staticmethod
+    def random_search(max_iter):
         """
-        -pair potential is roughly 12 Angstroms, so supercell should be safely
-        larger than that (at least 20 in each direction) so you don't get artifacts
-        from periodic boundary conditions (i.e. atoms being double-counted in the
-        pair potential)
-        -"most likely" at least 4 nearest neighbor distances is ok
-        -
-        -150+ atom-supercell
-        -for low symmetry, more atoms = finer displacement linspace (0.02 - 0.05 in
-        steps of 0.01 or 0.005)
-        -9-12 lattice parameters for pair cutoffs, triplets usually a little more than half of pairs
-        - -1 meV phonon mode is
-    	-change cutoff diameter (easiest, probably increase)
-    	-either increase supercells or relax primitive cell better (check total drift)
-
-    	CSLD CHECKS: IF FITTING IS BAD...
-        Option 1.
-        Play with cluster diameters
-            -random search? bayesopt?
-            -if tried some max number trials and still bad, pick the best one and move to Option 2
-
-        Option 2.
-        Include higher displacement supercells
-            1. If Natom>5, generate supercells at large displacements (>0.1 angstroms)
-            2. Fit up to 3rd order only with supercells perturbed <0.1 angstroms
-                -If good, run SBTE
-                -If bad, then fit including supercells >0.1 angstroms
-                    -If good, run SBTE
-                    -If bad, redo step 2 with 4th order
+        Generates a tuple of cluster diameter, max order, and submodel1 input
+        settings for CSLD using a random search. The length of each returned
+        list of settings is the number of total settings to try.
+
+        Args:
+            max_iter (int): Number of settings to try
+
+        Returns:
+            cluster_diam_settings (list[str]): List of cluster diameter settings
+            max_order_settings (list[int]): List of max order settings
+            submodel1_settings (list[str]): List of submodel1 settings
         """
         import random
 
-        if maxIter % 2 != 0 or maxIter <= 0:
+        if max_iter % 2 != 0 or max_iter <= 0:
             raise AttributeError('maxIter must be even.')
 
         cluster_diam_settings = []
-        for _ in range(maxIter):
+        for _ in range(max_iter):
             pair_diam = random.uniform(8, 12) #self["supercell_smallest_dim"])
             triplet_diam = random.uniform(5.5, 7)
             quadruplet_diam = random.uniform(triplet_diam * 0.6, triplet_diam)
@@ -1884,25 +1892,86 @@ def random_search(self, maxIter):
                 str(pair_diam) + ' ' + str(triplet_diam) + ' ' + str(
                     quadruplet_diam)]
 
-        max_order_settings = [3] * int(maxIter / 2) + [4] * int(maxIter / 2)
-        submodel1_settings = ['anh 0 1 2 3'] * int(maxIter / 2) + \
-                             ['anh 0 1 2 3 4'] * int(maxIter / 2)
+        max_order_settings = [3] * int(max_iter / 2) + [4] * int(max_iter / 2)
+        submodel1_settings = ['anh 0 1 2 3'] * int(max_iter / 2) + \
+                             ['anh 0 1 2 3 4'] * int(max_iter / 2)
 
         return cluster_diam_settings, max_order_settings, submodel1_settings
 
-    def set_params(self, iteration_number, disps,
-                   cluster_diam, max_order, submodel1, export_sbte):
+    def collect_successful_static_calcs_results(self, tasks):
+        """
+        Search a database's tasks collection for successful static calculations
+        and return a list of forces for each supercell
+
+        Args:
+            tasks (MongoDB collection): MongoDB collection containing static
+                perturbed supercells calculations
+
+        Returns:
+            supercells_forces (list[np.array]): List of forces for each
+                successful static perturbed supercell calculation
+            successful_disps (list[float]): List of displacement distances for
+                each successful static perturbed supercell calculation
+        """
+        uuid = self["wf_uuid"]
+        formula_pretty = self[
+            "parent_structure"].composition.reduced_formula
+        task_label = 'static'
+        supercells_dicts = list(
+            tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
+                        "task_label": {"$regex": task_label},
+                        "formula_pretty": formula_pretty,
+                        "state": 'successful'},
+                       ['task_id',
+                        'task_label',
+                        'output.forces']))
+        # list of dicts where each dict contains a task_id and a list of forces
+        #   for each supercell
+
+        supercells_forces = []
+        supercells_task_labels = []
+        successful_disps = []  # displacement values of successful static calcs
+        for supercell_dict in supercells_dicts:
+            # List of np.ndarrays where each np.ndarray is a matrix of forces
+            #  for a perturbed supercell
+            supercells_forces += [
+                np.asarray(supercell_dict['output']['forces'])]
+
+            # Supercell task labels
+            # e.g. 'InSb-perturbed supercell, idx: 0, disp_val: 0.010, static'
+            supercells_task_labels += [supercell_dict['task_label']]
+
+            # Store list of displacement values whose corresponding perturbed
+            # supercells successfully ran
+            successful_disp = re.search('disp_val: (\d+.\d+)',
+                                        supercell_dict['task_label'])
+            successful_disps += [successful_disp.group(1)]
+
+        # Sort the forces by their task label so CSLD correctly matches forces
+        # with their corresponding perturbed supercell
+        supercells_zip = sorted(
+            zip(supercells_task_labels, supercells_forces),
+            key=lambda pair: pair[0])
+        supercells_forces = [supercells_forces for
+                             (supercells_task_labels, supercells_forces) in
+                             supercells_zip]
+
+        return supercells_forces, successful_disps
+
+    def set_params(self, iteration_number, disps, cluster_diam,
+                   max_order, submodel1, export_sbte, supercells_forces,
+                   **kwargs):
         """
         This function deals with creating all the files, directories, and input
         parameters necessary for running CSLD.
 
         Specifically, it will save the transformation matrix (sc.txt) and parent
-        structure (POSCAR) in the current directory, create a folder for the current
-        iteration (e.g. Si_supercell_iter0) with subdirectories (e.g. disp0.010)
-        for each perturbed supercell. POSCARs of each perturbed supercell is written
-        inside the corresponding subdirectory. Next, all of CSLD's input parameters
-        are automatically generated in a format readable by CSLD and then saved to
-        the class' dictionary.
+        structure (POSCAR) in the current directory, create a folder for the
+        current iteration (e.g. Si_supercell_iter0) with subdirectories
+        (e.g. 'disp0.010') for each perturbed supercell. POSCARs of each
+        perturbed supercell is written inside the corresponding subdirectory.
+        Next, all of CSLD's input parameters are automatically generated in a
+        format readable by CSLD and then saved to the class' dictionary.
 
         Args:
             disps (list of floats): list of displacement distances for perturbed
@@ -1923,6 +1992,10 @@ def set_params(self, iteration_number, disps,
                 the force constant orders to consider. E.g. To output 2nd and
                 3rd order force constants for a 5x5x5 supercell, the
                 corresponding string must be '5 5 5 2 3'.
+            supercells_forces (list[np.array]): List of numpy arrays containing
+                forces for each static perturbed supercell calculation
+            kwargs: Any other CSLD settings that the user desires to update
+                from the default values (as found in atomate.vasp.analysis.csld)
         """
         from configparser import ConfigParser
         supercell_folder = self["parent_structure"].composition.reduced_formula + \
@@ -1958,145 +2031,271 @@ def set_params(self, iteration_number, disps,
         csld_traindat_string += csld_traindat_disp_folders
 
         # Create ConfigParser of all CSLD input settings
+        csld_settings_dict = deepcopy(default_csld_settings)
+
+        user_csld_settings = kwargs
+        if user_csld_settings is not None:
+            # recursively update settings dict
+            for k, v in user_csld_settings:
+                csld_settings_dict[k].update(v)
+
+        # update CSLD settings with dynamic options
+        # original structure poscar
+        csld_settings_dict["structure"]["prim"] = supercell_folder + '/POSCAR'
+        csld_settings_dict["model"].update({
+            'max_oder': max_order,
+            'cluster_diameter': cluster_diam,
+            'cluster_filter':
+                r"lambda cls: ((cls.order_uniq <= 2) or (cls.bond_counts(2.9) "
+                r">= 2)) and cls.is_small_in('" + supercell_folder + "/sc.txt')"
+        })
+
+        # directories of unperturbed followed by perturbed supercell poscars
+        # e.g., 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
+        csld_settings_dict["training"]['traindat1'] = csld_traindat_string
+        csld_settings_dict['fitting']['submodel1'] = submodel1
+
+        # e.g., '5 5 5 2 3' is a 5x5x5 supercell
+        csld_settings_dict['export_potential']['export_shengbte'] = export_sbte
+
         csld_settings = ConfigParser()
-        csld_settings['structure'] = {
-            'prim': supercell_folder + '/POSCAR', # original structure poscar
-            'sym_tol': '1e-3',
-            # 'epsilon_inf': None,  # check how it reads 3x3 matrix
-            # 'born_charge': None  # check reading n_atom*9 numbers
-        }
-        csld_settings['model'] = {
-            'model_type': 'LD',
-            'cluster_in': 'clusters.out',
-            'cluster_out': 'clusters.out',
-            'symC_in': 'Cmat.mtx',
-            'symC_out': 'Cmat.mtx',
-            'max_order': max_order, # 3,  # this should be variable
-            'fractional_distance': False,
-            'cluster_diameter': cluster_diam, # '11 6.5 5.0', #this should be variable
-            'cluster_filter': r"lambda cls: ((cls.order_uniq <= 2) or "
-                              r"(cls.bond_counts(2.9) >= 2)) and "
-                              r"cls.is_small_in('" + supercell_folder + "/sc.txt')"
-            # rewrote how it reads the trans_mat
-        }
-        csld_settings['training'] = {
-            'interface': 'VASP',
-            'corr_type': 'f',
-            'corr_in': 'Amat.mtx',
-            'corr_out': 'Amat.mtx',
-            'fval_in': 'fval.txt',
-            'fval_out': 'fval.txt',
-            'traindat1': csld_traindat_string # directories of unperturbed followed
-            # by perturbed supercell poscars
-            # 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
-            # Rewrote how it reads forces
-        }
-        csld_settings['fitting'] = {
-            'solution_in': 'solution_all',
-            'solution_out': 'solution_all',
-            'nsubset': 5,
-            'holdsize': 0.1,
-            ## 1 FPC 2 FPC sparse 3 split 4 sparse split
-            ## 5 split+ right preconditioning 6 sparse split + r preconditioning
-            ## 101 Bayesian CS
-            'method': 5,
-
-            # For weight of L1 or L2 regularization
-            'mulist': '1E-5 1E-6 1E-7 1E-9',
-            'maxIter': 300,
-            'tolerance': 1E-6,
-            'subsetsize': 0.85,
-            'lambda': 0.5,
-            'uscale_list': '0.03',
-            'submodel1': submodel1, # 'anh 0 1 2 3',  # this should be variable
-        }
-        csld_settings['phonon'] = {
-            'qpoint_fractional': False,
-            # 'Auto' or something like "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
-            'wavevector': 'Auto',
-            # "[[25,  [0,0,0],'\Gamma', [0,0.5,0.5], 'X'],"
-            #               " [25, [1,0.5,0.5], 'X', [0.75,0.375,0.375], "
-            #               "'K', [0,0,0], '\Gamma', [0.5, 0.5, 0.5], 'L']]",
-            'unit': 'meV',  # THz, meV, eV, cm
-
-            # number of grid points
-            'dos_grid': '15 15 15',
-
-            # number of points in DOS
-            'nE_dos': 500,
-
-            ## 0 (Gaussian), 1 (Lorentzian), -1 (tetrahedron method)
-            'ismear': -1,
-
-            ## width in THz of Gaussian/Lorentzian smearing
-            'epsilon': 0.05,
-            'pdos': True,
-
-            'thermal_T_range': '50 800 50',
-            'thermal_out': 'thermal_out.txt'
-        }
-        csld_settings['export_potential'] = {
-            'export_shengbte': export_sbte, # '5 5 5 2 3'  # 5x5x5 supercell
-            # 2 and 3 orders to be considered
-            # should be variable?
-        }
-        csld_settings['prediction'] = {
-            'interface': 'VASP',
-            'corr_type': 'f',
-            'corr_in': 'Amat_pred.mtx',
-            'corr_out': 'Amat_pred.mtx',
-            'fval_in': 'fval_pred.txt',
-            'fval_out': 'fval_pred.txt',
-            'traindat0': 'fcc222/POSCAR fcc222/traj*'
-        }
-        # set default values
-        csld_settings['DEFAULT'] = {
-            "qpoint_fractional": False,
-            "true_v_fit": 'true_fit.txt',
-            'epsilon': '0.05',
-            "bcs_reweight": 'True',
-            "bcs_penalty": 'arctan',
-            "bcs_jcutoff": '1E-8'}
-
-        csld_options = {}
-        csld_options['pdfout'] = 'plots.pdf'  # Name of pdf to output results
-        csld_options['ldff_step'] = 0
-        csld_options['phonon_step'] = 1
-        csld_options['phonon'] = False
-        csld_options['save_pot_step'] = 1  # usual default is 0. 1 means output to ShengBTE format.
-        csld_options['pot'] = False
-
-        # set default values
-        csld_options['log_level'] = 1
-        csld_options['symm_step'] = 2
-        csld_options['symm_prim'] = True
-        csld_options['clus_step'] = 3
-        csld_options['symC_step'] = 3
-        csld_options['train_step'] = 3
-        csld_options['fit_step'] = 3
-        csld_options['pred_step'] = 0
-        csld_options['refit'] = False
-        csld_options['cont'] = False
-        csld_options['predict'] = False
+        csld_settings.read_dict(csld_settings_dict)
+        csld_options = deepcopy(default_csld_options)
 
         self["csld_settings"] = csld_settings
         self["csld_options"] = csld_options
         self["forces_paths"] = disp_folders  # Paths to perturbed supercell folders
 
+        # Create force.txt files for perturbed supercells
+        for supercell_idx, supercell_force in enumerate(supercells_forces):
+            path = self["forces_paths"][supercell_idx]
+            np.savetxt(path + "/force.txt", supercell_force, fmt='%.6f')
+
+    def run_csld(self, iter):
+        """
+        Run CSLD, check for imaginary frequencies, and generate a summary of the
+        results.
+
+        Args:
+            iter (int): Current iteration of the grid/random search over CSLD
+                input parameters (0-indexed)
+        Return:
+            summary (dict): Summary of the results from CSLD
+        """
+        # Perform csld minimization now
+        from atomate.vasp.analysis.csld import csld_main
+        rel_err, freq_matrix = csld_main(self["csld_options"],
+                                         self["csld_settings"])
+
+        freq_matrix = np.asarray(freq_matrix)
+
+        # CHECK FOR IMAGINARY PHONON MODES
+        # For imaginary frequencies, w^2 is negative.
+        # CSLD handles these as w = sign(sqrt(abs(w^2)), w^2).
+        # i.e. if w < 0, it is imaginary.
+        # Here, we consider phonon frequencies < -1 meV to be imaginary
+        #  (numerical noise can sometimes make frequencies slightly negative,
+        #   so we ignore these)
+        imaginary_idx = freq_matrix < -1
+        imaginary_freqs = freq_matrix[imaginary_idx]
+        print('IMAGINARY FREQUENCIES')
+        print(imaginary_freqs)
+        num_imaginary_bands = np.sum(np.any(imaginary_idx, axis=1))
+        print(num_imaginary_bands)
+        if np.any(imaginary_freqs):
+            most_imaginary_freq = np.amin(imaginary_freqs)
+        else:
+            most_imaginary_freq = 0
+        print(most_imaginary_freq)
+
+        if num_imaginary_bands == 0:
+            not_converged = False
+
+        # Save to DB
+        summary = {
+            "date": datetime.now(),
+            "formula": self["parent_structure"].formula,
+            "formula_pretty": self[
+                "parent_structure"].composition.reduced_formula,
+            "parent_structure": self["parent_structure"].as_dict(),
+            "supercell_structure": self["supercell_structure"].as_dict(),
+            "supercell_transformation_matrix": self["trans_mat"],
+            "wf_meta": {"wf_uuid": self["wf_uuid"]},
+
+            # Store relevant CSLD settings
+            "iteration": iter,
+            "cluster_diam": self["csld_settings"]["model"][
+                "cluster_diameter"],
+            "max_order": self["csld_settings"]["model"]["max_order"],
+            "submodel1": self["csld_settings"]["fitting"]["submodel1"],
+            "export_potential": self["csld_settings"]["export_potential"][
+                "export_shengbte"],
+
+            # Store CSLD results
+            "cross_val_error": float(rel_err),
+            "num_imaginary_modes": int(num_imaginary_bands),
+            "most_imaginary_freq": float(most_imaginary_freq),
+            "imaginary_freq_sum": float(sum(imaginary_freqs))
+        }
+
+        # Store latest CSLD input settings tried
+        # TODO: If desired, store this information in a database to keep
+        #   track of what settings work and what doesn't for different materials
+        latest_settings = {str(self["convergence_info"]["iteration"]):
+                               {self["csld_settings"]["model"]["max_order"],
+                                self["csld_settings"]["fitting"][
+                                    "submodel1"],
+                                self["csld_settings"]["export_potential"][
+                                    "export_shengbte"]}}
+        self["convergence_info"]["iteration"] = iter
+        self["convergence_info"]["settings_tried"] += [latest_settings]
+        self["convergence_info"]["cross_val_errors"] += [rel_err]
+        self["convergence_info"]["most_imaginary_freqs"] += [
+            most_imaginary_freq]
+        self["convergence_info"]["imaginary_freqs_sum"] += [
+            sum(imaginary_freqs)]
+
+        return summary
+
+    def add_sbte_fw(self, fw_spec):
+        """
+        This function dynamically creates a ShengBTE firework for calculating
+        the lattice thermal conductivity matrix.
+
+        Args:
+            fw_spec (dict): The fw_spec for the CSLD firework.
+
+        Returns:
+            FWAction: Dynamically adds a ShengBTE Firework to the workflow
+        """
+        shengbte_fw = Firework(
+            ShengBTEToDB(
+                parent_structure=self["parent_structure"],
+                shengbte_cmd=">>shengbte_cmd<<",
+                db_file=self["db_file"],
+                wf_uuid=self["wf_uuid"],
+                t_range=self.get("shengbte_t_range", False),
+                trans_mat=self["trans_mat"]
+            ),
+            name="ShengBTE for Lattice Thermal Conductivity"
+        )
+
+        # Set the ShengBTE fworker
+        if isinstance(self["shengbte_fworker"], str):
+            shengbte_fw.spec["_fworker"] = self["shengbte_fworker"]
+        else:
+            shengbte_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
+
+        # Pass the CSLD launcher path to the ShengBTE FW
+        CSLD_path = self.get("path", os.getcwd())
+        shengbte_fw.spec["successful_CSLD_path"] = CSLD_path
+
+        # Add tags
+        if fw_spec.get("tags", None):
+            shengbte_fw.spec["tags"] = fw_spec["tags"]
+
+        return FWAction(additions=shengbte_fw)
+
+    def add_more_static_calcs(self, successful_disps, fw_spec):
+        """
+        This function will dynamically create more static perturbed supercell
+        calculations with displacement distances of 0.12, 0.14, 0.16, 0.18, and
+        0.20, and also append another CSLD Firework. A 'first_pass=False'
+        argument will be passed into the CSLD Firework to ensure that more
+        static perturbed supercell calculations will not be created.
+
+        Args:
+            successful_disps (list[float]): List of displacement distances of
+                previous successful static perturbed supercell calculations
+            fw_spec (dict): Firework spec of the first CSLD Firework
+
+        Returns:
+            FWAction: Dynamically adds a more static calculations and a CSLD
+                Firework to the workflow
+        """
+
+        new_fws = []
+
+        # Create new perturbed supercells
+        from atomate.vasp.analysis.csld import generate_perturbed_supercells
+        more_perturbed_supercells, more_disps = generate_perturbed_supercells(
+            self["supercell_structure"],
+            min_displacement=0.12,
+            max_displacement=0.2,
+            num_displacements=5
+            )
+
+        # Create new static FWs
+        for idx, more_perturbed_supercell in enumerate(
+                more_perturbed_supercells):
+            name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(
+                idx + len(self["perturbed_supercells"]),
+                more_disps)
+            static_vis = MPStaticSet(more_perturbed_supercell,
+                                     user_incar_settings=self[
+                                         "static_user_incar_settings"])
+
+            from atomate.vasp.fireworks.core import StaticFW
+            new_static_fw = StaticFW(
+                more_perturbed_supercell,
+                vasp_input_set=static_vis,
+                vasp_cmd=self["env_vars"]["VASP_CMD"],
+                db_file=self["env_vars"]["DB_FILE"],
+                name=name + " static"
+            )
+            new_static_fw.spec["_fworker"] = fw_spec["_fworker"]
+            new_static_fw.spec["displacement_value"] = more_disps[idx]
+            if fw_spec.get("tags", None):
+                new_static_fw.spec["tags"] = fw_spec["tags"]
+            new_fws.append(new_static_fw)
+
+        # Create new CSLD FW
+        # static_user_incar_settings and env_vars can be None since we
+        # are done trying more static calculations.
+        new_csld_fw = Firework(
+            CSLDForceConstantsToDB(
+                db_file=self["env_vars"]["DB_FILE"],
+                wf_uuid=self["wf_uuid"],
+                name='CSLDForceConstantsToDB',
+                parent_structure=self["parent_structure"],
+                trans_mat=self["trans_mat"],
+                supercell_structure=self["supercell_structure"],
+                supercell_smallest_dim=self["supercell_smallest_dim"],
+                perturbed_supercells=self[
+                                         "perturbed_supercells"] + more_perturbed_supercells,
+                disps=successful_disps + more_disps,
+                force_diagonal_transformation=self.force_diagonal_transformation,
+                first_pass=False,
+                do_shengbte=self.get("do_shengbte", False),
+                shengbte_t_range=self.get("shengbte_t_range", False),
+                shengbte_fworker=self.get("shengbte_fworker", None),
+                static_user_incar_settings=None,
+                env_vars=None
+            ),
+            name="Compressed Sensing Lattice Dynamics",
+            parents=new_fws[-len(more_perturbed_supercells):]
+        )
+        new_csld_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
+        if fw_spec.get("tags", None):
+            new_csld_fw.spec["tags"] = fw_spec["tags"]
+        new_fws.append(new_csld_fw)
+
+        # Dynamically add new fireworks to the workflow
+        return FWAction(additions=new_fws)
+
     def run_task(self, fw_spec):
         # Connect to the database
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        # tasks = mmdb["tasks"]
         tasks = mmdb.collection
 
         # Store information related to convergence of CSLD
-        iter = 0
+        iteration = 0
         not_converged = True
-        maxIter = 2
+        max_iter = 2
         summaries = []
         self['convergence_info'] = {
-            'iteration': iter,
+            'iteration': iteration,
             'settings_tried': [],
             'cross_val_errors': [],
             'most_imaginary_freqs': [],
@@ -2111,9 +2310,12 @@ def run_task(self, fw_spec):
                                  '9 6.5 5.0']
         max_order_settings = [3] * len(cluster_diam_settings)
         submodel1_settings = ['anh 0 1 2 3'] * len(cluster_diam_settings)
-        export_sbte_string = str(self["trans_mat"][0][0]) + ' ' + \
-                             str(self["trans_mat"][1][1]) + ' ' + \
-                             str(self["trans_mat"][2][2]) + ' 2 3'
+        if self["force_diagonal_transformation"]:
+            export_sbte_string = str(self["trans_mat"][0][0]) + ' ' + \
+                                 str(self["trans_mat"][1][1]) + ' ' + \
+                                 str(self["trans_mat"][2][2]) + ' 2 3'
+        else:
+            export_sbte_string = '5 5 5 2 3'
         export_sbte_settings = [export_sbte_string] * len(cluster_diam_settings)
         if self["first_pass"] is False:
             # If we are running CSLD a second time (i.e. with larger displaced
@@ -2124,150 +2326,41 @@ def run_task(self, fw_spec):
             submodel1_settings += submodel1_settings
             export_sbte_settings += export_sbte_settings
 
-        print('cluster_diam')
-        print(cluster_diam_settings)
-        print('max order')
-        print(max_order_settings)
-        print('submodel')
-        print(submodel1_settings)
+        logger.info('Cluster diameter settings to search over: '
+                    '{}'.format(cluster_diam_settings))
+        logger.info('Max order settings to search over: '
+                    '{}'.format(max_order_settings))
+        logger.info('"submodel1" settings to search over: '
+                    '{}'.format(submodel1_settings))
 
-        uuid = self["wf_uuid"]
-        formula = self["parent_structure"].formula
-        formula_pretty = self[
-            "parent_structure"].composition.reduced_formula
-        task_label = 'static'
-        supercells_dicts = list(
-            tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
-                        "task_label": {"$regex": task_label},
-                        "formula_pretty": formula_pretty,
-                        "state": 'successful'},
-                       ['task_id',
-                        'task_label',
-                        'output.forces']))
-        # list of dicts where each dict contains a task_id and a list of forces
-        #   for each supercell
-
-        supercells_forces = []
-        supercells_task_labels = []
-        successful_disps = [] #displacement values of successful static calcs
-        for supercell_dict in supercells_dicts:
-            # List of np.ndarrays where each np.ndarray is a matrix of forces
-            #  for a perturbed supercell
-            supercells_forces += [
-                np.asarray(supercell_dict['output']['forces'])]
-
-            # Supercell task labels
-            # e.g. 'InSb-perturbed supercell, idx: 0, disp_val: 0.010, static'
-            supercells_task_labels += [supercell_dict['task_label']]
-
-            # Store list of displacement values whose corresponding perturbed supercells successfully ran
-            successful_disp = re.search('disp_val: (\d+.\d+)', supercell_dict['task_label'])
-            successful_disps += [successful_disp.group(1)]
-
-        # Sort the forces by their task label so CSLD correctly matches forces
-        # with their corresponding perturbed supercell
-        supercells_zip = sorted(
-            zip(supercells_task_labels, supercells_forces),
-            key=lambda pair: pair[0])
-        supercells_forces = [supercells_forces for
-                             (supercells_task_labels, supercells_forces) in
-                             supercells_zip]
+        # Collect forces and successful displacement values from static
+        # perturbed supercell calculations
+        supercells_forces, successful_disps = \
+            self.collect_successful_static_calcs_results(tasks)
 
         # Iterate over CSLD settings until real solutions are found or max
         # iterations is reached.
-        while not_converged and iter < maxIter:
-            self.set_params(iter,
+        while not_converged and iteration < max_iter:
+            # For the current iteration, set the CSLD parameters and create the
+            # necessary folders/files
+            self.set_params(iteration,
                             successful_disps,
-                            cluster_diam_settings[iter],
-                            max_order_settings[iter],
-                            submodel1_settings[iter],
-                            export_sbte_settings[iter])
-            self["csld_options"]["pdfout"] = 'plots' + str(iter) + '.pdf'
-
-            # Create force.txt files for perturbed supercells
-            for supercell_idx, supercell_force in enumerate(supercells_forces):
-                path = self["forces_paths"][supercell_idx]
-                np.savetxt(path + "/force.txt", supercell_force, fmt='%.6f')
-
-            # Perform csld minimization now
-            # import scripts.csld_main_rees as csld_main
-            from atomate.vasp.workflows.base.csld import csld_main
-            rel_err, freq_matrix = csld_main(self["csld_options"],
-                                             self["csld_settings"])
-
-            freq_matrix = np.asarray(freq_matrix)
-
-            # CHECK FOR IMAGINARY PHONON MODES
-            # For imaginary frequencies, w^2 is negative.
-            # CSLD handles these as w = sign(sqrt(abs(w^2)), w^2).
-            # i.e. if w < 0, it is imaginary.
-            # Here, we consider phonon frequencies < -1 meV to be imaginary
-            #  (numerical noise can sometimes make frequencies slightly negative,
-            #   so we ignore these)
-            imaginary_idx = freq_matrix < -1
-            imaginary_freqs = freq_matrix[imaginary_idx]
-            print('IMAGINARY FREQUENCIES')
-            print(imaginary_freqs)
-            num_imaginary_bands = np.sum(np.any(imaginary_idx, axis=1))
-            print(num_imaginary_bands)
-            if np.any(imaginary_freqs):
-                most_imaginary_freq = np.amin(imaginary_freqs)
-            else:
-                most_imaginary_freq = 0
-            print(most_imaginary_freq)
-
-            if num_imaginary_bands == 0:
-                not_converged = False
-
-            # Save to DB
-            summary = {
-                "date": datetime.now(),
-                "formula": formula,
-                "formula_pretty": formula_pretty,
-                "parent_structure": self["parent_structure"].as_dict(),
-                "supercell_structure": self["supercell_structure"].as_dict(),
-                "supercell_transformation_matrix": self["trans_mat"],
-                "wf_meta": {"wf_uuid": uuid},
-
-                # Store relevant CSLD settings
-                "iteration": iter,
-                "cluster_diam": self["csld_settings"]["model"][
-                    "cluster_diameter"],
-                "max_order": self["csld_settings"]["model"]["max_order"],
-                "submodel1": self["csld_settings"]["fitting"]["submodel1"],
-                "export_potential": self["csld_settings"]["export_potential"][
-                    "export_shengbte"],
-
-                # Store CSLD results
-                "cross_val_error": float(rel_err),
-                "num_imaginary_modes": int(num_imaginary_bands),
-                "most_imaginary_freq": float(most_imaginary_freq),
-                "imaginary_freq_sum": float(sum(imaginary_freqs))
-            }
+                            cluster_diam_settings[iteration],
+                            max_order_settings[iteration],
+                            submodel1_settings[iteration],
+                            export_sbte_settings[iteration],
+                            supercells_forces)
+            self["csld_options"]["pdfout"] = 'plots' + str(iteration) + '.pdf'
 
-            # Store latest CSLD input settings tried
-            # TODO: If desired, store this information in a database to keep
-            #   track of what settings work and what doesn't for different materials
-            latest_settings = {str(self["convergence_info"]["iteration"]):
-                                   {self["csld_settings"]["model"]["max_order"],
-                                    self["csld_settings"]["fitting"][
-                                        "submodel1"],
-                                    self["csld_settings"]["export_potential"][
-                                        "export_shengbte"]}}
-            self["convergence_info"]["iteration"] = iter
-            self["convergence_info"]["settings_tried"] += [latest_settings]
-            self["convergence_info"]["cross_val_errors"] += [rel_err]
-            self["convergence_info"]["most_imaginary_freqs"] += [
-                most_imaginary_freq]
-            self["convergence_info"]["imaginary_freqs_sum"] += [
-                sum(imaginary_freqs)]
+            # Run CSLD, check for imaginary phonon frequencies, and generate a
+            # summary of results
+            summary = self.run_csld(iteration)
 
             if fw_spec.get("tags", None):
                 summary["tags"] = fw_spec["tags"]
-
             summaries.append(summary)
 
-            iter += 1
+            iteration += 1
 
         # Store the summaries in a "compressed_sensing_lattice_dynamics"
         #  collection of the database (if it does not exist, it will be created)
@@ -2283,98 +2376,33 @@ def run_task(self, fw_spec):
             self["convergence_info"]["settings_tried"][best_idx]))
 
         if not_converged is False:
-        # If CSLD converged to 0 imaginary frequencies, create the ShengBTE FW
-            logger.info("Compressed Sensing Lattice Dynamics calculation complete.")
-            shengbte_fw = Firework(
-                ShengBTEToDB(
-                    parent_structure=self["parent_structure"],
-                    shengbte_cmd=">>shengbte_cmd<<",
-                    db_file=self["db_file"],
-                    wf_uuid=self["wf_uuid"],
-                    t_range=self.get("shengbte_t_range", False),
-                    trans_mat=self["trans_mat"]
-                ),
-                name="ShengBTE for Lattice Thermal Conductivity"
-            )
-            if isinstance(self["shengbte_fworker"], str):
-                shengbte_fw.spec["_fworker"] = self["shengbte_fworker"]
-            else:
-                shengbte_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
-            CSLD_path = self.get("path", os.getcwd())
-            shengbte_fw.spec["successful_CSLD_path"] = CSLD_path
-            if fw_spec.get("tags", None):
-                shengbte_fw.spec["tags"] = fw_spec["tags"]
-            return FWAction(additions=shengbte_fw)
+            # If CSLD converged to 0 imaginary frequencies
+            logger.info("Compressed Sensing Lattice Dynamics calculation "
+                        "complete.")
+
+            # Dynamically create the ShengBTE Firework
+            if self.get("do_shengbte", False):
+                self.add_sbte_fw(fw_spec)
         else:
-            logger.info("Compressed Sensing Lattice Dynamics calculation failed."
-                        "Max iterations was reached.")
-            if self["parent_structure"].num_sites > 5 and self["first_pass"]:
-                logger.info("Compressed Sensing Lattice Dynamics calculation failed."
-                            " Max iterations was reached. Creating larger displacements"
-                            " and trying again.")
-                new_fws = []
-
-                # Create new perturbed supercells
-                from atomate.vasp.analysis.csld import generate_perturbed_supercells
-                more_perturbed_supercells, more_disps = generate_perturbed_supercells(self["supercell_structure"],
-                                                                                      min_displacement=0.12,
-                                                                                      max_displacement=0.2,
-                                                                                      num_displacements=5,
-                                                                                      )
-
-                # Create new static FWs
-                for idx, more_perturbed_supercell in enumerate(more_perturbed_supercells):
-                    name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(idx+len(self["perturbed_supercells"]),
-                                                                                    more_disps)
-                    static_vis = MPStaticSet(more_perturbed_supercell,
-                                             user_incar_settings=self["static_user_incar_settings"])
-
-                    from atomate.vasp.fireworks.core import StaticFW
-                    new_static_fw = StaticFW(
-                        more_perturbed_supercell,
-                        vasp_input_set=static_vis,
-                        vasp_cmd=self["env_vars"]["VASP_CMD"],
-                        db_file=self["env_vars"]["DB_FILE"],
-                        name=name + " static"
-                    )
-                    new_static_fw.spec["_fworker"] = fw_spec["_fworker"]
-                    new_static_fw.spec["displacement_value"] = more_disps[idx]
-                    if fw_spec.get("tags", None):
-                        new_static_fw.spec["tags"] = fw_spec["tags"]
-                    new_fws.append(new_static_fw)
-
-                # Create new CSLD FW
-                new_csld_fw = Firework(
-                    CSLDForceConstantsToDB(
-                        db_file=self["env_vars"]["DB_FILE"],
-                        wf_uuid=self["wf_uuid"],
-                        name='CSLDForceConstantsToDB',
-                        parent_structure=self["parent_structure"],
-                        trans_mat=self["trans_mat"],
-                        supercell_structure=self["supercell_structure"],
-                        supercell_smallest_dim=self["supercell_smallest_dim"],
-                        perturbed_supercells=self["perturbed_supercells"]+more_perturbed_supercells,
-                        disps=successful_disps+more_disps,
-                        first_pass=False
-                    ),
-                    name="Compressed Sensing Lattice Dynamics",
-                    parents=new_fws[-len(more_perturbed_supercells):]
-                )
-                new_csld_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
-                if fw_spec.get("tags", None):
-                    new_csld_fw.spec["tags"] = fw_spec["tags"]
-                new_fws.append(new_csld_fw)
+            logger.info("Compressed Sensing Lattice Dynamics calculation "
+                        "failed. Max iterations was reached.")
+            if self["parent_structure"].num_sites > 5 and self["first_pass"] \
+                    and self.get("dynamic_static_calcs", False):
+                logger.info("Compressed Sensing Lattice Dynamics calculation "
+                            "failed. Max iterations was reached. Creating "
+                            "larger displacements and trying again.")
 
-                # Dynamically add new fireworks to the workflow
-                return FWAction(additions=new_fws)
+                self.add_more_static_calcs(successful_disps, fw_spec)
 
             else:
-                raise TimeoutError("The workflow was unable to find a solution to CSLD"
-                    " for this material.")
+                raise TimeoutError("The workflow was unable to find a solution "
+                                   "to CSLD for this material.")
 
 @explicit_serialize
 class ShengBTEToDB(FiretaskBase):
-    #TODO: Test this firetask
+    #TODO: Rename this class to something more accurate (since this class only
+    #  calculates the lattice thermal conductivity matrix even though ShengBTE
+    #  has more capabilities)
     """
     Run ShengBTE and output the lattice thermal conductivity matrix to database.
 
@@ -2392,7 +2420,7 @@ class ShengBTEToDB(FiretaskBase):
     """
 
     required_params = ["parent_structure", "shengbte_cmd", "db_file",
-                       "wf_uuid", "trans_mat"]
+                       "wf_uuid", "trans_mat", "force_diagonal_transformation"]
     optional_params = ["t_range"]
 
     def run_task(self, fw_spec):
@@ -2418,7 +2446,7 @@ def run_task(self, fw_spec):
         shengbte_control_dict = {
             'nelements': self["parent_structure"].ntypesp,
             'natoms': self["parent_structure"].num_sites,
-            'ngrid': qpts.kpts[0], #[25, 25, 25],  # NEED TO GENERATE THIS BY DENSITY
+            'ngrid': qpts.kpts[0],
             'norientations': 0,
 
             'lfactor': 0.1,  # 0.1 nm = 1 Ang
@@ -2430,20 +2458,23 @@ def run_task(self, fw_spec):
                 self["parent_structure"].sites[i]._frac_coords.tolist()
                 for i in range(self["parent_structure"].num_sites)
             ],
-            'scell': [self["trans_mat"][0][0],
-                      self["trans_mat"][1][1],
-                      self["trans_mat"][2][2]],
             't': 300,
             'scalebroad': 0.5,
             'nonanalytic': False,
             'isotopes': False,
         }
+        if self["force_diagonal_transformation"]:
+            shengbte_control_dict['scell'] = [self["trans_mat"][0][0],
+                                              self["trans_mat"][1][1],
+                                              self["trans_mat"][2][2]]
+        else:
+            shengbte_control_dict['scell'] = [5, 5, 5]
         if self["t_range"]:
             shengbte_control_dict['t_min'] = 100
             shengbte_control_dict['t_max'] = 1000
             shengbte_control_dict['t_step'] = 100
         io = Control.from_dict(shengbte_control_dict)
-        io.to_file() #writes CONTROL file to current directory
+        io.to_file()  # writes CONTROL file to current directory
 
         # Copy force constants from previous CSLD firework
         force_constants_path = fw_spec["successful_CSLD_path"]
@@ -2461,10 +2492,12 @@ def run_task(self, fw_spec):
                 open("shengbte_err.txt", "w", buffering=1) as f_err:
             # use line buffering for stderr
             return_code = subprocess.call(shengbte_cmd, stdout=f_std, stderr=f_err)
-        logger.info("Command {} finished running with returncode: {}".format(shengbte_cmd, return_code))
+        logger.info("Command {} finished running "
+                    "with returncode: {}".format(shengbte_cmd, return_code))
         if return_code==1:
-            raise RuntimeError("Running ShengBTE failed. Check 'shengbte_err.txt'"
-                               " in the launch_dir for details.")
+            raise RuntimeError("Running ShengBTE failed. Check "
+                               "'shengbte_err.txt' in the launch_dir for "
+                               "details.")
 
         try:
             # Store lattice thermal conductivity matrix in the database
@@ -2479,7 +2512,8 @@ def run_task(self, fw_spec):
             summaries = []
             for temp in temps:
                 # xx, xy, xz, yx, yy, yz, zx, zy, zz
-                flattened_kappa = np.loadtxt('T'+str(int(temp))+'K/BTE.kappa_tensor')[1][1:]
+                flattened_kappa = np.loadtxt(
+                    'T'+str(int(temp))+'K/BTE.kappa_tensor')[1][1:]
                 flattened_kappa = flattened_kappa.reshape((3, 3)).tolist()
                 summary = {
                     "date": datetime.now(),
@@ -2495,7 +2529,8 @@ def run_task(self, fw_spec):
             mmdb.collection = mmdb.db["sheng_bte"]
             mmdb.collection.insert(summaries)
         except:
-            raise FileNotFoundError('BTE.kappa_tensor was not output from ShengBTE.')
+            raise FileNotFoundError('BTE.kappa_tensor was not output from '
+                                    'ShengBTE.')
 
 
 # the following definitions for backward compatibility
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 40d73dc96..e0edef612 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -1,42 +1,105 @@
 # coding: utf-8
 
-import os
-
 import numpy as np
 from uuid import uuid4
 
-from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.alchemy.materials import TransformedStructure
-from pymatgen.transformations.standard_transformations import \
-    PerturbStructureTransformation
 from pymatgen.transformations.advanced_transformations import (
-    CubicSupercellTransformation
-)
+    CubicSupercellTransformation)
+from pymatgen.io.vasp.sets import MPStaticSet
+
 from fireworks import Workflow, Firework
 from atomate.utils.utils import get_logger
-from atomate.vasp.config import VASP_CMD, DB_FILE, ADD_WF_METADATA #                what is this?
-from atomate.vasp.fireworks.core import StaticFW, OptimizeFW
+from atomate.vasp.config import VASP_CMD, DB_FILE
+from atomate.vasp.fireworks.core import StaticFW
 from atomate.vasp.firetasks.parse_outputs import CSLDForceConstantsToDB
-from atomate.vasp.powerups import (
-    add_additional_fields_to_taskdocs
-)
+from atomate.vasp.powerups import add_additional_fields_to_taskdocs
 from atomate.vasp.analysis.csld import generate_perturbed_supercells
 
-from pymatgen.io.vasp.sets import MPStaticSet, MPRelaxSet
-
-# NEW THINGS TO INSTALL?
-# from configparser import ConfigParser
-# from scripts import csld_main_rees #csld>scripts
-
-logger = get_logger(__name__)
-
 __author__ = "Rees Chang"
 __email__ = "rc564@cornell.edu"
 __date__ = "July 2019"
-
 __csld_wf_version__ = 1.0
 
+logger = get_logger(__name__)
+
+
 class CompressedSensingLatticeDynamicsWF:
+    """
+    This workflow will use compressed sensing lattice dynamics (CSLD)
+    (doi: 10.1103/PhysRevLett.113.185501) to generate interatomic force
+    constants from an input structure and output a summary to a database.
+
+    TODO: Implement 'tight_relaxation', 'dfpt_check', and 'nscf_check' options
+
+    A summary of the workflow is as follows:
+       1. Transform the input structure into a supercell
+       2. Transform the supercell into a list of supercells with all atoms
+           randomly perturbed from their original sites
+       3. Run static VASP calculations on each perturbed supercell to
+           calculate atomic forces.
+       4. Aggregate the forces and conduct the CSLD minimization algorithm
+           to compute interatomic force constants.
+       5. Output the interatomic force constants to the database.
+
+    Args:
+       parent_structure (Structure): Structure to conduct CSLD on
+       symmetrize (bool): If True, the parent_structure will be primitized
+           before running CSLD. Else, the parent_structure will be used
+           for CSLD as is.
+       tight_relaxation (bool): If True, run a tight relaxation step on the
+           parent_structure. Else, do not. TODO: IMPLEMENT
+       dfpt_check (bool): If True, run a DFPT calculation at the gamma
+           point to check for dynamic instabilities. TODO: IMPLEMENT
+       nscf_check (bool): If True, run a nscf electronic bands calculation to
+           determine if parent_structure is a metal or not. If metal, set
+           ISMEAR=1 for the static perturbed supercell calculations. Else, set
+           ISMEAR=0. TODO: IMPLEMENT
+       symprec (float): symmetry precision parameter for
+           SpacegroupAnalyzer's 'get_primitive_standard_structure()'
+           function
+       min_atoms (int): Minimum number of atoms to constrain the supercell
+       max_atoms (int): Maximum number of atoms to constrain the supercell
+       num_nn_dists (int or float): Number of nearest neighbor distances
+           that the shortest direction of the supercell must be as long as
+       force_diagonal_transformation (bool): If True, the supercell
+           transformation will be constrained to have a diagonal
+           transformation matrix. If False, the supercell transformation
+           will not be constrained to be diagonal (resulting in a more
+           cubic supercell).
+       max_displacement (float): Maximum displacement distance for
+           perturbing the supercell structure (Angstroms)
+       min_displacement (float): Minimum displacement distance for
+           perturbing the supercell structure (Angstroms)
+       num_displacements (int): Number of unique displacement distances to
+           generate uniformly between 'min_displacement' and
+           'max_displacement'
+       min_random_distance (Optional float): If None (default), then all
+           atoms in the supercell will move the same distance from their
+           original locations. If float, then for a given supercell, the
+           distances that atoms move will be uniformly distributed from a
+           minimum distance of 'min_random_distance' to one of the
+           displacement distances uniformly sampled between
+           'min_displacement' and 'max_displacement'.
+       supercells_per_displacement_distance (int): number of supercells to
+           generate for each unique displacement distance.
+       dynamic_static_calcs (bool): If True and CSLD fails to return all real
+            harmonic phonon frequencies on the first try, then the CSLD firework
+            will dynamically create more static perturbed supercell calculations
+            with larger displacements with the aim of handling materials with
+            loosely bound atoms (e.g. rattling modes).
+       do_shengbte (bool): If True and CSLD successfully returns all real
+            harmonic phonon frequencies, then the CSLD firework will dynamically
+            create a ShengBTE firework for calculating the lattice thermal
+            conductivity matrix and storing it to a database.
+       shengbte_t_range (bool): If False (default), calculate the lattice
+           thermal conductivity with ShengBTE at 300 K. If True, do the
+           calculation from 100-1000 K with 100 K steps (much slower).
+       shengbte_fworker (None or str): If None, the ShengBTE firework's
+           fworker will be set to all the previous fireworks' fworker. If
+           str, the ShengBTE firework's fworker will be set to
+           shengbte_fworker.
+   """
+
     def __init__(
             self,
             parent_structure,
@@ -51,84 +114,29 @@ def __init__(
             num_displacements=10,
             min_random_distance=None,
             supercells_per_displacement_distance=1,
+            dynamic_static_calcs=False,
+            do_shengbte=False,
             shengbte_t_range=False,
             shengbte_fworker=None
     ):
-        """
-        This workflow will use compressed sensing lattice dynamics (CSLD)
-        (doi: 10.1103/PhysRevLett.113.185501) to generate interatomic force
-        constants from an input structure and output a summary to a database.
-
-        A summary of the workflow is as follows:
-            1. Transform the input structure into a supercell
-            2. Transform the supercell into a list of supercells with all atoms
-                randomly perturbed from their original sites
-            3. Run static VASP calculations on each perturbed supercell to
-                calculate atomic forces.
-            4. Aggregate the forces and conduct the CSLD minimization algorithm
-                to compute interatomic force constants.
-            5. Output the interatomic force constants to the database.
-
-        Args:
-            parent_structure (Structure): Structure to conduct CSLD on
-            symmetrize (bool): If True, the parent_structure will be primitized
-                before running CSLD. Else, the parent_structure will be used
-                for CSLD as is.
-            tight_relaxation (bool): If True, run a tight relaxation step on the
-                parent_structure. Else, do not. TODO: IMPLEMENT
-            dfpt_check (bool): If True, run a DFPT calculation at the gamma
-                point to check for dynamic instabilities. TODO: IMPLEMENT
-            symprec (float): symmetry precision parameter for
-                SpacegroupAnalyzer's 'get_primitive_standard_structure()'
-                function
-            min_atoms (int): Minimum number of atoms to constrain the supercell
-            max_atoms (int): Maximum number of atoms to constrain the supercell
-            num_nn_dists (int or float): Number of nearest neighbor distances
-                that the shortest direction of the supercell must be as long as
-            force_diagonal_transformation (bool): If True, the supercell
-                transformation will be constrained to have a diagonal
-                transformation matrix. If False, the supercell transformation
-                will not be constrained to be diagonal (resulting in a more
-                cubic supercell).
-            max_displacement (float): Maximum displacement distance for
-                perturbing the supercell structure (Angstroms)
-            min_displacement (float): Minimum displacement distance for
-                perturbing the supercell structure (Angstroms)
-            num_displacements (int): Number of unique displacement distances to
-                generate uniformly between 'min_displacement' and
-                'max_displacement'
-            min_random_distance (Optional float): If None (default), then all
-                atoms in the supercell will move the same distance from their
-                original locations. If float, then for a given supercell, the
-                distances that atoms move will be uniformly distributed from a
-                minimum distance of 'min_random_distance' to one of the
-                displacement distances uniformly sampled between
-                'min_displacement' and 'max_displacement'.
-            supercells_per_displacement_distance (int): number of supercells to
-                generate for each unique displacement distance.
-            shengbte_t_range (bool): If False (default), calculate the lattice
-                thermal conductivity with ShengBTE at 300 K. If True, do the
-                calculation from 100-1000 K with 100 K steps (much slower).
-            shengbte_fworker (None or str): If None, the ShengBTE firework's
-                fworker will be set to all the previous fireworks' fworker. If
-                str, the ShengBTE firework's fworker will be set to
-                shengbte_fworker.
-        """
-        if force_diagonal_transformation is True and num_nn_dists==5:
+
+        if force_diagonal_transformation is True and num_nn_dists == 5:
             num_nn_dists = 6
 
+        # default name is CompressedSensingLatticeDynamicsWF
         self.uuid = str(uuid4())
         self.wf_meta = {
             "wf_uuid": self.uuid,
-            "wf_name": self.__class__.__name__, #"CompressedSensingLatticeDynamicsWF"
+            "wf_name": self.__class__.__name__,
         }
 
-    # Create supercell
+        # Create supercell
         self.parent_structure = parent_structure
         if symmetrize:
             sga = SpacegroupAnalyzer(parent_structure, symprec=symprec)
             self.parent_structure = sga.get_primitive_standard_structure()
 
+        self.force_diagonal_transformation = force_diagonal_transformation
         self.min_atoms = min_atoms
         self.max_atoms = max_atoms
         self.num_nn_dists = num_nn_dists
@@ -136,18 +144,19 @@ def __init__(
             self.min_atoms,
             self.max_atoms,
             self.num_nn_dists,
-            force_diagonal_transformation=force_diagonal_transformation
+            force_diagonal_transformation=self.force_diagonal_transformation
         )
 
-        # supercell (Structure)
-        self.supercell = supercell_transform.apply_transformation(self.parent_structure)
+        self.supercell = supercell_transform.apply_transformation(
+            self.parent_structure)
         self.nn_dist = supercell_transform.nn_dist
         self.trans_mat = supercell_transform.trans_mat.tolist()
         self.supercell_smallest_dim = supercell_transform.smallest_dim
 
-    # Generate list of perturbed supercells
-        # self.perturbed_supercells: list of perturbed supercells (list of Structures)
-        # self.disps: list of (non-unique) displacement values used in the perturbation (np.array)
+        # Generate list of perturbed supercells
+        # perturbed_supercells: list of perturbed supercells (list[Structures])
+        # disps: list of (non-unique) displacement values used in the
+        # perturbation (np.array)
         self.perturbed_supercells, self.disps = generate_perturbed_supercells(
             self.supercell,
             min_displacement=min_displacement,
@@ -157,42 +166,35 @@ def __init__(
             min_random_distance=min_random_distance
             )
 
+        self.dynamic_static_calcs = dynamic_static_calcs
+        self.do_shengbte = do_shengbte
         self.shengbte_t_range = shengbte_t_range
         self.shengbte_fworker = shengbte_fworker
 
-    def get_wf(
-            self,
-            c=None
-    ):
+    def get_wf(self, c=None):
         fws = []
         c = c or {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
 
-        def _add_metadata(structure):
-            """
-            Add metadata for easy querying from the database later.
-            """
-            return TransformedStructure(
-                structure, other_parameters={"wf_meta": self.wf_meta}
-            )
-
-
-        static_user_incar_settings = {"ADDGRID": True,
-                                      # Fast Fourier Transform grid
-                                      "LCHARG": False,
-                                      "ENCUT": 700,
-                                      "EDIFF": 1e-8,  # may need to tune this
-                                      "PREC": 'Accurate',
-                                      "LAECHG": False,
-                                      "LREAL": False,
-                                      "LASPH": True}
+        static_user_incar_settings = {
+            "ADDGRID": True,  # Fast Fourier Transform grid
+            "LCHARG": False,
+            "ENCUT": 700,
+            "EDIFF": 1e-8,  # may need to tune this
+            "PREC": 'Accurate',
+            "LAECHG": False,
+            "LREAL": False,
+            "LASPH": True}
         static_user_incar_settings.update(c.get("user_incar_settings", {}))
 
         for idx, perturbed_supercell in enumerate(self.perturbed_supercells):
-            # Run static calculations on the perturbed supercells to compute forces on each atom
-            name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(idx, self.disps[idx])
+            # Run static calculations on the perturbed supercells to compute
+            # forces on each atom
+            name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(
+                idx, self.disps[idx])
 
-            static_vis = MPStaticSet(perturbed_supercell,
-                                     user_incar_settings=static_user_incar_settings)
+            static_vis = MPStaticSet(
+                perturbed_supercell,
+                user_incar_settings=static_user_incar_settings)
             static_fw = StaticFW(
                 perturbed_supercell,
                 vasp_input_set=static_vis,
@@ -203,12 +205,13 @@ def _add_metadata(structure):
             static_fw.spec["displacement_value"] = self.disps[idx]
             fws.append(static_fw)
 
-        print('DISPS')
-        print(self.disps)
+        logger.debug("using {} displacements".format(len(self.disps)))
+        logger.debug("displacements: {}".format(self.disps))
+
         # Collect force constants from the DB and output on cluster
         csld_fw = Firework(
             CSLDForceConstantsToDB(
-                db_file=c["DB_FILE"], # wot
+                db_file=c["DB_FILE"],
                 wf_uuid=self.uuid,
                 parent_structure=self.parent_structure,
                 trans_mat=self.trans_mat,
@@ -216,9 +219,12 @@ def _add_metadata(structure):
                 supercell_smallest_dim=self.supercell_smallest_dim,
                 perturbed_supercells=self.perturbed_supercells,
                 disps=self.disps,
+                force_diagonal_transformation=self.force_diagonal_transformation,
                 first_pass=True,
                 static_user_incar_settings=static_user_incar_settings,
                 env_vars=c,
+                dynamic_static_calcs=self.dynamic_static_calcs,
+                do_shengbte=self.do_shengbte,
                 shengbte_t_range=self.shengbte_t_range,
                 shengbte_fworker=self.shengbte_fworker
             ),
@@ -231,33 +237,29 @@ def _add_metadata(structure):
         wf_name = "{} - compressed sensing lattice dynamics".format(formula)
         wf = Workflow(fws, name=wf_name)
 
-        wf = add_additional_fields_to_taskdocs(wf,
-                                               {"wf_meta": self.wf_meta},
-                                               task_name_constraint="VaspToDb"
-                                               #may need to change this to "CSLDForceConstantsToDB"?
-                                               )
-        #tag =   #insert anything relevant to every firework in the workflow
-        # wf = add_tags(wf, [tag, <insert whatever string you'd like>])
+        wf = add_additional_fields_to_taskdocs(
+            wf,  {"wf_meta": self.wf_meta}, task_name_constraint="VaspToDb")
+
         return wf
 
 
 # SCRIPT FOR CREATING THE WORKFLOW AND ADDING IT TO THE DATABASE
 if __name__ == "__main__":
 
-    from fireworks import LaunchPad
-    from atomate.vasp.powerups import add_tags, set_execution_options, add_modify_incar
+    from atomate.vasp.powerups import add_tags, set_execution_options
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
     from pymatgen.core.structure import Structure
 
     prim = Structure.from_file('POSCAR-well_relaxed_InSb_csld_primitivized')
 
-    csld_class = CompressedSensingLatticeDynamicsWF(prim,
-                                                    symmetrize=False,
-                                                    num_nn_dists=6,
-                                                    num_displacements=10,
-                                                    supercells_per_displacement_distance=1,
-                                                    force_diagonal_transformation=True
-                                                    )
+    csld_class = CompressedSensingLatticeDynamicsWF(
+        prim,
+        symmetrize=False,
+        num_nn_dists=6,
+        num_displacements=10,
+        supercells_per_displacement_distance=1,
+        force_diagonal_transformation=True
+        )
     print("uuid")
     print(csld_class.uuid)
 
@@ -275,69 +277,10 @@ def _add_metadata(structure):
     wf = add_tags(wf, ['csld', 'v1', 'rees',
                        'pre-relaxed insb', 'diagonal supercell',
                        'not symmetrized'])
-    wf = set_execution_options(wf, fworker_name="rees_the_fire_worker") #need this to run the fireworks
+    wf = set_execution_options(wf, fworker_name="rees_the_fire_worker")
     # wf = add_modify_incar(wf,
     #                       modify_incar_params={'incar_update': {'ENCUT': 500,
     #                                                             'ISPIN': 1}})
 
     # lpad = LaunchPad.auto_load()
     # lpad.add_wf(wf)
-
-#################custom csld_main below##################
-def csld_main(options, settings):
-    """
-    Runs CSLD minimization.
-
-    Changes from original version:
-        - Made 'prim' an argument in 'phonon_step()'
-        - Moved execution files to this main() function to be called from
-          atomate
-        - Rewrote 'add_common_parameter' in 'common_main' to treat 'options' as
-          a dictionary instead of ArgumentParser
-    """
-    import matplotlib
-    matplotlib.use('Agg')
-    from matplotlib.backends.backend_pdf import PdfPages
-    import atexit
-    import csld
-    from csld.symmetry_structure import SymmetrizedStructure
-
-    from csld.lattice_dynamics import init_ld_model
-
-    from csld.common_main import upon_exit, \
-        init_training
-    from csld.csld_main_functions import phonon_step, \
-        save_pot, predict, fit_data
-
-
-    freq_matrix = None #Rees
-    pdfout = PdfPages(
-        options['pdfout'].strip()) if options['pdfout'].strip() else None
-    atexit.register(upon_exit, pdfout)
-
-    prim = SymmetrizedStructure.init_structure(settings['structure'],
-                                               options['symm_step'],
-                                               options['symm_prim'],
-                                               options['log_level'])
-    model = init_ld_model(prim, settings['model'], settings[
-        'LDFF'] if 'LDFF' in settings.sections() else {}, options['clus_step'],
-                          options['symC_step'], options['ldff_step'])
-    Amat, fval = init_training(model, settings['training'], options['train_step'])
-    ibest, solutions, rel_err = fit_data(model, Amat, fval, settings['fitting'],
-                                options['fit_step'], pdfout)
-    if settings.has_section('phonon'):
-        phonon, freq_matrix = phonon_step(model, solutions, settings['phonon'],
-                             options['phonon_step'], pdfout, prim, return_eigen=True)
-    if settings.has_section('export_potential'):
-        save_pot(model, solutions[ibest], settings['export_potential'],
-                 options['save_pot_step'], phonon)
-    if settings.has_section('prediction'):
-        predict(model, solutions, settings['prediction'], options['pred_step'])
-
-    #OUTPUT
-    # freq_matrix is (nbands, nkpoints) = frequencies. Check for negative entries
-    # rel_err is cross validation error in percent
-    return rel_err, freq_matrix #also want to return force constants
-
-
-

From e7b2b68bd23e54b90fbe0e82f5eeda538c744234 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 11:13:33 -0700
Subject: [PATCH 040/207] Added csld_main to csld analysis file. Add beginnings
 of testing files

---
 atomate/vasp/analysis/csld.py                 |   145 +
 atomate/vasp/test_files/csld_wf/FW.json       | 55600 ++++++++++++++++
 .../test_files/csld_wf/POSCAR-well_relaxed_Si |    10 +
 atomate/vasp/test_files/csld_wf/__init__.py   |     0
 .../workflows/tests/test_csld_workflow.py     |    89 +
 5 files changed, 55844 insertions(+)
 create mode 100644 atomate/vasp/test_files/csld_wf/FW.json
 create mode 100644 atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si
 create mode 100644 atomate/vasp/test_files/csld_wf/__init__.py
 create mode 100644 atomate/vasp/workflows/tests/test_csld_workflow.py

diff --git a/atomate/vasp/analysis/csld.py b/atomate/vasp/analysis/csld.py
index 8f624bce7..a1b367d63 100644
--- a/atomate/vasp/analysis/csld.py
+++ b/atomate/vasp/analysis/csld.py
@@ -56,3 +56,148 @@ def generate_perturbed_supercells(supercell,
             supercell)
         perturbed_supercells += [perturbed_supercell]
     return perturbed_supercells, displacements
+
+
+def csld_main(options, settings):
+    """
+    Runs CSLD minimization.
+
+    Changes from original version:
+        - Made 'prim' an argument in 'phonon_step()'
+        - Moved execution files to this main() function to be called from
+          atomate
+        - Rewrote 'add_common_parameter' in 'common_main' to treat 'options' as
+          a dictionary instead of ArgumentParser
+    """
+    import matplotlib
+    matplotlib.use('Agg')
+    from matplotlib.backends.backend_pdf import PdfPages
+    import atexit
+    import csld
+    from csld.symmetry_structure import SymmetrizedStructure
+
+    from csld.lattice_dynamics import init_ld_model
+
+    from csld.common_main import upon_exit, \
+        init_training
+    from csld.csld_main_functions import phonon_step, \
+        save_pot, predict, fit_data
+
+
+    freq_matrix = None #Rees
+    pdfout = PdfPages(
+        options['pdfout'].strip()) if options['pdfout'].strip() else None
+    atexit.register(upon_exit, pdfout)
+
+    prim = SymmetrizedStructure.init_structure(settings['structure'],
+                                               options['symm_step'],
+                                               options['symm_prim'],
+                                               options['log_level'])
+    model = init_ld_model(prim, settings['model'], settings[
+        'LDFF'] if 'LDFF' in settings.sections() else {}, options['clus_step'],
+                          options['symC_step'], options['ldff_step'])
+    Amat, fval = init_training(model, settings['training'], options['train_step'])
+    ibest, solutions, rel_err = fit_data(model, Amat, fval, settings['fitting'],
+                                options['fit_step'], pdfout)
+    if settings.has_section('phonon'):
+        phonon, freq_matrix = phonon_step(model, solutions, settings['phonon'],
+                             options['phonon_step'], pdfout, prim, return_eigen=True)
+    if settings.has_section('export_potential'):
+        save_pot(model, solutions[ibest], settings['export_potential'],
+                 options['save_pot_step'], phonon)
+    if settings.has_section('prediction'):
+        predict(model, solutions, settings['prediction'], options['pred_step'])
+
+    #OUTPUT
+    # freq_matrix is (nbands, nkpoints) = frequencies. Check for negative entries
+    # rel_err is cross validation error in percent
+    return rel_err, freq_matrix  # also want to return force constants
+
+
+default_csld_settings = {
+    "structure": {"sym_tol": "1e-3"},
+    "model": {
+        'model_type': 'LD',
+        'cluster_in': 'clusters.out',
+        'cluster_out': 'clusters.out',
+        'symC_in': 'Cmat.mtx',
+        'symC_out': 'Cmat.mtx',
+        'fractional_distance': False,
+    },
+    "training":{
+        'interface': 'VASP',
+        'corr_type': 'f',
+        'corr_in': 'Amat.mtx',
+        'corr_out': 'Amat.mtx',
+        'fval_in': 'fval.txt',
+        'fval_out': 'fval.txt'
+    },
+    "fitting": {
+        'solution_in': 'solution_all',
+        'solution_out': 'solution_all',
+        'nsubset': 5,
+        'holdsize': 0.1,
+        ## 1 FPC 2 FPC sparse 3 split 4 sparse split
+        ## 5 split+ right preconditioning 6 sparse split + r preconditioning
+        ## 101 Bayesian CS
+        'method': 5,
+        # For weight of L1 or L2 regularization
+        'mulist': '1E-5 1E-6 1E-7 1E-9',
+        'maxIter': 300,
+        'tolerance': 1E-6,
+        'subsetsize': 0.85,
+        'lambda': 0.5,
+        'uscale_list': '0.03',
+    },
+    "phonon": {
+        'qpoint_fractional': False,
+        # 'Auto' or something like 
+        # "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
+        'wavevector': 'Auto',
+        'unit': 'cm',  # THz, meV, eV, cm
+        'dos_grid': '15 15 15',  # number of grid points
+        'nE_dos': 500, # number of points in DOS
+        'ismear': -1,  # 0 (Gaussian), 1 (Lorentzian), -1 (tetrahedron method)
+        'epsilon': 0.05,  # width in THz of Gaussian/Lorentzian smearing
+        'pdos': True,
+        'thermal_T_range': '50 800 50',
+        'thermal_out': 'thermal_out.txt'
+    },
+   'prediction': {
+        'interface': 'VASP',
+        'corr_type': 'f',
+        'corr_in': 'Amat_pred.mtx',
+        'corr_out': 'Amat_pred.mtx',
+        'fval_in': 'fval_pred.txt',
+        'fval_out': 'fval_pred.txt',
+        'traindat0': 'fcc222/POSCAR fcc222/traj*'
+    },
+    'DEFAULT': {
+        "qpoint_fractional": False,
+        "true_v_fit": 'true_fit.txt',
+        'epsilon': '0.05',
+        "bcs_reweight": 'True',
+        "bcs_penalty": 'arctan',
+        "bcs_jcutoff": '1E-8'
+    }
+}
+
+default_csld_options = {
+    'pdfout': 'plots.pdf',
+    'ldff_step': 0,
+    'phonon_step': 1,
+    'phonon': False,
+    'save_pot_step': 1,
+    'pot': False,
+    'log_level': 1,
+    'symm_step': 2,
+    'symm_prim': True,
+    'clus_step': 3,
+    'symC_step': 3,
+    'train_step': 3,
+    'fit_step': 3,
+    'pred_step': 0,
+    'refit': False,
+    'cont': False,
+    'predict': False
+}
\ No newline at end of file
diff --git a/atomate/vasp/test_files/csld_wf/FW.json b/atomate/vasp/test_files/csld_wf/FW.json
new file mode 100644
index 000000000..df18899c0
--- /dev/null
+++ b/atomate/vasp/test_files/csld_wf/FW.json
@@ -0,0 +1,55600 @@
+{
+    "spec": {
+        "tags": [
+            "csld",
+            "v1",
+            "rees",
+            "pre-relaxed si",
+            "diagonal supercell",
+            "not symmetrized",
+            "555"
+        ],
+        "_fworker": "rees_the_fire_worker",
+        "_tasks": [
+            {
+                "db_file": ">>db_file<<",
+                "wf_uuid": "b8ab536c-b75d-4011-a069-48cbab8b8bda",
+                "parent_structure": {
+                    "@module": "pymatgen.core.structure",
+                    "@class": "Structure",
+                    "charge": null,
+                    "lattice": {
+                        "matrix": [
+                            [
+                                0.0,
+                                2.734364,
+                                2.734364
+                            ],
+                            [
+                                2.734364,
+                                0.0,
+                                2.734364
+                            ],
+                            [
+                                2.734364,
+                                2.734364,
+                                0.0
+                            ]
+                        ],
+                        "a": 3.8669746532647453,
+                        "b": 3.8669746532647453,
+                        "c": 3.8669746532647453,
+                        "alpha": 59.99999999999999,
+                        "beta": 59.99999999999999,
+                        "gamma": 59.99999999999999,
+                        "volume": 40.88829284866483
+                    },
+                    "sites": [
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.5,
+                                0.5,
+                                0.5
+                            ],
+                            "xyz": [
+                                2.734364,
+                                2.734364,
+                                2.734364
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.75,
+                                0.75,
+                                0.75
+                            ],
+                            "xyz": [
+                                4.101546,
+                                4.101546,
+                                4.101546
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        }
+                    ]
+                },
+                "trans_mat": [
+                    [
+                        5,
+                        0,
+                        0
+                    ],
+                    [
+                        0,
+                        5,
+                        0
+                    ],
+                    [
+                        0,
+                        0,
+                        5
+                    ]
+                ],
+                "supercell_structure": {
+                    "@module": "pymatgen.core.structure",
+                    "@class": "Structure",
+                    "charge": null,
+                    "lattice": {
+                        "matrix": [
+                            [
+                                0.0,
+                                13.671819999999999,
+                                13.671819999999999
+                            ],
+                            [
+                                13.671819999999999,
+                                0.0,
+                                13.671819999999999
+                            ],
+                            [
+                                13.671819999999999,
+                                13.671819999999999,
+                                0.0
+                            ]
+                        ],
+                        "a": 19.334873266323726,
+                        "b": 19.334873266323726,
+                        "c": 19.334873266323726,
+                        "alpha": 59.99999999999999,
+                        "beta": 59.99999999999999,
+                        "gamma": 59.99999999999999,
+                        "volume": 5111.036606083104
+                    },
+                    "sites": [
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.1,
+                                0.1,
+                                0.1
+                            ],
+                            "xyz": [
+                                2.734364,
+                                2.734364,
+                                2.734364
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.1,
+                                0.1,
+                                0.3
+                            ],
+                            "xyz": [
+                                5.468728,
+                                5.468728,
+                                2.734364
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.1,
+                                0.10000000000000002,
+                                0.5000000000000001
+                            ],
+                            "xyz": [
+                                8.203092000000002,
+                                8.203092,
+                                2.734364
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.1,
+                                0.1,
+                                0.7000000000000001
+                            ],
+                            "xyz": [
+                                10.937456,
+                                10.937456,
+                                2.734364
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.10000000000000002,
+                                0.09999999999999999,
+                                0.9
+                            ],
+                            "xyz": [
+                                13.671819999999999,
+                                13.671819999999999,
+                                2.734364
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.1,
+                                0.30000000000000004,
+                                0.10000000000000003
+                            ],
+                            "xyz": [
+                                5.4687280000000005,
+                                2.7343640000000002,
+                                5.4687280000000005
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.09999999999999998,
+                                0.30000000000000004,
+                                0.3000000000000001
+                            ],
+                            "xyz": [
+                                8.203092000000002,
+                                5.4687280000000005,
+                                5.468728
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.10000000000000002,
+                                0.3,
+                                0.5
+                            ],
+                            "xyz": [
+                                10.937455999999997,
+                                8.203092,
+                                5.468728
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.09999999999999992,
+                                0.3000000000000001,
+                                0.7000000000000001
+                            ],
+                            "xyz": [
+                                13.67182,
+                                10.937456,
+                                5.468728
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.09999999999999994,
+                                0.3000000000000001,
+                                0.9
+                            ],
+                            "xyz": [
+                                16.406184,
+                                13.671819999999999,
+                                5.468728
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.09999999999999999,
+                                0.5000000000000001,
+                                0.10000000000000005
+                            ],
+                            "xyz": [
+                                8.203092000000002,
+                                2.7343640000000002,
+                                8.203092
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.10000000000000002,
+                                0.5,
+                                0.30000000000000004
+                            ],
+                            "xyz": [
+                                10.937456,
+                                5.4687280000000005,
+                                8.203092
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.10000000000000007,
+                                0.5,
+                                0.5
+                            ],
+                            "xyz": [
+                                13.671819999999999,
+                                8.203092,
+                                8.203092
+                            ],
+                            "label": "Si",
+                            "properties": {}
+                        },
+                        {
+                            "species": [
+                                {
+                                    "element": "Si",
+                                    "occu": 1
+                                }
+                            ],
+                            "abc": [
+                                0.09999999999999996,
+                                0.5000000000000001,
+                                0.7000000000000002
+                            ],
+                            "xyz": [
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+                                    17.86764514896959,
+                                    20.49501670256177
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9508420036388977,
+                                    0.5556380801760208,
+                                    0.5468171622240539
+                                ],
+                                "xyz": [
+                                    15.072569632150186,
+                                    20.475726537028414,
+                                    20.596324539502476
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9552987171994615,
+                                    0.5464575293404794,
+                                    0.7515021606060305
+                                ],
+                                "xyz": [
+                                    17.745471248204492,
+                                    23.33507437719868,
+                                    20.531741086569692
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9516031273730684,
+                                    0.5519316015293977,
+                                    0.9527576189685734
+                                ],
+                                "xyz": [
+                                    20.57184017858857,
+                                    26.036077339048582,
+                                    20.55605617730331
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.953101737548505,
+                                    0.7539617530754711,
+                                    0.14774035782855421
+                                ],
+                                "xyz": [
+                                    12.32790895389987,
+                                    15.050514976417984,
+                                    23.338664772382685
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9501612016322825,
+                                    0.7462586723974399,
+                                    0.35585620592232187
+                                ],
+                                "xyz": [
+                                    15.067916235709683,
+                                    17.85563491295319,
+                                    23.193147162157036
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9526934279377578,
+                                    0.74980693463005,
+                                    0.5441086189159127
+                                ],
+                                "xyz": [
+                                    17.69018054328076,
+                                    20.46400816021495,
+                                    23.276278506961805
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9507588976624178,
+                                    0.7519814187142847,
+                                    0.7533860269028283
+                                ],
+                                "xyz": [
+                                    20.581112750336956,
+                                    23.298762662569622,
+                                    23.279559112245327
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9512064107860795,
+                                    0.755460557714564,
+                                    0.946636069768628
+                                ],
+                                "xyz": [
+                                    23.270758713557253,
+                                    25.94696078249746,
+                                    23.333243593286465
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9521715102041416,
+                                    0.9442558736161951,
+                                    0.15395505983741078
+                                ],
+                                "xyz": [
+                                    15.014542204209677,
+                                    15.122763362825495,
+                                    25.92761383466255
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.946725952390455,
+                                    0.946383499493028,
+                                    0.35171887381365297
+                                ],
+                                "xyz": [
+                                    17.747421989421746,
+                                    17.752103943793845,
+                                    25.882251666449637
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9443562995011371,
+                                    0.9497555790132105,
+                                    0.5544023339843887
+                                ],
+                                "xyz": [
+                                    20.564576238078832,
+                                    20.490758260460076,
+                                    25.895956662910024
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.9489465364049484,
+                                    0.9561273575040368,
+                                    0.7464698987975502
+                                ],
+                                "xyz": [
+                                    23.27760322064916,
+                                    23.17942832713022,
+                                    26.04582736422274
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            },
+                            {
+                                "species": [
+                                    {
+                                        "element": "Si",
+                                        "occu": 1
+                                    }
+                                ],
+                                "abc": [
+                                    0.953772673061662,
+                                    0.952283975370427,
+                                    0.944169167504682
+                                ],
+                                "xyz": [
+                                    25.92796600782277,
+                                    25.94831921469175,
+                                    26.0592634071668
+                                ],
+                                "label": "Si",
+                                "properties": {}
+                            }
+                        ]
+                    }
+                ],
+                "disps": [
+                    0.01,
+                    0.020000000000000004,
+                    0.030000000000000006,
+                    0.04000000000000001,
+                    0.05000000000000001,
+                    0.06000000000000001,
+                    0.07,
+                    0.08,
+                    0.09000000000000001,
+                    0.1
+                ],
+                "first_pass": true,
+                "static_user_incar_settings": {
+                    "ADDGRID": true,
+                    "LCHARG": false,
+                    "ENCUT": 700,
+                    "EDIFF": 1e-08,
+                    "PREC": "Accurate",
+                    "LAECHG": false,
+                    "LREAL": false,
+                    "LASPH": true
+                },
+                "env_vars": {
+                    "VASP_CMD": ">>vasp_cmd<<",
+                    "DB_FILE": ">>db_file<<"
+                },
+                "shengbte_t_range": false,
+                "shengbte_fworker": null,
+                "_fw_name": "{{atomate.vasp.firetasks.parse_outputs.CSLDForceConstantsToDB}}"
+            }
+        ],
+        "calc_locs": [
+            {
+                "name": "perturbed supercell, idx: 0, disp_val: 0.010, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-00-47-30-571609/launcher_2019-08-03-01-06-49-396367"
+            },
+            {
+                "name": "perturbed supercell, idx: 1, disp_val: 0.020, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-01-00-10-536875/launcher_2019-08-03-01-15-54-768794"
+            },
+            {
+                "name": "perturbed supercell, idx: 2, disp_val: 0.030, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-00-47-30-571609/launcher_2019-08-03-01-53-25-787365"
+            },
+            {
+                "name": "perturbed supercell, idx: 4, disp_val: 0.050, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-02-00-31-887278/launcher_2019-08-03-02-10-39-900305"
+            },
+            {
+                "name": "perturbed supercell, idx: 3, disp_val: 0.040, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-01-00-10-536875/launcher_2019-08-03-02-03-16-191652"
+            },
+            {
+                "name": "perturbed supercell, idx: 5, disp_val: 0.060, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-00-47-30-571609/launcher_2019-08-03-02-41-13-527053"
+            },
+            {
+                "name": "perturbed supercell, idx: 6, disp_val: 0.070, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-02-00-31-887278/launcher_2019-08-03-02-51-25-930836"
+            },
+            {
+                "name": "perturbed supercell, idx: 7, disp_val: 0.080, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-01-00-10-536875/launcher_2019-08-03-03-14-04-415140"
+            },
+            {
+                "name": "perturbed supercell, idx: 8, disp_val: 0.090, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-03-00-15-983388/launcher_2019-08-03-03-20-49-969204"
+            },
+            {
+                "name": "perturbed supercell, idx: 9, disp_val: 0.100, static",
+                "filesystem": null,
+                "path": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-03-00-47-30-571609/launcher_2019-08-03-03-29-56-163076"
+            }
+        ]
+    },
+    "fw_id": 382,
+    "created_on": "2019-08-02T23:22:50.420334",
+    "updated_on": "2019-08-05T00:02:13.075974",
+    "launches": [
+        {
+            "fworker": {
+                "name": "rees_the_fire_worker",
+                "category": "",
+                "query": "{\"spec._fworker\": \"rees_the_fire_worker\"}",
+                "env": {
+                    "db_file": "/global/homes/r/rchang97/anywhere_called_anything/knl/db.json",
+                    "vasp_cmd": "srun -n64 -c16 --cpu_bind=cores vasp_std",
+                    "vasp_ncl": "srun -N 4 -n 32 -c16 --cpu_bind=cores vasp_ncl",
+                    "vasp_vtst": "srun -n 32 vasp_vtst",
+                    "shengbte_cmd": "srun -N 4 -n 32 --cpu_bind=cores ShengBTE",
+                    "scratch_dir": null,
+                    "incar_update": {
+                        "KPAR": 4
+                    },
+                    "MAPI_KEY": "auNIrJ23VLXCqbpl",
+                    "OMP_NUM_THREADS": 4
+                }
+            },
+            "fw_id": 382,
+            "launch_dir": "/global/project/projectdirs/m2439/rchang/test_CSLD_workflow_jul11/block_2019-07-11-20-46-47-559096/launcher_2019-08-04-23-48-07-539963/launcher_2019-08-05-00-02-10-420079",
+            "host": "nid02993",
+            "ip": "10.128.11.200",
+            "trackers": [],
+            "action": null,
+            "state": "RUNNING",
+            "state_history": [
+                {
+                    "state": "RUNNING",
+                    "created_on": "2019-08-05T00:02:12.925440",
+                    "updated_on": "2019-08-05T00:02:12.925456"
+                }
+            ],
+            "launch_id": 285
+        }
+    ],
+    "state": "RUNNING",
+    "name": "Compressed Sensing Lattice Dynamics"
+}
\ No newline at end of file
diff --git a/atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si b/atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si
new file mode 100644
index 000000000..283220155
--- /dev/null
+++ b/atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si
@@ -0,0 +1,10 @@
+Si2
+1.0
+0.0000000000000000 2.7343639999999998 2.7343639999999998
+2.7343639999999998 0.0000000000000000 2.7343639999999998
+2.7343639999999998 2.7343639999999998 0.0000000000000000
+Si
+2
+direct
+0.5000000000000000 0.5000000000000000 0.5000000000000000 Si
+0.7500000000000000 0.7500000000000000 0.7500000000000000 Si
diff --git a/atomate/vasp/test_files/csld_wf/__init__.py b/atomate/vasp/test_files/csld_wf/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/atomate/vasp/workflows/tests/test_csld_workflow.py b/atomate/vasp/workflows/tests/test_csld_workflow.py
new file mode 100644
index 000000000..da3d3db8b
--- /dev/null
+++ b/atomate/vasp/workflows/tests/test_csld_workflow.py
@@ -0,0 +1,89 @@
+# coding: utf-8
+
+from __future__ import division, print_function, unicode_literals, absolute_import
+
+import os
+import unittest
+
+from pymatgen import Structure
+from atomate.vasp.workflows.base.csld import CompressedSensingLatticeDynamicsWF
+from atomate.vasp.firetasks.parse_outputs import (
+    CSLDForceConstantsToDB,
+    ShengBTEToDB,
+)
+from atomate.utils.testing import AtomateTest, DB_DIR
+
+import json
+
+module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
+db_dir = os.path.join(module_dir, "..", "..", "..", "common", "test_files")
+ref_dir = os.path.join(module_dir, "..", "..", "test_files", "csld_wf")
+
+__author__ = "Rees Chang"
+__email__ = "rc564@cornell.edu"
+
+
+class TestCompressedSensingLatticeDynamicsWorkflow(AtomateTest):
+
+    # def test_CSLD(self):
+    #
+    #     structure = Structure.from_file(os.path.join(ref_dir, "POSCAR-well_relaxed_Si"))
+    #     wf = CompressedSensingLatticeDynamicsWF(structure,
+    #                                             symmetrize=False,
+    #                                             num_nn_dists=6,
+    #                                             num_displacements=10,
+    #                                             supercells_per_displacement_distance=1,
+    #                                             force_diagonal_transformation=True
+    #                                             )
+    #
+    #     tasks = self.get_task_collection()
+    #     with
+
+    def test_set_params(self):
+        # tasks = self.get_task_collection()
+        with open(os.path.join(ref_dir, "FW.json"),
+                  "r") as f:
+            sample_task = json.load(f)
+        wf_uuid = sample_task["spec"]["_tasks"][0]["wf_uuid"]
+        parent_structure = Structure.from_dict(
+            sample_task["spec"]["_tasks"][0]["parent_structure"])
+        trans_mat = sample_task["spec"]["_tasks"][0]["trans_mat"]
+        supercell_structure = sample_task["spec"]["_tasks"][0]["supercell_structure"]
+        supercell_smallest_dim = sample_task["spec"]["_tasks"][0]["supercell_smallest_dim"]
+        perturbed_supercells = sample_task["spec"]["_tasks"][0]["perturbed_supercells"]
+        disps = sample_task["spec"]["_tasks"][0]["disps"]
+        first_pass = sample_task["spec"]["_tasks"][0]["first_pass"]
+        static_user_incar_settings = sample_task["spec"]["_tasks"][0]["static_user_incar_settings"]
+        env_vars = sample_task["spec"]["_tasks"][0]["env_vars"]
+        shengbte_t_range = sample_task["spec"]["_tasks"][0]["shengbte_t_range"]
+        shengbte_fworker = sample_task["spec"]["_tasks"][0]["shengbte_fworker"]
+
+        print(wf_uuid)
+        print(parent_structure)
+        print(trans_mat)
+        print(supercell_structure)
+        print(supercell_smallest_dim)
+        print(perturbed_supercells)
+        print(disps)
+        print(first_pass)
+        print(static_user_incar_settings)
+        print(env_vars)
+        print(shengbte_t_range)
+        print(shengbte_fworker)
+
+        # csld_firetask = CSLDForceConstantsToDB(
+        #     db_file=os.path.join(DB_DIR, "db.json"),  # wot
+        #     wf_uuid=wf_uuid,
+        #     parent_structure=parent_structure,
+        #     trans_mat=trans_mat,
+        #     supercell_structure=supercell_structure,
+        #     supercell_smallest_dim=supercell_smallest_dim,
+        #     perturbed_supercells=perturbed_supercells,
+        #     disps=disps,
+        #     first_pass=first_pass,
+        #     static_user_incar_settings=static_user_incar_settings,
+        #     env_vars=env_vars,
+        #     shengbte_t_range=shengbte_t_range,
+        #     shengbte_fworker=shengbte_fworker
+        # )
+

From 8d9b7d1f4df8bf63123843ddf18f438ae549bd56 Mon Sep 17 00:00:00 2001
From: rees-c <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 11:11:04 -0700
Subject: [PATCH 041/207] Delete

---
 .../vasp/workflows/base/CSLD_sc_enumerator.py | 167 ------------------
 1 file changed, 167 deletions(-)
 delete mode 100644 atomate/vasp/workflows/base/CSLD_sc_enumerator.py

diff --git a/atomate/vasp/workflows/base/CSLD_sc_enumerator.py b/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
deleted file mode 100644
index b37f9ad54..000000000
--- a/atomate/vasp/workflows/base/CSLD_sc_enumerator.py
+++ /dev/null
@@ -1,167 +0,0 @@
-#!/usr/bin/env python3
-
-import numpy as np
-
-"""
-This module defines a script that generates perturbed supercells from a supercell structure
-"""
-
-class CSLDPerturbedSupercellEnumerator:
-    """
-    Uses a supercell Structure, a transformation matrix, a min/max displacement,
-    number of displacement values, and number of supercells per displacement
-    to generate a list of randomly perturbed supercells from a given supercell.
-
-        Args:
-            original_supercell (Structure): supercell to displace, typically already relaxed
-            max_displacement_val (float): maximum displacement value for perturbing the supercell (in Angstroms)
-            min_displacement_val (float): minimum displacement value for perturbing the supercell (in Angstroms)
-            num_displacements (int): number of unique displacement values to try, bounded by
-                min_displacement and max_displacement. This argument is ignored if min_displacement
-                is not passed as an argument.
-            scs_per_displacement_val (int): number of perturbed supercells to generate for each unique
-                displacement value.
-
-            floor_displacement (Optional float): If None (default), then for a given perturbed supercell, all atoms will
-                move the same distance from their original locations. If float, then for a given perturbed supercell,
-                the distances that atoms move will be uniformly distributed from a minimum value of 'floor_displacement'
-                to the displacement value 'displacement_val'.
-
-    """
-
-    def __init__(self, original_supercell,
-                 max_displacement_val,
-                 min_displacement_val,
-                 num_displacements,
-                 scs_per_displacement_val,
-                 floor_displacement=None):
-
-        self.original_supercell = original_supercell
-        self.max_disp_val = max_displacement_val
-        self.min_disp_val = min_displacement_val
-        self.num_disps = num_displacements
-        self.scs_per_disp_val = scs_per_displacement_val
-
-        if floor_displacement is not None:
-            self.floor_disp = float(floor_displacement)
-        else:
-            self.floor_disp = None
-
-        self.disp_vals = np.linspace(min_displacement_val, max_displacement_val, num=num_displacements)
-        self.perturbed_supercells = self.generate_transformations()
-
-
-    def random_displacements(self, natom, rmax, rmin, dim=3):
-        #*** Adapted from csld.util.mathtool
-
-        # Generate matrix of size (natom, 3) where each row is a Gaussian random vector
-        # If 'rmax'=None, then all vectors will have magnitude 'rmin'.
-        # Else, magnitudes are uniformly distributed between 'rmin' and 'rmax'.
-
-        dx = np.random.normal(size=(natom, dim)) #Gaussian sampled displacements. Matrix size: (natom, 3)
-        dx_norms = np.linalg.norm(dx, axis=1)
-        veclen = np.full(natom, rmax) if rmin is None else np.random.uniform(rmin, rmax, natom)
-
-        if not 0 in dx_norms:
-            return dx * (veclen / dx_norms)[:, None]
-        else:
-            self.random_displacements(natom, rmax, rmin, dim)
-
-
-    def perturb_supercell(self, structure, max_disp, floor_disp):
-        # *** Adapted from CSLD's 'polaron_main' file
-
-        na = structure.num_sites
-        max_disp = float(max_disp)
-        if isinstance(max_disp, float):
-            # from csld.util.mathtool import random_displacements
-            dr = self.random_displacements(na, max_disp, floor_disp) #generate random displacements
-
-            # Perturb structure with the random displacements
-            for i in range(len(structure._sites)):
-                structure.translate_sites([i], dr[i], frac_coords=False, to_unit_cell=True)
-            return structure
-        else:
-            print('displacement entered is not a float.')
-
-
-    def generate_transformations(self):
-        perturbed_supercells = []
-        for disp_val in self.disp_vals:
-            for cell in range(self.scs_per_disp_val):
-                sc = self.original_supercell.copy()
-                sc = self.perturb_supercell(sc, disp_val, self.floor_disp)
-                perturbed_supercells += [sc]
-        return perturbed_supercells
-
-
-####################################
-# BELOW IS FOR DEBUGGING PURPOSES #
-####################################
-def main():
-    # print('test')
-    # natom = 10
-    # dim = 3
-    # rmin = 0
-    # rmax = 0.1
-    # dx = np.random.normal(size=(natom, dim))  # Gaussian sampled displacements. Matrix size: (natom, 3)
-    # print(dx.shape)
-    # veclen = np.full(natom, rmin) if rmax is None else np.random.uniform(rmin, rmax, natom)  # vector of length natom
-    # dx *= (veclen / np.linalg.norm(dx, axis=1))[:, None]
-    # test = (veclen / np.linalg.norm(dx, axis=1))[:, None]
-    # print(test.shape)
-    #
-    # x = np.array([[1, 1, 1],
-    #               [1, 1, 1],
-    #               [1, 1, 1],
-    #               [1, 1, 1]])
-    # y = np.array([[1],
-    #               [2],
-    #               [3],
-    #               [4]])
-    # print(x*y)
-
-    from atomate.vasp.workflows.base.csld_sc_gen import gen_scaling_matrix
-
-    from pymatgen.ext.matproj import MPRester
-    from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
-    from pymatgen.transformations.standard_transformations import SupercellTransformation
-
-    mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
-    # structure = mpr.get_structure_by_material_id('mp-7814') #passed
-    structure = mpr.get_structure_by_material_id('mp-1101039')  # passed
-    # structure = mpr.get_structure_by_material_id('mp-20012')
-
-    print('structure loaded')
-    print(structure.num_sites)
-    # print('structure')
-    # print(structure)
-    # structure.to(fmt='poscar', filename='POSCAR-tlbise2-scraped')
-
-    # # Find Primitive
-    # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    # sga = SpacegroupAnalyzer(structure)
-    # # print(sga.find_primitive().lattice)
-    # sga.find_primitive().to(fmt='poscar', filename='POSCAR-tlbise2-scraped-prim')
-
-    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150, max_atoms=1000)
-    # ***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
-
-    print('~~~~~~~~~~~~~~~~~~~~~~~~~')
-    print("FINISHED2")
-    # print(T)
-
-    # Pymatgen version
-    superstructure = SupercellTransformation(T).apply_transformation(structure)
-
-    enum = CSLDPerturbedSupercellEnumerator(superstructure,
-                                            max_displacement_val=0.05,
-                                            min_displacement_val=0.01,
-                                            num_displacements=2,
-                                            scs_per_displacement_val=1)
-    print('perturbed supercells list:')
-    print(enum.perturbed_supercells)
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

From 685f2fb486f3269fa83206b6c09bc5c55ca925f2 Mon Sep 17 00:00:00 2001
From: rees-c <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 11:11:21 -0700
Subject: [PATCH 042/207] Delete

---
 atomate/vasp/workflows/base/csld_sc_gen.py | 257 ---------------------
 1 file changed, 257 deletions(-)
 delete mode 100644 atomate/vasp/workflows/base/csld_sc_gen.py

diff --git a/atomate/vasp/workflows/base/csld_sc_gen.py b/atomate/vasp/workflows/base/csld_sc_gen.py
deleted file mode 100644
index 6fa54d80e..000000000
--- a/atomate/vasp/workflows/base/csld_sc_gen.py
+++ /dev/null
@@ -1,257 +0,0 @@
-#!/usr/bin/env python3
-
-import math
-
-import numpy as np
-
-from pymatgen.ext.matproj import MPRester
-from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
-from pymatgen.transformations.standard_transformations import SupercellTransformation
-
-"""
-This module defines the Compressed Sensing Lattice Dynamics (CSLD) workflow.
-
-V3 added rounding of entries away from 0 if there are zero rows or columns in the transformation matrix.
-"""
-
-
-def round_away_from_zero(x):
-    aX = abs(x)
-    return math.ceil(aX)*(aX/x) if x is not 0 else 0
-
-def gen_scaling_matrix(structure=None, max_atoms=np.Inf, min_atoms=-np.Inf, length_cutoff=5):
-    """
-    Returns the transformation matrix of a Pymatgen structure into a suitable supercell for CSLD
-
-    Args:
-        structure (Structure): input structure.
-        max_atoms (int): maximum number of atoms allowed in the supercell
-        min_atoms (int): minimum number of atoms allowed in the supercell
-        length_cutoff (int): number of multiples of the unit cell nearest neighbor distance to
-            force all directions of the supercell to be at least as large
-
-    Returns:
-        Transformation matrix (numpy array)
-    """
-
-    if not structure:
-        print('No structure was passed into gen_scaling_matrix()')
-    else:
-
-        # -------- Store relevant structure data ----------
-        latVecs = structure.lattice.matrix #lattice vectors
-        bondLengths = get_max_bond_lengths(structure) #dictionary of bond lengths
-        bondMatrix = structure.distance_matrix #NxN matrix of bond distances (diagonal is 0)
-        # print(bondMatrix)
-        # print(structure.sites)
-        np.fill_diagonal(bondMatrix, np.Inf)
-        nnDist = np.amin(bondMatrix) #nearest neighbor bond length
-        print("nn Dist: " + str(nnDist))
-
-        # --------- Transform lattice vectors -------------
-        SCnotFound = True  # boolean indicator for whether a sufficiently large supercell has been created
-        hard_threshold = nnDist * length_cutoff
-        print("hard_threshold: " + str(hard_threshold))
-        target_threshold = hard_threshold  # target_threshold is used as the desired CUBE side lengths of
-                                            # the supercell (SC)
-        # note: if it is not possible to get a cubic SC, the real SC dimensions will be less
-        #      than the target
-        while SCnotFound:
-            print('---------------------------------------------------------')
-            print('target threshold: ' + str(target_threshold))
-            target_supercell = np.eye(3, 3) * target_threshold
-
-            T = np.linalg.inv(latVecs) @ target_supercell
-            # T = target_supercell @ np.linalg.inv(latVecs)
-            print('T before rounding:')
-            print(T)
-            print('T after rounding:')
-            T_rounded = np.around(T)
-            print(T_rounded)
-
-
-            # Zero columns or rows make T singular, so make them non-singular
-            if (~T_rounded.any(axis=1)).any(): #Check for zero rows
-                zero_row_idxs = np.where(~T_rounded.any(axis=1))[0]
-                for zero_row_idx in zero_row_idxs:
-                    # print(zero_row_idx)
-                    zero_row = T[zero_row_idx, :]
-                    # print('zero row:' + str(zero_row))
-                    col_idx_to_fix = np.where(np.absolute(zero_row) == np.amax(np.absolute(zero_row)))[0]
-                    # print('amax:')
-                    # print(np.amax(np.absolute(zero_row)))
-                    # print('col idx to fix:')
-                    # print(col_idx_to_fix)
-                    for j in col_idx_to_fix:
-                        T_rounded[zero_row_idx, j] = round_away_from_zero(T[zero_row_idx, j])
-            if (~T_rounded.any(axis=1)).any(): #Check for zero columns
-                zero_col_idxs = np.where(~T_rounded.any(axis=1))[0]
-                for zero_col_idx in zero_col_idxs:
-                    zero_col = T[:, zero_col_idx]
-                    row_idx_to_fix = np.where(np.absolute(zero_col) == np.amax(np.absolute(zero_col)))[0]
-                    for i in row_idx_to_fix:
-                        T_rounded[i, zero_col_idx] = round_away_from_zero(T[i, zero_col_idx])
-
-
-            T = T_rounded
-            print("proposed sc.txt:")
-            print(T)
-
-            print("\nSupercell dimensions:")
-            scBases = latVecs @ T
-            print(scBases)
-            print("Supercell volume:")
-            vol = np.cross(scBases[0],scBases[1]).T @ scBases[2]
-            print(vol)
-
-            # -------------------- Check how many nearest neighbors the supercell allows ---------------------------
-            def proj(b, a):
-                # Returns vector projection of b onto a
-                return (b.T @ (a / np.linalg.norm(a))) * (a / np.linalg.norm(a))
-
-            scBasesNorms = [np.linalg.norm(scBases[0]), np.linalg.norm(scBases[1]), np.linalg.norm(scBases[2])]
-            maxNorm = max(scBasesNorms)
-            maxIndex = scBasesNorms.index(maxNorm)
-            idx = list(range(3))
-            idx.remove(maxIndex)
-            a = scBases[maxIndex]
-            b = scBases[idx[0]]
-            c = scBases[idx[1]]
-            projb_a = proj(b, a)
-            projc_a = proj(c, a)
-
-            if np.linalg.norm(projb_a) > np.linalg.norm(projc_a):
-                length = np.linalg.norm(a - projb_a)
-            else:
-                length = np.linalg.norm(a - projc_a)
-            width = math.sqrt(np.linalg.norm(b) ** 2 - np.linalg.norm(projb_a) ** 2)
-            ab_normal = np.cross(a, b)  # get normal direction from AB plane
-            height = np.linalg.norm(proj(c, ab_normal))  # project c onto AB plane normal
-
-            cubeSide = min([length, width, height])
-            print('smallest dimension of proposed SC: ' + str(cubeSide))
-
-            # Get number of atoms
-            superstructure = SupercellTransformation(T).apply_transformation(structure)
-            num_at = superstructure.num_sites
-
-            if cubeSide >= hard_threshold and num_at >= min_atoms and num_at <= max_atoms:
-                print(T)
-                print("FINISHED")
-                return T
-            else:
-                # Increase threshold until
-                target_threshold += 1
-                if num_at > max_atoms:
-                    raise AttributeError('While trying to solve for the supercell, the max'
-                                         'number of atoms was exceeded. Try lowering the number'
-                                         'of nearest neighbor distances.')
-                    return
-
-
-def parallelipipedVol(a=[1, 0, 0], b=[0, 1, 0], c=[0, 0, 1]):
-    vol = np.cross(a,b).T @ c
-    return vol
-
-
-def main():
-    mpr = MPRester(api_key='auNIrJ23VLXCqbpl')
-    # structure = mpr.get_structure_by_material_id('mp-7814') #passed
-    structure = mpr.get_structure_by_material_id('mp-1101039') #passed
-    # structure = mpr.get_structure_by_material_id('mp-20012')
-
-    print('structure loaded')
-    print(structure.num_sites)
-    # print('structure')
-    # print(structure)
-    # structure.to(fmt='poscar', filename='POSCAR-tlbise2-scraped')
-
-    # # Find Primitive
-    # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    # sga = SpacegroupAnalyzer(structure)
-    # # print(sga.find_primitive().lattice)
-    # sga.find_primitive().to(fmt='poscar', filename='POSCAR-tlbise2-scraped-prim')
-
-
-    T = gen_scaling_matrix(structure, length_cutoff=5, min_atoms=150, max_atoms=1000)
-    #***my function, pymatgen's SupercellTransformation, and CSLD all yield different supercell lattice vectors
-
-    print('~~~~~~~~~~~~~~~~~~~~~~~~~')
-    print("FINISHED2")
-    # print(T)
-
-    # Pymatgen version
-    superstructure = SupercellTransformation(T).apply_transformation(structure)
-    print(superstructure.lattice)
-    # print(superstructure.volume)
-    # print(parallelipipedVol(superstructure.lattice.matrix[0],
-    #                         superstructure.lattice.matrix[1],
-    #                         superstructure.lattice.matrix[2]))
-    print(superstructure.num_sites)
-
-    # # Find Primitive
-    # from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    # sga = SpacegroupAnalyzer(superstructure)
-    # # print(sga.find_primitive().lattice)
-    # sga.find_primitive().to(fmt='poscar', filename='POSCAR-scTest-prim')
-
-    superstructure.to(fmt='poscar', filename='POSCAR-scTest')
-
-
-
-    # # CSLD version
-    # # *** Can't call CSLD Structure member functions because structure scraped is a Pymatgen Structure ***
-    # from csld.structure import Structure as CSLDStructure
-    # from csld.lattice import Lattice as CSLDLattice
-    # from csld.coord_utils import supercell_latticepoints
-    #
-    # def generate_supercell(CSLDStructure, scaling_matrix, scref=None):
-    #     """
-    #     Create a supercell.
-    #
-    #     Args:
-    #         scaling_matrix: A scaling matrix for transforming the lattice
-    #             vectors. Has to be all integers. Several options are possible:
-    #
-    #             a. A full 3x3 scaling matrix defining the linear combination
-    #                the old lattice vectors. E.g., [[2,1,0],[0,3,0],[0,0,
-    #                1]] generates a new structure with lattice vectors a' =
-    #                2a + b, b' = 3b, c' = c where a, b, and c are the lattice
-    #                vectors of the original structure.
-    #             b. An sequence of three scaling factors. E.g., [2, 1, 1]
-    #                specifies that the supercell should have dimensions 2a x b x
-    #                c.
-    #             c. A number, which simply scales all lattice vectors by the
-    #                same factor.
-    #     """
-    #     scmat = np.array(scaling_matrix, np.int16)
-    #     if scmat.shape != (3, 3):
-    #         scmat= np.array(scmat* np.eye(3), np.int16)
-    #     n_cell=int(round(np.linalg.det(scmat)))
-    #     old_lattice = CSLDStructure._lattice
-    #     new_lattice = CSLDLattice(np.dot(scmat, old_lattice.matrix))
-    #     tvects = supercell_latticepoints(scmat)
-    #     inv=np.linalg.inv(scmat)
-    #     if scref is None:
-    #         sc_ref= supercell_latticepoints(scmat)
-    #     else:
-    #         sc_ref= scref
-    #     return CSLDStructure(CSLDLattice(np.dot(scmat, CSLDStructure._lattice.matrix)),
-    #        [s.species_and_occu for s in CSLDStructure for _ in range(n_cell)],
-    #        (CSLDStructure.frac_coords[:,None,:]+sc_ref[None,:,:]).reshape((-1,3)).dot(inv),
-    #        coords_are_cartesian=False, to_unit_cell=True,
-    #        site_properties_T=[s.properties for s in CSLDStructure for _ in range(n_cell)],
-    #        intensive_properties=CSLDStructure.intensive_properties,extensive_properties=
-    #                        {k:v*CSLDStructure.n_cell for k,v in CSLDStructure.extensive_properties.items()})
-    #
-    # # csld_structure = csld.structure.Structure(structure.lattice, structure.species, structure.lattice.get_fractional_coords())
-    # csld_supercell = SupercellStructure.from_scmat(csld_structure, T)
-    # print("here:")
-    # print(csld_supercell)
-
-if __name__ == '__main__':
-    main()
-
-
-
-

From da91bdc5c8e04c5cb6da867e85a545f74d24378a Mon Sep 17 00:00:00 2001
From: rees-c <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 11:11:38 -0700
Subject: [PATCH 043/207] Delete

---
 atomate/vasp/workflows/base/sbte_IO.py | 180 -------------------------
 1 file changed, 180 deletions(-)
 delete mode 100644 atomate/vasp/workflows/base/sbte_IO.py

diff --git a/atomate/vasp/workflows/base/sbte_IO.py b/atomate/vasp/workflows/base/sbte_IO.py
deleted file mode 100644
index ffd465645..000000000
--- a/atomate/vasp/workflows/base/sbte_IO.py
+++ /dev/null
@@ -1,180 +0,0 @@
-#!/usr/bin/env python3
-
-import f90nml
-import numpy as np
-"""
-This module defines IO ShengBTE for making CONTROL file (i.e. a class that can read/write the ‘control’ file, f90ml)
-
-TO-DO: Test this thing
-"""
-
-class ShengBTE_CONTROL_IO:
-
-    """
-        Args:
-            nelements (int): number of elements in the material
-            natoms (int): number of atoms in the cell
-            ngrid (3 length list of ints): q-point mesh
-            ***norientations (int):
-            ***lfactor (float):
-            lattvec1 (3 length list of floats): first lattice vector
-            lattvec2 (3 length list of floats): second lattice vector
-            lattvec3 (3 length list of floats): third lattice vector
-            elements (comma-separated list of strings): list of elements present
-            types (natoms length list of ints): atom types listed in the same order as in 'elements' (first atom should be '1')
-            positions (natoms x 3 matrix): atomic positions of each atom
-            scell (3 length list of ints): dimensions of supercell input
-            ***temperature (int): temperature in Kelvin?
-            scalebroad (float): Gaussian broadening of allowable energies that can scatter a phonon to a certain state
-                (higher broadening = more scattering allowed. Too high is unphysical. For complex
-                materials, make 'scalebroad' smaller since there will be more scattering candidates
-                for any given phonon.
-            ***onlyharmonic (bool): Whether to only consider harmonic scattering (2-phonon?)
-            ***isotopes (bool): Whether to consider scattering from isotopic disorder.
-            ***nonanalytic (bool): Used for Born effective charge and dielectric constant.
-            nanowires (bool): Whether the structure input is a nanowire.
-
-        Returns:
-            IO reader/writer for ShengBTE's CONTROL file, composed of FORTRAN namelists
-    """
-
-    def read_CONTROL(self, filename):
-        nml = f90nml.read(filename)
-        return nml
-
-
-
-    def file_writer_helper_func(self, dict, filename):
-        nelements = str(dict['allocations']['nelements'])
-        natoms = str(dict['allocations']['natoms'])
-        ngrid = dict['allocations']['ngrid']
-        norientations = str(dict['allocations']['norientations'])
-
-        lfactor = str(dict['crystal']['lfactor'])
-        lattvec1 = dict['crystal']['lattvec'][0]
-        lattvec2 = dict['crystal']['lattvec'][1]
-        lattvec3 = dict['crystal']['lattvec'][2]
-        elements = dict['crystal']['elements'] #string or list of strings, needs to be parsed
-        types = dict['crystal']['types'] #list of ints, needs to be parsed
-        positions = np.asarray(dict['crystal']['positions']) #numpy array, needs to be parsed
-        num_sites, _ = positions.shape
-        scell = dict['crystal']['scell'] #list of ints, needs to be parsed
-
-        temperature = str(int(dict['parameters']['T']))
-        scalebroad = str(dict['parameters']['scalebroad'])
-
-        onlyharmonic = dict['flags']['onlyharmonic']
-        isotopes = dict['flags']['isotopes']
-        nonanalytic = dict['flags']['nonanalytic']
-        nanowires = dict['flags']['nanowires']
-
-        def boolean_to_string(boolean):
-            if boolean is True:
-                return '.TRUE.'
-            else:
-                return '.FALSE.'
-
-        indent = '        '
-        types_string ='types='
-        positions_string = ''
-        for line in range(num_sites):
-            if line != num_sites-1:
-                types_string += str(types[line])+' '
-            else:
-                types_string += str(types[line])+',\n'
-            positions_string += 'positions(:,' + str(line+1) + ')=' + str(positions[line,0]) + '  ' \
-                                + str(positions[line,1]) + '  ' + str(positions[line,2]) + ',\n' + indent
-
-        full_string = '&allocations\n'+indent+'nelements='+nelements+',\n'
-        full_string += indent+'natoms='+natoms+',\n'
-        full_string += indent+'ngrid(:)='+str(ngrid[0])+' '+str(ngrid[1])+' '+str(ngrid[2])+'\n'
-        full_string += indent+'norientations='+norientations+'\n'
-        full_string += '&end\n&crystal\n'
-        full_string += indent+'lfactor='+lfactor+',\n'
-        full_string += indent+'lattvec(:,1)='+str(lattvec1[0])+'  '+str(lattvec1[1])+'  '+str(lattvec1[2])+',\n'
-        full_string += indent+'lattvec(:,2)='+str(lattvec2[0])+'  '+str(lattvec2[1])+'  '+str(lattvec2[2])+',\n'
-        full_string += indent+'lattvec(:,3)='+str(lattvec3[0])+'  '+str(lattvec3[1])+'  '+str(lattvec3[2])+',\n'
-        full_string += indent+'elements='
-        if isinstance(elements, list):
-            for i in range(len(elements)):
-                full_string += '\"'+elements[i]+str('\"')
-                if i != (len(elements)-1):
-                    full_string += ' '
-                else:
-                    full_string += '\n'
-        else:
-            full_string += '\"'+elements+str('\"\n')
-        full_string += indent+types_string
-        full_string += indent+positions_string
-        full_string += 'scell(:)='+str(scell[0])+' '+str(scell[1])+' '+str(scell[2])+'\n'
-        full_string += '&end\n&parameters\n'
-        full_string += indent+'T='+temperature+'\n'
-        full_string += indent+'scalebroad='+scalebroad+'\n'
-        full_string += '&end\n&flags\n'
-        full_string += indent+'isotopes='+boolean_to_string(isotopes)+'\n'
-        full_string += indent+'onlyharmonic='+boolean_to_string(onlyharmonic)+'\n'
-        full_string += indent+'nonanalytic='+boolean_to_string(nonanalytic)+'\n'
-        full_string += indent+'nanowires='+boolean_to_string(nanowires)+'\n'
-        full_string += '&end'
-
-        file = open(filename, 'w+')
-        file.write(full_string)
-        file.close()
-
-
-    def write_CONTROL_from_dict(self, dict, filename='CONTROL', overwrite=True):
-        with open(filename, 'w') as control_file:
-            new_dict = {'allocations':
-                               {'nelements': dict.get('allocations', None).get('nelements', None),
-                                'natoms': dict.get('allocations', None).get('natoms', None),
-                                'ngrid': dict.get('allocations', [25, 25, 25]).get('ngrid', [25, 25, 25]),
-                                'norientations': dict.get('allocations', 0).get('norientations', 0)},
-                        'crystal':
-                               {'lfactor': dict.get('crystal', 0.1).get('lfactor', 0.1),
-                                # 'lattvec(:,1)': dict.get('crystal', None).get('lattvec(:,1)', None),
-                                # 'lattvec(:,2)': dict.get('crystal', None).get('lattvec(:,2)', None),
-                                # 'lattvec(:,3)': dict.get('crystal', None).get('lattvec(:,3)', None),
-                                'lattvec': dict.get('crystal', None).get('lattvec', None),
-                                'elements': dict.get('crystal', None).get('elements', None),
-                                'types': dict.get('crystal', None).get('types', None),
-                                'positions': dict.get('crystal', None).get('positions', None),
-                                'scell': dict.get('crystal', [5, 5, 5]).get('scell', [5, 5, 5])},
-                        'parameters':
-                               {'T': dict.get('parameters', 300).get('t', 300),
-                                'scalebroad': dict.get('parameters', 0.5).get('scalebroad', 0.5)},
-                        'flags':
-                               {'onlyharmonic': dict.get('flags', False).get('onlyharmonic', False),
-                                'isotopes': dict.get('flags', False).get('isotopes', False),
-                                'nonanalytic': dict.get('flags', True).get('nonanalytic', True),
-                                'nanowires': dict.get('flags', False).get('nanowires', False)}}
-
-            # nml = f90nml.namelist.Namelist(new_dict) #convert dict to namelist object
-            # nml.false_repr = '.FALSE.'
-            # nml.true_repr = '.TRUE.'
-            # nml.index_spacing = False
-            # nml.uppercase = False
-            # nml.indent = '        '
-            # f90nml.write(nml, control_file, force=overwrite, sort=False) #force=True overwrites an existing file
-            self.file_writer_helper_func(new_dict, filename=filename)
-
-
-def main():
-    # Read the CONTROL file into a Fortran namelist object
-    sbte_io = ShengBTE_CONTROL_IO()
-    namelist = sbte_io.read_CONTROL('CONTROL')
-    print(namelist)
-    print('---------------------')
-
-    # Convert the namelist object to a dict for easy access of contents
-    dict = namelist.todict()
-    print(dict)
-    print(dict['allocations']['nelements'])
-    print(dict['crystal']['lattvec'])
-    print(dict['crystal']['lattvec'][0])
-
-    # Write the dict back into a namelist file
-    sbte_io.write_CONTROL_from_dict(dict, filename='CONTROL_test2')
-
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

From 8b2c4e223efa2e3fe82c79c0e2c9ac3a0f62f26d Mon Sep 17 00:00:00 2001
From: rees-c <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 11:11:50 -0700
Subject: [PATCH 044/207] Delete

---
 .../workflows/base/scrape_forces_from_DB.py   | 85 -------------------
 1 file changed, 85 deletions(-)
 delete mode 100644 atomate/vasp/workflows/base/scrape_forces_from_DB.py

diff --git a/atomate/vasp/workflows/base/scrape_forces_from_DB.py b/atomate/vasp/workflows/base/scrape_forces_from_DB.py
deleted file mode 100644
index 90178a709..000000000
--- a/atomate/vasp/workflows/base/scrape_forces_from_DB.py
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env python3
-
-
-import numpy as np
-from pymongo import MongoClient
-
-
-# MongoDB database settings/details
-host = "brmyvxghlvvkgkx-mongodb.services.clever-cloud.com"
-port = 27017
-database_name = "brmyvxghlvvkgkx"
-username = "usxrmfzwh9ed1plwi027"
-password = "JJGXekEfnNYtXQSBYHv8"
-
-# Connect to the database
-db = MongoClient(host, port)[database_name]
-db.authenticate(username, password)
-tasks = db.tasks #connects to the 'tasks' collection
-
-"""
-This module defines IO ShengBTE for making CONTROL file (i.e. a class that can read/write the ‘control’ file, f90ml)
-
-TO-DO: Test this thing with csld_main
-"""
-
-def scrape_forces_to_txt(task_id):
-    # Input a Firetask task_id (int)
-    # Output a .txt with all the atomic forces
-
-    forces_list = tasks.find_one({'task_id': task_id})['calcs_reversed'][0]['output']['ionic_steps'][0]['forces']
-    # print(forces_list)
-    # print(len(forces_list))
-
-    num_atoms = len(forces_list)
-    forces = np.empty((num_atoms,3))
-    for atom in range(num_atoms):
-        forces[atom,:] = forces_list[atom][:]
-    # print(forces)
-    np.savetxt('forces.txt', forces, fmt='%.6f')
-
-
-def main():
-    scrape_forces_to_txt(2)
-
-
-if __name__ == '__main__':
-    main()
-
-# def get_structure_from_task_id(task_id):
-#     # Input a Firetask task_id (int)
-#     # Return the corresponding Pymatgen structure (Structure)
-#     try:
-#         return Structure.from_dict(tasks.find_one({"task_id": task_id})["input"]["structure"])
-#     except:
-#         print("No structure with task id '{}' was found.".format(task_id))
-#
-#
-#
-# def get_structures_from_formulaV2(formula, task_label=None):
-#     # Required:
-#     #   Input a Pymatgen 'pretty formula' (String)
-#     # Optional:
-#     #   Input a 'task_label' or substring of a 'task_label' (String)
-#     # Return the corresponding Pymatgen Structures (list)
-#
-#     structs = []
-#     try:
-#         query = {"formula_pretty": formula}
-#         if task_label is not None and isinstance(task_label, str):
-#             # query["$and"] += [{"task_label": task_label}]
-#             query["task_label"] = {"$regex": task_label}
-#         dicts = list(tasks.find(query, ["input.structure"]))
-#
-#         # dicts = list(tasks.find({"$and": [{"formula_pretty": formula},
-#         #                                   {"task_label": task_label}]},
-#         #                                 ["input.structure"]))
-#         for dict in dicts:
-#             struct = Structure.from_dict(dict["input"]["structure"])
-#             structs += [struct]
-#         return structs
-#     except:
-#         if isinstance(formula, str):
-#             print("No structures with the formula '{}' found.".format(formula))
-#         else:
-#             print("Entered formula is not a string.")

From d8af0551edeeae1c4c563bea2917b7a29dd4cebf Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Wed, 7 Aug 2019 22:52:14 -0700
Subject: [PATCH 045/207] updated script for creating workflows

---
 atomate/vasp/workflows/base/csld.py | 31 ++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index e0edef612..0c89d13a1 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -246,11 +246,13 @@ def get_wf(self, c=None):
 # SCRIPT FOR CREATING THE WORKFLOW AND ADDING IT TO THE DATABASE
 if __name__ == "__main__":
 
-    from atomate.vasp.powerups import add_tags, set_execution_options
+    from fireworks import LaunchPad
+    from atomate.vasp.powerups import add_tags, set_execution_options, \
+        add_modify_incar
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
     from pymatgen.core.structure import Structure
 
-    prim = Structure.from_file('POSCAR-well_relaxed_InSb_csld_primitivized')
+    prim = Structure.from_file('POSCAR-well_relaxed_KSnBi')
 
     csld_class = CompressedSensingLatticeDynamicsWF(
         prim,
@@ -258,7 +260,9 @@ def get_wf(self, c=None):
         num_nn_dists=6,
         num_displacements=10,
         supercells_per_displacement_distance=1,
-        force_diagonal_transformation=True
+        force_diagonal_transformation=True,
+        do_shengbte=True,
+        shengbte_fworker="rees_the_fire_worker_haswell"
         )
     print("uuid")
     print(csld_class.uuid)
@@ -272,15 +276,18 @@ def get_wf(self, c=None):
     print(csld_class.supercell_smallest_dim)
     print("supercell number of atoms")
     print(csld_class.supercell.num_sites)
-    csld_class.supercell.to("poscar", filename="SPOSCAR-InSb_diagonal")
+    csld_class.supercell.to("poscar", filename="SPOSCAR-KSnBi_diagonal")
 
     wf = add_tags(wf, ['csld', 'v1', 'rees',
-                       'pre-relaxed insb', 'diagonal supercell',
-                       'not symmetrized'])
+                       'pre-relaxed ksnbi', 'diagonal supercell',
+                       'not symmetrized', 'ismear manually set to 0'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker")
-    # wf = add_modify_incar(wf,
-    #                       modify_incar_params={'incar_update': {'ENCUT': 500,
-    #                                                             'ISPIN': 1}})
-
-    # lpad = LaunchPad.auto_load()
-    # lpad.add_wf(wf)
+    wf = add_modify_incar(wf,
+                          modify_incar_params={
+                              'incar_update': {
+                                  'ENCUT': 500,
+                                  'ISMEAR': 0,
+                                  'ISPIN': 1}})
+
+    lpad = LaunchPad.auto_load()
+    lpad.add_wf(wf)

From caeef025456446a61c4a112e7a3a9b012abd0f4c Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 8 Aug 2019 17:12:57 -0700
Subject: [PATCH 046/207] More unit tests and minor bug fixes

---
 atomate/vasp/analysis/csld.py                 |    1 +
 atomate/vasp/firetasks/parse_outputs.py       |   28 +-
 atomate/vasp/test_files/csld_wf/FW.json       | 1095 ++++++++++++++++-
 atomate/vasp/workflows/base/csld.py           |   25 +-
 .../workflows/tests/test_csld_workflow.py     |  175 ++-
 5 files changed, 1255 insertions(+), 69 deletions(-)

diff --git a/atomate/vasp/analysis/csld.py b/atomate/vasp/analysis/csld.py
index a1b367d63..799963108 100644
--- a/atomate/vasp/analysis/csld.py
+++ b/atomate/vasp/analysis/csld.py
@@ -172,6 +172,7 @@ def csld_main(options, settings):
         'fval_out': 'fval_pred.txt',
         'traindat0': 'fcc222/POSCAR fcc222/traj*'
     },
+    'export_potential': {},
     'DEFAULT': {
         "qpoint_fractional": False,
         "true_v_fit": 'true_fit.txt',
diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 25cbb8137..2037ab6d5 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1918,7 +1918,7 @@ def collect_successful_static_calcs_results(self, tasks):
             "parent_structure"].composition.reduced_formula
         task_label = 'static'
         supercells_dicts = list(
-            tasks.find({"wf_meta.wf_uuid": uuid,  # <insert
+            tasks.find({"wf_meta.wf_uuid": uuid,
                         "task_label": {"$regex": task_label},
                         "formula_pretty": formula_pretty,
                         "state": 'successful'},
@@ -1974,8 +1974,8 @@ def set_params(self, iteration_number, disps, cluster_diam,
         format readable by CSLD and then saved to the class' dictionary.
 
         Args:
-            disps (list of floats): list of displacement distances for perturbed
-                supercells that ran successfully
+            disps (list of str or floats): list of displacement distances for
+                perturbed supercells that ran successfully
             iteration_number (int): current iteration (0-indexed) of the CSLD
                 grid or random search
             cluster_diam (str): Space-separated string containing the spherical
@@ -2010,16 +2010,19 @@ def set_params(self, iteration_number, disps, cluster_diam,
         #   POSCAR to file
         np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
                    delimiter=" ")
-        self["supercell_structure"].to("poscar", filename=supercell_folder + "/SPOSCAR")
-        self["parent_structure"].to("poscar", filename=supercell_folder + "/POSCAR")
+        self["supercell_structure"].to("poscar",
+                                       filename=supercell_folder + "/SPOSCAR")
+        self["parent_structure"].to("poscar",
+                                    filename=supercell_folder + "/POSCAR")
 
-        # Create folders for perturbed supercell POSCARS and force.txt's (e.g. "Si_supercell_iter0/disp0.010")
+        # Create folders for perturbed supercell POSCARS and force.txt's
+        # (e.g. "Si_supercell_iter0/disp0.010")
         disp_folders = []
         csld_traindat_disp_folders = ''
         for idx, disp in enumerate(disps):
-            disp_folder = supercell_folder + '/disp' + str(disp)
+            disp_folder = supercell_folder + '/disp{:.2f}'.format(float(disp))
             disp_folders += [disp_folder] # list of folder paths
-            csld_traindat_disp_folders += ' ' + str(disp_folder) # Create string for CSLD input
+            csld_traindat_disp_folders += ' ' + str(disp_folder)
             if os.path.exists(disp_folder) and os.path.isdir(disp_folder):
                 shutil.rmtree(disp_folder)
             os.mkdir(disp_folder)
@@ -2043,7 +2046,7 @@ def set_params(self, iteration_number, disps, cluster_diam,
         # original structure poscar
         csld_settings_dict["structure"]["prim"] = supercell_folder + '/POSCAR'
         csld_settings_dict["model"].update({
-            'max_oder': max_order,
+            'max_order': max_order,
             'cluster_diameter': cluster_diam,
             'cluster_filter':
                 r"lambda cls: ((cls.order_uniq <= 2) or (cls.bond_counts(2.9) "
@@ -2051,7 +2054,8 @@ def set_params(self, iteration_number, disps, cluster_diam,
         })
 
         # directories of unperturbed followed by perturbed supercell poscars
-        # e.g., 'fcc333/SPOSCAR fcc333/dir*0.01 fcc333/dir*0.02 fcc333/dir*0.05'
+        # e.g., 'Si_supercell_iter0/SPOSCAR Si_supercell_iter0/disp0.01
+        #           Si_supercell_iter0/disp0.05'
         csld_settings_dict["training"]['traindat1'] = csld_traindat_string
         csld_settings_dict['fitting']['submodel1'] = submodel1
 
@@ -2370,9 +2374,9 @@ def run_task(self, fw_spec):
         # Output lowest validation error and corresponding CSLD input settings
         best_idx = self["convergence_info"]["cross_val_errors"].index(
             min(self["convergence_info"]["cross_val_errors"]))
-        print("The lowest error was {} percent.".format(
+        logger.info("The lowest error was {} percent.".format(
             min(self["convergence_info"]["cross_val_errors"])))
-        print("The corresponding settings were: {}".format(
+        logger.info("The corresponding settings were: {}".format(
             self["convergence_info"]["settings_tried"][best_idx]))
 
         if not_converged is False:
diff --git a/atomate/vasp/test_files/csld_wf/FW.json b/atomate/vasp/test_files/csld_wf/FW.json
index df18899c0..dfec54f0c 100644
--- a/atomate/vasp/test_files/csld_wf/FW.json
+++ b/atomate/vasp/test_files/csld_wf/FW.json
@@ -1,4 +1,4 @@
-{
+[{
     "spec": {
         "tags": [
             "csld",
@@ -55597,4 +55597,1095 @@
     ],
     "state": "RUNNING",
     "name": "Compressed Sensing Lattice Dynamics"
-}
\ No newline at end of file
+   },
+  {
+    "wf_meta":
+      {"wf_uuid": "b8ab536c-b75d-4011-a069-48cbab8b8bda"},
+    "task_id": 73,
+    "task_label": "perturbed supercell, idx:9, disp_val: 0.100, static",
+    "output":
+      {"forces": [
+      [
+        0.07831190000000000373,
+        0.13348752999999999314,
+        -0.7885310199999999714
+      ],
+      [
+        -0.23123856000000000965,
+        0.096098559999999999537,
+        -0.42135612000000000066
+      ],
+      [
+        0.58627600000000001934,
+        -0.54241695999999994804,
+        1.7035638600000000409
+      ],
+      [
+        -0.99997219000000003852,
+        -0.14053357999999999128,
+        0.20597187999999999608
+      ],
+      [
+        -0.084016499999999993964,
+        -0.66620157000000002068,
+        1.3024467399999999362
+      ],
+      [
+        0.042476250000000000118,
+        1.1488909899999999453,
+        1.790629919999999986
+      ],
+      [
+        0.79051106000000004315,
+        1.2691133900000000079,
+        -0.32494996999999997689
+      ],
+      [
+        0.5270944899999999711,
+        1.1274580000000000712,
+        -0.52687927000000001065
+      ],
+      [
+        1.3149132999999999516,
+        0.14895844999999999225,
+        -1.0134311000000000291
+      ],
+      [
+        0.64389313000000003573,
+        -0.48292942999999999287,
+        -1.1776767999999999681
+      ],
+      [
+        1.5145975300000000807,
+        0.5851555299999999793,
+        -1.061155279999999923
+      ],
+      [
+        -0.89103935000000000777,
+        0.50084167000000001657,
+        0.3583423299999999867
+      ],
+      [
+        0.64216777999999996585,
+        -0.35038510999999999962,
+        -0.29322418000000000093
+      ],
+      [
+        -1.2954094800000000021,
+        -0.97275754999999997086,
+        -1.9234877200000000119
+      ],
+      [
+        -0.62535890999999999007,
+        1.0499413399999999452,
+        0.13253425999999998708
+      ],
+      [
+        -0.087670300000000006557,
+        -0.68315850000000000186,
+        1.3583470200000000716
+      ],
+      [
+        1.5463132500000000835,
+        0.19501678000000000068,
+        -0.19524247999999999603
+      ],
+      [
+        -0.70032349999999998769,
+        0.0049489499999999997035,
+        0.66694388000000004446
+      ],
+      [
+        0.9796890700000000507,
+        -1.4648347200000000345,
+        -0.081083359999999993217
+      ],
+      [
+        -1.1092457300000000409,
+        1.7626276499999999903,
+        0.0014913599999999999513
+      ],
+      [
+        -0.12279756999999999478,
+        0.22585643999999999165,
+        0.91203732999999997944
+      ],
+      [
+        1.0306507300000000704,
+        -0.94734240999999996813,
+        0.81078428999999996307
+      ],
+      [
+        2.0477240600000001791,
+        0.77306264000000002312,
+        -0.37277839000000001501
+      ],
+      [
+        -0.12977749999999999009,
+        -1.1385224599999999029,
+        1.4968394000000000421
+      ],
+      [
+        0.21039493000000000777,
+        0.97166746999999997758,
+        0.59281391000000005498
+      ],
+      [
+        -0.78512747000000004949,
+        -1.2550078700000000254,
+        -0.33886599000000000581
+      ],
+      [
+        0.67743217000000000017,
+        -0.98036984000000004791,
+        -0.3980978900000000098
+      ],
+      [
+        -0.82411056999999998673,
+        -1.2909711100000000883,
+        -1.2323026500000000549
+      ],
+      [
+        -0.22584266000000000063,
+        1.6371852200000001076,
+        0.50890758000000002603
+      ],
+      [
+        -0.58444348999999995442,
+        1.8089793800000000257,
+        0.33931751999999998359
+      ],
+      [
+        0.60701552999999996985,
+        0.59774585999999996222,
+        0.048081379999999999952
+      ],
+      [
+        -0.035545699999999999519,
+        1.1661885000000000723,
+        0.86634655999999998777
+      ],
+      [
+        0.85057042999999998845,
+        0.46391482000000000552,
+        0.0076601999999999998217
+      ],
+      [
+        0.53596458000000002375,
+        1.4050670499999999841,
+        -0.21323982999999999133
+      ],
+      [
+        -1.2882882499999999126,
+        -0.71620264000000000149,
+        -1.2155741499999999089
+      ],
+      [
+        -0.091519009999999997862,
+        -0.5103751399999999494,
+        1.7366616399999998954
+      ],
+      [
+        0.10133767999999999943,
+        1.0869468799999999487,
+        -0.68463534999999997588
+      ],
+      [
+        -0.061204130000000002421,
+        0.58470761999999998348,
+        -0.15081370999999998972
+      ],
+      [
+        -0.19033634999999998749,
+        0.92370163999999999049,
+        0.88790815000000000712
+      ],
+      [
+        0.72283881000000005379,
+        1.3917510799999999183,
+        -0.93105172000000002708
+      ],
+      [
+        -1.4223688299999999174,
+        -0.99532498999999996503,
+        -1.1959716899999999207
+      ],
+      [
+        0.69786245000000002303,
+        0.20555810999999998834,
+        -1.1993644599999999656
+      ],
+      [
+        0.66534751999999997008,
+        -1.8806021399999999222,
+        0.074140209999999998058
+      ],
+      [
+        -0.70677151999999998644,
+        -1.2401579000000000352,
+        -0.60743424000000001417
+      ],
+      [
+        0.40725887999999998978,
+        0.22834728000000001358,
+        0.61086996000000004514
+      ],
+      [
+        0.62574004000000005288,
+        0.072553480000000003525,
+        -0.77714974000000003329
+      ],
+      [
+        -0.89136011000000003879,
+        -1.6358562999999999299,
+        -0.92497541999999999263
+      ],
+      [
+        1.4013913799999999643,
+        -0.096434980000000003475,
+        -1.0309077900000001016
+      ],
+      [
+        0.48585639000000002685,
+        -1.8281268200000000412,
+        0.29429448000000002494
+      ],
+      [
+        0.44854590999999999212,
+        -0.078582769999999996235,
+        -0.56651185999999997822
+      ],
+      [
+        1.5751037999999999428,
+        0.54963850999999996905,
+        1.0624619399999999381
+      ],
+      [
+        -0.22981135999999999231,
+        0.95532461000000001849,
+        -0.71957930000000003279
+      ],
+      [
+        0.30679977000000002718,
+        -0.51022266000000005004,
+        0.59013344000000000911
+      ],
+      [
+        0.95272164999999997548,
+        0.68642924000000005158,
+        -0.013147360000000000296
+      ],
+      [
+        -0.18585524999999999962,
+        1.146305490000000038,
+        0.59491990999999999623
+      ],
+      [
+        0.55832212999999997205,
+        1.0742693500000000117,
+        0.19820282999999999651
+      ],
+      [
+        1.0368665299999999529,
+        -0.69249707000000004786,
+        -0.16991117000000000026
+      ],
+      [
+        -1.1572808400000000884,
+        0.85230055999999998484,
+        -0.51185108000000001383
+      ],
+      [
+        -0.38697397000000000045,
+        0.56901707999999995291,
+        -0.78654011000000001452
+      ],
+      [
+        1.4335039099999999923,
+        -0.4602253700000000225,
+        1.4169320800000000382
+      ],
+      [
+        -0.80782277000000002332,
+        -0.49654826000000001907,
+        -0.6662061900000000314
+      ],
+      [
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+      ],
+      [
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+      ],
+      [
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+        0.034694469999999998089
+      ],
+      [
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+        0.87052498000000000378
+      ],
+      [
+        -0.67810042000000003704,
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+        0.96712319999999996067
+      ],
+      [
+        -0.44125513999999999015,
+        0.2097410500000000122,
+        0.076529910000000006542
+      ],
+      [
+        0.60216389000000003495,
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+      ],
+      [
+        0.26492007000000000749,
+        0.81453339999999996301,
+        1.0819854499999999042
+      ],
+      [
+        1.6347942600000000546,
+        -0.3844907900000000267,
+        -0.63217098999999998821
+      ]]},
+    "formula_pretty": "Si",
+    "state": "successful"
+  }
+]
\ No newline at end of file
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index 0c89d13a1..b7ac5ad8b 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -205,8 +205,8 @@ def get_wf(self, c=None):
             static_fw.spec["displacement_value"] = self.disps[idx]
             fws.append(static_fw)
 
-        logger.debug("using {} displacements".format(len(self.disps)))
-        logger.debug("displacements: {}".format(self.disps))
+        logger.debug("Using {} displacements".format(len(self.disps)))
+        logger.debug("Displacements: {}".format(self.disps))
 
         # Collect force constants from the DB and output on cluster
         csld_fw = Firework(
@@ -252,13 +252,19 @@ def get_wf(self, c=None):
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
     from pymatgen.core.structure import Structure
 
-    prim = Structure.from_file('POSCAR-well_relaxed_KSnBi')
+    prim = Structure.from_file('POSCAR-well_relaxed_Si')
+
+    sga = SpacegroupAnalyzer(prim)
+    prim = sga.get_conventional_standard_structure()
+    prim.to("poscar", filename="POSCAR-well_relaxed_conventional_Si")
 
     csld_class = CompressedSensingLatticeDynamicsWF(
         prim,
         symmetrize=False,
         num_nn_dists=6,
-        num_displacements=10,
+        num_displacements=2,
+        min_displacement=0.02,
+        max_displacement=0.05,
         supercells_per_displacement_distance=1,
         force_diagonal_transformation=True,
         do_shengbte=True,
@@ -276,10 +282,11 @@ def get_wf(self, c=None):
     print(csld_class.supercell_smallest_dim)
     print("supercell number of atoms")
     print(csld_class.supercell.num_sites)
-    csld_class.supercell.to("poscar", filename="SPOSCAR-KSnBi_diagonal")
+    csld_class.supercell.to("poscar",
+                            filename="SPOSCAR-conventional_Si_diagonal")
 
     wf = add_tags(wf, ['csld', 'v1', 'rees',
-                       'pre-relaxed ksnbi', 'diagonal supercell',
+                       'pre-relaxed conventional si', 'diagonal supercell',
                        'not symmetrized', 'ismear manually set to 0'])
     wf = set_execution_options(wf, fworker_name="rees_the_fire_worker")
     wf = add_modify_incar(wf,
@@ -288,6 +295,6 @@ def get_wf(self, c=None):
                                   'ENCUT': 500,
                                   'ISMEAR': 0,
                                   'ISPIN': 1}})
-
-    lpad = LaunchPad.auto_load()
-    lpad.add_wf(wf)
+    #
+    # lpad = LaunchPad.auto_load()
+    # lpad.add_wf(wf)
diff --git a/atomate/vasp/workflows/tests/test_csld_workflow.py b/atomate/vasp/workflows/tests/test_csld_workflow.py
index da3d3db8b..b0432d12f 100644
--- a/atomate/vasp/workflows/tests/test_csld_workflow.py
+++ b/atomate/vasp/workflows/tests/test_csld_workflow.py
@@ -4,6 +4,8 @@
 
 import os
 import unittest
+import numpy as np
+import shutil
 
 from pymatgen import Structure
 from atomate.vasp.workflows.base.csld import CompressedSensingLatticeDynamicsWF
@@ -25,32 +27,22 @@
 
 class TestCompressedSensingLatticeDynamicsWorkflow(AtomateTest):
 
-    # def test_CSLD(self):
-    #
-    #     structure = Structure.from_file(os.path.join(ref_dir, "POSCAR-well_relaxed_Si"))
-    #     wf = CompressedSensingLatticeDynamicsWF(structure,
-    #                                             symmetrize=False,
-    #                                             num_nn_dists=6,
-    #                                             num_displacements=10,
-    #                                             supercells_per_displacement_distance=1,
-    #                                             force_diagonal_transformation=True
-    #                                             )
-    #
-    #     tasks = self.get_task_collection()
-    #     with
-
-    def test_set_params(self):
-        # tasks = self.get_task_collection()
+    @staticmethod
+    def init():
         with open(os.path.join(ref_dir, "FW.json"),
                   "r") as f:
-            sample_task = json.load(f)
+            sample_task = json.load(f)[0]
         wf_uuid = sample_task["spec"]["_tasks"][0]["wf_uuid"]
         parent_structure = Structure.from_dict(
             sample_task["spec"]["_tasks"][0]["parent_structure"])
         trans_mat = sample_task["spec"]["_tasks"][0]["trans_mat"]
-        supercell_structure = sample_task["spec"]["_tasks"][0]["supercell_structure"]
+        supercell_structure = Structure.from_dict(
+            sample_task["spec"]["_tasks"][0]["supercell_structure"])
         supercell_smallest_dim = sample_task["spec"]["_tasks"][0]["supercell_smallest_dim"]
         perturbed_supercells = sample_task["spec"]["_tasks"][0]["perturbed_supercells"]
+        for i in range(len(perturbed_supercells)):
+            perturbed_supercells[i] = Structure.from_dict(
+                perturbed_supercells[i])
         disps = sample_task["spec"]["_tasks"][0]["disps"]
         first_pass = sample_task["spec"]["_tasks"][0]["first_pass"]
         static_user_incar_settings = sample_task["spec"]["_tasks"][0]["static_user_incar_settings"]
@@ -58,32 +50,123 @@ def test_set_params(self):
         shengbte_t_range = sample_task["spec"]["_tasks"][0]["shengbte_t_range"]
         shengbte_fworker = sample_task["spec"]["_tasks"][0]["shengbte_fworker"]
 
-        print(wf_uuid)
-        print(parent_structure)
-        print(trans_mat)
-        print(supercell_structure)
-        print(supercell_smallest_dim)
-        print(perturbed_supercells)
-        print(disps)
-        print(first_pass)
-        print(static_user_incar_settings)
-        print(env_vars)
-        print(shengbte_t_range)
-        print(shengbte_fworker)
-
-        # csld_firetask = CSLDForceConstantsToDB(
-        #     db_file=os.path.join(DB_DIR, "db.json"),  # wot
-        #     wf_uuid=wf_uuid,
-        #     parent_structure=parent_structure,
-        #     trans_mat=trans_mat,
-        #     supercell_structure=supercell_structure,
-        #     supercell_smallest_dim=supercell_smallest_dim,
-        #     perturbed_supercells=perturbed_supercells,
-        #     disps=disps,
-        #     first_pass=first_pass,
-        #     static_user_incar_settings=static_user_incar_settings,
-        #     env_vars=env_vars,
-        #     shengbte_t_range=shengbte_t_range,
-        #     shengbte_fworker=shengbte_fworker
-        # )
+        csld_firetask = CSLDForceConstantsToDB(
+            db_file=os.path.join(DB_DIR, "db.json"),
+            wf_uuid=wf_uuid,
+            parent_structure=parent_structure,
+            trans_mat=trans_mat,
+            supercell_structure=supercell_structure,
+            supercell_smallest_dim=supercell_smallest_dim,
+            perturbed_supercells=perturbed_supercells,
+            disps=disps,
+            first_pass=first_pass,
+            static_user_incar_settings=static_user_incar_settings,
+            env_vars=env_vars,
+            shengbte_t_range=shengbte_t_range,
+            shengbte_fworker=shengbte_fworker,
+            force_diagonal_transformation=True
+        )
+
+        return csld_firetask
+
+    def test_collect_successful_static_calcs_results(self):
+        tasks = self.get_task_collection()
+        csld_firetask = self.init()
+        with open(os.path.join(ref_dir, "FW.json"),
+                  "r") as f:
+            sample_task = json.load(f)[1]
+        tasks.insert_one(sample_task)
+
+        supercells_forces, successful_disps = csld_firetask.collect_successful_static_calcs_results(
+            tasks)
+
+        self.assertEqual(
+            float(successful_disps[0]),
+            0.1
+        )
+        self.assertTrue(
+            isinstance(supercells_forces, list)
+        )
+        self.assertEqual(
+            supercells_forces[0][0][0],
+            0.07831190000000000373
+        )
+        self.assertEqual(
+            supercells_forces[0][0][1],
+            0.13348752999999999314
+        )
+        self.assertEqual(
+            supercells_forces[0][0][2],
+            -0.7885310199999999714
+        )
+        self.assertEqual(
+            len(supercells_forces[0]),
+            216
+        )
+
+    def test_set_params(self):
+
+        csld_firetask = self.init()
+        csld_firetask.set_params(
+            iteration_number=0,
+            disps=[0.1],
+            cluster_diam='11 6.5 5.0',
+            max_order=3,
+            submodel1='anh 0 1 2 3',
+            export_sbte='5 5 5 2 3',
+            supercells_forces=[np.eye(3)]
+        )
+
+        self.assertEqual(
+            csld_firetask["csld_settings"]["structure"]["prim"],
+            "Si_supercell_iter0/POSCAR")
+        self.assertEqual(
+            csld_firetask["csld_settings"]["model"]["max_order"],
+            '3'
+        )
+        self.assertEqual(
+            csld_firetask["csld_settings"]["model"]["cluster_diameter"],
+            '11 6.5 5.0'
+        )
+        self.assertEqual(
+            csld_firetask["csld_settings"]["model"]["cluster_filter"],
+            r"lambda cls: ((cls.order_uniq <= 2) or (cls.bond_counts(2.9) "
+            r">= 2)) and cls.is_small_in('" + "Si_supercell_iter0" + "/sc.txt')"
+        )
+        self.assertEqual(
+            csld_firetask["csld_settings"]["training"]["traindat1"],
+            'Si_supercell_iter0/SPOSCAR Si_supercell_iter0/disp0.10'
+        )
+        self.assertEqual(
+            csld_firetask["csld_settings"]["fitting"]["submodel1"],
+            'anh 0 1 2 3'
+        )
+        self.assertEqual(
+            csld_firetask["csld_settings"]["export_potential"]["export_shengbte"],
+            '5 5 5 2 3'
+        )
+        self.assertEqual(
+            csld_firetask["forces_paths"],
+            ['Si_supercell_iter0/disp0.10']
+        )
+        self.assertTrue(
+            os.path.isfile(csld_firetask["forces_paths"][0] + "/force.txt")
+        )
+        self.assertTrue(
+            os.path.isfile('Si_supercell_iter0/POSCAR')
+        )
+        self.assertTrue(
+            os.path.isfile('Si_supercell_iter0/SPOSCAR')
+        )
+        self.assertTrue(
+            os.path.isfile('Si_supercell_iter0/sc.txt')
+        )
+        shutil.rmtree('Si_supercell_iter0')
+
+    def test_run_csld(self):
+
+
+
+
+
 

From 0bd0a6586ddc092504e9286a1938d7496eaec6fe Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 8 Aug 2019 17:13:51 -0700
Subject: [PATCH 047/207] Junsoo's

---
 atomate/vasp/workflows/tests/test_csld_workflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/tests/test_csld_workflow.py b/atomate/vasp/workflows/tests/test_csld_workflow.py
index b0432d12f..a50b7a9fa 100644
--- a/atomate/vasp/workflows/tests/test_csld_workflow.py
+++ b/atomate/vasp/workflows/tests/test_csld_workflow.py
@@ -164,7 +164,7 @@ def test_set_params(self):
         shutil.rmtree('Si_supercell_iter0')
 
     def test_run_csld(self):
-
+        print('hi')
 
 
 

From 2ce5a0357806922754cf72bf22e8f502b4dbda32 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Thu, 8 Aug 2019 19:29:10 -0700
Subject: [PATCH 048/207] debug

---
 atomate/vasp/firetasks/parse_outputs.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 2037ab6d5..fba355c9e 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -2036,6 +2036,7 @@ def set_params(self, iteration_number, disps, cluster_diam,
         # Create ConfigParser of all CSLD input settings
         csld_settings_dict = deepcopy(default_csld_settings)
 
+        # Update default settings if specified
         user_csld_settings = kwargs
         if user_csld_settings is not None:
             # recursively update settings dict
@@ -2060,7 +2061,8 @@ def set_params(self, iteration_number, disps, cluster_diam,
         csld_settings_dict['fitting']['submodel1'] = submodel1
 
         # e.g., '5 5 5 2 3' is a 5x5x5 supercell
-        csld_settings_dict['export_potential']['export_shengbte'] = export_sbte
+        csld_settings_dict['export_potential'] = {'export_shengbte':
+                                                      export_sbte}
 
         csld_settings = ConfigParser()
         csld_settings.read_dict(csld_settings_dict)

From e83cde83b92244adcf98194e463e95fdecc55d36 Mon Sep 17 00:00:00 2001
From: reeschang <rees.chang@gmail.com>
Date: Fri, 9 Aug 2019 10:21:33 -0700
Subject: [PATCH 049/207] last cleanup of the term

---
 atomate/vasp/firetasks/parse_outputs.py            |  6 +++---
 atomate/vasp/workflows/base/csld.py                | 13 +++++--------
 atomate/vasp/workflows/tests/test_csld_workflow.py |  5 ++++-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index fba355c9e..794fecc97 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -2089,6 +2089,7 @@ def run_csld(self, iter):
             summary (dict): Summary of the results from CSLD
         """
         # Perform csld minimization now
+        logger.info("Running CSLD...")
         from atomate.vasp.analysis.csld import csld_main
         rel_err, freq_matrix = csld_main(self["csld_options"],
                                          self["csld_settings"])
@@ -2104,10 +2105,9 @@ def run_csld(self, iter):
         #   so we ignore these)
         imaginary_idx = freq_matrix < -1
         imaginary_freqs = freq_matrix[imaginary_idx]
-        print('IMAGINARY FREQUENCIES')
-        print(imaginary_freqs)
+        logger.info('IMAGINARY FREQUENCIES: \n{}'.format(imaginary_freqs))
         num_imaginary_bands = np.sum(np.any(imaginary_idx, axis=1))
-        print(num_imaginary_bands)
+        logger.info('Number of imaginary bands: {}'.format(num_imaginary_bands))
         if np.any(imaginary_freqs):
             most_imaginary_freq = np.amin(imaginary_freqs)
         else:
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
index b7ac5ad8b..dcaaa7b02 100644
--- a/atomate/vasp/workflows/base/csld.py
+++ b/atomate/vasp/workflows/base/csld.py
@@ -252,19 +252,16 @@ def get_wf(self, c=None):
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
     from pymatgen.core.structure import Structure
 
-    prim = Structure.from_file('POSCAR-well_relaxed_Si')
+    prim = Structure.from_file('POSCAR-well_relaxed_KSnBi')
 
-    sga = SpacegroupAnalyzer(prim)
-    prim = sga.get_conventional_standard_structure()
-    prim.to("poscar", filename="POSCAR-well_relaxed_conventional_Si")
+    # sga = SpacegroupAnalyzer(prim)
+    # prim = sga.get_conventional_standard_structure()
+    # prim.to("poscar", filename="POSCAR-well_relaxed_KSnBi")
 
     csld_class = CompressedSensingLatticeDynamicsWF(
         prim,
         symmetrize=False,
         num_nn_dists=6,
-        num_displacements=2,
-        min_displacement=0.02,
-        max_displacement=0.05,
         supercells_per_displacement_distance=1,
         force_diagonal_transformation=True,
         do_shengbte=True,
@@ -283,7 +280,7 @@ def get_wf(self, c=None):
     print("supercell number of atoms")
     print(csld_class.supercell.num_sites)
     csld_class.supercell.to("poscar",
-                            filename="SPOSCAR-conventional_Si_diagonal")
+                            filename="SPOSCAR-KSnBi_diagonal")
 
     wf = add_tags(wf, ['csld', 'v1', 'rees',
                        'pre-relaxed conventional si', 'diagonal supercell',
diff --git a/atomate/vasp/workflows/tests/test_csld_workflow.py b/atomate/vasp/workflows/tests/test_csld_workflow.py
index a50b7a9fa..07471c7ab 100644
--- a/atomate/vasp/workflows/tests/test_csld_workflow.py
+++ b/atomate/vasp/workflows/tests/test_csld_workflow.py
@@ -3,6 +3,7 @@
 from __future__ import division, print_function, unicode_literals, absolute_import
 
 import os
+from monty.os.path import which
 import unittest
 import numpy as np
 import shutil
@@ -24,6 +25,7 @@
 __author__ = "Rees Chang"
 __email__ = "rc564@cornell.edu"
 
+csld_present = which("csld_main")
 
 class TestCompressedSensingLatticeDynamicsWorkflow(AtomateTest):
 
@@ -64,7 +66,7 @@ def init():
             env_vars=env_vars,
             shengbte_t_range=shengbte_t_range,
             shengbte_fworker=shengbte_fworker,
-            force_diagonal_transformation=True
+            force_diagonal_transformation=True,
         )
 
         return csld_firetask
@@ -163,6 +165,7 @@ def test_set_params(self):
         )
         shutil.rmtree('Si_supercell_iter0')
 
+    @unittest.skipIf(not csld_present, "CSLD not present")
     def test_run_csld(self):
         print('hi')
 

From 1a18f0819131bec40b648e339e1bc4ebad03b887 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Wed, 19 Feb 2020 14:40:45 -0800
Subject: [PATCH 050/207] Remove optional requirements

---
 requirements-optional.txt | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 requirements-optional.txt

diff --git a/requirements-optional.txt b/requirements-optional.txt
deleted file mode 100644
index a46c4ef70..000000000
--- a/requirements-optional.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-nose==1.3.7
-coverage==4.5.3
-coveralls==1.7.0
-f90nml==1.1.2
\ No newline at end of file

From 910b33fe25e0a104a4f540ba50d841e1e1fbeb90 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:01:59 -0800
Subject: [PATCH 051/207] Begin refactoring workflow

---
 .../analysis/{csld.py => lattice_dynamics.py} |  81 ++---
 atomate/vasp/workflows/base/csld.py           | 297 ------------------
 .../vasp/workflows/base/lattice_dynamics.py   | 264 ++++++++++++++++
 3 files changed, 306 insertions(+), 336 deletions(-)
 rename atomate/vasp/analysis/{csld.py => lattice_dynamics.py} (71%)
 delete mode 100644 atomate/vasp/workflows/base/csld.py
 create mode 100644 atomate/vasp/workflows/base/lattice_dynamics.py

diff --git a/atomate/vasp/analysis/csld.py b/atomate/vasp/analysis/lattice_dynamics.py
similarity index 71%
rename from atomate/vasp/analysis/csld.py
rename to atomate/vasp/analysis/lattice_dynamics.py
index 799963108..f0ab19acc 100644
--- a/atomate/vasp/analysis/csld.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -2,59 +2,61 @@
 
 from __future__ import division, print_function, unicode_literals, absolute_import
 
+from typing import Optional, Tuple, List
+
 import numpy as np
 
+from pymatgen import Structure
 from pymatgen.transformations.standard_transformations import PerturbStructureTransformation
 
-__author__ = 'Rees Chang'
-__email__ = 'rc564@cornell.edu'
+__author__ = 'Rees Chang, Alex Ganose'
+__email__ = 'rc564@cornell.edu, aganose@lbl.gov'
 
 
-def generate_perturbed_supercells(supercell,
-                                  min_displacement=0.01, max_displacement=0.1,
-                                  num_displacements=10,
-                                  supercells_per_displacement_distance=1,
-                                  min_random_distance=None):
+def generate_perturbed_supercells(
+    supercell: Structure,
+    min_displacement: float = 0.01,
+    max_displacement: float = 0.1,
+    num_displacements: int = 10,
+    n_cells_per_displacement_distance: int = 1,
+    min_random_distance: Optional[float] = None
+) -> Tuple[List[Structure], np.ndarray]:
     """
     Generate a list of supercells with perturbed atomic sites.
 
     Args:
-        supercell (Structure): original structure whose atomic sites are to be
-            perturbed
-        max_displacement (float): maximum displacement distance for
-            perturbing the structure (Angstroms)
-        min_displacement (float): minimum displacement distance for
-            perturbing the structure (Angstroms)
-        num_displacements (int): number of unique displacement distances to
-            try, uniformly distributed between 'min_displacement' and
-            'max_displacement'.
-        structures_per_displacement_distance (int): number of perturbed
+        supercell (Structure): Original structure whose atomic sites are to be
+            perturbed.
+        max_displacement: Maximum displacement distance for perturbing the
+            sites in Angstroms.
+        min_displacement: Minimum displacement distance for perturbing the
+            sites in Angstroms.
+        num_displacements: Number of unique displacement distances to
+            try, uniformly distributed between ``min_displacement`` and
+            ``max_displacement``.
+        n_cells_per_displacement_distance: Number of perturbed
             structures to generate for each unique displacement distance.
-        min_random_distance (Optional float): If None (default), then for a
-            given perturbed structure, all atoms will move the same distance
-            from their original locations. If float, then for a given
-            perturbed structure, the distances that atoms move will be
-            uniformly distributed from a minimum distance of
-            'min_random_distance' to one of the displacement distances
-            uniformly sampled between 'min_displacement' and
-            'max_displacement'.
+        min_random_distance: If None (default), then for a given perturbed
+            structure, all atoms will move the same distance from their original
+            locations. If float, then for a given perturbed structure, the
+            distances the atoms move will be uniformly distributed from a
+            minimum distance of ``min_random_distance`` to one of the
+            displacement distances uniformly sampled between
+            ``min_displacement`` and ``max_displacement``.
+
     Returns:
-        (List of randomly displaced structures (List of Structures),
-         List of corresponding displacements)
+        A tuple of the ``(structures, displacements)``. Where ``structures`` is
+        a list of randomly displaced structures, and ``displacements`` is
+        the displacement distance for each structure.
     """
-    displacements = np.repeat(
-        np.linspace(min_displacement, max_displacement, num_displacements),
-        supercells_per_displacement_distance
-    )
-    # self.min_random_distance = min_random_distance
-    perturbed_supercells = []  # list of perturbed supercell structures
+    dists = np.linspace(min_displacement, max_displacement, num_displacements)
+    displacements = np.repeat(dists, n_cells_per_displacement_distance)
+
+    perturbed_supercells = []
     for displacement in displacements:
-        perturb_structure_transformer = PerturbStructureTransformation(
-            displacement,
-            min_random_distance)
-        perturbed_supercell = perturb_structure_transformer.apply_transformation(
-            supercell)
-        perturbed_supercells += [perturbed_supercell]
+        pst = PerturbStructureTransformation(displacement, min_random_distance)
+        perturbed_supercells.append(pst.apply_transformation(supercell))
+
     return perturbed_supercells, displacements
 
 
@@ -67,6 +69,7 @@ def csld_main(options, settings):
         - Moved execution files to this main() function to be called from
           atomate
         - Rewrote 'add_common_parameter' in 'common_main' to treat 'options' as
+
           a dictionary instead of ArgumentParser
     """
     import matplotlib
diff --git a/atomate/vasp/workflows/base/csld.py b/atomate/vasp/workflows/base/csld.py
deleted file mode 100644
index dcaaa7b02..000000000
--- a/atomate/vasp/workflows/base/csld.py
+++ /dev/null
@@ -1,297 +0,0 @@
-# coding: utf-8
-
-import numpy as np
-from uuid import uuid4
-
-from pymatgen.transformations.advanced_transformations import (
-    CubicSupercellTransformation)
-from pymatgen.io.vasp.sets import MPStaticSet
-
-from fireworks import Workflow, Firework
-from atomate.utils.utils import get_logger
-from atomate.vasp.config import VASP_CMD, DB_FILE
-from atomate.vasp.fireworks.core import StaticFW
-from atomate.vasp.firetasks.parse_outputs import CSLDForceConstantsToDB
-from atomate.vasp.powerups import add_additional_fields_to_taskdocs
-from atomate.vasp.analysis.csld import generate_perturbed_supercells
-
-__author__ = "Rees Chang"
-__email__ = "rc564@cornell.edu"
-__date__ = "July 2019"
-__csld_wf_version__ = 1.0
-
-logger = get_logger(__name__)
-
-
-class CompressedSensingLatticeDynamicsWF:
-    """
-    This workflow will use compressed sensing lattice dynamics (CSLD)
-    (doi: 10.1103/PhysRevLett.113.185501) to generate interatomic force
-    constants from an input structure and output a summary to a database.
-
-    TODO: Implement 'tight_relaxation', 'dfpt_check', and 'nscf_check' options
-
-    A summary of the workflow is as follows:
-       1. Transform the input structure into a supercell
-       2. Transform the supercell into a list of supercells with all atoms
-           randomly perturbed from their original sites
-       3. Run static VASP calculations on each perturbed supercell to
-           calculate atomic forces.
-       4. Aggregate the forces and conduct the CSLD minimization algorithm
-           to compute interatomic force constants.
-       5. Output the interatomic force constants to the database.
-
-    Args:
-       parent_structure (Structure): Structure to conduct CSLD on
-       symmetrize (bool): If True, the parent_structure will be primitized
-           before running CSLD. Else, the parent_structure will be used
-           for CSLD as is.
-       tight_relaxation (bool): If True, run a tight relaxation step on the
-           parent_structure. Else, do not. TODO: IMPLEMENT
-       dfpt_check (bool): If True, run a DFPT calculation at the gamma
-           point to check for dynamic instabilities. TODO: IMPLEMENT
-       nscf_check (bool): If True, run a nscf electronic bands calculation to
-           determine if parent_structure is a metal or not. If metal, set
-           ISMEAR=1 for the static perturbed supercell calculations. Else, set
-           ISMEAR=0. TODO: IMPLEMENT
-       symprec (float): symmetry precision parameter for
-           SpacegroupAnalyzer's 'get_primitive_standard_structure()'
-           function
-       min_atoms (int): Minimum number of atoms to constrain the supercell
-       max_atoms (int): Maximum number of atoms to constrain the supercell
-       num_nn_dists (int or float): Number of nearest neighbor distances
-           that the shortest direction of the supercell must be as long as
-       force_diagonal_transformation (bool): If True, the supercell
-           transformation will be constrained to have a diagonal
-           transformation matrix. If False, the supercell transformation
-           will not be constrained to be diagonal (resulting in a more
-           cubic supercell).
-       max_displacement (float): Maximum displacement distance for
-           perturbing the supercell structure (Angstroms)
-       min_displacement (float): Minimum displacement distance for
-           perturbing the supercell structure (Angstroms)
-       num_displacements (int): Number of unique displacement distances to
-           generate uniformly between 'min_displacement' and
-           'max_displacement'
-       min_random_distance (Optional float): If None (default), then all
-           atoms in the supercell will move the same distance from their
-           original locations. If float, then for a given supercell, the
-           distances that atoms move will be uniformly distributed from a
-           minimum distance of 'min_random_distance' to one of the
-           displacement distances uniformly sampled between
-           'min_displacement' and 'max_displacement'.
-       supercells_per_displacement_distance (int): number of supercells to
-           generate for each unique displacement distance.
-       dynamic_static_calcs (bool): If True and CSLD fails to return all real
-            harmonic phonon frequencies on the first try, then the CSLD firework
-            will dynamically create more static perturbed supercell calculations
-            with larger displacements with the aim of handling materials with
-            loosely bound atoms (e.g. rattling modes).
-       do_shengbte (bool): If True and CSLD successfully returns all real
-            harmonic phonon frequencies, then the CSLD firework will dynamically
-            create a ShengBTE firework for calculating the lattice thermal
-            conductivity matrix and storing it to a database.
-       shengbte_t_range (bool): If False (default), calculate the lattice
-           thermal conductivity with ShengBTE at 300 K. If True, do the
-           calculation from 100-1000 K with 100 K steps (much slower).
-       shengbte_fworker (None or str): If None, the ShengBTE firework's
-           fworker will be set to all the previous fireworks' fworker. If
-           str, the ShengBTE firework's fworker will be set to
-           shengbte_fworker.
-   """
-
-    def __init__(
-            self,
-            parent_structure,
-            symmetrize=False,
-            symprec=0.1,
-            min_atoms=-np.Inf,
-            max_atoms=np.Inf,
-            num_nn_dists=5,
-            force_diagonal_transformation=True,
-            max_displacement=0.1,
-            min_displacement=0.01,
-            num_displacements=10,
-            min_random_distance=None,
-            supercells_per_displacement_distance=1,
-            dynamic_static_calcs=False,
-            do_shengbte=False,
-            shengbte_t_range=False,
-            shengbte_fworker=None
-    ):
-
-        if force_diagonal_transformation is True and num_nn_dists == 5:
-            num_nn_dists = 6
-
-        # default name is CompressedSensingLatticeDynamicsWF
-        self.uuid = str(uuid4())
-        self.wf_meta = {
-            "wf_uuid": self.uuid,
-            "wf_name": self.__class__.__name__,
-        }
-
-        # Create supercell
-        self.parent_structure = parent_structure
-        if symmetrize:
-            sga = SpacegroupAnalyzer(parent_structure, symprec=symprec)
-            self.parent_structure = sga.get_primitive_standard_structure()
-
-        self.force_diagonal_transformation = force_diagonal_transformation
-        self.min_atoms = min_atoms
-        self.max_atoms = max_atoms
-        self.num_nn_dists = num_nn_dists
-        supercell_transform = CubicSupercellTransformation(
-            self.min_atoms,
-            self.max_atoms,
-            self.num_nn_dists,
-            force_diagonal_transformation=self.force_diagonal_transformation
-        )
-
-        self.supercell = supercell_transform.apply_transformation(
-            self.parent_structure)
-        self.nn_dist = supercell_transform.nn_dist
-        self.trans_mat = supercell_transform.trans_mat.tolist()
-        self.supercell_smallest_dim = supercell_transform.smallest_dim
-
-        # Generate list of perturbed supercells
-        # perturbed_supercells: list of perturbed supercells (list[Structures])
-        # disps: list of (non-unique) displacement values used in the
-        # perturbation (np.array)
-        self.perturbed_supercells, self.disps = generate_perturbed_supercells(
-            self.supercell,
-            min_displacement=min_displacement,
-            max_displacement=max_displacement,
-            num_displacements=num_displacements,
-            supercells_per_displacement_distance=supercells_per_displacement_distance,
-            min_random_distance=min_random_distance
-            )
-
-        self.dynamic_static_calcs = dynamic_static_calcs
-        self.do_shengbte = do_shengbte
-        self.shengbte_t_range = shengbte_t_range
-        self.shengbte_fworker = shengbte_fworker
-
-    def get_wf(self, c=None):
-        fws = []
-        c = c or {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
-
-        static_user_incar_settings = {
-            "ADDGRID": True,  # Fast Fourier Transform grid
-            "LCHARG": False,
-            "ENCUT": 700,
-            "EDIFF": 1e-8,  # may need to tune this
-            "PREC": 'Accurate',
-            "LAECHG": False,
-            "LREAL": False,
-            "LASPH": True}
-        static_user_incar_settings.update(c.get("user_incar_settings", {}))
-
-        for idx, perturbed_supercell in enumerate(self.perturbed_supercells):
-            # Run static calculations on the perturbed supercells to compute
-            # forces on each atom
-            name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(
-                idx, self.disps[idx])
-
-            static_vis = MPStaticSet(
-                perturbed_supercell,
-                user_incar_settings=static_user_incar_settings)
-            static_fw = StaticFW(
-                perturbed_supercell,
-                vasp_input_set=static_vis,
-                vasp_cmd=c["VASP_CMD"],
-                db_file=c["DB_FILE"],
-                name=name + " static"
-            )
-            static_fw.spec["displacement_value"] = self.disps[idx]
-            fws.append(static_fw)
-
-        logger.debug("Using {} displacements".format(len(self.disps)))
-        logger.debug("Displacements: {}".format(self.disps))
-
-        # Collect force constants from the DB and output on cluster
-        csld_fw = Firework(
-            CSLDForceConstantsToDB(
-                db_file=c["DB_FILE"],
-                wf_uuid=self.uuid,
-                parent_structure=self.parent_structure,
-                trans_mat=self.trans_mat,
-                supercell_structure=self.supercell,
-                supercell_smallest_dim=self.supercell_smallest_dim,
-                perturbed_supercells=self.perturbed_supercells,
-                disps=self.disps,
-                force_diagonal_transformation=self.force_diagonal_transformation,
-                first_pass=True,
-                static_user_incar_settings=static_user_incar_settings,
-                env_vars=c,
-                dynamic_static_calcs=self.dynamic_static_calcs,
-                do_shengbte=self.do_shengbte,
-                shengbte_t_range=self.shengbte_t_range,
-                shengbte_fworker=self.shengbte_fworker
-            ),
-            name="Compressed Sensing Lattice Dynamics",
-            parents=fws[-len(self.perturbed_supercells):]
-        )
-        fws.append(csld_fw)
-
-        formula = self.parent_structure.composition.reduced_formula
-        wf_name = "{} - compressed sensing lattice dynamics".format(formula)
-        wf = Workflow(fws, name=wf_name)
-
-        wf = add_additional_fields_to_taskdocs(
-            wf,  {"wf_meta": self.wf_meta}, task_name_constraint="VaspToDb")
-
-        return wf
-
-
-# SCRIPT FOR CREATING THE WORKFLOW AND ADDING IT TO THE DATABASE
-if __name__ == "__main__":
-
-    from fireworks import LaunchPad
-    from atomate.vasp.powerups import add_tags, set_execution_options, \
-        add_modify_incar
-    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    from pymatgen.core.structure import Structure
-
-    prim = Structure.from_file('POSCAR-well_relaxed_KSnBi')
-
-    # sga = SpacegroupAnalyzer(prim)
-    # prim = sga.get_conventional_standard_structure()
-    # prim.to("poscar", filename="POSCAR-well_relaxed_KSnBi")
-
-    csld_class = CompressedSensingLatticeDynamicsWF(
-        prim,
-        symmetrize=False,
-        num_nn_dists=6,
-        supercells_per_displacement_distance=1,
-        force_diagonal_transformation=True,
-        do_shengbte=True,
-        shengbte_fworker="rees_the_fire_worker_haswell"
-        )
-    print("uuid")
-    print(csld_class.uuid)
-
-    wf = csld_class.get_wf()
-    print("trans mat")
-    print(csld_class.trans_mat)
-    print("nn dist")
-    print(csld_class.nn_dist)
-    print("supercell shortest direction (Angstroms)")
-    print(csld_class.supercell_smallest_dim)
-    print("supercell number of atoms")
-    print(csld_class.supercell.num_sites)
-    csld_class.supercell.to("poscar",
-                            filename="SPOSCAR-KSnBi_diagonal")
-
-    wf = add_tags(wf, ['csld', 'v1', 'rees',
-                       'pre-relaxed conventional si', 'diagonal supercell',
-                       'not symmetrized', 'ismear manually set to 0'])
-    wf = set_execution_options(wf, fworker_name="rees_the_fire_worker")
-    wf = add_modify_incar(wf,
-                          modify_incar_params={
-                              'incar_update': {
-                                  'ENCUT': 500,
-                                  'ISMEAR': 0,
-                                  'ISPIN': 1}})
-    #
-    # lpad = LaunchPad.auto_load()
-    # lpad.add_wf(wf)
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
new file mode 100644
index 000000000..43321a584
--- /dev/null
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -0,0 +1,264 @@
+# coding: utf-8
+from copy import deepcopy
+from typing import List, Dict, Optional
+
+from uuid import uuid4
+
+from pymatgen.transformations.advanced_transformations import (
+    CubicSupercellTransformation
+)
+from pymatgen.io.vasp.sets import MPStaticSet
+from pymatgen.core.structure import Structure
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+
+from fireworks import Workflow, Firework
+from atomate.utils.utils import get_logger
+from atomate.vasp.config import VASP_CMD, DB_FILE
+from atomate.vasp.fireworks.core import StaticFW
+from atomate.vasp.firetasks.parse_outputs import CSLDForceConstantsToDB
+from atomate.vasp.powerups import add_additional_fields_to_taskdocs
+from atomate.vasp.analysis.csld import generate_perturbed_supercells
+
+__author__ = "Rees Chang, Alex Ganose"
+__email__ = "rc564@cornell.edu, aganose@lbl.gov"
+__date__ = "July 2019"
+__csld_wf_version__ = 1.0
+
+logger = get_logger(__name__)
+
+_static_uis = {
+    "ADDGRID": True,  # Fast Fourier Transform grid
+    "LCHARG": False,
+    "ENCUT": 700,
+    "EDIFF": 1e-8,  # may need to tune this
+    "PREC": 'Accurate',
+    "LAECHG": False,
+    "LREAL": False,
+    "LASPH": True
+}
+
+# define shared constants
+_MAX_DISPLACEMENT = 0.1
+_MIN_DISPLACEMENT = 0.01
+_NUM_DISPLACEMENTS = 10
+_MIN_RANDOM_DISPLACEMENTS = None
+_CELLS_PER_DISPLACEMENT = 1
+_DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
+
+
+def get_lattice_dynamics_wf(
+    structure: Structure,
+    common_settings: Dict = None,
+    symprec: Optional[float] = None,
+    min_atoms: Optional[int] = None,
+    max_atoms: Optional[int] = None,
+    num_nn_dists: float = 5,
+    force_diagonal_transformation: bool = True,
+    max_displacement: float = _MAX_DISPLACEMENT,
+    min_displacement: float = _MIN_DISPLACEMENT,
+    num_displacements: int = _NUM_DISPLACEMENTS,
+    n_cells_per_displacement_distance: int = _CELLS_PER_DISPLACEMENT,
+    min_random_distance: Optional[float] = _MIN_RANDOM_DISPLACEMENTS,
+    dynamic_static_calcs: bool = False,
+    do_shengbte: bool = False,
+    shengbte_t_range: Optional[List[float]] = None,
+    shengbte_fworker: Optional[str] = None
+):
+    """
+    This workflow will calculate interatomic force constants and vibrational
+    properties using the hiPhive package.
+
+    A summary of the workflow is as follows:
+
+    1. Transform the input structure into a supercell
+    2. Transform the supercell into a list of supercells with all atoms
+       randomly perturbed from their original sites
+    3. Run static VASP calculations on each perturbed supercell to
+       calculate atomic forces.
+    4. Aggregate the forces and conduct the fit the force constants using
+       the minimization schemes in hiPhive.
+    5. Output the interatomic force constants, and phonon band structure and
+       density of states to the database.
+    6. Optional: Solve the lattice thermal conductivity using ShengBTE.
+
+    Args:
+        structure: Initial structure.
+        common_settings: Common settings dict.
+        symprec: Symmetry precision for symmetrizing the structure. If set to
+            ``None`` (the default), the structure will not be symmetrized.
+        min_atoms: Minimum number of atoms to constrain the supercell.
+        max_atoms: Maximum number of atoms to constrain the supercell.
+        num_nn_dists: Number of nearest neighbor distances that the shortest
+            direction of the supercell must be as long as.
+        force_diagonal_transformation: If True, the supercell
+            transformation will be constrained to have a diagonal
+            transformation matrix. If False, the supercell transformation
+            will not be constrained to be diagonal (resulting in a more
+            cubic supercell).
+        max_displacement: Maximum displacement distance for perturbing the
+            sites in Angstroms.
+        min_displacement: Minimum displacement distance for perturbing the
+            sites in Angstroms.
+        num_displacements: Number of unique displacement distances to
+            try, uniformly distributed between ``min_displacement`` and
+            ``max_displacement``.
+        n_cells_per_displacement_distance: Number of perturbed
+            structures to generate for each unique displacement distance.
+        min_random_distance: If None (default), then for a given perturbed
+            structure, all atoms will move the same distance from their original
+            locations. If float, then for a given perturbed structure, the
+            distances the atoms move will be uniformly distributed from a
+            minimum distance of ``min_random_distance`` to one of the
+            displacement distances uniformly sampled between
+            ``min_displacement`` and ``max_displacement``.
+        dynamic_static_calcs: If True and hiPhive fails to return all real
+             harmonic phonon frequencies on the first try, then the workflow
+             will dynamically create more static perturbed supercell
+             calculations with larger displacements to improve the fitting.
+        do_shengbte: If True and force constant fitting does not return
+            imaginary modes, then the workflow will dynamically create a
+            ShengBTE firework for calculating the lattice thermal conductivity.
+        shengbte_t_range: A list of temperatures at which to calculate the
+            lattice thermal conductivity using ShengBTE. If None (default),
+            then 300 K will be used.
+        shengbte_fworker: If None, the ShengBTE firework's fworker will be set
+            to all the previous fireworks' fworker. If str, the ShengBTE
+            firework's fworker will be set to shengbte_fworker.
+   """
+    common_settings = common_settings or _DEFAULT_SETTINGS
+    uis = deepcopy(_static_uis)
+    uis.update(common_settings.get("user_incar_settings", {}))
+
+    if force_diagonal_transformation is True and num_nn_dists == 5:
+        num_nn_dists = 6
+
+    if symprec is not None:
+        sga = SpacegroupAnalyzer(structure, symprec=symprec)
+        structure = sga.get_primitive_standard_structure()
+
+    st = CubicSupercellTransformation(
+        min_atoms,
+        max_atoms,
+        num_nn_dists,
+        force_diagonal_transformation=force_diagonal_transformation
+    )
+    supercell = st.apply_transformation(structure)
+
+    perturbed_supercells, disp_dists, fws = get_perturbed_supercell_fws(
+        supercell,
+        common_settings,
+        user_incar_settings=uis,
+        min_displacement=min_displacement,
+        max_displacement=max_displacement,
+        num_displacements=num_displacements,
+        min_random_distance=min_random_distance,
+        n_cells_per_displacement_distance=n_cells_per_displacement_distance,
+    )
+
+    logger.debug("Using {} displacements".format(len(disp_dists)))
+    logger.debug("Displacements: {}".format(disp_dists))
+
+    # Collect force constants from the DB and output on cluster
+    wf_meta = {"wf_uuid": str(uuid4()), "wf_name": "LatticeDynamicsWF"}
+    csld_fw = Firework(
+        CSLDForceConstantsToDB(
+            db_file=common_settings["DB_FILE"],
+            wf_uuid=wf_meta["wf_uuid"],
+            parent_structure=structure,
+            trans_mat=st.transformation_matrix.tolist(),
+            supercell_structure=supercell,
+            perturbed_supercells=perturbed_supercells,
+            disps=disp_dists,
+            force_diagonal_transformation=force_diagonal_transformation,
+            first_pass=True,
+            static_user_incar_settings=uis,
+            env_vars=common_settings,
+            dynamic_static_calcs=dynamic_static_calcs,
+            do_shengbte=do_shengbte,
+            shengbte_t_range=shengbte_t_range,
+            shengbte_fworker=shengbte_fworker
+        ),
+        name="Compressed Sensing Lattice Dynamics",
+        parents=fws[-len(perturbed_supercells):]
+    )
+    fws.append(csld_fw)
+
+    formula = structure.composition.reduced_formula
+    wf_name = "{} - compressed sensing lattice dynamics".format(formula)
+
+    wf = Workflow(fws, name=wf_name)
+    wf = add_additional_fields_to_taskdocs(
+        wf,  {"wf_meta": wf_meta}, task_name_constraint="VaspToDb"
+    )
+
+    return wf
+
+
+def get_perturbed_supercell_fws(
+    supercell: Structure,
+    common_settings: Optional[Dict] = None,
+    user_incar_settings: Optional[Dict] = None,
+    max_displacement: float = _MAX_DISPLACEMENT,
+    min_displacement: float = _MIN_DISPLACEMENT,
+    num_displacements: int = _NUM_DISPLACEMENTS,
+    n_cells_per_displacement_distance: int = _CELLS_PER_DISPLACEMENT,
+    min_random_distance: Optional[float] = _MIN_RANDOM_DISPLACEMENTS,
+) -> List[Firework]:
+    """
+    Get static calculations to calculate the forces on each perturbed supercell.
+
+    Args:
+        supercell: Parent supercell structure.
+        max_displacement: Maximum displacement distance for perturbing the
+            sites in Angstroms.
+        min_displacement: Minimum displacement distance for perturbing the
+            sites in Angstroms.
+        num_displacements: Number of unique displacement distances to
+            try, uniformly distributed between ``min_displacement`` and
+            ``max_displacement``.
+        n_cells_per_displacement_distance: Number of perturbed
+            structures to generate for each unique displacement distance.
+        min_random_distance: If None (default), then for a given perturbed
+            structure, all atoms will move the same distance from their original
+            locations. If float, then for a given perturbed structure, the
+            distances the atoms move will be uniformly distributed from a
+            minimum distance of ``min_random_distance`` to one of the
+            displacement distances uniformly sampled between
+            ``min_displacement`` and ``max_displacement``.
+        common_settings: Common settings dict
+        user_incar_settings: User incar settings override.
+
+    Returns:
+        A list of static fireworks.
+    """
+    user_incar_settings = user_incar_settings if user_incar_settings else {}
+
+    # Generate list of perturbed supercells
+    perturbed_supercells, disp_dists = generate_perturbed_supercells(
+        supercell,
+        min_displacement=min_displacement,
+        max_displacement=max_displacement,
+        num_displacements=num_displacements,
+        n_cells_per_displacement_distance=n_cells_per_displacement_distance,
+        min_random_distance=min_random_distance
+    )
+
+    fws = []
+    data = enumerate(zip(perturbed_supercells, disp_dists))
+    for i, (supercell, dist) in data:
+        name = "perturbed supercell, idx: {}, disp_val: {:.3f} static".format(
+            i, dist
+        )
+
+        vis = MPStaticSet(supercell, user_incar_settings=user_incar_settings)
+        static_fw = StaticFW(
+            supercell,
+            vasp_input_set=vis,
+            vasp_cmd=common_settings["VASP_CMD"],
+            db_file=common_settings["DB_FILE"],
+            name=name
+        )
+        static_fw.spec["displacement_value"] = dist
+        fws.append(static_fw)
+
+    return fws

From a74a2236f1f4c32cef2cb499e558a7994f215414 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:02:55 -0800
Subject: [PATCH 052/207] Remove old firetasks

---
 atomate/vasp/firetasks/parse_outputs.py | 765 +-----------------------
 1 file changed, 11 insertions(+), 754 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 794fecc97..488838577 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1,9 +1,12 @@
+<<<<<<< HEAD
+=======
+# coding: utf-8
+
+>>>>>>> 7a7f01df (Remove old firetasks)
 import json
 import os
-import shutil
 import re
 from collections import defaultdict
-from copy import deepcopy
 from datetime import datetime
 
 import numpy as np
@@ -13,18 +16,19 @@
 from monty.json import MontyEncoder, jsanitize
 from pydash.objects import has, get
 
-from atomate.vasp.analysis.csld import default_csld_options, \
-    default_csld_settings
 from atomate.vasp.config import DEFUSE_UNSUCCESSFUL
 >>>>>>> 816883c7 (Cleaned up code (made functions for CSLD firetask, adhered to PEP guidelines, etc.))
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 from fireworks.utilities.fw_serializers import DATETIME_HANDLER
 <<<<<<< HEAD
+<<<<<<< HEAD
 from monty.json import MontyEncoder, jsanitize
 from monty.os.path import zpath
 from pydash.objects import get, has
 =======
 from fireworks import Firework
+=======
+>>>>>>> 7a7f01df (Remove old firetasks)
 
 from pymatgen import Structure
 >>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
@@ -52,8 +56,11 @@
     EnergyTrend
 from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering, magnetic_deformation
 from pymatgen.command_line.bader_caller import bader_analysis_from_path
+<<<<<<< HEAD
 from pymatgen.io.vasp.sets import MPStaticSet
 >>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
+=======
+>>>>>>> 7a7f01df (Remove old firetasks)
 
 from atomate.common.firetasks.glue_tasks import get_calc_loc
 from atomate.utils.utils import env_chk, get_logger, get_meta_from_structure
@@ -1788,756 +1795,6 @@ def split_abc(var, var_name):
         coll = vaspdb.db["polarization_tasks"]
         coll.insert_one(polarization_dict)
 
-@explicit_serialize
-class CSLDForceConstantsToDB(FiretaskBase):
-    """
-    Used to aggregate atomic forces of perturbed supercells in compressed
-    sensing lattice dynamics (CSLD) workflow and generate/write interatomic
-    force constants up to 3rd order to file. The workflow uses a CSLD software
-    implemented by Zhou et al (https://github.com/LLNL/csld) and modified for
-    use in atomate (Aug 6, 2019: https://github.com/rees-c/csld).
-
-    TODO: Update this class once Fei's CSLD is modified correctly
-    TODO: Add to the summary inside 'run_CSLD()' as needed
-    TODO: Rename this class to something more accurate
-
-    Required parameters:
-        db_file (str): path to the db file that holds your tasks
-            collection specifying the database that the perturbed supercell
-            forces are stored and that CSLD results should be stored to
-        wf_uuid (str): auto-generated from CompressedSensingLatticeDynamicsWF,
-            used to make it easier to retrieve task docs
-        parent_structure (Structure): input (usually primitive) structure on
-            which CSLD is being done
-        perturbed_supercells (list of Structures): list of perturbed supercell
-            structures auto-generated from CompressedSensingLatticeDynamicsWF
-        trans_mat (3x3 nested list): supercell transformation matrix auto-
-            generated from CompressedSensingLatticeDynamicsWF
-        supercell_structure (Structure): supercell structure of parent_structure
-            auto-generated from CompressedSensingLatticeDynamicsWF
-        supercell_smallest_dim (float): length of shortest direction of the
-            supercell lattice, auto-generated from
-            CompressedSensingLatticeDynamicsWF
-        disps (list of floats): displacement values corresponding to
-            perturbed_supercells, auto-generated from
-            CompressedSensingLatticeDynamicsWF
-        force_diagonal_transformation (bool): Whether the transformation matrix
-            used to generate the supercell was diagonal (True) or not (False)
-        first_pass (boolean): indicator of whether this firetask has already
-            been attempted or if it is automatically running a second time
-            with larger perturbations
-        static_user_incar_settings (dict): incar settings used in static
-            calculations in CompressedSensingLatticeDynamicsWF
-        env_vars (dict): environmental variables used in static calculations in
-            CompressedSensingLatticeDynamicsWF
-
-    Optional parameters:
-        dynamic_static_calcs (bool): If True, dynamically create more static
-            perturbed supercell calculations with larger displacements if CSLD
-            fails. Default: False.
-        do_shengbte (bool): If True, dynamically create a ShengBTE firework
-            for computing lattice thermal conductivity if CSLD yields a good
-            solution. Default: False.
-        shengbte_t_range (bool): If True, pass to the ShengBTEToDB firetask
-            that lattice thermal conductivity should be calculated for 100 K to
-            1000 K in steps of 100 K. If False (default), only calculate at
-            300 K.
-        shengbte_fworker (str): If None (default), set the ShengBTE fworker to
-            the previous f_worker. Else, set it to the specified fworker
-            (allowing the user to run ShengBTE with different Fireworks
-            configurations than used to run the VASP static calculations).
-    """
-
-    logger = get_logger(__name__)
-
-    required_params = [
-        "db_file", "wf_uuid", "parent_structure",
-        "perturbed_supercells", "trans_mat", "supercell_structure",
-        "supercell_smallest_dim", "disps", "force_diagonal_transformation",
-        "first_pass", "static_user_incar_settings", "env_vars"
-        ]
-
-    optional_params = [
-        "dynamic_static_calcs", "do_shengbte", "shengbte_t_range",
-        "shengbte_fworker"
-        ]
-
-    @staticmethod
-    def random_search(max_iter):
-        """
-        Generates a tuple of cluster diameter, max order, and submodel1 input
-        settings for CSLD using a random search. The length of each returned
-        list of settings is the number of total settings to try.
-
-        Args:
-            max_iter (int): Number of settings to try
-
-        Returns:
-            cluster_diam_settings (list[str]): List of cluster diameter settings
-            max_order_settings (list[int]): List of max order settings
-            submodel1_settings (list[str]): List of submodel1 settings
-        """
-        import random
-
-        if max_iter % 2 != 0 or max_iter <= 0:
-            raise AttributeError('maxIter must be even.')
-
-        cluster_diam_settings = []
-        for _ in range(max_iter):
-            pair_diam = random.uniform(8, 12) #self["supercell_smallest_dim"])
-            triplet_diam = random.uniform(5.5, 7)
-            quadruplet_diam = random.uniform(triplet_diam * 0.6, triplet_diam)
-
-            cluster_diam_settings += [
-                str(pair_diam) + ' ' + str(triplet_diam) + ' ' + str(
-                    quadruplet_diam)]
-
-        max_order_settings = [3] * int(max_iter / 2) + [4] * int(max_iter / 2)
-        submodel1_settings = ['anh 0 1 2 3'] * int(max_iter / 2) + \
-                             ['anh 0 1 2 3 4'] * int(max_iter / 2)
-
-        return cluster_diam_settings, max_order_settings, submodel1_settings
-
-    def collect_successful_static_calcs_results(self, tasks):
-        """
-        Search a database's tasks collection for successful static calculations
-        and return a list of forces for each supercell
-
-        Args:
-            tasks (MongoDB collection): MongoDB collection containing static
-                perturbed supercells calculations
-
-        Returns:
-            supercells_forces (list[np.array]): List of forces for each
-                successful static perturbed supercell calculation
-            successful_disps (list[float]): List of displacement distances for
-                each successful static perturbed supercell calculation
-        """
-        uuid = self["wf_uuid"]
-        formula_pretty = self[
-            "parent_structure"].composition.reduced_formula
-        task_label = 'static'
-        supercells_dicts = list(
-            tasks.find({"wf_meta.wf_uuid": uuid,
-                        "task_label": {"$regex": task_label},
-                        "formula_pretty": formula_pretty,
-                        "state": 'successful'},
-                       ['task_id',
-                        'task_label',
-                        'output.forces']))
-        # list of dicts where each dict contains a task_id and a list of forces
-        #   for each supercell
-
-        supercells_forces = []
-        supercells_task_labels = []
-        successful_disps = []  # displacement values of successful static calcs
-        for supercell_dict in supercells_dicts:
-            # List of np.ndarrays where each np.ndarray is a matrix of forces
-            #  for a perturbed supercell
-            supercells_forces += [
-                np.asarray(supercell_dict['output']['forces'])]
-
-            # Supercell task labels
-            # e.g. 'InSb-perturbed supercell, idx: 0, disp_val: 0.010, static'
-            supercells_task_labels += [supercell_dict['task_label']]
-
-            # Store list of displacement values whose corresponding perturbed
-            # supercells successfully ran
-            successful_disp = re.search('disp_val: (\d+.\d+)',
-                                        supercell_dict['task_label'])
-            successful_disps += [successful_disp.group(1)]
-
-        # Sort the forces by their task label so CSLD correctly matches forces
-        # with their corresponding perturbed supercell
-        supercells_zip = sorted(
-            zip(supercells_task_labels, supercells_forces),
-            key=lambda pair: pair[0])
-        supercells_forces = [supercells_forces for
-                             (supercells_task_labels, supercells_forces) in
-                             supercells_zip]
-
-        return supercells_forces, successful_disps
-
-    def set_params(self, iteration_number, disps, cluster_diam,
-                   max_order, submodel1, export_sbte, supercells_forces,
-                   **kwargs):
-        """
-        This function deals with creating all the files, directories, and input
-        parameters necessary for running CSLD.
-
-        Specifically, it will save the transformation matrix (sc.txt) and parent
-        structure (POSCAR) in the current directory, create a folder for the
-        current iteration (e.g. Si_supercell_iter0) with subdirectories
-        (e.g. 'disp0.010') for each perturbed supercell. POSCARs of each
-        perturbed supercell is written inside the corresponding subdirectory.
-        Next, all of CSLD's input parameters are automatically generated in a
-        format readable by CSLD and then saved to the class' dictionary.
-
-        Args:
-            disps (list of str or floats): list of displacement distances for
-                perturbed supercells that ran successfully
-            iteration_number (int): current iteration (0-indexed) of the CSLD
-                grid or random search
-            cluster_diam (str): Space-separated string containing the spherical
-                length cutoffs for pair, triplet, and quadruplet interactions
-                 for CSLD (e.g. '11 6.5 5.0')
-            max_order (int): Max order of interatomic force constants to
-                consider (up to 6th order)
-            submodel1 (str): Anharmonicity orders to consider (e.g.
-                'anh 0 1 2 3')
-            export_sbte (str): Space-separated parameters for exporting CSLD's
-                interatomic force constants into a format readable by ShengBTE.
-                The first 3 numbers are the size of the supercell for which
-                interatomic force constants are exported. The next numbers are
-                the force constant orders to consider. E.g. To output 2nd and
-                3rd order force constants for a 5x5x5 supercell, the
-                corresponding string must be '5 5 5 2 3'.
-            supercells_forces (list[np.array]): List of numpy arrays containing
-                forces for each static perturbed supercell calculation
-            kwargs: Any other CSLD settings that the user desires to update
-                from the default values (as found in atomate.vasp.analysis.csld)
-        """
-        from configparser import ConfigParser
-        supercell_folder = self["parent_structure"].composition.reduced_formula + \
-                           "_supercell_iter" + str(iteration_number)
-
-        # Remove supercell_folder if it already exists, then make a new one
-        if os.path.exists(supercell_folder) and os.path.isdir(supercell_folder):
-            shutil.rmtree(supercell_folder)
-        os.mkdir(supercell_folder)
-
-        # Save transformation matrix, supercell POSCAR, and parent structure
-        #   POSCAR to file
-        np.savetxt(supercell_folder + "/sc.txt", self["trans_mat"], fmt="%.0f",
-                   delimiter=" ")
-        self["supercell_structure"].to("poscar",
-                                       filename=supercell_folder + "/SPOSCAR")
-        self["parent_structure"].to("poscar",
-                                    filename=supercell_folder + "/POSCAR")
-
-        # Create folders for perturbed supercell POSCARS and force.txt's
-        # (e.g. "Si_supercell_iter0/disp0.010")
-        disp_folders = []
-        csld_traindat_disp_folders = ''
-        for idx, disp in enumerate(disps):
-            disp_folder = supercell_folder + '/disp{:.2f}'.format(float(disp))
-            disp_folders += [disp_folder] # list of folder paths
-            csld_traindat_disp_folders += ' ' + str(disp_folder)
-            if os.path.exists(disp_folder) and os.path.isdir(disp_folder):
-                shutil.rmtree(disp_folder)
-            os.mkdir(disp_folder)
-            self["perturbed_supercells"][idx].to("poscar",
-                                                 filename=disp_folder + "/POSCAR")
-
-        # training>traindat1 setting for CSLD input
-        csld_traindat_string = supercell_folder + '/SPOSCAR'
-        csld_traindat_string += csld_traindat_disp_folders
-
-        # Create ConfigParser of all CSLD input settings
-        csld_settings_dict = deepcopy(default_csld_settings)
-
-        # Update default settings if specified
-        user_csld_settings = kwargs
-        if user_csld_settings is not None:
-            # recursively update settings dict
-            for k, v in user_csld_settings:
-                csld_settings_dict[k].update(v)
-
-        # update CSLD settings with dynamic options
-        # original structure poscar
-        csld_settings_dict["structure"]["prim"] = supercell_folder + '/POSCAR'
-        csld_settings_dict["model"].update({
-            'max_order': max_order,
-            'cluster_diameter': cluster_diam,
-            'cluster_filter':
-                r"lambda cls: ((cls.order_uniq <= 2) or (cls.bond_counts(2.9) "
-                r">= 2)) and cls.is_small_in('" + supercell_folder + "/sc.txt')"
-        })
-
-        # directories of unperturbed followed by perturbed supercell poscars
-        # e.g., 'Si_supercell_iter0/SPOSCAR Si_supercell_iter0/disp0.01
-        #           Si_supercell_iter0/disp0.05'
-        csld_settings_dict["training"]['traindat1'] = csld_traindat_string
-        csld_settings_dict['fitting']['submodel1'] = submodel1
-
-        # e.g., '5 5 5 2 3' is a 5x5x5 supercell
-        csld_settings_dict['export_potential'] = {'export_shengbte':
-                                                      export_sbte}
-
-        csld_settings = ConfigParser()
-        csld_settings.read_dict(csld_settings_dict)
-        csld_options = deepcopy(default_csld_options)
-
-        self["csld_settings"] = csld_settings
-        self["csld_options"] = csld_options
-        self["forces_paths"] = disp_folders  # Paths to perturbed supercell folders
-
-        # Create force.txt files for perturbed supercells
-        for supercell_idx, supercell_force in enumerate(supercells_forces):
-            path = self["forces_paths"][supercell_idx]
-            np.savetxt(path + "/force.txt", supercell_force, fmt='%.6f')
-
-    def run_csld(self, iter):
-        """
-        Run CSLD, check for imaginary frequencies, and generate a summary of the
-        results.
-
-        Args:
-            iter (int): Current iteration of the grid/random search over CSLD
-                input parameters (0-indexed)
-        Return:
-            summary (dict): Summary of the results from CSLD
-        """
-        # Perform csld minimization now
-        logger.info("Running CSLD...")
-        from atomate.vasp.analysis.csld import csld_main
-        rel_err, freq_matrix = csld_main(self["csld_options"],
-                                         self["csld_settings"])
-
-        freq_matrix = np.asarray(freq_matrix)
-
-        # CHECK FOR IMAGINARY PHONON MODES
-        # For imaginary frequencies, w^2 is negative.
-        # CSLD handles these as w = sign(sqrt(abs(w^2)), w^2).
-        # i.e. if w < 0, it is imaginary.
-        # Here, we consider phonon frequencies < -1 meV to be imaginary
-        #  (numerical noise can sometimes make frequencies slightly negative,
-        #   so we ignore these)
-        imaginary_idx = freq_matrix < -1
-        imaginary_freqs = freq_matrix[imaginary_idx]
-        logger.info('IMAGINARY FREQUENCIES: \n{}'.format(imaginary_freqs))
-        num_imaginary_bands = np.sum(np.any(imaginary_idx, axis=1))
-        logger.info('Number of imaginary bands: {}'.format(num_imaginary_bands))
-        if np.any(imaginary_freqs):
-            most_imaginary_freq = np.amin(imaginary_freqs)
-        else:
-            most_imaginary_freq = 0
-        print(most_imaginary_freq)
-
-        if num_imaginary_bands == 0:
-            not_converged = False
-
-        # Save to DB
-        summary = {
-            "date": datetime.now(),
-            "formula": self["parent_structure"].formula,
-            "formula_pretty": self[
-                "parent_structure"].composition.reduced_formula,
-            "parent_structure": self["parent_structure"].as_dict(),
-            "supercell_structure": self["supercell_structure"].as_dict(),
-            "supercell_transformation_matrix": self["trans_mat"],
-            "wf_meta": {"wf_uuid": self["wf_uuid"]},
-
-            # Store relevant CSLD settings
-            "iteration": iter,
-            "cluster_diam": self["csld_settings"]["model"][
-                "cluster_diameter"],
-            "max_order": self["csld_settings"]["model"]["max_order"],
-            "submodel1": self["csld_settings"]["fitting"]["submodel1"],
-            "export_potential": self["csld_settings"]["export_potential"][
-                "export_shengbte"],
-
-            # Store CSLD results
-            "cross_val_error": float(rel_err),
-            "num_imaginary_modes": int(num_imaginary_bands),
-            "most_imaginary_freq": float(most_imaginary_freq),
-            "imaginary_freq_sum": float(sum(imaginary_freqs))
-        }
-
-        # Store latest CSLD input settings tried
-        # TODO: If desired, store this information in a database to keep
-        #   track of what settings work and what doesn't for different materials
-        latest_settings = {str(self["convergence_info"]["iteration"]):
-                               {self["csld_settings"]["model"]["max_order"],
-                                self["csld_settings"]["fitting"][
-                                    "submodel1"],
-                                self["csld_settings"]["export_potential"][
-                                    "export_shengbte"]}}
-        self["convergence_info"]["iteration"] = iter
-        self["convergence_info"]["settings_tried"] += [latest_settings]
-        self["convergence_info"]["cross_val_errors"] += [rel_err]
-        self["convergence_info"]["most_imaginary_freqs"] += [
-            most_imaginary_freq]
-        self["convergence_info"]["imaginary_freqs_sum"] += [
-            sum(imaginary_freqs)]
-
-        return summary
-
-    def add_sbte_fw(self, fw_spec):
-        """
-        This function dynamically creates a ShengBTE firework for calculating
-        the lattice thermal conductivity matrix.
-
-        Args:
-            fw_spec (dict): The fw_spec for the CSLD firework.
-
-        Returns:
-            FWAction: Dynamically adds a ShengBTE Firework to the workflow
-        """
-        shengbte_fw = Firework(
-            ShengBTEToDB(
-                parent_structure=self["parent_structure"],
-                shengbte_cmd=">>shengbte_cmd<<",
-                db_file=self["db_file"],
-                wf_uuid=self["wf_uuid"],
-                t_range=self.get("shengbte_t_range", False),
-                trans_mat=self["trans_mat"]
-            ),
-            name="ShengBTE for Lattice Thermal Conductivity"
-        )
-
-        # Set the ShengBTE fworker
-        if isinstance(self["shengbte_fworker"], str):
-            shengbte_fw.spec["_fworker"] = self["shengbte_fworker"]
-        else:
-            shengbte_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
-
-        # Pass the CSLD launcher path to the ShengBTE FW
-        CSLD_path = self.get("path", os.getcwd())
-        shengbte_fw.spec["successful_CSLD_path"] = CSLD_path
-
-        # Add tags
-        if fw_spec.get("tags", None):
-            shengbte_fw.spec["tags"] = fw_spec["tags"]
-
-        return FWAction(additions=shengbte_fw)
-
-    def add_more_static_calcs(self, successful_disps, fw_spec):
-        """
-        This function will dynamically create more static perturbed supercell
-        calculations with displacement distances of 0.12, 0.14, 0.16, 0.18, and
-        0.20, and also append another CSLD Firework. A 'first_pass=False'
-        argument will be passed into the CSLD Firework to ensure that more
-        static perturbed supercell calculations will not be created.
-
-        Args:
-            successful_disps (list[float]): List of displacement distances of
-                previous successful static perturbed supercell calculations
-            fw_spec (dict): Firework spec of the first CSLD Firework
-
-        Returns:
-            FWAction: Dynamically adds a more static calculations and a CSLD
-                Firework to the workflow
-        """
-
-        new_fws = []
-
-        # Create new perturbed supercells
-        from atomate.vasp.analysis.csld import generate_perturbed_supercells
-        more_perturbed_supercells, more_disps = generate_perturbed_supercells(
-            self["supercell_structure"],
-            min_displacement=0.12,
-            max_displacement=0.2,
-            num_displacements=5
-            )
-
-        # Create new static FWs
-        for idx, more_perturbed_supercell in enumerate(
-                more_perturbed_supercells):
-            name = "perturbed supercell, idx: {}, disp_val: {:.3f},".format(
-                idx + len(self["perturbed_supercells"]),
-                more_disps)
-            static_vis = MPStaticSet(more_perturbed_supercell,
-                                     user_incar_settings=self[
-                                         "static_user_incar_settings"])
-
-            from atomate.vasp.fireworks.core import StaticFW
-            new_static_fw = StaticFW(
-                more_perturbed_supercell,
-                vasp_input_set=static_vis,
-                vasp_cmd=self["env_vars"]["VASP_CMD"],
-                db_file=self["env_vars"]["DB_FILE"],
-                name=name + " static"
-            )
-            new_static_fw.spec["_fworker"] = fw_spec["_fworker"]
-            new_static_fw.spec["displacement_value"] = more_disps[idx]
-            if fw_spec.get("tags", None):
-                new_static_fw.spec["tags"] = fw_spec["tags"]
-            new_fws.append(new_static_fw)
-
-        # Create new CSLD FW
-        # static_user_incar_settings and env_vars can be None since we
-        # are done trying more static calculations.
-        new_csld_fw = Firework(
-            CSLDForceConstantsToDB(
-                db_file=self["env_vars"]["DB_FILE"],
-                wf_uuid=self["wf_uuid"],
-                name='CSLDForceConstantsToDB',
-                parent_structure=self["parent_structure"],
-                trans_mat=self["trans_mat"],
-                supercell_structure=self["supercell_structure"],
-                supercell_smallest_dim=self["supercell_smallest_dim"],
-                perturbed_supercells=self[
-                                         "perturbed_supercells"] + more_perturbed_supercells,
-                disps=successful_disps + more_disps,
-                force_diagonal_transformation=self.force_diagonal_transformation,
-                first_pass=False,
-                do_shengbte=self.get("do_shengbte", False),
-                shengbte_t_range=self.get("shengbte_t_range", False),
-                shengbte_fworker=self.get("shengbte_fworker", None),
-                static_user_incar_settings=None,
-                env_vars=None
-            ),
-            name="Compressed Sensing Lattice Dynamics",
-            parents=new_fws[-len(more_perturbed_supercells):]
-        )
-        new_csld_fw.spec["_fworker"] = fw_spec.get("_fworker", None)
-        if fw_spec.get("tags", None):
-            new_csld_fw.spec["tags"] = fw_spec["tags"]
-        new_fws.append(new_csld_fw)
-
-        # Dynamically add new fireworks to the workflow
-        return FWAction(additions=new_fws)
-
-    def run_task(self, fw_spec):
-        # Connect to the database
-        db_file = env_chk(self.get("db_file"), fw_spec)
-        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        tasks = mmdb.collection
-
-        # Store information related to convergence of CSLD
-        iteration = 0
-        not_converged = True
-        max_iter = 2
-        summaries = []
-        self['convergence_info'] = {
-            'iteration': iteration,
-            'settings_tried': [],
-            'cross_val_errors': [],
-            'most_imaginary_freqs': [],
-            'imaginary_freqs_sum': []
-        }
-
-        # Set list of parameter settings to try (i.e. grid search settings)
-        # TODO: FILL THESE IN FURTHER WITH SETTINGS TO TRY, IN THE ORDER YOU WANT
-        #  TO TRY THEM. (May want to generate this with a grid search, depending
-        #  on what settings seem to work on many materials)
-        cluster_diam_settings = ['11 6.5 5.0',
-                                 '9 6.5 5.0']
-        max_order_settings = [3] * len(cluster_diam_settings)
-        submodel1_settings = ['anh 0 1 2 3'] * len(cluster_diam_settings)
-        if self["force_diagonal_transformation"]:
-            export_sbte_string = str(self["trans_mat"][0][0]) + ' ' + \
-                                 str(self["trans_mat"][1][1]) + ' ' + \
-                                 str(self["trans_mat"][2][2]) + ' 2 3'
-        else:
-            export_sbte_string = '5 5 5 2 3'
-        export_sbte_settings = [export_sbte_string] * len(cluster_diam_settings)
-        if self["first_pass"] is False:
-            # If we are running CSLD a second time (i.e. with larger displaced
-            #  supercells, then duplicate all the settings to try with 4th order
-            #  instead of 3rd order anharmonicity
-            max_order_settings += [4] * len(cluster_diam_settings)
-            cluster_diam_settings += cluster_diam_settings
-            submodel1_settings += submodel1_settings
-            export_sbte_settings += export_sbte_settings
-
-        logger.info('Cluster diameter settings to search over: '
-                    '{}'.format(cluster_diam_settings))
-        logger.info('Max order settings to search over: '
-                    '{}'.format(max_order_settings))
-        logger.info('"submodel1" settings to search over: '
-                    '{}'.format(submodel1_settings))
-
-        # Collect forces and successful displacement values from static
-        # perturbed supercell calculations
-        supercells_forces, successful_disps = \
-            self.collect_successful_static_calcs_results(tasks)
-
-        # Iterate over CSLD settings until real solutions are found or max
-        # iterations is reached.
-        while not_converged and iteration < max_iter:
-            # For the current iteration, set the CSLD parameters and create the
-            # necessary folders/files
-            self.set_params(iteration,
-                            successful_disps,
-                            cluster_diam_settings[iteration],
-                            max_order_settings[iteration],
-                            submodel1_settings[iteration],
-                            export_sbte_settings[iteration],
-                            supercells_forces)
-            self["csld_options"]["pdfout"] = 'plots' + str(iteration) + '.pdf'
-
-            # Run CSLD, check for imaginary phonon frequencies, and generate a
-            # summary of results
-            summary = self.run_csld(iteration)
-
-            if fw_spec.get("tags", None):
-                summary["tags"] = fw_spec["tags"]
-            summaries.append(summary)
-
-            iteration += 1
-
-        # Store the summaries in a "compressed_sensing_lattice_dynamics"
-        #  collection of the database (if it does not exist, it will be created)
-        mmdb.collection = mmdb.db["compressed_sensing_lattice_dynamics"]
-        mmdb.collection.insert(summaries)
-
-        # Output lowest validation error and corresponding CSLD input settings
-        best_idx = self["convergence_info"]["cross_val_errors"].index(
-            min(self["convergence_info"]["cross_val_errors"]))
-        logger.info("The lowest error was {} percent.".format(
-            min(self["convergence_info"]["cross_val_errors"])))
-        logger.info("The corresponding settings were: {}".format(
-            self["convergence_info"]["settings_tried"][best_idx]))
-
-        if not_converged is False:
-            # If CSLD converged to 0 imaginary frequencies
-            logger.info("Compressed Sensing Lattice Dynamics calculation "
-                        "complete.")
-
-            # Dynamically create the ShengBTE Firework
-            if self.get("do_shengbte", False):
-                self.add_sbte_fw(fw_spec)
-        else:
-            logger.info("Compressed Sensing Lattice Dynamics calculation "
-                        "failed. Max iterations was reached.")
-            if self["parent_structure"].num_sites > 5 and self["first_pass"] \
-                    and self.get("dynamic_static_calcs", False):
-                logger.info("Compressed Sensing Lattice Dynamics calculation "
-                            "failed. Max iterations was reached. Creating "
-                            "larger displacements and trying again.")
-
-                self.add_more_static_calcs(successful_disps, fw_spec)
-
-            else:
-                raise TimeoutError("The workflow was unable to find a solution "
-                                   "to CSLD for this material.")
-
-@explicit_serialize
-class ShengBTEToDB(FiretaskBase):
-    #TODO: Rename this class to something more accurate (since this class only
-    #  calculates the lattice thermal conductivity matrix even though ShengBTE
-    #  has more capabilities)
-    """
-    Run ShengBTE and output the lattice thermal conductivity matrix to database.
-
-    Required parameters:
-        parent_structure (Structure): material that ShengBTE is being run on
-        db_file (str): path to the db file that holds your tasks
-            collection specifying the database that ShengBTE results should be
-            stored to
-        shengbte_cmd (str): should be set to "<<shengbte_cmd>>"
-        wf_uuid (str): passed from the CSLDForceConstantsToDB firetask,
-            used for storing task docs
-    Optional parameters:
-        t_range (bool): If True, run lattice thermal conductivity calculations
-            at 100 K through 1000 K at steps of 100 K.
-    """
-
-    required_params = ["parent_structure", "shengbte_cmd", "db_file",
-                       "wf_uuid", "trans_mat", "force_diagonal_transformation"]
-    optional_params = ["t_range"]
-
-    def run_task(self, fw_spec):
-        from atomate.utils.utils import env_chk
-        import subprocess
-        from pymatgen.io.vasp.inputs import Kpoints
-        import six
-        import shlex
-
-        # Generate CONTROL file (a FORTRAN input file for ShengBTE)
-        from pymatgen.io.shengbte import Control
-        qpts = Kpoints.automatic_density(self["parent_structure"], 50000)
-        unique_elements = [
-            str(self["parent_structure"].types_of_specie[i])
-            for i in range(len(self["parent_structure"].types_of_specie))
-        ]
-        nonunique_elements_list = [
-            str(self["parent_structure"].species[i])
-            for i in range(len(self["parent_structure"].species))
-        ]
-        element_to_number = {ele: idx + 1 for (idx, ele) in
-                             enumerate(unique_elements)}
-        shengbte_control_dict = {
-            'nelements': self["parent_structure"].ntypesp,
-            'natoms': self["parent_structure"].num_sites,
-            'ngrid': qpts.kpts[0],
-            'norientations': 0,
-
-            'lfactor': 0.1,  # 0.1 nm = 1 Ang
-            'lattvec': self["parent_structure"].lattice.matrix.tolist(),
-            'elements': unique_elements,
-            'types': [element_to_number[ele] for ele in
-                      nonunique_elements_list],
-            'positions': [
-                self["parent_structure"].sites[i]._frac_coords.tolist()
-                for i in range(self["parent_structure"].num_sites)
-            ],
-            't': 300,
-            'scalebroad': 0.5,
-            'nonanalytic': False,
-            'isotopes': False,
-        }
-        if self["force_diagonal_transformation"]:
-            shengbte_control_dict['scell'] = [self["trans_mat"][0][0],
-                                              self["trans_mat"][1][1],
-                                              self["trans_mat"][2][2]]
-        else:
-            shengbte_control_dict['scell'] = [5, 5, 5]
-        if self["t_range"]:
-            shengbte_control_dict['t_min'] = 100
-            shengbte_control_dict['t_max'] = 1000
-            shengbte_control_dict['t_step'] = 100
-        io = Control.from_dict(shengbte_control_dict)
-        io.to_file()  # writes CONTROL file to current directory
-
-        # Copy force constants from previous CSLD firework
-        force_constants_path = fw_spec["successful_CSLD_path"]
-        shutil.copy(force_constants_path+"/FORCE_CONSTANTS_2ND", os.getcwd())
-        shutil.copy(force_constants_path+"/FORCE_CONSTANTS_3RD", os.getcwd())
-
-        # Run ShengBTE
-        shengbte_cmd = env_chk(self["shengbte_cmd"], fw_spec)
-        if isinstance(shengbte_cmd, six.string_types):
-            shengbte_cmd = os.path.expandvars(shengbte_cmd)
-            shengbte_cmd = shlex.split(shengbte_cmd)
-        shengbte_cmd = list(shengbte_cmd)
-        logger.info("Running command: {}".format(shengbte_cmd))
-        with open("shengbte.out", 'w') as f_std, \
-                open("shengbte_err.txt", "w", buffering=1) as f_err:
-            # use line buffering for stderr
-            return_code = subprocess.call(shengbte_cmd, stdout=f_std, stderr=f_err)
-        logger.info("Command {} finished running "
-                    "with returncode: {}".format(shengbte_cmd, return_code))
-        if return_code==1:
-            raise RuntimeError("Running ShengBTE failed. Check "
-                               "'shengbte_err.txt' in the launch_dir for "
-                               "details.")
-
-        try:
-            # Store lattice thermal conductivity matrix in the database
-            db_file = env_chk(self.get("db_file"), fw_spec)
-            mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-            if self["t_range"]:
-                temps = np.linspace(100, 1000, 10)
-            else:
-                temps = [300]
-
-            # Save to DB
-            summaries = []
-            for temp in temps:
-                # xx, xy, xz, yx, yy, yz, zx, zy, zz
-                flattened_kappa = np.loadtxt(
-                    'T'+str(int(temp))+'K/BTE.kappa_tensor')[1][1:]
-                flattened_kappa = flattened_kappa.reshape((3, 3)).tolist()
-                summary = {
-                    "date": datetime.now(),
-                    "temperature": temp,
-                    "parent_structure": self["parent_structure"].as_dict(),
-                    "wf_meta": {"wf_uuid": self["wf_uuid"]},
-                    str(temp)+" K": {"flattened_kappa": flattened_kappa}
-                }
-                if fw_spec.get("tags", None):
-                    summary["tags"] = fw_spec["tags"]
-                summaries.append(summary)
-
-            mmdb.collection = mmdb.db["sheng_bte"]
-            mmdb.collection.insert(summaries)
-        except:
-            raise FileNotFoundError('BTE.kappa_tensor was not output from '
-                                    'ShengBTE.')
-
 
 # the following definitions for backward compatibility
 class VaspToDbTask(VaspToDb):

From 1a4bb22c7a8b04be27b8b9ad59ada27659177b34 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:03:14 -0800
Subject: [PATCH 053/207] Add ShengBTE command to config

---
 atomate/vasp/config.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/atomate/vasp/config.py b/atomate/vasp/config.py
index 8a842d353..d5285726a 100644
--- a/atomate/vasp/config.py
+++ b/atomate/vasp/config.py
@@ -11,6 +11,7 @@
 VASP_CMD = ">>vasp_cmd<<"
 VDW_KERNEL_DIR = ">>vdw_kernel_dir<<"
 DB_FILE = ">>db_file<<"
+SHENGBTE_CMD = ">>shengbte_cmd<<"
 ADD_WF_METADATA = True
 LOBSTER_CMD = ">>lobster_cmd<<"
 

From 1db2992f6c587848b9387eb3908c7520c2ec7923 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:04:01 -0800
Subject: [PATCH 054/207] Add first pass at lattice_dynamics firetasks

---
 atomate/vasp/firetasks/lattice_dynamics.py | 437 +++++++++++++++++++++
 1 file changed, 437 insertions(+)
 create mode 100644 atomate/vasp/firetasks/lattice_dynamics.py

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
new file mode 100644
index 000000000..e99e21671
--- /dev/null
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -0,0 +1,437 @@
+import os
+import shlex
+
+from pathlib import Path
+
+from uuid import uuid4
+
+from datetime import datetime
+
+from monty.serialization import dumpfn, loadfn
+from monty.dev import requires
+
+from atomate.utils.utils import get_logger, env_chk
+from atomate.vasp.analysis.lattice_dynamics import (
+    fit_force_constants,
+    get_cutoffs,
+)
+from atomate.vasp.analysis.phonopy import (
+    get_phonon_dos,
+    get_phonon_band_structure,
+    get_line_mode_phonon_band_structure,
+)
+from atomate.vasp.database import VaspCalcDb
+from atomate.vasp.workflows.base.lattice_dynamics import (
+    MAX_N_IMAGINARY,
+    MAX_IMAGINARY_FREQ,
+    IMAGINARY_TOL,
+    FIT_METHOD,
+    DEFAULT_TEMPERATURE,
+    MESH_DENSITY)
+from fireworks import explicit_serialize, FiretaskBase, FWAction
+import numpy as np
+
+from pymatgen import Structure
+from pymatgen.io.ase import AseAtomsAdaptor
+from pymatgen.io.shengbte import Control
+from pymatgen.transformations.standard_transformations import (
+    SupercellTransformation,
+)
+
+try:
+    import hiphive
+except ImportError:
+    hiphive = False
+
+
+__author__ = "Alex Ganose"
+__email__ = "aganose@lbl.gov"
+
+logger = get_logger(__name__)
+
+
+@explicit_serialize
+class CollectPerturbedStructures(FiretaskBase):
+    """
+    Aggregate the structures and forces of perturbed supercells. Requires a
+    wf_uuid from which all perturbed static calculations will be compiled. The
+    initial structure and supercell transformation matrix will be extracted from
+    the perturbed structure tasks.
+
+    Required parameters:
+        db_file (str): Path to DB file for the database that contains the
+            perturbed structure calculations.
+        wf_uuid (str): Workflow unique identifier.
+    """
+
+    required_params = ["db_file", "wf_uuid"]
+
+    def run_task(self, fw_spec):
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+        tasks = mmdb.collection
+
+        query = {
+            "wf_meta.wf_uuid": self["wf_uuid"],
+            "task_label": {"$regex": "perturbed static"},
+            "state": "successful",
+        }
+        projection = ["output.structure", "output.forces", "transformations"]
+
+        logger.info("Fetching structure and forces data")
+        results = list(tasks.find(query, projection))
+
+        logger.info("Found {} perturbed structures".format(len(results)))
+        all_structures = []
+        all_forces = []
+        for result in results:
+            structure = Structure.from_dict(result["output"]["structure"])
+            forces = np.asarray(result["output"]["forces"])
+            all_structures.append(structure)
+            all_forces.append(forces)
+
+        if len(all_structures) == 0:
+            raise RuntimeError(
+                "Could not find any perturbed structures for workflow uuid: "
+                "{}".format(self["wf_uuid"])
+            )
+        else:
+            transformation = results[-1]["transformations"][0]
+            t_class = transformation["@class"]
+            if t_class != "SupercellTransformation":
+                raise ValueError(
+                    "Expecting SupercellTransformation not {}".format(t_class)
+                )
+            structure = Structure.from_dict(transformation["input_structure"])
+            supercell_matrix = transformation["deformation"]
+
+        # regenerate pure supercell structure
+        st = SupercellTransformation(supercell_matrix)
+        supercell_structure = st.apply_transformation(structure)
+
+        structure_data = {
+            "structure": structure,
+            "supercell_structure": supercell_structure,
+            "supercell_matrix": supercell_matrix,
+        }
+
+        logger.info("Writing structure and forces data.")
+        dumpfn(all_structures, "perturbed_structures.json")
+        dumpfn(all_forces, "perturbed_forces.json")
+        dumpfn(structure_data, "structure_data.json")
+
+
+@requires(hiphive, "hiphive is required for lattice dynamics workflow")
+@explicit_serialize
+class FitForceConstants(FiretaskBase):
+    """
+    Used to aggregate atomic forces of perturbed supercells in and fit
+    force constants using hiPhive. Requires "perturbed_structures.json",
+    "perturbed_forces.json", and "structure_data.json" files to be present
+    in the current working directory.
+
+    Optional parameters:
+        cutoffs (Optional[list[list]]): A list of cutoffs to trial. If None,
+            a set of trial cutoffs will be generated based on the structure
+            (default).
+        imaginary_tol (float): Tolerance used to decide if a phonon mode
+            is imaginary, in THz.
+        max_n_imaginary (int): Maximum number of imaginary modes allowed in the
+            the final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination this FireTask will fizzle.
+        max_imaginary_freq (float): Maximum allowed imaginary frequency in the
+            final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination this FireTask will fizzle.
+        fit_method (str): Method used for fitting force constants. This can be
+            any of the values allowed by the hiphive ``Optimizer`` class.
+    """
+
+    optional_params = [
+        "cutoffs",
+        "imaginary_tol",
+        "max_n_imaginary",
+        "max_imaginary_freq",
+        "fit_method",
+    ]
+
+    def run_task(self, fw_spec):
+        from hiphive.utilities import get_displacements
+
+        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
+        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
+        imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
+        fit_method = self.get("fit_method", FIT_METHOD)
+
+        all_structures = loadfn("perturbed_structures.json")
+        all_forces = loadfn("all_forces.json")
+        structure_data = loadfn("structure_data.json")
+        parent_structure = structure_data["structure"]
+        supercell_matrix = structure_data["supercell_matrix"]
+        supercell_structure = structure_data["supercell_structure"]
+
+        structures = []
+        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+        for structure, forces in zip(all_structures, all_forces):
+            atoms = AseAtomsAdaptor.get_atoms(structure)
+            displacements = get_displacements(atoms, supercell_atoms)
+            structure.new_array("displacements", displacements)
+            structure.new_array("forces", forces)
+            structure.positions = supercell_atoms.get_positions()
+            structures.append(structure)
+
+        cutoffs = self.get("cutoffs", get_cutoffs(supercell_structure))
+        force_constants, fitting_data = fit_force_constants(
+            parent_structure,
+            supercell_matrix,
+            structures,
+            cutoffs,
+            imaginary_tol,
+            max_n_imaginary,
+            max_imaginary_freq,
+            fit_method,
+        )
+
+        dumpfn(fitting_data, "fitting_data.json")
+
+        if force_constants is not None:
+            # fitting failed
+            raise RuntimeError(
+                "Could not find a force constant solution with less than {}"
+                "imaginary modes.\n"
+                "Fitting results: {}".format(max_n_imaginary, fitting_data)
+            )
+
+        else:
+            logger.info("Writing force constants.")
+            force_constants.write("force_constants.fcs")
+
+            atoms = AseAtomsAdaptor.get_atoms(parent_structure)
+            force_constants.write_to_shengBTE("FORCE_CONSTANTS_3ND", atoms)
+            force_constants.write_to_phonopy(
+                "FORCE_CONSTANTS_2ND", format="text"
+            )
+
+
+@requires(hiphive, "hiphive is required for lattice dynamics workflow")
+@explicit_serialize
+class ForceConstantsToDB(FiretaskBase):
+    """
+    Add force constants, phonon band structure and density of states
+    to the database.
+
+    Assumes you are in a directory with the force constants, fitting
+    data, and structure data written to files.
+
+    Required parameters:
+        db_file (str): Path to DB file for the database that contains the
+            perturbed structure calculations.
+
+    Optional parameters:
+        wf_uuid (str): Workflow unique identifier.
+        mesh_density (float): The density of the q-point mesh used to calculate
+            the phonon density of states. See the docstring for the ``mesh``
+            argument in Phonopy.init_mesh() for more details.
+        additional_fields (dict): Additional fields added to the document, such
+            as user-defined tags, name, ids, etc.
+    """
+
+    required_params = ["db_file"]
+    optional_params = ["wf_uuid", "mesh_density", "additional_fields"]
+
+    def run_task(self, fw_spec):
+        from hiphive.force_constants import ForceConstants
+
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+
+        force_constants = ForceConstants.read("force_constants.fcs")
+        fitting_data = loadfn("fitting_data.json")
+        structure_data = loadfn("structure_data.json")
+        structure = structure_data["structure"]
+        supercell_structure = structure_data["supercell_structure"]
+        supercell_matrix = structure_data["supercell_matrix"]
+
+        phonopy_fc = force_constants.get_fc_array(order=2)
+
+        logger.info("Getting uniform phonon band structure.")
+        uniform_bs = get_phonon_band_structure(
+            structure, supercell_matrix, phonopy_fc
+        )
+
+        logger.info("Getting line mode phonon band structure.")
+        lm_bs = get_line_mode_phonon_band_structure(
+            structure, supercell_matrix, phonopy_fc
+        )
+
+        logger.info("Getting phonon density of states.")
+        mesh_density = self.get("mesh_density", MESH_DENSITY)
+        dos = get_phonon_dos(
+            structure, supercell_matrix, phonopy_fc, mesh_density=mesh_density
+        )
+
+        logger.info("Inserting phonon objects into database.")
+        dos_fsid, _ = mmdb.insert_gridfs(
+            dos.to_json(), collection="phonon_dos_fs"
+        )
+        uniform_bs_fsid, _ = mmdb.insert_gridfs(
+            uniform_bs.to_json(), collection="phonon_bandstructure_fs"
+        )
+        lm_bs_fsid, _ = mmdb.insert_gridfs(
+            lm_bs.to_json(), collection="phonon_bandstructure_fs"
+        )
+
+        fc_uuid = str(uuid4())  # additional force constant identifier
+
+        data = {
+            "structure": structure.as_dict(),
+            "supercell_matrix": supercell_matrix.tolist(),
+            "supercell_structure": supercell_structure.as_dict(),
+            "fitting_data": fitting_data,
+            "force_constants": force_constants.get_fc_dict(),
+            "tags": fw_spec.get("tags", None),
+            "formula_pretty": structure.composition.reduced_formula,
+            "phonon_dos_fs_id": dos_fsid,
+            "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+            "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+            "wf_meta": {"wf_uuid": self["wf_uuid"], "fc_uuid": fc_uuid},
+            "created_at": datetime.utcnow(),
+        }
+        data.update(self.get("additional_fields", {}))
+
+        mmdb.collection = mmdb.db["lattice_dynamics"]
+        mmdb.collection.insert_one(data)
+
+        return FWAction(update_spec={"fc_uuid": fc_uuid})
+
+
+@explicit_serialize
+class RunShengBTE(FiretaskBase):
+    """
+    Run ShengBTE to calculate lattice thermal conductivity. Presumes
+    the FORCE_CONSTANTS_3ND and FORCE_CONSTANTS_2ND files in the current
+    directory. In addition, presumes a "structure_data.json" file, with they
+    keys "structure", " and "supercell_matrix" is in the current directory.
+
+    Required parameters:
+        shengbte_cmd (str): The name of the shengbte executable to run. Supports
+            env_chk.
+
+    Optional parameters:
+        temperature (float or dict): The temperature to calculate the lattice
+            thermal conductivity for. Can be given as a single float, or a
+            dictionary with the keys "min", "max", "step".
+        shengbte_control_kwargs (dict): Options to be included in the ShengBTE
+            control file.
+    """
+
+    required_params = ["shengbte_cmd"]
+    optional_params = ["temperature", "shengbte_control_kwargs"]
+
+    def run_task(self, fw_spec):
+        structure_data = loadfn("structure_data.json")
+        structure = structure_data["structure"]
+        supercell_matrix = structure_data["supercell_matrix"]
+
+        control_dict = {
+            "scalebroad": 0.5,
+            "nonanalytic": False,
+            "isotopes": False,
+            "temperature": self.get("temperature", DEFAULT_TEMPERATURE),
+            "scell": np.diag(supercell_matrix),
+        }
+        control_dict.update(self.get("shengbte_control_kwargs", {}))
+        control = Control.from_structure(structure, **control_dict)
+        control.to_file()
+
+        shengbte_cmd = env_chk(self["shengbte_cmd"], fw_spec)
+
+        if isinstance(shengbte_cmd, str):
+            shengbte_cmd = os.path.expandvars(shengbte_cmd)
+            shengbte_cmd = shlex.split(shengbte_cmd)
+
+        shengbte_cmd = list(shengbte_cmd)
+        logger.info("Running command: {}".format(shengbte_cmd))
+
+        with open("shengbte.out", "w") as f_std, open(
+            "shengbte_err.txt", "w", buffering=1
+        ) as f_err:
+            # use line buffering for stderr
+            return_code = os.subprocess.call(
+                shengbte_cmd, stdout=f_std, stderr=f_err
+            )
+        logger.info(
+            "Command {} finished running with returncode: {}".format(
+                shengbte_cmd, return_code
+            )
+        )
+
+        if return_code == 1:
+            raise RuntimeError(
+                "Running ShengBTE failed. Check '{}/shengbte_err.txt' for "
+                "details.".format(os.getcwd())
+            )
+
+
+@explicit_serialize
+class ShengBTEToDB(FiretaskBase):
+    """
+    Add lattice thermal conductivity results to database.
+
+    Assumes you are in a directory with the ShengBTE results in.
+
+    Required parameters:
+        db_file (str): Path to DB file for the database that contains the
+            perturbed structure calculations.
+
+    Optional parameters:
+        wf_uuid (str): Workflow unique identifier.
+        fc_uuid (str): Force constant identifier, used if workflow has multiple
+            force constants calculated (i.e., using different fit_methods).
+        additional_fields (dict): Additional fields added to the document, such
+            as user-defined tags, name, ids, etc.
+    """
+
+    required_params = ["db_file"]
+    optional_params = ["wf_uuid", "fc_uuid", "additional_fields"]
+
+    def run_task(self, fw_spec):
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+
+        control = Control.from_file("CONTROL")
+        structure = control.get_structure()
+        supercell_matrix = np.diag(control["scell"])
+
+        if Path("BTE.KappaTensorVsT_CONV").exists():
+            filename = "BTE.KappaTensorVsT_CONV"
+        elif Path("BTE.KappaTensorVsT_RTA").exists():
+            filename = "BTE.KappaTensorVsT_RTA"
+        else:
+            raise RuntimeError("Could not find ShengBTE output files.")
+
+        bte_data = np.loadtxt(filename)
+        temperatures = bte_data[:, 0].tolist()
+        kappa = bte_data[:, 1:10].reshape(-1, 3, 3)
+
+        wf_meta = {}
+        if self.get("wf_uuid"):
+            wf_meta["wf_uuid"] = self["wf_uuid"]
+
+        if self.get("fc_uuid") or fw_spec.get("fc_uuid"):
+            wf_meta["fc_uuid"] = self.get("fc_uuid", fw_spec.get("fc_uuid"))
+
+        data = {
+            "structure": structure.as_dict(),
+            "supercell_matrix": supercell_matrix.tolist(),
+            "temperatures": temperatures,
+            "lattice_thermal_conductivity": kappa,
+            "control": control.to_json(),
+            "tags": fw_spec.get("tags", None),
+            "formula_pretty": structure.composition.reduced_formula,
+            "wf_meta": wf_meta,
+            "created_at": datetime.utcnow(),
+        }
+        data.update(self.get("additional_fields", {}))
+
+        mmdb.collection = mmdb.db["lattice_thermal_conductivity"]
+        mmdb.collection.insert(data)

From 91c553382e680465428f0bb7a815bcbc2b2f0cfb Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:04:24 -0800
Subject: [PATCH 055/207] Add first pass at lattice_dynamics fireworks

---
 atomate/vasp/fireworks/lattice_dynamics.py | 148 +++++++++++++++++++++
 1 file changed, 148 insertions(+)
 create mode 100644 atomate/vasp/fireworks/lattice_dynamics.py

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
new file mode 100644
index 000000000..25b82f224
--- /dev/null
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -0,0 +1,148 @@
+from typing import Optional, List, Union
+
+from atomate.common.firetasks.glue_tasks import PassCalcLocs
+from atomate.vasp.firetasks.lattice_dynamics import CollectPerturbedStructures, \
+    FitForceConstants, ForceConstantsToDB
+from atomate.vasp.workflows.base.lattice_dynamics import IMAGINARY_TOL, \
+    MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, FIT_METHOD, MESH_DENSITY
+from fireworks import Firework
+
+__author__ = "Alex Ganose"
+__email__ = "aganose@lbl.gov"
+
+
+class FitForceConstantsFW(Firework):
+
+    def __init__(
+        self,
+        wf_uuid,
+        name="fit force constants",
+        parents: Union[Firework, List[Firework]] = None,
+        db_file: str = None,
+        cutoffs: Optional[List[List[float]]] = None,
+        imaginary_tol: float = IMAGINARY_TOL,
+        max_n_imaginary: int = MAX_N_IMAGINARY,
+        max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
+        fit_method: str = FIT_METHOD,
+        mesh_density: float = MESH_DENSITY,
+        additional_fields: dict = None,
+        **kwargs
+    ):
+        """
+        Compile perturbed supercell calculations and fit force constants
+        using hiPhive.
+
+        Args:
+            wf_uuid: Workflow identifier, from which the perturbed supercell
+                static calculations will be compiled.
+            parents: Parent(s) of this Firework.
+            name: Name of this FW.
+            db_file: Path to a db file.
+            cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
+                will be generated based on the structure (default).
+            imaginary_tol: Tolerance used to decide if a phonon mode is
+                imaginary, in THz.
+            max_n_imaginary: Maximum number of imaginary modes allowed in the
+                final fitted force constant solution. If this criteria is not
+                reached by any cutoff combination the Firework will fizzle.
+            max_imaginary_freq: Maximum allowed imaginary frequency in the
+                final fitted force constant solution. If this criteria is not
+                reached by any cutoff combination this FireTask will fizzle.
+            fit_method: Method used for fitting force constants. This can be
+                any of the values allowed by the hiphive ``Optimizer`` class.
+            mesh_density: The density of the q-point mesh used to calculate the
+                phonon density of states. See the docstring for the ``mesh``
+                argument in Phonopy.init_mesh() for more details.
+            additional_fields: Additional fields added to the document, such as
+                user-defined tags, name, ids, etc.
+            **kwargs: Other kwargs that are passed to Firework.__init__.
+        """
+        fw_name = "{}-{}".format(wf_uuid, name)
+        additional_fields = additional_fields or {}
+
+        collect_structures = CollectPerturbedStructures(db_file, wf_uuid)
+        fit_constants = FitForceConstants(
+            cutoffs=cutoffs,
+            imaginary_tol=imaginary_tol,
+            max_n_imaginary=max_n_imaginary,
+            max_imaginary_freq=max_imaginary_freq,
+            fit_method=fit_method
+        )
+        fc_to_db = ForceConstantsToDB(
+            db_file=db_file,
+            wf_uuid=wf_uuid,
+            mesh_density=mesh_density,
+            additional_fields=additional_fields
+        )
+        pass_locs = PassCalcLocs(name=name)
+
+        tasks = [collect_structures, fit_constants, fc_to_db, pass_locs]
+        super().__init__(tasks, parents=parents, name=fw_name, **kwargs)
+
+
+class LatticeThermalConductivityFW(Firework):
+
+    def __init__(
+            self,
+            name="fit force constants",
+            parents: Union[Firework, List[Firework]] = None,
+            db_file: str = None,
+            cutoffs: Optional[List[List[float]]] = None,
+            imaginary_tol: float = IMAGINARY_TOL,
+            max_n_imaginary: int = MAX_N_IMAGINARY,
+            max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
+            fit_method: str = FIT_METHOD,
+            mesh_density: float = MESH_DENSITY,
+            additional_fields: dict = None,
+            **kwargs
+    ):
+        """
+        Compile perturbed supercell calculations and fit force constants
+        using hiPhive.
+
+        Args:
+            wf_uuid: Workflow identifier, from which the perturbed supercell
+                static calculations will be compiled.
+            parents: Parent(s) of this Firework.
+            name: Name of this FW.
+            db_file: Path to a db file.
+            cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
+                will be generated based on the structure (default).
+            imaginary_tol: Tolerance used to decide if a phonon mode is
+                imaginary, in THz.
+            max_n_imaginary: Maximum number of imaginary modes allowed in the
+                final fitted force constant solution. If this criteria is not
+                reached by any cutoff combination the Firework will fizzle.
+            max_imaginary_freq: Maximum allowed imaginary frequency in the
+                final fitted force constant solution. If this criteria is not
+                reached by any cutoff combination this FireTask will fizzle.
+            fit_method: Method used for fitting force constants. This can be
+                any of the values allowed by the hiphive ``Optimizer`` class.
+            mesh_density: The density of the q-point mesh used to calculate the
+                phonon density of states. See the docstring for the ``mesh``
+                argument in Phonopy.init_mesh() for more details.
+            additional_fields: Additional fields added to the document, such as
+                user-defined tags, name, ids, etc.
+            **kwargs: Other kwargs that are passed to Firework.__init__.
+        """
+        fw_name = "{}-{}".format(wf_uuid, name)
+        additional_fields = additional_fields or {}
+
+        collect_structures = CollectPerturbedStructures(db_file, wf_uuid)
+        fit_constants = FitForceConstants(
+            cutoffs=cutoffs,
+            imaginary_tol=imaginary_tol,
+            max_n_imaginary=max_n_imaginary,
+            max_imaginary_freq=max_imaginary_freq,
+            fit_method=fit_method
+        )
+        fc_to_db = ForceConstantsToDB(
+            db_file=db_file,
+            wf_uuid=wf_uuid,
+            mesh_density=mesh_density,
+            additional_fields=additional_fields
+        )
+        pass_locs = PassCalcLocs(name=name)
+
+        tasks = [collect_structures, fit_constants, fc_to_db, pass_locs]
+        super().__init__(tasks, parents=parents, name=fw_name, **kwargs)

From 3ac59eb2000d0a0dceefabf6933b6cedb41de13d Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:04:39 -0800
Subject: [PATCH 056/207] Add methods for fitting force constants

---
 atomate/vasp/analysis/lattice_dynamics.py | 473 +++++++++++++---------
 1 file changed, 292 insertions(+), 181 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index f0ab19acc..c6d1a05ce 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -1,207 +1,318 @@
-# coding: utf-8
+import numpy as np
 
-from __future__ import division, print_function, unicode_literals, absolute_import
+from itertools import product
+from typing import Optional, Tuple, List, Dict
 
-from typing import Optional, Tuple, List
+from pymatgen import Structure
+from pymatgen.io.ase import AseAtomsAdaptor
+from pymatgen.io.phonopy import get_phonopy_structure
 
-import numpy as np
+from atomate.utils.utils import get_logger
+from atomate.vasp.workflows.base.lattice_dynamics import (
+    MIN_NN_SCALE,
+    FIT_METHOD,
+    MAX_IMAGINARY_FREQ,
+    IMAGINARY_TOL,
+    MAX_N_IMAGINARY,
+)
 
-from pymatgen import Structure
-from pymatgen.transformations.standard_transformations import PerturbStructureTransformation
+__author__ = "Rees Chang, Alex Ganose"
+__email__ = "rc564@cornell.edu, aganose@lbl.gov"
 
-__author__ = 'Rees Chang, Alex Ganose'
-__email__ = 'rc564@cornell.edu, aganose@lbl.gov'
 
+logger = get_logger(__name__)
 
-def generate_perturbed_supercells(
-    supercell: Structure,
-    min_displacement: float = 0.01,
-    max_displacement: float = 0.1,
-    num_displacements: int = 10,
-    n_cells_per_displacement_distance: int = 1,
-    min_random_distance: Optional[float] = None
+
+def generate_perturbed_structures(
+    structure: Structure,
+    rattle_stds: Optional[List[float]] = None,
+    n_configs_per_std: int = 1,
+    min_nn_scale: float = MIN_NN_SCALE,
 ) -> Tuple[List[Structure], np.ndarray]:
     """
-    Generate a list of supercells with perturbed atomic sites.
+    Generate a list of structures with perturbed atomic sites.
+
+    Rattling atom `i` is carried out as a Monte Carlo move that is accepted with
+    a probability determined from the minimum interatomic distance
+    :math:`d_{ij}`.  If :math:`\\min(d_{ij})` is smaller than :math:`d_{min}`
+    the move is only accepted with a low probability.
+
+    :math:`d_{min}` is calculated as the smallest nearest neighbor distance
+    times ``min_nn_fraction``.
 
     Args:
-        supercell (Structure): Original structure whose atomic sites are to be
-            perturbed.
-        max_displacement: Maximum displacement distance for perturbing the
-            sites in Angstroms.
-        min_displacement: Minimum displacement distance for perturbing the
-            sites in Angstroms.
-        num_displacements: Number of unique displacement distances to
-            try, uniformly distributed between ``min_displacement`` and
-            ``max_displacement``.
-        n_cells_per_displacement_distance: Number of perturbed
-            structures to generate for each unique displacement distance.
-        min_random_distance: If None (default), then for a given perturbed
-            structure, all atoms will move the same distance from their original
-            locations. If float, then for a given perturbed structure, the
-            distances the atoms move will be uniformly distributed from a
-            minimum distance of ``min_random_distance`` to one of the
-            displacement distances uniformly sampled between
-            ``min_displacement`` and ``max_displacement``.
+        structure: Structure whose atomic sites are to be perturbed.
+        rattle_stds: List of standard deviations (in normal distribution) to
+            to use when displacing the sites.
+        n_configs_per_std: Number of structures to generate per rattle standard
+            deviation.
+        min_nn_scale: Controls the minimum interatomic distance used for
+            computing the probability for each rattle move.
 
     Returns:
         A tuple of the ``(structures, displacements)``. Where ``structures`` is
         a list of randomly displaced structures, and ``displacements`` is
         the displacement distance for each structure.
     """
-    dists = np.linspace(min_displacement, max_displacement, num_displacements)
-    displacements = np.repeat(dists, n_cells_per_displacement_distance)
+    from hiphive.structure_generation import generate_mc_rattled_structures
+
+    if rattle_stds is None:
+        rattle_stds = np.linspace(0.01, 0.1, 5)
+
+    min_distance = np.min(structure.distance_matrix) * min_nn_scale
+    atoms = AseAtomsAdaptor.get_atoms(structure)
+
+    perturbed_structures = []
+    for rattle_std in rattle_stds:
+        seed = np.random.randint(1, 10000000000)
+        structures = generate_mc_rattled_structures(
+            atoms, n_configs_per_std, rattle_std, min_distance, seed=seed
+        )
+        perturbed_structures.extend(structures)
+
+    return perturbed_structures, rattle_stds
+
+
+def get_cutoffs(structure: Structure):
+    """
+    Get a list of trial cutoffs based on a structure.
+
+    An initial guess for the lower bound of the cutoffs is made based on the
+    period of the lightest element in the structure, according to:
+
+    ====== === === ===
+    .        Cutoff
+    ------ -----------
+    Period 2ND 3RD 4TH
+    ====== === === ===
+     1     5.5 3.0 3.0
+     2     5.5 3.0 3.0
+     3     6.5 4.0 3.5
+     4     7.5 5.0 4.0
+     5     8.5 6.0 4.5
+     6     9.5 7.0 5.0
+     7     9.5 7.0 5.0
+    ====== === === ===
+
+    The maximum cutoff for each order is determined by the minimum cutoff and
+    the following table. A full grid of all possible cutoff combinations is
+    generated based on the step size in the table below
+
+    ====== ==== =====
+    Cutoff Max  Step
+    ====== ==== =====
+    2ND    +3.0 0.5
+    3RD    +1.5 0.25
+    4TH    +1.0 0.25
+    ====== ==== =====
+
+    Args:
+        structure: A structure.
+
+    Returns:
+        A list of trial cutoffs.
+    """
+    # indexed as min_cutoffs[order][period]
+    min_cutoffs = {
+        2: {1: 5.5, 2: 5.5, 3: 6.5, 4: 7.5, 5: 8.5, 6: 9.5, 7: 9.5},
+        3: {1: 3.0, 2: 3.0, 3: 4.0, 4: 5.0, 5: 6.0, 6: 7.0, 7: 7.0},
+        4: {1: 3.0, 2: 3.0, 3: 3.5, 4: 4.0, 5: 4.5, 6: 5.0, 7: 5.0},
+    }
+    inc = {2: 3, 3: 1.5, 4: 1}
+    steps = {2: 0.5, 3: 0.25, 4: 0.25}
 
-    perturbed_supercells = []
-    for displacement in displacements:
-        pst = PerturbStructureTransformation(displacement, min_random_distance)
-        perturbed_supercells.append(pst.apply_transformation(supercell))
+    row = min([s.row for s in structure.species])
+    mins = (min_cutoffs[row][2], min_cutoffs[row][3], min_cutoffs[row][4])
 
-    return perturbed_supercells, displacements
+    range_two = np.arange(mins[0], mins[0] + inc[0] + steps[0], steps[0])
+    range_three = np.arange(mins[1], mins[1] + inc[1] + steps[1], steps[1])
+    range_four = np.arange(mins[2], mins[2] + inc[2] + steps[2], steps[2])
 
+    return list(product(range_two, range_three, range_four))
 
-def csld_main(options, settings):
+
+def fit_force_constants(
+    parent_structure: Structure,
+    supercell_matrix: np.ndarray,
+    structures: List["Atoms"],
+    all_cutoffs: List[List[float]],
+    imaginary_tol: float = IMAGINARY_TOL,
+    max_n_imaginary: int = MAX_N_IMAGINARY,
+    max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
+    fit_method: str = FIT_METHOD,
+) -> Tuple["SortedForceConstants", Dict]:
     """
-    Runs CSLD minimization.
+    Fit force constants using hiphive and select the optimum cutoff values.
+
+    The optimum cutoffs will be determined according to:
+    1. Number imaginary modes < ``max_n_imaginary``.
+    2. Most negative imaginary frequency < ``max_imaginary_freq``.
+    3. Least number of imaginary modes.
+    4. Lowest free energy at 300 K.
 
-    Changes from original version:
-        - Made 'prim' an argument in 'phonon_step()'
-        - Moved execution files to this main() function to be called from
-          atomate
-        - Rewrote 'add_common_parameter' in 'common_main' to treat 'options' as
+    If criteria 1 and 2 are not satisfied, None will be returned as the
+    force constants.
+
+    Args:
+        parent_structure: Initial input structure.
+        supercell_matrix: Supercell transformation matrix.
+        structures: A list of ase atoms objects with "forces" and
+            "displacements" arrays added, as required by hiPhive.
+        all_cutoffs: A nested list of cutoff values to trial. Each set of
+            cutoffs contains the radii for different orders starting with second
+            order.
+        imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
+            in THz.
+        max_n_imaginary: Maximum number of imaginary modes allowed in the
+            the final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination this FireTask will fizzle.
+        max_imaginary_freq: Maximum allowed imaginary frequency in the
+            final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination this FireTask will fizzle.
+        fit_method: Method used for fitting force constants. This can be
+            any of the values allowed by the hiphive ``Optimizer`` class.
 
-          a dictionary instead of ArgumentParser
+    Returns:
+        A tuple of the best fitted force constants as a hiphive
+        ``SortedForceConstants`` object and a dictionary of information on the
+        fitting process.
     """
-    import matplotlib
-    matplotlib.use('Agg')
-    from matplotlib.backends.backend_pdf import PdfPages
-    import atexit
-    import csld
-    from csld.symmetry_structure import SymmetrizedStructure
-
-    from csld.lattice_dynamics import init_ld_model
-
-    from csld.common_main import upon_exit, \
-        init_training
-    from csld.csld_main_functions import phonon_step, \
-        save_pot, predict, fit_data
-
-
-    freq_matrix = None #Rees
-    pdfout = PdfPages(
-        options['pdfout'].strip()) if options['pdfout'].strip() else None
-    atexit.register(upon_exit, pdfout)
-
-    prim = SymmetrizedStructure.init_structure(settings['structure'],
-                                               options['symm_step'],
-                                               options['symm_prim'],
-                                               options['log_level'])
-    model = init_ld_model(prim, settings['model'], settings[
-        'LDFF'] if 'LDFF' in settings.sections() else {}, options['clus_step'],
-                          options['symC_step'], options['ldff_step'])
-    Amat, fval = init_training(model, settings['training'], options['train_step'])
-    ibest, solutions, rel_err = fit_data(model, Amat, fval, settings['fitting'],
-                                options['fit_step'], pdfout)
-    if settings.has_section('phonon'):
-        phonon, freq_matrix = phonon_step(model, solutions, settings['phonon'],
-                             options['phonon_step'], pdfout, prim, return_eigen=True)
-    if settings.has_section('export_potential'):
-        save_pot(model, solutions[ibest], settings['export_potential'],
-                 options['save_pot_step'], phonon)
-    if settings.has_section('prediction'):
-        predict(model, solutions, settings['prediction'], options['pred_step'])
-
-    #OUTPUT
-    # freq_matrix is (nbands, nkpoints) = frequencies. Check for negative entries
-    # rel_err is cross validation error in percent
-    return rel_err, freq_matrix  # also want to return force constants
-
-
-default_csld_settings = {
-    "structure": {"sym_tol": "1e-3"},
-    "model": {
-        'model_type': 'LD',
-        'cluster_in': 'clusters.out',
-        'cluster_out': 'clusters.out',
-        'symC_in': 'Cmat.mtx',
-        'symC_out': 'Cmat.mtx',
-        'fractional_distance': False,
-    },
-    "training":{
-        'interface': 'VASP',
-        'corr_type': 'f',
-        'corr_in': 'Amat.mtx',
-        'corr_out': 'Amat.mtx',
-        'fval_in': 'fval.txt',
-        'fval_out': 'fval.txt'
-    },
-    "fitting": {
-        'solution_in': 'solution_all',
-        'solution_out': 'solution_all',
-        'nsubset': 5,
-        'holdsize': 0.1,
-        ## 1 FPC 2 FPC sparse 3 split 4 sparse split
-        ## 5 split+ right preconditioning 6 sparse split + r preconditioning
-        ## 101 Bayesian CS
-        'method': 5,
-        # For weight of L1 or L2 regularization
-        'mulist': '1E-5 1E-6 1E-7 1E-9',
-        'maxIter': 300,
-        'tolerance': 1E-6,
-        'subsetsize': 0.85,
-        'lambda': 0.5,
-        'uscale_list': '0.03',
-    },
-    "phonon": {
-        'qpoint_fractional': False,
-        # 'Auto' or something like 
-        # "[[10,  [0,0,0],'\\Gamma', [0.5,0.5,0.5], 'X', [0.5,0.5,0], 'K']]"
-        'wavevector': 'Auto',
-        'unit': 'cm',  # THz, meV, eV, cm
-        'dos_grid': '15 15 15',  # number of grid points
-        'nE_dos': 500, # number of points in DOS
-        'ismear': -1,  # 0 (Gaussian), 1 (Lorentzian), -1 (tetrahedron method)
-        'epsilon': 0.05,  # width in THz of Gaussian/Lorentzian smearing
-        'pdos': True,
-        'thermal_T_range': '50 800 50',
-        'thermal_out': 'thermal_out.txt'
-    },
-   'prediction': {
-        'interface': 'VASP',
-        'corr_type': 'f',
-        'corr_in': 'Amat_pred.mtx',
-        'corr_out': 'Amat_pred.mtx',
-        'fval_in': 'fval_pred.txt',
-        'fval_out': 'fval_pred.txt',
-        'traindat0': 'fcc222/POSCAR fcc222/traj*'
-    },
-    'export_potential': {},
-    'DEFAULT': {
-        "qpoint_fractional": False,
-        "true_v_fit": 'true_fit.txt',
-        'epsilon': '0.05',
-        "bcs_reweight": 'True',
-        "bcs_penalty": 'arctan',
-        "bcs_jcutoff": '1E-8'
+    from hiphive.fitting import Optimizer
+    from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
+
+    logger.info("Starting fitting force constants.")
+
+    fitting_data = {
+        "cutoffs": [],
+        "rmse_test": [],
+        "n_imaginary": [],
+        "min_frequency": [],
+        "300K_free_energy": [],
+        "fit_method": fit_method,
+        "imaginary_tol": imaginary_tol,
+        "max_n_imaginary": max_n_imaginary,
+        "max_imaginary_freq": max_imaginary_freq,
+    }
+
+    supercell_atoms = structures[0]
+
+    best_fit = {
+        "n_imaginary": np.inf,
+        "free_energy": np.inf,
+        "force_constants": None,
+        "cutoffs": None,
     }
-}
-
-default_csld_options = {
-    'pdfout': 'plots.pdf',
-    'ldff_step': 0,
-    'phonon_step': 1,
-    'phonon': False,
-    'save_pot_step': 1,
-    'pot': False,
-    'log_level': 1,
-    'symm_step': 2,
-    'symm_prim': True,
-    'clus_step': 3,
-    'symC_step': 3,
-    'train_step': 3,
-    'fit_step': 3,
-    'pred_step': 0,
-    'refit': False,
-    'cont': False,
-    'predict': False
-}
\ No newline at end of file
+    n_cutoffs = len(all_cutoffs)
+    for i, cutoffs in enumerate(all_cutoffs):
+        logger.info(
+            "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
+        )
+        sc = get_structure_container(cutoffs, structures)
+        opt = Optimizer(sc.get_fit_data(), fit_method)
+        opt.train()
+
+        parameters = enforce_rotational_sum_rules(
+            sc.cluster_space, opt.parameters, ["Huang", "Born-Huang"]
+        )
+        fcp = ForceConstantPotential(sc.cluster_space, parameters)
+        fcs = fcp.get_force_constants(supercell_atoms)
+
+        phonopy_fcs = fcs.get_fc_array(order=2)
+        n_imaginary, min_freq, free_energy = evaluate_force_constants(
+            parent_structure, supercell_matrix, phonopy_fcs, imaginary_tol
+        )
+
+        fitting_data["cutoffs"].append(cutoffs)
+        fitting_data["rmse_train"].append(opt.rmse_test)
+        fitting_data["n_imaginary"].append(n_imaginary)
+        fitting_data["min_frequency"].append(min_freq)
+        fitting_data["300K_free_energy"].append(free_energy)
+        fitting_data["force_constants"].append(fcs)
+
+        if (
+            min_freq < -np.abs(max_imaginary_freq)
+            and n_imaginary <= max_n_imaginary
+            and n_imaginary < best_fit["n_imaginary"]
+            and free_energy < best_fit["free_energy"]
+        ):
+
+            best_fit.update(
+                {
+                    "n_imaginary": n_imaginary,
+                    "free_energy": free_energy,
+                    "force_constants": fcs,
+                    "cutoffs": cutoffs,
+                }
+            )
+            fitting_data["best"] = cutoffs
+
+    logger.info("Finished fitting force constants.")
+
+    return best_fit["force_constants"], fitting_data
+
+
+def get_structure_container(
+    cutoffs: List[float], structures: List["Atoms"]
+) -> "StructureContainer":
+    """
+    Get a hiPhive StructureContainer from cutoffs and a list of atoms objects.
+
+    Args:
+        cutoffs: Cutoff radii for different orders starting with second order.
+        structures: A list of ase atoms objects with the "forces" and
+            "displacements" arrays included.
+
+    Returns:
+        A hiPhive StructureContainer.
+    """
+    from hiphive import ClusterSpace, StructureContainer
+
+    cs = ClusterSpace(structures[0], cutoffs)
+    logger.debug(cs.__repr__())
+
+    sc = StructureContainer(cs)
+    for structure in structures:
+        sc.add_structure(structure)
+    logger.debug(sc.__repr__())
+
+    return sc
+
+
+def evaluate_force_constants(
+    structure: Structure,
+    supercell_matrix: np.ndarray,
+    force_constants: np.ndarray,
+    imaginary_tol: float = IMAGINARY_TOL,
+) -> Tuple[int, float, float]:
+    """
+    Uses the force constants to extract phonon properties. Used for comparing
+    the accuracy of force constant fits.
+
+    Args:
+        structure: The parent structure.
+        supercell_matrix: The supercell transformation matrix.
+        force_constants: The force constants in numpy format.
+        imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
+            in THz.
+
+    Returns:
+        A tuple of the number of imaginary modes at Gamma, the minimum phonon
+        frequency at Gamma, and the free energy at 300 K.
+    """
+    from phonopy import Phonopy
+
+    parent_phonopy = get_phonopy_structure(structure)
+    phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
+
+    phonopy.set_force_constants(force_constants)
+    phonopy.run_mesh(is_gamma_center=True)
+    phonopy.run_thermal_properties(temperatures=[300])
+    free_energy = phonopy.get_thermal_properties_dict()["free_energy"][0]
+
+    # find imaginary modes at gamma
+    phonopy.run_qpoints([0, 0, 0])
+    gamma_eigs = phonopy.get_qpoints_dict()["frequencies"]
+    n_imaginary = int(np.sum(gamma_eigs < -np.abs(imaginary_tol)))
+    min_frequency = np.min(gamma_eigs)
+
+    return n_imaginary, min_frequency, free_energy

From 7919b9a014753f391f15adf85d3fcd27118f83a4 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:04:56 -0800
Subject: [PATCH 057/207] Add methods for generating phonon band structure &
 DOS

---
 atomate/vasp/analysis/phonopy.py | 182 +++++++++++++++++++++++++++++--
 1 file changed, 174 insertions(+), 8 deletions(-)

diff --git a/atomate/vasp/analysis/phonopy.py b/atomate/vasp/analysis/phonopy.py
index af386899b..3923895ab 100644
--- a/atomate/vasp/analysis/phonopy.py
+++ b/atomate/vasp/analysis/phonopy.py
@@ -1,7 +1,32 @@
+<<<<<<< HEAD
+=======
+# coding: utf-8
+
+>>>>>>> 728556b6 (Add methods for generating phonon band structure & DOS)
 import numpy as np
+from monty.dev import requires
 
+<<<<<<< HEAD
 __author__ = "Kiran Mathew"
 __email__ = "kmathew@lbl.gov"
+=======
+from pymatgen import Structure
+from pymatgen.io.phonopy import get_phonopy_structure
+from pymatgen.phonon.bandstructure import (
+    PhononBandStructure,
+    PhononBandStructureSymmLine,
+)
+from pymatgen.phonon.dos import PhononDos, CompletePhononDos
+from pymatgen.symmetry.bandstructure import HighSymmKpath
+
+try:
+    import phonopy
+except ImportError:
+    phonopy = False
+
+__author__ = "Kiran Mathew, Alex Ganose"
+__email__ = "kmathew@lbl.gov, aganose@lbl.gov"
+>>>>>>> 728556b6 (Add methods for generating phonon band structure & DOS)
 
 # TODO: @matk86 - unit tests?
 
@@ -30,8 +55,9 @@ def get_phonopy_gibbs(
         t_step (float): temperature step
         t_max (float): max temperature
         mesh (list/tuple): reciprocal space density
-        eos (str): equation of state used for fitting the energies and the volumes.
-            options supported by phonopy: vinet, murnaghan, birch_murnaghan
+        eos (str): equation of state used for fitting the energies and the
+            volumes. options supported by phonopy: vinet, murnaghan,
+            birch_murnaghan
         pressure (float): in GPa, optional.
 
     Returns:
@@ -59,6 +85,10 @@ def get_phonopy_gibbs(
     return G, T
 
 
+<<<<<<< HEAD
+=======
+@requires(phonopy, "phonopy is required to calculate the QHA")
+>>>>>>> 728556b6 (Add methods for generating phonon band structure & DOS)
 def get_phonopy_qha(
     energies,
     volumes,
@@ -83,8 +113,9 @@ def get_phonopy_qha(
         t_step (float): temperature step
         t_max (float): max temperature
         mesh (list/tuple): reciprocal space density
-        eos (str): equation of state used for fitting the energies and the volumes.
-            options supported by phonopy: vinet, murnaghan, birch_murnaghan
+        eos (str): equation of state used for fitting the energies and the
+            volumes. options supported by phonopy: vinet, murnaghan,
+            birch_murnaghan
         pressure (float): in GPa, optional.
 
     Returns:
@@ -117,7 +148,10 @@ def get_phonopy_qha(
         cv.append(c)
 
     # add pressure contribution
-    energies = np.array(energies) + np.array(volumes) * pressure / EVAngstromToGPa
+    energies = (
+        np.array(energies) + np.array(volumes) * pressure / EVAngstromToGPa
+    )
+
     # quasi-harmonic approx
     return PhonopyQHA(
         volumes,
@@ -155,12 +189,14 @@ def get_phonopy_thermal_expansion(
         t_step (float): temperature step
         t_max (float): max temperature
         mesh (list/tuple): reciprocal space density
-        eos (str): equation of state used for fitting the energies and the volumes.
-            options supported by phonopy: vinet, murnaghan, birch_murnaghan
+        eos (str): equation of state used for fitting the energies and the
+            volumes. options supported by phonopy: vinet, murnaghan,
+            birch_murnaghan
         pressure (float): in GPa, optional.
 
     Returns:
-        (numpy.ndarray, numpy.ndarray): thermal expansion coefficient, Temperature
+        (numpy.ndarray, numpy.ndarray): thermal expansion coefficient,
+        Temperature
     """
 
     # quasi-harmonic approx
@@ -182,3 +218,133 @@ def get_phonopy_thermal_expansion(
     alpha = phonopy_qha.get_thermal_expansion()[:max_t_index]
     T = phonopy_qha._qha._temperatures[:max_t_index]
     return alpha, T
+
+
+@requires(phonopy, "phonopy is required to calculate phonon density of states")
+def get_phonon_dos(
+    structure: Structure,
+    supercell_matrix: np.ndarray,
+    force_constants: np.ndarray,
+    mesh_density: float = MESH_DENSITY,
+    num_dos_steps: int = 200,
+) -> CompletePhononDos:
+    """
+    Get a projected phonon density of states.
+
+    Args:
+        structure: A structure.
+        supercell_matrix: The supercell matrix used to generate the force
+            constants.
+        force_constants: The force constants in phonopy format.
+        mesh_density: The density of the q-point mesh. See the docstring
+            for the ``mesh`` argument in Phonopy.init_mesh() for more details.
+        num_dos_steps: Number of frequency steps in the energy grid.
+
+    Returns:
+        The density of states.
+    """
+    from phonopy import Phonopy
+
+    structure_phonopy = get_phonopy_structure(structure)
+    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix)
+    phonon.set_force_constants(force_constants)
+    phonon.run_mesh(
+        mesh_density,
+        is_mesh_symmetry=False,
+        with_eigenvectors=True,
+        is_gamma_center=True,
+    )
+
+    # get min, max, step frequency
+    frequencies = phonon.get_mesh_dict()["frequencies"]
+    freq_min = frequencies.min()
+    freq_max = frequencies.max()
+    freq_pitch = (freq_max - freq_min) / num_dos_steps
+
+    phonon.run_projected_dos(
+        freq_min=freq_min, freq_max=freq_max, freq_pitch=freq_pitch
+    )
+
+    dos_raw = phonon.projected_dos.get_partial_dos()
+    pdoss = {s: dos for s, dos in zip(structure, dos_raw[1])}
+
+    total_dos = PhononDos(dos_raw[0], dos_raw[1].sum(axis=0))
+    return CompletePhononDos(structure, total_dos, pdoss)
+
+
+@requires(phonopy, "phonopy is required to calculate phonon band structures")
+def get_phonon_band_structure(
+    structure: Structure,
+    supercell_matrix: np.ndarray,
+    force_constants: np.ndarray,
+    mesh_density: float = 100.0,
+) -> PhononBandStructure:
+    """
+    Get a uniform phonon band structure.
+
+    Args:
+        structure: A structure.
+        supercell_matrix: The supercell matrix used to generate the force
+            constants.
+        force_constants: The force constants in phonopy format.
+        mesh_density: The density of the q-point mesh. See the docstring
+            for the ``mesh`` argument in Phonopy.init_mesh() for more details.
+
+    Returns:
+        The uniform phonon band structure.
+    """
+    from phonopy import Phonopy
+
+    structure_phonopy = get_phonopy_structure(structure)
+    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix)
+    phonon.set_force_constants(force_constants)
+    phonon.run_mesh(mesh_density, is_mesh_symmetry=False, is_gamma_center=True)
+    mesh = phonon.get_mesh_dict()
+
+    return PhononBandStructure(
+        mesh["qpoints"], mesh["frequencies"], structure.lattice
+    )
+
+
+@requires(phonopy, "phonopy is required to calculate phonon band structures")
+def get_line_mode_phonon_band_structure(
+    structure: Structure,
+    supercell_matrix: np.ndarray,
+    force_constants: np.ndarray,
+    line_density: float = 20.0,
+    symprec: float = 0.01,
+) -> PhononBandStructureSymmLine:
+    """
+    Get a projected phonon density of states.
+
+    Args:
+        structure: A structure.
+        supercell_matrix: The supercell matrix used to generate the force
+            constants.
+        force_constants: The force constants in phonopy format.
+        line_density: The density along the high symmetry path.
+        symprec: Symmetry precision for determining the band structure path.
+
+    Returns:
+        The line mode band structure.
+    """
+    from phonopy import Phonopy
+
+    structure_phonopy = get_phonopy_structure(structure)
+    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix)
+    phonon.set_force_constants(force_constants)
+
+    kpath = HighSymmKpath(structure, symprec=symprec)
+
+    kpoints, labels = kpath.get_kpoints(
+        line_density=line_density, coords_are_cartesian=False
+    )
+
+    phonon.run_qpoints(kpoints)
+    frequencies = phonon.qpoints.get_frequencies().T
+
+    labels_dict = dict([(a, k) for a, k in zip(labels, kpoints) if a != ""])
+
+    return PhononBandStructureSymmLine(
+        kpoints, frequencies, structure.lattice, labels_dict=labels_dict
+    )

From 8f1a9aeed262f61b48eb83d20de16fae61153957 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:05:38 -0800
Subject: [PATCH 058/207] Rewrite lattice dynamics workflow

---
 .../vasp/workflows/base/lattice_dynamics.py   | 304 +++++++++++-------
 1 file changed, 186 insertions(+), 118 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 43321a584..3c0417831 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -1,28 +1,40 @@
-# coding: utf-8
+import math
+
+import numpy as np
+
 from copy import deepcopy
-from typing import List, Dict, Optional
+
+from monty.dev import requires
+from typing import List, Dict, Optional, Union
 
 from uuid import uuid4
 
-from pymatgen.transformations.advanced_transformations import (
-    CubicSupercellTransformation
-)
+from atomate.vasp.firetasks.lattice_dynamics import FitForceConstants, \
+    ForceConstantsToDB, RunShengBTE, ShengBTEToDB
 from pymatgen.io.vasp.sets import MPStaticSet
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from pymatgen.transformations.advanced_transformations import (
+    CubicSupercellTransformation,
+)
 
 from fireworks import Workflow, Firework
+
 from atomate.utils.utils import get_logger
-from atomate.vasp.config import VASP_CMD, DB_FILE
+from atomate.vasp.config import VASP_CMD, DB_FILE, SHENGBTE_CMD
 from atomate.vasp.fireworks.core import StaticFW
-from atomate.vasp.firetasks.parse_outputs import CSLDForceConstantsToDB
 from atomate.vasp.powerups import add_additional_fields_to_taskdocs
-from atomate.vasp.analysis.csld import generate_perturbed_supercells
+from atomate.vasp.analysis.lattice_dynamics import generate_perturbed_structures
+
+try:
+    import hiphive
+except ImportError:
+    hiphive = False
 
 __author__ = "Rees Chang, Alex Ganose"
 __email__ = "rc564@cornell.edu, aganose@lbl.gov"
 __date__ = "July 2019"
-__csld_wf_version__ = 1.0
+__lattice_dynamics_wf_version__ = 1.0
 
 logger = get_logger(__name__)
 
@@ -31,38 +43,42 @@
     "LCHARG": False,
     "ENCUT": 700,
     "EDIFF": 1e-8,  # may need to tune this
-    "PREC": 'Accurate',
+    "PREC": "Accurate",
     "LAECHG": False,
     "LREAL": False,
-    "LASPH": True
+    "LASPH": True,
 }
 
 # define shared constants
-_MAX_DISPLACEMENT = 0.1
-_MIN_DISPLACEMENT = 0.01
-_NUM_DISPLACEMENTS = 10
-_MIN_RANDOM_DISPLACEMENTS = None
-_CELLS_PER_DISPLACEMENT = 1
+MIN_NN_SCALE = 0.85
+MAX_IMAGINARY_FREQ = 10  # in THz
+IMAGINARY_TOL = 0.025  # in THz
+MAX_N_IMAGINARY = 3
+DEFAULT_TEMPERATURE = 300
+FIT_METHOD = "least-squares"
+MESH_DENSITY = 100.  # should always be a float
 _DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
 
 
+@requires(hiphive, "hiphive is required for lattice dynamics workflow")
 def get_lattice_dynamics_wf(
     structure: Structure,
     common_settings: Dict = None,
-    symprec: Optional[float] = None,
+    symmetrize: bool = False,
+    symprec: float = 0.01,
     min_atoms: Optional[int] = None,
     max_atoms: Optional[int] = None,
-    num_nn_dists: float = 5,
+    num_nn_dists: float = 5.,
     force_diagonal_transformation: bool = True,
-    max_displacement: float = _MAX_DISPLACEMENT,
-    min_displacement: float = _MIN_DISPLACEMENT,
-    num_displacements: int = _NUM_DISPLACEMENTS,
-    n_cells_per_displacement_distance: int = _CELLS_PER_DISPLACEMENT,
-    min_random_distance: Optional[float] = _MIN_RANDOM_DISPLACEMENTS,
+    rattle_stds: Optional[List[float]] = None,
+    min_nn_scale: float = MIN_NN_SCALE,
+    min_num_equivalent_sites: int = 100,
+    max_num_supercells: int = 30,
     dynamic_static_calcs: bool = False,
-    do_shengbte: bool = False,
-    shengbte_t_range: Optional[List[float]] = None,
-    shengbte_fworker: Optional[str] = None
+    calculate_lattice_thermal_conductivity: bool = False,
+    thermal_conductivity_temperature: Union[float, Dict] = 300,
+    shengbte_cmd: str = SHENGBTE_CMD,
+    shengbte_fworker: Optional[str] = None,
 ):
     """
     This workflow will calculate interatomic force constants and vibrational
@@ -84,8 +100,10 @@ def get_lattice_dynamics_wf(
     Args:
         structure: Initial structure.
         common_settings: Common settings dict.
-        symprec: Symmetry precision for symmetrizing the structure. If set to
-            ``None`` (the default), the structure will not be symmetrized.
+        symmetrize: Whether to symmetrize the structure before running the
+            workflow.
+        symprec: Symmetry precision for determining the symmetry of the
+            structure.
         min_atoms: Minimum number of atoms to constrain the supercell.
         max_atoms: Maximum number of atoms to constrain the supercell.
         num_nn_dists: Number of nearest neighbor distances that the shortest
@@ -94,153 +112,163 @@ def get_lattice_dynamics_wf(
             transformation will be constrained to have a diagonal
             transformation matrix. If False, the supercell transformation
             will not be constrained to be diagonal (resulting in a more
-            cubic supercell).
-        max_displacement: Maximum displacement distance for perturbing the
-            sites in Angstroms.
-        min_displacement: Minimum displacement distance for perturbing the
-            sites in Angstroms.
-        num_displacements: Number of unique displacement distances to
-            try, uniformly distributed between ``min_displacement`` and
-            ``max_displacement``.
-        n_cells_per_displacement_distance: Number of perturbed
-            structures to generate for each unique displacement distance.
-        min_random_distance: If None (default), then for a given perturbed
-            structure, all atoms will move the same distance from their original
-            locations. If float, then for a given perturbed structure, the
-            distances the atoms move will be uniformly distributed from a
-            minimum distance of ``min_random_distance`` to one of the
-            displacement distances uniformly sampled between
-            ``min_displacement`` and ``max_displacement``.
+            cubic supercell). A diagonal supercell is required to calculate
+            lattice thermal conductivity.
+        rattle_stds: List of standard deviations (in normal distribution) to
+            to use when displacing the sites.
+        min_nn_scale: Controls the minimum interatomic distance used for
+            computing the probability for each rattle move.
+        min_num_equivalent_sites: The minimum number of equivalent sites for
+            each species. The aim is to have each equivalent site represented at
+            least ``min_num_equivalent_sites`` times. For example, if a symmetry
+            inequivalent site appears 26 times in the supercell structure,
+            and ``min_num_equivalent_sites`` is 100, then at least 4 supercells
+            are required for that site to appear over 100 times.
+        max_num_supercells: The maximum number of supercells per displacement.
+            For very unsymmetric structures, this imposes a hard limit on
+            the number of sites generated due to ``min_num_equivalent_sites``.
         dynamic_static_calcs: If True and hiPhive fails to return all real
              harmonic phonon frequencies on the first try, then the workflow
              will dynamically create more static perturbed supercell
              calculations with larger displacements to improve the fitting.
-        do_shengbte: If True and force constant fitting does not return
-            imaginary modes, then the workflow will dynamically create a
-            ShengBTE firework for calculating the lattice thermal conductivity.
-        shengbte_t_range: A list of temperatures at which to calculate the
-            lattice thermal conductivity using ShengBTE. If None (default),
-            then 300 K will be used.
+        calculate_lattice_thermal_conductivity: If True and force constant
+            fitting does not return imaginary modes, then use ShengBTE to
+            calculate the lattice thermal conductivity.
+        thermal_conductivity_temperature: The temperature to calculate the
+            lattice thermal conductivity for. Can be given as a single float, or
+            a dictionary with the keys "min", "max", "step".
+        shengbte_cmd: Command to run ShengBTE. Supports env_chk.
         shengbte_fworker: If None, the ShengBTE firework's fworker will be set
             to all the previous fireworks' fworker. If str, the ShengBTE
             firework's fworker will be set to shengbte_fworker.
    """
-    common_settings = common_settings or _DEFAULT_SETTINGS
+    common_settings = _get_common_settings(common_settings)
     uis = deepcopy(_static_uis)
     uis.update(common_settings.get("user_incar_settings", {}))
 
-    if force_diagonal_transformation is True and num_nn_dists == 5:
-        num_nn_dists = 6
+    if not force_diagonal_transformation and calculate_lattice_thermal_conductivity:
+        raise ValueError(
+            "Diagonal transformation required to calculate lattice thermal "
+            "conductivity"
+        )
 
-    if symprec is not None:
-        sga = SpacegroupAnalyzer(structure, symprec=symprec)
+    sga = SpacegroupAnalyzer(structure, symprec=symprec)
+    if symmetrize:
         structure = sga.get_primitive_standard_structure()
 
     st = CubicSupercellTransformation(
         min_atoms,
         max_atoms,
         num_nn_dists,
-        force_diagonal_transformation=force_diagonal_transformation
+        force_diagonal_transformation=force_diagonal_transformation,
     )
     supercell = st.apply_transformation(structure)
 
-    perturbed_supercells, disp_dists, fws = get_perturbed_supercell_fws(
+    n_cells = _get_n_cells(sga, min_num_equivalent_sites, max_num_supercells)
+    perturbed_supercells, disp_dists, fws = get_perturbed_structure_fws(
         supercell,
-        common_settings,
+        common_settings=common_settings,
         user_incar_settings=uis,
-        min_displacement=min_displacement,
-        max_displacement=max_displacement,
-        num_displacements=num_displacements,
-        min_random_distance=min_random_distance,
-        n_cells_per_displacement_distance=n_cells_per_displacement_distance,
+        rattle_stds=rattle_stds,
+        min_nn_scale=min_nn_scale,
+        n_configs_per_std=n_cells,
     )
 
+    logger.debug("Generating {} supercells per displacement".format(n_cells))
     logger.debug("Using {} displacements".format(len(disp_dists)))
     logger.debug("Displacements: {}".format(disp_dists))
 
-    # Collect force constants from the DB and output on cluster
-    wf_meta = {"wf_uuid": str(uuid4()), "wf_name": "LatticeDynamicsWF"}
-    csld_fw = Firework(
-        CSLDForceConstantsToDB(
-            db_file=common_settings["DB_FILE"],
-            wf_uuid=wf_meta["wf_uuid"],
-            parent_structure=structure,
-            trans_mat=st.transformation_matrix.tolist(),
-            supercell_structure=supercell,
-            perturbed_supercells=perturbed_supercells,
-            disps=disp_dists,
-            force_diagonal_transformation=force_diagonal_transformation,
-            first_pass=True,
-            static_user_incar_settings=uis,
-            env_vars=common_settings,
-            dynamic_static_calcs=dynamic_static_calcs,
-            do_shengbte=do_shengbte,
-            shengbte_t_range=shengbte_t_range,
-            shengbte_fworker=shengbte_fworker
-        ),
-        name="Compressed Sensing Lattice Dynamics",
-        parents=fws[-len(perturbed_supercells):]
+    wf_meta = {
+        "wf_uuid": str(uuid4()),
+        "wf_name": "LatticeDynamicsWF",
+        "wf_version": __lattice_dynamics_wf_version__,
+    }
+
+    # Add tasks to fit force constants
+    fit_forces = FitForceConstants(
+        db_file=common_settings["DB_FILE"],
+        wf_uuid=wf_meta["wf_uuid"],
+        parent_structure=structure,
+        supercell_structure=supercell,
+        supercell_matrix=st.transformation_matrix.tolist(),
+    )
+    forces_to_db = ForceConstantsToDB(
+        db_file=common_settings["DB_FILE"], wf_uuid=wf_meta["wf_uuid"],
+    )
+    fws.append(
+        Firework(
+            [fit_forces, forces_to_db],
+            name="Force Constant Fitting",
+            parents=fws[-len(perturbed_supercells):],
+        )
+    )
+
+    # Add ShengBTE tasks
+    run_shengbte = RunShengBTE(
+        db_file=common_settings["DB_FILE"],
+        wf_uuid=wf_meta["wf_uuid"],
+        structure=structure,
+        supercell_matrix=st.transformation_matrix.tolist(),
+        shengbte_cmd=shengbte_cmd,
+        temperature=thermal_conductivity_temperature,
+    )
+    shengbte_to_db = ShengBTEToDB(
+        db_file=common_settings["DB_FILE"],
+        wf_uuid=wf_meta["wf_uuid"],
+    )
+    fws.append(
+        Firework(
+            [run_shengbte, shengbte_to_db],
+            name="Lattice Thermal Conductivity",
+            parents=fws[-1]
+        )
     )
-    fws.append(csld_fw)
 
     formula = structure.composition.reduced_formula
-    wf_name = "{} - compressed sensing lattice dynamics".format(formula)
+    wf_name = "{} - lattice dynamics".format(formula)
 
     wf = Workflow(fws, name=wf_name)
     wf = add_additional_fields_to_taskdocs(
-        wf,  {"wf_meta": wf_meta}, task_name_constraint="VaspToDb"
+        wf, {"wf_meta": wf_meta}, task_name_constraint="VaspToDb"
     )
 
     return wf
 
 
-def get_perturbed_supercell_fws(
+def get_perturbed_structure_fws(
     supercell: Structure,
     common_settings: Optional[Dict] = None,
     user_incar_settings: Optional[Dict] = None,
-    max_displacement: float = _MAX_DISPLACEMENT,
-    min_displacement: float = _MIN_DISPLACEMENT,
-    num_displacements: int = _NUM_DISPLACEMENTS,
-    n_cells_per_displacement_distance: int = _CELLS_PER_DISPLACEMENT,
-    min_random_distance: Optional[float] = _MIN_RANDOM_DISPLACEMENTS,
+    rattle_stds: Optional[List[float]] = None,
+    n_configs_per_std: int = 1,
+    min_nn_scale: float = MIN_NN_SCALE,
 ) -> List[Firework]:
     """
     Get static calculations to calculate the forces on each perturbed supercell.
 
     Args:
         supercell: Parent supercell structure.
-        max_displacement: Maximum displacement distance for perturbing the
-            sites in Angstroms.
-        min_displacement: Minimum displacement distance for perturbing the
-            sites in Angstroms.
-        num_displacements: Number of unique displacement distances to
-            try, uniformly distributed between ``min_displacement`` and
-            ``max_displacement``.
-        n_cells_per_displacement_distance: Number of perturbed
-            structures to generate for each unique displacement distance.
-        min_random_distance: If None (default), then for a given perturbed
-            structure, all atoms will move the same distance from their original
-            locations. If float, then for a given perturbed structure, the
-            distances the atoms move will be uniformly distributed from a
-            minimum distance of ``min_random_distance`` to one of the
-            displacement distances uniformly sampled between
-            ``min_displacement`` and ``max_displacement``.
         common_settings: Common settings dict
         user_incar_settings: User incar settings override.
+        rattle_stds: List of standard deviations (in normal distribution) to
+            to use when displacing the sites.
+        n_configs_per_std: Number of structures to generate per rattle standard
+            deviation.
+        min_nn_scale: Controls the minimum interatomic distance used for
+            computing the probability for each rattle move.
 
     Returns:
         A list of static fireworks.
     """
     user_incar_settings = user_incar_settings if user_incar_settings else {}
+    common_settings = _get_common_settings(common_settings)
 
     # Generate list of perturbed supercells
-    perturbed_supercells, disp_dists = generate_perturbed_supercells(
+    perturbed_supercells, disp_dists = generate_perturbed_structures(
         supercell,
-        min_displacement=min_displacement,
-        max_displacement=max_displacement,
-        num_displacements=num_displacements,
-        n_cells_per_displacement_distance=n_cells_per_displacement_distance,
-        min_random_distance=min_random_distance
+        rattle_stds=rattle_stds,
+        n_configs_per_std=n_configs_per_std,
+        min_nn_scale=min_nn_scale
     )
 
     fws = []
@@ -256,9 +284,49 @@ def get_perturbed_supercell_fws(
             vasp_input_set=vis,
             vasp_cmd=common_settings["VASP_CMD"],
             db_file=common_settings["DB_FILE"],
-            name=name
+            name=name,
         )
         static_fw.spec["displacement_value"] = dist
         fws.append(static_fw)
 
     return fws
+
+
+def _get_common_settings(common_settings: Optional[Dict]):
+    common_settings = common_settings or {}
+    for k, v in _DEFAULT_SETTINGS.items():
+        if k not in common_settings:
+            common_settings[k] = v
+    return common_settings
+
+
+def _get_n_cells(
+    spacegroup_analyzer: SpacegroupAnalyzer,
+    min_num_equivalent_sites: int,
+    max_num_structure: int,
+) -> int:
+    """
+    Get the number of supercells to run per rattle standard deviation.
+
+    The aim is to have each equivalent site represented at least
+    ``min_num_equivalent_sites`` times. For example, if a symmetry inequivalent
+    site appears 26 times in the supercell structure, `n_configs` would be 4.
+    I.e., 4 * 26 > 100.
+
+    Args:
+        spacegroup_analyzer: A spacegroup analyzer object.
+        min_num_equivalent_sites: The minimum number of equivalent sites.
+        max_num_structure: The maximum number of cells.
+
+    Returns:
+        The number of supercells needed for all symmetry inequivalent sites to
+        be represented at least `min_num_equivalent_sites` times.
+    """
+    # get the equivalent sites in the structure and calculate the smallest
+    # site degeneracy
+    equiv_idxs = spacegroup_analyzer.get_symmetry_dataset()["equivalent_atoms"]
+    equiv_counts = np.unique(equiv_idxs, return_counts=True)
+    min_count = np.min(equiv_counts)
+
+    n_cells = math.ceil(min_num_equivalent_sites / min_count)
+    return min(n_cells, max_num_structure)

From dee5cc49b8f17f980572cca300a5ee3287dd40b4 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 11:05:49 -0800
Subject: [PATCH 059/207] Add optional requirements

---
 requirements-optional.txt | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 requirements-optional.txt

diff --git a/requirements-optional.txt b/requirements-optional.txt
new file mode 100644
index 000000000..8218f9e81
--- /dev/null
+++ b/requirements-optional.txt
@@ -0,0 +1,2 @@
+f90nml==1.1.2
+ase==3.19.0

From 4b482d629afea843b37bd2a8da8fafebc0ba909a Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 15:43:45 -0800
Subject: [PATCH 060/207] Refactor firetasks to not rely on wf_uuid

---
 atomate/vasp/firetasks/lattice_dynamics.py | 130 +++++++++------------
 1 file changed, 52 insertions(+), 78 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index e99e21671..eb59783ba 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -3,12 +3,11 @@
 
 from pathlib import Path
 
-from uuid import uuid4
-
 from datetime import datetime
 
 from monty.serialization import dumpfn, loadfn
 from monty.dev import requires
+from pymongo import ReturnDocument
 
 from atomate.utils.utils import get_logger, env_chk
 from atomate.vasp.analysis.lattice_dynamics import (
@@ -53,57 +52,31 @@
 @explicit_serialize
 class CollectPerturbedStructures(FiretaskBase):
     """
-    Aggregate the structures and forces of perturbed supercells. Requires a
-    wf_uuid from which all perturbed static calculations will be compiled. The
-    initial structure and supercell transformation matrix will be extracted from
-    the perturbed structure tasks.
+    Aggregate the structures and forces of perturbed supercells.
 
-    Required parameters:
-        db_file (str): Path to DB file for the database that contains the
-            perturbed structure calculations.
-        wf_uuid (str): Workflow unique identifier.
-    """
+    Requires a ``perturbed_tasks`` key to be set in the fw_spec, containing a
+    list of dictionaries, each with the keys:
 
-    required_params = ["db_file", "wf_uuid"]
+    - "parent_structure": The original structure.
+    - "supercell_matrix": The supercell transformation matrix.
+    - "structure": The perturbed supercell structure.
+    - "forces": The forces on each site in the supercell.
+    """
 
     def run_task(self, fw_spec):
-        db_file = env_chk(self.get("db_file"), fw_spec)
-        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        tasks = mmdb.collection
-
-        query = {
-            "wf_meta.wf_uuid": self["wf_uuid"],
-            "task_label": {"$regex": "perturbed static"},
-            "state": "successful",
-        }
-        projection = ["output.structure", "output.forces", "transformations"]
+        results = fw_spec.get("perturbed_tasks", [])
 
-        logger.info("Fetching structure and forces data")
-        results = list(tasks.find(query, projection))
+        if len(results) == 0:
+            # can happen if all parents fizzled
+            raise RuntimeError("No perturbed tasks found in firework spec")
 
         logger.info("Found {} perturbed structures".format(len(results)))
-        all_structures = []
-        all_forces = []
-        for result in results:
-            structure = Structure.from_dict(result["output"]["structure"])
-            forces = np.asarray(result["output"]["forces"])
-            all_structures.append(structure)
-            all_forces.append(forces)
-
-        if len(all_structures) == 0:
-            raise RuntimeError(
-                "Could not find any perturbed structures for workflow uuid: "
-                "{}".format(self["wf_uuid"])
-            )
-        else:
-            transformation = results[-1]["transformations"][0]
-            t_class = transformation["@class"]
-            if t_class != "SupercellTransformation":
-                raise ValueError(
-                    "Expecting SupercellTransformation not {}".format(t_class)
-                )
-            structure = Structure.from_dict(transformation["input_structure"])
-            supercell_matrix = transformation["deformation"]
+
+        structure = Structure.from_dict(results[0]["parent_structure"])
+        supercell_matrix = results[0]["supercell_matrix"]
+
+        structures = [Structure.from_dict(r["structure"]) for r in results]
+        forces = [np.asarray(r["forces"]) for r in results]
 
         # regenerate pure supercell structure
         st = SupercellTransformation(supercell_matrix)
@@ -116,19 +89,19 @@ def run_task(self, fw_spec):
         }
 
         logger.info("Writing structure and forces data.")
-        dumpfn(all_structures, "perturbed_structures.json")
-        dumpfn(all_forces, "perturbed_forces.json")
+        dumpfn(structures, "perturbed_structures.json")
+        dumpfn(forces, "perturbed_forces.json")
         dumpfn(structure_data, "structure_data.json")
 
 
 @requires(hiphive, "hiphive is required for lattice dynamics workflow")
 @explicit_serialize
-class FitForceConstants(FiretaskBase):
+class RunHiPhive(FiretaskBase):
     """
-    Used to aggregate atomic forces of perturbed supercells in and fit
-    force constants using hiPhive. Requires "perturbed_structures.json",
-    "perturbed_forces.json", and "structure_data.json" files to be present
-    in the current working directory.
+    Fit force constants using hiPhive.
+
+    Requires "perturbed_structures.json", "perturbed_forces.json", and
+    "structure_data.json" files to be present in the current working directory.
 
     Optional parameters:
         cutoffs (Optional[list[list]]): A list of cutoffs to trial. If None,
@@ -214,7 +187,7 @@ def run_task(self, fw_spec):
 
 @requires(hiphive, "hiphive is required for lattice dynamics workflow")
 @explicit_serialize
-class ForceConstantsToDB(FiretaskBase):
+class ForceConstantsToDb(FiretaskBase):
     """
     Add force constants, phonon band structure and density of states
     to the database.
@@ -227,7 +200,6 @@ class ForceConstantsToDB(FiretaskBase):
             perturbed structure calculations.
 
     Optional parameters:
-        wf_uuid (str): Workflow unique identifier.
         mesh_density (float): The density of the q-point mesh used to calculate
             the phonon density of states. See the docstring for the ``mesh``
             argument in Phonopy.init_mesh() for more details.
@@ -236,7 +208,7 @@ class ForceConstantsToDB(FiretaskBase):
     """
 
     required_params = ["db_file"]
-    optional_params = ["wf_uuid", "mesh_density", "additional_fields"]
+    optional_params = ["mesh_density", "additional_fields"]
 
     def run_task(self, fw_spec):
         from hiphive.force_constants import ForceConstants
@@ -247,6 +219,9 @@ def run_task(self, fw_spec):
         force_constants = ForceConstants.read("force_constants.fcs")
         fitting_data = loadfn("fitting_data.json")
         structure_data = loadfn("structure_data.json")
+        forces = loadfn("perturbed_forces.json")
+        structures = loadfn("perturbed_structures.json")
+
         structure = structure_data["structure"]
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = structure_data["supercell_matrix"]
@@ -280,12 +255,12 @@ def run_task(self, fw_spec):
             lm_bs.to_json(), collection="phonon_bandstructure_fs"
         )
 
-        fc_uuid = str(uuid4())  # additional force constant identifier
-
         data = {
             "structure": structure.as_dict(),
             "supercell_matrix": supercell_matrix.tolist(),
             "supercell_structure": supercell_structure.as_dict(),
+            "perturbed_structures": [s.to_json() for s in structures],
+            "perturbed_forces": [f.tolist() for f in forces],
             "fitting_data": fitting_data,
             "force_constants": force_constants.get_fc_dict(),
             "tags": fw_spec.get("tags", None),
@@ -293,24 +268,32 @@ def run_task(self, fw_spec):
             "phonon_dos_fs_id": dos_fsid,
             "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
             "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-            "wf_meta": {"wf_uuid": self["wf_uuid"], "fc_uuid": fc_uuid},
             "created_at": datetime.utcnow(),
         }
         data.update(self.get("additional_fields", {}))
 
+        # Get an id for the force constants
         mmdb.collection = mmdb.db["lattice_dynamics"]
+        fc_id = mmdb.db.counter.find_one_and_update(
+            {"_id": "taskid"}, {"$inc": {"c": 1}},
+            return_document=ReturnDocument.AFTER
+        )["c"]
+        metadata = {"fc_id": fc_id, "fc_dir": os.getcwd()}
+        data.update(metadata)
+
         mmdb.collection.insert_one(data)
+        logger.info("Finished inserting force constants")
 
-        return FWAction(update_spec={"fc_uuid": fc_uuid})
+        return FWAction(update_spec=metadata)
 
 
 @explicit_serialize
 class RunShengBTE(FiretaskBase):
     """
     Run ShengBTE to calculate lattice thermal conductivity. Presumes
-    the FORCE_CONSTANTS_3ND and FORCE_CONSTANTS_2ND files in the current
-    directory. In addition, presumes a "structure_data.json" file, with they
-    keys "structure", " and "supercell_matrix" is in the current directory.
+    the FORCE_CONSTANTS_3ND and FORCE_CONSTANTS_2ND, and a "structure_data.json"
+    file, with the keys "structure", " and "supercell_matrix" is in the current
+    directory.
 
     Required parameters:
         shengbte_cmd (str): The name of the shengbte executable to run. Supports
@@ -373,7 +356,7 @@ def run_task(self, fw_spec):
 
 
 @explicit_serialize
-class ShengBTEToDB(FiretaskBase):
+class ShengBTEToDb(FiretaskBase):
     """
     Add lattice thermal conductivity results to database.
 
@@ -384,15 +367,11 @@ class ShengBTEToDB(FiretaskBase):
             perturbed structure calculations.
 
     Optional parameters:
-        wf_uuid (str): Workflow unique identifier.
-        fc_uuid (str): Force constant identifier, used if workflow has multiple
-            force constants calculated (i.e., using different fit_methods).
-        additional_fields (dict): Additional fields added to the document, such
-            as user-defined tags, name, ids, etc.
+        additional_fields (dict): Additional fields added to the document.
     """
 
     required_params = ["db_file"]
-    optional_params = ["wf_uuid", "fc_uuid", "additional_fields"]
+    optional_params = ["additional_fields"]
 
     def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
@@ -413,13 +392,6 @@ def run_task(self, fw_spec):
         temperatures = bte_data[:, 0].tolist()
         kappa = bte_data[:, 1:10].reshape(-1, 3, 3)
 
-        wf_meta = {}
-        if self.get("wf_uuid"):
-            wf_meta["wf_uuid"] = self["wf_uuid"]
-
-        if self.get("fc_uuid") or fw_spec.get("fc_uuid"):
-            wf_meta["fc_uuid"] = self.get("fc_uuid", fw_spec.get("fc_uuid"))
-
         data = {
             "structure": structure.as_dict(),
             "supercell_matrix": supercell_matrix.tolist(),
@@ -428,7 +400,9 @@ def run_task(self, fw_spec):
             "control": control.to_json(),
             "tags": fw_spec.get("tags", None),
             "formula_pretty": structure.composition.reduced_formula,
-            "wf_meta": wf_meta,
+            "shengbte_dir": os.getcwd(),
+            "fc_id": fw_spec.get("fc_id", None),
+            "fc_dir": fw_spec.get("fc_dir", None),
             "created_at": datetime.utcnow(),
         }
         data.update(self.get("additional_fields", {}))

From c21dcc51ff145f9711061008b8fc9d84db6b9e92 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 15:44:22 -0800
Subject: [PATCH 061/207] Refactor lattice dynamics fireworks to remove wf_uuid

---
 atomate/vasp/fireworks/lattice_dynamics.py | 30 ++++++----------------
 1 file changed, 8 insertions(+), 22 deletions(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 25b82f224..827232d25 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -2,7 +2,7 @@
 
 from atomate.common.firetasks.glue_tasks import PassCalcLocs
 from atomate.vasp.firetasks.lattice_dynamics import CollectPerturbedStructures, \
-    FitForceConstants, ForceConstantsToDB
+    RunHiPhive, ForceConstantsToDb
 from atomate.vasp.workflows.base.lattice_dynamics import IMAGINARY_TOL, \
     MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, FIT_METHOD, MESH_DENSITY
 from fireworks import Firework
@@ -15,8 +15,7 @@ class FitForceConstantsFW(Firework):
 
     def __init__(
         self,
-        wf_uuid,
-        name="fit force constants",
+        name="Fit Force Constants",
         parents: Union[Firework, List[Firework]] = None,
         db_file: str = None,
         cutoffs: Optional[List[List[float]]] = None,
@@ -25,7 +24,6 @@ def __init__(
         max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
         fit_method: str = FIT_METHOD,
         mesh_density: float = MESH_DENSITY,
-        additional_fields: dict = None,
         **kwargs
     ):
         """
@@ -33,8 +31,6 @@ def __init__(
         using hiPhive.
 
         Args:
-            wf_uuid: Workflow identifier, from which the perturbed supercell
-                static calculations will be compiled.
             parents: Parent(s) of this Firework.
             name: Name of this FW.
             db_file: Path to a db file.
@@ -53,31 +49,21 @@ def __init__(
             mesh_density: The density of the q-point mesh used to calculate the
                 phonon density of states. See the docstring for the ``mesh``
                 argument in Phonopy.init_mesh() for more details.
-            additional_fields: Additional fields added to the document, such as
-                user-defined tags, name, ids, etc.
             **kwargs: Other kwargs that are passed to Firework.__init__.
         """
-        fw_name = "{}-{}".format(wf_uuid, name)
-        additional_fields = additional_fields or {}
-
-        collect_structures = CollectPerturbedStructures(db_file, wf_uuid)
-        fit_constants = FitForceConstants(
+        collect_structures = CollectPerturbedStructures(db_file)
+        fit_constants = RunHiPhive(
             cutoffs=cutoffs,
             imaginary_tol=imaginary_tol,
             max_n_imaginary=max_n_imaginary,
             max_imaginary_freq=max_imaginary_freq,
             fit_method=fit_method
         )
-        fc_to_db = ForceConstantsToDB(
-            db_file=db_file,
-            wf_uuid=wf_uuid,
-            mesh_density=mesh_density,
-            additional_fields=additional_fields
-        )
+        fc_to_db = ForceConstantsToDb(db_file=db_file,mesh_density=mesh_density)
         pass_locs = PassCalcLocs(name=name)
 
         tasks = [collect_structures, fit_constants, fc_to_db, pass_locs]
-        super().__init__(tasks, parents=parents, name=fw_name, **kwargs)
+        super().__init__(tasks, parents=parents, name=name, **kwargs)
 
 
 class LatticeThermalConductivityFW(Firework):
@@ -129,14 +115,14 @@ def __init__(
         additional_fields = additional_fields or {}
 
         collect_structures = CollectPerturbedStructures(db_file, wf_uuid)
-        fit_constants = FitForceConstants(
+        fit_constants = RunHiPhive(
             cutoffs=cutoffs,
             imaginary_tol=imaginary_tol,
             max_n_imaginary=max_n_imaginary,
             max_imaginary_freq=max_imaginary_freq,
             fit_method=fit_method
         )
-        fc_to_db = ForceConstantsToDB(
+        fc_to_db = ForceConstantsToDb(
             db_file=db_file,
             wf_uuid=wf_uuid,
             mesh_density=mesh_density,

From 960bf83d510a9593f7220c025f078a1d25ce19a1 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 15:44:59 -0800
Subject: [PATCH 062/207] Rewrite lattice dynamics workflow with chaining in
 mind

---
 .../vasp/workflows/base/lattice_dynamics.py   | 340 +++++++++---------
 1 file changed, 166 insertions(+), 174 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 3c0417831..a21daf112 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -1,30 +1,29 @@
+import warnings
 import math
 
 import numpy as np
 
 from copy import deepcopy
-
-from monty.dev import requires
 from typing import List, Dict, Optional, Union
 
-from uuid import uuid4
 
-from atomate.vasp.firetasks.lattice_dynamics import FitForceConstants, \
-    ForceConstantsToDB, RunShengBTE, ShengBTEToDB
-from pymatgen.io.vasp.sets import MPStaticSet
+from pymatgen.io.vasp.sets import MPStaticSet, VaspInputSet
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.transformations.advanced_transformations import (
     CubicSupercellTransformation,
 )
 
-from fireworks import Workflow, Firework
+from monty.dev import requires
+from fireworks import Workflow
 
 from atomate.utils.utils import get_logger
 from atomate.vasp.config import VASP_CMD, DB_FILE, SHENGBTE_CMD
-from atomate.vasp.fireworks.core import StaticFW
+from atomate.vasp.fireworks.core import TransmuterFW
 from atomate.vasp.powerups import add_additional_fields_to_taskdocs
-from atomate.vasp.analysis.lattice_dynamics import generate_perturbed_structures
+from atomate.vasp.firetasks import pass_vasp_result
+from atomate.vasp.fireworks.lattice_dynamics import FitForceConstantsFW, \
+    LatticeThermalConductivityFW
 
 try:
     import hiphive
@@ -34,11 +33,10 @@
 __author__ = "Rees Chang, Alex Ganose"
 __email__ = "rc564@cornell.edu, aganose@lbl.gov"
 __date__ = "July 2019"
-__lattice_dynamics_wf_version__ = 1.0
 
 logger = get_logger(__name__)
 
-_static_uis = {
+_static_user_incar_settings = {
     "ADDGRID": True,  # Fast Fourier Transform grid
     "LCHARG": False,
     "ENCUT": 700,
@@ -58,23 +56,17 @@
 FIT_METHOD = "least-squares"
 MESH_DENSITY = 100.  # should always be a float
 _DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
+_WF_VERSION = 1.0
 
 
 @requires(hiphive, "hiphive is required for lattice dynamics workflow")
 def get_lattice_dynamics_wf(
     structure: Structure,
     common_settings: Dict = None,
-    symmetrize: bool = False,
-    symprec: float = 0.01,
-    min_atoms: Optional[int] = None,
-    max_atoms: Optional[int] = None,
-    num_nn_dists: float = 5.,
-    force_diagonal_transformation: bool = True,
-    rattle_stds: Optional[List[float]] = None,
-    min_nn_scale: float = MIN_NN_SCALE,
-    min_num_equivalent_sites: int = 100,
-    max_num_supercells: int = 30,
-    dynamic_static_calcs: bool = False,
+    vasp_input_set: Optional[VaspInputSet] = None,
+    supercell_matrix_kwargs: Optional[dict] = None,
+    num_supercell_kwargs: Optional[dict] = None,
+    perturbed_structure_kwargs: Optional[dict] = None,
     calculate_lattice_thermal_conductivity: bool = False,
     thermal_conductivity_temperature: Union[float, Dict] = 300,
     shengbte_cmd: str = SHENGBTE_CMD,
@@ -99,38 +91,21 @@ def get_lattice_dynamics_wf(
 
     Args:
         structure: Initial structure.
-        common_settings: Common settings dict.
-        symmetrize: Whether to symmetrize the structure before running the
-            workflow.
-        symprec: Symmetry precision for determining the symmetry of the
-            structure.
-        min_atoms: Minimum number of atoms to constrain the supercell.
-        max_atoms: Maximum number of atoms to constrain the supercell.
-        num_nn_dists: Number of nearest neighbor distances that the shortest
-            direction of the supercell must be as long as.
-        force_diagonal_transformation: If True, the supercell
-            transformation will be constrained to have a diagonal
-            transformation matrix. If False, the supercell transformation
-            will not be constrained to be diagonal (resulting in a more
-            cubic supercell). A diagonal supercell is required to calculate
-            lattice thermal conductivity.
-        rattle_stds: List of standard deviations (in normal distribution) to
-            to use when displacing the sites.
-        min_nn_scale: Controls the minimum interatomic distance used for
-            computing the probability for each rattle move.
-        min_num_equivalent_sites: The minimum number of equivalent sites for
-            each species. The aim is to have each equivalent site represented at
-            least ``min_num_equivalent_sites`` times. For example, if a symmetry
-            inequivalent site appears 26 times in the supercell structure,
-            and ``min_num_equivalent_sites`` is 100, then at least 4 supercells
-            are required for that site to appear over 100 times.
-        max_num_supercells: The maximum number of supercells per displacement.
-            For very unsymmetric structures, this imposes a hard limit on
-            the number of sites generated due to ``min_num_equivalent_sites``.
-        dynamic_static_calcs: If True and hiPhive fails to return all real
-             harmonic phonon frequencies on the first try, then the workflow
-             will dynamically create more static perturbed supercell
-             calculations with larger displacements to improve the fitting.
+        common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
+            and "user_incar_settings" keys.
+        vasp_input_set: Vasp input set for perturbed structure calculations.
+        supercell_matrix_kwargs: Options that control the size of the supercell
+            that will be perturbed. Will be passed directly to
+            CubicSupercellTransformation in
+            pymatgen.transformations.advanced_transformations. Note, a diagonal
+            supercell is required to calculate lattice thermal conductivity.
+        num_supercell_kwargs: Options that control the number of supercells
+            generated per perturbation standard deviation distance. See the
+            docstring of ``get_num_supercells`` for more details.
+        perturbed_structure_kwargs: Options that control the number of
+            and magnitude of atomic displacements. Currently, the options are
+            "rattle_std", "n_configs_per_std", and "min_nn_scale". See the
+            docstring for ``get_perturbed_structure_wf`` for more details.
         calculate_lattice_thermal_conductivity: If True and force constant
             fitting does not return imaginary modes, then use ShengBTE to
             calculate the lattice thermal conductivity.
@@ -142,168 +117,170 @@ def get_lattice_dynamics_wf(
             to all the previous fireworks' fworker. If str, the ShengBTE
             firework's fworker will be set to shengbte_fworker.
    """
+    supercell_matrix_kwargs = supercell_matrix_kwargs or {}
+    num_supercell_kwargs = num_supercell_kwargs or {}
+    perturbed_structure_kwargs = perturbed_structure_kwargs or {}
     common_settings = _get_common_settings(common_settings)
-    uis = deepcopy(_static_uis)
-    uis.update(common_settings.get("user_incar_settings", {}))
-
-    if not force_diagonal_transformation and calculate_lattice_thermal_conductivity:
-        raise ValueError(
-            "Diagonal transformation required to calculate lattice thermal "
-            "conductivity"
-        )
+    db_file = common_settings["DB_FILE"]
 
-    sga = SpacegroupAnalyzer(structure, symprec=symprec)
-    if symmetrize:
-        structure = sga.get_primitive_standard_structure()
+    if calculate_lattice_thermal_conductivity:
+        if supercell_matrix_kwargs.get("force_diagonal", True):
+            warnings.warn(
+                "Diagonal transformation required to calculate lattice thermal "
+                "conductivity. Forcing diagonal matrix"
+            )
+        supercell_matrix_kwargs["force_diagonal"] = True
 
-    st = CubicSupercellTransformation(
-        min_atoms,
-        max_atoms,
-        num_nn_dists,
-        force_diagonal_transformation=force_diagonal_transformation,
-    )
+    st = CubicSupercellTransformation(**supercell_matrix_kwargs)
     supercell = st.apply_transformation(structure)
+    supercell_matrix = st.transformation_matrix
 
-    n_cells = _get_n_cells(sga, min_num_equivalent_sites, max_num_supercells)
-    perturbed_supercells, disp_dists, fws = get_perturbed_structure_fws(
-        supercell,
+    if "n_supercells" not in perturbed_structure_kwargs:
+        n_supercells = get_num_supercells(supercell, **num_supercell_kwargs)
+        perturbed_structure_kwargs["n_supercells"] = n_supercells
+
+    wf = get_perturbed_structure_wf(
+        structure,
+        supercell_matrix=supercell_matrix,
+        name="ld perturbed structure",
+        vasp_input_set=vasp_input_set,
         common_settings=common_settings,
-        user_incar_settings=uis,
-        rattle_stds=rattle_stds,
-        min_nn_scale=min_nn_scale,
-        n_configs_per_std=n_cells,
+        pass_forces=True,
+        **perturbed_structure_kwargs,
     )
 
-    logger.debug("Generating {} supercells per displacement".format(n_cells))
-    logger.debug("Using {} displacements".format(len(disp_dists)))
-    logger.debug("Displacements: {}".format(disp_dists))
-
-    wf_meta = {
-        "wf_uuid": str(uuid4()),
-        "wf_name": "LatticeDynamicsWF",
-        "wf_version": __lattice_dynamics_wf_version__,
-    }
-
-    # Add tasks to fit force constants
-    fit_forces = FitForceConstants(
-        db_file=common_settings["DB_FILE"],
-        wf_uuid=wf_meta["wf_uuid"],
-        parent_structure=structure,
-        supercell_structure=supercell,
-        supercell_matrix=st.transformation_matrix.tolist(),
-    )
-    forces_to_db = ForceConstantsToDB(
-        db_file=common_settings["DB_FILE"], wf_uuid=wf_meta["wf_uuid"],
-    )
-    fws.append(
-        Firework(
-            [fit_forces, forces_to_db],
-            name="Force Constant Fitting",
-            parents=fws[-len(perturbed_supercells):],
-        )
+    allow_fizzled = {"_allow_fizzled_parents": True}
+    fw_fit_force_constant = FitForceConstantsFW(
+        parents=wf.fws[wf.leaf_fw_ids], db_file=db_file, spec=allow_fizzled
     )
+    wf.fws.append(fw_fit_force_constant)
 
-    # Add ShengBTE tasks
-    run_shengbte = RunShengBTE(
-        db_file=common_settings["DB_FILE"],
-        wf_uuid=wf_meta["wf_uuid"],
-        structure=structure,
-        supercell_matrix=st.transformation_matrix.tolist(),
-        shengbte_cmd=shengbte_cmd,
-        temperature=thermal_conductivity_temperature,
-    )
-    shengbte_to_db = ShengBTEToDB(
-        db_file=common_settings["DB_FILE"],
-        wf_uuid=wf_meta["wf_uuid"],
-    )
-    fws.append(
-        Firework(
-            [run_shengbte, shengbte_to_db],
-            name="Lattice Thermal Conductivity",
-            parents=fws[-1]
+    if calculate_lattice_thermal_conductivity:
+        fw_lattice_conductivity = LatticeThermalConductivityFW(
+            parents=wf.fws[-1], db_file=db_file
         )
-    )
+        wf.fws.append(fw_lattice_conductivity)
 
     formula = structure.composition.reduced_formula
-    wf_name = "{} - lattice dynamics".format(formula)
+    wf.name = "{} - lattice dynamics".format(formula)
 
-    wf = Workflow(fws, name=wf_name)
-    wf = add_additional_fields_to_taskdocs(
-        wf, {"wf_meta": wf_meta}, task_name_constraint="VaspToDb"
-    )
+    # Add workflow meta data to all relevant *ToDb tasks.
+    wf_meta = {"wf_name": "LatticeDynamicsWF", "wf_version": _WF_VERSION}
+    for task_name in ["VaspToDb", "ShengBTEToDb", "ForceConstantsToDb"]:
+        wf = add_additional_fields_to_taskdocs(
+            wf, {"wf_meta": wf_meta}, task_name_constraint=task_name
+        )
 
     return wf
 
 
-def get_perturbed_structure_fws(
-    supercell: Structure,
+def get_perturbed_structure_wf(
+    structure: Structure,
+    supercell_matrix: Optional[np.ndarray],
+    name: str = "perturbed structure",
+    vasp_input_set: Optional[VaspInputSet] = None,
     common_settings: Optional[Dict] = None,
-    user_incar_settings: Optional[Dict] = None,
     rattle_stds: Optional[List[float]] = None,
     n_configs_per_std: int = 1,
     min_nn_scale: float = MIN_NN_SCALE,
-) -> List[Firework]:
+    pass_forces: bool = True,
+) -> Workflow:
     """
     Get static calculations to calculate the forces on each perturbed supercell.
 
     Args:
-        supercell: Parent supercell structure.
-        common_settings: Common settings dict
-        user_incar_settings: User incar settings override.
+        structure: Input structure.
+        supercell_matrix: Supercell transformation matrix
+        name: Transmuter firework name.
+        vasp_input_set: Vasp input set for perturbed structure calculations.
+        common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
+            and "user_incar_settings" keys.
         rattle_stds: List of standard deviations (in normal distribution) to
             to use when displacing the sites.
         n_configs_per_std: Number of structures to generate per rattle standard
             deviation.
         min_nn_scale: Controls the minimum interatomic distance used for
             computing the probability for each rattle move.
+        pass_forces: Whether to append the force and supercell structure
+            information into the perturbed_tasks key of the child fireworks.
 
     Returns:
-        A list of static fireworks.
+        The workflow.
     """
-    user_incar_settings = user_incar_settings if user_incar_settings else {}
     common_settings = _get_common_settings(common_settings)
+    vasp_cmd = common_settings["VASP_CMD"]
+    db_file = common_settings["DB_FILE"]
+    user_incar_settings = common_settings["user_incar_settings"]
 
-    # Generate list of perturbed supercells
-    perturbed_supercells, disp_dists = generate_perturbed_structures(
-        supercell,
-        rattle_stds=rattle_stds,
-        n_configs_per_std=n_configs_per_std,
-        min_nn_scale=min_nn_scale
-    )
+    if supercell_matrix is None:
+        supercell_matrix = np.eye(3)
 
-    fws = []
-    data = enumerate(zip(perturbed_supercells, disp_dists))
-    for i, (supercell, dist) in data:
-        name = "perturbed supercell, idx: {}, disp_val: {:.3f} static".format(
-            i, dist
-        )
+    supercell_matrix = np.asarray(supercell_matrix).tolist()
+
+    if rattle_stds is None:
+        rattle_stds = np.linspace(0.01, 0.1, 5)
+
+    if vasp_input_set is None:
+        vasp_input_set = MPStaticSet(structure)
+    else:
+        # ensure we don't override the user_incar_settings in the input set
+        user_incar_settings.update(vasp_input_set.user_incar_settings)
+    vasp_input_set.user_incar_settings = user_incar_settings
 
-        vis = MPStaticSet(supercell, user_incar_settings=user_incar_settings)
-        static_fw = StaticFW(
-            supercell,
-            vasp_input_set=vis,
-            vasp_cmd=common_settings["VASP_CMD"],
-            db_file=common_settings["DB_FILE"],
+    min_distance = np.min(structure.distance_matrix) * min_nn_scale
+    all_rattle_stds = np.repeat(rattle_stds, n_configs_per_std)
+
+    logger.debug("Using {} supercells / displacement".format(n_configs_per_std))
+    logger.debug("Using {} rattle stds".format(len(rattle_stds)))
+    logger.debug("Rattle stds: {}".format(rattle_stds))
+
+    fws = []
+    for i, rattle_std in all_rattle_stds:
+        name = "{} : i = {}; rattle_std : {:.3f}".format(name, i, rattle_std)
+        transformations = [
+            "SupercellTransformation", "MonteCarloRattleTransformation"
+        ]
+        transformation_params = [
+            {"scaling_matrix": supercell_matrix},
+            {"rattle_std": rattle_std, "min_distance": min_distance}
+        ]
+
+        fw = TransmuterFW(
             name=name,
+            structure=structure,
+            transformations=transformations,
+            transformation_params=transformation_params,
+            vasp_input_set=vasp_input_set,
+            copy_vasp_outputs=True,
+            vasp_cmd=vasp_cmd,
+            db_file=db_file,
         )
-        static_fw.spec["displacement_value"] = dist
-        fws.append(static_fw)
 
-    return fws
+        if pass_forces:
+            pass_dict = {
+                'parent_structure': structure.to_json(),
+                'supercell_matrix': supercell_matrix,
+                'forces': '>>output.ionic_steps.-1.forces',
+                'structure': '>>output.ionic_steps.-1.structure',
+            }
+            pass_task = pass_vasp_result(
+                pass_dict=pass_dict,
+                mod_spec_cmd="_push",
+                mod_spec_key="perturbed_tasks"
+            )
+            fw.tasks.append(pass_task)
 
+        fws.append(fw)
 
-def _get_common_settings(common_settings: Optional[Dict]):
-    common_settings = common_settings or {}
-    for k, v in _DEFAULT_SETTINGS.items():
-        if k not in common_settings:
-            common_settings[k] = v
-    return common_settings
+    wfname = "{}: {}".format(structure.composition.reduced_formula, name)
+    return Workflow(fws, name=wfname)
 
 
-def _get_n_cells(
-    spacegroup_analyzer: SpacegroupAnalyzer,
-    min_num_equivalent_sites: int,
-    max_num_structure: int,
+def get_num_supercells(
+    supercell_structure: Structure,
+    symprec: float = 0.01,
+    min_num_equivalent_sites: int = 100,
+    max_num_supercells: int = 30,
 ) -> int:
     """
     Get the number of supercells to run per rattle standard deviation.
@@ -314,9 +291,10 @@ def _get_n_cells(
     I.e., 4 * 26 > 100.
 
     Args:
-        spacegroup_analyzer: A spacegroup analyzer object.
+        supercell_structure: The ideal supercell structure.
+        symprec: The symmetry precision for determining if sites are equivalent.
         min_num_equivalent_sites: The minimum number of equivalent sites.
-        max_num_structure: The maximum number of cells.
+        max_num_supercells: The maximum number of cells.
 
     Returns:
         The number of supercells needed for all symmetry inequivalent sites to
@@ -324,9 +302,23 @@ def _get_n_cells(
     """
     # get the equivalent sites in the structure and calculate the smallest
     # site degeneracy
-    equiv_idxs = spacegroup_analyzer.get_symmetry_dataset()["equivalent_atoms"]
+    sga = SpacegroupAnalyzer(supercell_structure, symprec=symprec)
+    equiv_idxs = sga.get_symmetry_dataset()["equivalent_atoms"]
     equiv_counts = np.unique(equiv_idxs, return_counts=True)
     min_count = np.min(equiv_counts)
 
     n_cells = math.ceil(min_num_equivalent_sites / min_count)
-    return min(n_cells, max_num_structure)
+    return min(n_cells, max_num_supercells)
+
+
+def _get_common_settings(common_settings: Optional[Dict]):
+    common_settings = common_settings or {}
+    for k, v in _DEFAULT_SETTINGS.items():
+        if k not in common_settings:
+            common_settings[k] = v
+
+    user_incar_settings = deepcopy(_static_user_incar_settings)
+    user_incar_settings.update(common_settings.get("user_incar_settings", {}))
+    common_settings["user_incar_settings"] = user_incar_settings
+
+    return common_settings

From 6c56cea16ed8cb317016aed5c29c0ce68e34f3ff Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 15:45:12 -0800
Subject: [PATCH 063/207] Add pymongo to requirements

---
 requirements.txt | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 000000000..a8b26d3e4
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,16 @@
+numpy==1.16.4
+scipy==1.2.0
+FireWorks==1.9.0
+pymatgen_diffusion==2019.2.28
+monty==2.0.4
+paramiko==2.4.2
+tqdm==4.32.1
+six==1.12.0
+pybtex==0.22.2
+ruamel.yaml==0.15.96
+pandas==0.24.2
+pymatgen==2019.5.8
+custodian==2019.2.10
+networkx==2.2
+pydash==4.7.4
+pymongo==3.10.1

From 294602dff6d2b1eea7c08a70ed62e2a504873a57 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 15:55:52 -0800
Subject: [PATCH 064/207] Remove circular imports

---
 atomate/vasp/analysis/lattice_dynamics.py     | 68 ++-----------------
 atomate/vasp/analysis/phonopy.py              |  2 +
 atomate/vasp/firetasks/lattice_dynamics.py    | 12 ++--
 .../vasp/workflows/base/lattice_dynamics.py   | 15 ++--
 4 files changed, 16 insertions(+), 81 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index c6d1a05ce..bdb425160 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -1,76 +1,22 @@
 import numpy as np
 
 from itertools import product
-from typing import Optional, Tuple, List, Dict
+from typing import Tuple, List, Dict
 
 from pymatgen import Structure
-from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.phonopy import get_phonopy_structure
 
 from atomate.utils.utils import get_logger
-from atomate.vasp.workflows.base.lattice_dynamics import (
-    MIN_NN_SCALE,
-    FIT_METHOD,
-    MAX_IMAGINARY_FREQ,
-    IMAGINARY_TOL,
-    MAX_N_IMAGINARY,
-)
 
 __author__ = "Rees Chang, Alex Ganose"
 __email__ = "rc564@cornell.edu, aganose@lbl.gov"
 
-
 logger = get_logger(__name__)
 
-
-def generate_perturbed_structures(
-    structure: Structure,
-    rattle_stds: Optional[List[float]] = None,
-    n_configs_per_std: int = 1,
-    min_nn_scale: float = MIN_NN_SCALE,
-) -> Tuple[List[Structure], np.ndarray]:
-    """
-    Generate a list of structures with perturbed atomic sites.
-
-    Rattling atom `i` is carried out as a Monte Carlo move that is accepted with
-    a probability determined from the minimum interatomic distance
-    :math:`d_{ij}`.  If :math:`\\min(d_{ij})` is smaller than :math:`d_{min}`
-    the move is only accepted with a low probability.
-
-    :math:`d_{min}` is calculated as the smallest nearest neighbor distance
-    times ``min_nn_fraction``.
-
-    Args:
-        structure: Structure whose atomic sites are to be perturbed.
-        rattle_stds: List of standard deviations (in normal distribution) to
-            to use when displacing the sites.
-        n_configs_per_std: Number of structures to generate per rattle standard
-            deviation.
-        min_nn_scale: Controls the minimum interatomic distance used for
-            computing the probability for each rattle move.
-
-    Returns:
-        A tuple of the ``(structures, displacements)``. Where ``structures`` is
-        a list of randomly displaced structures, and ``displacements`` is
-        the displacement distance for each structure.
-    """
-    from hiphive.structure_generation import generate_mc_rattled_structures
-
-    if rattle_stds is None:
-        rattle_stds = np.linspace(0.01, 0.1, 5)
-
-    min_distance = np.min(structure.distance_matrix) * min_nn_scale
-    atoms = AseAtomsAdaptor.get_atoms(structure)
-
-    perturbed_structures = []
-    for rattle_std in rattle_stds:
-        seed = np.random.randint(1, 10000000000)
-        structures = generate_mc_rattled_structures(
-            atoms, n_configs_per_std, rattle_std, min_distance, seed=seed
-        )
-        perturbed_structures.extend(structures)
-
-    return perturbed_structures, rattle_stds
+MAX_IMAGINARY_FREQ = 10  # in THz
+IMAGINARY_TOL = 0.025  # in THz
+MAX_N_IMAGINARY = 3
+FIT_METHOD = "least-squares"
 
 
 def get_cutoffs(structure: Structure):
@@ -204,9 +150,7 @@ def fit_force_constants(
     }
     n_cutoffs = len(all_cutoffs)
     for i, cutoffs in enumerate(all_cutoffs):
-        logger.info(
-            "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
-        )
+        logger.info("Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs))
         sc = get_structure_container(cutoffs, structures)
         opt = Optimizer(sc.get_fit_data(), fit_method)
         opt.train()
diff --git a/atomate/vasp/analysis/phonopy.py b/atomate/vasp/analysis/phonopy.py
index 3923895ab..451a05b08 100644
--- a/atomate/vasp/analysis/phonopy.py
+++ b/atomate/vasp/analysis/phonopy.py
@@ -28,6 +28,8 @@
 __email__ = "kmathew@lbl.gov, aganose@lbl.gov"
 >>>>>>> 728556b6 (Add methods for generating phonon band structure & DOS)
 
+MESH_DENSITY = 100.  # should always be a float
+
 # TODO: @matk86 - unit tests?
 
 
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index eb59783ba..afac7df2d 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -13,20 +13,13 @@
 from atomate.vasp.analysis.lattice_dynamics import (
     fit_force_constants,
     get_cutoffs,
-)
+    MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, IMAGINARY_TOL, FIT_METHOD)
 from atomate.vasp.analysis.phonopy import (
     get_phonon_dos,
     get_phonon_band_structure,
     get_line_mode_phonon_band_structure,
 )
 from atomate.vasp.database import VaspCalcDb
-from atomate.vasp.workflows.base.lattice_dynamics import (
-    MAX_N_IMAGINARY,
-    MAX_IMAGINARY_FREQ,
-    IMAGINARY_TOL,
-    FIT_METHOD,
-    DEFAULT_TEMPERATURE,
-    MESH_DENSITY)
 from fireworks import explicit_serialize, FiretaskBase, FWAction
 import numpy as np
 
@@ -48,6 +41,9 @@
 
 logger = get_logger(__name__)
 
+# define shared constants
+DEFAULT_TEMPERATURE = 300
+
 
 @explicit_serialize
 class CollectPerturbedStructures(FiretaskBase):
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a21daf112..a3d186df4 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -6,7 +6,7 @@
 from copy import deepcopy
 from typing import List, Dict, Optional, Union
 
-
+from atomate.vasp.firetasks.lattice_dynamics import DEFAULT_TEMPERATURE
 from pymatgen.io.vasp.sets import MPStaticSet, VaspInputSet
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
@@ -47,14 +47,7 @@
     "LASPH": True,
 }
 
-# define shared constants
-MIN_NN_SCALE = 0.85
-MAX_IMAGINARY_FREQ = 10  # in THz
-IMAGINARY_TOL = 0.025  # in THz
-MAX_N_IMAGINARY = 3
-DEFAULT_TEMPERATURE = 300
-FIT_METHOD = "least-squares"
-MESH_DENSITY = 100.  # should always be a float
+
 _DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
 _WF_VERSION = 1.0
 
@@ -68,7 +61,7 @@ def get_lattice_dynamics_wf(
     num_supercell_kwargs: Optional[dict] = None,
     perturbed_structure_kwargs: Optional[dict] = None,
     calculate_lattice_thermal_conductivity: bool = False,
-    thermal_conductivity_temperature: Union[float, Dict] = 300,
+    thermal_conductivity_temperature: Union[float, Dict] = DEFAULT_TEMPERATURE,
     shengbte_cmd: str = SHENGBTE_CMD,
     shengbte_fworker: Optional[str] = None,
 ):
@@ -182,7 +175,7 @@ def get_perturbed_structure_wf(
     common_settings: Optional[Dict] = None,
     rattle_stds: Optional[List[float]] = None,
     n_configs_per_std: int = 1,
-    min_nn_scale: float = MIN_NN_SCALE,
+    min_nn_scale: float = 0.85,
     pass_forces: bool = True,
 ) -> Workflow:
     """

From 95b2a6070abe9d42cee4ee6088262fa567a71cbe Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 16:37:12 -0800
Subject: [PATCH 065/207] Use proper name for 3rd order fc

---
 atomate/vasp/firetasks/lattice_dynamics.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index afac7df2d..3af069f71 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -18,7 +18,7 @@
     get_phonon_dos,
     get_phonon_band_structure,
     get_line_mode_phonon_band_structure,
-)
+    MESH_DENSITY)
 from atomate.vasp.database import VaspCalcDb
 from fireworks import explicit_serialize, FiretaskBase, FWAction
 import numpy as np
@@ -175,7 +175,7 @@ def run_task(self, fw_spec):
             force_constants.write("force_constants.fcs")
 
             atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-            force_constants.write_to_shengBTE("FORCE_CONSTANTS_3ND", atoms)
+            force_constants.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
             force_constants.write_to_phonopy(
                 "FORCE_CONSTANTS_2ND", format="text"
             )
@@ -287,7 +287,7 @@ def run_task(self, fw_spec):
 class RunShengBTE(FiretaskBase):
     """
     Run ShengBTE to calculate lattice thermal conductivity. Presumes
-    the FORCE_CONSTANTS_3ND and FORCE_CONSTANTS_2ND, and a "structure_data.json"
+    the FORCE_CONSTANTS_3RD and FORCE_CONSTANTS_2ND, and a "structure_data.json"
     file, with the keys "structure", " and "supercell_matrix" is in the current
     directory.
 
@@ -299,12 +299,12 @@ class RunShengBTE(FiretaskBase):
         temperature (float or dict): The temperature to calculate the lattice
             thermal conductivity for. Can be given as a single float, or a
             dictionary with the keys "min", "max", "step".
-        shengbte_control_kwargs (dict): Options to be included in the ShengBTE
-            control file.
+        control_kwargs (dict): Options to be included in the ShengBTE control
+            file.
     """
 
     required_params = ["shengbte_cmd"]
-    optional_params = ["temperature", "shengbte_control_kwargs"]
+    optional_params = ["temperature", "control_kwargs"]
 
     def run_task(self, fw_spec):
         structure_data = loadfn("structure_data.json")
@@ -318,7 +318,7 @@ def run_task(self, fw_spec):
             "temperature": self.get("temperature", DEFAULT_TEMPERATURE),
             "scell": np.diag(supercell_matrix),
         }
-        control_dict.update(self.get("shengbte_control_kwargs", {}))
+        control_dict.update(self.get("control_kwargs", {}))
         control = Control.from_structure(structure, **control_dict)
         control.to_file()
 

From a3ad5f2c11cd7c336a74fa7fbc8aed53658c346b Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 16:37:44 -0800
Subject: [PATCH 066/207] Refactor lattice dynamics fireworks

---
 atomate/vasp/fireworks/lattice_dynamics.py | 103 ++++++++++-----------
 1 file changed, 47 insertions(+), 56 deletions(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 827232d25..f0beb661f 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -1,10 +1,14 @@
 from typing import Optional, List, Union
 
-from atomate.common.firetasks.glue_tasks import PassCalcLocs
+from atomate.common.firetasks.glue_tasks import PassCalcLocs, \
+    CopyFilesFromCalcLoc, CopyFiles
+from atomate.vasp.analysis.lattice_dynamics import IMAGINARY_TOL, \
+    MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, FIT_METHOD
+from atomate.vasp.analysis.phonopy import MESH_DENSITY
+from atomate.vasp.config import SHENGBTE_CMD
 from atomate.vasp.firetasks.lattice_dynamics import CollectPerturbedStructures, \
-    RunHiPhive, ForceConstantsToDb
-from atomate.vasp.workflows.base.lattice_dynamics import IMAGINARY_TOL, \
-    MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, FIT_METHOD, MESH_DENSITY
+    RunHiPhive, ForceConstantsToDb, DEFAULT_TEMPERATURE, ShengBTEToDb, \
+    RunShengBTE
 from fireworks import Firework
 
 __author__ = "Alex Ganose"
@@ -16,7 +20,7 @@ class FitForceConstantsFW(Firework):
     def __init__(
         self,
         name="Fit Force Constants",
-        parents: Union[Firework, List[Firework]] = None,
+        parents: Optional[Union[Firework, List[Firework]]] = None,
         db_file: str = None,
         cutoffs: Optional[List[List[float]]] = None,
         imaginary_tol: float = IMAGINARY_TOL,
@@ -59,10 +63,10 @@ def __init__(
             max_imaginary_freq=max_imaginary_freq,
             fit_method=fit_method
         )
-        fc_to_db = ForceConstantsToDb(db_file=db_file,mesh_density=mesh_density)
+        to_db = ForceConstantsToDb(db_file=db_file, mesh_density=mesh_density)
         pass_locs = PassCalcLocs(name=name)
 
-        tasks = [collect_structures, fit_constants, fc_to_db, pass_locs]
+        tasks = [collect_structures, fit_constants, to_db, pass_locs]
         super().__init__(tasks, parents=parents, name=name, **kwargs)
 
 
@@ -70,65 +74,52 @@ class LatticeThermalConductivityFW(Firework):
 
     def __init__(
             self,
-            name="fit force constants",
-            parents: Union[Firework, List[Firework]] = None,
+            name="Lattice Thermal Conductivity",
+            parents: Optional[Union[Firework, List[Firework]]] = None,
+            prev_calc_dir: Optional[str] = None,
             db_file: str = None,
-            cutoffs: Optional[List[List[float]]] = None,
-            imaginary_tol: float = IMAGINARY_TOL,
-            max_n_imaginary: int = MAX_N_IMAGINARY,
-            max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
-            fit_method: str = FIT_METHOD,
-            mesh_density: float = MESH_DENSITY,
-            additional_fields: dict = None,
+            shengbte_cmd: str = SHENGBTE_CMD,
+            temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
+            shengbte_control_kwargs: Optional[dict] = None,
             **kwargs
     ):
         """
-        Compile perturbed supercell calculations and fit force constants
-        using hiPhive.
+        Calculate the lattice thermal conductivity using ShengBTE.
 
         Args:
-            wf_uuid: Workflow identifier, from which the perturbed supercell
-                static calculations will be compiled.
-            parents: Parent(s) of this Firework.
             name: Name of this FW.
+            parents: Parent(s) of this Firework.
+            prev_calc_dir: Path to a directory containing the force constant
+                information. Will override ``parents`` when collecting the force
+                constants to run ShengBTE.
             db_file: Path to a db file.
-            cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
-                will be generated based on the structure (default).
-            imaginary_tol: Tolerance used to decide if a phonon mode is
-                imaginary, in THz.
-            max_n_imaginary: Maximum number of imaginary modes allowed in the
-                final fitted force constant solution. If this criteria is not
-                reached by any cutoff combination the Firework will fizzle.
-            max_imaginary_freq: Maximum allowed imaginary frequency in the
-                final fitted force constant solution. If this criteria is not
-                reached by any cutoff combination this FireTask will fizzle.
-            fit_method: Method used for fitting force constants. This can be
-                any of the values allowed by the hiphive ``Optimizer`` class.
-            mesh_density: The density of the q-point mesh used to calculate the
-                phonon density of states. See the docstring for the ``mesh``
-                argument in Phonopy.init_mesh() for more details.
-            additional_fields: Additional fields added to the document, such as
-                user-defined tags, name, ids, etc.
+            shengbte_cmd: The name of the shengbte executable to run. Supports
+                env_chk.
+            temperature: The temperature to calculate the lattice thermal
+                conductivity for. Can be given as a single float, or a
+                dictionary with the keys "min", "max", "step".
+            shengbte_control_kwargs: Options to be included in the ShengBTE
+                control file.
             **kwargs: Other kwargs that are passed to Firework.__init__.
         """
-        fw_name = "{}-{}".format(wf_uuid, name)
-        additional_fields = additional_fields or {}
+        # files needed to run ShengBTE
+        files = [
+            "structure_data.json", "FORCE_CONSTANTS_2ND", "FORCE_CONSTANTS_3RD"
+        ]
 
-        collect_structures = CollectPerturbedStructures(db_file, wf_uuid)
-        fit_constants = RunHiPhive(
-            cutoffs=cutoffs,
-            imaginary_tol=imaginary_tol,
-            max_n_imaginary=max_n_imaginary,
-            max_imaginary_freq=max_imaginary_freq,
-            fit_method=fit_method
-        )
-        fc_to_db = ForceConstantsToDb(
-            db_file=db_file,
-            wf_uuid=wf_uuid,
-            mesh_density=mesh_density,
-            additional_fields=additional_fields
+        if prev_calc_dir:
+            copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+        elif parents:
+            copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+        else:
+            raise ValueError("Must specify parents or prev_calc_dir.")
+
+        run_shengbte = RunShengBTE(
+            shengbte_cmd=shengbte_cmd,
+            temperature=temperature,
+            control_kwargs=shengbte_control_kwargs
         )
-        pass_locs = PassCalcLocs(name=name)
+        shengbte_to_db = ShengBTEToDb(db_file=db_file)
 
-        tasks = [collect_structures, fit_constants, fc_to_db, pass_locs]
-        super().__init__(tasks, parents=parents, name=fw_name, **kwargs)
+        tasks = [copy_files, run_shengbte, shengbte_to_db]
+        super().__init__(tasks, parents=parents, name=name, **kwargs)

From 159c6f9bcde8333b9f1b045d6a9d3aac24d466c8 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 16:38:05 -0800
Subject: [PATCH 067/207] Use latest fireworks in LD workflow

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a3d186df4..6e1101bc1 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -14,7 +14,6 @@
     CubicSupercellTransformation,
 )
 
-from monty.dev import requires
 from fireworks import Workflow
 
 from atomate.utils.utils import get_logger
@@ -25,11 +24,6 @@
 from atomate.vasp.fireworks.lattice_dynamics import FitForceConstantsFW, \
     LatticeThermalConductivityFW
 
-try:
-    import hiphive
-except ImportError:
-    hiphive = False
-
 __author__ = "Rees Chang, Alex Ganose"
 __email__ = "rc564@cornell.edu, aganose@lbl.gov"
 __date__ = "July 2019"
@@ -52,7 +46,6 @@
 _WF_VERSION = 1.0
 
 
-@requires(hiphive, "hiphive is required for lattice dynamics workflow")
 def get_lattice_dynamics_wf(
     structure: Structure,
     common_settings: Dict = None,
@@ -150,14 +143,20 @@ def get_lattice_dynamics_wf(
 
     if calculate_lattice_thermal_conductivity:
         fw_lattice_conductivity = LatticeThermalConductivityFW(
-            parents=wf.fws[-1], db_file=db_file
+            parents=wf.fws[-1],
+            db_file=db_file,
+            shengbte_cmd=shengbte_cmd,
+            temperature=thermal_conductivity_temperature
         )
+        if shengbte_fworker:
+            fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
+
         wf.fws.append(fw_lattice_conductivity)
 
     formula = structure.composition.reduced_formula
     wf.name = "{} - lattice dynamics".format(formula)
 
-    # Add workflow meta data to all relevant *ToDb tasks.
+    # Add workflow metadata to all relevant *ToDb tasks.
     wf_meta = {"wf_name": "LatticeDynamicsWF", "wf_version": _WF_VERSION}
     for task_name in ["VaspToDb", "ShengBTEToDb", "ForceConstantsToDb"]:
         wf = add_additional_fields_to_taskdocs(

From 705e4ac69127b5cc002ba72dddcdb0ba28afbe82 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 16:41:12 -0800
Subject: [PATCH 068/207] Run isort and black

---
 atomate/vasp/analysis/lattice_dynamics.py     |  13 +-
 atomate/vasp/analysis/phonopy.py              |   4 +-
 atomate/vasp/firetasks/lattice_dynamics.py    |  31 ++--
 atomate/vasp/fireworks/lattice_dynamics.py    | 142 ++++++++++--------
 .../vasp/workflows/base/lattice_dynamics.py   |  46 +++---
 5 files changed, 127 insertions(+), 109 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index bdb425160..8f5c6f71a 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -1,12 +1,11 @@
-import numpy as np
-
 from itertools import product
-from typing import Tuple, List, Dict
+from typing import Dict, List, Tuple
 
-from pymatgen import Structure
-from pymatgen.io.phonopy import get_phonopy_structure
+import numpy as np
 
 from atomate.utils.utils import get_logger
+from pymatgen import Structure
+from pymatgen.io.phonopy import get_phonopy_structure
 
 __author__ = "Rees Chang, Alex Ganose"
 __email__ = "rc564@cornell.edu, aganose@lbl.gov"
@@ -150,7 +149,9 @@ def fit_force_constants(
     }
     n_cutoffs = len(all_cutoffs)
     for i, cutoffs in enumerate(all_cutoffs):
-        logger.info("Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs))
+        logger.info(
+            "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
+        )
         sc = get_structure_container(cutoffs, structures)
         opt = Optimizer(sc.get_fit_data(), fit_method)
         opt.train()
diff --git a/atomate/vasp/analysis/phonopy.py b/atomate/vasp/analysis/phonopy.py
index 451a05b08..490dad612 100644
--- a/atomate/vasp/analysis/phonopy.py
+++ b/atomate/vasp/analysis/phonopy.py
@@ -16,7 +16,7 @@
     PhononBandStructure,
     PhononBandStructureSymmLine,
 )
-from pymatgen.phonon.dos import PhononDos, CompletePhononDos
+from pymatgen.phonon.dos import CompletePhononDos, PhononDos
 from pymatgen.symmetry.bandstructure import HighSymmKpath
 
 try:
@@ -28,7 +28,7 @@
 __email__ = "kmathew@lbl.gov, aganose@lbl.gov"
 >>>>>>> 728556b6 (Add methods for generating phonon band structure & DOS)
 
-MESH_DENSITY = 100.  # should always be a float
+MESH_DENSITY = 100.0  # should always be a float
 
 # TODO: @matk86 - unit tests?
 
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 3af069f71..70b792145 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -1,28 +1,30 @@
 import os
 import shlex
-
-from pathlib import Path
-
 from datetime import datetime
+from pathlib import Path
 
-from monty.serialization import dumpfn, loadfn
+import numpy as np
 from monty.dev import requires
+from monty.serialization import dumpfn, loadfn
 from pymongo import ReturnDocument
 
-from atomate.utils.utils import get_logger, env_chk
+from atomate.utils.utils import env_chk, get_logger
 from atomate.vasp.analysis.lattice_dynamics import (
+    FIT_METHOD,
+    IMAGINARY_TOL,
+    MAX_IMAGINARY_FREQ,
+    MAX_N_IMAGINARY,
     fit_force_constants,
     get_cutoffs,
-    MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, IMAGINARY_TOL, FIT_METHOD)
+)
 from atomate.vasp.analysis.phonopy import (
-    get_phonon_dos,
-    get_phonon_band_structure,
+    MESH_DENSITY,
     get_line_mode_phonon_band_structure,
-    MESH_DENSITY)
+    get_phonon_band_structure,
+    get_phonon_dos,
+)
 from atomate.vasp.database import VaspCalcDb
-from fireworks import explicit_serialize, FiretaskBase, FWAction
-import numpy as np
-
+from fireworks import FiretaskBase, FWAction, explicit_serialize
 from pymatgen import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.shengbte import Control
@@ -271,8 +273,9 @@ def run_task(self, fw_spec):
         # Get an id for the force constants
         mmdb.collection = mmdb.db["lattice_dynamics"]
         fc_id = mmdb.db.counter.find_one_and_update(
-            {"_id": "taskid"}, {"$inc": {"c": 1}},
-            return_document=ReturnDocument.AFTER
+            {"_id": "taskid"},
+            {"$inc": {"c": 1}},
+            return_document=ReturnDocument.AFTER,
         )["c"]
         metadata = {"fc_id": fc_id, "fc_dir": os.getcwd()}
         data.update(metadata)
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index f0beb661f..360e98c45 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -1,14 +1,26 @@
-from typing import Optional, List, Union
+from typing import List, Optional, Union
 
-from atomate.common.firetasks.glue_tasks import PassCalcLocs, \
-    CopyFilesFromCalcLoc, CopyFiles
-from atomate.vasp.analysis.lattice_dynamics import IMAGINARY_TOL, \
-    MAX_N_IMAGINARY, MAX_IMAGINARY_FREQ, FIT_METHOD
+from atomate.common.firetasks.glue_tasks import (
+    CopyFiles,
+    CopyFilesFromCalcLoc,
+    PassCalcLocs,
+)
+from atomate.vasp.analysis.lattice_dynamics import (
+    FIT_METHOD,
+    IMAGINARY_TOL,
+    MAX_IMAGINARY_FREQ,
+    MAX_N_IMAGINARY,
+)
 from atomate.vasp.analysis.phonopy import MESH_DENSITY
 from atomate.vasp.config import SHENGBTE_CMD
-from atomate.vasp.firetasks.lattice_dynamics import CollectPerturbedStructures, \
-    RunHiPhive, ForceConstantsToDb, DEFAULT_TEMPERATURE, ShengBTEToDb, \
-    RunShengBTE
+from atomate.vasp.firetasks.lattice_dynamics import (
+    DEFAULT_TEMPERATURE,
+    CollectPerturbedStructures,
+    ForceConstantsToDb,
+    RunHiPhive,
+    RunShengBTE,
+    ShengBTEToDb,
+)
 from fireworks import Firework
 
 __author__ = "Alex Ganose"
@@ -16,6 +28,31 @@
 
 
 class FitForceConstantsFW(Firework):
+    """
+    Compile perturbed supercell calculations and fit force constants
+    using hiPhive.
+
+    Args:
+        parents: Parent(s) of this Firework.
+        name: Name of this FW.
+        db_file: Path to a db file.
+        cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
+            will be generated based on the structure (default).
+        imaginary_tol: Tolerance used to decide if a phonon mode is
+            imaginary, in THz.
+        max_n_imaginary: Maximum number of imaginary modes allowed in the
+            final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination the Firework will fizzle.
+        max_imaginary_freq: Maximum allowed imaginary frequency in the
+            final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination this FireTask will fizzle.
+        fit_method: Method used for fitting force constants. This can be
+            any of the values allowed by the hiphive ``Optimizer`` class.
+        mesh_density: The density of the q-point mesh used to calculate the
+            phonon density of states. See the docstring for the ``mesh``
+            argument in Phonopy.init_mesh() for more details.
+        **kwargs: Other kwargs that are passed to Firework.__init__.
+    """
 
     def __init__(
         self,
@@ -30,38 +67,13 @@ def __init__(
         mesh_density: float = MESH_DENSITY,
         **kwargs
     ):
-        """
-        Compile perturbed supercell calculations and fit force constants
-        using hiPhive.
-
-        Args:
-            parents: Parent(s) of this Firework.
-            name: Name of this FW.
-            db_file: Path to a db file.
-            cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
-                will be generated based on the structure (default).
-            imaginary_tol: Tolerance used to decide if a phonon mode is
-                imaginary, in THz.
-            max_n_imaginary: Maximum number of imaginary modes allowed in the
-                final fitted force constant solution. If this criteria is not
-                reached by any cutoff combination the Firework will fizzle.
-            max_imaginary_freq: Maximum allowed imaginary frequency in the
-                final fitted force constant solution. If this criteria is not
-                reached by any cutoff combination this FireTask will fizzle.
-            fit_method: Method used for fitting force constants. This can be
-                any of the values allowed by the hiphive ``Optimizer`` class.
-            mesh_density: The density of the q-point mesh used to calculate the
-                phonon density of states. See the docstring for the ``mesh``
-                argument in Phonopy.init_mesh() for more details.
-            **kwargs: Other kwargs that are passed to Firework.__init__.
-        """
         collect_structures = CollectPerturbedStructures(db_file)
         fit_constants = RunHiPhive(
             cutoffs=cutoffs,
             imaginary_tol=imaginary_tol,
             max_n_imaginary=max_n_imaginary,
             max_imaginary_freq=max_imaginary_freq,
-            fit_method=fit_method
+            fit_method=fit_method,
         )
         to_db = ForceConstantsToDb(db_file=db_file, mesh_density=mesh_density)
         pass_locs = PassCalcLocs(name=name)
@@ -71,40 +83,42 @@ def __init__(
 
 
 class LatticeThermalConductivityFW(Firework):
+    """
+    Calculate the lattice thermal conductivity using ShengBTE.
+
+    Args:
+        name: Name of this FW.
+        parents: Parent(s) of this Firework.
+        prev_calc_dir: Path to a directory containing the force constant
+            information. Will override ``parents`` when collecting the force
+            constants to run ShengBTE.
+        db_file: Path to a db file.
+        shengbte_cmd: The name of the shengbte executable to run. Supports
+            env_chk.
+        temperature: The temperature to calculate the lattice thermal
+            conductivity for. Can be given as a single float, or a
+            dictionary with the keys "min", "max", "step".
+        shengbte_control_kwargs: Options to be included in the ShengBTE
+            control file.
+        **kwargs: Other kwargs that are passed to Firework.__init__.
+    """
 
     def __init__(
-            self,
-            name="Lattice Thermal Conductivity",
-            parents: Optional[Union[Firework, List[Firework]]] = None,
-            prev_calc_dir: Optional[str] = None,
-            db_file: str = None,
-            shengbte_cmd: str = SHENGBTE_CMD,
-            temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
-            shengbte_control_kwargs: Optional[dict] = None,
-            **kwargs
+        self,
+        name="Lattice Thermal Conductivity",
+        parents: Optional[Union[Firework, List[Firework]]] = None,
+        prev_calc_dir: Optional[str] = None,
+        db_file: str = None,
+        shengbte_cmd: str = SHENGBTE_CMD,
+        temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
+        shengbte_control_kwargs: Optional[dict] = None,
+        **kwargs
     ):
-        """
-        Calculate the lattice thermal conductivity using ShengBTE.
-
-        Args:
-            name: Name of this FW.
-            parents: Parent(s) of this Firework.
-            prev_calc_dir: Path to a directory containing the force constant
-                information. Will override ``parents`` when collecting the force
-                constants to run ShengBTE.
-            db_file: Path to a db file.
-            shengbte_cmd: The name of the shengbte executable to run. Supports
-                env_chk.
-            temperature: The temperature to calculate the lattice thermal
-                conductivity for. Can be given as a single float, or a
-                dictionary with the keys "min", "max", "step".
-            shengbte_control_kwargs: Options to be included in the ShengBTE
-                control file.
-            **kwargs: Other kwargs that are passed to Firework.__init__.
-        """
         # files needed to run ShengBTE
         files = [
-            "structure_data.json", "FORCE_CONSTANTS_2ND", "FORCE_CONSTANTS_3RD"
+            "structure_data.json",
+            "FORCE_CONSTANTS_2ND",
+            "FORCE_CONSTANTS_3RD",
         ]
 
         if prev_calc_dir:
@@ -117,7 +131,7 @@ def __init__(
         run_shengbte = RunShengBTE(
             shengbte_cmd=shengbte_cmd,
             temperature=temperature,
-            control_kwargs=shengbte_control_kwargs
+            control_kwargs=shengbte_control_kwargs,
         )
         shengbte_to_db = ShengBTEToDb(db_file=db_file)
 
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 6e1101bc1..1d020b548 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -1,29 +1,28 @@
-import warnings
 import math
+import warnings
+from copy import deepcopy
+from typing import Dict, List, Optional, Union
 
 import numpy as np
 
-from copy import deepcopy
-from typing import List, Dict, Optional, Union
-
+from atomate.utils.utils import get_logger
+from atomate.vasp.config import DB_FILE, SHENGBTE_CMD, VASP_CMD
+from atomate.vasp.firetasks import pass_vasp_result
 from atomate.vasp.firetasks.lattice_dynamics import DEFAULT_TEMPERATURE
-from pymatgen.io.vasp.sets import MPStaticSet, VaspInputSet
+from atomate.vasp.fireworks.core import TransmuterFW
+from atomate.vasp.fireworks.lattice_dynamics import (
+    FitForceConstantsFW,
+    LatticeThermalConductivityFW,
+)
+from atomate.vasp.powerups import add_additional_fields_to_taskdocs
+from fireworks import Workflow
 from pymatgen.core.structure import Structure
+from pymatgen.io.vasp.sets import MPStaticSet, VaspInputSet
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.transformations.advanced_transformations import (
     CubicSupercellTransformation,
 )
 
-from fireworks import Workflow
-
-from atomate.utils.utils import get_logger
-from atomate.vasp.config import VASP_CMD, DB_FILE, SHENGBTE_CMD
-from atomate.vasp.fireworks.core import TransmuterFW
-from atomate.vasp.powerups import add_additional_fields_to_taskdocs
-from atomate.vasp.firetasks import pass_vasp_result
-from atomate.vasp.fireworks.lattice_dynamics import FitForceConstantsFW, \
-    LatticeThermalConductivityFW
-
 __author__ = "Rees Chang, Alex Ganose"
 __email__ = "rc564@cornell.edu, aganose@lbl.gov"
 __date__ = "July 2019"
@@ -146,7 +145,7 @@ def get_lattice_dynamics_wf(
             parents=wf.fws[-1],
             db_file=db_file,
             shengbte_cmd=shengbte_cmd,
-            temperature=thermal_conductivity_temperature
+            temperature=thermal_conductivity_temperature,
         )
         if shengbte_fworker:
             fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
@@ -230,11 +229,12 @@ def get_perturbed_structure_wf(
     for i, rattle_std in all_rattle_stds:
         name = "{} : i = {}; rattle_std : {:.3f}".format(name, i, rattle_std)
         transformations = [
-            "SupercellTransformation", "MonteCarloRattleTransformation"
+            "SupercellTransformation",
+            "MonteCarloRattleTransformation",
         ]
         transformation_params = [
             {"scaling_matrix": supercell_matrix},
-            {"rattle_std": rattle_std, "min_distance": min_distance}
+            {"rattle_std": rattle_std, "min_distance": min_distance},
         ]
 
         fw = TransmuterFW(
@@ -250,15 +250,15 @@ def get_perturbed_structure_wf(
 
         if pass_forces:
             pass_dict = {
-                'parent_structure': structure.to_json(),
-                'supercell_matrix': supercell_matrix,
-                'forces': '>>output.ionic_steps.-1.forces',
-                'structure': '>>output.ionic_steps.-1.structure',
+                "parent_structure": structure.to_json(),
+                "supercell_matrix": supercell_matrix,
+                "forces": ">>output.ionic_steps.-1.forces",
+                "structure": ">>output.ionic_steps.-1.structure",
             }
             pass_task = pass_vasp_result(
                 pass_dict=pass_dict,
                 mod_spec_cmd="_push",
-                mod_spec_key="perturbed_tasks"
+                mod_spec_key="perturbed_tasks",
             )
             fw.tasks.append(pass_task)
 

From 20cf9e322a5da35b00a3ad0c38c7a78db8daccc5 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 16:47:05 -0800
Subject: [PATCH 069/207] Update docstrings

---
 .../vasp/workflows/base/lattice_dynamics.py   | 25 +++++++++++--------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 1d020b548..44f806793 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -63,25 +63,30 @@ def get_lattice_dynamics_wf(
 
     A summary of the workflow is as follows:
 
-    1. Transform the input structure into a supercell
-    2. Transform the supercell into a list of supercells with all atoms
-       randomly perturbed from their original sites
-    3. Run static VASP calculations on each perturbed supercell to
-       calculate atomic forces.
-    4. Aggregate the forces and conduct the fit the force constants using
+    1. Calculate a supercell transformation matrix that brings the
+       structure as close as cubic as possible, with all lattice lengths
+       greater than 5 nearest neighbor distances.
+    2. Perturb the atomic sites for each supercell using a Monte Carlo
+       rattle procedure. The atoms are perturbed roughly according to a
+       normal deviation. A number of standard deviation perturbation distances
+       are included. Multiple supercells may be generated for each perturbation
+       distance.
+    3. Run static VASP calculations on each perturbed supercell to calculate
+       atomic forces.
+    4. Aggregate the forces and conduct the fit atomic force constants using
        the minimization schemes in hiPhive.
     5. Output the interatomic force constants, and phonon band structure and
        density of states to the database.
-    6. Optional: Solve the lattice thermal conductivity using ShengBTE.
+    6. Optional: Solve the lattice thermal conductivity using ShengBTE and
+       output to the database.
 
     Args:
         structure: Initial structure.
         common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
             and "user_incar_settings" keys.
         vasp_input_set: Vasp input set for perturbed structure calculations.
-        supercell_matrix_kwargs: Options that control the size of the supercell
-            that will be perturbed. Will be passed directly to
-            CubicSupercellTransformation in
+        supercell_matrix_kwargs: Options that control the size of the supercell.
+            Will be passed directly to CubicSupercellTransformation in
             pymatgen.transformations.advanced_transformations. Note, a diagonal
             supercell is required to calculate lattice thermal conductivity.
         num_supercell_kwargs: Options that control the number of supercells

From a9155057cda2cbf5662fefb5322a0db5ed5ce0e9 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 17:03:07 -0800
Subject: [PATCH 070/207] Rewrite preset workflow

---
 atomate/vasp/workflows/presets/core.py | 80 +++++++++++++++++---------
 1 file changed, 52 insertions(+), 28 deletions(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 6e91dcb62..a75f34427 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -1,6 +1,20 @@
+<<<<<<< HEAD
 from uuid import uuid4
 
 import numpy as np
+=======
+# coding: utf-8
+from typing import Optional
+
+from uuid import uuid4
+
+import numpy as np
+
+from atomate.vasp.workflows.base.lattice_dynamics import get_lattice_dynamics_wf
+from fireworks import Workflow
+from pymatgen import Structure
+from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPHSERelaxSet
+>>>>>>> 7cb526cb (Rewrite preset workflow)
 from pymatgen.io.vasp.inputs import Kpoints
 from pymatgen.io.vasp.sets import MPHSERelaxSet, MPRelaxSet, MPStaticSet
 
@@ -828,46 +842,56 @@ def wf_nudged_elastic_band(structures, parent, c=None):
     return wf
 
 
-def wf_lattice_thermal_conductivity(structure, c=None):
+def wf_lattice_thermal_conductivity(
+    structure: Structure,
+    c: Optional[dict] = None,
+    **ld_kwargs
+) -> Workflow:
     """
-    Lattice thermal conductivity workflow from the given structure and config
-    dict.
+    Get a workflow to calculate lattice thermal conductivity, including a tight
+    structure optimization.
 
     Args:
-        structure (Structure): input structure
-        c (dict): workflow config dict
+        structure: The input structure.
+        c: Workflow common settings dict. Supports the keys: "VASP_CMD",
+            "DB_FILE", and "user_incar_settings", "ADD_WF_METADATA", and the
+            options supported by "add_common_powerups".
+        **ld_kwargs: Keyword arguments to be passed directly to the lattice
+            dynamics base workflow.
 
     Returns:
-        Workflow
+        A workflow to calculate lattice thermal conductivity.
     """
-    from atomate.vasp.workflows.base.csld import CompressedSensingLatticeDynamicsWF
-    c = c or {}
-    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
-    db_file = c.get("DB_FILE", DB_FILE)
+    optimize_uis = {
+        "LAECHG": False,
+        'ENCUT': 700,
+        'ADDGRID': True,
+        'EDIFFG': -5e-4,
+        'PREC': 'Accurate',
+        "LREAL": False,
+        'EDIFF': 1e-8,
+        "ISMEAR": 0,
+        'LCHARG': False,
+        'LASPH': True
+    }
+    # wf_structure_optimization expects user incar settings in capitals
+    c["USER_INCAR_SETTINGS"].update(optimize_uis)
+    c["USER_INCAR_SETTINGS"].update(c.get("user_incar_settings", {}))
+    wf = wf_structure_optimization(structure, c=c)
 
-    ## DFPT AT GAMMA POINT
-
-    optimize = {"LAECHG": False, 'ENCUT': 700,
-                'ADDGRID': True, 'EDIFFG': -5e-4,
-                'PREC': 'Accurate', "LREAL": False,
-                'EDIFF': 1e-8, "ISMEAR": 0,
-                'LCHARG': False, 'LASPH': True}
-    vis_relax = MPRelaxSet(structure, user_incar_settings=optimize)
-    wf = get_wf(structure, "optimize_only.yaml", vis=vis_relax,
-                      params=[{"vasp_cmd": vasp_cmd, "db_file": db_file,
-                               "name": "phonon structure optimization"}])
-    wf_csld = CompressedSensingLatticeDynamicsWF(structure,
-                                                 num_nn_dists=5,
-                                                 num_displacements=10,
-                                                 supercells_per_displacement_distance=1).get_wf()
-
-    wf.append_wf(wf_csld, wf.leaf_fw_ids)
-    wf = add_common_powerups(wf, c)
+    wf_ld = get_lattice_dynamics_wf(
+        structure,
+        common_settings=c,
+        calculate_lattice_thermal_conductivity=True,
+        **ld_kwargs
+    )
+    wf.append_wf(wf_ld, wf.leaf_fw_ids)
 
     formula = structure.composition.reduced_formula
     wf_name = "{} - lattice thermal conductivity preset".format(formula)
     wf.name = wf_name
 
+    wf = add_common_powerups(wf, c)
     if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
         wf = add_wf_metadata(wf, structure)
 

From fda14fe2b0a7502593176528d4be31bdc105dd2b Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 17:24:21 -0800
Subject: [PATCH 071/207] Move most phonopy functions to pymatgen

---
 atomate/vasp/analysis/phonopy.py           | 138 ---------------------
 atomate/vasp/firetasks/lattice_dynamics.py |  15 +--
 2 files changed, 6 insertions(+), 147 deletions(-)

diff --git a/atomate/vasp/analysis/phonopy.py b/atomate/vasp/analysis/phonopy.py
index 490dad612..6871b199e 100644
--- a/atomate/vasp/analysis/phonopy.py
+++ b/atomate/vasp/analysis/phonopy.py
@@ -11,13 +11,6 @@
 __email__ = "kmathew@lbl.gov"
 =======
 from pymatgen import Structure
-from pymatgen.io.phonopy import get_phonopy_structure
-from pymatgen.phonon.bandstructure import (
-    PhononBandStructure,
-    PhononBandStructureSymmLine,
-)
-from pymatgen.phonon.dos import CompletePhononDos, PhononDos
-from pymatgen.symmetry.bandstructure import HighSymmKpath
 
 try:
     import phonopy
@@ -28,7 +21,6 @@
 __email__ = "kmathew@lbl.gov, aganose@lbl.gov"
 >>>>>>> 728556b6 (Add methods for generating phonon band structure & DOS)
 
-MESH_DENSITY = 100.0  # should always be a float
 
 # TODO: @matk86 - unit tests?
 
@@ -220,133 +212,3 @@ def get_phonopy_thermal_expansion(
     alpha = phonopy_qha.get_thermal_expansion()[:max_t_index]
     T = phonopy_qha._qha._temperatures[:max_t_index]
     return alpha, T
-
-
-@requires(phonopy, "phonopy is required to calculate phonon density of states")
-def get_phonon_dos(
-    structure: Structure,
-    supercell_matrix: np.ndarray,
-    force_constants: np.ndarray,
-    mesh_density: float = MESH_DENSITY,
-    num_dos_steps: int = 200,
-) -> CompletePhononDos:
-    """
-    Get a projected phonon density of states.
-
-    Args:
-        structure: A structure.
-        supercell_matrix: The supercell matrix used to generate the force
-            constants.
-        force_constants: The force constants in phonopy format.
-        mesh_density: The density of the q-point mesh. See the docstring
-            for the ``mesh`` argument in Phonopy.init_mesh() for more details.
-        num_dos_steps: Number of frequency steps in the energy grid.
-
-    Returns:
-        The density of states.
-    """
-    from phonopy import Phonopy
-
-    structure_phonopy = get_phonopy_structure(structure)
-    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix)
-    phonon.set_force_constants(force_constants)
-    phonon.run_mesh(
-        mesh_density,
-        is_mesh_symmetry=False,
-        with_eigenvectors=True,
-        is_gamma_center=True,
-    )
-
-    # get min, max, step frequency
-    frequencies = phonon.get_mesh_dict()["frequencies"]
-    freq_min = frequencies.min()
-    freq_max = frequencies.max()
-    freq_pitch = (freq_max - freq_min) / num_dos_steps
-
-    phonon.run_projected_dos(
-        freq_min=freq_min, freq_max=freq_max, freq_pitch=freq_pitch
-    )
-
-    dos_raw = phonon.projected_dos.get_partial_dos()
-    pdoss = {s: dos for s, dos in zip(structure, dos_raw[1])}
-
-    total_dos = PhononDos(dos_raw[0], dos_raw[1].sum(axis=0))
-    return CompletePhononDos(structure, total_dos, pdoss)
-
-
-@requires(phonopy, "phonopy is required to calculate phonon band structures")
-def get_phonon_band_structure(
-    structure: Structure,
-    supercell_matrix: np.ndarray,
-    force_constants: np.ndarray,
-    mesh_density: float = 100.0,
-) -> PhononBandStructure:
-    """
-    Get a uniform phonon band structure.
-
-    Args:
-        structure: A structure.
-        supercell_matrix: The supercell matrix used to generate the force
-            constants.
-        force_constants: The force constants in phonopy format.
-        mesh_density: The density of the q-point mesh. See the docstring
-            for the ``mesh`` argument in Phonopy.init_mesh() for more details.
-
-    Returns:
-        The uniform phonon band structure.
-    """
-    from phonopy import Phonopy
-
-    structure_phonopy = get_phonopy_structure(structure)
-    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix)
-    phonon.set_force_constants(force_constants)
-    phonon.run_mesh(mesh_density, is_mesh_symmetry=False, is_gamma_center=True)
-    mesh = phonon.get_mesh_dict()
-
-    return PhononBandStructure(
-        mesh["qpoints"], mesh["frequencies"], structure.lattice
-    )
-
-
-@requires(phonopy, "phonopy is required to calculate phonon band structures")
-def get_line_mode_phonon_band_structure(
-    structure: Structure,
-    supercell_matrix: np.ndarray,
-    force_constants: np.ndarray,
-    line_density: float = 20.0,
-    symprec: float = 0.01,
-) -> PhononBandStructureSymmLine:
-    """
-    Get a projected phonon density of states.
-
-    Args:
-        structure: A structure.
-        supercell_matrix: The supercell matrix used to generate the force
-            constants.
-        force_constants: The force constants in phonopy format.
-        line_density: The density along the high symmetry path.
-        symprec: Symmetry precision for determining the band structure path.
-
-    Returns:
-        The line mode band structure.
-    """
-    from phonopy import Phonopy
-
-    structure_phonopy = get_phonopy_structure(structure)
-    phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix)
-    phonon.set_force_constants(force_constants)
-
-    kpath = HighSymmKpath(structure, symprec=symprec)
-
-    kpoints, labels = kpath.get_kpoints(
-        line_density=line_density, coords_are_cartesian=False
-    )
-
-    phonon.run_qpoints(kpoints)
-    frequencies = phonon.qpoints.get_frequencies().T
-
-    labels_dict = dict([(a, k) for a, k in zip(labels, kpoints) if a != ""])
-
-    return PhononBandStructureSymmLine(
-        kpoints, frequencies, structure.lattice, labels_dict=labels_dict
-    )
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 70b792145..92e7cea78 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -17,16 +17,12 @@
     fit_force_constants,
     get_cutoffs,
 )
-from atomate.vasp.analysis.phonopy import (
-    MESH_DENSITY,
-    get_line_mode_phonon_band_structure,
-    get_phonon_band_structure,
-    get_phonon_dos,
-)
 from atomate.vasp.database import VaspCalcDb
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 from pymatgen import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
+from pymatgen.io.phonopy import get_phonon_band_structure_from_fc, \
+    get_line_mode_phonon_band_structure_from_fc, get_phonon_dos_from_fc
 from pymatgen.io.shengbte import Control
 from pymatgen.transformations.standard_transformations import (
     SupercellTransformation,
@@ -45,6 +41,7 @@
 
 # define shared constants
 DEFAULT_TEMPERATURE = 300
+MESH_DENSITY = 100.0  # should always be a float
 
 
 @explicit_serialize
@@ -227,18 +224,18 @@ def run_task(self, fw_spec):
         phonopy_fc = force_constants.get_fc_array(order=2)
 
         logger.info("Getting uniform phonon band structure.")
-        uniform_bs = get_phonon_band_structure(
+        uniform_bs = get_phonon_band_structure_from_fc(
             structure, supercell_matrix, phonopy_fc
         )
 
         logger.info("Getting line mode phonon band structure.")
-        lm_bs = get_line_mode_phonon_band_structure(
+        lm_bs = get_line_mode_phonon_band_structure_from_fc(
             structure, supercell_matrix, phonopy_fc
         )
 
         logger.info("Getting phonon density of states.")
         mesh_density = self.get("mesh_density", MESH_DENSITY)
-        dos = get_phonon_dos(
+        dos = get_phonon_dos_from_fc(
             structure, supercell_matrix, phonopy_fc, mesh_density=mesh_density
         )
 

From 2fbab7dea25ff9637c929320340e0961df5d3173 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 19:13:21 -0800
Subject: [PATCH 072/207] Tidy polarization tests

---
 .../tests/test_polarization_to_db.py          | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/atomate/vasp/firetasks/tests/test_polarization_to_db.py b/atomate/vasp/firetasks/tests/test_polarization_to_db.py
index 519210fad..2bc839900 100644
--- a/atomate/vasp/firetasks/tests/test_polarization_to_db.py
+++ b/atomate/vasp/firetasks/tests/test_polarization_to_db.py
@@ -1,4 +1,12 @@
+<<<<<<< HEAD
 import os
+=======
+import bson
+import gzip
+import os
+
+from pathlib import Path
+>>>>>>> 45fcce62 (Tidy polarization tests)
 
 from atomate.utils.testing import AtomateTest
 from atomate.vasp.firetasks.parse_outputs import PolarizationToDb
@@ -6,6 +14,7 @@
 __author__ = "Tess Smidt"
 __email__ = "blondegeek@gmail.com"
 
+<<<<<<< HEAD
 module_dir = os.path.dirname(os.path.abspath(__file__))
 db_dir = os.path.join(module_dir, "..", "..", "..", "common", "test_files")
 ref_dir = os.path.join(module_dir, "..", "..", "test_files")
@@ -16,10 +25,16 @@
 )
 # If None, runs a "fake" VASP. Otherwise, runs VASP with this command...
 VASP_CMD = None
+=======
+module_dir = Path(__file__).resolve().parent
+db_dir = module_dir / "../../../common/test_files"
+ref_dir = module_dir / "../..//test_files"
+>>>>>>> 45fcce62 (Tidy polarization tests)
 
 
 class TestFerroelectricWorkflow(AtomateTest):
     def test_polarizationtodb(self):
+<<<<<<< HEAD
         import gzip
 
         import bson
@@ -27,6 +42,11 @@ def test_polarizationtodb(self):
         reference_dir = os.path.abspath(os.path.join(ref_dir, "ferroelectric_wf"))
 
         with gzip.open(os.path.join(reference_dir, "tasks.bson.gz")) as f:
+=======
+        wf_dir = ref_dir / "ferroelectric_wf"
+
+        with gzip.open(wf_dir / "tasks.bson.gz") as f:
+>>>>>>> 45fcce62 (Tidy polarization tests)
             coll_raw = f.read()
 
         coll = bson.decode_all(coll_raw)
@@ -46,4 +66,8 @@ def test_polarizationtodb(self):
         # Check recovered change in polarization
         coll = self.get_task_collection("polarization_tasks")
         d = coll.find_one()
+<<<<<<< HEAD
         self.assertAlmostEqual(d["polarization_change_norm"], 46.288752795325244, 5)
+=======
+        self.assertAlmostEqual(d["polarization_change_norm"], 46.28875279532, 5)
+>>>>>>> 45fcce62 (Tidy polarization tests)

From 792ceac1434426c15b7516303518d578e8027fd1 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 19:13:44 -0800
Subject: [PATCH 073/207] FIX: Use proper phonon function name

---
 atomate/vasp/firetasks/lattice_dynamics.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 92e7cea78..d845a46fc 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -22,7 +22,7 @@
 from pymatgen import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.phonopy import get_phonon_band_structure_from_fc, \
-    get_line_mode_phonon_band_structure_from_fc, get_phonon_dos_from_fc
+    get_phonon_dos_from_fc, get_phonon_band_structure_symm_line_from_fc
 from pymatgen.io.shengbte import Control
 from pymatgen.transformations.standard_transformations import (
     SupercellTransformation,
@@ -229,7 +229,7 @@ def run_task(self, fw_spec):
         )
 
         logger.info("Getting line mode phonon band structure.")
-        lm_bs = get_line_mode_phonon_band_structure_from_fc(
+        lm_bs = get_phonon_band_structure_symm_line_from_fc(
             structure, supercell_matrix, phonopy_fc
         )
 

From 54034c6beeccc0dd5f242235de2cf02ff9f0bc48 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 25 Feb 2020 19:18:41 -0800
Subject: [PATCH 074/207] Finish tidying polarization tests

---
 atomate/vasp/firetasks/tests/test_polarization_to_db.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/tests/test_polarization_to_db.py b/atomate/vasp/firetasks/tests/test_polarization_to_db.py
index 2bc839900..b85b0da70 100644
--- a/atomate/vasp/firetasks/tests/test_polarization_to_db.py
+++ b/atomate/vasp/firetasks/tests/test_polarization_to_db.py
@@ -3,7 +3,6 @@
 =======
 import bson
 import gzip
-import os
 
 from pathlib import Path
 >>>>>>> 45fcce62 (Tidy polarization tests)
@@ -28,11 +27,15 @@
 =======
 module_dir = Path(__file__).resolve().parent
 db_dir = module_dir / "../../../common/test_files"
+<<<<<<< HEAD
 ref_dir = module_dir / "../..//test_files"
 >>>>>>> 45fcce62 (Tidy polarization tests)
+=======
+ref_dir = module_dir / "../../test_files"
+>>>>>>> fcdf2e63 (Finish tidying polarization tests)
 
 
-class TestFerroelectricWorkflow(AtomateTest):
+class TestPolarizationFiretasks(AtomateTest):
     def test_polarizationtodb(self):
 <<<<<<< HEAD
         import gzip
@@ -56,7 +59,7 @@ def test_polarizationtodb(self):
             task_coll.insert_one(c)
 
         new_fw_spec = {
-            "_fw_env": {"db_file": os.path.join(db_dir, "db.json")},
+            "_fw_env": {"db_file": db_dir / "db.json"},
             "tags": ["wfid_1494203093.06934658"],
         }
 

From ff74e055b4a278ac38e4f1cd2ee5f09eb34c6a8b Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Wed, 26 Feb 2020 01:57:30 -0800
Subject: [PATCH 075/207] Add lattice dynamics test files

---
 atomate/vasp/test_files/csld_wf/FW.json       | 56691 ----------------
 .../test_files/csld_wf/POSCAR-well_relaxed_Si |    10 -
 atomate/vasp/test_files/csld_wf/__init__.py   |     0
 .../lattice_dynamics_wf/0/inputs/INCAR        |    21 +
 .../lattice_dynamics_wf/0/inputs/KPOINTS      |     4 +
 .../lattice_dynamics_wf/0/inputs/POSCAR       |   136 +
 .../lattice_dynamics_wf/0/inputs/POTCAR       |  1768 +
 .../lattice_dynamics_wf/0/outputs/INCAR       |    21 +
 .../lattice_dynamics_wf/0/outputs/KPOINTS     |     4 +
 .../lattice_dynamics_wf/0/outputs/POSCAR      |   136 +
 .../lattice_dynamics_wf/0/outputs/POTCAR      |  1768 +
 11 files changed, 3858 insertions(+), 56701 deletions(-)
 delete mode 100644 atomate/vasp/test_files/csld_wf/FW.json
 delete mode 100644 atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si
 delete mode 100644 atomate/vasp/test_files/csld_wf/__init__.py
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/INCAR
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/KPOINTS
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POSCAR
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POTCAR
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/INCAR
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/KPOINTS
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POSCAR
 create mode 100644 atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POTCAR

diff --git a/atomate/vasp/test_files/csld_wf/FW.json b/atomate/vasp/test_files/csld_wf/FW.json
deleted file mode 100644
index dfec54f0c..000000000
--- a/atomate/vasp/test_files/csld_wf/FW.json
+++ /dev/null
@@ -1,56691 +0,0 @@
-[{
-    "spec": {
-        "tags": [
-            "csld",
-            "v1",
-            "rees",
-            "pre-relaxed si",
-            "diagonal supercell",
-            "not symmetrized",
-            "555"
-        ],
-        "_fworker": "rees_the_fire_worker",
-        "_tasks": [
-            {
-                "db_file": ">>db_file<<",
-                "wf_uuid": "b8ab536c-b75d-4011-a069-48cbab8b8bda",
-                "parent_structure": {
-                    "@module": "pymatgen.core.structure",
-                    "@class": "Structure",
-                    "charge": null,
-                    "lattice": {
-                        "matrix": [
-                            [
-                                0.0,
-                                2.734364,
-                                2.734364
-                            ],
-                            [
-                                2.734364,
-                                0.0,
-                                2.734364
-                            ],
-                            [
-                                2.734364,
-                                2.734364,
-                                0.0
-                            ]
-                        ],
-                        "a": 3.8669746532647453,
-                        "b": 3.8669746532647453,
-                        "c": 3.8669746532647453,
-                        "alpha": 59.99999999999999,
-                        "beta": 59.99999999999999,
-                        "gamma": 59.99999999999999,
-                        "volume": 40.88829284866483
-                    },
-                    "sites": [
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.5,
-                                0.5,
-                                0.5
-                            ],
-                            "xyz": [
-                                2.734364,
-                                2.734364,
-                                2.734364
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.75,
-                                0.75,
-                                0.75
-                            ],
-                            "xyz": [
-                                4.101546,
-                                4.101546,
-                                4.101546
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        }
-                    ]
-                },
-                "trans_mat": [
-                    [
-                        5,
-                        0,
-                        0
-                    ],
-                    [
-                        0,
-                        5,
-                        0
-                    ],
-                    [
-                        0,
-                        0,
-                        5
-                    ]
-                ],
-                "supercell_structure": {
-                    "@module": "pymatgen.core.structure",
-                    "@class": "Structure",
-                    "charge": null,
-                    "lattice": {
-                        "matrix": [
-                            [
-                                0.0,
-                                13.671819999999999,
-                                13.671819999999999
-                            ],
-                            [
-                                13.671819999999999,
-                                0.0,
-                                13.671819999999999
-                            ],
-                            [
-                                13.671819999999999,
-                                13.671819999999999,
-                                0.0
-                            ]
-                        ],
-                        "a": 19.334873266323726,
-                        "b": 19.334873266323726,
-                        "c": 19.334873266323726,
-                        "alpha": 59.99999999999999,
-                        "beta": 59.99999999999999,
-                        "gamma": 59.99999999999999,
-                        "volume": 5111.036606083104
-                    },
-                    "sites": [
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.1,
-                                0.1,
-                                0.1
-                            ],
-                            "xyz": [
-                                2.734364,
-                                2.734364,
-                                2.734364
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.1,
-                                0.1,
-                                0.3
-                            ],
-                            "xyz": [
-                                5.468728,
-                                5.468728,
-                                2.734364
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.1,
-                                0.10000000000000002,
-                                0.5000000000000001
-                            ],
-                            "xyz": [
-                                8.203092000000002,
-                                8.203092,
-                                2.734364
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.1,
-                                0.1,
-                                0.7000000000000001
-                            ],
-                            "xyz": [
-                                10.937456,
-                                10.937456,
-                                2.734364
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000002,
-                                0.09999999999999999,
-                                0.9
-                            ],
-                            "xyz": [
-                                13.671819999999999,
-                                13.671819999999999,
-                                2.734364
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.1,
-                                0.30000000000000004,
-                                0.10000000000000003
-                            ],
-                            "xyz": [
-                                5.4687280000000005,
-                                2.7343640000000002,
-                                5.4687280000000005
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999998,
-                                0.30000000000000004,
-                                0.3000000000000001
-                            ],
-                            "xyz": [
-                                8.203092000000002,
-                                5.4687280000000005,
-                                5.468728
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000002,
-                                0.3,
-                                0.5
-                            ],
-                            "xyz": [
-                                10.937455999999997,
-                                8.203092,
-                                5.468728
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999992,
-                                0.3000000000000001,
-                                0.7000000000000001
-                            ],
-                            "xyz": [
-                                13.67182,
-                                10.937456,
-                                5.468728
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999994,
-                                0.3000000000000001,
-                                0.9
-                            ],
-                            "xyz": [
-                                16.406184,
-                                13.671819999999999,
-                                5.468728
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999999,
-                                0.5000000000000001,
-                                0.10000000000000005
-                            ],
-                            "xyz": [
-                                8.203092000000002,
-                                2.7343640000000002,
-                                8.203092
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000002,
-                                0.5,
-                                0.30000000000000004
-                            ],
-                            "xyz": [
-                                10.937456,
-                                5.4687280000000005,
-                                8.203092
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000007,
-                                0.5,
-                                0.5
-                            ],
-                            "xyz": [
-                                13.671819999999999,
-                                8.203092,
-                                8.203092
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999996,
-                                0.5000000000000001,
-                                0.7000000000000002
-                            ],
-                            "xyz": [
-                                16.406184000000003,
-                                10.937456000000001,
-                                8.203092
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999999,
-                                0.5000000000000001,
-                                0.9000000000000001
-                            ],
-                            "xyz": [
-                                19.140548000000003,
-                                13.67182,
-                                8.203092
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000003,
-                                0.7000000000000001,
-                                0.09999999999999998
-                            ],
-                            "xyz": [
-                                10.937456,
-                                2.734364,
-                                10.937456000000001
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000003,
-                                0.7000000000000001,
-                                0.30000000000000004
-                            ],
-                            "xyz": [
-                                13.67182,
-                                5.4687280000000005,
-                                10.937456000000001
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999998,
-                                0.7000000000000001,
-                                0.5000000000000001
-                            ],
-                            "xyz": [
-                                16.406184,
-                                8.203092,
-                                10.937456
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999998,
-                                0.7000000000000001,
-                                0.7000000000000001
-                            ],
-                            "xyz": [
-                                19.140548,
-                                10.937456,
-                                10.937456
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999998,
-                                0.7000000000000001,
-                                0.9
-                            ],
-                            "xyz": [
-                                21.874912,
-                                13.671819999999999,
-                                10.937456
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.10000000000000005,
-                                0.9,
-                                0.09999999999999996
-                            ],
-                            "xyz": [
-                                13.671819999999999,
-                                2.734364,
-                                13.67182
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999994,
-                                0.9000000000000001,
-                                0.30000000000000016
-                            ],
-                            "xyz": [
-                                16.406184000000003,
-                                5.4687280000000005,
-                                13.67182
-                            ],
-                            "label": "Si",
-                            "properties": {}
-                        },
-                        {
-                            "species": [
-                                {
-                                    "element": "Si",
-                                    "occu": 1
-                                }
-                            ],
-                            "abc": [
-                                0.09999999999999999,
-                                0.9,
-                                0.5
-                            ],
-                            "xyz": [
-                                19.140548,
-                                8.203091999999998,
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-    "formula_pretty": "Si",
-    "state": "successful"
-  }
-]
\ No newline at end of file
diff --git a/atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si b/atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si
deleted file mode 100644
index 283220155..000000000
--- a/atomate/vasp/test_files/csld_wf/POSCAR-well_relaxed_Si
+++ /dev/null
@@ -1,10 +0,0 @@
-Si2
-1.0
-0.0000000000000000 2.7343639999999998 2.7343639999999998
-2.7343639999999998 0.0000000000000000 2.7343639999999998
-2.7343639999999998 2.7343639999999998 0.0000000000000000
-Si
-2
-direct
-0.5000000000000000 0.5000000000000000 0.5000000000000000 Si
-0.7500000000000000 0.7500000000000000 0.7500000000000000 Si
diff --git a/atomate/vasp/test_files/csld_wf/__init__.py b/atomate/vasp/test_files/csld_wf/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/INCAR b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/INCAR
new file mode 100644
index 000000000..2d049b275
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/INCAR
@@ -0,0 +1,21 @@
+ADDGRID = True
+ALGO = Normal
+EDIFF = 1e-08
+ENCUT = 700
+IBRION = -1
+ICHARG = 0
+ISIF = 3
+ISMEAR = -5
+ISPIN = 2
+LAECHG = False
+LASPH = True
+LCHARG = False
+LORBIT = 11
+LREAL = False
+LVHAR = True
+LWAVE = False
+MAGMOM = 128*0.6
+NELM = 100
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/KPOINTS b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/KPOINTS
new file mode 100644
index 000000000..6677fab59
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/KPOINTS
@@ -0,0 +1,4 @@
+pymatgen v2020.1.28 with grid density = 1239 / atom
+0
+Monkhorst
+2 2 2
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POSCAR b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POSCAR
new file mode 100644
index 000000000..56a563b58
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POSCAR
@@ -0,0 +1,136 @@
+Si128
+1.0
+15.360792 0.000000 0.000000
+7.680396 13.302841 0.000000
+0.000000 -8.868554 12.542036
+Si
+128
+direct
+0.002404 -0.002517 0.000123 Si
+0.000357 -0.000777 0.252550 Si
+0.004490 -0.001628 0.500263 Si
+0.002106 -0.006496 0.747226 Si
+0.002968 0.251340 -0.000424 Si
+-0.003427 0.250985 0.250110 Si
+-0.000782 0.251244 0.499624 Si
+0.000512 0.249102 0.751360 Si
+0.006130 0.492281 -0.004097 Si
+-0.002867 0.504654 0.250646 Si
+-0.002557 0.504956 0.501778 Si
+-0.002017 0.505049 0.753557 Si
+-0.000990 0.749992 0.002984 Si
+-0.002484 0.747893 0.249024 Si
+0.001491 0.747627 0.499072 Si
+-0.002745 0.752763 0.751308 Si
+0.250543 0.002043 0.002689 Si
+0.250263 0.001233 0.251568 Si
+0.249181 0.003382 0.499683 Si
+0.252592 0.000338 0.750248 Si
+0.248235 0.253531 0.002630 Si
+0.251371 0.246532 0.246163 Si
+0.247689 0.250186 0.499295 Si
+0.248728 0.252353 0.751770 Si
+0.247456 0.501566 0.000831 Si
+0.245919 0.510981 0.258069 Si
+0.250265 0.499354 0.499871 Si
+0.248424 0.501149 0.748379 Si
+0.247168 0.753267 -0.000149 Si
+0.249007 0.747189 0.248607 Si
+0.250103 0.751187 0.502381 Si
+0.250548 0.753120 0.750159 Si
+0.504837 -0.004255 -0.001475 Si
+0.502158 0.000984 0.253542 Si
+0.493063 0.004233 0.502475 Si
+0.496057 0.004024 0.754290 Si
+0.500139 0.251115 -0.000257 Si
+0.496737 0.251876 0.254678 Si
+0.496044 0.254600 0.500845 Si
+0.497132 0.256958 0.752534 Si
+0.496869 0.505817 0.003930 Si
+0.500507 0.500335 0.248215 Si
+0.497799 0.501539 0.498221 Si
+0.498527 0.502456 0.752570 Si
+0.499691 0.748601 -0.000097 Si
+0.498840 0.750386 0.249273 Si
+0.499950 0.751666 0.499152 Si
+0.496771 0.749795 0.751294 Si
+0.749428 0.001949 -0.000458 Si
+0.751229 -0.002795 0.249361 Si
+0.750397 -0.002559 0.500299 Si
+0.748756 -0.000843 0.749283 Si
+0.749923 0.249533 0.000966 Si
+0.753039 0.243413 0.251122 Si
+0.747658 0.252684 0.503283 Si
+0.753566 0.247640 0.749662 Si
+0.747313 0.502195 0.004115 Si
+0.750050 0.499140 0.251465 Si
+0.742704 0.506149 0.502660 Si
+0.748272 0.506458 0.752443 Si
+0.744373 0.752620 -0.001382 Si
+0.749078 0.750121 0.249336 Si
+0.750750 0.747982 0.499201 Si
+0.747734 0.749730 0.746002 Si
+0.187469 0.122464 0.189217 Si
+0.184052 0.126282 0.437630 Si
+0.180841 0.131891 0.692717 Si
+0.187955 0.126552 0.941521 Si
+0.190406 0.372753 0.187942 Si
+0.185969 0.375798 0.438707 Si
+0.190932 0.369119 0.683643 Si
+0.184574 0.379973 0.942675 Si
+0.186188 0.629074 0.191760 Si
+0.186757 0.629134 0.443758 Si
+0.189067 0.624236 0.687615 Si
+0.185067 0.627484 0.938558 Si
+0.188650 0.875055 0.188436 Si
+0.189488 0.872896 0.434502 Si
+0.188558 0.874926 0.687882 Si
+0.189431 0.877489 0.938528 Si
+0.434486 0.127784 0.186098 Si
+0.437186 0.126922 0.436987 Si
+0.430043 0.128728 0.693003 Si
+0.435968 0.126353 0.933531 Si
+0.439790 0.371458 0.184592 Si
+0.435504 0.378703 0.441008 Si
+0.440051 0.376642 0.688726 Si
+0.438845 0.375748 0.937328 Si
+0.441756 0.618757 0.184083 Si
+0.440481 0.623350 0.435743 Si
+0.434662 0.624163 0.686391 Si
+0.438961 0.626271 0.940724 Si
+0.436167 0.873872 0.183818 Si
+0.442474 0.870235 0.433385 Si
+0.433970 0.877630 0.687396 Si
+0.437553 0.876921 0.938552 Si
+0.685077 0.128538 0.190597 Si
+0.688620 0.123968 0.436125 Si
+0.686134 0.129310 0.685286 Si
+0.686645 0.132644 0.943020 Si
+0.687873 0.373540 0.186993 Si
+0.689695 0.374393 0.438742 Si
+0.686614 0.376172 0.689488 Si
+0.687637 0.374833 0.938885 Si
+0.690119 0.620944 0.187764 Si
+0.685863 0.624962 0.438326 Si
+0.687946 0.625392 0.686429 Si
+0.688831 0.626261 0.939012 Si
+0.688685 0.873769 0.186379 Si
+0.690407 0.872704 0.436420 Si
+0.690068 0.868895 0.681756 Si
+0.689423 0.869237 0.939286 Si
+0.934735 0.127559 0.186834 Si
+0.939562 0.125044 0.437563 Si
+0.935312 0.129003 0.689791 Si
+0.940475 0.127166 0.937939 Si
+0.942430 0.373299 0.186505 Si
+0.937508 0.372289 0.436061 Si
+0.936880 0.371913 0.686790 Si
+0.935704 0.377405 0.934935 Si
+0.935908 0.624800 0.189670 Si
+0.940868 0.623802 0.437307 Si
+0.939283 0.623943 0.684337 Si
+0.936195 0.626949 0.942072 Si
+0.936474 0.875867 0.187693 Si
+0.939995 0.871104 0.436789 Si
+0.938360 0.874652 0.687098 Si
+0.938896 0.873531 0.937362 Si
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POTCAR b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POTCAR
new file mode 100644
index 000000000..ae2291fdf
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/inputs/POTCAR
@@ -0,0 +1,1768 @@
+ PAW_PBE Si 05Jan2001
+ 4.00000000000000000
+ parameters from PSCTR are:
+   VRHFIN =Si: s2p2
+   LEXCH  = PE
+   EATOM  =   103.0669 eV,    7.5752 Ry
+
+   TITEL  = PAW_PBE Si 05Jan2001
+   LULTRA =        F    use ultrasoft PP ?
+   IUNSCR =        1    unscreen: 0-lin 1-nonlin 2-no
+   RPACOR =    1.500    partial core radius
+   POMASS =   28.085; ZVAL   =    4.000    mass and valenz
+   RCORE  =    1.900    outmost cutoff radius
+   RWIGS  =    2.480; RWIGS  =    1.312    wigner-seitz radius (au A)
+   ENMAX  =  245.345; ENMIN  =  184.009 eV
+   ICORE  =        2    local potential
+   LCOR   =        T    correct aug charges
+   LPAW   =        T    paw PP
+   EAUG   =  322.069
+   DEXC   =    -.007
+   RMAX   =    2.944    core radius for proj-oper
+   RAUG   =    1.300    factor for augmentation sphere
+   RDEP   =    1.993    radius for radial grids
+   QCUT   =   -4.246; QGAM   =    8.493    optimization parameters
+ 
+   Description
+     l     E      TYP  RCUT    TYP  RCUT
+     0   .000     23  1.900
+     0   .000     23  1.900
+     1   .000     23  1.900
+     1   .000     23  1.900
+     2   .000      7  1.900
+   Error from kinetic energy argument (eV)
+   NDATA  =      100
+   STEP   =   20.000   1.050
+  10.1      9.04      8.56      7.65      7.23      6.44      5.73      5.40
+  4.79      4.25      4.00      3.54      3.13      2.77      2.45      2.16
+  1.91      1.69      1.50      1.24      1.10      .975      .812      .718
+  .636      .529      .440      .388      .322      .266      .219      .180
+  .148      .121      .986E-01  .804E-01  .614E-01  .504E-01  .392E-01  .328E-01
+  .265E-01  .220E-01  .189E-01  .166E-01  .149E-01  .135E-01  .123E-01  .109E-01
+  .977E-02  .840E-02  .707E-02  .605E-02  .488E-02  .387E-02  .290E-02  .229E-02
+  .185E-02  .152E-02  .134E-02  .125E-02  .121E-02  .117E-02  .112E-02  .102E-02
+  .915E-03  .776E-03  .640E-03  .524E-03  .425E-03  .369E-03  .331E-03  .310E-03
+  .294E-03  .273E-03  .242E-03  .210E-03  .175E-03  .146E-03  .124E-03  .113E-03
+  .105E-03  .973E-04  .879E-04  .755E-04  .633E-04  .539E-04  .478E-04  .438E-04
+  .404E-04  .362E-04  .308E-04  .264E-04  .229E-04  .209E-04  .192E-04  .170E-04
+  .145E-04  .126E-04  .112E-04  .103E-04
+END of PSCTR-controll parameters
+ local part
+ 98.2657514061040160
+   .84157696E+01   .84210616E+01   .84276868E+01   .84387430E+01   .84542501E+01
+   .84742336E+01   .84987229E+01   .85277486E+01   .85613410E+01   .85995276E+01
+   .86423322E+01   .86897735E+01   .87418643E+01   .87986117E+01   .88600162E+01
+   .89260725E+01   .89967686E+01   .90720854E+01   .91519966E+01   .92364669E+01
+   .93254512E+01   .94188926E+01   .95167214E+01   .96188530E+01   .97251866E+01
+   .98356042E+01   .99499691E+01   .10068126E+02   .10189900E+02   .10315095E+02
+   .10443498E+02   .10574872E+02   .10708964E+02   .10845497E+02   .10984178E+02
+   .11124691E+02   .11266702E+02   .11409858E+02   .11553785E+02   .11698096E+02
+   .11842382E+02   .11986223E+02   .12129182E+02   .12270810E+02   .12410650E+02
+   .12548232E+02   .12683081E+02   .12814718E+02   .12942658E+02   .13066416E+02
+   .13185509E+02   .13299456E+02   .13407780E+02   .13510014E+02   .13605699E+02
+   .13694388E+02   .13775652E+02   .13849074E+02   .13914259E+02   .13970835E+02
+   .14018449E+02   .14056778E+02   .14085523E+02   .14104415E+02   .14113216E+02
+   .14111719E+02   .14099752E+02   .14077176E+02   .14043889E+02   .13999825E+02
+   .13944955E+02   .13879288E+02   .13802872E+02   .13715793E+02   .13618173E+02
+   .13510175E+02   .13391996E+02   .13263872E+02   .13126073E+02   .12978903E+02
+   .12822702E+02   .12657838E+02   .12484712E+02   .12303753E+02   .12115415E+02
+   .11920177E+02   .11718543E+02   .11511033E+02   .11298186E+02   .11080557E+02
+   .10858712E+02   .10633228E+02   .10404688E+02   .10173679E+02   .99407918E+01
+   .97066146E+01   .94717325E+01   .92367246E+01   .90021609E+01   .87686001E+01
+   .85365874E+01   .83066514E+01   .80793026E+01   .78550308E+01   .76343035E+01
+   .74175636E+01   .72052280E+01   .69976861E+01   .67952984E+01   .65983952E+01
+   .64072758E+01   .62222076E+01   .60434252E+01   .58711303E+01   .57054911E+01
+   .55466426E+01   .53946862E+01   .52496902E+01   .51116906E+01   .49806911E+01
+   .48566645E+01   .47395534E+01   .46292712E+01   .45257038E+01   .44287105E+01
+   .43381258E+01   .42537607E+01   .41754049E+01   .41028282E+01   .40357822E+01
+   .39740031E+01   .39172124E+01   .38651203E+01   .38174267E+01   .37738238E+01
+   .37339979E+01   .36976315E+01   .36644056E+01   .36340010E+01   .36061008E+01
+   .35803917E+01   .35565663E+01   .35343243E+01   .35133745E+01   .34934357E+01
+   .34742388E+01   .34555274E+01   .34370596E+01   .34186083E+01   .33999627E+01
+   .33809285E+01   .33613290E+01   .33410052E+01   .33198164E+01   .32976401E+01
+   .32743723E+01   .32499276E+01   .32242387E+01   .31972561E+01   .31689481E+01
+   .31393000E+01   .31083133E+01   .30760055E+01   .30424087E+01   .30075693E+01
+   .29715463E+01   .29344112E+01   .28962459E+01   .28571426E+01   .28172018E+01
+   .27765317E+01   .27352466E+01   .26934662E+01   .26513138E+01   .26089155E+01
+   .25663991E+01   .25238927E+01   .24815236E+01   .24394173E+01   .23976966E+01
+   .23564804E+01   .23158831E+01   .22760134E+01   .22369739E+01   .21988600E+01
+   .21617599E+01   .21257533E+01   .20909116E+01   .20572974E+01   .20249638E+01
+   .19939548E+01   .19643045E+01   .19360379E+01   .19091701E+01   .18837069E+01
+   .18596450E+01   .18369720E+01   .18156670E+01   .17957010E+01   .17770368E+01
+   .17596305E+01   .17434311E+01   .17283816E+01   .17144193E+01   .17014768E+01
+   .16894823E+01   .16783607E+01   .16680338E+01   .16584212E+01   .16494415E+01
+   .16410120E+01   .16330504E+01   .16254746E+01   .16182040E+01   .16111597E+01
+   .16042653E+01   .15974473E+01   .15906355E+01   .15837638E+01   .15767703E+01
+   .15695978E+01   .15621941E+01   .15545123E+01   .15465111E+01   .15381544E+01
+   .15294125E+01   .15202610E+01   .15106817E+01   .15006619E+01   .14901947E+01
+   .14792788E+01   .14679182E+01   .14561221E+01   .14439046E+01   .14312844E+01
+   .14182846E+01   .14049321E+01   .13912574E+01   .13772942E+01   .13630791E+01
+   .13486509E+01   .13340503E+01   .13193195E+01   .13045019E+01   .12896412E+01
+   .12747815E+01   .12599666E+01   .12452397E+01   .12306428E+01   .12162167E+01
+   .12020006E+01   .11880314E+01   .11743437E+01   .11609697E+01   .11479386E+01
+   .11352766E+01   .11230067E+01   .11111486E+01   .10997186E+01   .10887293E+01
+   .10781902E+01   .10681067E+01   .10584813E+01   .10493127E+01   .10405964E+01
+   .10323246E+01   .10244865E+01   .10170685E+01   .10100542E+01   .10034245E+01
+   .99715846E+00   .99123280E+00   .98562260E+00   .98030145E+00   .97524173E+00
+   .97041488E+00   .96579171E+00   .96134265E+00   .95703806E+00   .95284844E+00
+   .94874473E+00   .94469858E+00   .94068254E+00   .93667031E+00   .93263696E+00
+   .92855909E+00   .92441506E+00   .92018509E+00   .91585142E+00   .91139842E+00
+   .90681263E+00   .90208291E+00   .89720039E+00   .89215854E+00   .88695315E+00
+   .88158229E+00   .87604630E+00   .87034770E+00   .86449110E+00   .85848313E+00
+   .85233229E+00   .84604884E+00   .83964465E+00   .83313300E+00   .82652847E+00
+   .81984671E+00   .81310428E+00   .80631845E+00   .79950703E+00   .79268813E+00
+   .78588003E+00   .77910097E+00   .77236895E+00   .76570159E+00   .75911593E+00
+   .75262828E+00   .74625407E+00   .74000773E+00   .73390251E+00   .72795041E+00
+   .72216209E+00   .71654675E+00   .71111209E+00   .70586428E+00   .70080787E+00
+   .69594584E+00   .69127954E+00   .68680877E+00   .68253173E+00   .67844513E+00
+   .67454418E+00   .67082274E+00   .66727331E+00   .66388721E+00   .66065462E+00
+   .65756473E+00   .65460586E+00   .65176555E+00   .64903076E+00   .64638795E+00
+   .64382325E+00   .64132257E+00   .63887178E+00   .63645678E+00   .63406371E+00
+   .63167900E+00   .62928956E+00   .62688288E+00   .62444710E+00   .62197118E+00
+   .61944494E+00   .61685919E+00   .61420575E+00   .61147755E+00   .60866866E+00
+   .60577434E+00   .60279104E+00   .59971643E+00   .59654939E+00   .59329003E+00
+   .58993961E+00   .58650056E+00   .58297643E+00   .57937181E+00   .57569230E+00
+   .57194440E+00   .56813547E+00   .56427363E+00   .56036764E+00   .55642683E+00
+   .55246099E+00   .54848026E+00   .54449503E+00   .54051583E+00   .53655322E+00
+   .53261771E+00   .52871961E+00   .52486898E+00   .52107551E+00   .51734843E+00
+   .51369641E+00   .51012750E+00   .50664907E+00   .50326768E+00   .49998911E+00
+   .49681824E+00   .49375908E+00   .49081468E+00   .48798715E+00   .48527763E+00
+   .48268632E+00   .48021244E+00   .47785431E+00   .47560930E+00   .47347392E+00
+   .47144387E+00   .46951402E+00   .46767855E+00   .46593095E+00   .46426412E+00
+   .46267047E+00   .46114194E+00   .45967012E+00   .45824632E+00   .45686169E+00
+   .45550723E+00   .45417395E+00   .45285292E+00   .45153535E+00   .45021267E+00
+   .44887661E+00   .44751931E+00   .44613331E+00   .44471171E+00   .44324816E+00
+   .44173692E+00   .44017295E+00   .43855190E+00   .43687017E+00   .43512491E+00
+   .43331405E+00   .43143631E+00   .42949120E+00   .42747899E+00   .42540073E+00
+   .42325823E+00   .42105400E+00   .41879126E+00   .41647384E+00   .41410622E+00
+   .41169341E+00   .40924089E+00   .40675462E+00   .40424088E+00   .40170629E+00
+   .39915769E+00   .39660209E+00   .39404660E+00   .39149835E+00   .38896445E+00
+   .38645189E+00   .38396749E+00   .38151784E+00   .37910923E+00   .37674758E+00
+   .37443844E+00   .37218685E+00   .36999739E+00   .36787409E+00   .36582039E+00
+   .36383915E+00   .36193261E+00   .36010239E+00   .35834945E+00   .35667414E+00
+   .35507613E+00   .35355450E+00   .35210772E+00   .35073362E+00   .34942953E+00
+   .34819219E+00   .34701788E+00   .34590241E+00   .34484117E+00   .34382921E+00
+   .34286125E+00   .34193178E+00   .34103506E+00   .34016522E+00   .33931629E+00
+   .33848229E+00   .33765725E+00   .33683525E+00   .33601054E+00   .33517754E+00
+   .33433091E+00   .33346559E+00   .33257683E+00   .33166028E+00   .33071198E+00
+   .32972841E+00   .32870651E+00   .32764370E+00   .32653791E+00   .32538758E+00
+   .32419168E+00   .32294968E+00   .32166161E+00   .32032797E+00   .31894980E+00
+   .31752862E+00   .31606640E+00   .31456556E+00   .31302895E+00   .31145977E+00
+   .30986158E+00   .30823823E+00   .30659385E+00   .30493275E+00   .30325946E+00
+   .30157859E+00   .29989486E+00   .29821301E+00   .29653778E+00   .29487386E+00
+   .29322581E+00   .29159807E+00   .28999490E+00   .28842031E+00   .28687807E+00
+   .28537164E+00   .28390415E+00   .28247839E+00   .28109677E+00   .27976132E+00
+   .27847363E+00   .27723491E+00   .27604592E+00   .27490700E+00   .27381809E+00
+   .27277867E+00   .27178784E+00   .27084428E+00   .26994630E+00   .26909186E+00
+   .26827855E+00   .26750369E+00   .26676430E+00   .26605715E+00   .26537882E+00
+   .26472568E+00   .26409398E+00   .26347988E+00   .26287945E+00   .26228874E+00
+   .26170381E+00   .26112076E+00   .26053579E+00   .25994520E+00   .25934545E+00
+   .25873320E+00   .25810531E+00   .25745888E+00   .25679129E+00   .25610022E+00
+   .25538363E+00   .25463983E+00   .25386744E+00   .25306545E+00   .25223318E+00
+   .25137030E+00   .25047684E+00   .24955316E+00   .24859996E+00   .24761829E+00
+   .24660949E+00   .24557519E+00   .24451731E+00   .24343801E+00   .24233971E+00
+   .24122498E+00   .24009659E+00   .23895746E+00   .23781060E+00   .23665912E+00
+   .23550617E+00   .23435492E+00   .23320855E+00   .23207016E+00   .23094281E+00
+   .22982945E+00   .22873289E+00   .22765579E+00   .22660063E+00   .22556967E+00
+   .22456498E+00   .22358834E+00   .22264131E+00   .22172517E+00   .22084092E+00
+   .21998928E+00   .21917068E+00   .21838526E+00   .21763287E+00   .21691308E+00
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+   .21322111E+00   .21269560E+00   .21219035E+00   .21170297E+00   .21123098E+00
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+ gradient corrections used for XC
+ 5
+ core charge-density (partial)
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+ Real Space Part
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+   .47404142E+03   .47502541E+03   .47573899E+03   .47598368E+03   .47554935E+03
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+ Non local Part
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+ 2.65859659160385764 -0.504801881867953453E-01 -0.504801881867953453E-01 0.892956271679604986E-02
+ Reciprocal Space Part
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+   .28801366E-03   .16363396E-02   .27990903E-02   .37452630E-02   .44552150E-02
+ Real Space Part
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+ Reciprocal Space Part
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+ Real Space Part
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+ PAW radial sets
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+(5E20.12)                                
+ augmentation charges (non sperical)
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+ core charge-density (pseudized)
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+ pseudo wavefunction
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+  -.755315101746E-01  -.952062316141E-01  -.115210910670E+00  -.135484516518E+00  -.155960703517E+00
+  -.176567793429E+00  -.197228772403E+00  -.217861306439E+00  -.238377786432E+00  -.258685421094E+00
+  -.278686400098E+00  -.298278147634E+00  -.317353677390E+00  -.335802046575E+00  -.353508895291E+00
+  -.370357053514E+00  -.386227201622E+00  -.400998577469E+00  -.414549728634E+00  -.426759310469E+00
+  -.437506929404E+00  -.446674028239E+00  -.454144807390E+00  -.459807173979E+00  -.463553709570E+00
+  -.465282646961E+00  -.464898846615E+00  -.462314763759E+00  -.457451397642E+00  -.450239215005E+00
+  -.440619040214E+00  -.428542904958E+00  -.413974850650E+00  -.396891676910E+00  -.377283629551E+00
+  -.355155021405E+00  -.330524779042E+00  -.303426907952E+00  -.273910868147E+00  -.242041851308E+00
+  -.207900949827E+00  -.171585207413E+00  -.133207540559E+00  -.928965205479E-01  -.507960069887E-01
+  -.706462660247E-02   .381249046254E-01   .845866118155E-01   .132122232827E+00   .180522312943E+00
+   .229567399836E+00   .279029316983E+00   .328672503777E+00   .378255433412E+00   .427532158406E+00
+   .476254091096E+00   .524172202057E+00   .571039898221E+00   .616616860053E+00   .660673895312E+00
+   .702998092998E+00   .743396069181E+00   .781691750831E+00   .817716502043E+00   .851295258407E+00
+   .882238299672E+00   .910345743397E+00   .935421491735E+00   .957287299205E+00   .975791213531E+00
+   .990810701652E+00   .100225314042E+01   .101005569012E+01   .101418535258E+01   .101463927777E+01
+   .101144510801E+01   .100466111560E+01   .994375951175E+00
+ pseudo wavefunction
+   .138848147713E-05   .143363143073E-05   .148024954817E-05   .152838357046E-05   .157808279106E-05
+   .162939810629E-05   .168238206754E-05   .173708893499E-05   .179357473326E-05   .185189730873E-05
+   .191211638882E-05   .197429364312E-05   .203849274656E-05   .210477944463E-05   .217322162069E-05
+   .224388936550E-05   .231685504901E-05   .239219339443E-05   .246998155480E-05   .255029919199E-05
+   .263322855826E-05   .271885458052E-05   .280726494727E-05   .289855019843E-05   .299280381807E-05
+   .309012233011E-05   .319060539717E-05   .329435592268E-05   .340148015621E-05   .351208780231E-05
+   .362629213282E-05   .374421010294E-05   .386596247091E-05   .399167392177E-05   .412147319496E-05
+   .425549321623E-05   .439387123372E-05   .453674895855E-05   .468427270993E-05   .483659356497E-05
+   .499386751345E-05   .515625561753E-05   .532392417672E-05   .549704489814E-05   .567579507240E-05
+   .586035775516E-05   .605092195456E-05   .624768282482E-05   .645084186605E-05   .666060713066E-05
+   .687719343636E-05   .710082258618E-05   .733172359563E-05   .757013292719E-05   .781629473250E-05
+   .807046110236E-05   .833289232491E-05   .860385715220E-05   .888363307535E-05   .917250660878E-05
+   .947077358361E-05   .977873945059E-05   .100967195929E-04   .104250396492E-04   .107640358469E-04
+   .111140553467E-04   .114754565982E-04   .118486097064E-04   .122338968115E-04   .126317124796E-04
+   .130424641070E-04   .134665723375E-04   .139044714931E-04   .143566100184E-04   .148234509404E-04
+   .153054723424E-04   .158031678534E-04   .163170471539E-04   .168476364977E-04   .173954792507E-04
+   .179611364475E-04   .185451873656E-04   .191482301190E-04   .197708822706E-04   .204137814640E-04
+   .210775860774E-04   .217629758970E-04   .224706528134E-04   .232013415404E-04   .239557903567E-04
+   .247347718727E-04   .255390838211E-04   .263695498740E-04   .272270204861E-04   .281123737658E-04
+   .290265163739E-04   .299703844525E-04   .309449445827E-04   .319511947751E-04   .329901654910E-04
+   .340629206980E-04   .351705589586E-04   .363142145555E-04   .374950586529E-04   .387143004951E-04
+   .399731886447E-04   .412730122609E-04   .426151024191E-04   .440008334734E-04   .454316244639E-04
+   .469089405685E-04   .484342946036E-04   .500092485720E-04   .516354152616E-04   .533144598965E-04
+   .550481018409E-04   .568381163590E-04   .586863364318E-04   .605946546324E-04   .625650250632E-04
+   .645994653551E-04   .667000587319E-04   .688689561416E-04   .711083784571E-04   .734206187480E-04
+   .758080446262E-04   .782731006675E-04   .808183109118E-04   .834462814443E-04   .861597030606E-04
+   .889613540173E-04   .918541028731E-04   .948409114207E-04   .979248377142E-04   .101109039194E-03
+   .104396775914E-03   .107791413872E-03   .111296428448E-03   .114915407952E-03   .118652057294E-03
+   .122510201760E-03   .126493790920E-03   .130606902659E-03   .134853747338E-03   .139238672088E-03
+   .143766165242E-03   .148440860915E-03   .153267543723E-03   .158251153660E-03   .163396791131E-03
+   .168709722144E-03   .174195383669E-03   .179859389171E-03   .185707534319E-03   .191745802874E-03
+   .197980372773E-03   .204417622402E-03   .211064137063E-03   .217926715664E-03   .225012377598E-03
+   .232328369866E-03   .239882174401E-03   .247681515644E-03   .255734368344E-03   .264048965612E-03
+   .272633807228E-03   .281497668203E-03   .290649607612E-03   .300098977705E-03   .309855433294E-03
+   .319928941443E-03   .330329791440E-03   .341068605095E-03   .352156347338E-03   .363604337150E-03
+   .375424258823E-03   .387628173562E-03   .400228531432E-03   .413238183671E-03   .426670395356E-03
+   .440538858462E-03   .454857705282E-03   .469641522262E-03   .484905364210E-03   .500664768938E-03
+   .516935772296E-03   .533734923645E-03   .551079301749E-03   .568986531105E-03   .587474798722E-03
+   .606562871331E-03   .626270113061E-03   .646616503561E-03   .667622656585E-03   .689309839028E-03
+   .711699990427E-03   .734815742920E-03   .758680441650E-03   .783318165627E-03   .808753749025E-03
+   .835012802915E-03   .862121737409E-03   .890107784211E-03   .918999019551E-03   .948824387471E-03
+   .979613723446E-03   .101139777830E-02   .104420824237E-02   .107807776989E-02   .111304000356E-02
+   .114912959911E-02   .118638225005E-02   .122483471218E-02   .126452482815E-02   .130549155155E-02
+   .134777497086E-02   .139141633267E-02   .143645806444E-02   .148294379626E-02   .153091838171E-02
+   .158042791736E-02   .163151976091E-02   .168424254740E-02   .173864620342E-02   .179478195889E-02
+   .185270235589E-02   .191246125433E-02   .197411383369E-02   .203771659049E-02   .210332733071E-02
+   .217100515649E-02   .224081044631E-02   .231280482772E-02   .238705114166E-02   .246361339709E-02
+   .254255671485E-02   .262394725904E-02   .270785215452E-02   .279433938855E-02   .288347769449E-02
+   .297533641527E-02   .306998534399E-02   .316749453861E-02   .326793410732E-02   .337137396094E-02
+   .347788352781E-02   .358753142647E-02   .370038509052E-02   .381651033932E-02   .393597088755E-02
+   .405882778553E-02   .418513878099E-02   .431495759219E-02   .444833308019E-02   .458530830718E-02
+   .472591946529E-02   .487019465868E-02   .501815251889E-02   .516980063105E-02   .532513374505E-02
+   .548413174236E-02   .564675732521E-02   .581295338964E-02   .598264003926E-02   .615571118988E-02
+   .633203070846E-02   .651142802188E-02   .669369312193E-02   .687857088273E-02   .706575459498E-02
+   .725487860842E-02   .744550995872E-02   .763713883827E-02   .782916775105E-02   .802089917058E-02
+   .821152149574E-02   .840009307223E-02   .858552401783E-02   .876655555604E-02   .894173652625E-02
+   .910939669822E-02   .926761647490E-02   .941419252015E-02   .954659879722E-02   .966194244997E-02
+   .975691390319E-02   .982773050077E-02   .987007294359E-02   .987901373415E-02   .984893678510E-02
+   .977344730712E-02   .964527106365E-02   .945614207061E-02   .919667783672E-02   .885624129362E-02
+   .842278866608E-02   .788270269565E-02   .722061087326E-02   .641918867735E-02   .545894827979E-02
+   .431801379800E-02   .297188497289E-02   .139319217287E-02  -.448553094467E-03  -.258720639694E-02
+  -.506022962024E-02  -.790891121518E-02  -.111785546697E-01  -.149186192039E-01  -.191827929812E-01
+  -.240289749478E-01  -.295191367867E-01  -.357190314954E-01  -.426977099021E-01  -.505268012579E-01
+  -.592795092078E-01  -.690292703957E-01  -.798480203107E-01  -.918040104754E-01  -.104959123678E+00
+  -.119365640755E+00  -.135052537078E+00  -.152079847668E+00
+ ae wavefunction
+  -.536934453859E-05  -.554283679026E-05  -.572192904881E-05  -.590680169358E-05  -.609764089026E-05
+  -.629463877488E-05  -.649799364359E-05  -.670791014832E-05  -.692459949849E-05  -.714827966909E-05
+  -.737917561507E-05  -.761751949247E-05  -.786355088640E-05  -.811751704595E-05  -.837967312645E-05
+  -.865028243916E-05  -.892961670862E-05  -.921795633789E-05  -.951559068196E-05  -.982281832946E-05
+  -.101399473930E-04  -.104672958085E-04  -.108051916432E-04  -.111539734135E-04  -.115139904123E-04
+  -.118856030458E-04  -.122691831813E-04  -.126651145043E-04  -.130737928877E-04  -.134956267708E-04
+  -.139310375502E-04  -.143804599824E-04  -.148443425977E-04  -.153231481275E-04  -.158173539430E-04
+  -.163274525071E-04  -.168539518402E-04  -.173973759985E-04  -.179582655672E-04  -.185371781670E-04
+  -.191346889761E-04  -.197513912662E-04  -.203878969549E-04  -.210448371726E-04  -.217228628465E-04
+  -.224226453000E-04  -.231448768698E-04  -.238902715395E-04  -.246595655907E-04  -.254535182727E-04
+  -.262729124892E-04  -.271185555052E-04  -.279912796712E-04  -.288919431682E-04  -.298214307715E-04
+  -.307806546346E-04  -.317705550946E-04  -.327921014965E-04  -.338462930403E-04  -.349341596486E-04
+  -.360567628560E-04  -.372151967208E-04  -.384105887585E-04  -.396441008986E-04  -.409169304631E-04
+  -.422303111689E-04  -.435855141531E-04  -.449838490212E-04  -.464266649193E-04  -.479153516296E-04
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+  -.317135695765E-03  -.326748438899E-03  -.336630805319E-03  -.346788912276E-03  -.357228914847E-03
+  -.367956997739E-03  -.378979366308E-03  -.390302236747E-03  -.401931825406E-03  -.413874337166E-03
+  -.426135952835E-03  -.438722815493E-03  -.451641015734E-03  -.464896575730E-03  -.478495432072E-03
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+  -.851716921913E-03  -.873877109413E-03  -.896429619485E-03  -.919368663237E-03  -.942687315069E-03
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+  -.122088688052E-02  -.124769519669E-02  -.127465142868E-02  -.130172355576E-02  -.132887701736E-02
+  -.135607460649E-02  -.138327636352E-02  -.141043947082E-02  -.143751814883E-02  -.146446355430E-02
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+  -.173475841814E-02  -.175506034127E-02  -.177427815611E-02  -.179231278583E-02  -.180906147281E-02
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+  -.187570210923E-02  -.186784332698E-02  -.185709744495E-02  -.184333027040E-02  -.182640799755E-02
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+  -.139579887503E-02  -.133148115055E-02  -.126256128768E-02  -.118897044893E-02  -.111064820449E-02
+  -.102754275349E-02  -.939611039582E-03  -.846818745856E-03  -.749140153709E-03  -.646557849671E-03
+  -.539062263517E-03  -.426651020394E-03  -.309328089220E-03  -.187102709897E-03  -.599880838515E-04
+   .720001825600E-04   .208845882540E-03   .350534246572E-03   .497054178393E-03   .648400632914E-03
+   .804577064382E-03   .965597871782E-03   .113149078626E-02   .130229918063E-02   .147808432308E-02
+   .165892762793E-02   .184493295336E-02   .203622894624E-02   .223297134696E-02   .243534507736E-02
+   .264356588222E-02   .285788129106E-02   .307857069465E-02   .330594435780E-02   .354034119917E-02
+   .378212515797E-02   .403167994363E-02   .428940193867E-02   .455569100166E-02   .483093890027E-02
+   .511551509457E-02   .540974958539E-02   .571391254373E-02   .602819044082E-02   .635265840777E-02
+   .668724856637E-02   .703171409088E-02   .738558878481E-02   .774814198662E-02   .811832865644E-02
+   .849473454000E-02   .887551635833E-02   .925833702998E-02   .964029599629E-02   .100178547868E-01
+   .103867580288E-01   .107419501671E-01   .110774882165E-01   .113864509092E-01   .116608446298E-01
+   .118915065430E-01   .120680053329E-01   .121785399967E-01   .122098372057E-01   .121470479066E-01
+   .119736441032E-01   .116713171792E-01   .112198796429E-01   .105971727185E-01   .977898257453E-02
+   .873896786599E-02   .744860013681E-02   .587711563848E-02   .399147119709E-02   .175628797936E-02
+  -.866239019038E-03  -.391647408054E-02  -.743746940754E-02  -.114749637066E-01  -.160771276901E-01
+  -.212941062664E-01  -.271776042085E-01  -.337807161610E-01  -.411579574899E-01  -.493653243621E-01
+  -.584602786172E-01  -.685016626504E-01  -.795495976261E-01  -.916654172796E-01  -.104911674326E+00
+  -.119352243438E+00  -.135052537078E+00  -.152079847668E+00
+ pseudo wavefunction
+   .291401328267E-08   .310660741021E-08   .331193054558E-08   .353082397944E-08   .376418460535E-08
+   .401296859474E-08   .427819531469E-08   .456095150469E-08   .486239572944E-08   .518376312600E-08
+   .552637046455E-08   .589162154379E-08   .628101294285E-08   .669614015334E-08   .713870411675E-08
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+ End of Dataset
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/INCAR b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/INCAR
new file mode 100644
index 000000000..1a9f52780
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/INCAR
@@ -0,0 +1,21 @@
+ADDGRID = True
+ALGO = Normal
+EDIFF = 1e-08
+ENCUT = 700
+IBRION = -1
+ICHARG = 0
+ISIF = 3
+ISMEAR = 0
+ISPIN = 2
+LAECHG = False
+LASPH = True
+LCHARG = False
+LORBIT = 11
+LREAL = False
+LVHAR = True
+LWAVE = False
+MAGMOM = 128*0.6
+NELM = 100
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/KPOINTS b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/KPOINTS
new file mode 100644
index 000000000..6677fab59
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/KPOINTS
@@ -0,0 +1,4 @@
+pymatgen v2020.1.28 with grid density = 1239 / atom
+0
+Monkhorst
+2 2 2
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POSCAR b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POSCAR
new file mode 100644
index 000000000..eb785ce7e
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POSCAR
@@ -0,0 +1,136 @@
+Si128
+1.0
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+0.686764 0.378560 0.190140 Si
+0.689784 0.379171 0.436946 Si
+0.686554 0.380682 0.688244 Si
+0.686129 0.374762 0.936997 Si
+0.687256 0.620816 0.184061 Si
+0.686313 0.628028 0.439813 Si
+0.687753 0.626497 0.688568 Si
+0.685704 0.628037 0.937508 Si
+0.686470 0.877937 0.186396 Si
+0.686007 0.878400 0.438826 Si
+0.687927 0.872425 0.690325 Si
+0.685678 0.873399 0.937346 Si
+0.939966 0.121715 0.184463 Si
+0.938280 0.125985 0.439959 Si
+0.935714 0.125861 0.688139 Si
+0.941256 0.121740 0.934856 Si
+0.940509 0.370740 0.184174 Si
+0.934583 0.375952 0.438550 Si
+0.933805 0.375006 0.691141 Si
+0.939116 0.373552 0.936880 Si
+0.938269 0.626982 0.190164 Si
+0.944814 0.622757 0.438232 Si
+0.935640 0.629382 0.687222 Si
+0.933990 0.629804 0.937675 Si
+0.935086 0.877005 0.189286 Si
+0.938269 0.874576 0.437978 Si
+0.939148 0.875524 0.684622 Si
+0.935925 0.874399 0.934462 Si
diff --git a/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POTCAR b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POTCAR
new file mode 100644
index 000000000..ae2291fdf
--- /dev/null
+++ b/atomate/vasp/test_files/lattice_dynamics_wf/0/outputs/POTCAR
@@ -0,0 +1,1768 @@
+ PAW_PBE Si 05Jan2001
+ 4.00000000000000000
+ parameters from PSCTR are:
+   VRHFIN =Si: s2p2
+   LEXCH  = PE
+   EATOM  =   103.0669 eV,    7.5752 Ry
+
+   TITEL  = PAW_PBE Si 05Jan2001
+   LULTRA =        F    use ultrasoft PP ?
+   IUNSCR =        1    unscreen: 0-lin 1-nonlin 2-no
+   RPACOR =    1.500    partial core radius
+   POMASS =   28.085; ZVAL   =    4.000    mass and valenz
+   RCORE  =    1.900    outmost cutoff radius
+   RWIGS  =    2.480; RWIGS  =    1.312    wigner-seitz radius (au A)
+   ENMAX  =  245.345; ENMIN  =  184.009 eV
+   ICORE  =        2    local potential
+   LCOR   =        T    correct aug charges
+   LPAW   =        T    paw PP
+   EAUG   =  322.069
+   DEXC   =    -.007
+   RMAX   =    2.944    core radius for proj-oper
+   RAUG   =    1.300    factor for augmentation sphere
+   RDEP   =    1.993    radius for radial grids
+   QCUT   =   -4.246; QGAM   =    8.493    optimization parameters
+ 
+   Description
+     l     E      TYP  RCUT    TYP  RCUT
+     0   .000     23  1.900
+     0   .000     23  1.900
+     1   .000     23  1.900
+     1   .000     23  1.900
+     2   .000      7  1.900
+   Error from kinetic energy argument (eV)
+   NDATA  =      100
+   STEP   =   20.000   1.050
+  10.1      9.04      8.56      7.65      7.23      6.44      5.73      5.40
+  4.79      4.25      4.00      3.54      3.13      2.77      2.45      2.16
+  1.91      1.69      1.50      1.24      1.10      .975      .812      .718
+  .636      .529      .440      .388      .322      .266      .219      .180
+  .148      .121      .986E-01  .804E-01  .614E-01  .504E-01  .392E-01  .328E-01
+  .265E-01  .220E-01  .189E-01  .166E-01  .149E-01  .135E-01  .123E-01  .109E-01
+  .977E-02  .840E-02  .707E-02  .605E-02  .488E-02  .387E-02  .290E-02  .229E-02
+  .185E-02  .152E-02  .134E-02  .125E-02  .121E-02  .117E-02  .112E-02  .102E-02
+  .915E-03  .776E-03  .640E-03  .524E-03  .425E-03  .369E-03  .331E-03  .310E-03
+  .294E-03  .273E-03  .242E-03  .210E-03  .175E-03  .146E-03  .124E-03  .113E-03
+  .105E-03  .973E-04  .879E-04  .755E-04  .633E-04  .539E-04  .478E-04  .438E-04
+  .404E-04  .362E-04  .308E-04  .264E-04  .229E-04  .209E-04  .192E-04  .170E-04
+  .145E-04  .126E-04  .112E-04  .103E-04
+END of PSCTR-controll parameters
+ local part
+ 98.2657514061040160
+   .84157696E+01   .84210616E+01   .84276868E+01   .84387430E+01   .84542501E+01
+   .84742336E+01   .84987229E+01   .85277486E+01   .85613410E+01   .85995276E+01
+   .86423322E+01   .86897735E+01   .87418643E+01   .87986117E+01   .88600162E+01
+   .89260725E+01   .89967686E+01   .90720854E+01   .91519966E+01   .92364669E+01
+   .93254512E+01   .94188926E+01   .95167214E+01   .96188530E+01   .97251866E+01
+   .98356042E+01   .99499691E+01   .10068126E+02   .10189900E+02   .10315095E+02
+   .10443498E+02   .10574872E+02   .10708964E+02   .10845497E+02   .10984178E+02
+   .11124691E+02   .11266702E+02   .11409858E+02   .11553785E+02   .11698096E+02
+   .11842382E+02   .11986223E+02   .12129182E+02   .12270810E+02   .12410650E+02
+   .12548232E+02   .12683081E+02   .12814718E+02   .12942658E+02   .13066416E+02
+   .13185509E+02   .13299456E+02   .13407780E+02   .13510014E+02   .13605699E+02
+   .13694388E+02   .13775652E+02   .13849074E+02   .13914259E+02   .13970835E+02
+   .14018449E+02   .14056778E+02   .14085523E+02   .14104415E+02   .14113216E+02
+   .14111719E+02   .14099752E+02   .14077176E+02   .14043889E+02   .13999825E+02
+   .13944955E+02   .13879288E+02   .13802872E+02   .13715793E+02   .13618173E+02
+   .13510175E+02   .13391996E+02   .13263872E+02   .13126073E+02   .12978903E+02
+   .12822702E+02   .12657838E+02   .12484712E+02   .12303753E+02   .12115415E+02
+   .11920177E+02   .11718543E+02   .11511033E+02   .11298186E+02   .11080557E+02
+   .10858712E+02   .10633228E+02   .10404688E+02   .10173679E+02   .99407918E+01
+   .97066146E+01   .94717325E+01   .92367246E+01   .90021609E+01   .87686001E+01
+   .85365874E+01   .83066514E+01   .80793026E+01   .78550308E+01   .76343035E+01
+   .74175636E+01   .72052280E+01   .69976861E+01   .67952984E+01   .65983952E+01
+   .64072758E+01   .62222076E+01   .60434252E+01   .58711303E+01   .57054911E+01
+   .55466426E+01   .53946862E+01   .52496902E+01   .51116906E+01   .49806911E+01
+   .48566645E+01   .47395534E+01   .46292712E+01   .45257038E+01   .44287105E+01
+   .43381258E+01   .42537607E+01   .41754049E+01   .41028282E+01   .40357822E+01
+   .39740031E+01   .39172124E+01   .38651203E+01   .38174267E+01   .37738238E+01
+   .37339979E+01   .36976315E+01   .36644056E+01   .36340010E+01   .36061008E+01
+   .35803917E+01   .35565663E+01   .35343243E+01   .35133745E+01   .34934357E+01
+   .34742388E+01   .34555274E+01   .34370596E+01   .34186083E+01   .33999627E+01
+   .33809285E+01   .33613290E+01   .33410052E+01   .33198164E+01   .32976401E+01
+   .32743723E+01   .32499276E+01   .32242387E+01   .31972561E+01   .31689481E+01
+   .31393000E+01   .31083133E+01   .30760055E+01   .30424087E+01   .30075693E+01
+   .29715463E+01   .29344112E+01   .28962459E+01   .28571426E+01   .28172018E+01
+   .27765317E+01   .27352466E+01   .26934662E+01   .26513138E+01   .26089155E+01
+   .25663991E+01   .25238927E+01   .24815236E+01   .24394173E+01   .23976966E+01
+   .23564804E+01   .23158831E+01   .22760134E+01   .22369739E+01   .21988600E+01
+   .21617599E+01   .21257533E+01   .20909116E+01   .20572974E+01   .20249638E+01
+   .19939548E+01   .19643045E+01   .19360379E+01   .19091701E+01   .18837069E+01
+   .18596450E+01   .18369720E+01   .18156670E+01   .17957010E+01   .17770368E+01
+   .17596305E+01   .17434311E+01   .17283816E+01   .17144193E+01   .17014768E+01
+   .16894823E+01   .16783607E+01   .16680338E+01   .16584212E+01   .16494415E+01
+   .16410120E+01   .16330504E+01   .16254746E+01   .16182040E+01   .16111597E+01
+   .16042653E+01   .15974473E+01   .15906355E+01   .15837638E+01   .15767703E+01
+   .15695978E+01   .15621941E+01   .15545123E+01   .15465111E+01   .15381544E+01
+   .15294125E+01   .15202610E+01   .15106817E+01   .15006619E+01   .14901947E+01
+   .14792788E+01   .14679182E+01   .14561221E+01   .14439046E+01   .14312844E+01
+   .14182846E+01   .14049321E+01   .13912574E+01   .13772942E+01   .13630791E+01
+   .13486509E+01   .13340503E+01   .13193195E+01   .13045019E+01   .12896412E+01
+   .12747815E+01   .12599666E+01   .12452397E+01   .12306428E+01   .12162167E+01
+   .12020006E+01   .11880314E+01   .11743437E+01   .11609697E+01   .11479386E+01
+   .11352766E+01   .11230067E+01   .11111486E+01   .10997186E+01   .10887293E+01
+   .10781902E+01   .10681067E+01   .10584813E+01   .10493127E+01   .10405964E+01
+   .10323246E+01   .10244865E+01   .10170685E+01   .10100542E+01   .10034245E+01
+   .99715846E+00   .99123280E+00   .98562260E+00   .98030145E+00   .97524173E+00
+   .97041488E+00   .96579171E+00   .96134265E+00   .95703806E+00   .95284844E+00
+   .94874473E+00   .94469858E+00   .94068254E+00   .93667031E+00   .93263696E+00
+   .92855909E+00   .92441506E+00   .92018509E+00   .91585142E+00   .91139842E+00
+   .90681263E+00   .90208291E+00   .89720039E+00   .89215854E+00   .88695315E+00
+   .88158229E+00   .87604630E+00   .87034770E+00   .86449110E+00   .85848313E+00
+   .85233229E+00   .84604884E+00   .83964465E+00   .83313300E+00   .82652847E+00
+   .81984671E+00   .81310428E+00   .80631845E+00   .79950703E+00   .79268813E+00
+   .78588003E+00   .77910097E+00   .77236895E+00   .76570159E+00   .75911593E+00
+   .75262828E+00   .74625407E+00   .74000773E+00   .73390251E+00   .72795041E+00
+   .72216209E+00   .71654675E+00   .71111209E+00   .70586428E+00   .70080787E+00
+   .69594584E+00   .69127954E+00   .68680877E+00   .68253173E+00   .67844513E+00
+   .67454418E+00   .67082274E+00   .66727331E+00   .66388721E+00   .66065462E+00
+   .65756473E+00   .65460586E+00   .65176555E+00   .64903076E+00   .64638795E+00
+   .64382325E+00   .64132257E+00   .63887178E+00   .63645678E+00   .63406371E+00
+   .63167900E+00   .62928956E+00   .62688288E+00   .62444710E+00   .62197118E+00
+   .61944494E+00   .61685919E+00   .61420575E+00   .61147755E+00   .60866866E+00
+   .60577434E+00   .60279104E+00   .59971643E+00   .59654939E+00   .59329003E+00
+   .58993961E+00   .58650056E+00   .58297643E+00   .57937181E+00   .57569230E+00
+   .57194440E+00   .56813547E+00   .56427363E+00   .56036764E+00   .55642683E+00
+   .55246099E+00   .54848026E+00   .54449503E+00   .54051583E+00   .53655322E+00
+   .53261771E+00   .52871961E+00   .52486898E+00   .52107551E+00   .51734843E+00
+   .51369641E+00   .51012750E+00   .50664907E+00   .50326768E+00   .49998911E+00
+   .49681824E+00   .49375908E+00   .49081468E+00   .48798715E+00   .48527763E+00
+   .48268632E+00   .48021244E+00   .47785431E+00   .47560930E+00   .47347392E+00
+   .47144387E+00   .46951402E+00   .46767855E+00   .46593095E+00   .46426412E+00
+   .46267047E+00   .46114194E+00   .45967012E+00   .45824632E+00   .45686169E+00
+   .45550723E+00   .45417395E+00   .45285292E+00   .45153535E+00   .45021267E+00
+   .44887661E+00   .44751931E+00   .44613331E+00   .44471171E+00   .44324816E+00
+   .44173692E+00   .44017295E+00   .43855190E+00   .43687017E+00   .43512491E+00
+   .43331405E+00   .43143631E+00   .42949120E+00   .42747899E+00   .42540073E+00
+   .42325823E+00   .42105400E+00   .41879126E+00   .41647384E+00   .41410622E+00
+   .41169341E+00   .40924089E+00   .40675462E+00   .40424088E+00   .40170629E+00
+   .39915769E+00   .39660209E+00   .39404660E+00   .39149835E+00   .38896445E+00
+   .38645189E+00   .38396749E+00   .38151784E+00   .37910923E+00   .37674758E+00
+   .37443844E+00   .37218685E+00   .36999739E+00   .36787409E+00   .36582039E+00
+   .36383915E+00   .36193261E+00   .36010239E+00   .35834945E+00   .35667414E+00
+   .35507613E+00   .35355450E+00   .35210772E+00   .35073362E+00   .34942953E+00
+   .34819219E+00   .34701788E+00   .34590241E+00   .34484117E+00   .34382921E+00
+   .34286125E+00   .34193178E+00   .34103506E+00   .34016522E+00   .33931629E+00
+   .33848229E+00   .33765725E+00   .33683525E+00   .33601054E+00   .33517754E+00
+   .33433091E+00   .33346559E+00   .33257683E+00   .33166028E+00   .33071198E+00
+   .32972841E+00   .32870651E+00   .32764370E+00   .32653791E+00   .32538758E+00
+   .32419168E+00   .32294968E+00   .32166161E+00   .32032797E+00   .31894980E+00
+   .31752862E+00   .31606640E+00   .31456556E+00   .31302895E+00   .31145977E+00
+   .30986158E+00   .30823823E+00   .30659385E+00   .30493275E+00   .30325946E+00
+   .30157859E+00   .29989486E+00   .29821301E+00   .29653778E+00   .29487386E+00
+   .29322581E+00   .29159807E+00   .28999490E+00   .28842031E+00   .28687807E+00
+   .28537164E+00   .28390415E+00   .28247839E+00   .28109677E+00   .27976132E+00
+   .27847363E+00   .27723491E+00   .27604592E+00   .27490700E+00   .27381809E+00
+   .27277867E+00   .27178784E+00   .27084428E+00   .26994630E+00   .26909186E+00
+   .26827855E+00   .26750369E+00   .26676430E+00   .26605715E+00   .26537882E+00
+   .26472568E+00   .26409398E+00   .26347988E+00   .26287945E+00   .26228874E+00
+   .26170381E+00   .26112076E+00   .26053579E+00   .25994520E+00   .25934545E+00
+   .25873320E+00   .25810531E+00   .25745888E+00   .25679129E+00   .25610022E+00
+   .25538363E+00   .25463983E+00   .25386744E+00   .25306545E+00   .25223318E+00
+   .25137030E+00   .25047684E+00   .24955316E+00   .24859996E+00   .24761829E+00
+   .24660949E+00   .24557519E+00   .24451731E+00   .24343801E+00   .24233971E+00
+   .24122498E+00   .24009659E+00   .23895746E+00   .23781060E+00   .23665912E+00
+   .23550617E+00   .23435492E+00   .23320855E+00   .23207016E+00   .23094281E+00
+   .22982945E+00   .22873289E+00   .22765579E+00   .22660063E+00   .22556967E+00
+   .22456498E+00   .22358834E+00   .22264131E+00   .22172517E+00   .22084092E+00
+   .21998928E+00   .21917068E+00   .21838526E+00   .21763287E+00   .21691308E+00
+   .21622517E+00   .21556818E+00   .21494086E+00   .21434175E+00   .21376913E+00
+   .21322111E+00   .21269560E+00   .21219035E+00   .21170297E+00   .21123098E+00
+   .21077179E+00   .21032276E+00   .20988120E+00   .20944443E+00   .20900979E+00
+   .20857462E+00   .20813639E+00   .20769262E+00   .20724095E+00   .20677916E+00
+   .20630522E+00   .20581722E+00   .20531350E+00   .20479256E+00   .20425315E+00
+   .20369424E+00   .20311502E+00   .20251496E+00   .20189372E+00   .20125124E+00
+   .20058769E+00   .19990349E+00   .19919926E+00   .19847589E+00   .19773443E+00
+   .19697618E+00   .19620258E+00   .19541527E+00   .19461602E+00   .19380673E+00
+   .19298941E+00   .19216618E+00   .19133918E+00   .19051063E+00   .18968276E+00
+   .18885780E+00   .18803797E+00   .18722542E+00   .18642227E+00   .18563052E+00
+   .18485209E+00   .18408877E+00   .18334220E+00   .18261388E+00   .18190512E+00
+   .18121707E+00   .18055068E+00   .17990670E+00   .17928569E+00   .17868800E+00
+   .17811376E+00   .17756291E+00   .17703518E+00   .17653009E+00   .17604697E+00
+   .17558497E+00   .17514306E+00   .17472002E+00   .17431452E+00   .17392507E+00
+   .17355005E+00   .17318776E+00   .17283640E+00   .17249410E+00   .17215895E+00
+   .17182901E+00   .17150232E+00   .17117693E+00   .17085094E+00   .17052245E+00
+   .17018966E+00   .16985084E+00   .16950435E+00   .16914867E+00   .16878242E+00
+   .16840433E+00   .16801331E+00   .16760841E+00   .16718886E+00   .16675406E+00
+   .16630358E+00   .16583717E+00   .16535477E+00   .16485650E+00   .16434264E+00
+   .16381366E+00   .16327018E+00   .16271301E+00   .16214308E+00   .16156147E+00
+   .16096939E+00   .16036817E+00   .15975923E+00   .15914407E+00   .15852427E+00
+   .15790145E+00   .15727728E+00   .15665345E+00   .15603163E+00   .15541350E+00
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+ gradient corrections used for XC
+ 5
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+  -.73622006E-01  -.50254001E-01  -.31070866E-01  -.16212387E-01  -.54900275E-02
+ Non local Part
+ 1 2 1.55770284366884382
+ 2.65859659160385764 -0.504801881867953453E-01 -0.504801881867953453E-01 0.892956271679604986E-02
+ Reciprocal Space Part
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+   .28801366E-03   .16363396E-02   .27990903E-02   .37452630E-02   .44552150E-02
+ Real Space Part
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+ Reciprocal Space Part
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+ Real Space Part
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+ PAW radial sets
+ 323 0.989218471734281124
+(5E20.12)                                
+ augmentation charges (non sperical)
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+ core charge-density (pseudized)
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+   .386374464823E-01   .411484508237E-01   .438196346781E-01   .466608047400E-01   .496823112734E-01
+   .528950701615E-01   .563105846042E-01   .599409662088E-01   .637989551781E-01   .678979392487E-01
+   .722519709725E-01   .768757828747E-01   .817847999463E-01   .869951488479E-01   .925236631107E-01
+   .983878835213E-01   .104606052760E+00   .111197103239E+00   .118180636950E+00   .125576895976E+00
+   .133406722150E+00   .141691504177E+00   .150453110317E+00   .159713804529E+00   .169496143740E+00
+   .179822853659E+00   .190716680317E+00   .202200214208E+00   .214295683694E+00   .227024713996E+00
+   .240408047883E+00   .254465223863E+00   .269214207487E+00   .284670971153E+00   .300849017672E+00
+   .317758842779E+00   .335407331821E+00   .353797086014E+00   .372925673998E+00   .392784804976E+00
+   .413359420546E+00   .434626703479E+00   .456555003242E+00   .479102680107E+00   .502216872244E+00
+   .525832193516E+00   .549869373680E+00   .574233857642E+00   .598814386387E+00   .623481589187E+00
+   .648086625061E+00   .672459920978E+00   .696410065316E+00   .719722927378E+00   .742161087375E+00
+   .763463676005E+00   .783346738217E+00   .801504251502E+00   .817609944243E+00   .831320073323E+00
+   .842277330789E+00   .850116055018E+00   .854468920152E+00   .854975265373E+00   .851291199249E+00
+   .843101569433E+00   .830133819226E+00   .812173654295E+00   .789082308931E+00   .760815025548E+00
+   .727440137991E+00   .689157874534E+00   .646317668655E+00   .599432387566E+00   .549187469489E+00
+   .496442519212E+00   .442222478719E+00   .387695112852E+00   .334131296257E+00   .282844548501E+00
+   .235106556397E+00   .192036190812E+00   .154460937507E+00   .122751901168E+00   .966509456742E-01
+   .754197389551E-01   .583105713293E-01   .446553155083E-01   .338641489723E-01   .254227504169E-01
+   .188882123217E-01   .138839144900E-01   .100936595806E-01
+ pseudo wavefunction
+   .575355356415E-04   .594064477253E-04   .613381972024E-04   .633327623533E-04   .653921857868E-04
+   .675185765325E-04   .697141122004E-04   .719810412106E-04   .743216850967E-04   .767384408824E-04
+   .792337835369E-04   .818102685089E-04   .844705343442E-04   .872173053874E-04   .900533945721E-04
+   .929817063013E-04   .960052394220E-04   .991270902962E-04   .102350455972E-03   .105678637457E-03
+   .109115043101E-03   .112663192082E-03   .116326718016E-03   .120109372672E-03   .124015029819E-03
+   .128047689192E-03   .132211480586E-03   .136510668086E-03   .140949654437E-03   .145532985548E-03
+   .150265355149E-03   .155151609602E-03   .160196752857E-03   .165405951581E-03   .170784540448E-03
+   .176338027603E-03   .182072100302E-03   .187992630735E-03   .194105682043E-03   .200417514522E-03
+   .206934592042E-03   .213663588656E-03   .220611395446E-03   .227785127571E-03   .235192131559E-03
+   .242839992828E-03   .250736543454E-03   .258889870194E-03   .267308322765E-03   .276000522397E-03
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+   .120279413821E-02   .124190598731E-02   .128228965460E-02   .132398649626E-02   .136703921328E-02
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+   .314132971901E-02   .324347764574E-02   .334894714010E-02   .345784620834E-02   .357028636854E-02
+   .368638276474E-02   .380625428484E-02   .393002368229E-02   .405781770175E-02   .418976720886E-02
+   .432600732415E-02   .446667756139E-02   .461192197039E-02   .476188928438E-02   .491673307231E-02
+   .507661189599E-02   .524168947234E-02   .541213484098E-02   .558812253715E-02   .576983277035E-02
+   .595745160873E-02   .615117116944E-02   .635118981518E-02   .655771235717E-02   .677095026461E-02
+   .699112188101E-02   .721845264752E-02   .745317533347E-02   .769553027439E-02   .794576561781E-02
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+   .962761239135E-02   .994067029381E-02   .102639072487E-01   .105976541719E-01   .109422527315E-01
+   .112980556968E-01   .116654272983E-01   .120447435995E-01   .124363928804E-01   .128407760336E-01
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+   .182580030081E-01   .188516529119E-01   .194646013071E-01   .200974751761E-01   .207509218330E-01
+   .214256095793E-01   .221222283799E-01   .228414905610E-01   .235841315294E-01   .243509105150E-01
+   .251426113360E-01   .259600431889E-01   .268040414619E-01   .276754685752E-01   .285752148462E-01
+   .295041993818E-01   .304633709985E-01   .314537091706E-01   .324762250072E-01   .335319622594E-01
+   .346219983579E-01   .357474454814E-01   .369094516585E-01   .381092019006E-01   .393479193701E-01
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+   .476721504277E-01   .492213531363E-01   .508208336098E-01   .524722168313E-01   .541771796234E-01
+   .559374522328E-01   .577548199563E-01   .596311248087E-01   .615682672319E-01   .635682078464E-01
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+   .903388029198E-01   .932697257982E-01   .962952821862E-01   .994184814074E-01   .102642423774E+00
+   .105970302852E+00   .109405407722E+00   .112951125248E+00   .116610942317E+00   .120388448077E+00
+   .124287336121E+00   .128311406648E+00   .132464568547E+00   .136750841429E+00   .141174357551E+00
+   .145739363643E+00   .150450222608E+00   .155311415056E+00   .160327540676E+00   .165503319382E+00
+   .170843592230E+00   .176353322051E+00   .182037593757E+00   .187901614291E+00   .193950712150E+00
+   .200190336440E+00   .206626055381E+00   .213263554212E+00   .220108632399E+00   .227167200068E+00
+   .234445273557E+00   .241948969987E+00   .249684500724E+00   .257658163593E+00   .265876333703E+00
+   .274345452710E+00   .283072016330E+00   .292062559898E+00   .301323641738E+00   .310861824101E+00
+   .320683651362E+00   .330795625188E+00   .341204176307E+00   .351915632491E+00   .362936182330E+00
+   .374271834305E+00   .385928370642E+00   .397911295339E+00   .410225775742E+00   .422876576925E+00
+   .435867988095E+00   .449203740138E+00   .462886913351E+00   .476919834292E+00   .491303960597E+00
+   .506039752485E+00   .521126529587E+00   .536562311577E+00   .552343640997E+00   .568465386534E+00
+   .584920524858E+00   .601699899070E+00   .618791951638E+00   .636182429658E+00   .653854060191E+00
+   .671786193400E+00   .689954411226E+00   .708330099434E+00   .726879981021E+00   .745565609229E+00
+   .764342818847E+00   .783161135014E+00   .801963139531E+00   .820683795679E+00   .839249733873E+00
+   .857578502086E+00   .875577787069E+00   .893144614848E+00   .910164542018E+00   .926510852941E+00
+   .942043782108E+00   .956609785792E+00   .970040892551E+00   .982154168203E+00   .992751337468E+00
+   .100161861137E+01   .100852677652E+01   .101323160906E+01   .101547468225E+01   .101498464091E+01
+   .101147901878E+01   .100466111560E+01   .994375951175E+00
+ ae wavefunction
+   .723210491674E-03   .746578583504E-03   .770700951777E-03   .795601892046E-03   .821306479222E-03
+   .847840592364E-03   .875230940233E-03   .903505087646E-03   .932691482648E-03   .962819484530E-03
+   .993919392710E-03   .102602247652E-02   .105916100589E-02   .109336828301E-02   .112867867496E-02
+   .116512764731E-02   .120275179882E-02   .124158889712E-02   .128167791559E-02   .132305907123E-02
+   .136577386383E-02   .140986511623E-02   .145537701585E-02   .150235515746E-02   .155084658728E-02
+   .160089984836E-02   .165256502735E-02   .170589380272E-02   .176093949434E-02   .181775711461E-02
+   .187640342107E-02   .193693697064E-02   .199941817539E-02   .206390935997E-02   .213047482081E-02
+   .219918088694E-02   .227009598271E-02   .234329069219E-02   .241883782559E-02   .249681248751E-02
+   .257729214718E-02   .266035671067E-02   .274608859525E-02   .283457280576E-02   .292589701322E-02
+   .302015163557E-02   .311742992074E-02   .321782803195E-02   .332144513543E-02   .342838349055E-02
+   .353874854230E-02   .365264901643E-02   .377019701702E-02   .389150812670E-02   .401670150953E-02
+   .414590001658E-02   .427923029422E-02   .441682289522E-02   .455881239271E-02   .470533749697E-02
+   .485654117518E-02   .501257077409E-02   .517357814572E-02   .533971977604E-02   .551115691676E-02
+   .568805572017E-02   .587058737709E-02   .605892825797E-02   .625326005711E-02   .645376994004E-02
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+   .427067744540E-01   .440007359916E-01   .453309406888E-01   .466982057375E-01   .481033527959E-01
+   .495472068255E-01   .510305948176E-01   .525543444026E-01   .541192823346E-01   .557262328435E-01
+   .573760158460E-01   .590694450081E-01   .608073256492E-01   .625904524789E-01   .644196071575E-01
+   .662955556690E-01   .682190454976E-01   .701908025956E-01   .722115281337E-01   .742818950192E-01
+   .764025441734E-01   .785740805545E-01   .807970689137E-01   .830720292724E-01   .853994321068E-01
+   .877796932277E-01   .902131683422E-01   .927001472824E-01   .952408478902E-01   .978354095427E-01
+   .100483886305E+00   .103186239701E+00   .105942331082E+00   .108751913586E+00   .111614623678E+00
+   .114529972255E+00   .117497335304E+00   .120515944107E+00   .123584874990E+00   .126703038594E+00
+   .129869168677E+00   .133081810436E+00   .136339308348E+00   .139639793532E+00   .142981170636E+00
+   .146361104253E+00   .149777004875E+00   .153226014404E+00   .156704991228E+00   .160210494897E+00
+   .163738770409E+00   .167285732154E+00   .170846947546E+00   .174417620387E+00   .177992574025E+00
+   .181566234348E+00   .185132612703E+00   .188685288794E+00   .192217393669E+00   .195721592871E+00
+   .199190069873E+00   .202614509914E+00   .205986084362E+00   .209295435754E+00   .212532663666E+00
+   .215687311579E+00   .218748354949E+00   .221704190648E+00   .224542628026E+00   .227250881804E+00
+   .229815567059E+00   .232222696565E+00   .234457680772E+00   .236505330719E+00   .238349864209E+00
+   .239974915563E+00   .241363549317E+00   .242498278209E+00   .243361085852E+00   .243933454457E+00
+   .244196398032E+00   .244130501447E+00   .243715965781E+00   .242932660377E+00   .241760182005E+00
+   .240177921559E+00   .238165138679E+00   .235701044686E+00   .232764894196E+00   .229336085751E+00
+   .225394271769E+00   .220919478069E+00   .215892233186E+00   .210293707615E+00   .204105863065E+00
+   .197311611722E+00   .189894985412E+00   .181841314484E+00   .173137416083E+00   .163771791405E+00
+   .153734831344E+00   .143019029848E+00   .131619204110E+00   .119532720583E+00   .106759725623E+00
+   .933033793783E-01   .791700913290E-01   .643697556467E-01   .489159842705E-01   .328263352823E-01
+   .161225338086E-01  -.116931769311E-02  -.190185432589E-01  -.373897150652E-01  -.562424965567E-01
+  -.755315101746E-01  -.952062316141E-01  -.115210910670E+00  -.135484516518E+00  -.155960703517E+00
+  -.176567793429E+00  -.197228772403E+00  -.217861306439E+00  -.238377786432E+00  -.258685421094E+00
+  -.278686400098E+00  -.298278147634E+00  -.317353677390E+00  -.335802046575E+00  -.353508895291E+00
+  -.370357053514E+00  -.386227201622E+00  -.400998577469E+00  -.414549728634E+00  -.426759310469E+00
+  -.437506929404E+00  -.446674028239E+00  -.454144807390E+00  -.459807173979E+00  -.463553709570E+00
+  -.465282646961E+00  -.464898846615E+00  -.462314763759E+00  -.457451397642E+00  -.450239215005E+00
+  -.440619040214E+00  -.428542904958E+00  -.413974850650E+00  -.396891676910E+00  -.377283629551E+00
+  -.355155021405E+00  -.330524779042E+00  -.303426907952E+00  -.273910868147E+00  -.242041851308E+00
+  -.207900949827E+00  -.171585207413E+00  -.133207540559E+00  -.928965205479E-01  -.507960069887E-01
+  -.706462660247E-02   .381249046254E-01   .845866118155E-01   .132122232827E+00   .180522312943E+00
+   .229567399836E+00   .279029316983E+00   .328672503777E+00   .378255433412E+00   .427532158406E+00
+   .476254091096E+00   .524172202057E+00   .571039898221E+00   .616616860053E+00   .660673895312E+00
+   .702998092998E+00   .743396069181E+00   .781691750831E+00   .817716502043E+00   .851295258407E+00
+   .882238299672E+00   .910345743397E+00   .935421491735E+00   .957287299205E+00   .975791213531E+00
+   .990810701652E+00   .100225314042E+01   .101005569012E+01   .101418535258E+01   .101463927777E+01
+   .101144510801E+01   .100466111560E+01   .994375951175E+00
+ pseudo wavefunction
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+ pseudo wavefunction
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+  -.209065329490E-01  -.274826407059E-01  -.349943660481E-01  -.435353202661E-01  -.532033034353E-01
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+  -.140490455867E+00  -.160752140242E+00  -.182838197398E+00
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+   .490228207127E-03   .518142385893E-03   .547514626344E-03   .578409478292E-03   .610893360173E-03
+   .645034529359E-03   .680903044093E-03   .718570716657E-03   .758111057440E-03   .799599209646E-03
+   .843111874437E-03   .888727226421E-03   .936524819495E-03   .986585483195E-03   .103899120984E-02
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+   .140737775294E-02   .147856502718E-02   .155277915525E-02   .163010640797E-02   .171063280434E-02
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+   .283163793710E-02   .295706690745E-02   .308676787920E-02   .322082403378E-02   .335932059220E-02
+   .350234561239E-02   .364999093291E-02   .380235327479E-02   .395953550720E-02   .412164806889E-02
+   .428881051644E-02   .446115314045E-02   .463881855679E-02   .482196315214E-02   .501075825528E-02
+   .520539093344E-02   .540606438254E-02   .561299798267E-02   .582642719909E-02   .604660358714E-02
+   .627379516452E-02   .650828731395E-02   .675038417942E-02   .700041028844E-02   .725871197647E-02
+   .752565817955E-02   .780164027316E-02   .808707077981E-02   .838238086423E-02   .868801655628E-02
+   .900443360736E-02   .933209082854E-02   .967144170169E-02   .100229240120E-01   .103869472209E-01
+   .107638772809E-01   .111540185848E-01   .115575927342E-01   .119747138083E-01   .124053598104E-01
+   .128493399678E-01   .133062575600E-01   .137754679559E-01   .142560315452E-01   .147466612667E-01
+   .152456644480E-01   .157508787005E-01   .162596016357E-01   .167685142012E-01   .172735974648E-01
+   .177700427009E-01   .182521546525E-01   .187132478523E-01   .191455358726E-01   .195400133505E-01
+   .198863305955E-01   .201726605474E-01   .203855578566E-01   .205098099183E-01   .205282799298E-01
+   .204217424344E-01   .201687124905E-01   .197452704861E-01   .191248856466E-01   .182782422416E-01
+   .171730730409E-01   .157740040676E-01   .140424119477E-01   .119362882257E-01   .941009223694E-02
+   .641455956391E-02   .289643672970E-02  -.120182972349E-02  -.594230845433E-02  -.113915061558E-01
+  -.176199584845E-01  -.247017208792E-01  -.327140327375E-01  -.417371826148E-01  -.518544026197E-01
+  -.631516436073E-01  -.757171941354E-01  -.896411710603E-01  -.105014918512E+00  -.121930338317E+00
+  -.140479159189E+00  -.160752140242E+00  -.182838197398E+00
+ End of Dataset

From 8693997a619bd52a008be8f06e47e89b8c07c5ee Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Wed, 26 Feb 2020 01:58:27 -0800
Subject: [PATCH 076/207] Remove parents options from ld fireworks

---
 atomate/vasp/fireworks/lattice_dynamics.py | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 360e98c45..18cdd4664 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -11,7 +11,6 @@
     MAX_IMAGINARY_FREQ,
     MAX_N_IMAGINARY,
 )
-from atomate.vasp.analysis.phonopy import MESH_DENSITY
 from atomate.vasp.config import SHENGBTE_CMD
 from atomate.vasp.firetasks.lattice_dynamics import (
     DEFAULT_TEMPERATURE,
@@ -20,7 +19,7 @@
     RunHiPhive,
     RunShengBTE,
     ShengBTEToDb,
-)
+    MESH_DENSITY)
 from fireworks import Firework
 
 __author__ = "Alex Ganose"
@@ -67,7 +66,7 @@ def __init__(
         mesh_density: float = MESH_DENSITY,
         **kwargs
     ):
-        collect_structures = CollectPerturbedStructures(db_file)
+        collect_structures = CollectPerturbedStructures()
         fit_constants = RunHiPhive(
             cutoffs=cutoffs,
             imaginary_tol=imaginary_tol,
@@ -75,7 +74,9 @@ def __init__(
             max_imaginary_freq=max_imaginary_freq,
             fit_method=fit_method,
         )
-        to_db = ForceConstantsToDb(db_file=db_file, mesh_density=mesh_density)
+        to_db = ForceConstantsToDb(
+            db_file=db_file, mesh_density=mesh_density, additional_fields={}
+        )
         pass_locs = PassCalcLocs(name=name)
 
         tasks = [collect_structures, fit_constants, to_db, pass_locs]
@@ -88,7 +89,6 @@ class LatticeThermalConductivityFW(Firework):
 
     Args:
         name: Name of this FW.
-        parents: Parent(s) of this Firework.
         prev_calc_dir: Path to a directory containing the force constant
             information. Will override ``parents`` when collecting the force
             constants to run ShengBTE.
@@ -106,7 +106,6 @@ class LatticeThermalConductivityFW(Firework):
     def __init__(
         self,
         name="Lattice Thermal Conductivity",
-        parents: Optional[Union[Firework, List[Firework]]] = None,
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
         shengbte_cmd: str = SHENGBTE_CMD,
@@ -123,17 +122,15 @@ def __init__(
 
         if prev_calc_dir:
             copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
-        elif parents:
-            copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
         else:
-            raise ValueError("Must specify parents or prev_calc_dir.")
+            copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
 
         run_shengbte = RunShengBTE(
             shengbte_cmd=shengbte_cmd,
             temperature=temperature,
             control_kwargs=shengbte_control_kwargs,
         )
-        shengbte_to_db = ShengBTEToDb(db_file=db_file)
+        shengbte_to_db = ShengBTEToDb(db_file=db_file, additional_fields={})
 
         tasks = [copy_files, run_shengbte, shengbte_to_db]
-        super().__init__(tasks, parents=parents, name=name, **kwargs)
+        super().__init__(tasks, name=name, **kwargs)

From 9279f8bcd41b53be583e329284a79b7bc058ec06 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Wed, 26 Feb 2020 01:59:59 -0800
Subject: [PATCH 077/207] BUG: Fixes for lattice dynamics workflow

---
 .../vasp/workflows/base/lattice_dynamics.py   | 66 +++++++++++--------
 1 file changed, 38 insertions(+), 28 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 44f806793..a5d893e3a 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -23,32 +23,32 @@
     CubicSupercellTransformation,
 )
 
-__author__ = "Rees Chang, Alex Ganose"
-__email__ = "rc564@cornell.edu, aganose@lbl.gov"
-__date__ = "July 2019"
+__author__ = "Alex Ganose, Rees Chang"
+__email__ = "aganose@lbl.gov, rc564@cornell.edu"
+__date__ = "February 2020"
 
 logger = get_logger(__name__)
 
 _static_user_incar_settings = {
-    "ADDGRID": True,  # Fast Fourier Transform grid
+    "ADDGRID": True,
     "LCHARG": False,
     "ENCUT": 700,
-    "EDIFF": 1e-8,  # may need to tune this
+    "ISMEAR": 0,
+    "EDIFF": 1e-8,
     "PREC": "Accurate",
     "LAECHG": False,
     "LREAL": False,
     "LASPH": True,
 }
-
-
 _DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
-_WF_VERSION = 1.0
+_WF_VERSION = 0.1
 
 
 def get_lattice_dynamics_wf(
     structure: Structure,
     common_settings: Dict = None,
     vasp_input_set: Optional[VaspInputSet] = None,
+    copy_vasp_outputs: bool = False,
     supercell_matrix_kwargs: Optional[dict] = None,
     num_supercell_kwargs: Optional[dict] = None,
     perturbed_structure_kwargs: Optional[dict] = None,
@@ -85,6 +85,7 @@ def get_lattice_dynamics_wf(
         common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
             and "user_incar_settings" keys.
         vasp_input_set: Vasp input set for perturbed structure calculations.
+        copy_vasp_outputs: Whether or not to copy previous vasp outputs.
         supercell_matrix_kwargs: Options that control the size of the supercell.
             Will be passed directly to CubicSupercellTransformation in
             pymatgen.transformations.advanced_transformations. Note, a diagonal
@@ -125,29 +126,28 @@ def get_lattice_dynamics_wf(
     supercell = st.apply_transformation(structure)
     supercell_matrix = st.transformation_matrix
 
-    if "n_supercells" not in perturbed_structure_kwargs:
+    if "n_configs_per_std" not in perturbed_structure_kwargs:
         n_supercells = get_num_supercells(supercell, **num_supercell_kwargs)
-        perturbed_structure_kwargs["n_supercells"] = n_supercells
+        perturbed_structure_kwargs["n_configs_per_std"] = n_supercells
 
     wf = get_perturbed_structure_wf(
         structure,
         supercell_matrix=supercell_matrix,
-        name="ld perturbed structure",
         vasp_input_set=vasp_input_set,
         common_settings=common_settings,
+        copy_vasp_outputs=copy_vasp_outputs,
         pass_forces=True,
         **perturbed_structure_kwargs,
     )
 
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
-        parents=wf.fws[wf.leaf_fw_ids], db_file=db_file, spec=allow_fizzled
+        db_file=db_file, spec=allow_fizzled
     )
-    wf.fws.append(fw_fit_force_constant)
+    wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 
     if calculate_lattice_thermal_conductivity:
         fw_lattice_conductivity = LatticeThermalConductivityFW(
-            parents=wf.fws[-1],
             db_file=db_file,
             shengbte_cmd=shengbte_cmd,
             temperature=thermal_conductivity_temperature,
@@ -155,7 +155,9 @@ def get_lattice_dynamics_wf(
         if shengbte_fworker:
             fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
 
-        wf.fws.append(fw_lattice_conductivity)
+        wf.append_wf(
+            Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
+        )
 
     formula = structure.composition.reduced_formula
     wf.name = "{} - lattice dynamics".format(formula)
@@ -176,6 +178,7 @@ def get_perturbed_structure_wf(
     name: str = "perturbed structure",
     vasp_input_set: Optional[VaspInputSet] = None,
     common_settings: Optional[Dict] = None,
+    copy_vasp_outputs: bool = False,
     rattle_stds: Optional[List[float]] = None,
     n_configs_per_std: int = 1,
     min_nn_scale: float = 0.85,
@@ -191,6 +194,7 @@ def get_perturbed_structure_wf(
         vasp_input_set: Vasp input set for perturbed structure calculations.
         common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
             and "user_incar_settings" keys.
+        copy_vasp_outputs: Whether or not to copy previous vasp outputs.
         rattle_stds: List of standard deviations (in normal distribution) to
             to use when displacing the sites.
         n_configs_per_std: Number of structures to generate per rattle standard
@@ -206,7 +210,9 @@ def get_perturbed_structure_wf(
     common_settings = _get_common_settings(common_settings)
     vasp_cmd = common_settings["VASP_CMD"]
     db_file = common_settings["DB_FILE"]
-    user_incar_settings = common_settings["user_incar_settings"]
+    override_vasp_params = {
+        "user_incar_settings": common_settings["user_incar_settings"]
+    }
 
     if supercell_matrix is None:
         supercell_matrix = np.eye(3)
@@ -218,21 +224,24 @@ def get_perturbed_structure_wf(
 
     if vasp_input_set is None:
         vasp_input_set = MPStaticSet(structure)
-    else:
-        # ensure we don't override the user_incar_settings in the input set
-        user_incar_settings.update(vasp_input_set.user_incar_settings)
-    vasp_input_set.user_incar_settings = user_incar_settings
 
-    min_distance = np.min(structure.distance_matrix) * min_nn_scale
+    # find the smallest nearest neighbor distance taking into account PBC
+    min_distance = np.min(
+        [d.nn_distance for d in structure.get_all_neighbors(10)[0]]
+    )
+    min_distance *= min_nn_scale
     all_rattle_stds = np.repeat(rattle_stds, n_configs_per_std)
 
-    logger.debug("Using {} supercells / displacement".format(n_configs_per_std))
+    logger.debug("Using supercell_matrix of: {}".format(supercell_matrix))
+    logger.debug(
+        "Using {} supercells per displacement".format(n_configs_per_std)
+    )
     logger.debug("Using {} rattle stds".format(len(rattle_stds)))
     logger.debug("Rattle stds: {}".format(rattle_stds))
 
     fws = []
-    for i, rattle_std in all_rattle_stds:
-        name = "{} : i = {}; rattle_std : {:.3f}".format(name, i, rattle_std)
+    for i, rattle_std in enumerate(all_rattle_stds):
+        fw_name = "{}: i={}; rattle_std={:.3f}".format(name, i, rattle_std)
         transformations = [
             "SupercellTransformation",
             "MonteCarloRattleTransformation",
@@ -243,12 +252,13 @@ def get_perturbed_structure_wf(
         ]
 
         fw = TransmuterFW(
-            name=name,
+            name=fw_name,
             structure=structure,
             transformations=transformations,
             transformation_params=transformation_params,
             vasp_input_set=vasp_input_set,
-            copy_vasp_outputs=True,
+            override_default_vasp_params=override_vasp_params,
+            copy_vasp_outputs=copy_vasp_outputs,
             vasp_cmd=vasp_cmd,
             db_file=db_file,
         )
@@ -301,11 +311,11 @@ def get_num_supercells(
     # site degeneracy
     sga = SpacegroupAnalyzer(supercell_structure, symprec=symprec)
     equiv_idxs = sga.get_symmetry_dataset()["equivalent_atoms"]
-    equiv_counts = np.unique(equiv_idxs, return_counts=True)
+    _, equiv_counts = np.unique(equiv_idxs, return_counts=True)
     min_count = np.min(equiv_counts)
 
     n_cells = math.ceil(min_num_equivalent_sites / min_count)
-    return min(n_cells, max_num_supercells)
+    return min([n_cells, max_num_supercells])
 
 
 def _get_common_settings(common_settings: Optional[Dict]):

From a67b01cbd0d06a882aff7082f45d39ea9235f252 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Wed, 26 Feb 2020 02:00:25 -0800
Subject: [PATCH 078/207] Add lattice dynamics workflow test

---
 .../tests/test_lattice_dynamics_workflow.py   | 93 +++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py

diff --git a/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py b/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
new file mode 100644
index 000000000..1f0bb7254
--- /dev/null
+++ b/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
@@ -0,0 +1,93 @@
+
+from pathlib import Path
+
+from atomate.vasp.workflows import get_lattice_dynamics_wf
+from fireworks import FWorker
+from fireworks.core.rocket_launcher import rapidfire
+
+from atomate.vasp.powerups import use_fake_vasp, use_potcar_spec
+from atomate.utils.testing import AtomateTest
+
+from pymatgen.util.testing import PymatgenTest
+
+__author__ = 'Alex Ganose'
+__email__ = 'aganose@lbl.gov'
+
+module_dir = Path(__file__).resolve().parent
+db_dir = module_dir / "../../../common/test_files"
+ref_dir = module_dir / "../../test_files"
+wf_dir = ref_dir / "lattice_dynamics_wf"
+
+test_fworker = FWorker(env={"db_file": db_dir / "db.json"})
+
+
+class TestRamanWorkflow(AtomateTest):
+
+    def setUp(self, lpad=True):
+        super().setUp(lpad=lpad)
+
+        self.struct_si = PymatgenTest.get_structure("Si")
+
+        self.wf = get_lattice_dynamics_wf(
+            self.struct_si,
+            perturbed_structure_kwargs={"rattle_stds": [0.01]},
+            calculate_lattice_thermal_conductivity=True
+        )
+
+    def test_wf(self):
+        self.wf = get_simulated_wf(self.wf)
+        self.lp.add_wf(self.wf)
+        rapidfire(self.lp, fworker=test_fworker)
+
+        self.assertEqual(len(self.wf.fws), 3)
+
+        # check static calculation
+        result = self.get_task_collection().find_one(
+            {"task_label": "perturbed structure: i=0; rattle_std=0.010"}
+        )
+        self.check_run(result, mode="structure optimization")
+
+        wf = self.lp.get_wf_by_fw_id(1)
+        self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
+
+    def check_run(self, d, mode):
+        pass
+        # if mode not in ["structure optimization", "static dielectric",
+        #                 "raman_0_0.005", "raman analysis"]:
+        #     raise ValueError("Invalid mode!")
+        #
+        # if mode not in ["raman analysis"]:
+        #     self.assertEqual(d["formula_pretty"], "Si")
+        #     self.assertEqual(d["formula_anonymous"], "A")
+        #     self.assertEqual(d["nelements"], 1)
+        #     self.assertEqual(d["state"], "successful")
+        #     self.assertAlmostEqual(d["calcs_reversed"][0]["output"]["structure"]["lattice"]["a"], 3.867, 2)
+        #
+        # if mode in ["structure optimization"]:
+        #     self.assertAlmostEqual(d["output"]["energy"], -10.850, 2)
+        #     self.assertAlmostEqual(d["output"]["energy_per_atom"], -5.425, 2)
+        #
+        # elif mode in ["static dielectric"]:
+        #     epsilon = [[13.23245131, -1.98e-06, -1.4e-06],
+        #                [-1.98e-06, 13.23245913, 8.38e-06],
+        #                [-1.4e-06, 8.38e-06, 13.23245619]]
+        #     np.testing.assert_allclose(epsilon, d["output"]["epsilon_static"], rtol=1e-5)
+        #
+        # elif mode in ["raman_0_0.005"]:
+        #     epsilon = [[13.16509632, 0.00850098, 0.00597267],
+        #                [0.00850097, 13.25477303, -0.02979572],
+        #                [0.00597267, -0.0297953, 13.28883867]]
+        #     np.testing.assert_allclose(epsilon, d["output"]["epsilon_static"], rtol=1e-5)
+
+
+
+def get_simulated_wf(wf):
+    ref_dirs = {"perturbed structure: i=0; rattle_std=0.010": wf_dir / "0"}
+
+    params_to_check = ["ENCUT", "NSW", "EDIFF"]
+    wf = use_potcar_spec(wf)
+    wf = use_fake_vasp(
+        wf, ref_dirs, params_to_check=params_to_check, check_potcar=False
+    )
+
+    return wf

From 1e2f67db2f9c4b647248ff68631f6d6d75d9f6ef Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Fri, 28 Feb 2020 12:22:50 -0800
Subject: [PATCH 079/207] BUG: Fix bugs in lattice dynamics firetasks

---
 atomate/vasp/analysis/lattice_dynamics.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 8f5c6f71a..e644482dc 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -7,8 +7,8 @@
 from pymatgen import Structure
 from pymatgen.io.phonopy import get_phonopy_structure
 
-__author__ = "Rees Chang, Alex Ganose"
-__email__ = "rc564@cornell.edu, aganose@lbl.gov"
+__author__ = "Alex Ganose, Rees Chang"
+__email__ = "aganose@lbl.gov, rc564@cornell.edu"
 
 logger = get_logger(__name__)
 
@@ -67,13 +67,15 @@ def get_cutoffs(structure: Structure):
     steps = {2: 0.5, 3: 0.25, 4: 0.25}
 
     row = min([s.row for s in structure.species])
-    mins = (min_cutoffs[row][2], min_cutoffs[row][3], min_cutoffs[row][4])
+    mins = {
+        2: min_cutoffs[row][2], 3: min_cutoffs[row][3], 4: min_cutoffs[row][4]
+    }
 
-    range_two = np.arange(mins[0], mins[0] + inc[0] + steps[0], steps[0])
-    range_three = np.arange(mins[1], mins[1] + inc[1] + steps[1], steps[1])
-    range_four = np.arange(mins[2], mins[2] + inc[2] + steps[2], steps[2])
+    range_two = np.arange(mins[2], mins[2] + inc[2] + steps[2], steps[2])
+    range_three = np.arange(mins[3], mins[3] + inc[3] + steps[3], steps[3])
+    range_four = np.arange(mins[4], mins[4] + inc[4] + steps[4], steps[4])
 
-    return list(product(range_two, range_three, range_four))
+    return list(map(list, product(range_two, range_three, range_four)))
 
 
 def fit_force_constants(
@@ -168,19 +170,17 @@ def fit_force_constants(
         )
 
         fitting_data["cutoffs"].append(cutoffs)
-        fitting_data["rmse_train"].append(opt.rmse_test)
+        fitting_data["rmse_test"].append(opt.rmse_test)
         fitting_data["n_imaginary"].append(n_imaginary)
         fitting_data["min_frequency"].append(min_freq)
         fitting_data["300K_free_energy"].append(free_energy)
-        fitting_data["force_constants"].append(fcs)
 
         if (
-            min_freq < -np.abs(max_imaginary_freq)
+            min_freq > -np.abs(max_imaginary_freq)
             and n_imaginary <= max_n_imaginary
             and n_imaginary < best_fit["n_imaginary"]
             and free_energy < best_fit["free_energy"]
         ):
-
             best_fit.update(
                 {
                     "n_imaginary": n_imaginary,

From a414460037b1c75501017bd4278382d21fc32526 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Fri, 28 Feb 2020 12:23:06 -0800
Subject: [PATCH 080/207] Fix bugs in lattice dynamics workflow

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a5d893e3a..1f89ac2ce 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -265,7 +265,7 @@ def get_perturbed_structure_wf(
 
         if pass_forces:
             pass_dict = {
-                "parent_structure": structure.to_json(),
+                "parent_structure": structure.as_dict(),
                 "supercell_matrix": supercell_matrix,
                 "forces": ">>output.ionic_steps.-1.forces",
                 "structure": ">>output.ionic_steps.-1.structure",

From 048ccf2f350bf2c6358b013d5eaac9cf4fa10325 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Fri, 28 Feb 2020 12:29:13 -0800
Subject: [PATCH 081/207] Update firetasks

---
 atomate/vasp/firetasks/lattice_dynamics.py | 95 ++++++++++++++--------
 1 file changed, 60 insertions(+), 35 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index d845a46fc..cefa4e166 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -1,4 +1,6 @@
+import json
 import os
+import subprocess
 import shlex
 from datetime import datetime
 from pathlib import Path
@@ -19,7 +21,6 @@
 )
 from atomate.vasp.database import VaspCalcDb
 from fireworks import FiretaskBase, FWAction, explicit_serialize
-from pymatgen import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.phonopy import get_phonon_band_structure_from_fc, \
     get_phonon_dos_from_fc, get_phonon_band_structure_symm_line_from_fc
@@ -67,10 +68,10 @@ def run_task(self, fw_spec):
 
         logger.info("Found {} perturbed structures".format(len(results)))
 
-        structure = Structure.from_dict(results[0]["parent_structure"])
+        structure = results[0]["parent_structure"]
         supercell_matrix = results[0]["supercell_matrix"]
 
-        structures = [Structure.from_dict(r["structure"]) for r in results]
+        structures = [r["structure"] for r in results]
         forces = [np.asarray(r["forces"]) for r in results]
 
         # regenerate pure supercell structure
@@ -89,7 +90,6 @@ def run_task(self, fw_spec):
         dumpfn(structure_data, "structure_data.json")
 
 
-@requires(hiphive, "hiphive is required for lattice dynamics workflow")
 @explicit_serialize
 class RunHiPhive(FiretaskBase):
     """
@@ -122,6 +122,7 @@ class RunHiPhive(FiretaskBase):
         "fit_method",
     ]
 
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
         from hiphive.utilities import get_displacements
 
@@ -131,7 +132,7 @@ def run_task(self, fw_spec):
         fit_method = self.get("fit_method", FIT_METHOD)
 
         all_structures = loadfn("perturbed_structures.json")
-        all_forces = loadfn("all_forces.json")
+        all_forces = loadfn("perturbed_forces.json")
         structure_data = loadfn("structure_data.json")
         parent_structure = structure_data["structure"]
         supercell_matrix = structure_data["supercell_matrix"]
@@ -142,12 +143,12 @@ def run_task(self, fw_spec):
         for structure, forces in zip(all_structures, all_forces):
             atoms = AseAtomsAdaptor.get_atoms(structure)
             displacements = get_displacements(atoms, supercell_atoms)
-            structure.new_array("displacements", displacements)
-            structure.new_array("forces", forces)
-            structure.positions = supercell_atoms.get_positions()
-            structures.append(structure)
+            atoms.new_array("displacements", displacements)
+            atoms.new_array("forces", forces)
+            atoms.positions = supercell_atoms.get_positions()
+            structures.append(atoms)
 
-        cutoffs = self.get("cutoffs", get_cutoffs(supercell_structure))
+        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
         force_constants, fitting_data = fit_force_constants(
             parent_structure,
             supercell_matrix,
@@ -161,10 +162,10 @@ def run_task(self, fw_spec):
 
         dumpfn(fitting_data, "fitting_data.json")
 
-        if force_constants is not None:
+        if force_constants is None:
             # fitting failed
             raise RuntimeError(
-                "Could not find a force constant solution with less than {}"
+                "Could not find a force constant solution with less than {} "
                 "imaginary modes.\n"
                 "Fitting results: {}".format(max_n_imaginary, fitting_data)
             )
@@ -180,7 +181,6 @@ def run_task(self, fw_spec):
             )
 
 
-@requires(hiphive, "hiphive is required for lattice dynamics workflow")
 @explicit_serialize
 class ForceConstantsToDb(FiretaskBase):
     """
@@ -205,13 +205,14 @@ class ForceConstantsToDb(FiretaskBase):
     required_params = ["db_file"]
     optional_params = ["mesh_density", "additional_fields"]
 
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
         from hiphive.force_constants import ForceConstants
 
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
 
-        force_constants = ForceConstants.read("force_constants.fcs")
+        fc = ForceConstants.read("force_constants.fcs")
         fitting_data = loadfn("fitting_data.json")
         structure_data = loadfn("structure_data.json")
         forces = loadfn("perturbed_forces.json")
@@ -221,7 +222,7 @@ def run_task(self, fw_spec):
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = structure_data["supercell_matrix"]
 
-        phonopy_fc = force_constants.get_fc_array(order=2)
+        phonopy_fc = fc.get_fc_array(order=2)
 
         logger.info("Getting uniform phonon band structure.")
         uniform_bs = get_phonon_band_structure_from_fc(
@@ -250,14 +251,22 @@ def run_task(self, fw_spec):
             lm_bs.to_json(), collection="phonon_bandstructure_fs"
         )
 
+        logger.info("Inserting force constants into database.")
+        fc_json = json.dumps(
+            {str(k): v.tolist() for k, v in fc.get_fc_dict().items()}
+        )
+        fc_fsid, _ = mmdb.insert_gridfs(
+            fc_json, collection="phonon_force_constants_fs"
+        )
+
         data = {
             "structure": structure.as_dict(),
-            "supercell_matrix": supercell_matrix.tolist(),
+            "supercell_matrix": supercell_matrix,
             "supercell_structure": supercell_structure.as_dict(),
-            "perturbed_structures": [s.to_json() for s in structures],
+            "perturbed_structures": [s.as_dict() for s in structures],
             "perturbed_forces": [f.tolist() for f in forces],
             "fitting_data": fitting_data,
-            "force_constants": force_constants.get_fc_dict(),
+            "force_constants_fs_id": fc_fsid,
             "tags": fw_spec.get("tags", None),
             "formula_pretty": structure.composition.reduced_formula,
             "phonon_dos_fs_id": dos_fsid,
@@ -268,16 +277,11 @@ def run_task(self, fw_spec):
         data.update(self.get("additional_fields", {}))
 
         # Get an id for the force constants
-        mmdb.collection = mmdb.db["lattice_dynamics"]
-        fc_id = mmdb.db.counter.find_one_and_update(
-            {"_id": "taskid"},
-            {"$inc": {"c": 1}},
-            return_document=ReturnDocument.AFTER,
-        )["c"]
-        metadata = {"fc_id": fc_id, "fc_dir": os.getcwd()}
+        fitting_id = _get_fc_fitting_id(mmdb)
+        metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
         data.update(metadata)
 
-        mmdb.collection.insert_one(data)
+        mmdb.db.lattice_dynamics.insert_one(data)
         logger.info("Finished inserting force constants")
 
         return FWAction(update_spec=metadata)
@@ -316,10 +320,11 @@ def run_task(self, fw_spec):
             "nonanalytic": False,
             "isotopes": False,
             "temperature": self.get("temperature", DEFAULT_TEMPERATURE),
-            "scell": np.diag(supercell_matrix),
+            "scell": np.diag(supercell_matrix).tolist(),
         }
-        control_dict.update(self.get("control_kwargs", {}))
-        control = Control.from_structure(structure, **control_dict)
+        control_kwargs = self.get("control_kwargs") or {}
+        control_dict.update(control_kwargs)
+        control = Control().from_structure(structure, **control_dict)
         control.to_file()
 
         shengbte_cmd = env_chk(self["shengbte_cmd"], fw_spec)
@@ -335,7 +340,7 @@ def run_task(self, fw_spec):
             "shengbte_err.txt", "w", buffering=1
         ) as f_err:
             # use line buffering for stderr
-            return_code = os.subprocess.call(
+            return_code = subprocess.call(
                 shengbte_cmd, stdout=f_std, stderr=f_err
             )
         logger.info(
@@ -373,7 +378,7 @@ def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
 
-        control = Control.from_file("CONTROL")
+        control = Control().from_file("CONTROL")
         structure = control.get_structure()
         supercell_matrix = np.diag(control["scell"])
 
@@ -385,23 +390,43 @@ def run_task(self, fw_spec):
             raise RuntimeError("Could not find ShengBTE output files.")
 
         bte_data = np.loadtxt(filename)
+        if len(bte_data.shape) == 1:
+            # pad extra axis to make compatible with multiple temperatures
+            bte_data = bte_data[None, :]
+
         temperatures = bte_data[:, 0].tolist()
-        kappa = bte_data[:, 1:10].reshape(-1, 3, 3)
+        kappa = bte_data[:, 1:10].reshape(-1, 3, 3).tolist()
 
         data = {
             "structure": structure.as_dict(),
             "supercell_matrix": supercell_matrix.tolist(),
             "temperatures": temperatures,
             "lattice_thermal_conductivity": kappa,
-            "control": control.to_json(),
+            "control": control.as_dict(),
             "tags": fw_spec.get("tags", None),
             "formula_pretty": structure.composition.reduced_formula,
             "shengbte_dir": os.getcwd(),
-            "fc_id": fw_spec.get("fc_id", None),
-            "fc_dir": fw_spec.get("fc_dir", None),
+            "fc_fitting_id": fw_spec.get("fc_fitting_id", None),
+            "fc_fitting_dir": fw_spec.get("fc_fitting_dir", None),
             "created_at": datetime.utcnow(),
         }
         data.update(self.get("additional_fields", {}))
 
         mmdb.collection = mmdb.db["lattice_thermal_conductivity"]
         mmdb.collection.insert(data)
+
+
+def _get_fc_fitting_id(mmdb: VaspCalcDb) -> int:
+    """Helper method to get a force constant fitting id."""
+    fc_id = mmdb.db.counter.find_one_and_update(
+        {"_id": "fc_fitting_id"},
+        {"$inc": {"c": 1}},
+        return_document=ReturnDocument.AFTER,
+    )
+    if fc_id is None:
+        mmdb.db.counter.insert({"_id": "fc_fitting_id", "c": 1})
+        fc_id = 1
+    else:
+        fc_id = fc_id["c"]
+
+    return fc_id

From c748e2703df441041fd72974352c15ac36ba1d70 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Fri, 28 Feb 2020 12:29:38 -0800
Subject: [PATCH 082/207] Update lattice dynamics workflow test

---
 .../tests/test_lattice_dynamics_workflow.py    | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py b/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
index 1f0bb7254..55da5cde4 100644
--- a/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
+++ b/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
@@ -18,10 +18,12 @@
 ref_dir = module_dir / "../../test_files"
 wf_dir = ref_dir / "lattice_dynamics_wf"
 
-test_fworker = FWorker(env={"db_file": db_dir / "db.json"})
+test_fworker = FWorker(
+    env={"db_file": db_dir / "db.json", "shengbte_cmd": "ShengBTE"}
+)
 
 
-class TestRamanWorkflow(AtomateTest):
+class TestLatticeThermalConductivityWorkflow(AtomateTest):
 
     def setUp(self, lpad=True):
         super().setUp(lpad=lpad)
@@ -34,6 +36,14 @@ def setUp(self, lpad=True):
             calculate_lattice_thermal_conductivity=True
         )
 
+        # change the cutoffs for fit CSLD
+        self.wf.fws[-2].tasks[1].update({"cutoffs": [[5., 3., 3.]]})
+
+        # change shengbte mesh density
+        self.wf.fws[-1].tasks[1].update(
+            {"control_kwargs": {"reciprocal_density": 500}}
+        )
+
     def test_wf(self):
         self.wf = get_simulated_wf(self.wf)
         self.lp.add_wf(self.wf)
@@ -51,7 +61,7 @@ def test_wf(self):
         self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
 
     def check_run(self, d, mode):
-        pass
+        return 1
         # if mode not in ["structure optimization", "static dielectric",
         #                 "raman_0_0.005", "raman analysis"]:
         #     raise ValueError("Invalid mode!")
@@ -80,7 +90,6 @@ def check_run(self, d, mode):
         #     np.testing.assert_allclose(epsilon, d["output"]["epsilon_static"], rtol=1e-5)
 
 
-
 def get_simulated_wf(wf):
     ref_dirs = {"perturbed structure: i=0; rattle_std=0.010": wf_dir / "0"}
 
@@ -91,3 +100,4 @@ def get_simulated_wf(wf):
     )
 
     return wf
+

From 8f238d558281484fa5e9012a21b82a0875e65cee Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 11:44:40 -0700
Subject: [PATCH 083/207] Add powerup for updating any firetask

---
 atomate/common/powerups.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/atomate/common/powerups.py b/atomate/common/powerups.py
index d76db63b5..f9658f89f 100644
--- a/atomate/common/powerups.py
+++ b/atomate/common/powerups.py
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 """
 This module defines general powerups that can be used for all workflows
 """
@@ -318,3 +319,40 @@ def powerup_by_kwargs(
         if not found:
             raise RuntimeError(f"Could not find powerup {name}.")
     return original_wf
+=======
+from typing import Dict, Any, Optional
+
+from fireworks import Workflow
+from atomate.utils.utils import get_fws_and_tasks
+
+
+def update_firetask(
+    original_wf: Workflow,
+    update_params: Dict[str, Any],
+    task_name_constraint: str,
+    fw_name_constraint: Optional[str] = None,
+) -> Workflow:
+    """
+    General powerup for arbitrary updates to a Firetask.
+
+    Args:
+        original_wf: The original workflow.
+        update_params: A dictionary of the keyword arguments to update.
+        task_name_constraint: Only apply changes to the Firetasks where the
+            Firetask class name contains this string.
+        fw_name_constraint: Only apply changes to Fireworks where the Firework
+            name contains this substring.
+
+    Returns:
+       Workflow
+    """
+    idx_list = get_fws_and_tasks(
+        original_wf,
+        fw_name_constraint=fw_name_constraint,
+        task_name_constraint=task_name_constraint,
+    )
+    for idx_fw, idx_t in idx_list:
+        original_wf.fws[idx_fw].tasks[idx_t].update(update_params)
+
+    return original_wf
+>>>>>>> bd235a73 (Add powerup for updating any firetask)

From 98c0c243cc04f363d678650bc7c9f69125ac62ac Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 11:45:26 -0700
Subject: [PATCH 084/207] Tidy docstrings

---
 atomate/vasp/fireworks/core.py | 74 ++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/atomate/vasp/fireworks/core.py b/atomate/vasp/fireworks/core.py
index 7292a64dc..e99d18925 100644
--- a/atomate/vasp/fireworks/core.py
+++ b/atomate/vasp/fireworks/core.py
@@ -99,8 +99,13 @@ def __init__(
             and job_type == "double_relaxation"
         ):
             warnings.warn(
+<<<<<<< HEAD
                 f"A double relaxation run might not be appropriate with ISIF {vasp_input_set.incar['ISIF']}"
             )
+=======
+                "A double relaxation run might not be appropriate with ISIF {}".format(
+                    vasp_input_set.incar["ISIF"]))
+>>>>>>> 23b88a18 (Tidy docstrings)
 
         t = []
         t.append(WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set))
@@ -140,11 +145,26 @@ def __init__(
         **kwargs,
     ):
         """
+<<<<<<< HEAD
         Structure optimization using the SCAN metaGGA functional. If this Firework is
         initialized with no parents, it will perform a GGA optimization of the provided
         structure using the PBESol functional. This GGA-relaxed structure is intended
         to be passed to a second instance of this Firework for optimization with SCAN.
         (see workflow definition in metagga_optimization.yaml)
+=======
+        Structure optimization using the SCAN metaGGA functional.
+
+        This workflow performs a 3-step optmization. The first step ('relax1')
+        is a conventional GGA run relaxation that initializes the geometry and
+        calculates the bandgap of the structure. The bandgap is used to update
+        the KSPACING parameter, which sets the appropriate number of k-points
+        for the structure. The second step ('.relax2') is a static GGA
+        calculation that computes wavefunctions using the updated number of
+        k-points. The third step ('relax3') is a SCAN relaxation.
+
+        By default, .relax1 and .relax2 are force converged with
+        EDIFFG = -0.05, and .relax3 is force converged with EDIFFG=-0.02.
+>>>>>>> 23b88a18 (Tidy docstrings)
 
         Args:
             structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
@@ -188,6 +208,7 @@ def __init__(
                  is not supported by this InputSet."
             )
 
+<<<<<<< HEAD
         if prev_calc_dir:
             has_previous_calc = True
             # Copy the CHGCAR from previous calc directory (usually PBE)
@@ -218,6 +239,59 @@ def __init__(
             raise UserWarning(
                 "You specified prev_calc_loc but did not provide a parent Firework. Set "
                 "parents and try again."
+=======
+        t = []
+        # write the VASP input files based on MPScanRelaxSet
+        t.append(WriteVaspFromIOSet(structure=structure,
+                                    vasp_input_set=orig_input_set
+                                    )
+                 )
+
+        # pass the CalcLoc so that CopyFilesFromCalcLoc can find the directory
+        t.append(PassCalcLocs(name=name))
+
+        # Copy the pre-compiled VdW kernel for VASP, if required
+        if orig_input_set.vdw is not None:
+            t.append(CopyFiles(from_dir=vdw_kernel_dir))
+
+        # Copy original inputs with the ".orig" suffix
+        t.append(
+            CopyFilesFromCalcLoc(
+                calc_loc=True,
+                name_append=".orig",
+                exclude_files=["vdw_kernel.bindat", "FW.json", "FW--*"],
+            )
+        )
+
+        # Update the INCAR for the GGA preconditioning step
+        # Disable writing the WAVECAR because the no. of k-points will likely
+        # change before the next step in the calculation
+        pre_opt_settings = {"_set": {"METAGGA": None,
+                                     "EDIFFG": -0.05,
+                                     "LWAVE": False}}
+
+        # Disable vdW for the precondition step
+        if orig_input_set.incar.get("LUSE_VDW", None):
+            pre_opt_settings.update({"_unset": {"LUSE_VDW": True,
+                                                "BPARAM": 15.7}})
+
+        t.append(ModifyIncar(incar_dictmod=pre_opt_settings))
+
+        # Run the GGA .relax1 step
+        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
+                                  job_type="normal_no_backup",
+                                  gzip_output=False
+                                  )
+                 )
+
+        # Copy GGA outputs with '.relax1' suffix
+        # by the subsequent UpdateScanRelaxBandgap Firetask
+        t.append(
+            CopyFilesFromCalcLoc(
+                calc_loc=True,
+                name_append=".relax1",
+                exclude_files=["vdw_kernel.bindat", "FW.json", "FW--*", "*.orig"],
+>>>>>>> 23b88a18 (Tidy docstrings)
             )
 
         if has_previous_calc:

From a9acd1e0996d4c0c12ea81d02fe6d4cd3f7b833f Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 11:47:10 -0700
Subject: [PATCH 085/207] Tweak lattice dynamics settings

---
 atomate/vasp/workflows/presets/core.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index a75f34427..8c5326f1a 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -332,6 +332,7 @@ def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False):
 
     uis_optimize = {"ENCUT": 700, "EDIFF": 1e-6, "LAECHG": False, "LREAL": False}
     if order > 2:
+<<<<<<< HEAD
         uis_optimize.update(
             {
                 "EDIFF": 1e-10,
@@ -341,6 +342,10 @@ def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False):
                 "ISYM": 0,
             }
         )
+=======
+        uis_optimize.update({"EDIFF": 1e-8, "EDIFFG": -0.001,
+                             "ADDGRID": True, "LREAL": False, "ISYM": 0})
+>>>>>>> 16220e12 (Tweak lattice dynamics settings)
         # This ensures a consistent k-point mesh across all calculations
         # We also turn off symmetry to prevent VASP from changing the
         # mesh internally
@@ -888,7 +893,7 @@ def wf_lattice_thermal_conductivity(
     wf.append_wf(wf_ld, wf.leaf_fw_ids)
 
     formula = structure.composition.reduced_formula
-    wf_name = "{} - lattice thermal conductivity preset".format(formula)
+    wf_name = "{} - lattice thermal conductivity".format(formula)
     wf.name = wf_name
 
     wf = add_common_powerups(wf, c)

From 792755dd34cf46ef53f5deabbbec66b1302307d2 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 11:48:01 -0700
Subject: [PATCH 086/207] Change imaginary mode requirements

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index e644482dc..a313c877f 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -14,7 +14,7 @@
 
 MAX_IMAGINARY_FREQ = 10  # in THz
 IMAGINARY_TOL = 0.025  # in THz
-MAX_N_IMAGINARY = 3
+MAX_N_IMAGINARY = np.inf
 FIT_METHOD = "least-squares"
 
 

From cf98cc168aa3846b4cf4a76eda968e1b4ffe5b00 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 11:48:41 -0700
Subject: [PATCH 087/207] Lattice dynamics settings tweaks

---
 .../vasp/workflows/base/lattice_dynamics.py   | 25 +++++++++++++++----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 1f89ac2ce..6617f758c 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -115,7 +115,7 @@ def get_lattice_dynamics_wf(
     db_file = common_settings["DB_FILE"]
 
     if calculate_lattice_thermal_conductivity:
-        if supercell_matrix_kwargs.get("force_diagonal", True):
+        if supercell_matrix_kwargs.get("force_diagonal", False):
             warnings.warn(
                 "Diagonal transformation required to calculate lattice thermal "
                 "conductivity. Forcing diagonal matrix"
@@ -218,6 +218,7 @@ def get_perturbed_structure_wf(
         supercell_matrix = np.eye(3)
 
     supercell_matrix = np.asarray(supercell_matrix).tolist()
+    natoms = len(structure * supercell_matrix)
 
     if rattle_stds is None:
         rattle_stds = np.linspace(0.01, 0.1, 5)
@@ -227,12 +228,13 @@ def get_perturbed_structure_wf(
 
     # find the smallest nearest neighbor distance taking into account PBC
     min_distance = np.min(
-        [d.nn_distance for d in structure.get_all_neighbors(10)[0]]
+        [n.nn_distance for d in structure.get_all_neighbors(10) for n in d]
     )
-    min_distance *= min_nn_scale
+    scaled_min_distance = min_distance * min_nn_scale
     all_rattle_stds = np.repeat(rattle_stds, n_configs_per_std)
 
     logger.debug("Using supercell_matrix of: {}".format(supercell_matrix))
+    logger.debug("Supercell has {} atoms".format(natoms))
     logger.debug(
         "Using {} supercells per displacement".format(n_configs_per_std)
     )
@@ -242,13 +244,19 @@ def get_perturbed_structure_wf(
     fws = []
     for i, rattle_std in enumerate(all_rattle_stds):
         fw_name = "{}: i={}; rattle_std={:.3f}".format(name, i, rattle_std)
+
+        # make sure the minimum distance is at least min_dist - 2 * rattle_std
+        # as a sanity check
+        rattle_min_distance = min_distance - 2 * rattle_std
+        rattle_min_distance = min(scaled_min_distance, rattle_min_distance)
+
         transformations = [
             "SupercellTransformation",
             "MonteCarloRattleTransformation",
         ]
         transformation_params = [
             {"scaling_matrix": supercell_matrix},
-            {"rattle_std": rattle_std, "min_distance": min_distance},
+            {"rattle_std": rattle_std, "min_distance": rattle_min_distance},
         ]
 
         fw = TransmuterFW(
@@ -263,6 +271,11 @@ def get_perturbed_structure_wf(
             db_file=db_file,
         )
 
+        # don't store CHGCAR and other volumetric data in the VASP drone
+        for task in fw.tasks:
+            if "VaspToDb" in str(task):
+                task.update({"store_volumetric_data": tuple()})
+
         if pass_forces:
             pass_dict = {
                 "parent_structure": structure.as_dict(),
@@ -287,7 +300,7 @@ def get_num_supercells(
     supercell_structure: Structure,
     symprec: float = 0.01,
     min_num_equivalent_sites: int = 100,
-    max_num_supercells: int = 30,
+    max_num_supercells: int = 6,
 ) -> int:
     """
     Get the number of supercells to run per rattle standard deviation.
@@ -329,3 +342,5 @@ def _get_common_settings(common_settings: Optional[Dict]):
     common_settings["user_incar_settings"] = user_incar_settings
 
     return common_settings
+
+

From 67bd581481e2e84d2d6519bf103f6b8c966ea0f6 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 12:16:24 -0700
Subject: [PATCH 088/207] Copy vasp outputs

---
 atomate/vasp/workflows/presets/core.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 8c5326f1a..3b4d03fd5 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -888,6 +888,7 @@ def wf_lattice_thermal_conductivity(
         structure,
         common_settings=c,
         calculate_lattice_thermal_conductivity=True,
+        copy_vasp_outputs=True,
         **ld_kwargs
     )
     wf.append_wf(wf_ld, wf.leaf_fw_ids)

From 103e46c88012bf9bbc444a7f49d7c154dccf6664 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Tue, 7 Apr 2020 12:59:43 -0700
Subject: [PATCH 089/207] Fix bug in lattice dynamics wf

---
 atomate/vasp/workflows/presets/core.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 3b4d03fd5..76fd7cfe3 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -879,6 +879,10 @@ def wf_lattice_thermal_conductivity(
         'LCHARG': False,
         'LASPH': True
     }
+    c = c if c is not None else {}
+    if "USER_INCAR_SETTINGS" not in c:
+        c["USER_INCAR_SETTINGS"] = {}
+
     # wf_structure_optimization expects user incar settings in capitals
     c["USER_INCAR_SETTINGS"].update(optimize_uis)
     c["USER_INCAR_SETTINGS"].update(c.get("user_incar_settings", {}))

From b7804b97b50a49f524acd622cf55f7d5f380cf78 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Fri, 10 Apr 2020 10:38:12 -0700
Subject: [PATCH 090/207] Tweak VaspToDb params

---
 atomate/vasp/firetasks/parse_outputs.py       | 23 +++++++++++++++++++
 .../vasp/workflows/base/lattice_dynamics.py   | 10 ++++++--
 atomate/vasp/workflows/presets/core.py        |  8 ++++++-
 3 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 488838577..25fd107a6 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -117,6 +117,7 @@ class VaspToDb(FiretaskBase):
             Format: {key : path} -> fw.spec[key] = task_doc[path]
             The path is a full mongo-style path so subdocuments can be referenced
             using dot notation and array keys can be referenced using the index.
+<<<<<<< HEAD
             E.g "calcs_reversed.0.output.outcar.run_stats"
     """
 
@@ -136,6 +137,17 @@ class VaspToDb(FiretaskBase):
         "parse_bader",
         "store_volumetric_data",
     ]
+=======
+            E.g "calcs_reversed.0.output.outar.run_stats"
+        vasp_drone_params (dict): Additional keyword arguments to pass to the
+            VaspDrone.
+    """
+    optional_params = ["calc_dir", "calc_loc", "parse_dos", "bandstructure_mode",
+                       "additional_fields", "db_file", "fw_spec_field", "defuse_unsuccessful",
+                       "task_fields_to_push", "parse_chgcar", "parse_aeccar",
+                       "parse_potcar_file",
+                       "store_volumetric_data", "vasp_drone_params"]
+>>>>>>> cf160919 (Tweak VaspToDb params)
 
     def run_task(self, fw_spec):
         # get the directory that contains the VASP dir to parse
@@ -148,6 +160,7 @@ def run_task(self, fw_spec):
         # parse the VASP directory
         logger.info(f"PARSING DIRECTORY: {calc_dir}")
 
+<<<<<<< HEAD
         drone = VaspDrone(
             additional_fields=self.get("additional_fields"),
             parse_dos=self.get("parse_dos", False),
@@ -160,6 +173,16 @@ def run_task(self, fw_spec):
                 "store_volumetric_data", STORE_VOLUMETRIC_DATA
             ),
         )
+=======
+        drone = VaspDrone(additional_fields=self.get("additional_fields"),
+                          parse_dos=self.get("parse_dos", False),
+                          parse_potcar_file=self.get("parse_potcar_file", True),
+                          bandstructure_mode=self.get("bandstructure_mode", False),
+                          parse_chgcar=self.get("parse_chgcar", False),  # deprecated
+                          parse_aeccar=self.get("parse_aeccar", False),  # deprecated
+                          store_volumetric_data=self.get("store_volumetric_data", STORE_VOLUMETRIC_DATA),
+                          **self.get("vasp_drone_params", {}))
+>>>>>>> cf160919 (Tweak VaspToDb params)
 
         # assimilate (i.e., parse)
         task_doc = drone.assimilate(calc_dir)
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 6617f758c..6bead2a7e 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -40,6 +40,12 @@
     "LREAL": False,
     "LASPH": True,
 }
+
+vasp_to_db_params = {
+    "store_volumetric_data": tuple(),
+    "vasp_drone_params": {"parse_bader": False, "parse_locpot": False}
+}
+
 _DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
 _WF_VERSION = 0.1
 
@@ -221,7 +227,7 @@ def get_perturbed_structure_wf(
     natoms = len(structure * supercell_matrix)
 
     if rattle_stds is None:
-        rattle_stds = np.linspace(0.01, 0.1, 5)
+        rattle_stds = np.linspace(0.008, 0.08, 5)
 
     if vasp_input_set is None:
         vasp_input_set = MPStaticSet(structure)
@@ -274,7 +280,7 @@ def get_perturbed_structure_wf(
         # don't store CHGCAR and other volumetric data in the VASP drone
         for task in fw.tasks:
             if "VaspToDb" in str(task):
-                task.update({"store_volumetric_data": tuple()})
+                task.update(vasp_to_db_params)
 
         if pass_forces:
             pass_dict = {
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 76fd7cfe3..6e98f1194 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -10,7 +10,8 @@
 
 import numpy as np
 
-from atomate.vasp.workflows.base.lattice_dynamics import get_lattice_dynamics_wf
+from atomate.vasp.workflows.base.lattice_dynamics import \
+    get_lattice_dynamics_wf, vasp_to_db_params
 from fireworks import Workflow
 from pymatgen import Structure
 from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPHSERelaxSet
@@ -888,6 +889,11 @@ def wf_lattice_thermal_conductivity(
     c["USER_INCAR_SETTINGS"].update(c.get("user_incar_settings", {}))
     wf = wf_structure_optimization(structure, c=c)
 
+    # don't store CHGCAR and other volumetric data in the VASP drone
+    for task in wf.fws[0].tasks:
+        if "VaspToDb" in str(task):
+            task.update(vasp_to_db_params)
+
     wf_ld = get_lattice_dynamics_wf(
         structure,
         common_settings=c,

From fc248e2a508c2f0268b7f7fdc92fab2f2bfeb1a3 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Sat, 11 Apr 2020 12:29:22 -0700
Subject: [PATCH 091/207] Handle prior structural relaxations

---
 atomate/vasp/firetasks/lattice_dynamics.py     | 18 +++++++++++++++---
 .../vasp/workflows/base/lattice_dynamics.py    |  2 ++
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index cefa4e166..bd63afcb6 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -20,7 +20,9 @@
     get_cutoffs,
 )
 from atomate.vasp.database import VaspCalcDb
+from atomate.vasp.drones import VaspDrone
 from fireworks import FiretaskBase, FWAction, explicit_serialize
+from pymatgen import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.phonopy import get_phonon_band_structure_from_fc, \
     get_phonon_dos_from_fc, get_phonon_band_structure_symm_line_from_fc
@@ -68,12 +70,22 @@ def run_task(self, fw_spec):
 
         logger.info("Found {} perturbed structures".format(len(results)))
 
-        structure = results[0]["parent_structure"]
-        supercell_matrix = results[0]["supercell_matrix"]
-
         structures = [r["structure"] for r in results]
         forces = [np.asarray(r["forces"]) for r in results]
 
+        # if relaxation, get original structure from that calculation
+        calc_locs = fw_spec.get("calc_locs", [])
+        opt_calc_locs = [c for c in calc_locs if "optimiz" in c["name"]]
+        if opt_calc_locs:
+            opt_loc = opt_calc_locs[-1]["path"]
+            logger.info("Parsing optimization directory: {}".format(opt_loc))
+            opt_doc = VaspDrone().assimilate(opt_loc)
+            opt_output = opt_doc["calcs_reversed"][0]["output"]
+            structure = Structure.from_dict(opt_output["structure"])
+        else:
+            structure = results[0]["parent_structure"]
+        supercell_matrix = results[0]["supercell_matrix"]
+
         # regenerate pure supercell structure
         st = SupercellTransformation(supercell_matrix)
         supercell_structure = st.apply_transformation(structure)
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 6bead2a7e..ec063f094 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -39,6 +39,8 @@
     "LAECHG": False,
     "LREAL": False,
     "LASPH": True,
+    "LVTOT": False,
+    "LVHAR": False,
 }
 
 vasp_to_db_params = {

From 6fa622eda379bcaf2b093568c755d2efa8308265 Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Sat, 11 Apr 2020 16:16:53 -0700
Subject: [PATCH 092/207] optimize drone parsing

---
 atomate/vasp/firetasks/lattice_dynamics.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index bd63afcb6..b91ebdb42 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -79,7 +79,10 @@ def run_task(self, fw_spec):
         if opt_calc_locs:
             opt_loc = opt_calc_locs[-1]["path"]
             logger.info("Parsing optimization directory: {}".format(opt_loc))
-            opt_doc = VaspDrone().assimilate(opt_loc)
+            opt_doc = VaspDrone(
+                parse_dos=False, parse_locpot=False,
+                parse_bader=False, store_volumetric_data=[],
+            ).assimilate(opt_loc)
             opt_output = opt_doc["calcs_reversed"][0]["output"]
             structure = Structure.from_dict(opt_output["structure"])
         else:

From 83b4837321c6110b606ce86738be398e0a26d0aa Mon Sep 17 00:00:00 2001
From: Alex Ganose <alexganose@googlemail.com>
Date: Sat, 11 Apr 2020 17:00:06 -0700
Subject: [PATCH 093/207] fix typo in hiphive analysis

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index a313c877f..8ba57c551 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -68,7 +68,7 @@ def get_cutoffs(structure: Structure):
 
     row = min([s.row for s in structure.species])
     mins = {
-        2: min_cutoffs[row][2], 3: min_cutoffs[row][3], 4: min_cutoffs[row][4]
+        2: min_cutoffs[2][row], 3: min_cutoffs[3][row], 4: min_cutoffs[4][row]
     }
 
     range_two = np.arange(mins[2], mins[2] + inc[2] + steps[2], steps[2])

From 2eca8765190fed7528c9b5d1d0c0dd41f8401a37 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Tue, 25 May 2021 23:04:25 -0700
Subject: [PATCH 094/207] gruneisen and CTE

---
 atomate/vasp/analysis/lattice_dynamics.py     | 193 ++++++++++++++++--
 .../vasp/workflows/base/lattice_dynamics.py   |   5 +-
 2 files changed, 179 insertions(+), 19 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 8ba57c551..10ca27fbe 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -4,11 +4,18 @@
 import numpy as np
 
 from atomate.utils.utils import get_logger
+<<<<<<< HEAD
 from pymatgen import Structure
+=======
+from hiphive.cutoffs import is_cutoff_allowed, estimate_maximum_cutoff
+from hiphive import ForceConstants
+from pymatgen.core.structure import Structure
+from pymatgen.io.ase import AseAtomsAdaptor
+>>>>>>> 8f4f7e37 (gruneisen and CTE)
 from pymatgen.io.phonopy import get_phonopy_structure
 
-__author__ = "Alex Ganose, Rees Chang"
-__email__ = "aganose@lbl.gov, rc564@cornell.edu"
+__author__ = "Alex Ganose, Rees Chang, Junsoo Park"
+__email__ = "aganose@lbl.gov, rc564@cornell.edu, jsyony37@lbl.gov"
 
 logger = get_logger(__name__)
 
@@ -124,17 +131,24 @@ def fit_force_constants(
         ``SortedForceConstants`` object and a dictionary of information on the
         fitting process.
     """
+<<<<<<< HEAD
     from hiphive.fitting import Optimizer
     from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
 
     logger.info("Starting fitting force constants.")
+=======
+    logger.info("Starting force constant fitting.")
+>>>>>>> 8f4f7e37 (gruneisen and CTE)
 
     fitting_data = {
         "cutoffs": [],
         "rmse_test": [],
         "n_imaginary": [],
         "min_frequency": [],
-        "300K_free_energy": [],
+        "temperature": [],
+        "free_energy": [],
+        "entropy": [],
+        "heat_capacity": [],
         "fit_method": fit_method,
         "imaginary_tol": imaginary_tol,
         "max_n_imaginary": max_n_imaginary,
@@ -150,7 +164,66 @@ def fit_force_constants(
         "cutoffs": None,
     }
     n_cutoffs = len(all_cutoffs)
+<<<<<<< HEAD
     for i, cutoffs in enumerate(all_cutoffs):
+=======
+
+    fit_kwargs = fit_kwargs if fit_kwargs else {}
+    if fit_method == "rfe" and n_jobs == -1:
+        fit_kwargs["n_jobs"] = 1
+
+    cutoff_results = Parallel(n_jobs=-1, backend="multiprocessing")(delayed(_run_cutoffs)(
+        i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix,
+        fit_method, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
+
+    for result in cutoff_results:
+        if result is None:
+            pass
+
+        fitting_data["cutoffs"].append(result["cutoffs"])
+        fitting_data["rmse_test"].append(result["rmse_test"])
+        fitting_data["n_imaginary"].append(result["n_imaginary"])
+        fitting_data["min_frequency"].append(result["min_frequency"])
+        fitting_data["temperature"].append(result["temperature"])
+        fitting_data["free_energy"].append(result["free_energy"])
+        fitting_data["entropy"].append(result["entropy"])
+        fitting_data["heat_capcity"].append(result["heat_capacity"])
+
+        if (
+            result["min_frequency"] > -np.abs(max_imaginary_freq)
+#            and result["n_imaginary"] <= max_n_imaginary
+#            and result["n_imaginary"] < best_fit["n_imaginary"]
+            and result["rmse_test"] < best_fit["rmse_test"]
+        ):
+            best_fit.update(result)
+            fitting_data["best"] = result["cutoffs"]
+
+    logger.info("Finished fitting force constants.")
+
+    return best_fit["force_constants"], fitting_data
+
+
+def _run_cutoffs(
+    i,
+    cutoffs,
+    n_cutoffs,
+    parent_structure,
+    structures,
+    supercell_matrix,
+    fit_method,
+    imaginary_tol,
+    fit_kwargs
+):
+    from hiphive.fitting import Optimizer
+    from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
+
+    logger.info(
+        "Testing cutoffs {} out of {}: {}".format(i + 1, n_cutoffs, cutoffs)
+    )
+    supercell_atoms = structures[0]
+
+    if not is_cutoff_allowed(supercell_atoms, max(cutoffs)):
+>>>>>>> 8f4f7e37 (gruneisen and CTE)
         logger.info(
             "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
         )
@@ -164,10 +237,12 @@ def fit_force_constants(
         fcp = ForceConstantPotential(sc.cluster_space, parameters)
         fcs = fcp.get_force_constants(supercell_atoms)
 
-        phonopy_fcs = fcs.get_fc_array(order=2)
-        n_imaginary, min_freq, free_energy = evaluate_force_constants(
-            parent_structure, supercell_matrix, phonopy_fcs, imaginary_tol
+        T_qha = [i*100 for i in range(16)]
+#        phonopy_fcs = fcs.get_fc_array(order=2)
+        n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
+            parent_structure, supercell_matrix, fcs, imaginary_tol, T_qha
         )
+<<<<<<< HEAD
 
         fitting_data["cutoffs"].append(cutoffs)
         fitting_data["rmse_test"].append(opt.rmse_test)
@@ -194,6 +269,22 @@ def fit_force_constants(
     logger.info("Finished fitting force constants.")
 
     return best_fit["force_constants"], fitting_data
+=======
+        return {
+            "cutoffs": cutoffs,
+            "rmse_test": opt.rmse_test,
+            "n_imaginary": n_imaginary,
+            "min_frequency": min_freq,
+            "temperature": T_qha,
+            "free_energy": free_energy,
+            "entropy": entropy,
+            "heat_capacity": Cv,
+            "thermal_expansion": cte,
+            "force_constants": fcp
+        }
+    except Exception:
+        return None
+>>>>>>> 8f4f7e37 (gruneisen and CTE)
 
 
 def get_structure_container(
@@ -226,9 +317,10 @@ def get_structure_container(
 def evaluate_force_constants(
     structure: Structure,
     supercell_matrix: np.ndarray,
-    force_constants: np.ndarray,
+    force_constants: ForceConstants,
     imaginary_tol: float = IMAGINARY_TOL,
-) -> Tuple[int, float, float]:
+    T: List
+) -> Tuple[int, float, List, List, List]:
     """
     Uses the force constants to extract phonon properties. Used for comparing
     the accuracy of force constant fits.
@@ -242,22 +334,87 @@ def evaluate_force_constants(
 
     Returns:
         A tuple of the number of imaginary modes at Gamma, the minimum phonon
-        frequency at Gamma, and the free energy at 300 K.
+        frequency at Gamma, and the free energy, entropy, and heat capacity
     """
     from phonopy import Phonopy
 
+    fcs2 = fcs.get_fc_array(2)
+    fcs3 = fcs.get_fc_array(3)
     parent_phonopy = get_phonopy_structure(structure)
     phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
 
-    phonopy.set_force_constants(force_constants)
+    phonopy.set_force_constants(fcs2)
     phonopy.run_mesh(is_gamma_center=True)
-    phonopy.run_thermal_properties(temperatures=[300])
-    free_energy = phonopy.get_thermal_properties_dict()["free_energy"][0]
-
+    phonopy.run_thermal_properties(temperatures=T)
+    free_energy = phonopy.get_thermal_properties_dict()["free_energy"]
+    entropy = phonopy.get_thermal_properties_dict()["entropy"]
+    Cv = phonopy.get_thermal_properties_dict()["heat_capacity"]
+    freq = phonopy.mesh.frequencies
     # find imaginary modes at gamma
-    phonopy.run_qpoints([0, 0, 0])
-    gamma_eigs = phonopy.get_qpoints_dict()["frequencies"]
-    n_imaginary = int(np.sum(gamma_eigs < -np.abs(imaginary_tol)))
-    min_frequency = np.min(gamma_eigs)
+#    phonopy.run_qpoints([0, 0, 0])
+#    gamma_eigs = phonopy.get_qpoints_dict()["frequencies"]
+    n_imaginary = int(np.sum(freq < -np.abs(imaginary_tol)))
+    min_frequency = np.min(freq)
+
+    if n_imeginary > 0:
+        grun, cte = gruneisen(phonopy,fcs2,fcs3,mesh,T,Cv,bulk_mod,vol)
+        dLfrac = thermal_expansion(T,cte)
+    else:
+        grun = np.zeros((len(T),3))
+        cte = np.zeros((len(T),3))
+        dLfrac = np.zeros((len(T),3))
+        
+    return n_imaginary, min_frequency, free_energy, entropy, Cv, grun, cte, dLfrac
+
+
+def gruneisen(
+        phonopy: Phonopy,
+        fcs2: np.ndarray,
+        fcs3: np.ndarray,
+        mesh: List,
+        temperature: List,
+        Cv: List, # in J
+        bulk_mod: float, # in GPa
+        vol: float # in A^3
+) -> Tuple[List,List]:
+    
+    from phono3py.phonon3.gruneisen import Gruneisen
+    
+    gruneisen = Gruneisen(fcs2,fcs3,phonopy.supercell,phonopy.primitive)
+    gruneisen.set_sampling_mesh(mesh,is_gamma_center=True)
+    gruneisen.run()
+    grun = gruneisen.get_gruneisen_parameters() # (nptk,nmode,3,3)
+    omega = gruneisen._frequencies
+    qp = gruneisen._qpoints
+    kweight = gruneisen._weights
+    grun_tot = list()
+    for temp in temperature:
+        grun_tot.append(get_total_grun(omega,grun,kweight,temp))
+    grun_tot = np.array(np.nan_to_num(np.array(grun_tot)))
+    # linear thermal expansion coefficient     
+    cte = grun_tot*(Cv.repeat(3).reshape((len(Cv),3)))/(vol/10**30)/(bulk_mod*10**9)/3
+    cte = np.nan_to_num(cte)    
+    logger.info('Frequency : {}'.format(np.sort(omega.flatten())))
+    logger.info('Gruneisen : {}'.format(grun_tot))
+    logger.info('CTE : {}'.format(cte))    
+    return grun_tot, cte
+
+
+def thermal_expansion(
+        temperature: List,
+        cte: List
+) -> List:
+    assert len(temperature)==len(cte)
+    if 0 not in temperature:
+        temperature = [0] + temperature
+        cte = [[0,0,0]] + cte
+    temperature = np.array(temperature)
+    cte = np.array(cte)
+    # linear expansion fraction
+    dLfrac = copy(cte)
+    for t in range(len(temperature)):
+        dLfrac[t,:] = np.trapz(cte[:t+1,:],temperature[:t+1],axis=0)
+    dLfrac = np.nan_to_num(dLfrac)
+    logger.info('dLfrac : {}'.format(dLfrac))
+    return dLfrac
 
-    return n_imaginary, min_frequency, free_energy
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index ec063f094..e7c7d842f 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -126,7 +126,7 @@ def get_lattice_dynamics_wf(
         if supercell_matrix_kwargs.get("force_diagonal", False):
             warnings.warn(
                 "Diagonal transformation required to calculate lattice thermal "
-                "conductivity. Forcing diagonal matrix"
+                "conductivity using ShengBTE. Forcing diagonal matrix"
             )
         supercell_matrix_kwargs["force_diagonal"] = True
 
@@ -138,6 +138,7 @@ def get_lattice_dynamics_wf(
         n_supercells = get_num_supercells(supercell, **num_supercell_kwargs)
         perturbed_structure_kwargs["n_configs_per_std"] = n_supercells
 
+    # 1. Start by pertrubing supercell and calculating forces
     wf = get_perturbed_structure_wf(
         structure,
         supercell_matrix=supercell_matrix,
@@ -148,12 +149,14 @@ def get_lattice_dynamics_wf(
         **perturbed_structure_kwargs,
     )
 
+    # 2. Fit interatomic force constants from pertrubed structures
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
         db_file=db_file, spec=allow_fizzled
     )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 
+    # 3. Lattice thermal conductivity calculation (optional)
     if calculate_lattice_thermal_conductivity:
         fw_lattice_conductivity = LatticeThermalConductivityFW(
             db_file=db_file,

From f5bf0eeb3af8bdbc4066272bc597d51afe3efd11 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 26 May 2021 13:35:09 -0700
Subject: [PATCH 095/207] gruneisen

---
 atomate/vasp/analysis/lattice_dynamics.py | 24 ++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 10ca27fbe..63e183cda 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -240,7 +240,7 @@ def _run_cutoffs(
         T_qha = [i*100 for i in range(16)]
 #        phonopy_fcs = fcs.get_fc_array(order=2)
         n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
-            parent_structure, supercell_matrix, fcs, imaginary_tol, T_qha
+            parent_structure, supercell_matrix, fcs, T_qha, imaginary_tol
         )
 <<<<<<< HEAD
 
@@ -318,8 +318,8 @@ def evaluate_force_constants(
     structure: Structure,
     supercell_matrix: np.ndarray,
     force_constants: ForceConstants,
-    imaginary_tol: float = IMAGINARY_TOL,
-    T: List
+    T: List,
+    imaginary_tol: float = IMAGINARY_TOL
 ) -> Tuple[int, float, List, List, List]:
     """
     Uses the force constants to extract phonon properties. Used for comparing
@@ -402,19 +402,29 @@ def gruneisen(
 
 def thermal_expansion(
         temperature: List,
-        cte: List
-) -> List:
+        cte: List,
+        T=None: float 
+) -> np.ndarray:
     assert len(temperature)==len(cte)
     if 0 not in temperature:
         temperature = [0] + temperature
         cte = [[0,0,0]] + cte
     temperature = np.array(temperature)
-    cte = np.array(cte)
+    ind = np.argsort(temperature)
+    temperature = temperature[ind]
+    cte = np.array(cte)[ind]
     # linear expansion fraction
     dLfrac = copy(cte)
     for t in range(len(temperature)):
         dLfrac[t,:] = np.trapz(cte[:t+1,:],temperature[:t+1],axis=0)
     dLfrac = np.nan_to_num(dLfrac)
     logger.info('dLfrac : {}'.format(dLfrac))
-    return dLfrac
+    if T is None:
+        return dLfrac
+    else:
+        try:
+            T_ind = np.where(temperature==T)[0][0]
+            return [dLfrac[T_ind]]
+        except:
+            raise ValueError('Designated T does not exist in the temperature array!')
 

From 6ea285bbe3248f373453c505fd11d361295c6022 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 26 May 2021 14:00:04 -0700
Subject: [PATCH 096/207] gruneisen

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 63e183cda..2714571a1 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -424,7 +424,7 @@ def thermal_expansion(
     else:
         try:
             T_ind = np.where(temperature==T)[0][0]
-            return [dLfrac[T_ind]]
+            return np.array([dLfrac[T_ind]])
         except:
             raise ValueError('Designated T does not exist in the temperature array!')
 

From 8f767d9229bbd8ac510b89dc0e4b45bea828da32 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 26 May 2021 15:05:18 -0700
Subject: [PATCH 097/207] gruneisen

---
 atomate/vasp/analysis/lattice_dynamics.py | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 2714571a1..8222d73d8 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -2,6 +2,7 @@
 from typing import Dict, List, Tuple
 
 import numpy as np
+import scipy as sp
 
 from atomate.utils.utils import get_logger
 <<<<<<< HEAD
@@ -23,7 +24,7 @@
 IMAGINARY_TOL = 0.025  # in THz
 MAX_N_IMAGINARY = np.inf
 FIT_METHOD = "least-squares"
-
+eV2J = 1.602e-19
 
 def get_cutoffs(structure: Structure):
     """
@@ -342,14 +343,21 @@ def evaluate_force_constants(
     fcs3 = fcs.get_fc_array(3)
     parent_phonopy = get_phonopy_structure(structure)
     phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
-
+    vol = phonopy.primitive.get_volume()
+    natom = phonopy.primitive.get_number_of_atoms()
+    
     phonopy.set_force_constants(fcs2)
     phonopy.run_mesh(is_gamma_center=True)
     phonopy.run_thermal_properties(temperatures=T)
+
     free_energy = phonopy.get_thermal_properties_dict()["free_energy"]
+    free_energy *= 1000/sp.constants.Avogadro/eV2J/natom # kJ/mol to eV/atom
     entropy = phonopy.get_thermal_properties_dict()["entropy"]
+    entropy *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
     Cv = phonopy.get_thermal_properties_dict()["heat_capacity"]
-    freq = phonopy.mesh.frequencies
+    Cv *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
+    
+    freq = phonopy.mesh.frequencies # in THz
     # find imaginary modes at gamma
 #    phonopy.run_qpoints([0, 0, 0])
 #    gamma_eigs = phonopy.get_qpoints_dict()["frequencies"]
@@ -359,7 +367,7 @@ def evaluate_force_constants(
     if n_imeginary > 0:
         grun, cte = gruneisen(phonopy,fcs2,fcs3,mesh,T,Cv,bulk_mod,vol)
         dLfrac = thermal_expansion(T,cte)
-    else:
+    else: # do not calculate these if imaginary modes exist
         grun = np.zeros((len(T),3))
         cte = np.zeros((len(T),3))
         dLfrac = np.zeros((len(T),3))
@@ -373,11 +381,11 @@ def gruneisen(
         fcs3: np.ndarray,
         mesh: List,
         temperature: List,
-        Cv: List, # in J
+        Cv: np.ndarray, # in eV/K/atom
         bulk_mod: float, # in GPa
         vol: float # in A^3
 ) -> Tuple[List,List]:
-    
+
     from phono3py.phonon3.gruneisen import Gruneisen
     
     gruneisen = Gruneisen(fcs2,fcs3,phonopy.supercell,phonopy.primitive)
@@ -391,6 +399,7 @@ def gruneisen(
     for temp in temperature:
         grun_tot.append(get_total_grun(omega,grun,kweight,temp))
     grun_tot = np.array(np.nan_to_num(np.array(grun_tot)))
+    Cv *= eV2J*phonopy.primitive.get_number_of_atoms() # eV/K/atom to J/K
     # linear thermal expansion coefficient     
     cte = grun_tot*(Cv.repeat(3).reshape((len(Cv),3)))/(vol/10**30)/(bulk_mod*10**9)/3
     cte = np.nan_to_num(cte)    
@@ -403,7 +412,7 @@ def gruneisen(
 def thermal_expansion(
         temperature: List,
         cte: List,
-        T=None: float 
+        T: Optional[float]=None
 ) -> np.ndarray:
     assert len(temperature)==len(cte)
     if 0 not in temperature:

From bdc514356abf506b479921666475baa797660e32 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 26 May 2021 17:59:39 -0700
Subject: [PATCH 098/207] imports

---
 atomate/vasp/analysis/lattice_dynamics.py | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 8222d73d8..269891ac4 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -6,15 +6,27 @@
 
 from atomate.utils.utils import get_logger
 <<<<<<< HEAD
+<<<<<<< HEAD
 from pymatgen import Structure
 =======
+=======
+
+from hiphive import (ForceConstants, ForceConstantPotential,
+                     enforce_rotational_sum_rules, ClusterSpace,
+                     StructureContainer)
+>>>>>>> 1e75a82a (imports)
 from hiphive.cutoffs import is_cutoff_allowed, estimate_maximum_cutoff
-from hiphive import ForceConstants
+from hiphive.fitting import Optimizer
+
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 >>>>>>> 8f4f7e37 (gruneisen and CTE)
 from pymatgen.io.phonopy import get_phonopy_structure
 
+from phonopy import Phonopy
+from phono3py.phonon3.gruneisen import Gruneisen
+
+
 __author__ = "Alex Ganose, Rees Chang, Junsoo Park"
 __email__ = "aganose@lbl.gov, rc564@cornell.edu, jsyony37@lbl.gov"
 
@@ -215,8 +227,6 @@ def _run_cutoffs(
     imaginary_tol,
     fit_kwargs
 ):
-    from hiphive.fitting import Optimizer
-    from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
 
     logger.info(
         "Testing cutoffs {} out of {}: {}".format(i + 1, n_cutoffs, cutoffs)
@@ -302,7 +312,6 @@ def get_structure_container(
     Returns:
         A hiPhive StructureContainer.
     """
-    from hiphive import ClusterSpace, StructureContainer
 
     cs = ClusterSpace(structures[0], cutoffs)
     logger.debug(cs.__repr__())
@@ -337,7 +346,6 @@ def evaluate_force_constants(
         A tuple of the number of imaginary modes at Gamma, the minimum phonon
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
-    from phonopy import Phonopy
 
     fcs2 = fcs.get_fc_array(2)
     fcs3 = fcs.get_fc_array(3)
@@ -385,8 +393,6 @@ def gruneisen(
         bulk_mod: float, # in GPa
         vol: float # in A^3
 ) -> Tuple[List,List]:
-
-    from phono3py.phonon3.gruneisen import Gruneisen
     
     gruneisen = Gruneisen(fcs2,fcs3,phonopy.supercell,phonopy.primitive)
     gruneisen.set_sampling_mesh(mesh,is_gamma_center=True)

From d12802dda421e415eae99a5b2a071e3c07172b37 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 26 May 2021 19:52:55 -0700
Subject: [PATCH 099/207] FW

---
 atomate/vasp/analysis/lattice_dynamics.py  |   8 +-
 atomate/vasp/firetasks/lattice_dynamics.py | 102 ++++++++++++++++++++-
 atomate/vasp/fireworks/lattice_dynamics.py |  54 +++++++++++
 3 files changed, 156 insertions(+), 8 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 269891ac4..28cc37a87 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -35,6 +35,9 @@
 MAX_IMAGINARY_FREQ = 10  # in THz
 IMAGINARY_TOL = 0.025  # in THz
 MAX_N_IMAGINARY = np.inf
+T_QHA = [i*100 for i in range(16)]
+T_RENORM = [i*100 for i in range(0,16,3)]
+
 FIT_METHOD = "least-squares"
 eV2J = 1.602e-19
 
@@ -248,10 +251,9 @@ def _run_cutoffs(
         fcp = ForceConstantPotential(sc.cluster_space, parameters)
         fcs = fcp.get_force_constants(supercell_atoms)
 
-        T_qha = [i*100 for i in range(16)]
 #        phonopy_fcs = fcs.get_fc_array(order=2)
         n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
-            parent_structure, supercell_matrix, fcs, T_qha, imaginary_tol
+            parent_structure, supercell_matrix, fcs, T_QHA, imaginary_tol
         )
 <<<<<<< HEAD
 
@@ -286,7 +288,7 @@ def _run_cutoffs(
             "rmse_test": opt.rmse_test,
             "n_imaginary": n_imaginary,
             "min_frequency": min_freq,
-            "temperature": T_qha,
+            "temperature": T_QHA,
             "free_energy": free_energy,
             "entropy": entropy,
             "heat_capacity": Cv,
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index b91ebdb42..dad1a4fa4 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -16,13 +16,17 @@
     IMAGINARY_TOL,
     MAX_IMAGINARY_FREQ,
     MAX_N_IMAGINARY,
+    T_QHA,
+    T_RENORM,
     fit_force_constants,
     get_cutoffs,
 )
 from atomate.vasp.database import VaspCalcDb
 from atomate.vasp.drones import VaspDrone
+
 from fireworks import FiretaskBase, FWAction, explicit_serialize
-from pymatgen import Structure
+
+from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.phonopy import get_phonon_band_structure_from_fc, \
     get_phonon_dos_from_fc, get_phonon_band_structure_symm_line_from_fc
@@ -33,17 +37,18 @@
 
 try:
     import hiphive
+    from hiphive.utilities import get_displacements
+    from hiphive import Renormalization
 except ImportError:
     hiphive = False
 
 
-__author__ = "Alex Ganose"
-__email__ = "aganose@lbl.gov"
+__author__ = "Alex Ganose, Junsoo Park"
+__email__ = "aganose@lbl.gov, jsyony37@lbl.gov"
 
 logger = get_logger(__name__)
 
 # define shared constants
-DEFAULT_TEMPERATURE = 300
 MESH_DENSITY = 100.0  # should always be a float
 
 
@@ -196,6 +201,93 @@ def run_task(self, fw_spec):
             )
 
 
+
+@explicit_serialize
+class RunHiPhiveRenorm(FiretaskBase):
+    """
+    Perform phonon renormalization to obtain temperature-dependent force constants
+    using hiPhive. Requires "structure_data.json" to be present in the current working
+    directory.
+
+    cs,supercell,fcs,param,T,
+
+    Required parameters:
+        cs (hiphive.ClusterSpace): A list of cutoffs to trial. If None,
+            a set of trial cutoffs will be generated based on the structure
+            (default).
+        supercell (ase.Atoms): Tolerance used to decide if a phonon mode
+            is imaginary, in THz.
+        fcs (hiphive.ForceConstants): Maximum number of imaginary modes allowed in the
+            the final fitted force constant solution. If this criteria is not
+            reached by any cutoff combination this FireTask will fizzle.
+        param (np.ndarray): array of force constant parameters
+    Optional parameter:
+        T_renorm (List): list of temperatures to perform renormalization - default is T_RENORM
+    """
+
+    required_params = ["cs","supercell","fcs","param"]
+    optional_params = ["T_renorm"]
+
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
+    def run_task(self, fw_spec):
+        from hiphive.utilities import get_displacements
+
+        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
+        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
+        imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
+        fit_method = self.get("T_renorm", T_RENORM)
+
+        all_structures = loadfn("perturbed_structures.json")
+        all_forces = loadfn("perturbed_forces.json")
+        structure_data = loadfn("structure_data.json")
+        parent_structure = structure_data["structure"]
+        supercell_matrix = structure_data["supercell_matrix"]
+        supercell_structure = structure_data["supercell_structure"]
+
+        structures = []
+        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+        for structure, forces in zip(all_structures, all_forces):
+            atoms = AseAtomsAdaptor.get_atoms(structure)
+            displacements = get_displacements(atoms, supercell_atoms)
+            atoms.new_array("displacements", displacements)
+            atoms.new_array("forces", forces)
+            atoms.positions = supercell_atoms.get_positions()
+            structures.append(atoms)
+
+        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
+        force_constants, fitting_data = fit_force_constants(
+            parent_structure,
+            supercell_matrix,
+            structures,
+            cutoffs,
+            imaginary_tol,
+            max_n_imaginary,
+            max_imaginary_freq,
+            fit_method,
+        )
+
+        dumpfn(fitting_data, "fitting_data.json")        
+
+        if force_constants is None:
+            # fitting failed
+            raise RuntimeError(
+                "Could not find a force constant solution with less than {} "
+                "imaginary modes.\n"
+                "Fitting results: {}".format(max_n_imaginary, fitting_data)
+            )
+        
+        else:
+            logger.info("Writing force constants.")
+            force_constants.write("force_constants.fcs")
+
+            atoms = AseAtomsAdaptor.get_atoms(parent_structure)
+            force_constants.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
+            force_constants.write_to_phonopy(
+                "FORCE_CONSTANTS_2ND", format="text"
+            )
+            
+
+        
 @explicit_serialize
 class ForceConstantsToDb(FiretaskBase):
     """
@@ -334,7 +426,7 @@ def run_task(self, fw_spec):
             "scalebroad": 0.5,
             "nonanalytic": False,
             "isotopes": False,
-            "temperature": self.get("temperature", DEFAULT_TEMPERATURE),
+            "temperature": self.get("temperature", T_QHA),
             "scell": np.diag(supercell_matrix).tolist(),
         }
         control_kwargs = self.get("control_kwargs") or {}
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 18cdd4664..6e7d4e621 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -134,3 +134,57 @@ def __init__(
 
         tasks = [copy_files, run_shengbte, shengbte_to_db]
         super().__init__(tasks, name=name, **kwargs)
+
+
+
+class RenormalizationFW(Firework):        
+    """
+    Performs temperature-dependent phonon renormalization to obtain phonons
+    at finite temperatures. Can be used to stabilize dynamically unstable modes
+                                                                                                                                                                                                
+    Args:
+        name: Name of this FW.
+        prev_calc_dir: Path to a directory containing the force constant
+            information. Will override ``parents`` when collecting the force
+            constants to run ShengBTE.
+        db_file: Path to a db file.
+        shengbte_cmd: The name of the shengbte executable to run. Supports
+            env_chk.
+        temperature: The temperature to perform phonon renormalization at
+            Can be given as a single float, or a dictionary with the keys 
+            "min", "max", "step".
+        shengbte_control_kwargs: Options to be included in the ShengBTE
+            control file.
+        **kwargs: Other kwargs that are passed to Firework.__init__.
+    """
+    
+    def __init__(
+        self,
+        name="Renormalization",
+        prev_calc_dir: Optional[str] = None,
+        db_file: str = None,
+        shengbte_cmd: str = SHENGBTE_CMD,
+        temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
+        shengbte_control_kwargs: Optional[dict] = None,
+        **kwargs
+    ):    
+    
+    # files needed to run ShengBTE                                                                                                                                                                      
+    files = [
+        "structure_data.json",
+        "FORCE_CONSTANTS_2ND",
+        "FORCE_CONSTANTS_3RD",
+    ]
+    
+    if prev_calc_dir:
+        copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+    else:
+        copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+
+    fit_constants = RunHiPhiveRenorm(
+        cutoffs=cutoffs,
+        imaginary_tol=imaginary_tol,
+        max_n_imaginary=max_n_imaginary,
+        max_imaginary_freq=max_imaginary_freq,
+        fit_method=fit_method,
+    )        

From f9bc14cc6ab985a882160c5e49212d620d6f25df Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 19:34:13 -0700
Subject: [PATCH 100/207] VASP runs successfully

---
 atomate/vasp/analysis/lattice_dynamics.py  | 60 +++++++++++++++++++---
 atomate/vasp/drones.py                     |  1 +
 atomate/vasp/firetasks/lattice_dynamics.py | 46 +++++++++--------
 atomate/vasp/firetasks/parse_outputs.py    |  8 ++-
 atomate/vasp/fireworks/lattice_dynamics.py | 28 ++++------
 5 files changed, 97 insertions(+), 46 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 28cc37a87..7c969c8ac 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -107,7 +107,7 @@ def fit_force_constants(
     structures: List["Atoms"],
     all_cutoffs: List[List[float]],
     imaginary_tol: float = IMAGINARY_TOL,
-    max_n_imaginary: int = MAX_N_IMAGINARY,
+#    max_n_imaginary: int = MAX_N_IMAGINARY,
     max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
     fit_method: str = FIT_METHOD,
 ) -> Tuple["SortedForceConstants", Dict]:
@@ -194,7 +194,7 @@ def fit_force_constants(
 
     for result in cutoff_results:
         if result is None:
-            pass
+            continue
 
         fitting_data["cutoffs"].append(result["cutoffs"])
         fitting_data["rmse_test"].append(result["rmse_test"])
@@ -206,17 +206,17 @@ def fit_force_constants(
         fitting_data["heat_capcity"].append(result["heat_capacity"])
 
         if (
-            result["min_frequency"] > -np.abs(max_imaginary_freq)
+            result["rmse_test"] < best_fit["rmse_test"]
+#            and result["min_frequency"] > -np.abs(max_imaginary_freq)
 #            and result["n_imaginary"] <= max_n_imaginary
 #            and result["n_imaginary"] < best_fit["n_imaginary"]
-            and result["rmse_test"] < best_fit["rmse_test"]
         ):
             best_fit.update(result)
             fitting_data["best"] = result["cutoffs"]
 
     logger.info("Finished fitting force constants.")
 
-    return best_fit["force_constants"], fitting_data
+    return best_fit["force_constants"], best_fit["parameters"], best_fit["cluster_space"], fitting_data
 
 
 def _run_cutoffs(
@@ -293,7 +293,9 @@ def _run_cutoffs(
             "entropy": entropy,
             "heat_capacity": Cv,
             "thermal_expansion": cte,
-            "force_constants": fcp
+            "cluster_space": sc.cluster_space,
+            "parameters": parameters,
+            "force_constants": fcs
         }
     except Exception:
         return None
@@ -385,6 +387,52 @@ def evaluate_force_constants(
     return n_imaginary, min_frequency, free_energy, entropy, Cv, grun, cte, dLfrac
 
 
+def get_total_grun(
+        omega: np.ndarray,
+        grun: np.ndarray,
+        kweight: np.ndarray,
+        T: float
+) -> np.ndarray:
+    total = 0
+    weight = 0
+    nptk = omega.shape[0]
+    nbands = omega.shape[1]
+    omega = abs(omega)*1e12*2*np.pi
+    if T==0:
+        total = np.zeros((3,3))
+        grun_total_diag = np.zeros(3)
+    else:
+        for i in range(nptk):
+            for j in range(nbands):
+                x = hbar*omega[i,j]/(2.0*kB*T)
+                dBE = (x/np.sinh(x))**2
+                weight += dBE*kweight[i]
+                total += dBE*kweight[i]*grun[i,j]
+        total = total/weight
+        grun_total_diag = np.array([total[0,2],total[1,1],total[2,0]])
+
+        def percent_diff(a,b):
+            return abs((a-b)/b)
+        # This process preserves cell symmetry upon thermal expansion, i.e., it prevents
+        # symmetry-identical directions from inadvertently expanding by different ratios
+        # when the Gruneisen routine returns slighlty different ratios for those directions
+        if percent_diff(grun_total_diag[0],grun_total_diag[1]) < 0.1:
+            avg = np.mean((grun_total_diag[0],grun_total_diag[1]))
+            grun_total_diag[0] = avg
+            grun_total_diag[1] = avg
+        elif percent_diff(grun_total_diag[0],grun_total_diag[2]) < 0.1:
+            avg = np.mean((grun_total_diag[0],grun_total_diag[2]))
+            grun_total_diag[0] = avg
+            grun_total_diag[2] = avg
+        elif percent_diff(grun_total_diag[1],grun_total_diag[2]) < 0.1:
+            avg = np.mean((grun_total_diag[1],grun_total_diag[2]))
+            grun_total_diag[1] = avg
+            grun_total_diag[2] = avg
+        else:
+            pass
+    return grun_total_diag
+
+
 def gruneisen(
         phonopy: Phonopy,
         fcs2: np.ndarray,
diff --git a/atomate/vasp/drones.py b/atomate/vasp/drones.py
index 0c5714fa1..ada98aedf 100644
--- a/atomate/vasp/drones.py
+++ b/atomate/vasp/drones.py
@@ -575,6 +575,7 @@ def process_vasprun(self, dir_name, taskname, filename):
 
         # perform Bader analysis using Henkelman bader
         if self.parse_bader and "chgcar" in d["output_file_paths"]:
+            print(self.parse_bader)
             suffix = "" if taskname == "standard" else f".{taskname}"
             bader = bader_analysis_from_path(dir_name, suffix=suffix)
             d["bader"] = bader
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index dad1a4fa4..e91691617 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -144,9 +144,8 @@ class RunHiPhive(FiretaskBase):
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
-        from hiphive.utilities import get_displacements
 
-        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
+#        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
         max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
         fit_method = self.get("fit_method", FIT_METHOD)
@@ -169,36 +168,42 @@ def run_task(self, fw_spec):
             structures.append(atoms)
 
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        force_constants, fitting_data = fit_force_constants(
+        fcs, param, cs, fitting_data = fit_force_constants(
             parent_structure,
             supercell_matrix,
             structures,
             cutoffs,
             imaginary_tol,
-            max_n_imaginary,
+#            max_n_imaginary,
             max_imaginary_freq,
             fit_method,
         )
 
         dumpfn(fitting_data, "fitting_data.json")
 
-        if force_constants is None:
-            # fitting failed
-            raise RuntimeError(
-                "Could not find a force constant solution with less than {} "
-                "imaginary modes.\n"
-                "Fitting results: {}".format(max_n_imaginary, fitting_data)
-            )
+#        if force_constants is None:
+#            # fitting failed
+#            raise RuntimeError(
+#                "Could not find a force constant solution with less than {} "
+#                "imaginary modes.\n"
+#                "Fitting results: {}".format(max_n_imaginary, fitting_data)
+#            )
 
-        else:
-            logger.info("Writing force constants.")
-            force_constants.write("force_constants.fcs")
+        logger.info("Writing cluster space and force_constants")
+        fcs.write("force_constants.fcs")
+        np.savetxt('parameters',parameters)
+        cs.write('cluster_space.cs')
 
+        if fitting_data["n_imaginary"] == 0:
             atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-            force_constants.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
-            force_constants.write_to_phonopy(
-                "FORCE_CONSTANTS_2ND", format="text"
-            )
+            fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
+        elif fitting_data["n_imaginary"] > 0 and renormalization:
+            logger.info("Imaginary modes exist!")
+            logger.info("Performing phonon renormalization at temperatures {}".format(T_renorm))
+            renorm = Renormalization(cs,fcs,param,T)
+        else:
+            logger.info("Imaginary modes exist! ShengBTE files not written. Not performing renormalization.")
 
 
 
@@ -215,8 +220,6 @@ class RunHiPhiveRenorm(FiretaskBase):
         cs (hiphive.ClusterSpace): A list of cutoffs to trial. If None,
             a set of trial cutoffs will be generated based on the structure
             (default).
-        supercell (ase.Atoms): Tolerance used to decide if a phonon mode
-            is imaginary, in THz.
         fcs (hiphive.ForceConstants): Maximum number of imaginary modes allowed in the
             the final fitted force constant solution. If this criteria is not
             reached by any cutoff combination this FireTask will fizzle.
@@ -225,12 +228,11 @@ class RunHiPhiveRenorm(FiretaskBase):
         T_renorm (List): list of temperatures to perform renormalization - default is T_RENORM
     """
 
-    required_params = ["cs","supercell","fcs","param"]
+    required_params = ["cs","fcs","param"]
     optional_params = ["T_renorm"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
-        from hiphive.utilities import get_displacements
 
         max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
         max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 25fd107a6..1efb2b28c 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -67,6 +67,7 @@
 from atomate.vasp.config import DEFUSE_UNSUCCESSFUL, STORE_VOLUMETRIC_DATA
 from atomate.vasp.database import VaspCalcDb
 <<<<<<< HEAD
+<<<<<<< HEAD
 from atomate.vasp.drones import BADER_EXE_EXISTS, VaspDrone
 =======
 from atomate.vasp.drones import VaspDrone
@@ -75,12 +76,17 @@
 >>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 =======
 >>>>>>> fd3cc888 (Added fw_spec updates to all dynamically added fireworks and wrote a ShengBTE firetask)
+=======
+from atomate.vasp.drones import VaspDrone, BADER_EXE_EXISTS
+from atomate.vasp.config import STORE_VOLUMETRIC_DATA, STORE_BADER
+>>>>>>> 13ec960c (VASP runs successfully)
 
 __author__ = "Anubhav Jain, Kiran Mathew, Shyam Dwaraknath"
 __email__ = "ajain@lbl.gov, kmathew@lbl.gov, shyamd@lbl.gov"
 
 logger = get_logger(__name__)
 
+STORE_BADER = STORE_BADER and BADER_EXE_EXISTS
 
 @explicit_serialize
 class VaspToDb(FiretaskBase):
@@ -166,7 +172,7 @@ def run_task(self, fw_spec):
             parse_dos=self.get("parse_dos", False),
             parse_potcar_file=self.get("parse_potcar_file", True),
             bandstructure_mode=self.get("bandstructure_mode", False),
-            parse_bader=self.get("parse_bader", BADER_EXE_EXISTS),
+            parse_bader=STORE_BADER, #self.get("parse_bader", BADER_EXE_EXISTS),
             parse_chgcar=self.get("parse_chgcar", False),  # deprecated
             parse_aeccar=self.get("parse_aeccar", False),  # deprecated
             store_volumetric_data=self.get(
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 6e7d4e621..637370abf 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -10,6 +10,8 @@
     IMAGINARY_TOL,
     MAX_IMAGINARY_FREQ,
     MAX_N_IMAGINARY,
+    T_QHA,
+    T_RENORM
 )
 from atomate.vasp.config import SHENGBTE_CMD
 from atomate.vasp.firetasks.lattice_dynamics import (
@@ -22,8 +24,8 @@
     MESH_DENSITY)
 from fireworks import Firework
 
-__author__ = "Alex Ganose"
-__email__ = "aganose@lbl.gov"
+__author__ = "Alex Ganose, Junsoo Park"
+__email__ = "aganose@lbl.gov, jsyony37@lbl.gov"
 
 
 class FitForceConstantsFW(Firework):
@@ -148,8 +150,6 @@ class RenormalizationFW(Firework):
             information. Will override ``parents`` when collecting the force
             constants to run ShengBTE.
         db_file: Path to a db file.
-        shengbte_cmd: The name of the shengbte executable to run. Supports
-            env_chk.
         temperature: The temperature to perform phonon renormalization at
             Can be given as a single float, or a dictionary with the keys 
             "min", "max", "step".
@@ -163,28 +163,22 @@ def __init__(
         name="Renormalization",
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
-        shengbte_cmd: str = SHENGBTE_CMD,
         temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
         shengbte_control_kwargs: Optional[dict] = None,
         **kwargs
     ):    
     
-    # files needed to run ShengBTE                                                                                                                                                                      
-    files = [
-        "structure_data.json",
-        "FORCE_CONSTANTS_2ND",
-        "FORCE_CONSTANTS_3RD",
-    ]
+    # files needed to run renormalization
+    files = ["cluster_space.cs","parameters","force_constants.fcs"]
     
     if prev_calc_dir:
         copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
     else:
         copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
 
-    fit_constants = RunHiPhiveRenorm(
-        cutoffs=cutoffs,
-        imaginary_tol=imaginary_tol,
-        max_n_imaginary=max_n_imaginary,
-        max_imaginary_freq=max_imaginary_freq,
-        fit_method=fit_method,
+    fit_renorm_constants = RunHiPhiveRenorm(
+        cs=cluster_space.cs,
+        param=parameters,
+        fcs=force_constants.fcs,
+        T_renorm=T_renorm,
     )        

From 045a35f4ca2c1864c4d54c021414fbb0a2ea8e41 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 19:40:26 -0700
Subject: [PATCH 101/207] no DEFAULT TEMPERATURE

---
 atomate/vasp/analysis/lattice_dynamics.py  |  4 ++-
 atomate/vasp/firetasks/lattice_dynamics.py |  1 +
 atomate/vasp/fireworks/lattice_dynamics.py | 32 +++++++++++-----------
 3 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 7c969c8ac..1bf5b141d 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -35,8 +35,10 @@
 MAX_IMAGINARY_FREQ = 10  # in THz
 IMAGINARY_TOL = 0.025  # in THz
 MAX_N_IMAGINARY = np.inf
+
 T_QHA = [i*100 for i in range(16)]
-T_RENORM = [i*100 for i in range(0,16,3)]
+T_RENORM = [i*100 for i in range(0,16)]
+T_KLAT = [i*100 for i in range(0,16)]
 
 FIT_METHOD = "least-squares"
 eV2J = 1.602e-19
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index e91691617..68b08dd70 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -18,6 +18,7 @@
     MAX_N_IMAGINARY,
     T_QHA,
     T_RENORM,
+    T_KLAT,
     fit_force_constants,
     get_cutoffs,
 )
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 637370abf..f38766c61 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -11,11 +11,11 @@
     MAX_IMAGINARY_FREQ,
     MAX_N_IMAGINARY,
     T_QHA,
-    T_RENORM
+    T_RENORM,
+    T_KLAT
 )
 from atomate.vasp.config import SHENGBTE_CMD
 from atomate.vasp.firetasks.lattice_dynamics import (
-    DEFAULT_TEMPERATURE,
     CollectPerturbedStructures,
     ForceConstantsToDb,
     RunHiPhive,
@@ -168,17 +168,17 @@ def __init__(
         **kwargs
     ):    
     
-    # files needed to run renormalization
-    files = ["cluster_space.cs","parameters","force_constants.fcs"]
-    
-    if prev_calc_dir:
-        copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
-    else:
-        copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
-
-    fit_renorm_constants = RunHiPhiveRenorm(
-        cs=cluster_space.cs,
-        param=parameters,
-        fcs=force_constants.fcs,
-        T_renorm=T_renorm,
-    )        
+        # files needed to run renormalization
+        files = ["cluster_space.cs","parameters","force_constants.fcs"]
+        
+        if prev_calc_dir:
+            copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+        else:
+            copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+            
+            fit_renorm_constants = RunHiPhiveRenorm(
+                cs=cluster_space.cs,
+                param=parameters,
+                fcs=force_constants.fcs,
+                T_renorm=T_renorm,
+            )        

From 5fe792baca08be629cbf0ad69eaf64e472067f8e Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 19:41:58 -0700
Subject: [PATCH 102/207] T_KLAT

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index f38766c61..59ea68da4 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -111,7 +111,7 @@ def __init__(
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
         shengbte_cmd: str = SHENGBTE_CMD,
-        temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
+        temperature: Union[float, dict] = T_KLAT,
         shengbte_control_kwargs: Optional[dict] = None,
         **kwargs
     ):

From 832a947d8342ea1161c71bd2a6b55a8779a73113 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 19:42:59 -0700
Subject: [PATCH 103/207] T_RENORM

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 59ea68da4..d2edb4f40 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -163,7 +163,7 @@ def __init__(
         name="Renormalization",
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
-        temperature: Union[float, dict] = DEFAULT_TEMPERATURE,
+        temperature: Union[float, dict] = T_RENORM,
         shengbte_control_kwargs: Optional[dict] = None,
         **kwargs
     ):    

From 85eef6c837d86bfb011dbe073994ff04ea24c8bc Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 20:17:54 -0700
Subject: [PATCH 104/207] import renormalization

---
 atomate/vasp/analysis/lattice_dynamics.py  | 2 +-
 atomate/vasp/firetasks/lattice_dynamics.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 1bf5b141d..606fbe3fa 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -40,7 +40,7 @@
 T_RENORM = [i*100 for i in range(0,16)]
 T_KLAT = [i*100 for i in range(0,16)]
 
-FIT_METHOD = "least-squares"
+FIT_METHOD = "rfe" #"least-squares"
 eV2J = 1.602e-19
 
 def get_cutoffs(structure: Structure):
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 68b08dd70..d120e1e01 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -39,7 +39,7 @@
 try:
     import hiphive
     from hiphive.utilities import get_displacements
-    from hiphive import Renormalization
+    from hiphive.renormalization import Renormalization
 except ImportError:
     hiphive = False
 

From 6359a632a3a2114b70346f3d5f66adb1bb327d19 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 20:49:19 -0700
Subject: [PATCH 105/207] parameters to best_fit

---
 atomate/vasp/analysis/lattice_dynamics.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 606fbe3fa..0567d1864 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -169,7 +169,7 @@ def fit_force_constants(
         "heat_capacity": [],
         "fit_method": fit_method,
         "imaginary_tol": imaginary_tol,
-        "max_n_imaginary": max_n_imaginary,
+#        "max_n_imaginary": max_n_imaginary,
         "max_imaginary_freq": max_imaginary_freq,
     }
 
@@ -179,6 +179,7 @@ def fit_force_constants(
         "n_imaginary": np.inf,
         "free_energy": np.inf,
         "force_constants": None,
+        "parameters":None,
         "cutoffs": None,
     }
     n_cutoffs = len(all_cutoffs)

From 9a7928ce999be1a488135337a405bd9bb445cd67 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 28 May 2021 20:55:52 -0700
Subject: [PATCH 106/207] cluster_space to best_fit

---
 atomate/vasp/analysis/lattice_dynamics.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 0567d1864..cd319959b 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -177,7 +177,12 @@ def fit_force_constants(
 
     best_fit = {
         "n_imaginary": np.inf,
+<<<<<<< HEAD
         "free_energy": np.inf,
+=======
+        "rmse_test": np.inf,
+        "cluster_space": None,
+>>>>>>> cd00c732 (cluster_space to best_fit)
         "force_constants": None,
         "parameters":None,
         "cutoffs": None,

From 1ba2a949af6de18e5b37d84cef3e8121e580a534 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sat, 29 May 2021 12:15:15 -0700
Subject: [PATCH 107/207] get_cutoffs

---
 atomate/vasp/analysis/lattice_dynamics.py     | 35 +++++++++++++++----
 atomate/vasp/firetasks/lattice_dynamics.py    | 29 ++++++++-------
 atomate/vasp/fireworks/lattice_dynamics.py    |  1 +
 .../vasp/workflows/base/lattice_dynamics.py   |  2 ++
 4 files changed, 48 insertions(+), 19 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index cd319959b..d45fa8769 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -112,7 +112,13 @@ def fit_force_constants(
 #    max_n_imaginary: int = MAX_N_IMAGINARY,
     max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
     fit_method: str = FIT_METHOD,
+<<<<<<< HEAD
 ) -> Tuple["SortedForceConstants", Dict]:
+=======
+    n_jobs: int = -1,
+    fit_kwargs: Optional[Dict] = None
+) -> Tuple["SortedForceConstants", np.ndarray, ClusterSpace, Dict]:
+>>>>>>> fddd9681 (get_cutoffs)
     """
     Fit force constants using hiphive and select the optimum cutoff values.
 
@@ -146,8 +152,8 @@ def fit_force_constants(
 
     Returns:
         A tuple of the best fitted force constants as a hiphive
-        ``SortedForceConstants`` object and a dictionary of information on the
-        fitting process.
+        ``SortedForceConstants`` object, array of parameters, cluster space,
+        and a dictionary of information on the fitting results.
     """
 <<<<<<< HEAD
     from hiphive.fitting import Optimizer
@@ -192,14 +198,17 @@ def fit_force_constants(
     for i, cutoffs in enumerate(all_cutoffs):
 =======
 
-    fit_kwargs = fit_kwargs if fit_kwargs else {}
-    if fit_method == "rfe" and n_jobs == -1:
-        fit_kwargs["n_jobs"] = 1
+#    fit_kwargs = fit_kwargs if fit_kwargs else {}
+#    if fit_method == "rfe" and n_jobs == -1:
+#        fit_kwargs["n_jobs"] = 1
 
+    logger.info('cutoff_results')
     cutoff_results = Parallel(n_jobs=-1, backend="multiprocessing")(delayed(_run_cutoffs)(
         i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix,
         fit_method, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
+    logger.info(cutoff_results)
+    
     for result in cutoff_results:
         if result is None:
             continue
@@ -250,19 +259,28 @@ def _run_cutoffs(
             "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
         )
         sc = get_structure_container(cutoffs, structures)
+<<<<<<< HEAD
         opt = Optimizer(sc.get_fit_data(), fit_method)
+=======
+        logger.info('{}, {}: FINE UNTIL SC'.format(i,cutoffs))
+        opt = Optimizer(sc.get_fit_data(), fit_method, **fit_kwargs)
+        logger.info('{}, {}: FINE UNTIL OPT'.format(i,cutoffs))
+>>>>>>> fddd9681 (get_cutoffs)
         opt.train()
+        logger.info('{}, {}: FINE UNTIL TRAIN'.format(i,cutoffs))
 
         parameters = enforce_rotational_sum_rules(
             sc.cluster_space, opt.parameters, ["Huang", "Born-Huang"]
         )
+        logger.info('{}, {}: FINE UNTIL SUM RULE'.format(i,cutoffs))
         fcp = ForceConstantPotential(sc.cluster_space, parameters)
+        logger.info('{}, {}: FINE UNTIL FCP'.format(i,cutoffs))
         fcs = fcp.get_force_constants(supercell_atoms)
-
-#        phonopy_fcs = fcs.get_fc_array(order=2)
+        logger.info('{}, {}: FINE UNTIL FCS'.format(i,cutoffs))
         n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
             parent_structure, supercell_matrix, fcs, T_QHA, imaginary_tol
         )
+<<<<<<< HEAD
 <<<<<<< HEAD
 
         fitting_data["cutoffs"].append(cutoffs)
@@ -291,6 +309,9 @@ def _run_cutoffs(
 
     return best_fit["force_constants"], fitting_data
 =======
+=======
+        logger.info('evaluate_force_constants success!')
+>>>>>>> fddd9681 (get_cutoffs)
         return {
             "cutoffs": cutoffs,
             "rmse_test": opt.rmse_test,
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index d120e1e01..67547ee69 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -20,7 +20,7 @@
     T_RENORM,
     T_KLAT,
     fit_force_constants,
-    get_cutoffs,
+    get_cutoffs
 )
 from atomate.vasp.database import VaspCalcDb
 from atomate.vasp.drones import VaspDrone
@@ -157,6 +157,7 @@ def run_task(self, fw_spec):
         parent_structure = structure_data["structure"]
         supercell_matrix = structure_data["supercell_matrix"]
         supercell_structure = structure_data["supercell_structure"]
+        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
 
         structures = []
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
@@ -168,7 +169,13 @@ def run_task(self, fw_spec):
             atoms.positions = supercell_atoms.get_positions()
             structures.append(atoms)
 
-        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
+        logger.info(parent_structure)
+        logger.info(supercell_structure)
+        logger.info(fit_method)
+        from_get_cutoffs = get_cutoffs(supercell_structure)
+        logger.info('SELF.GET_CUTOFFS \n {}'.format(self.get("cutoffs")))
+        logger.info('FROM GET_CUTOFFS \n {}'.format(from_get_cutoffs))
+        logger.info('FINAL INPUT CUTOFFS \n {}'.format(cutoffs))
         fcs, param, cs, fitting_data = fit_force_constants(
             parent_structure,
             supercell_matrix,
@@ -177,7 +184,7 @@ def run_task(self, fw_spec):
             imaginary_tol,
 #            max_n_imaginary,
             max_imaginary_freq,
-            fit_method,
+            fit_method
         )
 
         dumpfn(fitting_data, "fitting_data.json")
@@ -191,20 +198,18 @@ def run_task(self, fw_spec):
 #            )
 
         logger.info("Writing cluster space and force_constants")
+        logger.info("{}".format(type(fcs)))
         fcs.write("force_constants.fcs")
-        np.savetxt('parameters',parameters)
+        np.savetxt('parameters.txt',parameters)
         cs.write('cluster_space.cs')
 
         if fitting_data["n_imaginary"] == 0:
+            logger.info("No imaginary modes! Writing ShengBTE files")
             atoms = AseAtomsAdaptor.get_atoms(parent_structure)
             fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
-        elif fitting_data["n_imaginary"] > 0 and renormalization:
-            logger.info("Imaginary modes exist!")
-            logger.info("Performing phonon renormalization at temperatures {}".format(T_renorm))
-            renorm = Renormalization(cs,fcs,param,T)
-        else:
-            logger.info("Imaginary modes exist! ShengBTE files not written. Not performing renormalization.")
+        elif fitting_data["n_imaginary"] > 0:
+            logger.info("Imaginary modes exist! ShengBTE files not written. You may want to perform phonon renormalization.")
 
 
 
@@ -238,7 +243,7 @@ def run_task(self, fw_spec):
         max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
         max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
-        fit_method = self.get("T_renorm", T_RENORM)
+        T_renorm = self.get("T_renorm", T_RENORM)
 
         all_structures = loadfn("perturbed_structures.json")
         all_forces = loadfn("perturbed_forces.json")
@@ -264,7 +269,7 @@ def run_task(self, fw_spec):
             structures,
             cutoffs,
             imaginary_tol,
-            max_n_imaginary,
+#            max_n_imaginary,
             max_imaginary_freq,
             fit_method,
         )
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index d2edb4f40..9a42dfc1f 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -69,6 +69,7 @@ def __init__(
         **kwargs
     ):
         collect_structures = CollectPerturbedStructures()
+        logger.info("INPUT CUTOFF \n {}".format(cutoffs))
         fit_constants = RunHiPhive(
             cutoffs=cutoffs,
             imaginary_tol=imaginary_tol,
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index e7c7d842f..5d76a979b 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -156,6 +156,8 @@ def get_lattice_dynamics_wf(
     )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 
+    # RenormalizeFW(pass_inputs like bulk modulus)
+    
     # 3. Lattice thermal conductivity calculation (optional)
     if calculate_lattice_thermal_conductivity:
         fw_lattice_conductivity = LatticeThermalConductivityFW(

From 505479f3c7bd6a9b3076eecfe55d120d408c6b50 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 30 May 2021 20:42:10 -0700
Subject: [PATCH 108/207] cutoff vs cell_size

---
 atomate/vasp/analysis/lattice_dynamics.py     | 12 +++++++-
 atomate/vasp/firetasks/lattice_dynamics.py    |  7 +++--
 atomate/vasp/fireworks/lattice_dynamics.py    | 29 +++++++++++++------
 .../vasp/workflows/base/lattice_dynamics.py   |  2 +-
 4 files changed, 36 insertions(+), 14 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index d45fa8769..21536d189 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -34,7 +34,7 @@
 
 MAX_IMAGINARY_FREQ = 10  # in THz
 IMAGINARY_TOL = 0.025  # in THz
-MAX_N_IMAGINARY = np.inf
+#MAX_N_IMAGINARY = np.inf
 
 T_QHA = [i*100 for i in range(16)]
 T_RENORM = [i*100 for i in range(0,16)]
@@ -100,7 +100,17 @@ def get_cutoffs(structure: Structure):
     range_three = np.arange(mins[3], mins[3] + inc[3] + steps[3], steps[3])
     range_four = np.arange(mins[4], mins[4] + inc[4] + steps[4], steps[4])
 
+<<<<<<< HEAD
     return list(map(list, product(range_two, range_three, range_four)))
+=======
+    cutoffs = np.array(list(map(list, product(range_two, range_three, range_four))))
+    logger.info('CUTOFFS \n {}'.format(cutoffs))
+    max_cutoff = estimate_maximum_cutoff(AseAtomsAdaptor.get_atoms(supercell_structure))
+    logger.info('MAX_CUTOFF \n {}'.format(max_cutoff))    
+    good_cutoffs = np.all(cutoffs < np.around(max_cutoff, 4) - 0.0001, axis=1)
+    logger.info('GOOD CUTOFFS \n {}'.format(good_cutoffs))
+    return cutoffs[good_cutoffs].tolist()
+>>>>>>> c094a175 (cutoff vs cell_size)
 
 
 def fit_force_constants(
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 67547ee69..ddde2a512 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -15,7 +15,7 @@
     FIT_METHOD,
     IMAGINARY_TOL,
     MAX_IMAGINARY_FREQ,
-    MAX_N_IMAGINARY,
+#    MAX_N_IMAGINARY,
     T_QHA,
     T_RENORM,
     T_KLAT,
@@ -41,6 +41,7 @@
     from hiphive.utilities import get_displacements
     from hiphive.renormalization import Renormalization
 except ImportError:
+    logger.info('Could not import hiphive!')
     hiphive = False
 
 
@@ -169,8 +170,8 @@ def run_task(self, fw_spec):
             atoms.positions = supercell_atoms.get_positions()
             structures.append(atoms)
 
-        logger.info(parent_structure)
-        logger.info(supercell_structure)
+        logger.info('PARENT \n {}'.format(parent_structure))
+        logger.info('SUPERCELL \n {}'.format(supercell_structure))
         logger.info(fit_method)
         from_get_cutoffs = get_cutoffs(supercell_structure)
         logger.info('SELF.GET_CUTOFFS \n {}'.format(self.get("cutoffs")))
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 9a42dfc1f..4defbdfac 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -75,7 +75,7 @@ def __init__(
             imaginary_tol=imaginary_tol,
             max_n_imaginary=max_n_imaginary,
             max_imaginary_freq=max_imaginary_freq,
-            fit_method=fit_method,
+            fit_method=fit_method
         )
         to_db = ForceConstantsToDb(
             db_file=db_file, mesh_density=mesh_density, additional_fields={}
@@ -170,16 +170,27 @@ def __init__(
     ):    
     
         # files needed to run renormalization
-        files = ["cluster_space.cs","parameters","force_constants.fcs"]
+        files = ["cluster_space.cs","parameters.txt","force_constants.fcs"]
         
         if prev_calc_dir:
             copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
         else:
             copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
-            
-            fit_renorm_constants = RunHiPhiveRenorm(
-                cs=cluster_space.cs,
-                param=parameters,
-                fcs=force_constants.fcs,
-                T_renorm=T_renorm,
-            )        
+
+        cs = ClusterSpace.read('cluster_space.cs')
+        fcs = ForceConstants.read('force_constants.fcs')
+        param = np.loadtxt('parameters.txt')
+        renorm_force_constants = RunHiPhiveRenorm(
+            cs=cluster_space.cs,
+            param=parameters,
+            fcs=force_constants.fcs,
+            T_renorm=T_renorm
+        )        
+
+        to_db = ForceConstantsToDb(
+            db_file=db_file, mesh_density=mesh_density, additional_fields={}
+	)
+        pass_locs = PassCalcLocs(name=name)
+
+	tasks = [collect_structures, renorm_force_constants, to_db, pass_locs]
+        super().__init__(tasks, name=name, **kwargs)
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 5d76a979b..e26199890 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -228,7 +228,7 @@ def get_perturbed_structure_wf(
     }
 
     if supercell_matrix is None:
-        supercell_matrix = np.eye(3)
+        supercell_matrix = np.eye(4)
 
     supercell_matrix = np.asarray(supercell_matrix).tolist()
     natoms = len(structure * supercell_matrix)

From 53875933533c84485be670a4fa7dc9a16891efec Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Tue, 1 Jun 2021 21:52:51 -0700
Subject: [PATCH 109/207] bulk_mod input

---
 atomate/vasp/analysis/lattice_dynamics.py     | 100 ++++++++++++------
 atomate/vasp/firetasks/lattice_dynamics.py    |   7 +-
 atomate/vasp/fireworks/lattice_dynamics.py    |   2 +
 .../vasp/workflows/base/lattice_dynamics.py   |  10 +-
 4 files changed, 78 insertions(+), 41 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 21536d189..699d507c3 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -55,13 +55,13 @@ def get_cutoffs(structure: Structure):
     ------ -----------
     Period 2ND 3RD 4TH
     ====== === === ===
-     1     5.5 3.0 3.0
-     2     5.5 3.0 3.0
-     3     6.5 4.0 3.5
-     4     7.5 5.0 4.0
-     5     8.5 6.0 4.5
-     6     9.5 7.0 5.0
-     7     9.5 7.0 5.0
+     1     5.0 3.0 2.0
+     2     5.5 3.5 2.5
+     3     6.0 4.0 3.0
+     4     6.5 4.5 3.0
+     5     7.0 5.0 3.5
+     6     8.0 5.5 4.0
+     7     9.0 6.0 4.5
     ====== === === ===
 
     The maximum cutoff for each order is determined by the minimum cutoff and
@@ -84,9 +84,9 @@ def get_cutoffs(structure: Structure):
     """
     # indexed as min_cutoffs[order][period]
     min_cutoffs = {
-        2: {1: 5.5, 2: 5.5, 3: 6.5, 4: 7.5, 5: 8.5, 6: 9.5, 7: 9.5},
-        3: {1: 3.0, 2: 3.0, 3: 4.0, 4: 5.0, 5: 6.0, 6: 7.0, 7: 7.0},
-        4: {1: 3.0, 2: 3.0, 3: 3.5, 4: 4.0, 5: 4.5, 6: 5.0, 7: 5.0},
+        2: {1: 5.0, 2: 5.5, 3: 6.0, 4: 6.5, 5: 7.0, 6: 8.0, 7: 9.0},
+        3: {1: 3.0, 2: 3.5, 3: 4.0, 4: 4.5, 5: 5.0, 6: 5.5, 7: 6.0},
+        4: {1: 2.0, 2: 2.5, 3: 3.0, 4: 3.0, 5: 3.5, 6: 4.0, 7: 4.5},
     }
     inc = {2: 3, 3: 1.5, 4: 1}
     steps = {2: 0.5, 3: 0.25, 4: 0.25}
@@ -104,11 +104,9 @@ def get_cutoffs(structure: Structure):
     return list(map(list, product(range_two, range_three, range_four)))
 =======
     cutoffs = np.array(list(map(list, product(range_two, range_three, range_four))))
-    logger.info('CUTOFFS \n {}'.format(cutoffs))
     max_cutoff = estimate_maximum_cutoff(AseAtomsAdaptor.get_atoms(supercell_structure))
     logger.info('MAX_CUTOFF \n {}'.format(max_cutoff))    
     good_cutoffs = np.all(cutoffs < np.around(max_cutoff, 4) - 0.0001, axis=1)
-    logger.info('GOOD CUTOFFS \n {}'.format(good_cutoffs))
     return cutoffs[good_cutoffs].tolist()
 >>>>>>> c094a175 (cutoff vs cell_size)
 
@@ -118,6 +116,7 @@ def fit_force_constants(
     supercell_matrix: np.ndarray,
     structures: List["Atoms"],
     all_cutoffs: List[List[float]],
+    bulk_modulus: float,
     imaginary_tol: float = IMAGINARY_TOL,
 #    max_n_imaginary: int = MAX_N_IMAGINARY,
     max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
@@ -208,16 +207,15 @@ def fit_force_constants(
     for i, cutoffs in enumerate(all_cutoffs):
 =======
 
-#    fit_kwargs = fit_kwargs if fit_kwargs else {}
-#    if fit_method == "rfe" and n_jobs == -1:
-#        fit_kwargs["n_jobs"] = 1
+    fit_kwargs = fit_kwargs if fit_kwargs else {}
+    if fit_method == "rfe" and n_jobs == -1:
+        fit_kwargs["n_jobs"] = 1
 
-    logger.info('cutoff_results')
-    cutoff_results = Parallel(n_jobs=-1, backend="multiprocessing")(delayed(_run_cutoffs)(
-        i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix,
+    cutoff_results = Parallel(n_jobs=5, backend="multiprocessing")(delayed(_run_cutoffs)(
+        i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, bulk_modulus,
         fit_method, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
-    logger.info(cutoff_results)
+    logger.info('CUTOFF RESULTS \n {}'.format(cutoff_results))
     
     for result in cutoff_results:
         if result is None:
@@ -253,6 +251,7 @@ def _run_cutoffs(
     parent_structure,
     structures,
     supercell_matrix,
+    bulk_modulus,
     fit_method,
     imaginary_tol,
     fit_kwargs
@@ -268,6 +267,7 @@ def _run_cutoffs(
         logger.info(
             "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
         )
+<<<<<<< HEAD
         sc = get_structure_container(cutoffs, structures)
 <<<<<<< HEAD
         opt = Optimizer(sc.get_fit_data(), fit_method)
@@ -276,21 +276,33 @@ def _run_cutoffs(
         opt = Optimizer(sc.get_fit_data(), fit_method, **fit_kwargs)
         logger.info('{}, {}: FINE UNTIL OPT'.format(i,cutoffs))
 >>>>>>> fddd9681 (get_cutoffs)
+=======
+        return None
+
+    try:
+        sc, cs = get_structure_container(cutoffs, structures)
+        ncut = cs.n_dofs
+        logger.info('SC and CS generated for cutoff: {}, {}'.format(i,cutoffs))
+        opt = Optimizer(sc.get_fit_data(),
+                        fit_method,
+                        [0,ncut],
+                        **fit_kwargs)
+        logger.info('Optimizer set up for cutoff: {}, {}'.format(i,cutoffs))
+>>>>>>> 79348b89 (bulk_mod input)
         opt.train()
-        logger.info('{}, {}: FINE UNTIL TRAIN'.format(i,cutoffs))
+        logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
 
         parameters = enforce_rotational_sum_rules(
             sc.cluster_space, opt.parameters, ["Huang", "Born-Huang"]
         )
-        logger.info('{}, {}: FINE UNTIL SUM RULE'.format(i,cutoffs))
         fcp = ForceConstantPotential(sc.cluster_space, parameters)
-        logger.info('{}, {}: FINE UNTIL FCP'.format(i,cutoffs))
         fcs = fcp.get_force_constants(supercell_atoms)
-        logger.info('{}, {}: FINE UNTIL FCS'.format(i,cutoffs))
+        logger.info('FCS generated for cutoff {}, {}'.format(i,cutoffs))
         n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
-            parent_structure, supercell_matrix, fcs, T_QHA, imaginary_tol
+            parent_structure, supercell_matrix, fcs, bulk_modulus, T_QHA, imaginary_tol
         )
 <<<<<<< HEAD
+<<<<<<< HEAD
 <<<<<<< HEAD
 
         fitting_data["cutoffs"].append(cutoffs)
@@ -322,6 +334,9 @@ def _run_cutoffs(
 =======
         logger.info('evaluate_force_constants success!')
 >>>>>>> fddd9681 (get_cutoffs)
+=======
+        logger.info('evaluate_force_constants success: {}, {}'.format(i,cutoffs))
+>>>>>>> 79348b89 (bulk_mod input)
         return {
             "cutoffs": cutoffs,
             "rmse_test": opt.rmse_test,
@@ -356,7 +371,7 @@ def get_structure_container(
         A hiPhive StructureContainer.
     """
 
-    cs = ClusterSpace(structures[0], cutoffs)
+    cs = ClusterSpace(structures[0], cutoffs, symprec=1e-3, acoustic_sum_rules=True)
     logger.debug(cs.__repr__())
 
     sc = StructureContainer(cs)
@@ -364,13 +379,14 @@ def get_structure_container(
         sc.add_structure(structure)
     logger.debug(sc.__repr__())
 
-    return sc
+    return sc, cs
 
 
 def evaluate_force_constants(
     structure: Structure,
     supercell_matrix: np.ndarray,
-    force_constants: ForceConstants,
+    fcs: ForceConstants,
+    bulk_modulus: float,
     T: List,
     imaginary_tol: float = IMAGINARY_TOL
 ) -> Tuple[int, float, List, List, List]:
@@ -390,40 +406,54 @@ def evaluate_force_constants(
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
 
+    logger.info('EVALUATE FC STARTING')
     fcs2 = fcs.get_fc_array(2)
     fcs3 = fcs.get_fc_array(3)
     parent_phonopy = get_phonopy_structure(structure)
     phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
     vol = phonopy.primitive.get_volume()
     natom = phonopy.primitive.get_number_of_atoms()
+    mesh = supercell_matrix.diagonal()*5
     
     phonopy.set_force_constants(fcs2)
-    phonopy.run_mesh(is_gamma_center=True)
+    logger.info('FCS2 SET')
+    phonopy.set_mesh(mesh,is_eigenvectors=True,is_mesh_symmetry=False) #run_mesh(is_gamma_center=True)
+    logger.info('MESH SET')
     phonopy.run_thermal_properties(temperatures=T)
+    logger.info('Thermal properties successfully run!')
 
-    free_energy = phonopy.get_thermal_properties_dict()["free_energy"]
+    _, free_energy, entropy, Cv = phonopy.get_thermal_properties()
     free_energy *= 1000/sp.constants.Avogadro/eV2J/natom # kJ/mol to eV/atom
-    entropy = phonopy.get_thermal_properties_dict()["entropy"]
     entropy *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
-    Cv = phonopy.get_thermal_properties_dict()["heat_capacity"]
     Cv *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
+    logger.info('Units converted!')
     
     freq = phonopy.mesh.frequencies # in THz
     # find imaginary modes at gamma
 #    phonopy.run_qpoints([0, 0, 0])
 #    gamma_eigs = phonopy.get_qpoints_dict()["frequencies"]
+    logger.info('FREQ \n {}:'.format(freq))
     n_imaginary = int(np.sum(freq < -np.abs(imaginary_tol)))
-    min_frequency = np.min(freq)
+    logger.info('N_IMAGINARY: {}'.format(n_imaginary))
+    min_freq = np.min(freq)
 
-    if n_imeginary > 0:
-        grun, cte = gruneisen(phonopy,fcs2,fcs3,mesh,T,Cv,bulk_mod,vol)
+    if n_imeginary > 0 and bulk_modulus is not None:
+        logger.info('No imaginary modes! Computing Gruneisen and thermal expansion.')
+        grun, cte = gruneisen(phonopy,fcs2,fcs3,mesh,T,Cv,bulk_modulus,vol)
         dLfrac = thermal_expansion(T,cte)
+    elif n_imeginary > 0 and bulk_modulus is None: # need bulk modulus input
+        logger.warning('No imaginary modes, but bulk modulus is not supplied!')
+        logger.warning('Gruneisen and thermal expansion are not calculated.')
+        grun = np.zeros((len(T),3))
+        cte = np.zeros((len(T),3))
+        dLfrac = np.zeros((len(T),3))
     else: # do not calculate these if imaginary modes exist
+        logger.warning('Imaginary modes found!')
         grun = np.zeros((len(T),3))
         cte = np.zeros((len(T),3))
         dLfrac = np.zeros((len(T),3))
         
-    return n_imaginary, min_frequency, free_energy, entropy, Cv, grun, cte, dLfrac
+    return n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac
 
 
 def get_total_grun(
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index ddde2a512..87a5c8305 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -156,8 +156,8 @@ def run_task(self, fw_spec):
         all_forces = loadfn("perturbed_forces.json")
         structure_data = loadfn("structure_data.json")
         parent_structure = structure_data["structure"]
-        supercell_matrix = structure_data["supercell_matrix"]
         supercell_structure = structure_data["supercell_structure"]
+        supercell_matrix = np.array(structure_data["supercell_matrix"])
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
 
         structures = []
@@ -172,7 +172,8 @@ def run_task(self, fw_spec):
 
         logger.info('PARENT \n {}'.format(parent_structure))
         logger.info('SUPERCELL \n {}'.format(supercell_structure))
-        logger.info(fit_method)
+        logger.info('SUPERCELL MATRIX \n {}'.format(supercell_matrix))
+        logger.info('FIT_METHOD {}'.format(fit_method))
         from_get_cutoffs = get_cutoffs(supercell_structure)
         logger.info('SELF.GET_CUTOFFS \n {}'.format(self.get("cutoffs")))
         logger.info('FROM GET_CUTOFFS \n {}'.format(from_get_cutoffs))
@@ -182,6 +183,7 @@ def run_task(self, fw_spec):
             supercell_matrix,
             structures,
             cutoffs,
+            bulk_modulus,
             imaginary_tol,
 #            max_n_imaginary,
             max_imaginary_freq,
@@ -269,6 +271,7 @@ def run_task(self, fw_spec):
             supercell_matrix,
             structures,
             cutoffs,
+            bulk_modulus,
             imaginary_tol,
 #            max_n_imaginary,
             max_imaginary_freq,
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 4defbdfac..59ffc56c0 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -61,6 +61,7 @@ def __init__(
         parents: Optional[Union[Firework, List[Firework]]] = None,
         db_file: str = None,
         cutoffs: Optional[List[List[float]]] = None,
+        bulk_modulus:float = None,
         imaginary_tol: float = IMAGINARY_TOL,
         max_n_imaginary: int = MAX_N_IMAGINARY,
         max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
@@ -72,6 +73,7 @@ def __init__(
         logger.info("INPUT CUTOFF \n {}".format(cutoffs))
         fit_constants = RunHiPhive(
             cutoffs=cutoffs,
+            bulk_modulus=bulk_modulus,
             imaginary_tol=imaginary_tol,
             max_n_imaginary=max_n_imaginary,
             max_imaginary_freq=max_imaginary_freq,
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index e26199890..f7308bb71 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -8,7 +8,7 @@
 from atomate.utils.utils import get_logger
 from atomate.vasp.config import DB_FILE, SHENGBTE_CMD, VASP_CMD
 from atomate.vasp.firetasks import pass_vasp_result
-from atomate.vasp.firetasks.lattice_dynamics import DEFAULT_TEMPERATURE
+from atomate.vasp.firetasks.lattice_dynamics import T_KLAT
 from atomate.vasp.fireworks.core import TransmuterFW
 from atomate.vasp.fireworks.lattice_dynamics import (
     FitForceConstantsFW,
@@ -54,6 +54,7 @@
 
 def get_lattice_dynamics_wf(
     structure: Structure,
+    bulk_modulus: float = None
     common_settings: Dict = None,
     vasp_input_set: Optional[VaspInputSet] = None,
     copy_vasp_outputs: bool = False,
@@ -61,7 +62,7 @@ def get_lattice_dynamics_wf(
     num_supercell_kwargs: Optional[dict] = None,
     perturbed_structure_kwargs: Optional[dict] = None,
     calculate_lattice_thermal_conductivity: bool = False,
-    thermal_conductivity_temperature: Union[float, Dict] = DEFAULT_TEMPERATURE,
+    thermal_conductivity_temperature: Union[float, Dict] = T_Klat,
     shengbte_cmd: str = SHENGBTE_CMD,
     shengbte_fworker: Optional[str] = None,
 ):
@@ -122,11 +123,12 @@ def get_lattice_dynamics_wf(
     common_settings = _get_common_settings(common_settings)
     db_file = common_settings["DB_FILE"]
 
+
     if calculate_lattice_thermal_conductivity:
         if supercell_matrix_kwargs.get("force_diagonal", False):
             warnings.warn(
                 "Diagonal transformation required to calculate lattice thermal "
-                "conductivity using ShengBTE. Forcing diagonal matrix"
+                "conductivity using ShengBTE. Forcing diagonal matrix."
             )
         supercell_matrix_kwargs["force_diagonal"] = True
 
@@ -152,7 +154,7 @@ def get_lattice_dynamics_wf(
     # 2. Fit interatomic force constants from pertrubed structures
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
-        db_file=db_file, spec=allow_fizzled
+        db_file=db_file, spec=allow_fizzled, bulk_modulus=bulk_modulus
     )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 

From c4241109309feb114f2f0a21d089b60ef95e8b82 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 08:52:01 -0700
Subject: [PATCH 110/207] separate fitting

---
 atomate/vasp/analysis/lattice_dynamics.py     | 358 ++++++++++++++----
 atomate/vasp/firetasks/lattice_dynamics.py    | 335 +++++++++-------
 atomate/vasp/fireworks/lattice_dynamics.py    |  30 +-
 .../vasp/workflows/base/lattice_dynamics.py   |  36 +-
 4 files changed, 537 insertions(+), 222 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 699d507c3..1419c6fbd 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -3,6 +3,9 @@
 
 import numpy as np
 import scipy as sp
+import os
+import psutil
+from copy import copy
 
 from atomate.utils.utils import get_logger
 <<<<<<< HEAD
@@ -17,12 +20,16 @@
 >>>>>>> 1e75a82a (imports)
 from hiphive.cutoffs import is_cutoff_allowed, estimate_maximum_cutoff
 from hiphive.fitting import Optimizer
+from hiphive.renormalization import Renormalization
+from hiphive.utilities import get_displacements
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 >>>>>>> 8f4f7e37 (gruneisen and CTE)
 from pymatgen.io.phonopy import get_phonopy_structure
 
+from ase.cell import Cell
+
 from phonopy import Phonopy
 from phono3py.phonon3.gruneisen import Gruneisen
 
@@ -32,16 +39,19 @@
 
 logger = get_logger(__name__)
 
-MAX_IMAGINARY_FREQ = 10  # in THz
 IMAGINARY_TOL = 0.025  # in THz
 #MAX_N_IMAGINARY = np.inf
+#MAX_IMAGINARY_FREQ = 10  # in THz
 
 T_QHA = [i*100 for i in range(16)]
 T_RENORM = [i*100 for i in range(0,16)]
 T_KLAT = [i*100 for i in range(0,16)]
 
 FIT_METHOD = "rfe" #"least-squares"
+
 eV2J = 1.602e-19
+hbar = sp.constants.hbar
+kB = sp.constants.Boltzmann
 
 def get_cutoffs(structure: Structure):
     """
@@ -58,10 +68,10 @@ def get_cutoffs(structure: Structure):
      1     5.0 3.0 2.0
      2     5.5 3.5 2.5
      3     6.0 4.0 3.0
-     4     6.5 4.5 3.0
-     5     7.0 5.0 3.5
-     6     8.0 5.5 4.0
-     7     9.0 6.0 4.5
+     4     7.0 4.5 3.0
+     5     8.0 5.0 3.5
+     6     9.0 5.5 4.0
+     7     10.0 6.0 4.5
     ====== === === ===
 
     The maximum cutoff for each order is determined by the minimum cutoff and
@@ -84,21 +94,29 @@ def get_cutoffs(structure: Structure):
     """
     # indexed as min_cutoffs[order][period]
     min_cutoffs = {
-        2: {1: 5.0, 2: 5.5, 3: 6.0, 4: 6.5, 5: 7.0, 6: 8.0, 7: 9.0},
+        2: {1: 5.0, 2: 5.5, 3: 6.0, 4: 7.0, 5: 8.0, 6: 9.0, 7: 10.0},
         3: {1: 3.0, 2: 3.5, 3: 4.0, 4: 4.5, 5: 5.0, 6: 5.5, 7: 6.0},
         4: {1: 2.0, 2: 2.5, 3: 3.0, 4: 3.0, 5: 3.5, 6: 4.0, 7: 4.5},
     }
+<<<<<<< HEAD
     inc = {2: 3, 3: 1.5, 4: 1}
     steps = {2: 0.5, 3: 0.25, 4: 0.25}
 
     row = min([s.row for s in structure.species])
+=======
+    inc = {2: 2, 3: 1, 4: 0.5}
+    steps = {2: 1, 3: 0.5, 4: 0.5}
+
+    row = min([s.row for s in supercell_structure.species])
+    factor = row/4
+>>>>>>> cc7520c5 (separate fitting)
     mins = {
         2: min_cutoffs[2][row], 3: min_cutoffs[3][row], 4: min_cutoffs[4][row]
     }
 
-    range_two = np.arange(mins[2], mins[2] + inc[2] + steps[2], steps[2])
-    range_three = np.arange(mins[3], mins[3] + inc[3] + steps[3], steps[3])
-    range_four = np.arange(mins[4], mins[4] + inc[4] + steps[4], steps[4])
+    range_two = np.arange(mins[2], mins[2] + factor*(inc[2]+steps[2]), factor*steps[2])
+    range_three = np.arange(mins[3], mins[3] + factor*(inc[3]+steps[3]), factor*steps[3])
+    range_four = np.arange(mins[4], mins[4] + factor*(inc[4]+steps[4]), factor*steps[4])
 
 <<<<<<< HEAD
     return list(map(list, product(range_two, range_three, range_four)))
@@ -116,10 +134,10 @@ def fit_force_constants(
     supercell_matrix: np.ndarray,
     structures: List["Atoms"],
     all_cutoffs: List[List[float]],
-    bulk_modulus: float,
+    separate_fit: bool,
     imaginary_tol: float = IMAGINARY_TOL,
 #    max_n_imaginary: int = MAX_N_IMAGINARY,
-    max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
+#    max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
     fit_method: str = FIT_METHOD,
 <<<<<<< HEAD
 ) -> Tuple["SortedForceConstants", Dict]:
@@ -176,16 +194,15 @@ def fit_force_constants(
     fitting_data = {
         "cutoffs": [],
         "rmse_test": [],
-        "n_imaginary": [],
-        "min_frequency": [],
-        "temperature": [],
-        "free_energy": [],
-        "entropy": [],
-        "heat_capacity": [],
+#        "n_imaginary": [],
+#        "min_frequency": [],
+#        "temperature": [],
+#        "free_energy": [],
+#        "entropy": [],
+#        "heat_capacity": [],
         "fit_method": fit_method,
         "imaginary_tol": imaginary_tol,
 #        "max_n_imaginary": max_n_imaginary,
-        "max_imaginary_freq": max_imaginary_freq,
     }
 
     supercell_atoms = structures[0]
@@ -211,9 +228,10 @@ def fit_force_constants(
     if fit_method == "rfe" and n_jobs == -1:
         fit_kwargs["n_jobs"] = 1
 
-    cutoff_results = Parallel(n_jobs=5, backend="multiprocessing")(delayed(_run_cutoffs)(
-        i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, bulk_modulus,
-        fit_method, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
+    logger.info('CPU COUNT: {}'.format(os.cpu_count()))
+    cutoff_results = Parallel(n_jobs=12, backend="multiprocessing")(delayed(_run_cutoffs)(
+        i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, fit_method,
+        separate_fit, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
     logger.info('CUTOFF RESULTS \n {}'.format(cutoff_results))
     
@@ -223,12 +241,8 @@ def fit_force_constants(
 
         fitting_data["cutoffs"].append(result["cutoffs"])
         fitting_data["rmse_test"].append(result["rmse_test"])
-        fitting_data["n_imaginary"].append(result["n_imaginary"])
-        fitting_data["min_frequency"].append(result["min_frequency"])
-        fitting_data["temperature"].append(result["temperature"])
-        fitting_data["free_energy"].append(result["free_energy"])
-        fitting_data["entropy"].append(result["entropy"])
-        fitting_data["heat_capcity"].append(result["heat_capacity"])
+#        fitting_data["n_imaginary"].append(result["n_imaginary"])
+#        fitting_data["min_frequency"].append(result["min_frequency"])
 
         if (
             result["rmse_test"] < best_fit["rmse_test"]
@@ -251,11 +265,11 @@ def _run_cutoffs(
     parent_structure,
     structures,
     supercell_matrix,
-    bulk_modulus,
     fit_method,
+    separate_fit,
     imaginary_tol,
     fit_kwargs
-):
+) -> Dict:
 
     logger.info(
         "Testing cutoffs {} out of {}: {}".format(i + 1, n_cutoffs, cutoffs)
@@ -279,19 +293,36 @@ def _run_cutoffs(
 =======
         return None
 
-    try:
-        sc, cs = get_structure_container(cutoffs, structures)
-        ncut = cs.n_dofs
-        logger.info('SC and CS generated for cutoff: {}, {}'.format(i,cutoffs))
+    cs = ClusterSpace(supercell_atoms, cutoffs, symprec=1e-3, acoustic_sum_rules=True)
+    logger.debug(cs.__repr__())
+    n2nd = cs.get_n_dofs_by_order(2)
+    nall = cs.n_dofs
+    
+    if separate_fit:
+        logger.info('Fitting harmonic force constants separately')
+        sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=None)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
-                        [0,ncut],
+                        [0,2nd],
                         **fit_kwargs)
+<<<<<<< HEAD
         logger.info('Optimizer set up for cutoff: {}, {}'.format(i,cutoffs))
 >>>>>>> 79348b89 (bulk_mod input)
+=======
+>>>>>>> cc7520c5 (separate fitting)
         opt.train()
-        logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
+        param_harmonic = opt.parameters # harmonic force constant parameters
+        
+        logger.info('Fitting anharmonic force constants separately')
+        sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=param2)
+        opt = Optimizer(sc.get_fit_data(),
+                        fit_method,
+                        [2nd,nall],
+                        **fit_kwargs)
+        opt.train()
+        param_anharmonic = opt.parameters # anharmonic force constant parameters
 
+<<<<<<< HEAD
         parameters = enforce_rotational_sum_rules(
             sc.cluster_space, opt.parameters, ["Huang", "Born-Huang"]
         )
@@ -358,6 +389,58 @@ def _run_cutoffs(
 
 def get_structure_container(
     cutoffs: List[float], structures: List["Atoms"]
+=======
+        parameters = np.concatenate((param_harmonic,param_anharmonic)) # combine 
+        assert(nall==len(parameters))
+        logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
+        
+    else:
+        logger.info('Fitting all force constants in one shot')
+        sc = get_structure_container(cs, structures, separate_fit, ncut=None, param2=None)
+        opt = Optimizer(sc.get_fit_data(),
+                        fit_method,
+                        [0,nall],
+                        **fit_kwargs)
+        opt.train()
+        parameters = opt.parameters
+        logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
+    
+    parameters = enforce_rotational_sum_rules(
+        sc.cluster_space, parameters, ["Huang", "Born-Huang"]
+    )
+    fcp = ForceConstantPotential(cs, parameters)
+    fcs = fcp.get_force_constants(supercell_atoms)
+    logger.info('FCS generated for cutoff {}, {}'.format(i,cutoffs))
+
+#    n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
+#        parent_structure, supercell_matrix, fcs, bulk_modulus, T_QHA, imaginary_tol
+#    )
+
+    return {
+        "cutoffs": cutoffs,
+        "rmse_test": opt.rmse_test,
+#        "n_imaginary": n_imaginary,
+#        "min_frequency": min_freq,
+#        "temperature": T_QHA,
+#        "free_energy": free_energy,
+#        "entropy": entropy,
+#        "heat_capacity": Cv,
+#        "thermal_expansion": cte,
+        "cluster_space": sc.cluster_space,
+        "parameters": parameters,
+        "force_constants": fcs
+    }
+    #except Exception:
+    #    return None
+
+
+def get_structure_container(
+        cs: ClusterSpace,
+        structures: List["Atoms"],
+        separate_fit: bool,
+        ncut: int,
+        param2: np.ndarray
+>>>>>>> cc7520c5 (separate fitting)
 ) -> "StructureContainer":
     """
     Get a hiPhive StructureContainer from cutoffs and a list of atoms objects.
@@ -371,25 +454,42 @@ def get_structure_container(
         A hiPhive StructureContainer.
     """
 
-    cs = ClusterSpace(structures[0], cutoffs, symprec=1e-3, acoustic_sum_rules=True)
-    logger.debug(cs.__repr__())
-
     sc = StructureContainer(cs)
+    saved_strutures = []
     for structure in structures:
-        sc.add_structure(structure)
+        displacements = get_displacements(atoms, supercell_atoms)
+        mean_displacements = np.linalg.norm(displacements,axis=1).mean()
+        if not separate_fit: # fit all
+            sc.add_structure(structure)
+        else: # fit separately
+            if param2 is None: # for harmonic fitting
+                sc.add_structure(structure) if mean_displacements <= 0.05
+            else: # for anharmonic fitting
+                sc.add_structure(structure) if mean_displacements >= 0.2
+                saved_structures.append(structure) if mean_displacements >= 0.2
+    if separate_fit and param2 is not None:
+        A_mat = sc.get_fit_data()[0] # displacement matrix
+        f_vec = sc.get_fit_data()[1] # force vector
+        new_force = f_vec - np.dot(A_mat[:,:ncut],param2) # subract harmonic forces
+        sc.delete_all_structures()
+        for i, structure in enumerate(saved_structures):
+            naroms = structure.et_global_number_of_atoms()
+            ndisp = natoms*3
+            structure.set_array('forces',new_force[i*ndisp:(i+1)*ndisp].reshape(natoms,3))
+            sc.add_structure(structure)
+
     logger.debug(sc.__repr__())
 
-    return sc, cs
+    return sc
 
 
-def evaluate_force_constants(
+def harmonic_properties(
     structure: Structure,
     supercell_matrix: np.ndarray,
     fcs: ForceConstants,
-    bulk_modulus: float,
     T: List,
     imaginary_tol: float = IMAGINARY_TOL
-) -> Tuple[int, float, List, List, List]:
+) -> Tuple[Dict,Phonopy]:
     """
     Uses the force constants to extract phonon properties. Used for comparing
     the accuracy of force constant fits.
@@ -406,19 +506,16 @@ def evaluate_force_constants(
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
 
-    logger.info('EVALUATE FC STARTING')
+    logger.info('Evaluating harmonic properties.')
     fcs2 = fcs.get_fc_array(2)
     fcs3 = fcs.get_fc_array(3)
     parent_phonopy = get_phonopy_structure(structure)
     phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
-    vol = phonopy.primitive.get_volume()
     natom = phonopy.primitive.get_number_of_atoms()
-    mesh = supercell_matrix.diagonal()*5
+    mesh = supercell_matrix.diagonal()*4
     
     phonopy.set_force_constants(fcs2)
-    logger.info('FCS2 SET')
     phonopy.set_mesh(mesh,is_eigenvectors=True,is_mesh_symmetry=False) #run_mesh(is_gamma_center=True)
-    logger.info('MESH SET')
     phonopy.run_thermal_properties(temperatures=T)
     logger.info('Thermal properties successfully run!')
 
@@ -426,34 +523,60 @@ def evaluate_force_constants(
     free_energy *= 1000/sp.constants.Avogadro/eV2J/natom # kJ/mol to eV/atom
     entropy *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
     Cv *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
-    logger.info('Units converted!')
     
     freq = phonopy.mesh.frequencies # in THz
     # find imaginary modes at gamma
 #    phonopy.run_qpoints([0, 0, 0])
 #    gamma_eigs = phonopy.get_qpoints_dict()["frequencies"]
-    logger.info('FREQ \n {}:'.format(freq))
     n_imaginary = int(np.sum(freq < -np.abs(imaginary_tol)))
-    logger.info('N_IMAGINARY: {}'.format(n_imaginary))
     min_freq = np.min(freq)
 
-    if n_imeginary > 0 and bulk_modulus is not None:
-        logger.info('No imaginary modes! Computing Gruneisen and thermal expansion.')
-        grun, cte = gruneisen(phonopy,fcs2,fcs3,mesh,T,Cv,bulk_modulus,vol)
-        dLfrac = thermal_expansion(T,cte)
-    elif n_imeginary > 0 and bulk_modulus is None: # need bulk modulus input
-        logger.warning('No imaginary modes, but bulk modulus is not supplied!')
-        logger.warning('Gruneisen and thermal expansion are not calculated.')
-        grun = np.zeros((len(T),3))
-        cte = np.zeros((len(T),3))
-        dLfrac = np.zeros((len(T),3))
+    if n_imaginary == 0:
+        logger.info('No imaginary modes!')
     else: # do not calculate these if imaginary modes exist
         logger.warning('Imaginary modes found!')
+
+    return {
+        "temperature": T,
+        "free_energy": free_energy,
+        "entropy": entropy,
+        "heat_capacity": Cv,
+        "n_imaginary": n_imaginary
+        }, phonopy
+
+
+def anharmonic_properties(
+    phonopy: Phonopy,
+    fcs: ForceConstants,
+    T: List,
+    Cv: np.ndarray,
+    n_imaginary: float,
+    bulk_modulus: float = None
+) -> Tuple[Dict, Phonopy]:
+
+    if n_imaginary == 0:
+        logger.info('Evaluating anharmonic properties')
+        fcs2 = fcs.get_fc_array(2)
+        fcs3 = fcs.get_fc_array(3)
+        grun, cte = gruneisen(phonopy,fcs2,fcs3,T,Cv,bulk_modulus=bulk_modulus)
+        if type(bulk_modulus) is float or int:
+            dLfrac = thermal_expansion(T,cte)
+        else:
+            logger.warning('Thermal expansion cannot be calculated without bulk modulus input. Set to 0.')
+            cte = np.zeros((len(T),3))
+            dLfrac = np.zeros((len(T),3))
+    else: # do not calculate these if imaginary modes exist
+        logger.warning('Gruneisen and thermal expansion cannot be calculated with imaginary modes. All set to 0.')
         grun = np.zeros((len(T),3))
         cte = np.zeros((len(T),3))
         dLfrac = np.zeros((len(T),3))
-        
-    return n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac
+
+    return {
+        "temperature": T,
+        "gruneisen": grun,
+        "thermal_expansion": cte,
+        "expansion_ratio": dLfrac,
+        }, phonopy
 
 
 def get_total_grun(
@@ -506,16 +629,16 @@ def gruneisen(
         phonopy: Phonopy,
         fcs2: np.ndarray,
         fcs3: np.ndarray,
-        mesh: List,
         temperature: List,
         Cv: np.ndarray, # in eV/K/atom
-        bulk_mod: float, # in GPa
-        vol: float # in A^3
+        bulk_modulus: float = None # in GPa
 ) -> Tuple[List,List]:
-    
+
     gruneisen = Gruneisen(fcs2,fcs3,phonopy.supercell,phonopy.primitive)
-    gruneisen.set_sampling_mesh(mesh,is_gamma_center=True)
+    gruneisen.set_sampling_mesh(phonopy.mesh_numbers,is_gamma_center=True)
+    logger.info('Memory use before Gruneisen: {} %'.format(psutil.virtual_memory().percent))
     gruneisen.run()
+    logger.info('Memory use after Gruneisen: {} %'.format(psutil.virtual_memory().percent))
     grun = gruneisen.get_gruneisen_parameters() # (nptk,nmode,3,3)
     omega = gruneisen._frequencies
     qp = gruneisen._qpoints
@@ -523,14 +646,18 @@ def gruneisen(
     grun_tot = list()
     for temp in temperature:
         grun_tot.append(get_total_grun(omega,grun,kweight,temp))
-    grun_tot = np.array(np.nan_to_num(np.array(grun_tot)))
-    Cv *= eV2J*phonopy.primitive.get_number_of_atoms() # eV/K/atom to J/K
-    # linear thermal expansion coefficient     
-    cte = grun_tot*(Cv.repeat(3).reshape((len(Cv),3)))/(vol/10**30)/(bulk_mod*10**9)/3
-    cte = np.nan_to_num(cte)    
-    logger.info('Frequency : {}'.format(np.sort(omega.flatten())))
-    logger.info('Gruneisen : {}'.format(grun_tot))
-    logger.info('CTE : {}'.format(cte))    
+    grun_tot = np.nan_to_num(np.array(grun_tot))
+    
+    # linear thermal expansion coefficient
+    if bulk_modulus is None:
+        cte = None
+    else:
+        Cv *= eV2J*phonopy.primitive.get_number_of_atoms() # eV/K/atom to J/K 
+        vol = phonopy.primitive.get_volume()
+        cte = grun_tot*(Cv.repeat(3).reshape((len(Cv),3)))/(vol/10**30)/(bulk_modulus*10**9)/3
+        cte = np.nan_to_num(cte)    
+        logger.info('Gruneisen : {}'.format(grun_tot))
+        logger.info('CTE : {}'.format(cte))    
     return grun_tot, cte
 
 
@@ -562,3 +689,82 @@ def thermal_expansion(
         except:
             raise ValueError('Designated T does not exist in the temperature array!')
 
+
+def renormalization(
+        structure: Structure,
+        supercell_matrix: np.ndarray,
+        cs: ClusterSpace,
+        fcs: ForceConstants,
+        param: np.ndarray,
+        T: float,
+        nconfig: int,
+        conv_tresh: float,
+        bulk_modulus: float = None,
+        imaginary_tol: float = IMAGINARY_TOL,
+        fit_method: str = None
+) -> Dict:
+    """
+    Uses the force constants to extract phonon properties. Used for comparing
+    the accuracy of force constant fits.
+
+    Args:
+        structure: The parent structure.
+        supercell_matrix: The supercell transformation matrix.
+        fcs: ForceConstants from previous fitting or renormalization
+        imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
+            in THz.                                                                                                                                                                                        
+
+    Returns:
+        A tuple of the number of imaginary modes at Gamma, the minimum phonon
+        frequency at Gamma, and the free energy, entropy, and heat capacity
+    """
+    renorm = Renormalization(cs,fcs,param,T,fit_method)
+    fcp, fcs, param = renorm.renormalize(nconfig,'pseudoinverse',conv_tresh)
+
+    renorm_data, phonopy = harmonic_properties(
+        structure, supercell_matrix, fcs, [T], imaginary_tol
+    )
+
+    if renorm_data["n_imaginary"] ==0:
+        logger.info('Renormalized phonon is completely real at T = {} K!'.format(T))
+        anharmonic_data, phonopy = anharmonic_properties(
+            phonopy, fcs, [T], thermal_data["heat_capacity"], n_imaginary, bulk_modulus=bulk_modulus
+	)
+    else:
+        anharmonic_data = dict()
+        anharmonic_data["gruneisen"] = np.array([[0,0,0]])
+        anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
+    renorm_data.update(anharmonic_data)
+    renorm_data["fcp"] = fcp
+    renorm_data["fcs"] = fcs
+    renorm_data["param"] = param
+    
+    return renorm_data
+
+
+
+def setup_TE_renorm(parent_structure,temperatures,dLfracs):
+    parent_structure_TE = []
+    cs_TE = []
+    fcs_TE = []
+    for t, (T,dLfrac) in enumerate(zip(temperatures,dLfracs)):
+        new_atoms = AseAtomsAdaptor.get_atoms(parent_structure)
+        new_cell = Cell(np.transpose([new_atoms.get_cell()[:,i]*(1+dLfrac[0,i]) for i in range(3)]))
+        new_atoms.set_cell(new_cell,scale_atoms=True)
+        new_parent_structure = AseAtomsAdaptor.get_structure(new_atoms)
+        new_supercell_atoms = AseAtomsAdaptor.get_atoms(new_parent_structure*supercell_matrix)
+        new_cutoffs = [i*(1+np.linalg.norm(dLfrac)) for i in cutoffs]
+        while True:
+            new_cs = ClusterSpace(atoms,new_cutoffs,1e-3,acoustic_sum_rules=True)
+            if cs_TD.n_dofs == cs.n_dofs:
+                break
+            elif cs_TD.n_dofs > cs.n_dofs:
+                new_cutoffs = [i*0.999 for i in new_cutoffs]
+            elif cs_TD.n_dofs < cs.n_dofs:
+                new_cutoffs = [i*1.001 for i in new_cutoffs]
+        cs_TE.append(new_cs)
+        parent_structure_TE.append(new_parent_structure)
+        new_fcp = ForceConstantsPotential(new_cs,param_real[t])
+        fcs_TE.append(new_fcp.get_force_constants(new_supercell_atoms))
+
+        return parent_structure_TE, cs_TE, fcs_TE
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 87a5c8305..5a5752cee 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -6,24 +6,29 @@
 from pathlib import Path
 
 import numpy as np
+from joblib import Parallel, delayed
+
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
 from pymongo import ReturnDocument
 
 from atomate.utils.utils import env_chk, get_logger
+from atomate.vasp.database import VaspCalcDb
+from atomate.vasp.drones import VaspDrone
 from atomate.vasp.analysis.lattice_dynamics import (
     FIT_METHOD,
     IMAGINARY_TOL,
-    MAX_IMAGINARY_FREQ,
+#    MAX_IMAGINARY_FREQ,
 #    MAX_N_IMAGINARY,
     T_QHA,
     T_RENORM,
     T_KLAT,
     fit_force_constants,
+    harmonic_properties,
+    anharmonic_properties,
+    renormalization,
     get_cutoffs
 )
-from atomate.vasp.database import VaspCalcDb
-from atomate.vasp.drones import VaspDrone
 
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 
@@ -38,8 +43,8 @@
 
 try:
     import hiphive
+    from hiphive import ForceConstants
     from hiphive.utilities import get_displacements
-    from hiphive.renormalization import Renormalization
 except ImportError:
     logger.info('Could not import hiphive!')
     hiphive = False
@@ -124,6 +129,9 @@ class RunHiPhive(FiretaskBase):
         cutoffs (Optional[list[list]]): A list of cutoffs to trial. If None,
             a set of trial cutoffs will be generated based on the structure
             (default).
+        separate_fit: If True, harmonic and anharmonic force constants are fit
+            separately and sequentially, harmonic first then anharmonic. If
+            False, then they are all fit in one go. Default is False.
         imaginary_tol (float): Tolerance used to decide if a phonon mode
             is imaginary, in THz.
         max_n_imaginary (int): Maximum number of imaginary modes allowed in the
@@ -138,9 +146,11 @@ class RunHiPhive(FiretaskBase):
 
     optional_params = [
         "cutoffs",
+        "separate_fit",
+        "bulk_modulus",
         "imaginary_tol",
-        "max_n_imaginary",
-        "max_imaginary_freq",
+#        "max_n_imaginary",
+#        "max_imaginary_freq",
         "fit_method",
     ]
 
@@ -148,10 +158,11 @@ class RunHiPhive(FiretaskBase):
     def run_task(self, fw_spec):
 
 #        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
-        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
+#        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
         fit_method = self.get("fit_method", FIT_METHOD)
-
+        separate_fit = self.get('separate_fit', False)
+        
         all_structures = loadfn("perturbed_structures.json")
         all_forces = loadfn("perturbed_forces.json")
         structure_data = loadfn("structure_data.json")
@@ -159,6 +170,7 @@ def run_task(self, fw_spec):
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = np.array(structure_data["supercell_matrix"])
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
+        bulk_modulus = self.get("bulk_modulus")
 
         structures = []
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
@@ -174,23 +186,32 @@ def run_task(self, fw_spec):
         logger.info('SUPERCELL \n {}'.format(supercell_structure))
         logger.info('SUPERCELL MATRIX \n {}'.format(supercell_matrix))
         logger.info('FIT_METHOD {}'.format(fit_method))
-        from_get_cutoffs = get_cutoffs(supercell_structure)
-        logger.info('SELF.GET_CUTOFFS \n {}'.format(self.get("cutoffs")))
-        logger.info('FROM GET_CUTOFFS \n {}'.format(from_get_cutoffs))
         logger.info('FINAL INPUT CUTOFFS \n {}'.format(cutoffs))
+        
         fcs, param, cs, fitting_data = fit_force_constants(
             parent_structure,
             supercell_matrix,
             structures,
             cutoffs,
-            bulk_modulus,
+            separate_fit,
             imaginary_tol,
 #            max_n_imaginary,
-            max_imaginary_freq,
+#            max_imaginary_freq,
             fit_method
         )
 
+        thermal_data, phonopy = harmonic_properties(
+            parent_structure, supercell_matrix, fcs, T_QHA, imaginary_tol
+        )
+        anharmonic_data, phonopy = anharmonic_properties(
+            phonopy, fcs, T_QHA, thermal_data["heat_capacity"],
+            thermal_data["n_imaginary"], bulk_modulus=bulk_modulus
+        )
+
+        fitting_data["n_imaginary"] = thermal_data.pop("n_imaginary")
+        thermal_data.update(anharmonic_data)
         dumpfn(fitting_data, "fitting_data.json")
+        dumpfn(thermal_data, "thermal_data_qha.json")
 
 #        if force_constants is None:
 #            # fitting failed
@@ -203,15 +224,15 @@ def run_task(self, fw_spec):
         logger.info("Writing cluster space and force_constants")
         logger.info("{}".format(type(fcs)))
         fcs.write("force_constants.fcs")
-        np.savetxt('parameters.txt',parameters)
+        np.savetxt('parameters.txt',param)
         cs.write('cluster_space.cs')
 
         if fitting_data["n_imaginary"] == 0:
             logger.info("No imaginary modes! Writing ShengBTE files")
             atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-            fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
+            fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms, order=3)
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
-        elif fitting_data["n_imaginary"] > 0:
+        elif n_imaginary > 0:
             logger.info("Imaginary modes exist! ShengBTE files not written. You may want to perform phonon renormalization.")
 
 
@@ -233,71 +254,94 @@ class RunHiPhiveRenorm(FiretaskBase):
             the final fitted force constant solution. If this criteria is not
             reached by any cutoff combination this FireTask will fizzle.
         param (np.ndarray): array of force constant parameters
+        cutoffs (np.ndarray): cutoffs used for best fitting
+   
     Optional parameter:
         T_renorm (List): list of temperatures to perform renormalization - default is T_RENORM
+        bulk_modulus (float): manually input bulk modulus - necessary for thermal expansion
+        renorm_with_te (bool): if True, 
     """
 
-    required_params = ["cs","fcs","param"]
-    optional_params = ["T_renorm"]
+    required_params = ["cs","fcs","param","cutoff"]
+    optional_params = ["T_renorm","bulk_modulus","renorm_with_te","fit_method"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
 
-        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
-        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
+#        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
+#        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
-        T_renorm = self.get("T_renorm", T_RENORM)
+        fit_method = self.get("fit_method", FIT_METHOD)
 
-        all_structures = loadfn("perturbed_structures.json")
-        all_forces = loadfn("perturbed_forces.json")
         structure_data = loadfn("structure_data.json")
         parent_structure = structure_data["structure"]
-        supercell_matrix = structure_data["supercell_matrix"]
         supercell_structure = structure_data["supercell_structure"]
-
-        structures = []
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
-        for structure, forces in zip(all_structures, all_forces):
-            atoms = AseAtomsAdaptor.get_atoms(structure)
-            displacements = get_displacements(atoms, supercell_atoms)
-            atoms.new_array("displacements", displacements)
-            atoms.new_array("forces", forces)
-            atoms.positions = supercell_atoms.get_positions()
-            structures.append(atoms)
-
-        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        force_constants, fitting_data = fit_force_constants(
-            parent_structure,
-            supercell_matrix,
-            structures,
-            cutoffs,
-            bulk_modulus,
-            imaginary_tol,
-#            max_n_imaginary,
-            max_imaginary_freq,
-            fit_method,
-        )
+        supercell_matrix = np.array(structure_data["supercell_matrix"])
 
-        dumpfn(fitting_data, "fitting_data.json")        
+        cs = self.get("cs")
+        fcs = self.get("fcs")
+        param = self.get("param")
+        bulk_modulus = self.get("bulk_modulus")
+        T_renorm = self.get("T_renorm", T_RENORM)
 
-        if force_constants is None:
-            # fitting failed
-            raise RuntimeError(
-                "Could not find a force constant solution with less than {} "
-                "imaginary modes.\n"
-                "Fitting results: {}".format(max_n_imaginary, fitting_data)
-            )
-        
+        renorm_results = Parallel(n_jobs=2, backend="multiprocessing")(delayed(renormalization)(
+            parent_structure, supercell_matrix, cs, fcs, param, T, nconfig, conv_thresh, imaginary_tol
+        ) for t, T in enumerate(T_renorm))
+
+        T_real = []
+        cte_real = []
+        fcs_real = []
+        param_real = []
+        for result in renorm_results:
+            if result is None:
+                continue
+            elif result["n_imaginary"] > 0 or bulk_modulus is None:
+                fcs = result["fcs"][0]
+                fcs.write("force_constants_{}K.fcs".format(T))
+                np.savetxt('parameters_{}K.txt'.format(T),result["param"][0])
+            else:
+                T_real = T_real + result["temperature"]
+                cte_real = cte_real + result["thermal_expansion"]
+                fcs_real = fcs_real + result["fcs"]
+                param_real = param_real + result["param"]
+        if len(T_real)==0:
+            pass
+        elif len(T_real)==1 and T_real[0]==0:
+            fcs = result["fcs"][0]
+            fcs.write("force_constants_{}K.fcs".format(T))
+            np.savetxt('parameters_{}K.txt'.format(T),result["param"][0])
         else:
-            logger.info("Writing force constants.")
-            force_constants.write("force_constants.fcs")
-
-            atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-            force_constants.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms)
-            force_constants.write_to_phonopy(
-                "FORCE_CONSTANTS_2ND", format="text"
-            )
-            
+            ind = np.argsort(np.array(T_real))
+            T_real = list(np.array(T_real)[ind])
+            cte_real = list(np.array(cte_real)[ind])
+            dLfrac_real = thermal_expansion(T_real,cte_real)
+            parent_structure_TE, cs_TE, fcs_TE = setup_TE_renorm(parent_structure,T_real,dLfrac_real)
+            renorm_results = Parallel(n_jobs=2, backend="multiprocessing")(delayed(renormalization)(
+                parent_structure_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param, T, nconfig, conv_thresh, imaginary_tol
+            ) for t, T in enumerate(T_real))
+
+            logger.info("Writing renormalized results")
+            thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
+                            "gruneisen","thermal_expansion","expansion_ratio"]
+            thermal_data = {key: [] for key in thermal_keys}
+            for t, result in enumerate(renorm_results):
+                T = result["temperature"][0]
+                fcs = result["fcs"][0]
+                fcs.write("force_constants_{}K.fcs".format(T))
+                np.savetxt('parameters_{}K.txt'.format(T),result["param"][0])
+                for key in thermal_keys:
+                    thermal_data[key].append(result[key][0])
+                if result["n_imaginary"] > 0:
+                    logger.warning('Imaginary modes generated for {} K!'.format(T))
+                    logger.warning('Renormalization with thermal expansion may have failed')
+                    logger.warning('ShengBTE files not written')
+                else:
+                    logger.info("No imaginary modes! Writing ShengBTE files")
+                    fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(T), format="text")
+
+            thermal_data.pop("n_imaginary")                    
+            dumpfn(thermal_data, "thermal_data_renorm.json")
 
         
 @explicit_serialize
@@ -314,6 +358,9 @@ class ForceConstantsToDb(FiretaskBase):
             perturbed structure calculations.
 
     Optional parameters:
+        renormalized (bool): Whether FC resulted from original fitting (False)
+            or renormalization process (True) determines how data are stored. 
+            Default is False.
         mesh_density (float): The density of the q-point mesh used to calculate
             the phonon density of states. See the docstring for the ``mesh``
             argument in Phonopy.init_mesh() for more details.
@@ -322,17 +369,16 @@ class ForceConstantsToDb(FiretaskBase):
     """
 
     required_params = ["db_file"]
-    optional_params = ["mesh_density", "additional_fields"]
+    optional_params = ["renormalized","mesh_density", "additional_fields"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
-        from hiphive.force_constants import ForceConstants
 
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+        renormalized = self.get("renormalized", False)
+        mesh_density = self.get("mesh_density", MESH_DENSITY)
 
-        fc = ForceConstants.read("force_constants.fcs")
-        fitting_data = loadfn("fitting_data.json")
         structure_data = loadfn("structure_data.json")
         forces = loadfn("perturbed_forces.json")
         structures = loadfn("perturbed_structures.json")
@@ -341,66 +387,61 @@ def run_task(self, fw_spec):
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = structure_data["supercell_matrix"]
 
-        phonopy_fc = fc.get_fc_array(order=2)
-
-        logger.info("Getting uniform phonon band structure.")
-        uniform_bs = get_phonon_band_structure_from_fc(
-            structure, supercell_matrix, phonopy_fc
-        )
-
-        logger.info("Getting line mode phonon band structure.")
-        lm_bs = get_phonon_band_structure_symm_line_from_fc(
-            structure, supercell_matrix, phonopy_fc
-        )
-
-        logger.info("Getting phonon density of states.")
-        mesh_density = self.get("mesh_density", MESH_DENSITY)
-        dos = get_phonon_dos_from_fc(
-            structure, supercell_matrix, phonopy_fc, mesh_density=mesh_density
-        )
-
-        logger.info("Inserting phonon objects into database.")
-        dos_fsid, _ = mmdb.insert_gridfs(
-            dos.to_json(), collection="phonon_dos_fs"
-        )
-        uniform_bs_fsid, _ = mmdb.insert_gridfs(
-            uniform_bs.to_json(), collection="phonon_bandstructure_fs"
-        )
-        lm_bs_fsid, _ = mmdb.insert_gridfs(
-            lm_bs.to_json(), collection="phonon_bandstructure_fs"
-        )
-
-        logger.info("Inserting force constants into database.")
-        fc_json = json.dumps(
-            {str(k): v.tolist() for k, v in fc.get_fc_dict().items()}
-        )
-        fc_fsid, _ = mmdb.insert_gridfs(
-            fc_json, collection="phonon_force_constants_fs"
-        )
-
-        data = {
-            "structure": structure.as_dict(),
-            "supercell_matrix": supercell_matrix,
-            "supercell_structure": supercell_structure.as_dict(),
-            "perturbed_structures": [s.as_dict() for s in structures],
-            "perturbed_forces": [f.tolist() for f in forces],
-            "fitting_data": fitting_data,
-            "force_constants_fs_id": fc_fsid,
-            "tags": fw_spec.get("tags", None),
-            "formula_pretty": structure.composition.reduced_formula,
-            "phonon_dos_fs_id": dos_fsid,
-            "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-            "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-            "created_at": datetime.utcnow(),
-        }
-        data.update(self.get("additional_fields", {}))
-
-        # Get an id for the force constants
-        fitting_id = _get_fc_fitting_id(mmdb)
-        metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
-        data.update(metadata)
+        if renormalized: # FC from renormalization
+            thermal_data = loadfn("thermal_data_renorm.json")
+            temperature = thermal_data["temperature"]
+            for t, T in enumerate(temperature):
+                ## err should I collect results for all T and push data at once,
+                ## or push data for each T individually?
+                fcs = ForceConstants.read("force_constants_{}K.fcs")
+                phonopy_fc = fcs.get_fc_array(order=2)
+                dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                    structure, supercell_matrix, phonopy_fc, mesh_density, mmdb
+                )
+                data = {
+                    "thermal_data": thermal_data,
+                    "force_constants_fs_id": fc_fsid,
+                    "tags": fw_spec.get("tags", None),
+                    "phonon_dos_fs_id": dos_fsid,
+                    "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+                    "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+                    "created_at": datetime.utcnow(),
+                }
+                data.update(self.get("additional_fields", {}))                
+        else: # FC directly from fitting
+            fitting_data = loadfn("fitting_data.json")
+            thermal_data = loadfn("thermal_data_qha.json")
+            fcs = ForceConstants.read("force_constants.fcs")
+
+            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                structure, supercell_matrix, fcs, mesh_density, mmdb
+            )
 
-        mmdb.db.lattice_dynamics.insert_one(data)
+            data = {
+                "structure": structure.as_dict(),
+                "supercell_matrix": supercell_matrix,
+                "supercell_structure": supercell_structure.as_dict(),
+                "perturbed_structures": [s.as_dict() for s in structures],
+                "perturbed_forces": [f.tolist() for f in forces],
+                "fitting_data": fitting_data,
+                "thermal_data": thermal_data,
+                "force_constants_fs_id": fc_fsid,
+                "tags": fw_spec.get("tags", None),
+                "formula_pretty": structure.composition.reduced_formula,
+                "phonon_dos_fs_id": dos_fsid,
+                "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+                "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+                "created_at": datetime.utcnow(),
+            }
+            data.update(self.get("additional_fields", {}))
+
+            # Get an id for the force constants
+            fitting_id = _get_fc_fitting_id(mmdb)
+            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+            data.update(metadata)
+            mmdb.db.lattice_dynamics.insert_many(data)  # WHAT TO DO HERE?
+#            mmdb.db.lattice_dynamics.insert_one(data)
+            
         logger.info("Finished inserting force constants")
 
         return FWAction(update_spec=metadata)
@@ -549,3 +590,43 @@ def _get_fc_fitting_id(mmdb: VaspCalcDb) -> int:
         fc_id = fc_id["c"]
 
     return fc_id
+
+
+def _get_fc_fsid(structure, supercell_matrix, fcs, mesh_density, mmdb):
+    phonopy_fc = fcs.get_fc_array(order=2)
+    
+    logger.info("Getting uniform phonon band structure.")
+    uniform_bs = get_phonon_band_structure_from_fc(
+        structure, supercell_matrix, phonopy_fc
+    )
+    
+    logger.info("Getting line mode phonon band structure.")
+    lm_bs = get_phonon_band_structure_symm_line_from_fc(
+        structure, supercell_matrix, phonopy_fc
+    )
+    
+    logger.info("Getting phonon density of states.")
+    dos = get_phonon_dos_from_fc(
+        structure, supercell_matrix, phonopy_fc, mesh_density=mesh_density
+    )
+    
+    logger.info("Inserting phonon objects into database.")
+    dos_fsid, _ = mmdb.insert_gridfs(
+        dos.to_json(), collection="phonon_dos_fs"
+    )
+    uniform_bs_fsid, _ = mmdb.insert_gridfs(
+        uniform_bs.to_json(), collection="phonon_bandstructure_fs"
+    )
+    lm_bs_fsid, _ = mmdb.insert_gridfs(
+        lm_bs.to_json(), collection="phonon_bandstructure_fs"
+    )
+    
+    logger.info("Inserting force constants into database.")
+    fc_json = json.dumps(
+        {str(k): v.tolist() for k, v in fcs.get_fc_dict().items()}
+    )
+    fc_fsid, _ = mmdb.insert_gridfs(
+        fc_json, collection="phonon_force_constants_fs"
+    )
+
+    return dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 59ffc56c0..34b2057e3 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -19,6 +19,7 @@
     CollectPerturbedStructures,
     ForceConstantsToDb,
     RunHiPhive,
+    RunHiPhiveRenorm,
     RunShengBTE,
     ShengBTEToDb,
     MESH_DENSITY)
@@ -39,6 +40,10 @@ class FitForceConstantsFW(Firework):
         db_file: Path to a db file.
         cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
             will be generated based on the structure (default).
+        separate_fit: If True, harmonic and anharmonic force constants are fit
+            separately and sequentially, harmonic first then anharmonic. If
+            False, then they are all fit in one go. Default is False.
+        bulk_modulus: Must be supplied (in GPa) to copute thermal expansion
         imaginary_tol: Tolerance used to decide if a phonon mode is
             imaginary, in THz.
         max_n_imaginary: Maximum number of imaginary modes allowed in the
@@ -61,6 +66,7 @@ def __init__(
         parents: Optional[Union[Firework, List[Firework]]] = None,
         db_file: str = None,
         cutoffs: Optional[List[List[float]]] = None,
+        separate_fit: bool = False,
         bulk_modulus:float = None,
         imaginary_tol: float = IMAGINARY_TOL,
         max_n_imaginary: int = MAX_N_IMAGINARY,
@@ -71,20 +77,22 @@ def __init__(
     ):
         collect_structures = CollectPerturbedStructures()
         logger.info("INPUT CUTOFF \n {}".format(cutoffs))
-        fit_constants = RunHiPhive(
+        
+        fit_force_constants = RunHiPhive(
             cutoffs=cutoffs,
+            separate_fit=separate_fit
             bulk_modulus=bulk_modulus,
             imaginary_tol=imaginary_tol,
-            max_n_imaginary=max_n_imaginary,
-            max_imaginary_freq=max_imaginary_freq,
+#            max_n_imaginary=max_n_imaginary,
+#            max_imaginary_freq=max_imaginary_freq,
             fit_method=fit_method
         )
         to_db = ForceConstantsToDb(
-            db_file=db_file, mesh_density=mesh_density, additional_fields={}
+            db_file=db_file, renormalized=False, mesh_density=mesh_density, additional_fields={}
         )
         pass_locs = PassCalcLocs(name=name)
 
-        tasks = [collect_structures, fit_constants, to_db, pass_locs]
+        tasks = [collect_structures, fit_force_constants, to_db, pass_locs]
         super().__init__(tasks, parents=parents, name=name, **kwargs)
 
 
@@ -167,7 +175,6 @@ def __init__(
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
         temperature: Union[float, dict] = T_RENORM,
-        shengbte_control_kwargs: Optional[dict] = None,
         **kwargs
     ):    
     
@@ -182,17 +189,18 @@ def __init__(
         cs = ClusterSpace.read('cluster_space.cs')
         fcs = ForceConstants.read('force_constants.fcs')
         param = np.loadtxt('parameters.txt')
+        
         renorm_force_constants = RunHiPhiveRenorm(
-            cs=cluster_space.cs,
-            param=parameters,
-            fcs=force_constants.fcs,
+            cs=cs,
+            param=param,
+            fcs=fcs,
             T_renorm=T_renorm
         )        
 
         to_db = ForceConstantsToDb(
-            db_file=db_file, mesh_density=mesh_density, additional_fields={}
+            db_file=db_file, renormalized=True, mesh_density=mesh_density, additional_fields={}
 	)
         pass_locs = PassCalcLocs(name=name)
 
-	tasks = [collect_structures, renorm_force_constants, to_db, pass_locs]
+	tasks = [renorm_force_constants, to_db, pass_locs]
         super().__init__(tasks, name=name, **kwargs)
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index f7308bb71..a711e4d5f 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -4,11 +4,12 @@
 from typing import Dict, List, Optional, Union
 
 import numpy as np
+from monty.serialization import loadfn, dumpfn
 
 from atomate.utils.utils import get_logger
 from atomate.vasp.config import DB_FILE, SHENGBTE_CMD, VASP_CMD
 from atomate.vasp.firetasks import pass_vasp_result
-from atomate.vasp.firetasks.lattice_dynamics import T_KLAT
+from atomate.vasp.firetasks.lattice_dynamics import T_KLAT, T_RENORM
 from atomate.vasp.fireworks.core import TransmuterFW
 from atomate.vasp.fireworks.lattice_dynamics import (
     FitForceConstantsFW,
@@ -54,7 +55,8 @@
 
 def get_lattice_dynamics_wf(
     structure: Structure,
-    bulk_modulus: float = None
+    separate_fit: bool = False
+    bulk_modulus: float = None,
     common_settings: Dict = None,
     vasp_input_set: Optional[VaspInputSet] = None,
     copy_vasp_outputs: bool = False,
@@ -62,7 +64,9 @@ def get_lattice_dynamics_wf(
     num_supercell_kwargs: Optional[dict] = None,
     perturbed_structure_kwargs: Optional[dict] = None,
     calculate_lattice_thermal_conductivity: bool = False,
-    thermal_conductivity_temperature: Union[float, Dict] = T_Klat,
+    thermal_conductivity_temperature: Union[float, Dict] = T_KLAT,
+    renormalize: bool =	False,
+    renormalization_temperature: Union[float, Dict] = T_RENORM,
     shengbte_cmd: str = SHENGBTE_CMD,
     shengbte_fworker: Optional[str] = None,
 ):
@@ -109,9 +113,15 @@ def get_lattice_dynamics_wf(
         calculate_lattice_thermal_conductivity: If True and force constant
             fitting does not return imaginary modes, then use ShengBTE to
             calculate the lattice thermal conductivity.
-        thermal_conductivity_temperature: The temperature to calculate the
+        renormalize: If True and force constant fitting returns imaginary modes, 
+            then use HiPhiveRenorm to obtain phonons and force constants at
+            finite temperatures, which at some temperatures are hopefully real.
+        thermal_conductivity_temperature: The temperature at which to calculate
             lattice thermal conductivity for. Can be given as a single float, or
             a dictionary with the keys "min", "max", "step".
+        renormalization_temperature: The temperature at which to perform phonon 
+            renormalization. Can be given as a single float, or a dictionary
+            with the keys "min", "max", "step".
         shengbte_cmd: Command to run ShengBTE. Supports env_chk.
         shengbte_fworker: If None, the ShengBTE firework's fworker will be set
             to all the previous fireworks' fworker. If str, the ShengBTE
@@ -154,13 +164,23 @@ def get_lattice_dynamics_wf(
     # 2. Fit interatomic force constants from pertrubed structures
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
-        db_file=db_file, spec=allow_fizzled, bulk_modulus=bulk_modulus
+        db_file=db_file, spec=allow_fizzled,
+        separate_fit=separate_fit, bulk_modulus=bulk_modulus
     )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 
-    # RenormalizeFW(pass_inputs like bulk modulus)
-    
-    # 3. Lattice thermal conductivity calculation (optional)
+    # 3. RenormalizeFW (pass_inputs like bulk modulus)
+#    fitting_data = loadfn(fitting_data, "fitting_data.json")
+#    if fitting_data["n_imaginary"] > 0 and renormalize:
+#        fw_renormalization = RenormalizationFW(
+#            db_file=db_file,
+#            temperature=renormalization_temperature
+#        )
+#        wf.append_wf(
+#            Workflow.from_Firework(fw_fw_renormalization), [wf.fws[-1].fw_id]
+#        )
+
+    # 4. Lattice thermal conductivity calculation (optional)
     if calculate_lattice_thermal_conductivity:
         fw_lattice_conductivity = LatticeThermalConductivityFW(
             db_file=db_file,

From 989affbaf540173eac7d4065f74ba80385231714 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 13:16:59 -0700
Subject: [PATCH 111/207] separate fitting

---
 atomate/vasp/analysis/lattice_dynamics.py       | 4 ++--
 atomate/vasp/workflows/base/lattice_dynamics.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 1419c6fbd..c91cd8119 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -303,7 +303,7 @@ def _run_cutoffs(
         sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=None)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
-                        [0,2nd],
+                        [0,n2nd],
                         **fit_kwargs)
 <<<<<<< HEAD
         logger.info('Optimizer set up for cutoff: {}, {}'.format(i,cutoffs))
@@ -317,7 +317,7 @@ def _run_cutoffs(
         sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=param2)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
-                        [2nd,nall],
+                        [n2nd,nall],
                         **fit_kwargs)
         opt.train()
         param_anharmonic = opt.parameters # anharmonic force constant parameters
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a711e4d5f..d800076e1 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -55,7 +55,7 @@
 
 def get_lattice_dynamics_wf(
     structure: Structure,
-    separate_fit: bool = False
+    separate_fit: bool = False,
     bulk_modulus: float = None,
     common_settings: Dict = None,
     vasp_input_set: Optional[VaspInputSet] = None,

From 3f88a26c76e059171e849afcc139e6b392b04458 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 13:19:15 -0700
Subject: [PATCH 112/207] separate fitting

---
 atomate/vasp/analysis/lattice_dynamics.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index c91cd8119..e07c7027f 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -463,10 +463,12 @@ def get_structure_container(
             sc.add_structure(structure)
         else: # fit separately
             if param2 is None: # for harmonic fitting
-                sc.add_structure(structure) if mean_displacements <= 0.05
+                if mean_displacements <= 0.05:
+                    sc.add_structure(structure) 
             else: # for anharmonic fitting
-                sc.add_structure(structure) if mean_displacements >= 0.2
-                saved_structures.append(structure) if mean_displacements >= 0.2
+                if mean_displacements >= 0.15:
+                    sc.add_structure(structure) 
+                    saved_structures.append(structure) 
     if separate_fit and param2 is not None:
         A_mat = sc.get_fit_data()[0] # displacement matrix
         f_vec = sc.get_fit_data()[1] # force vector

From 1107deb9c8f23eaa0a53c5cb1f72c87eb3cbbb63 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 13:27:18 -0700
Subject: [PATCH 113/207] separate fitting

---
 atomate/vasp/firetasks/lattice_dynamics.py | 2 +-
 atomate/vasp/fireworks/lattice_dynamics.py | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 5a5752cee..205a399cd 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -205,7 +205,7 @@ def run_task(self, fw_spec):
         )
         anharmonic_data, phonopy = anharmonic_properties(
             phonopy, fcs, T_QHA, thermal_data["heat_capacity"],
-            thermal_data["n_imaginary"], bulk_modulus=bulk_modulus
+            thermal_data["n_imaginary"], bulk_modulus
         )
 
         fitting_data["n_imaginary"] = thermal_data.pop("n_imaginary")
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 34b2057e3..74615c0a8 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -67,7 +67,7 @@ def __init__(
         db_file: str = None,
         cutoffs: Optional[List[List[float]]] = None,
         separate_fit: bool = False,
-        bulk_modulus:float = None,
+        bulk_modulus: float = None,
         imaginary_tol: float = IMAGINARY_TOL,
         max_n_imaginary: int = MAX_N_IMAGINARY,
         max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
@@ -76,11 +76,10 @@ def __init__(
         **kwargs
     ):
         collect_structures = CollectPerturbedStructures()
-        logger.info("INPUT CUTOFF \n {}".format(cutoffs))
         
         fit_force_constants = RunHiPhive(
             cutoffs=cutoffs,
-            separate_fit=separate_fit
+            separate_fit=separate_fit,
             bulk_modulus=bulk_modulus,
             imaginary_tol=imaginary_tol,
 #            max_n_imaginary=max_n_imaginary,

From ae4ed812d83f58b1068c0b3c48bc6dd8cec03b06 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 13:28:39 -0700
Subject: [PATCH 114/207] separate fitting

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 74615c0a8..4445616fb 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -201,5 +201,5 @@ def __init__(
 	)
         pass_locs = PassCalcLocs(name=name)
 
-	tasks = [renorm_force_constants, to_db, pass_locs]
+        tasks = [renorm_force_constants, to_db, pass_locs]
         super().__init__(tasks, name=name, **kwargs)

From 170b96ec9626a4b127e48badf1894dbe55de59e8 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 13:31:20 -0700
Subject: [PATCH 115/207] separate fitting

---
 atomate/vasp/analysis/lattice_dynamics.py  |  4 ----
 atomate/vasp/firetasks/lattice_dynamics.py | 16 ----------------
 2 files changed, 20 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index e07c7027f..e3f51acf9 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -40,8 +40,6 @@
 logger = get_logger(__name__)
 
 IMAGINARY_TOL = 0.025  # in THz
-#MAX_N_IMAGINARY = np.inf
-#MAX_IMAGINARY_FREQ = 10  # in THz
 
 T_QHA = [i*100 for i in range(16)]
 T_RENORM = [i*100 for i in range(0,16)]
@@ -136,8 +134,6 @@ def fit_force_constants(
     all_cutoffs: List[List[float]],
     separate_fit: bool,
     imaginary_tol: float = IMAGINARY_TOL,
-#    max_n_imaginary: int = MAX_N_IMAGINARY,
-#    max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
     fit_method: str = FIT_METHOD,
 <<<<<<< HEAD
 ) -> Tuple["SortedForceConstants", Dict]:
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 205a399cd..5e8f3d207 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -18,8 +18,6 @@
 from atomate.vasp.analysis.lattice_dynamics import (
     FIT_METHOD,
     IMAGINARY_TOL,
-#    MAX_IMAGINARY_FREQ,
-#    MAX_N_IMAGINARY,
     T_QHA,
     T_RENORM,
     T_KLAT,
@@ -134,12 +132,6 @@ class RunHiPhive(FiretaskBase):
             False, then they are all fit in one go. Default is False.
         imaginary_tol (float): Tolerance used to decide if a phonon mode
             is imaginary, in THz.
-        max_n_imaginary (int): Maximum number of imaginary modes allowed in the
-            the final fitted force constant solution. If this criteria is not
-            reached by any cutoff combination this FireTask will fizzle.
-        max_imaginary_freq (float): Maximum allowed imaginary frequency in the
-            final fitted force constant solution. If this criteria is not
-            reached by any cutoff combination this FireTask will fizzle.
         fit_method (str): Method used for fitting force constants. This can be
             any of the values allowed by the hiphive ``Optimizer`` class.
     """
@@ -149,16 +141,12 @@ class RunHiPhive(FiretaskBase):
         "separate_fit",
         "bulk_modulus",
         "imaginary_tol",
-#        "max_n_imaginary",
-#        "max_imaginary_freq",
         "fit_method",
     ]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
 
-#        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
-#        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
         fit_method = self.get("fit_method", FIT_METHOD)
         separate_fit = self.get('separate_fit', False)
@@ -195,8 +183,6 @@ def run_task(self, fw_spec):
             cutoffs,
             separate_fit,
             imaginary_tol,
-#            max_n_imaginary,
-#            max_imaginary_freq,
             fit_method
         )
 
@@ -268,8 +254,6 @@ class RunHiPhiveRenorm(FiretaskBase):
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
 
-#        max_n_imaginary = self.get("max_n_imaginary", MAX_N_IMAGINARY)
-#        max_imaginary_freq = self.get("max_imaginary_freq", MAX_IMAGINARY_FREQ)
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
         fit_method = self.get("fit_method", FIT_METHOD)
 

From 6cd23c7a2f0950316fe9710d03763d062a8c4029 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Jun 2021 13:32:36 -0700
Subject: [PATCH 116/207] separate fitting

---
 atomate/vasp/fireworks/lattice_dynamics.py | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 4445616fb..a14003177 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -8,8 +8,6 @@
 from atomate.vasp.analysis.lattice_dynamics import (
     FIT_METHOD,
     IMAGINARY_TOL,
-    MAX_IMAGINARY_FREQ,
-    MAX_N_IMAGINARY,
     T_QHA,
     T_RENORM,
     T_KLAT
@@ -46,12 +44,6 @@ class FitForceConstantsFW(Firework):
         bulk_modulus: Must be supplied (in GPa) to copute thermal expansion
         imaginary_tol: Tolerance used to decide if a phonon mode is
             imaginary, in THz.
-        max_n_imaginary: Maximum number of imaginary modes allowed in the
-            final fitted force constant solution. If this criteria is not
-            reached by any cutoff combination the Firework will fizzle.
-        max_imaginary_freq: Maximum allowed imaginary frequency in the
-            final fitted force constant solution. If this criteria is not
-            reached by any cutoff combination this FireTask will fizzle.
         fit_method: Method used for fitting force constants. This can be
             any of the values allowed by the hiphive ``Optimizer`` class.
         mesh_density: The density of the q-point mesh used to calculate the
@@ -69,8 +61,6 @@ def __init__(
         separate_fit: bool = False,
         bulk_modulus: float = None,
         imaginary_tol: float = IMAGINARY_TOL,
-        max_n_imaginary: int = MAX_N_IMAGINARY,
-        max_imaginary_freq: float = MAX_IMAGINARY_FREQ,
         fit_method: str = FIT_METHOD,
         mesh_density: float = MESH_DENSITY,
         **kwargs
@@ -82,8 +72,6 @@ def __init__(
             separate_fit=separate_fit,
             bulk_modulus=bulk_modulus,
             imaginary_tol=imaginary_tol,
-#            max_n_imaginary=max_n_imaginary,
-#            max_imaginary_freq=max_imaginary_freq,
             fit_method=fit_method
         )
         to_db = ForceConstantsToDb(

From 5da14aa553b7ff985312784d77d3225beb8dbef5 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 9 Jun 2021 08:10:59 -0700
Subject: [PATCH 117/207] presets + other things

---
 atomate/vasp/analysis/lattice_dynamics.py     | 100 ++++----
 atomate/vasp/firetasks/lattice_dynamics.py    | 214 ++++++++++++------
 .../vasp/workflows/base/lattice_dynamics.py   |  13 +-
 atomate/vasp/workflows/presets/core.py        |   9 +-
 4 files changed, 218 insertions(+), 118 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index e3f51acf9..cc6626c26 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -42,8 +42,8 @@
 IMAGINARY_TOL = 0.025  # in THz
 
 T_QHA = [i*100 for i in range(16)]
-T_RENORM = [i*100 for i in range(0,16)]
-T_KLAT = [i*100 for i in range(0,16)]
+T_RENORM = [0,100,200,300,500,700,1000,1500]#[i*100 for i in range(0,16)]
+T_KLAT = [i*100 for i in range(0,11)]
 
 FIT_METHOD = "rfe" #"least-squares"
 
@@ -268,7 +268,7 @@ def _run_cutoffs(
 ) -> Dict:
 
     logger.info(
-        "Testing cutoffs {} out of {}: {}".format(i + 1, n_cutoffs, cutoffs)
+        "Testing cutoffs {} out of {}: {}".format(i+1, n_cutoffs, cutoffs)
     )
     supercell_atoms = structures[0]
 
@@ -310,7 +310,7 @@ def _run_cutoffs(
         param_harmonic = opt.parameters # harmonic force constant parameters
         
         logger.info('Fitting anharmonic force constants separately')
-        sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=param2)
+        sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=param_harmonic)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [n2nd,nall],
@@ -402,32 +402,22 @@ def get_structure_container(
         logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
     
     parameters = enforce_rotational_sum_rules(
-        sc.cluster_space, parameters, ["Huang", "Born-Huang"]
+        cs, parameters, ["Huang", "Born-Huang"]
     )
     fcp = ForceConstantPotential(cs, parameters)
     fcs = fcp.get_force_constants(supercell_atoms)
     logger.info('FCS generated for cutoff {}, {}'.format(i,cutoffs))
 
-#    n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
-#        parent_structure, supercell_matrix, fcs, bulk_modulus, T_QHA, imaginary_tol
-#    )
-
-    return {
-        "cutoffs": cutoffs,
-        "rmse_test": opt.rmse_test,
-#        "n_imaginary": n_imaginary,
-#        "min_frequency": min_freq,
-#        "temperature": T_QHA,
-#        "free_energy": free_energy,
-#        "entropy": entropy,
-#        "heat_capacity": Cv,
-#        "thermal_expansion": cte,
-        "cluster_space": sc.cluster_space,
-        "parameters": parameters,
-        "force_constants": fcs
-    }
-    #except Exception:
-    #    return None
+    try:
+        return {
+            "cutoffs": cutoffs,
+            "rmse_test": opt.rmse_test,
+            "cluster_space": sc.cluster_space,
+            "parameters": parameters,
+            "force_constants": fcs
+        }
+    except Exception:
+        return None
 
 
 def get_structure_container(
@@ -452,8 +442,11 @@ def get_structure_container(
 
     sc = StructureContainer(cs)
     saved_strutures = []
-    for structure in structures:
-        displacements = get_displacements(atoms, supercell_atoms)
+    structure_orig = structures[0]
+    for i, structure in enumerate(structures):
+        if i==0:
+            continue
+        displacements = get_displacements(structure_orig, structure)
         mean_displacements = np.linalg.norm(displacements,axis=1).mean()
         if not separate_fit: # fit all
             sc.add_structure(structure)
@@ -465,7 +458,7 @@ def get_structure_container(
                 if mean_displacements >= 0.15:
                     sc.add_structure(structure) 
                     saved_structures.append(structure) 
-    if separate_fit and param2 is not None:
+    if separate_fit and param2 is not None: # do after anharmonic fitting
         A_mat = sc.get_fit_data()[0] # displacement matrix
         f_vec = sc.get_fit_data()[1] # force vector
         new_force = f_vec - np.dot(A_mat[:,:ncut],param2) # subract harmonic forces
@@ -504,7 +497,7 @@ def harmonic_properties(
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
 
-    logger.info('Evaluating harmonic properties.')
+    logger.info('Evaluating harmonic properties...')
     fcs2 = fcs.get_fc_array(2)
     fcs3 = fcs.get_fc_array(3)
     parent_phonopy = get_phonopy_structure(structure)
@@ -553,7 +546,7 @@ def anharmonic_properties(
 ) -> Tuple[Dict, Phonopy]:
 
     if n_imaginary == 0:
-        logger.info('Evaluating anharmonic properties')
+        logger.info('Evaluating anharmonic properties...')
         fcs2 = fcs.get_fc_array(2)
         fcs3 = fcs.get_fc_array(3)
         grun, cte = gruneisen(phonopy,fcs2,fcs3,T,Cv,bulk_modulus=bulk_modulus)
@@ -606,20 +599,41 @@ def percent_diff(a,b):
         # This process preserves cell symmetry upon thermal expansion, i.e., it prevents
         # symmetry-identical directions from inadvertently expanding by different ratios
         # when the Gruneisen routine returns slighlty different ratios for those directions
-        if percent_diff(grun_total_diag[0],grun_total_diag[1]) < 0.1:
-            avg = np.mean((grun_total_diag[0],grun_total_diag[1]))
-            grun_total_diag[0] = avg
-            grun_total_diag[1] = avg
-        elif percent_diff(grun_total_diag[0],grun_total_diag[2]) < 0.1:
-            avg = np.mean((grun_total_diag[0],grun_total_diag[2]))
-            grun_total_diag[0] = avg
-            grun_total_diag[2] = avg
-        elif percent_diff(grun_total_diag[1],grun_total_diag[2]) < 0.1:
-            avg = np.mean((grun_total_diag[1],grun_total_diag[2]))
-            grun_total_diag[1] = avg
-            grun_total_diag[2] = avg
-        else:
+        avg012 = np.mean((grun_total_diag[0],grun_total_diag[1],grun_total_diag[2]))
+        avg01 = np.mean((grun_total_diag[0],grun_total_diag[1]))
+        avg02 = np.mean((grun_total_diag[0],grun_total_diag[2]))
+        avg12 = np.mean((grun_total_diag[1],grun_total_diag[2]))
+        if percent_diff(grun_total_diag[0],avg012) < 0.1:
+            if percent_diff(grun_total_diag[1],avg012) < 0.1:
+                if percent_diff(grun_total_diag[2],avg012) < 0.1: # all siilar
+                    grun_total_diag[0] = avg012
+                    grun_total_diag[1] = avg012
+                    grun_total_diag[2] = avg012
+                elif percent_diff(grun_total_diag[2],avg02) < 0.1: # 0 and 2 similar
+                    grun_total_diag[0] = avg02
+                    grun_total_diag[2] = avg02
+                elif percent_diff(grun_total_diag[2],avg12) < 0.1: # 1 and 2 similar
+                    grun_total_diag[1] = avg12
+                    grun_total_diag[2] = avg12
+                else:
+                    pass
+            elif percent_diff(grun_total_diag[1],avg01) < 0.1: # 0 and 1 similar
+                grun_total_diag[0] = avg01
+                grun_total_diag[1] = avg01
+            elif percent_diff(grun_total_diag[1],avg12) < 0.1: # 1 and 2 similar
+                grun_total_diag[1] = avg12
+                grun_total_diag[2] = avg12
+            else:
+                pass
+        elif percent_diff(grun_total_diag[0],avg01) < 0.1: # 0 and 1 similar
+            grun_total_diag[0] = avg01
+            grun_total_diag[1] = avg01
+        elif percent_diff(grun_total_diag[0],avg02) < 0.1: # 0 and 2 similar
+            grun_total_diag[0] = avg02
+            grun_total_diag[2] = avg02
+        else: # nothing similar
             pass
+        
     return grun_total_diag
 
 
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 5e8f3d207..edf6e26e0 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -10,6 +10,7 @@
 
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
+from monty.json import jsanitize
 from pymongo import ReturnDocument
 
 from atomate.utils.utils import env_chk, get_logger
@@ -170,12 +171,6 @@ def run_task(self, fw_spec):
             atoms.positions = supercell_atoms.get_positions()
             structures.append(atoms)
 
-        logger.info('PARENT \n {}'.format(parent_structure))
-        logger.info('SUPERCELL \n {}'.format(supercell_structure))
-        logger.info('SUPERCELL MATRIX \n {}'.format(supercell_matrix))
-        logger.info('FIT_METHOD {}'.format(fit_method))
-        logger.info('FINAL INPUT CUTOFFS \n {}'.format(cutoffs))
-        
         fcs, param, cs, fitting_data = fit_force_constants(
             parent_structure,
             supercell_matrix,
@@ -186,6 +181,12 @@ def run_task(self, fw_spec):
             fit_method
         )
 
+        if fcs is None:
+            # fitting failed for some reason
+            raise RuntimeError(
+                "Could not find a force constant solution"
+            )
+        
         thermal_data, phonopy = harmonic_properties(
             parent_structure, supercell_matrix, fcs, T_QHA, imaginary_tol
         )
@@ -199,14 +200,6 @@ def run_task(self, fw_spec):
         dumpfn(fitting_data, "fitting_data.json")
         dumpfn(thermal_data, "thermal_data_qha.json")
 
-#        if force_constants is None:
-#            # fitting failed
-#            raise RuntimeError(
-#                "Could not find a force constant solution with less than {} "
-#                "imaginary modes.\n"
-#                "Fitting results: {}".format(max_n_imaginary, fitting_data)
-#            )
-
         logger.info("Writing cluster space and force_constants")
         logger.info("{}".format(type(fcs)))
         fcs.write("force_constants.fcs")
@@ -218,8 +211,8 @@ def run_task(self, fw_spec):
             atoms = AseAtomsAdaptor.get_atoms(parent_structure)
             fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms, order=3)
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
-        elif n_imaginary > 0:
-            logger.info("Imaginary modes exist! ShengBTE files not written. You may want to perform phonon renormalization.")
+        else:
+            logger.info("ShengBTE files not written due to imaginary modes. You may want to perform phonon renormalization.")
 
 
 
@@ -371,66 +364,132 @@ def run_task(self, fw_spec):
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = structure_data["supercell_matrix"]
 
-        if renormalized: # FC from renormalization
-            thermal_data = loadfn("thermal_data_renorm.json")
-            temperature = thermal_data["temperature"]
-            for t, T in enumerate(temperature):
-                ## err should I collect results for all T and push data at once,
-                ## or push data for each T individually?
-                fcs = ForceConstants.read("force_constants_{}K.fcs")
-                phonopy_fc = fcs.get_fc_array(order=2)
-                dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-                    structure, supercell_matrix, phonopy_fc, mesh_density, mmdb
-                )
-                data = {
-                    "thermal_data": thermal_data,
-                    "force_constants_fs_id": fc_fsid,
-                    "tags": fw_spec.get("tags", None),
-                    "phonon_dos_fs_id": dos_fsid,
-                    "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-                    "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-                    "created_at": datetime.utcnow(),
-                }
-                data.update(self.get("additional_fields", {}))                
-        else: # FC directly from fitting
-            fitting_data = loadfn("fitting_data.json")
-            thermal_data = loadfn("thermal_data_qha.json")
-            fcs = ForceConstants.read("force_constants.fcs")
+        fitting_data = loadfn("fitting_data.json")
+        thermal_data = loadfn("thermal_data_qha.json")
+        fcs = ForceConstants.read("force_constants.fcs")
+        
+        dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+            structure, supercell_matrix, fcs, mesh_density, mmdb
+        )
+        
+        data = {
+            "created_at": datetime.utcnow(),            
+            "tags": fw_spec.get("tags", None),
+            "formula_pretty": structure.composition.reduced_formula,            
+            "structure": structure.as_dict(),
+            "supercell_matrix": supercell_matrix,
+            "supercell_structure": supercell_structure.as_dict(),
+            "perturbed_structures": [s.as_dict() for s in structures],
+            "perturbed_forces": [f.tolist() for f in forces],
+            "fitting_data": fitting_data,
+            "thermal_data": thermal_data,
+            "force_constants_fs_id": fc_fsid,
+            "phonon_dos_fs_id": dos_fsid,
+            "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+            "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+        }
+        data.update(self.get("additional_fields", {}))
+
+        # Get an id for the force constants
+        fitting_id = _get_fc_fitting_id(mmdb)
+        metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+        data.update(metadata)
+        data = jsanitize(data,strict=True,allow_bson=True)
+        
+        mmdb.db.lattice_dynamics.insert_one(data)
+            
+        logger.info("Finished inserting force constants")
+
+        return FWAction(update_spec=metadata)
+
+
+
+class ForceConstantsRenormToDb(FiretaskBase):
+    """
+    Add force constants, phonon band structure and density of states
+    to the database.
+
+    Assumes you are in a directory with the force constants, fitting
+    data, and structure data written to files.
 
+    Required parameters:
+        db_file (str): Path to DB file for the database that contains the
+            perturbed structure calculations.
+    Optional parameters:
+        renormalized (bool): Whether FC resulted from original fitting (False)
+            or renormalization process (True) determines how data are stored.
+            Default is False.                                                                                                                                                                                      mesh_density (float): The density of the q-point mesh used to calculate
+            the phonon density of states. See the docstring for the ``mesh``
+            argument in Phonopy.init_mesh() for more details.
+        additional_fields (dict): Additional fields added to the document, such
+            as user-defined tags, name, ids, etc.                                                                                                                                                              """
+
+    required_params = ["db_file"]
+    optional_params = ["renormalized","mesh_density", "additional_fields"]
+
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
+    def run_task(self, fw_spec):
+
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+        renormalized = self.get("renormalized", False)
+        mesh_density = self.get("mesh_density", MESH_DENSITY)
+
+        structure_data = loadfn("structure_data.json")
+        forces = loadfn("perturbed_forces.json")
+        structures = loadfn("perturbed_structures.json")
+
+        structure = structure_data["structure"]
+        supercell_structure = structure_data["supercell_structure"]
+        supercell_matrix = structure_data["supercell_matrix"]
+
+        thermal_data = loadfn("thermal_data_renorm.json")
+        temperature = thermal_data["temperature"]
+
+        data = {
+            "created_at": datetime.utcnow(),
+            "tags": fw_spec.get("tags", None),
+            "formula_pretty": structure.composition.reduced_formula,
+            "structure": structure.as_dict(),
+            "thermal_data": thermal_data,
+            }
+        
+        temperature_to_keep = []
+        renormalized_data = []
+        for t, T in enumerate(temperature):
+            ## err should I collect results for all T and push data at once,                                                                                                                            
+            ## or push data for each T individually?                                                                                                                                                    
+            fcs = ForceConstants.read("force_constants_{}K.fcs")
+            phonopy_fc = fcs.get_fc_array(order=2)
             dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-                structure, supercell_matrix, fcs, mesh_density, mmdb
+                structure, supercell_matrix, phonopy_fc, mesh_density, mmdb
             )
-
-            data = {
-                "structure": structure.as_dict(),
-                "supercell_matrix": supercell_matrix,
-                "supercell_structure": supercell_structure.as_dict(),
-                "perturbed_structures": [s.as_dict() for s in structures],
-                "perturbed_forces": [f.tolist() for f in forces],
-                "fitting_data": fitting_data,
-                "thermal_data": thermal_data,
+            
+            data_at_T = {
                 "force_constants_fs_id": fc_fsid,
-                "tags": fw_spec.get("tags", None),
-                "formula_pretty": structure.composition.reduced_formula,
                 "phonon_dos_fs_id": dos_fsid,
                 "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
                 "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-                "created_at": datetime.utcnow(),
             }
-            data.update(self.get("additional_fields", {}))
-
-            # Get an id for the force constants
-            fitting_id = _get_fc_fitting_id(mmdb)
-            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
-            data.update(metadata)
-            mmdb.db.lattice_dynamics.insert_many(data)  # WHAT TO DO HERE?
-#            mmdb.db.lattice_dynamics.insert_one(data)
-            
-        logger.info("Finished inserting force constants")
+            temperature_to_keep.append(T)
+            renormalized_data.append(data_at_T)
+        data["temperatures"] = temperature_to_keep
+        data["renormalized_data"] = renormalized_data
+        data.update(self.get("additional_fields", {}))
 
-        return FWAction(update_spec=metadata)
+        # Get an id for the force constants
+        fitting_id = _get_fc_fitting_id(mmdb)
+        metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+        data.update(metadata)
+        data = jsanitize(data,strict=True,allow_bson=True)
+
+        mmdb.db.renormalized_lattice_dynamics.insert_one(data)
 
+        logger.info("Finished inserting renormalized force constants")
 
+        return FWAction(update_spec=metadata)        
+
+    
 @explicit_serialize
 class RunShengBTE(FiretaskBase):
     """
@@ -458,12 +517,33 @@ def run_task(self, fw_spec):
         structure_data = loadfn("structure_data.json")
         structure = structure_data["structure"]
         supercell_matrix = structure_data["supercell_matrix"]
-
+        temperature = self.get("temperature", T_KLAT)
+
+        if isinstance(temperature, (int, float)):
+            self["t"] = temperature
+        elif isinstance(temperature, (list, np.ndarray)):
+            t_max = np.max(np.array(temperature))
+            t_min = np.min(np.array(temperature))
+            if t_min==0:
+                t_min = np.partition(temperature,1)[1]
+                t_step = (t_max-t_min)/(len(temperature)-2)
+            else:
+                t_step = (t_max-t_min)/(len(temperature)-1)
+            self["t_min"] = t_min
+            self["t_max"] = t_max
+            self["t_step"] = t_step
+        elif isinstance(temperature, dict):
+            self["t_min"] = temperature["min"]
+            self["t_max"] = temperature["max"]
+            self["t_step"] = temperature["step"]
+        else:
+            raise ValueError("Unsupported temperature type, must be float or dict")
+        
         control_dict = {
             "scalebroad": 0.5,
             "nonanalytic": False,
             "isotopes": False,
-            "temperature": self.get("temperature", T_QHA),
+            "temperature": self.get("temperature", T_KLAT),
             "scell": np.diag(supercell_matrix).tolist(),
         }
         control_kwargs = self.get("control_kwargs") or {}
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index d800076e1..9ced8bb86 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -10,7 +10,7 @@
 from atomate.vasp.config import DB_FILE, SHENGBTE_CMD, VASP_CMD
 from atomate.vasp.firetasks import pass_vasp_result
 from atomate.vasp.firetasks.lattice_dynamics import T_KLAT, T_RENORM
-from atomate.vasp.fireworks.core import TransmuterFW
+from atomate.vasp.fireworks.core import TransmuterFW, OptimizeFW
 from atomate.vasp.fireworks.lattice_dynamics import (
     FitForceConstantsFW,
     LatticeThermalConductivityFW,
@@ -31,12 +31,13 @@
 logger = get_logger(__name__)
 
 _static_user_incar_settings = {
+    "PREC": "Accurate",
     "ADDGRID": True,
     "LCHARG": False,
-    "ENCUT": 700,
+    "ENCUT": 520,
     "ISMEAR": 0,
-    "EDIFF": 1e-8,
-    "PREC": "Accurate",
+    "SIGMA": 0.1,
+    "EDIFF": 1e-6,
     "LAECHG": False,
     "LREAL": False,
     "LASPH": True,
@@ -150,7 +151,7 @@ def get_lattice_dynamics_wf(
         n_supercells = get_num_supercells(supercell, **num_supercell_kwargs)
         perturbed_structure_kwargs["n_configs_per_std"] = n_supercells
 
-    # 1. Start by pertrubing supercell and calculating forces
+    # 1. Perturb supercell and calculae forces
     wf = get_perturbed_structure_wf(
         structure,
         supercell_matrix=supercell_matrix,
@@ -180,7 +181,7 @@ def get_lattice_dynamics_wf(
 #            Workflow.from_Firework(fw_fw_renormalization), [wf.fws[-1].fw_id]
 #        )
 
-    # 4. Lattice thermal conductivity calculation (optional)
+    # 4. Lattice thermal conductivity calculation
     if calculate_lattice_thermal_conductivity:
         fw_lattice_conductivity = LatticeThermalConductivityFW(
             db_file=db_file,
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 6e98f1194..ab3e57137 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -848,8 +848,10 @@ def wf_nudged_elastic_band(structures, parent, c=None):
     return wf
 
 
-def wf_lattice_thermal_conductivity(
+def wf_lattice_dynamics(
     structure: Structure,
+    separate_fit: bool = False,
+    bulk_modulus: float = None,
     c: Optional[dict] = None,
     **ld_kwargs
 ) -> Workflow:
@@ -870,13 +872,14 @@ def wf_lattice_thermal_conductivity(
     """
     optimize_uis = {
         "LAECHG": False,
-        'ENCUT': 700,
+        'ENCUT': 520,
         'ADDGRID': True,
         'EDIFFG': -5e-4,
         'PREC': 'Accurate',
         "LREAL": False,
         'EDIFF': 1e-8,
         "ISMEAR": 0,
+        "SIGMA": 0.1,
         'LCHARG': False,
         'LASPH': True
     }
@@ -896,6 +899,8 @@ def wf_lattice_thermal_conductivity(
 
     wf_ld = get_lattice_dynamics_wf(
         structure,
+        separate_fit: bool = separate_fit,
+        bulk_modulus: float = bulk_modulus,
         common_settings=c,
         calculate_lattice_thermal_conductivity=True,
         copy_vasp_outputs=True,

From 5d56a502110f5e33c4aea5f9ac924bb2a7edaf53 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 9 Jun 2021 08:23:26 -0700
Subject: [PATCH 118/207] presets

---
 atomate/vasp/workflows/base/lattice_dynamics.py |  2 +-
 atomate/vasp/workflows/presets/core.py          | 13 ++++++++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 9ced8bb86..54a5b6fba 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -151,7 +151,7 @@ def get_lattice_dynamics_wf(
         n_supercells = get_num_supercells(supercell, **num_supercell_kwargs)
         perturbed_structure_kwargs["n_configs_per_std"] = n_supercells
 
-    # 1. Perturb supercell and calculae forces
+    # 1. Perturb supercell and calculate forces
     wf = get_perturbed_structure_wf(
         structure,
         supercell_matrix=supercell_matrix,
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index ab3e57137..c85d7f2da 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -853,6 +853,12 @@ def wf_lattice_dynamics(
     separate_fit: bool = False,
     bulk_modulus: float = None,
     c: Optional[dict] = None,
+    supercell_matrix_kwargs: Optional[dict] = None,
+    num_supercell_kwargs: Optional[dict] = None,
+    calculate_lattice_thermal_conductivity=True,
+    thermal_conductivity_temperature=None,
+    renormalize=False,
+    renormalization_temperature=None,        
     **ld_kwargs
 ) -> Workflow:
     """
@@ -902,7 +908,12 @@ def wf_lattice_dynamics(
         separate_fit: bool = separate_fit,
         bulk_modulus: float = bulk_modulus,
         common_settings=c,
-        calculate_lattice_thermal_conductivity=True,
+        supercell_matrix_kwargs: supercell_matrix_kwargs,
+        num_supercell_kwargs: num_supercell_kwargs,
+        calculate_lattice_thermal_conductivity=calculate_lattice_thermal_conductivity,
+        thermal_conductivity_temperature=thermal_conductivity_temperature,
+        renormalize=renormalize,
+        renormalization_temperature=renormalization_temperature,
         copy_vasp_outputs=True,
         **ld_kwargs
     )

From 128ff50e3e97d198e50f05fa5da22ce4f59bd0d2 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 9 Jun 2021 08:31:18 -0700
Subject: [PATCH 119/207] preset

---
 atomate/vasp/workflows/presets/core.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index c85d7f2da..055095914 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -905,8 +905,8 @@ def wf_lattice_dynamics(
 
     wf_ld = get_lattice_dynamics_wf(
         structure,
-        separate_fit: bool = separate_fit,
-        bulk_modulus: float = bulk_modulus,
+        separate_fit = separate_fit,
+        bulk_modulus = bulk_modulus,
         common_settings=c,
         supercell_matrix_kwargs: supercell_matrix_kwargs,
         num_supercell_kwargs: num_supercell_kwargs,

From ef8880f86628b7701917ecded6c148c55d56e8ea Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 9 Jun 2021 08:34:14 -0700
Subject: [PATCH 120/207] preset

---
 atomate/vasp/workflows/presets/core.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 055095914..21095a194 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -908,8 +908,8 @@ def wf_lattice_dynamics(
         separate_fit = separate_fit,
         bulk_modulus = bulk_modulus,
         common_settings=c,
-        supercell_matrix_kwargs: supercell_matrix_kwargs,
-        num_supercell_kwargs: num_supercell_kwargs,
+        supercell_matrix_kwargs=supercell_matrix_kwargs,
+        num_supercell_kwargs=num_supercell_kwargs,
         calculate_lattice_thermal_conductivity=calculate_lattice_thermal_conductivity,
         thermal_conductivity_temperature=thermal_conductivity_temperature,
         renormalize=renormalize,

From 43cd4fe12cd863df70b5c75e1aa998890176bad8 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 17 Jun 2021 21:54:39 -0700
Subject: [PATCH 121/207] update

---
 atomate/vasp/analysis/lattice_dynamics.py     |  2 +-
 atomate/vasp/firetasks/lattice_dynamics.py    | 47 +++++++-------
 atomate/vasp/fireworks/lattice_dynamics.py    | 60 +++++++++++++-----
 .../vasp/workflows/base/lattice_dynamics.py   | 63 ++++++++++++-------
 4 files changed, 111 insertions(+), 61 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index cc6626c26..39bc5e35c 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -43,7 +43,7 @@
 
 T_QHA = [i*100 for i in range(16)]
 T_RENORM = [0,100,200,300,500,700,1000,1500]#[i*100 for i in range(0,16)]
-T_KLAT = [i*100 for i in range(0,11)]
+T_KLAT = {"t_min":100,"t_max":1000,"t_step":100} #[i*100 for i in range(0,11)]
 
 FIT_METHOD = "rfe" #"least-squares"
 
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index edf6e26e0..f9fe08811 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -262,7 +262,7 @@ def run_task(self, fw_spec):
         bulk_modulus = self.get("bulk_modulus")
         T_renorm = self.get("T_renorm", T_RENORM)
 
-        renorm_results = Parallel(n_jobs=2, backend="multiprocessing")(delayed(renormalization)(
+        renorm_results = Parallel(n_jobs=4, backend="multiprocessing")(delayed(renormalization)(
             parent_structure, supercell_matrix, cs, fcs, param, T, nconfig, conv_thresh, imaginary_tol
         ) for t, T in enumerate(T_renorm))
 
@@ -505,45 +505,50 @@ class RunShengBTE(FiretaskBase):
     Optional parameters:
         temperature (float or dict): The temperature to calculate the lattice
             thermal conductivity for. Can be given as a single float, or a
-            dictionary with the keys "min", "max", "step".
+            dictionary with the keys "t_min", "t_max", "t_step".
         control_kwargs (dict): Options to be included in the ShengBTE control
             file.
     """
 
     required_params = ["shengbte_cmd"]
-    optional_params = ["temperature", "control_kwargs"]
+    optional_params = ["renormalized","temperature", "control_kwargs"]
 
     def run_task(self, fw_spec):
         structure_data = loadfn("structure_data.json")
         structure = structure_data["structure"]
         supercell_matrix = structure_data["supercell_matrix"]
         temperature = self.get("temperature", T_KLAT)
+        renormalized = self.get("renormalized", False)
 
-        if isinstance(temperature, (int, float)):
+        if renormalized:
+            assert isinstance(temperature, (int, float))
             self["t"] = temperature
-        elif isinstance(temperature, (list, np.ndarray)):
-            t_max = np.max(np.array(temperature))
-            t_min = np.min(np.array(temperature))
-            if t_min==0:
-                t_min = np.partition(temperature,1)[1]
-                t_step = (t_max-t_min)/(len(temperature)-2)
-            else:
-                t_step = (t_max-t_min)/(len(temperature)-1)
-            self["t_min"] = t_min
-            self["t_max"] = t_max
-            self["t_step"] = t_step
-        elif isinstance(temperature, dict):
-            self["t_min"] = temperature["min"]
-            self["t_max"] = temperature["max"]
-            self["t_step"] = temperature["step"]
         else:
-            raise ValueError("Unsupported temperature type, must be float or dict")
+            if isinstance(temperature, (int, float)):
+                self["t"] = temperature
+            elif isinstance(temperature, (list, np.ndarray)):
+                t_max = np.max(np.array(temperature))
+                t_min = np.min(np.array(temperature))
+                if t_min==0:
+                    t_min = np.partition(temperature,1)[1]
+                    t_step = (t_max-t_min)/(len(temperature)-2)
+                else:
+                    t_step = (t_max-t_min)/(len(temperature)-1)
+                self["t_min"] = t_min
+                self["t_max"] = t_max
+                self["t_step"] = t_step
+            elif isinstance(temperature, dict):
+                self["t_min"] = temperature["t_min"]
+                self["t_max"] = temperature["t_max"]
+                self["t_step"] = temperature["t_step"]
+            else:
+                raise ValueError("Unsupported temperature type, must be float or dict")
         
         control_dict = {
             "scalebroad": 0.5,
             "nonanalytic": False,
             "isotopes": False,
-            "temperature": self.get("temperature", T_KLAT),
+            "temperature": temperature,
             "scell": np.diag(supercell_matrix).tolist(),
         }
         control_kwargs = self.get("control_kwargs") or {}
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index a14003177..a03d28d86 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -109,27 +109,53 @@ def __init__(
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
         shengbte_cmd: str = SHENGBTE_CMD,
+        renormalized: bool = False,
         temperature: Union[float, dict] = T_KLAT,
         shengbte_control_kwargs: Optional[dict] = None,
         **kwargs
     ):
         # files needed to run ShengBTE
-        files = [
-            "structure_data.json",
-            "FORCE_CONSTANTS_2ND",
-            "FORCE_CONSTANTS_3RD",
-        ]
-
-        if prev_calc_dir:
-            copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
-        else:
-            copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
-
-        run_shengbte = RunShengBTE(
-            shengbte_cmd=shengbte_cmd,
-            temperature=temperature,
-            control_kwargs=shengbte_control_kwargs,
-        )
+        if renormalized: # must check if FORCE_CONSTANTS_2ND_{T}K can be copied individually
+            files = [
+                "structure_data.json",
+                "FORCE_CONSTANTS_2ND_{}K".format(temperature),
+                "FORCE_CONSTANTS_3RD"
+            ]
+            if prev_calc_dir:
+                try:
+                    copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+                except:
+                    raise IOError("FORCE_CONSTANTS_2ND_{}K not found! Abandoning ShengBTE run."
+                                  .format(temperature))
+            else:
+                try:
+                    copy_files = CopyFilesFromCalcLoc(calc_loc=True, files_to_copy=files)
+                except:
+                    raise IOError("FORCE_CONSTANTS_2ND_{}K not found! Abandoning ShengBTE run."
+                                  .format(temperature))
+            run_shengbte = RunShengBTE(
+                shengbte_cmd=shengbte_cmd,
+                temperature=temperature,
+                renormlized=renormalized,
+                control_kwargs=shengbte_control_kwargs,
+            )
+        else: # only the default files are needed
+            files = [
+                "structure_data.json",
+                "FORCE_CONSTANTS_2ND",
+                "FORCE_CONSTANTS_3RD",
+            ]
+            if prev_calc_dir:
+                copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+            else:
+                copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+            run_shengbte = RunShengBTE(
+                shengbte_cmd=shengbte_cmd,
+                renormlized=renormalized,
+                temperature=temperature,
+                control_kwargs=shengbte_control_kwargs,
+            )
+            
         shengbte_to_db = ShengBTEToDb(db_file=db_file, additional_fields={})
 
         tasks = [copy_files, run_shengbte, shengbte_to_db]
@@ -158,10 +184,10 @@ class RenormalizationFW(Firework):
     
     def __init__(
         self,
+        temperature: Union[float, list],
         name="Renormalization",
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
-        temperature: Union[float, dict] = T_RENORM,
         **kwargs
     ):    
     
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 54a5b6fba..abfe38a8a 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -24,8 +24,8 @@
     CubicSupercellTransformation,
 )
 
-__author__ = "Alex Ganose, Rees Chang"
-__email__ = "aganose@lbl.gov, rc564@cornell.edu"
+__author__ = "Alex Ganose, Rees Chang, Junsoo Park"
+__email__ = "aganose@lbl.gov, rc564@cornell.edu, jsyony37@lbl.gov"
 __date__ = "February 2020"
 
 logger = get_logger(__name__)
@@ -91,7 +91,9 @@ def get_lattice_dynamics_wf(
        the minimization schemes in hiPhive.
     5. Output the interatomic force constants, and phonon band structure and
        density of states to the database.
-    6. Optional: Solve the lattice thermal conductivity using ShengBTE and
+    6. Optional: Perform phonon renormalization at finite temperature - useful
+       when unstable modes exist 
+    7. Optional: Solve the lattice thermal conductivity using ShengBTE and
        output to the database.
 
     Args:
@@ -171,30 +173,47 @@ def get_lattice_dynamics_wf(
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 
     # 3. RenormalizeFW (pass_inputs like bulk modulus)
-#    fitting_data = loadfn(fitting_data, "fitting_data.json")
-#    if fitting_data["n_imaginary"] > 0 and renormalize:
-#        fw_renormalization = RenormalizationFW(
-#            db_file=db_file,
-#            temperature=renormalization_temperature
-#        )
-#        wf.append_wf(
-#            Workflow.from_Firework(fw_fw_renormalization), [wf.fws[-1].fw_id]
-#        )
-
-    # 4. Lattice thermal conductivity calculation
-    if calculate_lattice_thermal_conductivity:
-        fw_lattice_conductivity = LatticeThermalConductivityFW(
+    if renormalize:
+        fw_renormalization = RenormalizationFW(
+            temperature=renormalization_temperature,
             db_file=db_file,
-            shengbte_cmd=shengbte_cmd,
-            temperature=thermal_conductivity_temperature,
         )
-        if shengbte_fworker:
-            fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
-
         wf.append_wf(
-            Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
+            Workflow.from_Firework(fw_renormalization), [wf.fws[-1].fw_id]
         )
 
+    # 4. Lattice thermal conductivity calculation
+    if calculate_lattice_thermal_conductivity:
+        if renormalize:
+            # Because of the way ShengBTE works, a temperature array that is not
+            # equally spaced out (T_step) requires submission for each temperature
+            fw_lattice_conductivity = []
+            for T in renormalization_temperature:
+                fw = LatticeThermalConductivityFW(
+                    db_file=db_file,
+                    shengbte_cmd=shengbte_cmd,
+                    renormalized=True,
+                    temperature=T
+                )
+                if shengbte_fworker:
+                    fw.spec["_fworker"] = shengbte_fworker
+                fw_lattice_conductivity.append(fw)
+            wf.append_wf(
+                Workflow.from_Firework(fw_lattice_conductivity), wf.leaf_fw_ids
+            )                
+        else:
+            fw_lattice_conductivity = LatticeThermalConductivityFW(
+                db_file=db_file,
+                shengbte_cmd=shengbte_cmd,
+                renormalized=False,
+                temperature=thermal_conductivity_temperature,
+            )
+            if shengbte_fworker:
+                fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
+            wf.append_wf(
+                Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
+            )
+
     formula = structure.composition.reduced_formula
     wf.name = "{} - lattice dynamics".format(formula)
 

From 6ad697c528c0cebbe520ac5e6cc178c50a379f06 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 17 Jun 2021 22:11:28 -0700
Subject: [PATCH 122/207] update

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index abfe38a8a..672f42be8 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -67,7 +67,7 @@ def get_lattice_dynamics_wf(
     calculate_lattice_thermal_conductivity: bool = False,
     thermal_conductivity_temperature: Union[float, Dict] = T_KLAT,
     renormalize: bool =	False,
-    renormalization_temperature: Union[float, Dict] = T_RENORM,
+    renormalization_temperature: Union[float, List, Dict] = T_RENORM,
     shengbte_cmd: str = SHENGBTE_CMD,
     shengbte_fworker: Optional[str] = None,
 ):
@@ -123,7 +123,7 @@ def get_lattice_dynamics_wf(
             lattice thermal conductivity for. Can be given as a single float, or
             a dictionary with the keys "min", "max", "step".
         renormalization_temperature: The temperature at which to perform phonon 
-            renormalization. Can be given as a single float, or a dictionary
+            renormalization. Can be given as a single float, list, or a dictionary
             with the keys "min", "max", "step".
         shengbte_cmd: Command to run ShengBTE. Supports env_chk.
         shengbte_fworker: If None, the ShengBTE firework's fworker will be set

From d6b0f7b2218240a8002e9a3f820535a6dac3f9a2 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 17 Jun 2021 22:14:41 -0700
Subject: [PATCH 123/207] update

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index a03d28d86..d32af3052 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -95,6 +95,8 @@ class LatticeThermalConductivityFW(Firework):
         db_file: Path to a db file.
         shengbte_cmd: The name of the shengbte executable to run. Supports
             env_chk.
+        renormalized: boolean to denote whether force constants are from 
+            phonon renormalization (True) or directly from fitting (False)
         temperature: The temperature to calculate the lattice thermal
             conductivity for. Can be given as a single float, or a
             dictionary with the keys "min", "max", "step".

From 5a859b3409ca87943932c91911b95e460e0c4ba0 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 17 Jun 2021 22:20:23 -0700
Subject: [PATCH 124/207] update

---
 atomate/vasp/firetasks/lattice_dynamics.py | 2 ++
 atomate/vasp/fireworks/lattice_dynamics.py | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index f9fe08811..99822ca8e 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -503,6 +503,8 @@ class RunShengBTE(FiretaskBase):
             env_chk.
 
     Optional parameters:
+        renormalized: boolean to denote whether force constants are from
+            phonon renormalization (True) or directly from fitting (False)  
         temperature (float or dict): The temperature to calculate the lattice
             thermal conductivity for. Can be given as a single float, or a
             dictionary with the keys "t_min", "t_max", "t_step".
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index d32af3052..44816a534 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -137,8 +137,8 @@ def __init__(
                                   .format(temperature))
             run_shengbte = RunShengBTE(
                 shengbte_cmd=shengbte_cmd,
+                renormalized=renormalized,
                 temperature=temperature,
-                renormlized=renormalized,
                 control_kwargs=shengbte_control_kwargs,
             )
         else: # only the default files are needed
@@ -153,7 +153,7 @@ def __init__(
                 copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
             run_shengbte = RunShengBTE(
                 shengbte_cmd=shengbte_cmd,
-                renormlized=renormalized,
+                renormalized=renormalized,
                 temperature=temperature,
                 control_kwargs=shengbte_control_kwargs,
             )

From 2be7628a7bc202aedc7fdb2e2f305e2456a936a5 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 1 Jul 2021 22:32:53 -0700
Subject: [PATCH 125/207] fixed cutoff

---
 atomate/vasp/analysis/lattice_dynamics.py     | 44 +++++++++++--------
 .../vasp/workflows/base/lattice_dynamics.py   |  6 +--
 atomate/vasp/workflows/presets/core.py        |  2 +-
 3 files changed, 29 insertions(+), 23 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 39bc5e35c..588f0fe1a 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -92,10 +92,11 @@ def get_cutoffs(structure: Structure):
     """
     # indexed as min_cutoffs[order][period]
     min_cutoffs = {
-        2: {1: 5.0, 2: 5.5, 3: 6.0, 4: 7.0, 5: 8.0, 6: 9.0, 7: 10.0},
+        2: {1: 5.0, 2: 6.0, 3: 7.0, 4: 8.0, 5: 9.0, 6: 9.0, 7: 10.0},
         3: {1: 3.0, 2: 3.5, 3: 4.0, 4: 4.5, 5: 5.0, 6: 5.5, 7: 6.0},
         4: {1: 2.0, 2: 2.5, 3: 3.0, 4: 3.0, 5: 3.5, 6: 4.0, 7: 4.5},
     }
+<<<<<<< HEAD
 <<<<<<< HEAD
     inc = {2: 3, 3: 1.5, 4: 1}
     steps = {2: 0.5, 3: 0.25, 4: 0.25}
@@ -104,6 +105,10 @@ def get_cutoffs(structure: Structure):
 =======
     inc = {2: 2, 3: 1, 4: 0.5}
     steps = {2: 1, 3: 0.5, 4: 0.5}
+=======
+    inc = {2: 2, 3: 1.5, 4: 0.5}
+    steps = {2: 1, 3: 0.75, 4: 0.5}
+>>>>>>> c69d0316 (fixed cutoff)
 
     row = min([s.row for s in supercell_structure.species])
     factor = row/4
@@ -121,8 +126,10 @@ def get_cutoffs(structure: Structure):
 =======
     cutoffs = np.array(list(map(list, product(range_two, range_three, range_four))))
     max_cutoff = estimate_maximum_cutoff(AseAtomsAdaptor.get_atoms(supercell_structure))
+    logger.info('CUTOFFS \n {}'.format(cutoffs))
     logger.info('MAX_CUTOFF \n {}'.format(max_cutoff))    
-    good_cutoffs = np.all(cutoffs < np.around(max_cutoff, 4) - 0.0001, axis=1)
+    good_cutoffs = np.all(cutoffs < max_cutoff-0.1, axis=1)
+    logger.info('GOOD CUTOFFS \n{}'.format(good_cutoffs))
     return cutoffs[good_cutoffs].tolist()
 >>>>>>> c094a175 (cutoff vs cell_size)
 
@@ -197,6 +204,7 @@ def fit_force_constants(
 #        "entropy": [],
 #        "heat_capacity": [],
         "fit_method": fit_method,
+        "separate_fit": separate_fit,
         "imaginary_tol": imaginary_tol,
 #        "max_n_imaginary": max_n_imaginary,
     }
@@ -228,6 +236,7 @@ def fit_force_constants(
     cutoff_results = Parallel(n_jobs=12, backend="multiprocessing")(delayed(_run_cutoffs)(
         i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, fit_method,
         separate_fit, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
+#        separate_fit, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
     logger.info('CUTOFF RESULTS \n {}'.format(cutoff_results))
     
@@ -400,14 +409,15 @@ def get_structure_container(
         opt.train()
         parameters = opt.parameters
         logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
-    
+
+    logger.info('Memory use: {} %'.format(psutil.virtual_memory().percent))
     parameters = enforce_rotational_sum_rules(
         cs, parameters, ["Huang", "Born-Huang"]
     )
     fcp = ForceConstantPotential(cs, parameters)
     fcs = fcp.get_force_constants(supercell_atoms)
     logger.info('FCS generated for cutoff {}, {}'.format(i,cutoffs))
-
+    
     try:
         return {
             "cutoffs": cutoffs,
@@ -441,32 +451,30 @@ def get_structure_container(
     """
 
     sc = StructureContainer(cs)
-    saved_strutures = []
-    structure_orig = structures[0]
+    saved_structures = []
     for i, structure in enumerate(structures):
-        if i==0:
-            continue
-        displacements = get_displacements(structure_orig, structure)
+        displacements = structure.get_array('displacements')
         mean_displacements = np.linalg.norm(displacements,axis=1).mean()
+        logger.info('Mean displacements: {}'.format(mean_displacements))
         if not separate_fit: # fit all
             sc.add_structure(structure)
         else: # fit separately
             if param2 is None: # for harmonic fitting
-                if mean_displacements <= 0.05:
+                if mean_displacements < 0.07:
                     sc.add_structure(structure) 
             else: # for anharmonic fitting
-                if mean_displacements >= 0.15:
+                if mean_displacements >= 0.07:
                     sc.add_structure(structure) 
                     saved_structures.append(structure) 
     if separate_fit and param2 is not None: # do after anharmonic fitting
         A_mat = sc.get_fit_data()[0] # displacement matrix
         f_vec = sc.get_fit_data()[1] # force vector
-        new_force = f_vec - np.dot(A_mat[:,:ncut],param2) # subract harmonic forces
+        anh_force = f_vec - np.dot(A_mat[:,:ncut],param2) # subtract harmonic forces
         sc.delete_all_structures()
         for i, structure in enumerate(saved_structures):
-            naroms = structure.et_global_number_of_atoms()
+            natoms = structure.get_global_number_of_atoms()
             ndisp = natoms*3
-            structure.set_array('forces',new_force[i*ndisp:(i+1)*ndisp].reshape(natoms,3))
+            structure.set_array('forces',anh_force[i*ndisp:(i+1)*ndisp].reshape(natoms,3))
             sc.add_structure(structure)
 
     logger.debug(sc.__repr__())
@@ -648,9 +656,7 @@ def gruneisen(
 
     gruneisen = Gruneisen(fcs2,fcs3,phonopy.supercell,phonopy.primitive)
     gruneisen.set_sampling_mesh(phonopy.mesh_numbers,is_gamma_center=True)
-    logger.info('Memory use before Gruneisen: {} %'.format(psutil.virtual_memory().percent))
     gruneisen.run()
-    logger.info('Memory use after Gruneisen: {} %'.format(psutil.virtual_memory().percent))
     grun = gruneisen.get_gruneisen_parameters() # (nptk,nmode,3,3)
     omega = gruneisen._frequencies
     qp = gruneisen._qpoints
@@ -668,8 +674,8 @@ def gruneisen(
         vol = phonopy.primitive.get_volume()
         cte = grun_tot*(Cv.repeat(3).reshape((len(Cv),3)))/(vol/10**30)/(bulk_modulus*10**9)/3
         cte = np.nan_to_num(cte)    
-        logger.info('Gruneisen : {}'.format(grun_tot))
-        logger.info('CTE : {}'.format(cte))    
+        logger.info('Gruneisen: \n {}'.format(grun_tot))
+        logger.info('CTE: \n {}'.format(cte))    
     return grun_tot, cte
 
 
@@ -691,7 +697,7 @@ def thermal_expansion(
     for t in range(len(temperature)):
         dLfrac[t,:] = np.trapz(cte[:t+1,:],temperature[:t+1],axis=0)
     dLfrac = np.nan_to_num(dLfrac)
-    logger.info('dLfrac : {}'.format(dLfrac))
+    logger.info('dLfrac: \n {}'.format(dLfrac))
     if T is None:
         return dLfrac
     else:
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 672f42be8..eaff6de48 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -34,10 +34,10 @@
     "PREC": "Accurate",
     "ADDGRID": True,
     "LCHARG": False,
-    "ENCUT": 520,
+    "ENCUT": 600,
     "ISMEAR": 0,
     "SIGMA": 0.1,
-    "EDIFF": 1e-6,
+    "EDIFF": 1e-7,
     "LAECHG": False,
     "LREAL": False,
     "LASPH": True,
@@ -200,7 +200,7 @@ def get_lattice_dynamics_wf(
                 fw_lattice_conductivity.append(fw)
             wf.append_wf(
                 Workflow.from_Firework(fw_lattice_conductivity), wf.leaf_fw_ids
-            )                
+            )
         else:
             fw_lattice_conductivity = LatticeThermalConductivityFW(
                 db_file=db_file,
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 21095a194..524b049d2 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -878,7 +878,7 @@ def wf_lattice_dynamics(
     """
     optimize_uis = {
         "LAECHG": False,
-        'ENCUT': 520,
+        'ENCUT': 600,
         'ADDGRID': True,
         'EDIFFG': -5e-4,
         'PREC': 'Accurate',

From aa9d488aefa4333c4a38b961006216e64a33ce8c Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 7 Jul 2021 19:37:32 -0700
Subject: [PATCH 126/207] update

---
 atomate/vasp/analysis/lattice_dynamics.py | 45 +++++++++++++++--------
 1 file changed, 30 insertions(+), 15 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 588f0fe1a..b815c1ec0 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -53,35 +53,45 @@
 
 def get_cutoffs(structure: Structure):
     """
+<<<<<<< HEAD
     Get a list of trial cutoffs based on a structure.
+=======
+    Get a list of trial cutoffs based on a supercell structure for grid search.
+>>>>>>> b637d9a8 (update)
 
     An initial guess for the lower bound of the cutoffs is made based on the
-    period of the lightest element in the structure, according to:
+    average period (row) of the elements in the structure, according to:
 
     ====== === === ===
     .        Cutoff
     ------ -----------
     Period 2ND 3RD 4TH
     ====== === === ===
-     1     5.0 3.0 2.0
-     2     5.5 3.5 2.5
-     3     6.0 4.0 3.0
-     4     7.0 4.5 3.0
-     5     8.0 5.0 3.5
-     6     9.0 5.5 4.0
-     7     10.0 6.0 4.5
+     1     5.0 3.0 2.5
+     2     6.0 3.5 3.0
+     3     7.0 4.5 3.5
+     4     8.0 5.5 4.0
+     5     9.0 6.0 4.5
+     6     10.0 6.5 5.0
+     7     11.0 7.0 5.5
     ====== === === ===
 
     The maximum cutoff for each order is determined by the minimum cutoff and
     the following table. A full grid of all possible cutoff combinations is
-    generated based on the step size in the table below
+    generated based on the step size in the table below times a row factor
 
     ====== ==== =====
     Cutoff Max  Step
     ====== ==== =====
+<<<<<<< HEAD
     2ND    +3.0 0.5
     3RD    +1.5 0.25
     4TH    +1.0 0.25
+=======
+    2ND    +2.0 1.0
+    3RD    +1.5 0.75
+    4TH    +0.6 0.6
+>>>>>>> b637d9a8 (update)
     ====== ==== =====
 
     Args:
@@ -92,11 +102,12 @@ def get_cutoffs(structure: Structure):
     """
     # indexed as min_cutoffs[order][period]
     min_cutoffs = {
-        2: {1: 5.0, 2: 6.0, 3: 7.0, 4: 8.0, 5: 9.0, 6: 9.0, 7: 10.0},
-        3: {1: 3.0, 2: 3.5, 3: 4.0, 4: 4.5, 5: 5.0, 6: 5.5, 7: 6.0},
-        4: {1: 2.0, 2: 2.5, 3: 3.0, 4: 3.0, 5: 3.5, 6: 4.0, 7: 4.5},
+        2: {1: 5.0, 2: 6.0, 3: 7.0, 4: 8.0, 5: 9.0, 6: 10.0, 7: 11.0},
+        3: {1: 3.0, 2: 3.5, 3: 4.5, 4: 5.5, 5: 6.0, 6: 6.5, 7: 7.0},
+        4: {1: 2.5, 2: 3.0, 3: 3.5, 4: 4.0, 5: 4.5, 6: 5.0, 7: 5.5},
     }
 <<<<<<< HEAD
+<<<<<<< HEAD
 <<<<<<< HEAD
     inc = {2: 3, 3: 1.5, 4: 1}
     steps = {2: 0.5, 3: 0.25, 4: 0.25}
@@ -109,8 +120,12 @@ def get_cutoffs(structure: Structure):
     inc = {2: 2, 3: 1.5, 4: 0.5}
     steps = {2: 1, 3: 0.75, 4: 0.5}
 >>>>>>> c69d0316 (fixed cutoff)
+=======
+    inc = {2: 2, 3: 1.5, 4: 0.6}
+    steps = {2: 1, 3: 0.75, 4: 0.6}
+>>>>>>> b637d9a8 (update)
 
-    row = min([s.row for s in supercell_structure.species])
+    row = int(np.around(np.array([s.row for s in supercell_structure.species]).mean(),0))
     factor = row/4
 >>>>>>> cc7520c5 (separate fitting)
     mins = {
@@ -460,10 +475,10 @@ def get_structure_container(
             sc.add_structure(structure)
         else: # fit separately
             if param2 is None: # for harmonic fitting
-                if mean_displacements < 0.07:
+                if mean_displacements < 0.04:
                     sc.add_structure(structure) 
             else: # for anharmonic fitting
-                if mean_displacements >= 0.07:
+                if mean_displacements >= 0.04:
                     sc.add_structure(structure) 
                     saved_structures.append(structure) 
     if separate_fit and param2 is not None: # do after anharmonic fitting

From 805071438b79cfe11ded0720588cb35d9e337efa Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 7 Jul 2021 21:44:17 -0700
Subject: [PATCH 127/207] disp_cut

---
 atomate/vasp/analysis/lattice_dynamics.py     | 30 ++++++++++++++-----
 atomate/vasp/firetasks/lattice_dynamics.py    |  5 ++++
 atomate/vasp/fireworks/lattice_dynamics.py    | 11 ++++---
 .../vasp/workflows/base/lattice_dynamics.py   |  6 ++++
 4 files changed, 41 insertions(+), 11 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index b815c1ec0..3ec64d673 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -155,6 +155,7 @@ def fit_force_constants(
     structures: List["Atoms"],
     all_cutoffs: List[List[float]],
     separate_fit: bool,
+    disp_cut: float = None,
     imaginary_tol: float = IMAGINARY_TOL,
     fit_method: str = FIT_METHOD,
 <<<<<<< HEAD
@@ -184,6 +185,10 @@ def fit_force_constants(
         all_cutoffs: A nested list of cutoff values to trial. Each set of
             cutoffs contains the radii for different orders starting with second
             order.
+        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
+            are to be done separately (True) or in one shot (False)
+        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting
         imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
             in THz.
         max_n_imaginary: Maximum number of imaginary modes allowed in the
@@ -220,6 +225,7 @@ def fit_force_constants(
 #        "heat_capacity": [],
         "fit_method": fit_method,
         "separate_fit": separate_fit,
+        "disp_cut": disp_cut,
         "imaginary_tol": imaginary_tol,
 #        "max_n_imaginary": max_n_imaginary,
     }
@@ -250,8 +256,7 @@ def fit_force_constants(
     logger.info('CPU COUNT: {}'.format(os.cpu_count()))
     cutoff_results = Parallel(n_jobs=12, backend="multiprocessing")(delayed(_run_cutoffs)(
         i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, fit_method,
-        separate_fit, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
-#        separate_fit, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
+        separate_fit, disp_cut, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
     logger.info('CUTOFF RESULTS \n {}'.format(cutoff_results))
     
@@ -287,6 +292,7 @@ def _run_cutoffs(
     supercell_matrix,
     fit_method,
     separate_fit,
+    disp_cut,
     imaginary_tol,
     fit_kwargs
 ) -> Dict:
@@ -320,7 +326,8 @@ def _run_cutoffs(
     
     if separate_fit:
         logger.info('Fitting harmonic force constants separately')
-        sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=None)
+        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+                                     ncut=n2nd, param2=None)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [0,n2nd],
@@ -334,7 +341,8 @@ def _run_cutoffs(
         param_harmonic = opt.parameters # harmonic force constant parameters
         
         logger.info('Fitting anharmonic force constants separately')
-        sc = get_structure_container(cs, structures, separate_fit, ncut=n2nd, param2=param_harmonic)
+        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+                                     ncut=n2nd, param2=param_harmonic)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [n2nd,nall],
@@ -416,7 +424,8 @@ def get_structure_container(
         
     else:
         logger.info('Fitting all force constants in one shot')
-        sc = get_structure_container(cs, structures, separate_fit, ncut=None, param2=None)
+        sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
+                                     ncut=None, param2=None)
         opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [0,nall],
@@ -449,6 +458,7 @@ def get_structure_container(
         cs: ClusterSpace,
         structures: List["Atoms"],
         separate_fit: bool,
+        disp_cut: float,
         ncut: int,
         param2: np.ndarray
 >>>>>>> cc7520c5 (separate fitting)
@@ -460,6 +470,12 @@ def get_structure_container(
         cutoffs: Cutoff radii for different orders starting with second order.
         structures: A list of ase atoms objects with the "forces" and
             "displacements" arrays included.
+        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
+            are to be done separately (True) or in one shot (False)
+        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting 
+        ncut: the parameter index where fitting separation occurs
+        param2: previously fit parameter array (harmonic only for now, hence 2)
 
     Returns:
         A hiPhive StructureContainer.
@@ -475,10 +491,10 @@ def get_structure_container(
             sc.add_structure(structure)
         else: # fit separately
             if param2 is None: # for harmonic fitting
-                if mean_displacements < 0.04:
+                if mean_displacements < disp_cut:
                     sc.add_structure(structure) 
             else: # for anharmonic fitting
-                if mean_displacements >= 0.04:
+                if mean_displacements >= disp_cut:
                     sc.add_structure(structure) 
                     saved_structures.append(structure) 
     if separate_fit and param2 is not None: # do after anharmonic fitting
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 99822ca8e..900e1b710 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -131,6 +131,8 @@ class RunHiPhive(FiretaskBase):
         separate_fit: If True, harmonic and anharmonic force constants are fit
             separately and sequentially, harmonic first then anharmonic. If
             False, then they are all fit in one go. Default is False.
+        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting  
         imaginary_tol (float): Tolerance used to decide if a phonon mode
             is imaginary, in THz.
         fit_method (str): Method used for fitting force constants. This can be
@@ -140,6 +142,7 @@ class RunHiPhive(FiretaskBase):
     optional_params = [
         "cutoffs",
         "separate_fit",
+        "disp_cut",
         "bulk_modulus",
         "imaginary_tol",
         "fit_method",
@@ -151,6 +154,7 @@ def run_task(self, fw_spec):
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
         fit_method = self.get("fit_method", FIT_METHOD)
         separate_fit = self.get('separate_fit', False)
+        disp_cut = self.get('disp_cut',None)
         
         all_structures = loadfn("perturbed_structures.json")
         all_forces = loadfn("perturbed_forces.json")
@@ -177,6 +181,7 @@ def run_task(self, fw_spec):
             structures,
             cutoffs,
             separate_fit,
+            disp_cut,
             imaginary_tol,
             fit_method
         )
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 44816a534..8f6c10bdd 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -38,10 +38,11 @@ class FitForceConstantsFW(Firework):
         db_file: Path to a db file.
         cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
             will be generated based on the structure (default).
-        separate_fit: If True, harmonic and anharmonic force constants are fit
-            separately and sequentially, harmonic first then anharmonic. If
-            False, then they are all fit in one go. Default is False.
-        bulk_modulus: Must be supplied (in GPa) to copute thermal expansion
+        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
+            are to be done separately (True) or in one shot (False)
+        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting  
+        bulk_modulus: in GPa, necessary for thermal expansion
         imaginary_tol: Tolerance used to decide if a phonon mode is
             imaginary, in THz.
         fit_method: Method used for fitting force constants. This can be
@@ -59,6 +60,7 @@ def __init__(
         db_file: str = None,
         cutoffs: Optional[List[List[float]]] = None,
         separate_fit: bool = False,
+        disp_cut: float = None,
         bulk_modulus: float = None,
         imaginary_tol: float = IMAGINARY_TOL,
         fit_method: str = FIT_METHOD,
@@ -70,6 +72,7 @@ def __init__(
         fit_force_constants = RunHiPhive(
             cutoffs=cutoffs,
             separate_fit=separate_fit,
+            disp_cut=disp_cut,
             bulk_modulus=bulk_modulus,
             imaginary_tol=imaginary_tol,
             fit_method=fit_method
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index eaff6de48..22fc3b336 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -57,6 +57,7 @@
 def get_lattice_dynamics_wf(
     structure: Structure,
     separate_fit: bool = False,
+    disp_cut: float = None,
     bulk_modulus: float = None,
     common_settings: Dict = None,
     vasp_input_set: Optional[VaspInputSet] = None,
@@ -98,6 +99,11 @@ def get_lattice_dynamics_wf(
 
     Args:
         structure: Initial structure.
+        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
+            are to be done separately (True) or in one shot (False)
+        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting  
+        bulk_modulus: bulk modulus in GPa, necessary for thermal expansion
         common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
             and "user_incar_settings" keys.
         vasp_input_set: Vasp input set for perturbed structure calculations.

From 01695f5a66fc3c0e0b8aa544bc3fc30df6585981 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 8 Jul 2021 00:23:42 -0700
Subject: [PATCH 128/207] disp_cut fix

---
 atomate/vasp/workflows/presets/core.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 524b049d2..56f95809a 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -851,6 +851,7 @@ def wf_nudged_elastic_band(structures, parent, c=None):
 def wf_lattice_dynamics(
     structure: Structure,
     separate_fit: bool = False,
+    disp_cut: float = None,
     bulk_modulus: float = None,
     c: Optional[dict] = None,
     supercell_matrix_kwargs: Optional[dict] = None,
@@ -906,6 +907,7 @@ def wf_lattice_dynamics(
     wf_ld = get_lattice_dynamics_wf(
         structure,
         separate_fit = separate_fit,
+        disp_cut = disp_cut,
         bulk_modulus = bulk_modulus,
         common_settings=c,
         supercell_matrix_kwargs=supercell_matrix_kwargs,

From 2fcbfcce9ae360f0de7fb7df81efcd34885c6a57 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 8 Jul 2021 16:15:12 -0700
Subject: [PATCH 129/207] disp_cut in FitForceConstantsFW

---
 atomate/vasp/firetasks/lattice_dynamics.py      | 2 +-
 atomate/vasp/workflows/base/lattice_dynamics.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 900e1b710..ca65a2378 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -154,7 +154,7 @@ def run_task(self, fw_spec):
         imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
         fit_method = self.get("fit_method", FIT_METHOD)
         separate_fit = self.get('separate_fit', False)
-        disp_cut = self.get('disp_cut',None)
+        disp_cut = self.get('disp_cut', None)
         
         all_structures = loadfn("perturbed_structures.json")
         all_forces = loadfn("perturbed_forces.json")
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 22fc3b336..4ff7cb4d1 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -173,8 +173,8 @@ def get_lattice_dynamics_wf(
     # 2. Fit interatomic force constants from pertrubed structures
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
-        db_file=db_file, spec=allow_fizzled,
-        separate_fit=separate_fit, bulk_modulus=bulk_modulus
+        db_file=db_file, spec=allow_fizzled, separate_fit=separate_fit,
+        disp_cut=disp_cut, bulk_modulus=bulk_modulus
     )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 

From a817a0072893667696c68472f18b9a035bdc6e03 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Thu, 27 Oct 2022 11:17:41 -0400
Subject: [PATCH 130/207] renormalization

---
 atomate/vasp/analysis/lattice_dynamics.py     |  46 +-
 atomate/vasp/firetasks/lattice_dynamics.py    | 396 ++++++++----------
 atomate/vasp/fireworks/lattice_dynamics.py    | 125 +++---
 .../vasp/workflows/base/lattice_dynamics.py   |  83 ++--
 atomate/vasp/workflows/presets/core.py        |  29 +-
 5 files changed, 352 insertions(+), 327 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 3ec64d673..589f9cab6 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -22,12 +22,14 @@
 from hiphive.fitting import Optimizer
 from hiphive.renormalization import Renormalization
 from hiphive.utilities import get_displacements
+from hiphive.run_tools import FE_correction
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 >>>>>>> 8f4f7e37 (gruneisen and CTE)
 from pymatgen.io.phonopy import get_phonopy_structure
 
+from ase.atoms import Atoms
 from ase.cell import Cell
 
 from phonopy import Phonopy
@@ -39,13 +41,19 @@
 
 logger = get_logger(__name__)
 
+# Define some shared constants
 IMAGINARY_TOL = 0.025  # in THz
+MESH_DENSITY = 100.0  # should always be a float 
 
-T_QHA = [i*100 for i in range(16)]
-T_RENORM = [0,100,200,300,500,700,1000,1500]#[i*100 for i in range(0,16)]
-T_KLAT = {"t_min":100,"t_max":1000,"t_step":100} #[i*100 for i in range(0,11)]
+T_QHA = [i*100 for i in range(21)]
+T_RENORM = [0,50,100,200,300,500,700,1000,1500]#[i*100 for i in range(0,16)]
+T_KLAT = {"t_min":100,"t_max":1500,"t_step":100} #[i*100 for i in range(0,11)]
 
-FIT_METHOD = "rfe" #"least-squares"
+FIT_METHOD = "rfe" 
+RENORM_METHOD = 'pseudoinverse'
+RENORM_NCONFIG = 50
+RENORM_CONV_THRESH = 0.1 # meV/atom
+RENORM_MAX_ITER = 20
 
 eV2J = 1.602e-19
 hbar = sp.constants.hbar
@@ -553,7 +561,7 @@ def harmonic_properties(
     free_energy *= 1000/sp.constants.Avogadro/eV2J/natom # kJ/mol to eV/atom
     entropy *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
     Cv *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
-    
+
     freq = phonopy.mesh.frequencies # in THz
     # find imaginary modes at gamma
 #    phonopy.run_qpoints([0, 0, 0])
@@ -739,25 +747,32 @@ def thermal_expansion(
             raise ValueError('Designated T does not exist in the temperature array!')
 
 
-def renormalization(
+def run_renormalization(
         structure: Structure,
+        supercell: Atoms,
         supercell_matrix: np.ndarray,
         cs: ClusterSpace,
         fcs: ForceConstants,
         param: np.ndarray,
         T: float,
         nconfig: int,
+        max_iter: int,
         conv_tresh: float,
+        renorm_method: str,
+        fit_method: str,
         bulk_modulus: float = None,
+        phonopy_orig: Phonopy = None,
         imaginary_tol: float = IMAGINARY_TOL,
-        fit_method: str = None
 ) -> Dict:
     """
     Uses the force constants to extract phonon properties. Used for comparing
     the accuracy of force constant fits.
 
     Args:
-        structure: The parent structure.
+        structure: pymatgen Structure
+            The parent structure.
+        supercell : ase Atoms
+            Original supercell object  
         supercell_matrix: The supercell transformation matrix.
         fcs: ForceConstants from previous fitting or renormalization
         imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
@@ -767,14 +782,14 @@ def renormalization(
         A tuple of the number of imaginary modes at Gamma, the minimum phonon
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
-    renorm = Renormalization(cs,fcs,param,T,fit_method)
-    fcp, fcs, param = renorm.renormalize(nconfig,'pseudoinverse',conv_tresh)
+    renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
+    fcp, fcs, param = renorm.renormalize(nconfig,conv_tresh)
 
     renorm_data, phonopy = harmonic_properties(
         structure, supercell_matrix, fcs, [T], imaginary_tol
     )
 
-    if renorm_data["n_imaginary"] ==0:
+    if renorm_data["n_imaginary"] == 0:
         logger.info('Renormalized phonon is completely real at T = {} K!'.format(T))
         anharmonic_data, phonopy = anharmonic_properties(
             phonopy, fcs, [T], thermal_data["heat_capacity"], n_imaginary, bulk_modulus=bulk_modulus
@@ -783,7 +798,14 @@ def renormalization(
         anharmonic_data = dict()
         anharmonic_data["gruneisen"] = np.array([[0,0,0]])
         anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
+
+    omega0 = phonopy_orig.mesh.frequencies # THz
+    omega_TD = phonopy.mesh.frequencies # THz
+    natom = phonopy.primitive.get_number_of_atoms()
+    correction = FE_correction(omega0,omega_TD,T)/natom # eV/atom
+
     renorm_data.update(anharmonic_data)
+    renorm_data["free_energy_correction"] = correction
     renorm_data["fcp"] = fcp
     renorm_data["fcs"] = fcs
     renorm_data["param"] = param
@@ -792,7 +814,7 @@ def renormalization(
 
 
 
-def setup_TE_renorm(parent_structure,temperatures,dLfracs):
+def setup_TE_iter(cutoffs,parent_structure,temperatures,dLfracs):
     parent_structure_TE = []
     cs_TE = []
     fcs_TE = []
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index ca65a2378..53d87fb2c 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -7,25 +7,26 @@
 
 import numpy as np
 from joblib import Parallel, delayed
+from copy import copy, deepcopy
 
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
 from monty.json import jsanitize
 from pymongo import ReturnDocument
 
+import phonopy as phpy
+
 from atomate.utils.utils import env_chk, get_logger
 from atomate.vasp.database import VaspCalcDb
 from atomate.vasp.drones import VaspDrone
 from atomate.vasp.analysis.lattice_dynamics import (
-    FIT_METHOD,
-    IMAGINARY_TOL,
     T_QHA,
-    T_RENORM,
     T_KLAT,
     fit_force_constants,
     harmonic_properties,
     anharmonic_properties,
-    renormalization,
+    run_renormalization,
+    setup_TE_iter,
     get_cutoffs
 )
 
@@ -54,9 +55,6 @@
 
 logger = get_logger(__name__)
 
-# define shared constants
-MESH_DENSITY = 100.0  # should always be a float
-
 
 @explicit_serialize
 class CollectPerturbedStructures(FiretaskBase):
@@ -131,12 +129,12 @@ class RunHiPhive(FiretaskBase):
         separate_fit: If True, harmonic and anharmonic force constants are fit
             separately and sequentially, harmonic first then anharmonic. If
             False, then they are all fit in one go. Default is False.
-        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+        disp_cut: if separate_fit=True, determines the mean displacement of perturbed
             structure to be included in harmonic (<) or anharmonic (>) fitting  
         imaginary_tol (float): Tolerance used to decide if a phonon mode
             is imaginary, in THz.
-        fit_method (str): Method used for fitting force constants. This can be
-            any of the values allowed by the hiphive ``Optimizer`` class.
+        fit_method (str): Method used for fitting force constants. This can
+            be any of the values allowed by the hiphive ``Optimizer`` class.
     """
 
     optional_params = [
@@ -151,19 +149,21 @@ class RunHiPhive(FiretaskBase):
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
 
-        imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
-        fit_method = self.get("fit_method", FIT_METHOD)
         separate_fit = self.get('separate_fit', False)
         disp_cut = self.get('disp_cut', None)
-        
+        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
+        T_qha = np.array(self.get("T_qha"))
+        T_qha.sort()
+        imaginary_tol = self.get("imaginary_tol")
+        bulk_modulus = self.get("bulk_modulus")
+        fit_method = self.get("fit_method")
+
         all_structures = loadfn("perturbed_structures.json")
         all_forces = loadfn("perturbed_forces.json")
         structure_data = loadfn("structure_data.json")
         parent_structure = structure_data["structure"]
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = np.array(structure_data["supercell_matrix"])
-        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        bulk_modulus = self.get("bulk_modulus")
 
         structures = []
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
@@ -200,10 +200,11 @@ def run_task(self, fw_spec):
             thermal_data["n_imaginary"], bulk_modulus
         )
 
+        phonopy.save("phonopy_params.yaml")
         fitting_data["n_imaginary"] = thermal_data.pop("n_imaginary")
         thermal_data.update(anharmonic_data)
         dumpfn(fitting_data, "fitting_data.json")
-        dumpfn(thermal_data, "thermal_data_qha.json")
+        dumpfn(thermal_data, "thermal_data.json")
 
         logger.info("Writing cluster space and force_constants")
         logger.info("{}".format(type(fcs)))
@@ -217,7 +218,8 @@ def run_task(self, fw_spec):
             fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms, order=3)
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
         else:
-            logger.info("ShengBTE files not written due to imaginary modes. You may want to perform phonon renormalization.")
+            logger.info("ShengBTE files not written due to imaginary modes.")
+            logger.info("You may want to perform phonon renormalization.")
 
 
 
@@ -228,102 +230,114 @@ class RunHiPhiveRenorm(FiretaskBase):
     using hiPhive. Requires "structure_data.json" to be present in the current working
     directory.
 
-    cs,supercell,fcs,param,T,
-
     Required parameters:
-        cs (hiphive.ClusterSpace): A list of cutoffs to trial. If None,
-            a set of trial cutoffs will be generated based on the structure
-            (default).
-        fcs (hiphive.ForceConstants): Maximum number of imaginary modes allowed in the
-            the final fitted force constant solution. If this criteria is not
-            reached by any cutoff combination this FireTask will fizzle.
-        param (np.ndarray): array of force constant parameters
-        cutoffs (np.ndarray): cutoffs used for best fitting
    
     Optional parameter:
-        T_renorm (List): list of temperatures to perform renormalization - default is T_RENORM
-        bulk_modulus (float): manually input bulk modulus - necessary for thermal expansion
-        renorm_with_te (bool): if True, 
+        renorm_temp (List): list of temperatures to perform renormalization - defaults to T_RENORM
+        renorm_with_te (bool): if True, perform outer iteration over thermally expanded volumes
+        bulk_modulus (float): input bulk modulus - required for thermal expansion iterations
     """
 
-    required_params = ["cs","fcs","param","cutoff"]
-    optional_params = ["T_renorm","bulk_modulus","renorm_with_te","fit_method"]
+    optional_params = ["renorm_method","renorm_temp","nconfig","conv_thresh","max_iter",
+                       "renorm_TE_iter","bulk_modulus","imaginary_tol"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
 
-        imaginary_tol = self.get("imaginary_tol", IMAGINARY_TOL)
-        fit_method = self.get("fit_method", FIT_METHOD)
-
+        cs = ClusterSpace.read('cluster_space.cs')
+        fcs = ForceConstants.read('force_constants.fcs')
+        param = np.loadtxt('parameters.txt')
+        fitting_data = loadfn("fitting_data.json")
         structure_data = loadfn("structure_data.json")
+        phonopy_orig = phpy.load("phonopy_params.yaml")
+
+        cutoffs = fitting_data["cutoffs"]
+        fit_method = fitting_data["fit_method"]
+        imaginary_tol = fitting_data["imaginary_tol"]
+
         parent_structure = structure_data["structure"]
         supercell_structure = structure_data["supercell_structure"]
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
         supercell_matrix = np.array(structure_data["supercell_matrix"])
 
-        cs = self.get("cs")
-        fcs = self.get("fcs")
-        param = self.get("param")
+        renorm_temp = np.array(self.get("renorm_temp"))
+        renorm_temp.sort()
+        renorm_method = self.get("renorm_method")
+        nconfig = self.get("nconfig")
+        conv_thresh = self.get("conv_thresh")
+        max_iter = self.get("max_iter")
+        renorm_TE_iter = self.get("renorm_TE_iter")
         bulk_modulus = self.get("bulk_modulus")
-        T_renorm = self.get("T_renorm", T_RENORM)
-
-        renorm_results = Parallel(n_jobs=4, backend="multiprocessing")(delayed(renormalization)(
-            parent_structure, supercell_matrix, cs, fcs, param, T, nconfig, conv_thresh, imaginary_tol
-        ) for t, T in enumerate(T_renorm))
-
-        T_real = []
-        cte_real = []
-        fcs_real = []
-        param_real = []
-        for result in renorm_results:
-            if result is None:
-                continue
-            elif result["n_imaginary"] > 0 or bulk_modulus is None:
-                fcs = result["fcs"][0]
-                fcs.write("force_constants_{}K.fcs".format(T))
-                np.savetxt('parameters_{}K.txt'.format(T),result["param"][0])
-            else:
-                T_real = T_real + result["temperature"]
-                cte_real = cte_real + result["thermal_expansion"]
-                fcs_real = fcs_real + result["fcs"]
-                param_real = param_real + result["param"]
-        if len(T_real)==0:
-            pass
-        elif len(T_real)==1 and T_real[0]==0:
-            fcs = result["fcs"][0]
-            fcs.write("force_constants_{}K.fcs".format(T))
-            np.savetxt('parameters_{}K.txt'.format(T),result["param"][0])
-        else:
-            ind = np.argsort(np.array(T_real))
-            T_real = list(np.array(T_real)[ind])
-            cte_real = list(np.array(cte_real)[ind])
-            dLfrac_real = thermal_expansion(T_real,cte_real)
-            parent_structure_TE, cs_TE, fcs_TE = setup_TE_renorm(parent_structure,T_real,dLfrac_real)
-            renorm_results = Parallel(n_jobs=2, backend="multiprocessing")(delayed(renormalization)(
-                parent_structure_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param, T, nconfig, conv_thresh, imaginary_tol
-            ) for t, T in enumerate(T_real))
-
-            logger.info("Writing renormalized results")
-            thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
-                            "gruneisen","thermal_expansion","expansion_ratio"]
-            thermal_data = {key: [] for key in thermal_keys}
-            for t, result in enumerate(renorm_results):
-                T = result["temperature"][0]
-                fcs = result["fcs"][0]
-                fcs.write("force_constants_{}K.fcs".format(T))
-                np.savetxt('parameters_{}K.txt'.format(T),result["param"][0])
-                for key in thermal_keys:
-                    thermal_data[key].append(result[key][0])
-                if result["n_imaginary"] > 0:
-                    logger.warning('Imaginary modes generated for {} K!'.format(T))
-                    logger.warning('Renormalization with thermal expansion may have failed')
-                    logger.warning('ShengBTE files not written')
+
+        # First renormalization with DFT lattice 
+        renorm_data = Parallel(n_jobs=4, backend="multiprocessing")(delayed(run_renormalization)(
+            parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, max_iter,
+            conv_thresh, bulk_modulus, phonopy_orig) for t, T in enumerate(renorm_temp))
+
+        # Additional renormalization with thermal expansion - optional - just single "iteration" for now
+        if renorm_TE_iter:
+            n_TE_iter = 1            
+            for i in range(n_TE_iter):
+                logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
+
+                if i==0: # first iteration - pull only cases where phonon is all real and order by temperature
+                    T_real = []
+                    dLfrac_real = []
+                    param_real = []
+                    for result in renorm_data:
+                        if result is None: # failed or incomplete 
+                            continue 
+                        elif result["n_imaginary"] < 0: # still imaginary
+                            continue
+                        else:
+                            T_real = T_real + result["temperature"]
+                            dLfrac_real = dLfrac_real + result["expansion_ratio"]
+                            param_real = param_real + result["param"]
+                    if len(T_real)==0: 
+                        logger.info("No cases with real phonons - cannot do thermal expansion for any temperature")
+                        break
                 else:
-                    logger.info("No imaginary modes! Writing ShengBTE files")
-                    fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(T), format="text")
+                    for t,result in enumerate(renorm_data):
+                        dLfrac_real[t] = result["expansion_ratio"]  
+                        param_real[t] = result["param"]
+
+                parent_structure_TE, cs_TE, fcs_TE = setup_TE_iter(cutoffs,parent_structure,T_real,dLfrac_real)
+                param_TE = copy(param_real)
+                
+                renorm_data = Parallel(n_jobs=4, backend="multiprocessing")(delayed(run_renormalization)(
+                    parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param_TE[t],
+                    T, nconfig, max_iter, conv_thresh, bulk_modulus
+                    ) for t, T in enumerate(T_real)
+                )
+
+            if len(T_real) > 0:
+                for t, result in enumerate(renorm_data):
+                    temp_index = np.where(renorm_temp==T_real[t])[0][0]
+                    renorm_data[temp_index] = result
+
+        # write results
+        logger.info("Writing renormalized results")
+        thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
+        "gruneisen","thermal_expansion","expansion_ratio","free_energy_correction"]
+        renorm_thermal_data = {key: [] for key in thermal_keys}
+        for t, result in enumerate(renorm_data):
+            logger.info("DEBUG: ",result)
+            T = result["temperature"]
+            fcs = result["fcs"]
+            fcs.write("force_constants_{}K.fcs".format(T))
+            np.savetxt('parameters_{}K.txt'.format(T),result["param"])
+            for key in thermal_keys:
+                renorm_thermal_data[key].append(result[key])
+            if result["n_imaginary"] > 0:
+                logger.warning('Imaginary modes exist for {} K!'.format(T))
+                logger.warning('ShengBTE files not written')
+                logger.warning('No renormalization with thermal expansion')
+            else:
+                logger.info("No imaginary modes! Writing ShengBTE files")
+                fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(T), format="text")
 
-            thermal_data.pop("n_imaginary")                    
-            dumpfn(thermal_data, "thermal_data_renorm.json")
+        renorm_thermal_data.pop("n_imaginary")                    
+        dumpfn(thermal_data, "renorm_thermal_data.json")
 
         
 @explicit_serialize
@@ -359,138 +373,89 @@ def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
         renormalized = self.get("renormalized", False)
-        mesh_density = self.get("mesh_density", MESH_DENSITY)
+        mesh_density = self.get("mesh_density", 100.0)
 
         structure_data = loadfn("structure_data.json")
         forces = loadfn("perturbed_forces.json")
         structures = loadfn("perturbed_structures.json")
-
-        structure = structure_data["structure"]
-        supercell_structure = structure_data["supercell_structure"]
-        supercell_matrix = structure_data["supercell_matrix"]
-
-        fitting_data = loadfn("fitting_data.json")
-        thermal_data = loadfn("thermal_data_qha.json")
-        fcs = ForceConstants.read("force_constants.fcs")
-        
-        dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-            structure, supercell_matrix, fcs, mesh_density, mmdb
-        )
-        
-        data = {
-            "created_at": datetime.utcnow(),            
-            "tags": fw_spec.get("tags", None),
-            "formula_pretty": structure.composition.reduced_formula,            
-            "structure": structure.as_dict(),
-            "supercell_matrix": supercell_matrix,
-            "supercell_structure": supercell_structure.as_dict(),
-            "perturbed_structures": [s.as_dict() for s in structures],
-            "perturbed_forces": [f.tolist() for f in forces],
-            "fitting_data": fitting_data,
-            "thermal_data": thermal_data,
-            "force_constants_fs_id": fc_fsid,
-            "phonon_dos_fs_id": dos_fsid,
-            "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-            "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-        }
-        data.update(self.get("additional_fields", {}))
-
-        # Get an id for the force constants
-        fitting_id = _get_fc_fitting_id(mmdb)
-        metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
-        data.update(metadata)
-        data = jsanitize(data,strict=True,allow_bson=True)
         
-        mmdb.db.lattice_dynamics.insert_one(data)
-            
-        logger.info("Finished inserting force constants")
-
-        return FWAction(update_spec=metadata)
-
-
-
-class ForceConstantsRenormToDb(FiretaskBase):
-    """
-    Add force constants, phonon band structure and density of states
-    to the database.
-
-    Assumes you are in a directory with the force constants, fitting
-    data, and structure data written to files.
-
-    Required parameters:
-        db_file (str): Path to DB file for the database that contains the
-            perturbed structure calculations.
-    Optional parameters:
-        renormalized (bool): Whether FC resulted from original fitting (False)
-            or renormalization process (True) determines how data are stored.
-            Default is False.                                                                                                                                                                                      mesh_density (float): The density of the q-point mesh used to calculate
-            the phonon density of states. See the docstring for the ``mesh``
-            argument in Phonopy.init_mesh() for more details.
-        additional_fields (dict): Additional fields added to the document, such
-            as user-defined tags, name, ids, etc.                                                                                                                                                              """
-
-    required_params = ["db_file"]
-    optional_params = ["renormalized","mesh_density", "additional_fields"]
-
-    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
-    def run_task(self, fw_spec):
-
-        db_file = env_chk(self.get("db_file"), fw_spec)
-        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        renormalized = self.get("renormalized", False)
-        mesh_density = self.get("mesh_density", MESH_DENSITY)
-
-        structure_data = loadfn("structure_data.json")
-        forces = loadfn("perturbed_forces.json")
-        structures = loadfn("perturbed_structures.json")
-
         structure = structure_data["structure"]
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = structure_data["supercell_matrix"]
 
-        thermal_data = loadfn("thermal_data_renorm.json")
-        temperature = thermal_data["temperature"]
-
-        data = {
-            "created_at": datetime.utcnow(),
-            "tags": fw_spec.get("tags", None),
-            "formula_pretty": structure.composition.reduced_formula,
-            "structure": structure.as_dict(),
-            "thermal_data": thermal_data,
-            }
-        
-        temperature_to_keep = []
-        renormalized_data = []
-        for t, T in enumerate(temperature):
-            ## err should I collect results for all T and push data at once,                                                                                                                            
-            ## or push data for each T individually?                                                                                                                                                    
-            fcs = ForceConstants.read("force_constants_{}K.fcs")
-            phonopy_fc = fcs.get_fc_array(order=2)
-            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-                structure, supercell_matrix, phonopy_fc, mesh_density, mmdb
-            )
+        if not renormalized:
+            
+            fitting_data = loadfn("fitting_data.json")
+            thermal_data = loadfn("thermal_data.json")
+            fcs = ForceConstants.read("force_constants.fcs")
             
-            data_at_T = {
+            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                structure, supercell_matrix, fcs, mesh_density, mmdb
+                )
+        
+            data = {
+                "created_at": datetime.utcnow(),            
+                "tags": fw_spec.get("tags", None),
+                "formula_pretty": structure.composition.reduced_formula,            
+                "structure": structure.as_dict(),
+                "supercell_matrix": supercell_matrix,
+                "supercell_structure": supercell_structure.as_dict(),
+                "perturbed_structures": [s.as_dict() for s in structures],
+                "perturbed_forces": [f.tolist() for f in forces],
+                "fitting_data": fitting_data,
+                "thermal_data": thermal_data,
                 "force_constants_fs_id": fc_fsid,
                 "phonon_dos_fs_id": dos_fsid,
                 "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
                 "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-            }
-            temperature_to_keep.append(T)
-            renormalized_data.append(data_at_T)
-        data["temperatures"] = temperature_to_keep
-        data["renormalized_data"] = renormalized_data
-        data.update(self.get("additional_fields", {}))
+                }
+            data.update(self.get("additional_fields", {}))
+
+            # Get an id for the force constants
+            fitting_id = _get_fc_fitting_id(mmdb)
+            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+            data.update(metadata)
+            data = jsanitize(data,strict=True,allow_bson=True)
+            
+            mmdb.db.lattice_dynamics.insert_one(data)
+            
+            logger.info("Finished inserting force constants and phonon data")
 
-        # Get an id for the force constants
-        fitting_id = _get_fc_fitting_id(mmdb)
-        metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
-        data.update(metadata)
-        data = jsanitize(data,strict=True,allow_bson=True)
+        else:
+            renorm_thermal_data = loadfn("renorm_thermal_data.json")
+            temperature = renorm_thermal_data["temperature"]
+
+            # pushing data for individual temperature  
+            for t, T in enumerate(temperature):
+                fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
+                phonopy_fc = fcs.get_fc_array(order=2)
+                dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                    structure, supercell_matrix, phonopy_fc, mesh_density, mmdb
+                    )
+                
+                data_at_T = {
+                    "created_at": datetime.utcnow(),
+                    "tags": fw_spec.get("tags", None),
+                    "formula_pretty": structure.composition.reduced_formula,
+                    "renormalized": renormalized,
+                    "temperature": T,
+                    "force_constants_fs_id": fc_fsid,
+                    "thermal_data": renorm_thermal_data[t],
+                    "phonon_dos_fs_id": dos_fsid,
+                    "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+                    "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+                    }
+                data_at_T.update(self.get("additional_fields", {}))
+        
+                # Get an id for the force constants
+                fitting_id = _get_fc_fitting_id(mmdb)
+                metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+                data_at_T.update(metadata)
+                data_at_T = jsanitize(data,strict=True,allow_bson=True)
 
-        mmdb.db.renormalized_lattice_dynamics.insert_one(data)
+                mmdb.db.renormalized_lattice_dynamics.insert_one(data_at_T)
 
-        logger.info("Finished inserting renormalized force constants")
+                logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
 
         return FWAction(update_spec=metadata)        
 
@@ -533,17 +498,6 @@ def run_task(self, fw_spec):
         else:
             if isinstance(temperature, (int, float)):
                 self["t"] = temperature
-            elif isinstance(temperature, (list, np.ndarray)):
-                t_max = np.max(np.array(temperature))
-                t_min = np.min(np.array(temperature))
-                if t_min==0:
-                    t_min = np.partition(temperature,1)[1]
-                    t_step = (t_max-t_min)/(len(temperature)-2)
-                else:
-                    t_step = (t_max-t_min)/(len(temperature)-1)
-                self["t_min"] = t_min
-                self["t_max"] = t_max
-                self["t_step"] = t_step
             elif isinstance(temperature, dict):
                 self["t_min"] = temperature["t_min"]
                 self["t_max"] = temperature["t_max"]
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 8f6c10bdd..fe9648232 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -1,17 +1,11 @@
-from typing import List, Optional, Union
+from typing import List, Optional, Union, Dict
 
 from atomate.common.firetasks.glue_tasks import (
     CopyFiles,
     CopyFilesFromCalcLoc,
     PassCalcLocs,
 )
-from atomate.vasp.analysis.lattice_dynamics import (
-    FIT_METHOD,
-    IMAGINARY_TOL,
-    T_QHA,
-    T_RENORM,
-    T_KLAT
-)
+
 from atomate.vasp.config import SHENGBTE_CMD
 from atomate.vasp.firetasks.lattice_dynamics import (
     CollectPerturbedStructures,
@@ -19,10 +13,13 @@
     RunHiPhive,
     RunHiPhiveRenorm,
     RunShengBTE,
-    ShengBTEToDb,
-    MESH_DENSITY)
+    ShengBTEToDb
+    )
+
 from fireworks import Firework
 
+from hiphive import ClusterSpace, ForceConstants
+
 __author__ = "Alex Ganose, Junsoo Park"
 __email__ = "aganose@lbl.gov, jsyony37@lbl.gov"
 
@@ -55,16 +52,16 @@ class FitForceConstantsFW(Firework):
 
     def __init__(
         self,
+        fit_method: str,
+        separate_fit: bool,
+        disp_cut: float,
+        bulk_modulus: float,
+        imaginary_tol: float,
+        mesh_density: float,
+        cutoffs: Optional[List[List[float]]] = None,
         name="Fit Force Constants",
         parents: Optional[Union[Firework, List[Firework]]] = None,
         db_file: str = None,
-        cutoffs: Optional[List[List[float]]] = None,
-        separate_fit: bool = False,
-        disp_cut: float = None,
-        bulk_modulus: float = None,
-        imaginary_tol: float = IMAGINARY_TOL,
-        fit_method: str = FIT_METHOD,
-        mesh_density: float = MESH_DENSITY,
         **kwargs
     ):
         collect_structures = CollectPerturbedStructures()
@@ -72,10 +69,10 @@ def __init__(
         fit_force_constants = RunHiPhive(
             cutoffs=cutoffs,
             separate_fit=separate_fit,
+            fit_method=fit_method,
             disp_cut=disp_cut,
             bulk_modulus=bulk_modulus,
             imaginary_tol=imaginary_tol,
-            fit_method=fit_method
         )
         to_db = ForceConstantsToDb(
             db_file=db_file, renormalized=False, mesh_density=mesh_density, additional_fields={}
@@ -110,40 +107,38 @@ class LatticeThermalConductivityFW(Firework):
 
     def __init__(
         self,
+        shengbte_cmd: str,
+        temperature: Union[float, dict],
+        renormalized: bool,
         name="Lattice Thermal Conductivity",
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
-        shengbte_cmd: str = SHENGBTE_CMD,
-        renormalized: bool = False,
-        temperature: Union[float, dict] = T_KLAT,
         shengbte_control_kwargs: Optional[dict] = None,
         **kwargs
-    ):
+        ):
+
         # files needed to run ShengBTE
         if renormalized: # must check if FORCE_CONSTANTS_2ND_{T}K can be copied individually
+            assert type(temperature) in [float,int]
             files = [
                 "structure_data.json",
                 "FORCE_CONSTANTS_2ND_{}K".format(temperature),
                 "FORCE_CONSTANTS_3RD"
             ]
+#            temperature_copy = temperature[:]
+#            for t,T in enumerate(temperature_copy):
+#                try:
+#                    files = files.append("FORCE_CONSTANTS_2ND_{}K".format(T))
+#                except:
+#                    logger.info("FORCE_CONSTANTS_2ND_{}K is missing".format(T))
+#                    logger.info("Renormalization must have failed at {} K".format(T))
+#                    logger.info("Cannot calculate thermal conductivity at {} K".format(T))
+#                    temperature.remove(T)
             if prev_calc_dir:
-                try:
-                    copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
-                except:
-                    raise IOError("FORCE_CONSTANTS_2ND_{}K not found! Abandoning ShengBTE run."
-                                  .format(temperature))
+                copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
-                try:
-                    copy_files = CopyFilesFromCalcLoc(calc_loc=True, files_to_copy=files)
-                except:
-                    raise IOError("FORCE_CONSTANTS_2ND_{}K not found! Abandoning ShengBTE run."
-                                  .format(temperature))
-            run_shengbte = RunShengBTE(
-                shengbte_cmd=shengbte_cmd,
-                renormalized=renormalized,
-                temperature=temperature,
-                control_kwargs=shengbte_control_kwargs,
-            )
+                copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+
         else: # only the default files are needed
             files = [
                 "structure_data.json",
@@ -151,20 +146,24 @@ def __init__(
                 "FORCE_CONSTANTS_3RD",
             ]
             if prev_calc_dir:
-                copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+                copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
                 copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
-            run_shengbte = RunShengBTE(
-                shengbte_cmd=shengbte_cmd,
-                renormalized=renormalized,
-                temperature=temperature,
-                control_kwargs=shengbte_control_kwargs,
+
+        run_shengbte = RunShengBTE(
+            shengbte_cmd=shengbte_cmd,
+            renormalized=renormalized,
+            temperature=temperature,
+            control_kwargs=shengbte_control_kwargs,
             )
             
         shengbte_to_db = ShengBTEToDb(db_file=db_file, additional_fields={})
 
         tasks = [copy_files, run_shengbte, shengbte_to_db]
-        super().__init__(tasks, name=name, **kwargs)
+        if renormalized:
+            super().__init__(tasks, name=name+' at {}K'.format(temperature), **kwargs)
+        else:
+            super().__init__(tasks, name=name, **kwargs)
 
 
 
@@ -189,31 +188,39 @@ class RenormalizationFW(Firework):
     
     def __init__(
         self,
-        temperature: Union[float, list],
+        temperature: Union[float, Dict], 
+        renorm_method: str,
+        renorm_nconfig: int,
+        renorm_conv_thresh: float,
+        renorm_max_iter: float,
+        renorm_TE_iter: bool,
+        bulk_modulus: float,
+        mesh_density: float,
         name="Renormalization",
         prev_calc_dir: Optional[str] = None,
         db_file: str = None,
         **kwargs
-    ):    
-    
+        ):
+        
         # files needed to run renormalization
-        files = ["cluster_space.cs","parameters.txt","force_constants.fcs"]
+        files = ["cluster_space.cs","parameters.txt","force_constants.fcs",
+                 "structure_data.json","fitting_data.json","phonopy_params.yaml"]
         
         if prev_calc_dir:
-            copy_files = CopyFiles(from_dir=prev_calc_dir, files_to_copy=files)
+            copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
         else:
             copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
 
-        cs = ClusterSpace.read('cluster_space.cs')
-        fcs = ForceConstants.read('force_constants.fcs')
-        param = np.loadtxt('parameters.txt')
-        
         renorm_force_constants = RunHiPhiveRenorm(
-            cs=cs,
-            param=param,
-            fcs=fcs,
-            T_renorm=T_renorm
-        )        
+            renorm_temp=temperature,
+            renorm_method=renorm_method,
+            nconfig=renorm_nconfig,
+            conv_thresh=renorm_conv_thresh,
+            max_iter=renorm_max_iter,
+            renorm_TE_iter=renorm_TE_iter,
+            bulk_modulus=bulk_modulus,
+            **kwargs
+            )        
 
         to_db = ForceConstantsToDb(
             db_file=db_file, renormalized=True, mesh_density=mesh_density, additional_fields={}
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 4ff7cb4d1..535d5f5be 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -9,11 +9,23 @@
 from atomate.utils.utils import get_logger
 from atomate.vasp.config import DB_FILE, SHENGBTE_CMD, VASP_CMD
 from atomate.vasp.firetasks import pass_vasp_result
-from atomate.vasp.firetasks.lattice_dynamics import T_KLAT, T_RENORM
+from atomate.vasp.analysis.lattice_dynamics import (
+    FIT_METHOD,
+    MESH_DENSITY,
+    IMAGINARY_TOL,
+    T_QHA,
+    T_KLAT,
+    T_RENORM,
+    RENORM_METHOD,
+    RENORM_NCONFIG,
+    RENORM_MAX_ITER,
+    RENORM_CONV_THRESH,
+)
 from atomate.vasp.fireworks.core import TransmuterFW, OptimizeFW
 from atomate.vasp.fireworks.lattice_dynamics import (
     FitForceConstantsFW,
     LatticeThermalConductivityFW,
+    RenormalizationFW,
 )
 from atomate.vasp.powerups import add_additional_fields_to_taskdocs
 from fireworks import Workflow
@@ -37,6 +49,7 @@
     "ENCUT": 600,
     "ISMEAR": 0,
     "SIGMA": 0.1,
+    "ISPIN": 2,
     "EDIFF": 1e-7,
     "LAECHG": False,
     "LREAL": False,
@@ -56,6 +69,7 @@
 
 def get_lattice_dynamics_wf(
     structure: Structure,
+    fit_method:str = FIT_METHOD,
     separate_fit: bool = False,
     disp_cut: float = None,
     bulk_modulus: float = None,
@@ -65,10 +79,16 @@ def get_lattice_dynamics_wf(
     supercell_matrix_kwargs: Optional[dict] = None,
     num_supercell_kwargs: Optional[dict] = None,
     perturbed_structure_kwargs: Optional[dict] = None,
-    calculate_lattice_thermal_conductivity: bool = False,
+    calculate_lattice_thermal_conductivity: bool = True,
     thermal_conductivity_temperature: Union[float, Dict] = T_KLAT,
     renormalize: bool =	False,
-    renormalization_temperature: Union[float, List, Dict] = T_RENORM,
+    renormalize_temperature: Union[float, List, Dict] = T_RENORM,
+    renormalize_method: str = RENORM_METHOD,
+    renormalize_nconfig: int = RENORM_NCONFIG,
+    renormalize_conv_thresh: float = RENORM_CONV_THRESH,
+    renormalize_max_iter: int = RENORM_MAX_ITER,
+    renormalize_thermal_expansion_iter: bool = False,
+    mesh_density: float = MESH_DENSITY,
     shengbte_cmd: str = SHENGBTE_CMD,
     shengbte_fworker: Optional[str] = None,
 ):
@@ -128,7 +148,7 @@ def get_lattice_dynamics_wf(
         thermal_conductivity_temperature: The temperature at which to calculate
             lattice thermal conductivity for. Can be given as a single float, or
             a dictionary with the keys "min", "max", "step".
-        renormalization_temperature: The temperature at which to perform phonon 
+        renormalize_temperature: The temperature at which to perform phonon 
             renormalization. Can be given as a single float, list, or a dictionary
             with the keys "min", "max", "step".
         shengbte_cmd: Command to run ShengBTE. Supports env_chk.
@@ -143,12 +163,12 @@ def get_lattice_dynamics_wf(
     db_file = common_settings["DB_FILE"]
 
 
-    if calculate_lattice_thermal_conductivity:
+    if calculate_lattice_thermal_conductivity or renormalize:
         if supercell_matrix_kwargs.get("force_diagonal", False):
             warnings.warn(
                 "Diagonal transformation required to calculate lattice thermal "
                 "conductivity using ShengBTE. Forcing diagonal matrix."
-            )
+                )
         supercell_matrix_kwargs["force_diagonal"] = True
 
     st = CubicSupercellTransformation(**supercell_matrix_kwargs)
@@ -168,58 +188,69 @@ def get_lattice_dynamics_wf(
         copy_vasp_outputs=copy_vasp_outputs,
         pass_forces=True,
         **perturbed_structure_kwargs,
-    )
+        )
 
     # 2. Fit interatomic force constants from pertrubed structures
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
-        db_file=db_file, spec=allow_fizzled, separate_fit=separate_fit,
-        disp_cut=disp_cut, bulk_modulus=bulk_modulus
-    )
+        db_file=db_file,
+        spec=allow_fizzled,
+        separate_fit=separate_fit,
+        fit_method=fit_method,
+        disp_cut=disp_cut,
+        bulk_modulus=bulk_modulus, 
+        mesh_density=mesh_density,
+        imaginary_tol=IMAGINARY_TOL,
+        )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
 
-    # 3. RenormalizeFW (pass_inputs like bulk modulus)
+    # 3. Renormalization FW (pass_inputs like bulk modulus)
     if renormalize:
         fw_renormalization = RenormalizationFW(
-            temperature=renormalization_temperature,
             db_file=db_file,
-        )
+            temperature=renormalize_temperature,
+            renorm_method=renormalize_method,
+            renorm_nconfig=renormalize_nconfig,
+            renorm_conv_thresh=renormalize_conv_thresh,
+            renorm_max_iter=renormalize_max_iter,
+            renorm_TE_iter=renormalize_thermal_expansion_iter,
+            bulk_modulus=bulk_modulus,
+            mesh_density=mesh_density,
+            )
         wf.append_wf(
             Workflow.from_Firework(fw_renormalization), [wf.fws[-1].fw_id]
-        )
+            )
 
     # 4. Lattice thermal conductivity calculation
     if calculate_lattice_thermal_conductivity:
         if renormalize:
             # Because of the way ShengBTE works, a temperature array that is not
             # equally spaced out (T_step) requires submission for each temperature
-            fw_lattice_conductivity = []
-            for T in renormalization_temperature:
-                fw = LatticeThermalConductivityFW(
+            for T in renormalize_temperature:
+                fw_lattice_conductivity = LatticeThermalConductivityFW(
                     db_file=db_file,
                     shengbte_cmd=shengbte_cmd,
                     renormalized=True,
                     temperature=T
-                )
+                    )
                 if shengbte_fworker:
-                    fw.spec["_fworker"] = shengbte_fworker
-                fw_lattice_conductivity.append(fw)
-            wf.append_wf(
-                Workflow.from_Firework(fw_lattice_conductivity), wf.leaf_fw_ids
-            )
+                    fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
+                wf.append_wf(
+                    Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
+                    )
         else:
             fw_lattice_conductivity = LatticeThermalConductivityFW(
                 db_file=db_file,
                 shengbte_cmd=shengbte_cmd,
                 renormalized=False,
                 temperature=thermal_conductivity_temperature,
-            )
+                )
             if shengbte_fworker:
                 fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
             wf.append_wf(
                 Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
-            )
-
+                )
+                
     formula = structure.composition.reduced_formula
     wf.name = "{} - lattice dynamics".format(formula)
 
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 56f95809a..2b5aa70b8 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -851,6 +851,7 @@ def wf_nudged_elastic_band(structures, parent, c=None):
 def wf_lattice_dynamics(
     structure: Structure,
     separate_fit: bool = False,
+    fit_method: str = False,
     disp_cut: float = None,
     bulk_modulus: float = None,
     c: Optional[dict] = None,
@@ -859,7 +860,8 @@ def wf_lattice_dynamics(
     calculate_lattice_thermal_conductivity=True,
     thermal_conductivity_temperature=None,
     renormalize=False,
-    renormalization_temperature=None,        
+    renormalize_temperature=None,        
+    renormalize_thermal_expansion_iter=False,
     **ld_kwargs
 ) -> Workflow:
     """
@@ -877,18 +879,22 @@ def wf_lattice_dynamics(
     Returns:
         A workflow to calculate lattice thermal conductivity.
     """
+
+    # start with defining the relaxation workflow
     optimize_uis = {
         "LAECHG": False,
         'ENCUT': 600,
         'ADDGRID': True,
+        'EDIFF': 1e-8,
         'EDIFFG': -5e-4,
         'PREC': 'Accurate',
         "LREAL": False,
-        'EDIFF': 1e-8,
-        "ISMEAR": 0,
-        "SIGMA": 0.1,
+        'LASPH': True,
+        'ISPIN': 2,
+        'ISMEAR': 0,
+        'SIGMA': 0.1,
         'LCHARG': False,
-        'LASPH': True
+        'LWAVE': False
     }
     c = c if c is not None else {}
     if "USER_INCAR_SETTINGS" not in c:
@@ -904,21 +910,26 @@ def wf_lattice_dynamics(
         if "VaspToDb" in str(task):
             task.update(vasp_to_db_params)
 
+    # define lattice dynamics workflow
     wf_ld = get_lattice_dynamics_wf(
         structure,
-        separate_fit = separate_fit,
-        disp_cut = disp_cut,
-        bulk_modulus = bulk_modulus,
+        fit_method=fit_method,
+        separate_fit=separate_fit,
+        disp_cut=disp_cut,
+        bulk_modulus=bulk_modulus,
         common_settings=c,
         supercell_matrix_kwargs=supercell_matrix_kwargs,
         num_supercell_kwargs=num_supercell_kwargs,
         calculate_lattice_thermal_conductivity=calculate_lattice_thermal_conductivity,
         thermal_conductivity_temperature=thermal_conductivity_temperature,
         renormalize=renormalize,
-        renormalization_temperature=renormalization_temperature,
+        renormalize_temperature=renormalize_temperature,
+        renormalize_thermal_expansion_iter=bool(renormalize_thermal_expansion_iter and bulk_modulus),
         copy_vasp_outputs=True,
         **ld_kwargs
     )
+
+    # join the workflows
     wf.append_wf(wf_ld, wf.leaf_fw_ids)
 
     formula = structure.composition.reduced_formula

From f2c5dc2e6310858f5b70397150355107dc61d79d Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Tue, 1 Nov 2022 10:17:27 -0400
Subject: [PATCH 131/207] any changes?

---
 atomate/vasp/analysis/lattice_dynamics.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 589f9cab6..dfb226973 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -45,8 +45,12 @@
 IMAGINARY_TOL = 0.025  # in THz
 MESH_DENSITY = 100.0  # should always be a float 
 
+# Temperature for straight-up phonopy calculation of thermodynamic properties (free energy etc.)
 T_QHA = [i*100 for i in range(21)]
+# Temperature at which renormalization is to be performed
 T_RENORM = [0,50,100,200,300,500,700,1000,1500]#[i*100 for i in range(0,16)]
+# Temperature at which lattice thermal conductivity is calculated
+# If renormalization is performed, T_RENORM overrides T_KLAT for lattice thermal conductivity
 T_KLAT = {"t_min":100,"t_max":1500,"t_step":100} #[i*100 for i in range(0,11)]
 
 FIT_METHOD = "rfe" 
@@ -56,8 +60,8 @@
 RENORM_MAX_ITER = 20
 
 eV2J = 1.602e-19
-hbar = sp.constants.hbar
-kB = sp.constants.Boltzmann
+hbar = sp.constants.hbar # J-s
+kB = sp.constants.Boltzmann # J/K
 
 def get_cutoffs(structure: Structure):
     """

From f81a71804774ef962eaf1f10a43bffb1335faf1c Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Tue, 1 Nov 2022 10:53:38 -0400
Subject: [PATCH 132/207] workflow name

---
 atomate/vasp/workflows/presets/core.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 2b5aa70b8..d301c20bf 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -933,7 +933,7 @@ def wf_lattice_dynamics(
     wf.append_wf(wf_ld, wf.leaf_fw_ids)
 
     formula = structure.composition.reduced_formula
-    wf_name = "{} - lattice thermal conductivity".format(formula)
+    wf_name = "{} - lattice dynamics".format(formula)
     wf.name = wf_name
 
     wf = add_common_powerups(wf, c)

From 6792750adec3fba3251f2ac1638592942ab696d1 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Wed, 2 Nov 2022 09:21:18 -0400
Subject: [PATCH 133/207] firetask error fix

---
 atomate/vasp/firetasks/lattice_dynamics.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 53d87fb2c..b3e1e1a00 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -149,6 +149,13 @@ class RunHiPhive(FiretaskBase):
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
 
+        all_structures = loadfn("perturbed_structures.json")
+        all_forces = loadfn("perturbed_forces.json")
+        structure_data = loadfn("structure_data.json")
+        parent_structure = structure_data["structure"]
+        supercell_structure = structure_data["supercell_structure"]
+        supercell_matrix = np.array(structure_data["supercell_matrix"])
+
         separate_fit = self.get('separate_fit', False)
         disp_cut = self.get('disp_cut', None)
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
@@ -158,13 +165,6 @@ def run_task(self, fw_spec):
         bulk_modulus = self.get("bulk_modulus")
         fit_method = self.get("fit_method")
 
-        all_structures = loadfn("perturbed_structures.json")
-        all_forces = loadfn("perturbed_forces.json")
-        structure_data = loadfn("structure_data.json")
-        parent_structure = structure_data["structure"]
-        supercell_structure = structure_data["supercell_structure"]
-        supercell_matrix = np.array(structure_data["supercell_matrix"])
-
         structures = []
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
         for structure, forces in zip(all_structures, all_forces):

From eba90589f724b0c285a98d0abcd1b459bfe673c9 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Fri, 4 Nov 2022 14:33:19 -0400
Subject: [PATCH 134/207] T_qha

---
 atomate/vasp/firetasks/lattice_dynamics.py      | 2 +-
 atomate/vasp/fireworks/lattice_dynamics.py      | 2 ++
 atomate/vasp/workflows/base/lattice_dynamics.py | 1 +
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index b3e1e1a00..b99df0ad5 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -159,7 +159,7 @@ def run_task(self, fw_spec):
         separate_fit = self.get('separate_fit', False)
         disp_cut = self.get('disp_cut', None)
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        T_qha = np.array(self.get("T_qha"))
+        T_qha = np.array(self.get("temperature_qha"))
         T_qha.sort()
         imaginary_tol = self.get("imaginary_tol")
         bulk_modulus = self.get("bulk_modulus")
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index fe9648232..c1bfc7534 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -58,6 +58,7 @@ def __init__(
         bulk_modulus: float,
         imaginary_tol: float,
         mesh_density: float,
+        temperature_qha: float,
         cutoffs: Optional[List[List[float]]] = None,
         name="Fit Force Constants",
         parents: Optional[Union[Firework, List[Firework]]] = None,
@@ -72,6 +73,7 @@ def __init__(
             fit_method=fit_method,
             disp_cut=disp_cut,
             bulk_modulus=bulk_modulus,
+            temperature_qha=temperature_qha,
             imaginary_tol=imaginary_tol,
         )
         to_db = ForceConstantsToDb(
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 535d5f5be..04a4f79fb 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -199,6 +199,7 @@ def get_lattice_dynamics_wf(
         fit_method=fit_method,
         disp_cut=disp_cut,
         bulk_modulus=bulk_modulus, 
+        temperature_qha=T_QHA,
         mesh_density=mesh_density,
         imaginary_tol=IMAGINARY_TOL,
         )

From 5660096b5fd98842d5ed780ad6f674d612011987 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 6 Nov 2022 20:13:23 -0800
Subject: [PATCH 135/207] T_qha

---
 atomate/vasp/firetasks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index b99df0ad5..99af4b775 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -159,7 +159,7 @@ def run_task(self, fw_spec):
         separate_fit = self.get('separate_fit', False)
         disp_cut = self.get('disp_cut', None)
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        T_qha = np.array(self.get("temperature_qha"))
+        T_qha = self.get("temperature_qha")
         T_qha.sort()
         imaginary_tol = self.get("imaginary_tol")
         bulk_modulus = self.get("bulk_modulus")

From bca664297b78ae17da30052e8d76bac2f199eab0 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Sun, 6 Nov 2022 23:16:31 -0500
Subject: [PATCH 136/207] T_qha

---
 atomate/vasp/firetasks/lattice_dynamics.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 99af4b775..10d6b45fb 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -141,6 +141,7 @@ class RunHiPhive(FiretaskBase):
         "cutoffs",
         "separate_fit",
         "disp_cut",
+        "temperature_qha",
         "bulk_modulus",
         "imaginary_tol",
         "fit_method",

From e3e5347911644550036dd699a9baca24c21068d3 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 7 Nov 2022 16:54:24 -0500
Subject: [PATCH 137/207] max cutoff

---
 atomate/vasp/analysis/lattice_dynamics.py  | 2 ++
 atomate/vasp/firetasks/lattice_dynamics.py | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index dfb226973..aacea0d18 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -113,6 +113,7 @@ def get_cutoffs(structure: Structure):
         A list of trial cutoffs.
     """
     # indexed as min_cutoffs[order][period]
+    # DO NOT CHANGE unless you know what you are doing
     min_cutoffs = {
         2: {1: 5.0, 2: 6.0, 3: 7.0, 4: 8.0, 5: 9.0, 6: 10.0, 7: 11.0},
         3: {1: 3.0, 2: 3.5, 3: 4.5, 4: 5.5, 5: 6.0, 6: 6.5, 7: 7.0},
@@ -153,6 +154,7 @@ def get_cutoffs(structure: Structure):
 =======
     cutoffs = np.array(list(map(list, product(range_two, range_three, range_four))))
     max_cutoff = estimate_maximum_cutoff(AseAtomsAdaptor.get_atoms(supercell_structure))
+    cutoffs[cutoffs>max_cutoff] = max_cutoff
     logger.info('CUTOFFS \n {}'.format(cutoffs))
     logger.info('MAX_CUTOFF \n {}'.format(max_cutoff))    
     good_cutoffs = np.all(cutoffs < max_cutoff-0.1, axis=1)
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 10d6b45fb..09316fb12 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -160,7 +160,7 @@ def run_task(self, fw_spec):
         separate_fit = self.get('separate_fit', False)
         disp_cut = self.get('disp_cut', None)
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        T_qha = self.get("temperature_qha")
+        T_qha = self.get("temperature_qha", T_QHA)
         T_qha.sort()
         imaginary_tol = self.get("imaginary_tol")
         bulk_modulus = self.get("bulk_modulus")
@@ -194,10 +194,10 @@ def run_task(self, fw_spec):
             )
         
         thermal_data, phonopy = harmonic_properties(
-            parent_structure, supercell_matrix, fcs, T_QHA, imaginary_tol
+            parent_structure, supercell_matrix, fcs, T_qha, imaginary_tol
         )
         anharmonic_data, phonopy = anharmonic_properties(
-            phonopy, fcs, T_QHA, thermal_data["heat_capacity"],
+            phonopy, fcs, T_qha, thermal_data["heat_capacity"],
             thermal_data["n_imaginary"], bulk_modulus
         )
 

From 3a6bdde3cf466333783becc2bbe1ee7145932316 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Tue, 15 Nov 2022 00:29:15 -0500
Subject: [PATCH 138/207] file copy

---
 atomate/vasp/fireworks/lattice_dynamics.py      | 3 +++
 atomate/vasp/workflows/base/lattice_dynamics.py | 6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index c1bfc7534..bb26644e7 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -1,5 +1,7 @@
 from typing import List, Optional, Union, Dict
 
+import os
+
 from atomate.common.firetasks.glue_tasks import (
     CopyFiles,
     CopyFilesFromCalcLoc,
@@ -140,6 +142,7 @@ def __init__(
                 copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
                 copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+            os.system('mv FORCE_CONSTANTS_2ND_{}K FORCE_CONSTANTS_2ND'.format(temperature))
 
         else: # only the default files are needed
             files = [
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 04a4f79fb..fa9acb534 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -163,7 +163,7 @@ def get_lattice_dynamics_wf(
     db_file = common_settings["DB_FILE"]
 
 
-    if calculate_lattice_thermal_conductivity or renormalize:
+    if calculate_lattice_thermal_conductivity:
         if supercell_matrix_kwargs.get("force_diagonal", False):
             warnings.warn(
                 "Diagonal transformation required to calculate lattice thermal "
@@ -227,7 +227,7 @@ def get_lattice_dynamics_wf(
         if renormalize:
             # Because of the way ShengBTE works, a temperature array that is not
             # equally spaced out (T_step) requires submission for each temperature
-            for T in renormalize_temperature:
+            for t,T in enumerate(renormalize_temperature):
                 fw_lattice_conductivity = LatticeThermalConductivityFW(
                     db_file=db_file,
                     shengbte_cmd=shengbte_cmd,
@@ -237,7 +237,7 @@ def get_lattice_dynamics_wf(
                 if shengbte_fworker:
                     fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
                 wf.append_wf(
-                    Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
+                    Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-(t+1)].fw_id]
                     )
         else:
             fw_lattice_conductivity = LatticeThermalConductivityFW(

From 54acf2af57ef09ac3300124ae7f59845366e0cfc Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Sun, 20 Nov 2022 21:34:49 -0500
Subject: [PATCH 139/207] clusterspace

---
 atomate/vasp/firetasks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 09316fb12..2d10f3a2c 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -43,7 +43,7 @@
 
 try:
     import hiphive
-    from hiphive import ForceConstants
+    from hiphive import ForceConstants, ClusterSpace
     from hiphive.utilities import get_displacements
 except ImportError:
     logger.info('Could not import hiphive!')

From 43db85f44a9274f152eefd47395945c2252339df Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.local>
Date: Tue, 22 Nov 2022 22:54:02 -0500
Subject: [PATCH 140/207] calc_loc

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index bb26644e7..24a60f0de 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -214,7 +214,7 @@ def __init__(
         if prev_calc_dir:
             copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
         else:
-            copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+            copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
 
         renorm_force_constants = RunHiPhiveRenorm(
             renorm_temp=temperature,

From c9fc23293e8c3d7c1ced01b218ea66f0f52e025e Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Thu, 1 Dec 2022 15:40:08 -0500
Subject: [PATCH 141/207] renormalization calc_loc

---
 atomate/vasp/firetasks/lattice_dynamics.py      |  3 ++-
 atomate/vasp/fireworks/lattice_dynamics.py      | 14 +++++++-------
 atomate/vasp/workflows/base/lattice_dynamics.py |  2 ++
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 2d10f3a2c..ad11a39dd 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -414,7 +414,7 @@ def run_task(self, fw_spec):
 
             # Get an id for the force constants
             fitting_id = _get_fc_fitting_id(mmdb)
-            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+            metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
             data.update(metadata)
             data = jsanitize(data,strict=True,allow_bson=True)
             
@@ -599,6 +599,7 @@ def run_task(self, fw_spec):
             "shengbte_dir": os.getcwd(),
             "fc_fitting_id": fw_spec.get("fc_fitting_id", None),
             "fc_fitting_dir": fw_spec.get("fc_fitting_dir", None),
+            "renormalization_dir": fw_spec.get("renormalization_dir", None),
             "created_at": datetime.utcnow(),
         }
         data.update(self.get("additional_fields", {}))
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 24a60f0de..14ad484dc 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -112,7 +112,7 @@ class LatticeThermalConductivityFW(Firework):
     def __init__(
         self,
         shengbte_cmd: str,
-        temperature: Union[float, dict],
+        temperature: Union[float, int, dict],
         renormalized: bool,
         name="Lattice Thermal Conductivity",
         prev_calc_dir: Optional[str] = None,
@@ -141,7 +141,7 @@ def __init__(
             if prev_calc_dir:
                 copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
-                copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+                copy_files = CopyFilesFromCalcLoc(calc_loc='Renormalization', filenames=files)
             os.system('mv FORCE_CONSTANTS_2ND_{}K FORCE_CONSTANTS_2ND'.format(temperature))
 
         else: # only the default files are needed
@@ -153,7 +153,7 @@ def __init__(
             if prev_calc_dir:
                 copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
-                copy_files = CopyFilesFromCalcLoc(calc_loc=True, filenames=files)
+                copy_files = CopyFilesFromCalcLoc(calc_loc='Fit Force Constants', filenames=files)
 
         run_shengbte = RunShengBTE(
             shengbte_cmd=shengbte_cmd,
@@ -211,10 +211,10 @@ def __init__(
         files = ["cluster_space.cs","parameters.txt","force_constants.fcs",
                  "structure_data.json","fitting_data.json","phonopy_params.yaml"]
         
-        if prev_calc_dir:
-            copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
-        else:
-            copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
+#        if prev_calc_dir:
+#            copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
+#        else:
+        copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
 
         renorm_force_constants = RunHiPhiveRenorm(
             renorm_temp=temperature,
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index fa9acb534..9ab230816 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -228,6 +228,8 @@ def get_lattice_dynamics_wf(
             # Because of the way ShengBTE works, a temperature array that is not
             # equally spaced out (T_step) requires submission for each temperature
             for t,T in enumerate(renormalize_temperature):
+                if T == 0:
+                    continue
                 fw_lattice_conductivity = LatticeThermalConductivityFW(
                     db_file=db_file,
                     shengbte_cmd=shengbte_cmd,

From 388e7adf2df532b4e1e55aa8f0117cfa6424c890 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Mon, 27 Feb 2023 12:54:01 -0800
Subject: [PATCH 142/207] copy_files

---
 atomate/vasp/fireworks/lattice_dynamics.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 14ad484dc..530643973 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -210,11 +210,11 @@ def __init__(
         # files needed to run renormalization
         files = ["cluster_space.cs","parameters.txt","force_constants.fcs",
                  "structure_data.json","fitting_data.json","phonopy_params.yaml"]
-        
-#        if prev_calc_dir:
-#            copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
-#        else:
-        copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
+
+        if prev_calc_dir:
+            copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
+        else:
+            copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
 
         renorm_force_constants = RunHiPhiveRenorm(
             renorm_temp=temperature,
@@ -232,5 +232,5 @@ def __init__(
 	)
         pass_locs = PassCalcLocs(name=name)
 
-        tasks = [renorm_force_constants, to_db, pass_locs]
+        tasks = [copy_files, renorm_force_constants, to_db, pass_locs]
         super().__init__(tasks, name=name, **kwargs)

From 38a60c27e80b3ab1fc4cab419fa6452e475b0095 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 27 Feb 2023 16:32:04 -0500
Subject: [PATCH 143/207] add_attiaional_fields_to_taskdocs

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 9ab230816..e42345741 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -27,7 +27,7 @@
     LatticeThermalConductivityFW,
     RenormalizationFW,
 )
-from atomate.vasp.powerups import add_additional_fields_to_taskdocs
+from atomate.common.powerups import add_additional_fields_to_taskdocs
 from fireworks import Workflow
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.sets import MPStaticSet, VaspInputSet

From b5b7e7e4b1e4f4f3597e40799fbb56e156ef8cfb Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 27 Feb 2023 23:03:17 -0500
Subject: [PATCH 144/207] RunHiPhiveRenorm

---
 atomate/vasp/firetasks/lattice_dynamics.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index ad11a39dd..842c843eb 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -273,7 +273,7 @@ def run_task(self, fw_spec):
         # First renormalization with DFT lattice 
         renorm_data = Parallel(n_jobs=4, backend="multiprocessing")(delayed(run_renormalization)(
             parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, max_iter,
-            conv_thresh, bulk_modulus, phonopy_orig) for t, T in enumerate(renorm_temp))
+            conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig) for t, T in enumerate(renorm_temp))
 
         # Additional renormalization with thermal expansion - optional - just single "iteration" for now
         if renorm_TE_iter:
@@ -304,10 +304,13 @@ def run_task(self, fw_spec):
 
                 parent_structure_TE, cs_TE, fcs_TE = setup_TE_iter(cutoffs,parent_structure,T_real,dLfrac_real)
                 param_TE = copy(param_real)
-                
+                prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
+                prim_phonopy_TE = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
+                                               scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
+                phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
                 renorm_data = Parallel(n_jobs=4, backend="multiprocessing")(delayed(run_renormalization)(
                     parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param_TE[t],
-                    T, nconfig, max_iter, conv_thresh, bulk_modulus
+                    T, nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_TE
                     ) for t, T in enumerate(T_real)
                 )
 

From 346a86fb04affb3cfb8dc59db8d8112f53dc9bf7 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Wed, 1 Mar 2023 11:11:39 -0500
Subject: [PATCH 145/207] revert to structure container for fitting

---
 atomate/vasp/analysis/lattice_dynamics.py  | 89 ++++++++++++++++++++--
 atomate/vasp/firetasks/lattice_dynamics.py | 41 +++++++---
 2 files changed, 115 insertions(+), 15 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index aacea0d18..32f9248b1 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -17,12 +17,16 @@
 from hiphive import (ForceConstants, ForceConstantPotential,
                      enforce_rotational_sum_rules, ClusterSpace,
                      StructureContainer)
+<<<<<<< HEAD
 >>>>>>> 1e75a82a (imports)
+=======
+from hiphive.force_constant_model import ForceConstantModel
+>>>>>>> 0d613579 (revert to structure container for fitting)
 from hiphive.cutoffs import is_cutoff_allowed, estimate_maximum_cutoff
 from hiphive.fitting import Optimizer
 from hiphive.renormalization import Renormalization
 from hiphive.utilities import get_displacements
-from hiphive.run_tools import FE_correction
+from hiphive.run_tools import _clean_data, FE_correction
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
@@ -297,6 +301,75 @@ def fit_force_constants(
     return best_fit["force_constants"], best_fit["parameters"], best_fit["cluster_space"], fitting_data
 
 
+def _get_fit_data(
+        cs: ClusterSpace,
+        supercell: Atoms,
+        structures: List["Atoms"],
+        separate_fit: bool,
+        disp_cut: float,
+        ncut: int,
+        param2: np.ndarray = None
+) -> "List":
+    """ Constructs structure container of atom-displaced supercells
+    Args: 
+    cs: ClusterSpace
+    supercell: Atoms
+      Original undisplaced supercell
+    structures: A list of ase atoms objects with the "forces" and                                                                                                                                  
+      "displacements" arrays included.                                                                                                                                                           
+    separate_fit: Boolean to determine whether harmonic and anharmonic fitting                                                                                                                     
+      are to be done separately (True) or in one shot (False)                                                                                                                                    
+    disp_cut: if separate_fit true, determines the mean displacement of perturbed                                                                                                                  
+      structure to be included in harmonic (<) or anharmonic (>) fitting                                                                                                                         
+    ncut: the parameter index where fitting separation occurs                                                                                                                                      
+      param2: previously fit parameter array (harmonic only for now, hence 2)                                                                                                                        
+
+    Returns:
+    fit_data: List[A_mat,f_vec] 
+    """
+
+    saved_structures = []
+    fcm = ForceConstantModel(supercell,cs)
+    natom = supercell.get_global_number_of_atoms()
+    nrow_per = natom*3
+    nrow_all = nrow_per*len(saved_structures)
+    A_mat = np.memmap('A_mat_memmap', dtype=float, shape=(nrow_all,cs.n_dofs), mode='w+')
+    f_vec = np.memmap('f_vec_memmap', dtype=float, shape=(nrow_all), mode='w+')
+
+    for i, structure in enumerate(structures):
+        displacements = structure.get_array('displacements')
+        mean_displacements = np.linalg.norm(displacements,axis=1).mean()
+        logger.info('Mean displacements: {}'.format(mean_displacements))
+        if not separate_fit: # fit all
+            saved_structures.append(structure)
+        else: # fit separately
+            if param2 is None: # for harmonic fitting
+                if mean_displacements < disp_cut:
+                    saved_structures.append(structure)
+            else: # for anharmonic fitting
+                if mean_displacements >= disp_cut:
+                    saved_structures.append(structure)
+
+    Parallel(n_jobs=min(os.cpu_count(),max(1,len(saved_structures))))(#,prefer="threads")(
+        delayed(construct_fit_data)(fcm,structure,A_mat,f_vec,nrow_per,s,param=None)
+        for s,structure in enumerate(saved_structures)
+    )
+
+    if param2 is not None:
+        force_anh = f_vec - np.dot(A_mat[:,:ncut],param2) # subtract harmonic force from total
+        for i, structure in enumerate(saved_structures):
+            structure.set_array('forces', force_anh[i*nrow_per:(i+1)*nrow_per].reshape(natom,3))
+        Parallel(n_jobs=min(os.cpu_count(),max(1,len(saved_structures))))(#,prefer="threads")(
+            delayed(construct_fit_data)(fcm,structure,A_mat,f_vec,nrow_per,s,param=None)
+            for s,structure in enumerate(saved_structures)
+        )
+    os.remove('A_mat_memmap')
+    os.remove('f_vec_memmap')
+    logger.info('Fit_data dimensions: {}'.format(A_mat.shape))
+    fit_data = _clean_data(A_mat,f_vec,nrow_per)
+    return fit_data
+
+
 def _run_cutoffs(
     i,
     cutoffs,
@@ -340,6 +413,8 @@ def _run_cutoffs(
     
     if separate_fit:
         logger.info('Fitting harmonic force constants separately')
+#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                                disp_cut, ncut=n2nd, param2=None)
         sc = get_structure_container(cs, structures, separate_fit, disp_cut,
                                      ncut=n2nd, param2=None)
         opt = Optimizer(sc.get_fit_data(),
@@ -355,6 +430,8 @@ def _run_cutoffs(
         param_harmonic = opt.parameters # harmonic force constant parameters
         
         logger.info('Fitting anharmonic force constants separately')
+#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                                disp_cut, ncut=n2nd, param2=param_harmonic)
         sc = get_structure_container(cs, structures, separate_fit, disp_cut,
                                      ncut=n2nd, param2=param_harmonic)
         opt = Optimizer(sc.get_fit_data(),
@@ -438,6 +515,8 @@ def get_structure_container(
         
     else:
         logger.info('Fitting all force constants in one shot')
+#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                                disp_cut=None, ncut=None, param2=None)
         sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
                                      ncut=None, param2=None)
         opt = Optimizer(sc.get_fit_data(),
@@ -481,7 +560,7 @@ def get_structure_container(
     Get a hiPhive StructureContainer from cutoffs and a list of atoms objects.
 
     Args:
-        cutoffs: Cutoff radii for different orders starting with second order.
+        cs: ClusterSpace 
         structures: A list of ase atoms objects with the "forces" and
             "displacements" arrays included.
         separate_fit: Boolean to determine whether harmonic and anharmonic fitting
@@ -807,11 +886,11 @@ def run_renormalization(
 
     omega0 = phonopy_orig.mesh.frequencies # THz
     omega_TD = phonopy.mesh.frequencies # THz
-    natom = phonopy.primitive.get_number_of_atoms()
-    correction = FE_correction(omega0,omega_TD,T)/natom # eV/atom
+#    natom = phonopy.primitive.get_number_of_atoms()
+    correction_S, correction_4 = FE_correction(omega0,omega_TD,T) # eV/atom
 
     renorm_data.update(anharmonic_data)
-    renorm_data["free_energy_correction"] = correction
+    renorm_data["free_energy_correction_S"] = correction_S[0]
     renorm_data["fcp"] = fcp
     renorm_data["fcs"] = fcs
     renorm_data["param"] = param
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 842c843eb..07db589f8 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -270,10 +270,21 @@ def run_task(self, fw_spec):
         renorm_TE_iter = self.get("renorm_TE_iter")
         bulk_modulus = self.get("bulk_modulus")
 
-        # First renormalization with DFT lattice 
-        renorm_data = Parallel(n_jobs=4, backend="multiprocessing")(delayed(run_renormalization)(
-            parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, max_iter,
-            conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig) for t, T in enumerate(renorm_temp))
+        # Renormalization with DFT lattice 
+
+        # Parallel version
+#        renorm_data = Parallel(n_jobs=len(renorm_temp), backend="multiprocessing")(delayed(run_renormalization)(
+#            parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, max_iter,
+#            conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig) for t, T in enumerate(renorm_temp))
+
+        # Serial version - likely better because it allows parallelization over A matrix construction,
+        # which takes most of the time during renormalization, and leaves no process idling around when 
+        # low temperature renormalizations finish early
+        renorm_data = []
+        for t, T in enumerate(renorm_temp):
+            data_T = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, 
+                                max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
+            renorm_data.append(data_T)
 
         # Additional renormalization with thermal expansion - optional - just single "iteration" for now
         if renorm_TE_iter:
@@ -308,14 +319,24 @@ def run_task(self, fw_spec):
                 prim_phonopy_TE = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
                                                scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
                 phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
-                renorm_data = Parallel(n_jobs=4, backend="multiprocessing")(delayed(run_renormalization)(
-                    parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param_TE[t],
-                    T, nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_TE
-                    ) for t, T in enumerate(T_real)
-                )
 
+                # Parallel
+#                renorm_data = Parallel(n_jobs=len(T_real), backend="multiprocessing")(delayed(run_renormalization)(
+#                    parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param_TE[t],
+#                    T, nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_TE
+#                    ) for t, T in enumerate(T_real)
+#                )
+
+                # Serial
+                renorm_data_TE = []
+                for t, T in enumerate(T_real):
+                    data_T = run_renormalization(parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, 
+                                                 cs_TE[t], fcs_TE[t], param_TE[t], T, nconfig, max_iter, conv_thresh,
+                                                 renorm_method, fit_method, bulk_modulus, phonopy_TE)
+                    renorm_data_TE.append(data_T)
+                    
             if len(T_real) > 0:
-                for t, result in enumerate(renorm_data):
+                for t, result in enumerate(renorm_data_TE):
                     temp_index = np.where(renorm_temp==T_real[t])[0][0]
                     renorm_data[temp_index] = result
 

From ff4921282bca128e59f46ff52564b98896b4bb8d Mon Sep 17 00:00:00 2001
From: Junsoo Park <Aficionado37@Junsoos-MBP.vpn-dhcp.lbl.gov>
Date: Wed, 8 Mar 2023 11:29:11 -0500
Subject: [PATCH 146/207] fit_data parallel

---
 atomate/vasp/analysis/lattice_dynamics.py | 73 +++++++++++------------
 1 file changed, 34 insertions(+), 39 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 32f9248b1..7f1eb5a74 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -301,7 +301,7 @@ def fit_force_constants(
     return best_fit["force_constants"], best_fit["parameters"], best_fit["cluster_space"], fitting_data
 
 
-def _get_fit_data(
+def get_fit_data(
         cs: ClusterSpace,
         supercell: Atoms,
         structures: List["Atoms"],
@@ -315,14 +315,14 @@ def _get_fit_data(
     cs: ClusterSpace
     supercell: Atoms
       Original undisplaced supercell
-    structures: A list of ase atoms objects with the "forces" and                                                                                                                                  
-      "displacements" arrays included.                                                                                                                                                           
-    separate_fit: Boolean to determine whether harmonic and anharmonic fitting                                                                                                                     
-      are to be done separately (True) or in one shot (False)                                                                                                                                    
-    disp_cut: if separate_fit true, determines the mean displacement of perturbed                                                                                                                  
-      structure to be included in harmonic (<) or anharmonic (>) fitting                                                                                                                         
-    ncut: the parameter index where fitting separation occurs                                                                                                                                      
-      param2: previously fit parameter array (harmonic only for now, hence 2)                                                                                                                        
+    structures: A list of ase atoms objects with the "forces" and
+      "displacements" arrays included.
+    separate_fit: Boolean to determine whether harmonic and anharmonic fitting
+      are to be done separately (True) or in one shot (False)
+    disp_cut: if separate_fit true, determines the mean displacement of perturbed
+      structure to be included in harmonic (<) or anharmonic (>) fitting
+    ncut: the parameter index where fitting separation occurs
+      param2: previously fit parameter array (harmonic only for now, hence 2)
 
     Returns:
     fit_data: List[A_mat,f_vec] 
@@ -333,8 +333,8 @@ def _get_fit_data(
     natom = supercell.get_global_number_of_atoms()
     nrow_per = natom*3
     nrow_all = nrow_per*len(saved_structures)
-    A_mat = np.memmap('A_mat_memmap', dtype=float, shape=(nrow_all,cs.n_dofs), mode='w+')
-    f_vec = np.memmap('f_vec_memmap', dtype=float, shape=(nrow_all), mode='w+')
+    A_mat = np.zeros((nrow_all,cs.n_dofs))
+    f_vec = np.zeros(nrow_all)
 
     for i, structure in enumerate(structures):
         displacements = structure.get_array('displacements')
@@ -350,21 +350,16 @@ def _get_fit_data(
                 if mean_displacements >= disp_cut:
                     saved_structures.append(structure)
 
-    Parallel(n_jobs=min(os.cpu_count(),max(1,len(saved_structures))))(#,prefer="threads")(
-        delayed(construct_fit_data)(fcm,structure,A_mat,f_vec,nrow_per,s,param=None)
+    fit_data_tmp = Parallel(n_jobs=min(os.cpu_count(),max(1,len(saved_structures))))(#,prefer="threads")(
+        delayed(construct_fit_data)(fcm,structure,s)
         for s,structure in enumerate(saved_structures)
     )
+    for s,data in enumerate(fit_data_tmp)
+        A_mat[s*nrow_per:(s+1)*nrow_per] = data[0]
+        f_vec[s*nrow_per:(s+1)*nrow_per] = data[1]
 
     if param2 is not None:
-        force_anh = f_vec - np.dot(A_mat[:,:ncut],param2) # subtract harmonic force from total
-        for i, structure in enumerate(saved_structures):
-            structure.set_array('forces', force_anh[i*nrow_per:(i+1)*nrow_per].reshape(natom,3))
-        Parallel(n_jobs=min(os.cpu_count(),max(1,len(saved_structures))))(#,prefer="threads")(
-            delayed(construct_fit_data)(fcm,structure,A_mat,f_vec,nrow_per,s,param=None)
-            for s,structure in enumerate(saved_structures)
-        )
-    os.remove('A_mat_memmap')
-    os.remove('f_vec_memmap')
+        f_vec -= np.dot(A_mat[:,:ncut],param2) # subtract harmonic force from total
     logger.info('Fit_data dimensions: {}'.format(A_mat.shape))
     fit_data = _clean_data(A_mat,f_vec,nrow_per)
     return fit_data
@@ -413,11 +408,11 @@ def _run_cutoffs(
     
     if separate_fit:
         logger.info('Fitting harmonic force constants separately')
-#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-#                                disp_cut, ncut=n2nd, param2=None)
-        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
-                                     ncut=n2nd, param2=None)
-        opt = Optimizer(sc.get_fit_data(),
+        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+                                disp_cut, ncut=n2nd, param2=None)
+#        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+#                                     ncut=n2nd, param2=None)
+        opt = Optimizer(fit_data,#sc.get_fit_data(),
                         fit_method,
                         [0,n2nd],
                         **fit_kwargs)
@@ -430,11 +425,11 @@ def _run_cutoffs(
         param_harmonic = opt.parameters # harmonic force constant parameters
         
         logger.info('Fitting anharmonic force constants separately')
-#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-#                                disp_cut, ncut=n2nd, param2=param_harmonic)
-        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
-                                     ncut=n2nd, param2=param_harmonic)
-        opt = Optimizer(sc.get_fit_data(),
+        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+                                disp_cut, ncut=n2nd, param2=param_harmonic)
+#        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+#                                     ncut=n2nd, param2=param_harmonic)
+        opt = Optimizer(fit_data,#sc.get_fit_data(),
                         fit_method,
                         [n2nd,nall],
                         **fit_kwargs)
@@ -515,11 +510,11 @@ def get_structure_container(
         
     else:
         logger.info('Fitting all force constants in one shot')
-#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-#                                disp_cut=None, ncut=None, param2=None)
-        sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
-                                     ncut=None, param2=None)
-        opt = Optimizer(sc.get_fit_data(),
+        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+                                disp_cut=None, ncut=None, param2=None)
+#        sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
+#                                     ncut=None, param2=None)
+        opt = Optimizer(fit_data,#sc.get_fit_data(),
                         fit_method,
                         [0,nall],
                         **fit_kwargs)
@@ -593,7 +588,7 @@ def get_structure_container(
     if separate_fit and param2 is not None: # do after anharmonic fitting
         A_mat = sc.get_fit_data()[0] # displacement matrix
         f_vec = sc.get_fit_data()[1] # force vector
-        anh_force = f_vec - np.dot(A_mat[:,:ncut],param2) # subtract harmonic forces
+        f_vec -= np.dot(A_mat[:,:ncut],param2) # subtract harmonic forces
         sc.delete_all_structures()
         for i, structure in enumerate(saved_structures):
             natoms = structure.get_global_number_of_atoms()
@@ -861,7 +856,7 @@ def run_renormalization(
         supercell_matrix: The supercell transformation matrix.
         fcs: ForceConstants from previous fitting or renormalization
         imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
-            in THz.                                                                                                                                                                                        
+            in THz.
 
     Returns:
         A tuple of the number of imaginary modes at Gamma, the minimum phonon

From a26f235aa6ed14f325d44588f0970113fba646d7 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Aficionado37@Junsoos-MBP.vpn-dhcp.lbl.gov>
Date: Wed, 8 Mar 2023 11:30:28 -0500
Subject: [PATCH 147/207] typo

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 7f1eb5a74..7c41de133 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -354,7 +354,7 @@ def get_fit_data(
         delayed(construct_fit_data)(fcm,structure,s)
         for s,structure in enumerate(saved_structures)
     )
-    for s,data in enumerate(fit_data_tmp)
+    for s,data in enumerate(fit_data_tmp):
         A_mat[s*nrow_per:(s+1)*nrow_per] = data[0]
         f_vec[s*nrow_per:(s+1)*nrow_per] = data[1]
 

From 6671b07993fd51d465765489b2a29f2db89a823c Mon Sep 17 00:00:00 2001
From: Junsoo Park <Aficionado37@Junsoos-MBP.vpn-dhcp.lbl.gov>
Date: Wed, 8 Mar 2023 14:11:48 -0500
Subject: [PATCH 148/207] BTE.KappaTotalTensorVsT_CONV

---
 atomate/vasp/firetasks/lattice_dynamics.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 07db589f8..7aa27c033 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -597,7 +597,9 @@ def run_task(self, fw_spec):
         structure = control.get_structure()
         supercell_matrix = np.diag(control["scell"])
 
-        if Path("BTE.KappaTensorVsT_CONV").exists():
+        if Path("BTE.KappaTotalTensorVsT_CONV").exists():
+            filename = "BTE.KappaTotalTensorVsT_CONV"
+        elif Path("BTE.KappaTensorVsT_CONV").exists():
             filename = "BTE.KappaTensorVsT_CONV"
         elif Path("BTE.KappaTensorVsT_RTA").exists():
             filename = "BTE.KappaTensorVsT_RTA"

From 0b8d0b9aa1d2aec44a9cc688653f023c712ee99e Mon Sep 17 00:00:00 2001
From: Zhuoying Zhu <zzy@ZYZhu-M40.attlocal.net.vpn-dhcp.lbl.gov>
Date: Fri, 10 Mar 2023 15:31:51 -0800
Subject: [PATCH 149/207] small fix for cutoffs and fit_method

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 atomate/vasp/workflows/presets/core.py    | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 7c41de133..41025e18e 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -158,7 +158,7 @@ def get_cutoffs(structure: Structure):
 =======
     cutoffs = np.array(list(map(list, product(range_two, range_three, range_four))))
     max_cutoff = estimate_maximum_cutoff(AseAtomsAdaptor.get_atoms(supercell_structure))
-    cutoffs[cutoffs>max_cutoff] = max_cutoff
+    cutoffs[cutoffs>max_cutoff] = max_cutoff-0.2
     logger.info('CUTOFFS \n {}'.format(cutoffs))
     logger.info('MAX_CUTOFF \n {}'.format(max_cutoff))    
     good_cutoffs = np.all(cutoffs < max_cutoff-0.1, axis=1)
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index d301c20bf..6f206ef52 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -33,7 +33,11 @@
     add_stability_check,
     add_wf_metadata,
 )
+<<<<<<< HEAD
 from atomate.vasp.workflows.base.bulk_modulus import get_wf_bulk_modulus
+=======
+from atomate.vasp.analysis.lattice_dynamics import FIT_METHOD
+>>>>>>> 0da85957 (small fix for cutoffs and fit_method)
 from atomate.vasp.workflows.base.core import get_wf
 from atomate.vasp.workflows.base.elastic import get_wf_elastic_constant
 from atomate.vasp.workflows.base.gibbs import get_wf_gibbs_free_energy
@@ -851,7 +855,7 @@ def wf_nudged_elastic_band(structures, parent, c=None):
 def wf_lattice_dynamics(
     structure: Structure,
     separate_fit: bool = False,
-    fit_method: str = False,
+    fit_method: str = FIT_METHOD,
     disp_cut: float = None,
     bulk_modulus: float = None,
     c: Optional[dict] = None,

From 5ced537706f8f14a1dadb52ba158ef8b06a1c6c8 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Tue, 14 Mar 2023 14:56:46 -0400
Subject: [PATCH 150/207] construct_fit_data

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 41025e18e..eb1a5309a 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -26,7 +26,7 @@
 from hiphive.fitting import Optimizer
 from hiphive.renormalization import Renormalization
 from hiphive.utilities import get_displacements
-from hiphive.run_tools import _clean_data, FE_correction
+from hiphive.run_tools import _clean_data, FE_correction, construct_fit_data
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor

From 22fb19d26170d37b96f2cd4b96a7ccda8c2d306d Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Thu, 16 Mar 2023 21:00:50 -0400
Subject: [PATCH 151/207] fit_data unpack :

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index eb1a5309a..b0f68c8ef 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -355,7 +355,7 @@ def get_fit_data(
         for s,structure in enumerate(saved_structures)
     )
     for s,data in enumerate(fit_data_tmp):
-        A_mat[s*nrow_per:(s+1)*nrow_per] = data[0]
+        A_mat[s*nrow_per:(s+1)*nrow_per,:] = data[0]
         f_vec[s*nrow_per:(s+1)*nrow_per] = data[1]
 
     if param2 is not None:

From b65529548e1d2eca0a65d4d6ba8370b88b15b908 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Fri, 17 Mar 2023 18:05:46 -0400
Subject: [PATCH 152/207] debug

---
 atomate/vasp/analysis/lattice_dynamics.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index b0f68c8ef..78ff34979 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -331,8 +331,8 @@ def get_fit_data(
     saved_structures = []
     fcm = ForceConstantModel(supercell,cs)
     natom = supercell.get_global_number_of_atoms()
-    nrow_per = natom*3
-    nrow_all = nrow_per*len(saved_structures)
+    ndim = natom*3
+    nrow_all = ndim*len(saved_structures)
     A_mat = np.zeros((nrow_all,cs.n_dofs))
     f_vec = np.zeros(nrow_all)
 
@@ -355,13 +355,14 @@ def get_fit_data(
         for s,structure in enumerate(saved_structures)
     )
     for s,data in enumerate(fit_data_tmp):
-        A_mat[s*nrow_per:(s+1)*nrow_per,:] = data[0]
-        f_vec[s*nrow_per:(s+1)*nrow_per] = data[1]
+        print(s,ndim)
+        A_mat[s*ndim:(s+1)*ndim] = data[0]
+        f_vec[s*ndim:(s+1)*ndim] = data[1]
 
     if param2 is not None:
         f_vec -= np.dot(A_mat[:,:ncut],param2) # subtract harmonic force from total
     logger.info('Fit_data dimensions: {}'.format(A_mat.shape))
-    fit_data = _clean_data(A_mat,f_vec,nrow_per)
+    fit_data = _clean_data(A_mat,f_vec,ndim)
     return fit_data
 
 

From 7f0e8581058061e3bc8d23143a0d89846bd93304 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Fri, 17 Mar 2023 18:12:15 -0400
Subject: [PATCH 153/207] debug

---
 atomate/vasp/analysis/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 78ff34979..491adc23b 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -355,7 +355,7 @@ def get_fit_data(
         for s,structure in enumerate(saved_structures)
     )
     for s,data in enumerate(fit_data_tmp):
-        print(s,ndim)
+        print(s,data)
         A_mat[s*ndim:(s+1)*ndim] = data[0]
         f_vec[s*ndim:(s+1)*ndim] = data[1]
 

From 510d9f1a97c6d63dfb15bf8ab837a2851f558dbf Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 17 Mar 2023 20:06:55 -0700
Subject: [PATCH 154/207] sc

---
 atomate/vasp/analysis/lattice_dynamics.py | 34 +++++++++++------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 491adc23b..d0fbfbfda 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -355,7 +355,7 @@ def get_fit_data(
         for s,structure in enumerate(saved_structures)
     )
     for s,data in enumerate(fit_data_tmp):
-        print(s,data)
+        logger.info('DEBUG: {}, {}'.format(s,data[0]))
         A_mat[s*ndim:(s+1)*ndim] = data[0]
         f_vec[s*ndim:(s+1)*ndim] = data[1]
 
@@ -409,11 +409,11 @@ def _run_cutoffs(
     
     if separate_fit:
         logger.info('Fitting harmonic force constants separately')
-        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-                                disp_cut, ncut=n2nd, param2=None)
-#        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
-#                                     ncut=n2nd, param2=None)
-        opt = Optimizer(fit_data,#sc.get_fit_data(),
+#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                                disp_cut, ncut=n2nd, param2=None)
+        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+                                     ncut=n2nd, param2=None)
+        opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [0,n2nd],
                         **fit_kwargs)
@@ -426,11 +426,11 @@ def _run_cutoffs(
         param_harmonic = opt.parameters # harmonic force constant parameters
         
         logger.info('Fitting anharmonic force constants separately')
-        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-                                disp_cut, ncut=n2nd, param2=param_harmonic)
-#        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
-#                                     ncut=n2nd, param2=param_harmonic)
-        opt = Optimizer(fit_data,#sc.get_fit_data(),
+#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                                disp_cut, ncut=n2nd, param2=param_harmonic)
+        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+                                     ncut=n2nd, param2=param_harmonic)
+        opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [n2nd,nall],
                         **fit_kwargs)
@@ -511,11 +511,11 @@ def get_structure_container(
         
     else:
         logger.info('Fitting all force constants in one shot')
-        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-                                disp_cut=None, ncut=None, param2=None)
-#        sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
-#                                     ncut=None, param2=None)
-        opt = Optimizer(fit_data,#sc.get_fit_data(),
+#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                                disp_cut=None, ncut=None, param2=None)
+        sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
+                                     ncut=None, param2=None)
+        opt = Optimizer(sc.get_fit_data(),
                         fit_method,
                         [0,nall],
                         **fit_kwargs)
@@ -594,7 +594,7 @@ def get_structure_container(
         for i, structure in enumerate(saved_structures):
             natoms = structure.get_global_number_of_atoms()
             ndisp = natoms*3
-            structure.set_array('forces',anh_force[i*ndisp:(i+1)*ndisp].reshape(natoms,3))
+            structure.set_array('forces',f_vec[i*ndisp:(i+1)*ndisp].reshape(natoms,3))
             sc.add_structure(structure)
 
     logger.debug(sc.__repr__())

From 351010c505ee7cda445132ca6e340ac9d94cef8c Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 19 Mar 2023 20:17:34 -0700
Subject: [PATCH 155/207] changes

---
 atomate/vasp/analysis/lattice_dynamics.py  | 13 ++++++++-----
 atomate/vasp/firetasks/lattice_dynamics.py |  4 ++--
 atomate/vasp/fireworks/lattice_dynamics.py |  2 +-
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index d0fbfbfda..2fc79b40a 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -877,16 +877,19 @@ def run_renormalization(
 	)
     else:
         anharmonic_data = dict()
-        anharmonic_data["gruneisen"] = np.array([[0,0,0]])
-        anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
-
+#        anharmonic_data["temperature"] = T
+#        anharmonic_data["gruneisen"] = np.array([[0,0,0]])
+#        anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
+#        anharmonic_data["expansion_ratio"] = np.array([[0,0,0]])
+    renorm_data.update(anharmonic_data)
+    
     omega0 = phonopy_orig.mesh.frequencies # THz
     omega_TD = phonopy.mesh.frequencies # THz
 #    natom = phonopy.primitive.get_number_of_atoms()
-    correction_S, correction_4 = FE_correction(omega0,omega_TD,T) # eV/atom
+    correction_S, correction_SC = FE_correction(omega0,omega_TD,T) # eV/atom
 
-    renorm_data.update(anharmonic_data)
     renorm_data["free_energy_correction_S"] = correction_S[0]
+    renorm_data["free_energy_correction_SC"] = correction_SC[0]
     renorm_data["fcp"] = fcp
     renorm_data["fcs"] = fcs
     renorm_data["param"] = param
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 7aa27c033..72483b8e8 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -201,7 +201,7 @@ def run_task(self, fw_spec):
             thermal_data["n_imaginary"], bulk_modulus
         )
 
-        phonopy.save("phonopy_params.yaml")
+        phonopy.save("phonopy_orig.yaml")
         fitting_data["n_imaginary"] = thermal_data.pop("n_imaginary")
         thermal_data.update(anharmonic_data)
         dumpfn(fitting_data, "fitting_data.json")
@@ -250,7 +250,7 @@ def run_task(self, fw_spec):
         param = np.loadtxt('parameters.txt')
         fitting_data = loadfn("fitting_data.json")
         structure_data = loadfn("structure_data.json")
-        phonopy_orig = phpy.load("phonopy_params.yaml")
+        phonopy_orig = phpy.load("phonopy_orig.yaml")
 
         cutoffs = fitting_data["cutoffs"]
         fit_method = fitting_data["fit_method"]
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 530643973..a0f62bd9b 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -209,7 +209,7 @@ def __init__(
         
         # files needed to run renormalization
         files = ["cluster_space.cs","parameters.txt","force_constants.fcs",
-                 "structure_data.json","fitting_data.json","phonopy_params.yaml"]
+                 "structure_data.json","fitting_data.json","phonopy_orig.yaml"]
 
         if prev_calc_dir:
             copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)

From 8a2e573f65690941aab6ff949d96d52044d95713 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Sun, 19 Mar 2023 23:15:33 -0400
Subject: [PATCH 156/207] anharmonic properties return

---
 atomate/vasp/analysis/lattice_dynamics.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 2fc79b40a..2d286665b 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -671,7 +671,7 @@ def anharmonic_properties(
     Cv: np.ndarray,
     n_imaginary: float,
     bulk_modulus: float = None
-) -> Tuple[Dict, Phonopy]:
+) -> Dict:
 
     if n_imaginary == 0:
         logger.info('Evaluating anharmonic properties...')
@@ -695,7 +695,7 @@ def anharmonic_properties(
         "gruneisen": grun,
         "thermal_expansion": cte,
         "expansion_ratio": dLfrac,
-        }, phonopy
+        }
 
 
 def get_total_grun(
@@ -872,7 +872,7 @@ def run_renormalization(
 
     if renorm_data["n_imaginary"] == 0:
         logger.info('Renormalized phonon is completely real at T = {} K!'.format(T))
-        anharmonic_data, phonopy = anharmonic_properties(
+        anharmonic_data = anharmonic_properties(
             phonopy, fcs, [T], thermal_data["heat_capacity"], n_imaginary, bulk_modulus=bulk_modulus
 	)
     else:

From f15af74bcf365571d757470ddbe67655ca2ca0b8 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sun, 19 Mar 2023 20:42:45 -0700
Subject: [PATCH 157/207] anharmonic properties return

---
 atomate/vasp/firetasks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 72483b8e8..3336857be 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -196,7 +196,7 @@ def run_task(self, fw_spec):
         thermal_data, phonopy = harmonic_properties(
             parent_structure, supercell_matrix, fcs, T_qha, imaginary_tol
         )
-        anharmonic_data, phonopy = anharmonic_properties(
+        anharmonic_data = anharmonic_properties(
             phonopy, fcs, T_qha, thermal_data["heat_capacity"],
             thermal_data["n_imaginary"], bulk_modulus
         )

From 13856745ba16a959eea3b20071dd65deecab408d Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 20 Mar 2023 00:05:59 -0400
Subject: [PATCH 158/207] nconfig0 nconfig

---
 atomate/vasp/analysis/lattice_dynamics.py  | 4 ++--
 atomate/vasp/firetasks/lattice_dynamics.py | 3 ++-
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 2d286665b..535f55d88 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -59,9 +59,9 @@
 
 FIT_METHOD = "rfe" 
 RENORM_METHOD = 'pseudoinverse'
-RENORM_NCONFIG = 50
+RENORM_NCONFIG = 5
 RENORM_CONV_THRESH = 0.1 # meV/atom
-RENORM_MAX_ITER = 20
+RENORM_MAX_ITER = 30
 
 eV2J = 1.602e-19
 hbar = sp.constants.hbar # J-s
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 3336857be..e5a9b1b2b 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -264,7 +264,7 @@ def run_task(self, fw_spec):
         renorm_temp = np.array(self.get("renorm_temp"))
         renorm_temp.sort()
         renorm_method = self.get("renorm_method")
-        nconfig = self.get("nconfig")
+        nconfig0 = self.get("nconfig")
         conv_thresh = self.get("conv_thresh")
         max_iter = self.get("max_iter")
         renorm_TE_iter = self.get("renorm_TE_iter")
@@ -282,6 +282,7 @@ def run_task(self, fw_spec):
         # low temperature renormalizations finish early
         renorm_data = []
         for t, T in enumerate(renorm_temp):
+            nconfig = nconfig0*(1+np.mod(T,100))
             data_T = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, 
                                 max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
             renorm_data.append(data_T)
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index a0f62bd9b..d18d1cc23 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -219,7 +219,7 @@ def __init__(
         renorm_force_constants = RunHiPhiveRenorm(
             renorm_temp=temperature,
             renorm_method=renorm_method,
-            nconfig=renorm_nconfig,
+            nconfig0=renorm_nconfig,
             conv_thresh=renorm_conv_thresh,
             max_iter=renorm_max_iter,
             renorm_TE_iter=renorm_TE_iter,

From 04419a98de4da0cf3049f4a8acd21935f6080724 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 20 Mar 2023 00:35:34 -0400
Subject: [PATCH 159/207] parallel renormalization fireworks for each T

---
 atomate/vasp/firetasks/lattice_dynamics.py    | 121 ++++++------------
 atomate/vasp/fireworks/lattice_dynamics.py    |   2 +-
 .../vasp/workflows/base/lattice_dynamics.py   |  26 ++--
 3 files changed, 56 insertions(+), 93 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index e5a9b1b2b..8c9d6be5e 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -264,103 +264,64 @@ def run_task(self, fw_spec):
         renorm_temp = np.array(self.get("renorm_temp"))
         renorm_temp.sort()
         renorm_method = self.get("renorm_method")
-        nconfig0 = self.get("nconfig")
+        nconfig = self.get("nconfig")
         conv_thresh = self.get("conv_thresh")
         max_iter = self.get("max_iter")
         renorm_TE_iter = self.get("renorm_TE_iter")
         bulk_modulus = self.get("bulk_modulus")
 
         # Renormalization with DFT lattice 
-
-        # Parallel version
-#        renorm_data = Parallel(n_jobs=len(renorm_temp), backend="multiprocessing")(delayed(run_renormalization)(
-#            parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, max_iter,
-#            conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig) for t, T in enumerate(renorm_temp))
-
-        # Serial version - likely better because it allows parallelization over A matrix construction,
-        # which takes most of the time during renormalization, and leaves no process idling around when 
-        # low temperature renormalizations finish early
-        renorm_data = []
-        for t, T in enumerate(renorm_temp):
-            nconfig = nconfig0*(1+np.mod(T,100))
-            data_T = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, 
-                                max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
-            renorm_data.append(data_T)
+        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, 
+                                     max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
 
         # Additional renormalization with thermal expansion - optional - just single "iteration" for now
         if renorm_TE_iter:
-            n_TE_iter = 1            
-            for i in range(n_TE_iter):
-                logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
-
-                if i==0: # first iteration - pull only cases where phonon is all real and order by temperature
-                    T_real = []
-                    dLfrac_real = []
-                    param_real = []
-                    for result in renorm_data:
-                        if result is None: # failed or incomplete 
+            n_TE_iter = 1
+            if renorm_data is None: # failed or incomplete                                                                                                                                           
+                pass
+            elif result["n_imaginary"] > 0: # still has imaginary frequencies
+                pass
+            else:
+                for i in range(n_TE_iter):
+                    logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
+                    if i==0: # first iteration - pull only cases where phonon is all real and order by temperature
+                        if renorm_data is None: # failed or incomplete 
                             continue 
                         elif result["n_imaginary"] < 0: # still imaginary
                             continue
-                        else:
-                            T_real = T_real + result["temperature"]
-                            dLfrac_real = dLfrac_real + result["expansion_ratio"]
-                            param_real = param_real + result["param"]
-                    if len(T_real)==0: 
-                        logger.info("No cases with real phonons - cannot do thermal expansion for any temperature")
-                        break
-                else:
-                    for t,result in enumerate(renorm_data):
-                        dLfrac_real[t] = result["expansion_ratio"]  
-                        param_real[t] = result["param"]
-
-                parent_structure_TE, cs_TE, fcs_TE = setup_TE_iter(cutoffs,parent_structure,T_real,dLfrac_real)
-                param_TE = copy(param_real)
-                prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
-                prim_phonopy_TE = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
-                                               scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
-                phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
-
-                # Parallel
-#                renorm_data = Parallel(n_jobs=len(T_real), backend="multiprocessing")(delayed(run_renormalization)(
-#                    parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, cs_TE[t], fcs_TE[t], param_TE[t],
-#                    T, nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_TE
-#                    ) for t, T in enumerate(T_real)
-#                )
-
-                # Serial
-                renorm_data_TE = []
-                for t, T in enumerate(T_real):
-                    data_T = run_renormalization(parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, 
-                                                 cs_TE[t], fcs_TE[t], param_TE[t], T, nconfig, max_iter, conv_thresh,
-                                                 renorm_method, fit_method, bulk_modulus, phonopy_TE)
-                    renorm_data_TE.append(data_T)
-                    
-            if len(T_real) > 0:
-                for t, result in enumerate(renorm_data_TE):
-                    temp_index = np.where(renorm_temp==T_real[t])[0][0]
-                    renorm_data[temp_index] = result
-
+                    if i > 0:
+                        dLfrac = renorm_data["expansion_ratio"]  
+                        param = renorm_data["param"]
+
+                        parent_structure_TE, cs_TE, fcs_TE = setup_TE_iter(cutoffs,parent_structure,T,dLfrac)
+                        param_TE = copy(param)
+                        prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
+                        prim_phonopy_TE = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
+                                                       scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
+                        phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
+                        
+                        renorm_data = run_renormalization(parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, 
+                                                          cs_TE[t], fcs_TE[t], param_TE[t], T, nconfig, max_iter, conv_thresh,
+                                                          renorm_method, fit_method, bulk_modulus, phonopy_TE)
+                        
         # write results
         logger.info("Writing renormalized results")
         thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
         "gruneisen","thermal_expansion","expansion_ratio","free_energy_correction"]
         renorm_thermal_data = {key: [] for key in thermal_keys}
-        for t, result in enumerate(renorm_data):
-            logger.info("DEBUG: ",result)
-            T = result["temperature"]
-            fcs = result["fcs"]
-            fcs.write("force_constants_{}K.fcs".format(T))
-            np.savetxt('parameters_{}K.txt'.format(T),result["param"])
-            for key in thermal_keys:
-                renorm_thermal_data[key].append(result[key])
-            if result["n_imaginary"] > 0:
-                logger.warning('Imaginary modes exist for {} K!'.format(T))
-                logger.warning('ShengBTE files not written')
-                logger.warning('No renormalization with thermal expansion')
-            else:
-                logger.info("No imaginary modes! Writing ShengBTE files")
-                fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(T), format="text")
+        logger.info("DEBUG: ",renorm_data)
+        fcs = renorm_data["fcs"]
+        fcs.write("force_constants_{}K.fcs".format(T))
+        np.savetxt('parameters_{}K.txt'.format(T),renorm_data["param"])
+        for key in thermal_keys:
+            renorm_thermal_data[key].append(renorm_data[key])
+        if renorm_data["n_imaginary"] > 0:
+            logger.warning('Imaginary modes exist for {} K!'.format(T))
+            logger.warning('ShengBTE files not written')
+            logger.warning('No renormalization with thermal expansion')
+        else:
+            logger.info("No imaginary modes! Writing ShengBTE files")
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(T), format="text")
 
         renorm_thermal_data.pop("n_imaginary")                    
         dumpfn(thermal_data, "renorm_thermal_data.json")
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index d18d1cc23..a0f62bd9b 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -219,7 +219,7 @@ def __init__(
         renorm_force_constants = RunHiPhiveRenorm(
             renorm_temp=temperature,
             renorm_method=renorm_method,
-            nconfig0=renorm_nconfig,
+            nconfig=renorm_nconfig,
             conv_thresh=renorm_conv_thresh,
             max_iter=renorm_max_iter,
             renorm_TE_iter=renorm_TE_iter,
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index e42345741..c1b995960 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -207,19 +207,21 @@ def get_lattice_dynamics_wf(
 
     # 3. Renormalization FW (pass_inputs like bulk modulus)
     if renormalize:
-        fw_renormalization = RenormalizationFW(
-            db_file=db_file,
-            temperature=renormalize_temperature,
-            renorm_method=renormalize_method,
-            renorm_nconfig=renormalize_nconfig,
-            renorm_conv_thresh=renormalize_conv_thresh,
-            renorm_max_iter=renormalize_max_iter,
-            renorm_TE_iter=renormalize_thermal_expansion_iter,
-            bulk_modulus=bulk_modulus,
-            mesh_density=mesh_density,
+        for T in renormalize_temperature:
+            nconfig = renormalize_nconfig*(1+np.mod(T,100))
+            fw_renormalization = RenormalizationFW(
+                db_file=db_file,
+                temperature=temp,
+                renorm_method=renormalize_method,
+                renorm_nconfig=nconfig,
+                renorm_conv_thresh=renormalize_conv_thresh,
+                renorm_max_iter=renormalize_max_iter,
+                renorm_TE_iter=renormalize_thermal_expansion_iter,
+                bulk_modulus=bulk_modulus,
+                mesh_density=mesh_density,
             )
-        wf.append_wf(
-            Workflow.from_Firework(fw_renormalization), [wf.fws[-1].fw_id]
+            wf.append_wf(
+                Workflow.from_Firework(fw_renormalization), [wf.fws[-1].fw_id]
             )
 
     # 4. Lattice thermal conductivity calculation

From 7737ba7225a1b09dc44ee17383ccb69096d99779 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 20 Mar 2023 00:37:01 -0400
Subject: [PATCH 160/207] parallel renormalization fireworks for each T

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index c1b995960..eac66ed05 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -211,7 +211,7 @@ def get_lattice_dynamics_wf(
             nconfig = renormalize_nconfig*(1+np.mod(T,100))
             fw_renormalization = RenormalizationFW(
                 db_file=db_file,
-                temperature=temp,
+                temperature=T,
                 renorm_method=renormalize_method,
                 renorm_nconfig=nconfig,
                 renorm_conv_thresh=renormalize_conv_thresh,

From c1981f106a6b6bbf1045d61005e2856aef15761a Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 20 Mar 2023 00:39:46 -0400
Subject: [PATCH 161/207] parallel renormalization fireworks name

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index a0f62bd9b..658d1695b 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -233,4 +233,4 @@ def __init__(
         pass_locs = PassCalcLocs(name=name)
 
         tasks = [copy_files, renorm_force_constants, to_db, pass_locs]
-        super().__init__(tasks, name=name, **kwargs)
+        super().__init__(tasks, name="{}_{}K".format(name,temperature), **kwargs)

From 2ffa1c7fa8fb61c6848215132f196ea5566741c5 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Mon, 20 Mar 2023 00:41:21 -0400
Subject: [PATCH 162/207] renormalization klat dir link

---
 atomate/vasp/fireworks/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 658d1695b..f7f20ee2f 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -141,7 +141,7 @@ def __init__(
             if prev_calc_dir:
                 copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
-                copy_files = CopyFilesFromCalcLoc(calc_loc='Renormalization', filenames=files)
+                copy_files = CopyFilesFromCalcLoc(calc_loc='Renormalization_{}K'.format(temperature), filenames=files)
             os.system('mv FORCE_CONSTANTS_2ND_{}K FORCE_CONSTANTS_2ND'.format(temperature))
 
         else: # only the default files are needed

From 72de4a9cfd6b4f7f54e1482529d7bd9e5bd218a8 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Mon, 20 Mar 2023 07:53:18 -0700
Subject: [PATCH 163/207] TE iter fix

---
 atomate/vasp/analysis/lattice_dynamics.py  | 43 +++++++---------
 atomate/vasp/firetasks/lattice_dynamics.py | 57 ++++++++++------------
 2 files changed, 43 insertions(+), 57 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 535f55d88..77f954cf3 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -898,28 +898,21 @@ def run_renormalization(
 
 
 
-def setup_TE_iter(cutoffs,parent_structure,temperatures,dLfracs):
-    parent_structure_TE = []
-    cs_TE = []
-    fcs_TE = []
-    for t, (T,dLfrac) in enumerate(zip(temperatures,dLfracs)):
-        new_atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-        new_cell = Cell(np.transpose([new_atoms.get_cell()[:,i]*(1+dLfrac[0,i]) for i in range(3)]))
-        new_atoms.set_cell(new_cell,scale_atoms=True)
-        new_parent_structure = AseAtomsAdaptor.get_structure(new_atoms)
-        new_supercell_atoms = AseAtomsAdaptor.get_atoms(new_parent_structure*supercell_matrix)
-        new_cutoffs = [i*(1+np.linalg.norm(dLfrac)) for i in cutoffs]
-        while True:
-            new_cs = ClusterSpace(atoms,new_cutoffs,1e-3,acoustic_sum_rules=True)
-            if cs_TD.n_dofs == cs.n_dofs:
-                break
-            elif cs_TD.n_dofs > cs.n_dofs:
-                new_cutoffs = [i*0.999 for i in new_cutoffs]
-            elif cs_TD.n_dofs < cs.n_dofs:
-                new_cutoffs = [i*1.001 for i in new_cutoffs]
-        cs_TE.append(new_cs)
-        parent_structure_TE.append(new_parent_structure)
-        new_fcp = ForceConstantsPotential(new_cs,param_real[t])
-        fcs_TE.append(new_fcp.get_force_constants(new_supercell_atoms))
-
-        return parent_structure_TE, cs_TE, fcs_TE
+def setup_TE_iter(cs,cutoffs,parent_structure,param,temperatures,dLfrac):
+    new_atoms = AseAtomsAdaptor.get_atoms(parent_structure)
+    new_cell = Cell(np.transpose([new_atoms.get_cell()[:,i]*(1+dLfrac[0,i]) for i in range(3)]))
+    new_atoms.set_cell(new_cell,scale_atoms=True)
+    parent_structure_TE = AseAtomsAdaptor.get_structure(new_atoms)
+    supercell_atoms_TE = AseAtomsAdaptor.get_atoms(parent_structure_TE*supercell_matrix)
+    new_cutoffs = [i*(1+np.linalg.norm(dLfrac)) for i in cutoffs]
+    while True:
+        cs_TE = ClusterSpace(atoms,new_cutoffs,1e-3,acoustic_sum_rules=True)
+        if cs_TE.n_dofs == cs.n_dofs:
+            break
+        elif cs_TE.n_dofs > cs.n_dofs:
+            new_cutoffs = [i*0.999 for i in new_cutoffs]
+        elif cs_TE.n_dofs < cs.n_dofs:
+            new_cutoffs = [i*1.001 for i in new_cutoffs]
+        new_fcp = ForceConstantsPotential(cs_TE,param)
+        fcs_TE.append(new_fcp.get_force_constants(supercell_atoms_TE))
+    return parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 8c9d6be5e..a7ef4a594 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -262,7 +262,6 @@ def run_task(self, fw_spec):
         supercell_matrix = np.array(structure_data["supercell_matrix"])
 
         renorm_temp = np.array(self.get("renorm_temp"))
-        renorm_temp.sort()
         renorm_method = self.get("renorm_method")
         nconfig = self.get("nconfig")
         conv_thresh = self.get("conv_thresh")
@@ -271,38 +270,32 @@ def run_task(self, fw_spec):
         bulk_modulus = self.get("bulk_modulus")
 
         # Renormalization with DFT lattice 
-        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, T, nconfig, 
-                                     max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
+        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, renorm_temp,
+                                          nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
 
         # Additional renormalization with thermal expansion - optional - just single "iteration" for now
         if renorm_TE_iter:
             n_TE_iter = 1
-            if renorm_data is None: # failed or incomplete                                                                                                                                           
-                pass
-            elif result["n_imaginary"] > 0: # still has imaginary frequencies
-                pass
-            else:
-                for i in range(n_TE_iter):
+            for i in range(n_TE_iter):
+                if renorm_data is None: # failed or incomplete 
+                    break
+                elif result["n_imaginary"] < 0: # still imaginary
+                    break
+                else:
                     logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
-                    if i==0: # first iteration - pull only cases where phonon is all real and order by temperature
-                        if renorm_data is None: # failed or incomplete 
-                            continue 
-                        elif result["n_imaginary"] < 0: # still imaginary
-                            continue
-                    if i > 0:
-                        dLfrac = renorm_data["expansion_ratio"]  
-                        param = renorm_data["param"]
-
-                        parent_structure_TE, cs_TE, fcs_TE = setup_TE_iter(cutoffs,parent_structure,T,dLfrac)
-                        param_TE = copy(param)
-                        prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
-                        prim_phonopy_TE = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
-                                                       scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
-                        phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
-                        
-                        renorm_data = run_renormalization(parent_structure_TE[t], supercell_atoms_TE[t], supercell_matrix, 
-                                                          cs_TE[t], fcs_TE[t], param_TE[t], T, nconfig, max_iter, conv_thresh,
-                                                          renorm_method, fit_method, bulk_modulus, phonopy_TE)
+
+                dLfrac = renorm_data["expansion_ratio"]  
+                param = renorm_data["param"]
+
+                parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,renorm_temp,dLfrac)
+                prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
+                prim_TE_phonopy = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
+                                               scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
+                phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
+                
+                renorm_data = run_renormalization(parent_structure_TE, supercell_atoms_TE, supercell_matrix, 
+                                                  cs_TE, fcs_TE, param, renorm_temp, nconfig, max_iter,
+                                                  conv_thresh,  renorm_method, fit_method, bulk_modulus, phonopy_TE)
                         
         # write results
         logger.info("Writing renormalized results")
@@ -311,17 +304,17 @@ def run_task(self, fw_spec):
         renorm_thermal_data = {key: [] for key in thermal_keys}
         logger.info("DEBUG: ",renorm_data)
         fcs = renorm_data["fcs"]
-        fcs.write("force_constants_{}K.fcs".format(T))
-        np.savetxt('parameters_{}K.txt'.format(T),renorm_data["param"])
+        fcs.write("force_constants_{}K.fcs".format(renorm_temp))
+        np.savetxt('parameters_{}K.txt'.format(renorm_temp),renorm_data["param"])
         for key in thermal_keys:
             renorm_thermal_data[key].append(renorm_data[key])
         if renorm_data["n_imaginary"] > 0:
-            logger.warning('Imaginary modes exist for {} K!'.format(T))
+            logger.warning('Imaginary modes exist for {} K!'.format(renorm_temp))
             logger.warning('ShengBTE files not written')
             logger.warning('No renormalization with thermal expansion')
         else:
             logger.info("No imaginary modes! Writing ShengBTE files")
-            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(T), format="text")
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(renorm_temp), format="text")
 
         renorm_thermal_data.pop("n_imaginary")                    
         dumpfn(thermal_data, "renorm_thermal_data.json")

From a1e43e4859bfa952f3786e894d27c0e57d0dce9c Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Mon, 20 Mar 2023 09:11:03 -0700
Subject: [PATCH 164/207] anything?

---
 atomate/vasp/analysis/lattice_dynamics.py     |  4 +++
 atomate/vasp/firetasks/lattice_dynamics.py    | 27 ++++++++++---------
 atomate/vasp/fireworks/lattice_dynamics.py    | 15 ++++++-----
 .../vasp/workflows/base/lattice_dynamics.py   |  7 ++---
 4 files changed, 30 insertions(+), 23 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 77f954cf3..5a5fe1329 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -863,6 +863,10 @@ def run_renormalization(
         A tuple of the number of imaginary modes at Gamma, the minimum phonon
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
+
+    print("nconfig ANAL",type(nconfig),nconfig)
+    print('T ANAL',T)
+    nconfig = int(nconfig)
     renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
     fcp, fcs, param = renorm.renormalize(nconfig,conv_tresh)
 
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index a7ef4a594..45d8eadec 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -227,19 +227,19 @@ def run_task(self, fw_spec):
 @explicit_serialize
 class RunHiPhiveRenorm(FiretaskBase):
     """
-    Perform phonon renormalization to obtain temperature-dependent force constants
+    Perform phonon renormalization to obtain dependent-temperature force constants
     using hiPhive. Requires "structure_data.json" to be present in the current working
     directory.
 
     Required parameters:
    
     Optional parameter:
-        renorm_temp (List): list of temperatures to perform renormalization - defaults to T_RENORM
-        renorm_with_te (bool): if True, perform outer iteration over thermally expanded volumes
+        temperature (List): list of temperatures to perform renormalization - defaults to T_RENORM
+        renorm_TE_iter (bool): if True, perform outer iteration over thermally expanded volumes
         bulk_modulus (float): input bulk modulus - required for thermal expansion iterations
     """
 
-    optional_params = ["renorm_method","renorm_temp","nconfig","conv_thresh","max_iter",
+    optional_params = ["renorm_method","temperature","nconfig","conv_thresh","max_iter",
                        "renorm_TE_iter","bulk_modulus","imaginary_tol"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
@@ -261,7 +261,7 @@ def run_task(self, fw_spec):
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
         supercell_matrix = np.array(structure_data["supercell_matrix"])
 
-        renorm_temp = np.array(self.get("renorm_temp"))
+        temperature = np.array(self.get("temperature"))
         renorm_method = self.get("renorm_method")
         nconfig = self.get("nconfig")
         conv_thresh = self.get("conv_thresh")
@@ -269,8 +269,9 @@ def run_task(self, fw_spec):
         renorm_TE_iter = self.get("renorm_TE_iter")
         bulk_modulus = self.get("bulk_modulus")
 
-        # Renormalization with DFT lattice 
-        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, renorm_temp,
+        # Renormalization with DFT lattice
+        print("nconfig FT",type(nconfig),nconfig)
+        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, temperature,
                                           nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
 
         # Additional renormalization with thermal expansion - optional - just single "iteration" for now
@@ -287,14 +288,14 @@ def run_task(self, fw_spec):
                 dLfrac = renorm_data["expansion_ratio"]  
                 param = renorm_data["param"]
 
-                parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,renorm_temp,dLfrac)
+                parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,temperature,dLfrac)
                 prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
                 prim_TE_phonopy = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
                                                scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
                 phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
                 
                 renorm_data = run_renormalization(parent_structure_TE, supercell_atoms_TE, supercell_matrix, 
-                                                  cs_TE, fcs_TE, param, renorm_temp, nconfig, max_iter,
+                                                  cs_TE, fcs_TE, param, temperature, nconfig, max_iter,
                                                   conv_thresh,  renorm_method, fit_method, bulk_modulus, phonopy_TE)
                         
         # write results
@@ -304,17 +305,17 @@ def run_task(self, fw_spec):
         renorm_thermal_data = {key: [] for key in thermal_keys}
         logger.info("DEBUG: ",renorm_data)
         fcs = renorm_data["fcs"]
-        fcs.write("force_constants_{}K.fcs".format(renorm_temp))
-        np.savetxt('parameters_{}K.txt'.format(renorm_temp),renorm_data["param"])
+        fcs.write("force_constants_{}K.fcs".format(temperature))
+        np.savetxt('parameters_{}K.txt'.format(temperature),renorm_data["param"])
         for key in thermal_keys:
             renorm_thermal_data[key].append(renorm_data[key])
         if renorm_data["n_imaginary"] > 0:
-            logger.warning('Imaginary modes exist for {} K!'.format(renorm_temp))
+            logger.warning('Imaginary modes exist for {} K!'.format(temperature))
             logger.warning('ShengBTE files not written')
             logger.warning('No renormalization with thermal expansion')
         else:
             logger.info("No imaginary modes! Writing ShengBTE files")
-            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(renorm_temp), format="text")
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(temperature), format="text")
 
         renorm_thermal_data.pop("n_imaginary")                    
         dumpfn(thermal_data, "renorm_thermal_data.json")
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index f7f20ee2f..147dff8e5 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -195,9 +195,9 @@ def __init__(
         self,
         temperature: Union[float, Dict], 
         renorm_method: str,
-        renorm_nconfig: int,
-        renorm_conv_thresh: float,
-        renorm_max_iter: float,
+        nconfig: int,
+        conv_thresh: float,
+        max_iter: float,
         renorm_TE_iter: bool,
         bulk_modulus: float,
         mesh_density: float,
@@ -216,12 +216,13 @@ def __init__(
         else:
             copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
 
+        print('nconfig in FW',type(nconfig),nconfig)
         renorm_force_constants = RunHiPhiveRenorm(
-            renorm_temp=temperature,
+            temperature=temperature,
             renorm_method=renorm_method,
-            nconfig=renorm_nconfig,
-            conv_thresh=renorm_conv_thresh,
-            max_iter=renorm_max_iter,
+            nconfig=nconfig,
+            conv_thresh=conv_thresh,
+            max_iter=max_iter,
             renorm_TE_iter=renorm_TE_iter,
             bulk_modulus=bulk_modulus,
             **kwargs
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index eac66ed05..14077683f 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -209,13 +209,14 @@ def get_lattice_dynamics_wf(
     if renormalize:
         for T in renormalize_temperature:
             nconfig = renormalize_nconfig*(1+np.mod(T,100))
+            print("nconfig in WF",type(nconfig),nconfig)
             fw_renormalization = RenormalizationFW(
                 db_file=db_file,
                 temperature=T,
                 renorm_method=renormalize_method,
-                renorm_nconfig=nconfig,
-                renorm_conv_thresh=renormalize_conv_thresh,
-                renorm_max_iter=renormalize_max_iter,
+                nconfig=nconfig,
+                conv_thresh=renormalize_conv_thresh,
+                max_iter=renormalize_max_iter,
                 renorm_TE_iter=renormalize_thermal_expansion_iter,
                 bulk_modulus=bulk_modulus,
                 mesh_density=mesh_density,

From cb039d220b451840e36262bcef4a1251c9448be9 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Mon, 20 Mar 2023 13:58:53 -0700
Subject: [PATCH 165/207] ToDB

---
 atomate/vasp/analysis/lattice_dynamics.py     | 20 ++--
 atomate/vasp/firetasks/lattice_dynamics.py    | 95 ++++++++++---------
 atomate/vasp/fireworks/lattice_dynamics.py    |  7 +-
 .../vasp/workflows/base/lattice_dynamics.py   |  5 +-
 4 files changed, 64 insertions(+), 63 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 5a5fe1329..ab0f2bc25 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -271,8 +271,7 @@ def fit_force_constants(
     if fit_method == "rfe" and n_jobs == -1:
         fit_kwargs["n_jobs"] = 1
 
-    logger.info('CPU COUNT: {}'.format(os.cpu_count()))
-    cutoff_results = Parallel(n_jobs=12, backend="multiprocessing")(delayed(_run_cutoffs)(
+    cutoff_results = Parallel(n_jobs=min(os.cpu_count(),len(all_cutoffs)), backend="multiprocessing")(delayed(_run_cutoffs)(
         i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, fit_method,
         separate_fit, disp_cut, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
@@ -864,8 +863,6 @@ def run_renormalization(
         frequency at Gamma, and the free energy, entropy, and heat capacity
     """
 
-    print("nconfig ANAL",type(nconfig),nconfig)
-    print('T ANAL',T)
     nconfig = int(nconfig)
     renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
     fcp, fcs, param = renorm.renormalize(nconfig,conv_tresh)
@@ -881,16 +878,19 @@ def run_renormalization(
 	)
     else:
         anharmonic_data = dict()
-#        anharmonic_data["temperature"] = T
-#        anharmonic_data["gruneisen"] = np.array([[0,0,0]])
-#        anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
-#        anharmonic_data["expansion_ratio"] = np.array([[0,0,0]])
+        anharmonic_data["temperature"] = T
+        anharmonic_data["gruneisen"] = np.array([[0,0,0]])
+        anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
+        anharmonic_data["expansion_ratio"] = np.array([[0,0,0]])
     renorm_data.update(anharmonic_data)
-    
+
+    phonopy_orig.run_mesh()
+    phonopy.run_mesh()
     omega0 = phonopy_orig.mesh.frequencies # THz
     omega_TD = phonopy.mesh.frequencies # THz
+    evec = phonopy.mesh.eigenvectors
 #    natom = phonopy.primitive.get_number_of_atoms()
-    correction_S, correction_SC = FE_correction(omega0,omega_TD,T) # eV/atom
+    correction_S, correction_SC = FE_correction(omega0,omega_TD,evec,[T]) # eV/atom
 
     renorm_data["free_energy_correction_S"] = correction_S[0]
     renorm_data["free_energy_correction_SC"] = correction_SC[0]
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 45d8eadec..be8b4b48c 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -234,7 +234,7 @@ class RunHiPhiveRenorm(FiretaskBase):
     Required parameters:
    
     Optional parameter:
-        temperature (List): list of temperatures to perform renormalization - defaults to T_RENORM
+        temperature (float): temperature to perform renormalization
         renorm_TE_iter (bool): if True, perform outer iteration over thermally expanded volumes
         bulk_modulus (float): input bulk modulus - required for thermal expansion iterations
     """
@@ -261,7 +261,7 @@ def run_task(self, fw_spec):
         supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
         supercell_matrix = np.array(structure_data["supercell_matrix"])
 
-        temperature = np.array(self.get("temperature"))
+        temperature = self.get("temperature")
         renorm_method = self.get("renorm_method")
         nconfig = self.get("nconfig")
         conv_thresh = self.get("conv_thresh")
@@ -270,7 +270,6 @@ def run_task(self, fw_spec):
         bulk_modulus = self.get("bulk_modulus")
 
         # Renormalization with DFT lattice
-        print("nconfig FT",type(nconfig),nconfig)
         renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, temperature,
                                           nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
 
@@ -297,11 +296,14 @@ def run_task(self, fw_spec):
                 renorm_data = run_renormalization(parent_structure_TE, supercell_atoms_TE, supercell_matrix, 
                                                   cs_TE, fcs_TE, param, temperature, nconfig, max_iter,
                                                   conv_thresh,  renorm_method, fit_method, bulk_modulus, phonopy_TE)
+            structure_data["structure"] = parent_structure_TE
+            structure_data["supercell_structure"] = AseAtomsAdaptor.get_structure(supercell_atoms_TE)
                         
         # write results
         logger.info("Writing renormalized results")
         thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
-        "gruneisen","thermal_expansion","expansion_ratio","free_energy_correction"]
+                        "gruneisen","thermal_expansion","expansion_ratio",
+                        "free_energy_correction_S","free_energy_correction_SC"]
         renorm_thermal_data = {key: [] for key in thermal_keys}
         logger.info("DEBUG: ",renorm_data)
         fcs = renorm_data["fcs"]
@@ -310,15 +312,15 @@ def run_task(self, fw_spec):
         for key in thermal_keys:
             renorm_thermal_data[key].append(renorm_data[key])
         if renorm_data["n_imaginary"] > 0:
-            logger.warning('Imaginary modes exist for {} K!'.format(temperature))
+            logger.warning('Imaginary modes remain for {} K!'.format(temperature))
             logger.warning('ShengBTE files not written')
             logger.warning('No renormalization with thermal expansion')
         else:
             logger.info("No imaginary modes! Writing ShengBTE files")
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(temperature), format="text")
 
-        renorm_thermal_data.pop("n_imaginary")                    
-        dumpfn(thermal_data, "renorm_thermal_data.json")
+        dumpfn(structure_data, "structure_data_{}K.json".format(temperature))
+        dumpfn(renorm_thermal_data, "renorm_thermal_data_{}K.json".format(temperature))
 
         
 @explicit_serialize
@@ -346,7 +348,7 @@ class ForceConstantsToDb(FiretaskBase):
     """
 
     required_params = ["db_file"]
-    optional_params = ["renormalized","mesh_density", "additional_fields"]
+    optional_params = ["renormalized","renorm_temperature","mesh_density", "additional_fields"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
     def run_task(self, fw_spec):
@@ -354,18 +356,17 @@ def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
         renormalized = self.get("renormalized", False)
+        renorm_temperature = self.get("renorm_temperature", None)
         mesh_density = self.get("mesh_density", 100.0)
 
-        structure_data = loadfn("structure_data.json")
-        forces = loadfn("perturbed_forces.json")
-        structures = loadfn("perturbed_structures.json")
-        
+        structure_data = loadfn("structure_data.json")        
         structure = structure_data["structure"]
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = structure_data["supercell_matrix"]
 
         if not renormalized:
-            
+            perturbed_structures = loadfn("perturbed_structures.json")
+            forces = loadfn("perturbed_forces.json")
             fitting_data = loadfn("fitting_data.json")
             thermal_data = loadfn("thermal_data.json")
             fcs = ForceConstants.read("force_constants.fcs")
@@ -381,7 +382,7 @@ def run_task(self, fw_spec):
                 "structure": structure.as_dict(),
                 "supercell_matrix": supercell_matrix,
                 "supercell_structure": supercell_structure.as_dict(),
-                "perturbed_structures": [s.as_dict() for s in structures],
+                "perturbed_structures": [s.as_dict() for s in perturbed_structures],
                 "perturbed_forces": [f.tolist() for f in forces],
                 "fitting_data": fitting_data,
                 "thermal_data": thermal_data,
@@ -403,41 +404,41 @@ def run_task(self, fw_spec):
             logger.info("Finished inserting force constants and phonon data")
 
         else:
-            renorm_thermal_data = loadfn("renorm_thermal_data.json")
-            temperature = renorm_thermal_data["temperature"]
-
-            # pushing data for individual temperature  
-            for t, T in enumerate(temperature):
-                fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
-                phonopy_fc = fcs.get_fc_array(order=2)
-                dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-                    structure, supercell_matrix, phonopy_fc, mesh_density, mmdb
-                    )
+            T = renorm_temperature
+            renorm_thermal_data = loadfn("renorm_thermal_data_{}.json".format(T))
+            fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
+            
+            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                structure, supercell_matrix, fcs, mesh_density, mmdb
+            )
                 
-                data_at_T = {
-                    "created_at": datetime.utcnow(),
-                    "tags": fw_spec.get("tags", None),
-                    "formula_pretty": structure.composition.reduced_formula,
-                    "renormalized": renormalized,
-                    "temperature": T,
-                    "force_constants_fs_id": fc_fsid,
-                    "thermal_data": renorm_thermal_data[t],
-                    "phonon_dos_fs_id": dos_fsid,
-                    "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-                    "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-                    }
-                data_at_T.update(self.get("additional_fields", {}))
+            data_at_T = {
+                "created_at": datetime.utcnow(),
+                "tags": fw_spec.get("tags", None),
+                "formula_pretty": structure.composition.reduced_formula,
+                "structure": structure.as_dict(),
+                "supercell_matrix": supercell_matrix,
+                "supercell_structure": supercell_structure.as_dict(),
+                "renormalized": renormalized,
+                "temperature": T,
+                "thermal_data": renorm_thermal_data,
+                "force_constants_fs_id": fc_fsid,
+                "phonon_dos_fs_id": dos_fsid,
+                "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+                "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+            }
+            data_at_T.update(self.get("additional_fields", {}))
         
-                # Get an id for the force constants
-                fitting_id = _get_fc_fitting_id(mmdb)
-                metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
-                data_at_T.update(metadata)
-                data_at_T = jsanitize(data,strict=True,allow_bson=True)
-
-                mmdb.db.renormalized_lattice_dynamics.insert_one(data_at_T)
-
-                logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
-
+            # Get an id for the force constants
+            fitting_id = _get_fc_fitting_id(mmdb)
+            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+            data_at_T.update(metadata)
+            data_at_T = jsanitize(data,strict=True,allow_bson=True)
+            
+            mmdb.db.renormalized_lattice_dynamics.insert_one(data_at_T)
+            
+            logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
+            
         return FWAction(update_spec=metadata)        
 
     
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 147dff8e5..827f495f2 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -211,12 +211,12 @@ def __init__(
         files = ["cluster_space.cs","parameters.txt","force_constants.fcs",
                  "structure_data.json","fitting_data.json","phonopy_orig.yaml"]
 
+        name = name+"_{}K".format(temperature)
         if prev_calc_dir:
             copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
         else:
             copy_files = CopyFilesFromCalcLoc(calc_loc="Fit Force Constants", filenames=files)
 
-        print('nconfig in FW',type(nconfig),nconfig)
         renorm_force_constants = RunHiPhiveRenorm(
             temperature=temperature,
             renorm_method=renorm_method,
@@ -229,9 +229,10 @@ def __init__(
             )        
 
         to_db = ForceConstantsToDb(
-            db_file=db_file, renormalized=True, mesh_density=mesh_density, additional_fields={}
+            db_file=db_file, renormalized=True, renorm_temperature = temperature,
+            mesh_density=mesh_density, additional_fields={}
 	)
         pass_locs = PassCalcLocs(name=name)
 
         tasks = [copy_files, renorm_force_constants, to_db, pass_locs]
-        super().__init__(tasks, name="{}_{}K".format(name,temperature), **kwargs)
+        super().__init__(tasks, name=name, **kwargs)
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 14077683f..5ccf75b17 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -207,12 +207,11 @@ def get_lattice_dynamics_wf(
 
     # 3. Renormalization FW (pass_inputs like bulk modulus)
     if renormalize:
-        for T in renormalize_temperature:
+        for temperature in renormalize_temperature:
             nconfig = renormalize_nconfig*(1+np.mod(T,100))
-            print("nconfig in WF",type(nconfig),nconfig)
             fw_renormalization = RenormalizationFW(
                 db_file=db_file,
-                temperature=T,
+                temperature=temperature,
                 renorm_method=renormalize_method,
                 nconfig=nconfig,
                 conv_thresh=renormalize_conv_thresh,

From 6b8f0b77c6ae58a0a9ff33509bd7580d396731cc Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Mon, 20 Mar 2023 14:00:25 -0700
Subject: [PATCH 166/207] error fix

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 5ccf75b17..b73f59fc2 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -208,7 +208,7 @@ def get_lattice_dynamics_wf(
     # 3. Renormalization FW (pass_inputs like bulk modulus)
     if renormalize:
         for temperature in renormalize_temperature:
-            nconfig = renormalize_nconfig*(1+np.mod(T,100))
+            nconfig = renormalize_nconfig*(1+np.mod(temperature,100))
             fw_renormalization = RenormalizationFW(
                 db_file=db_file,
                 temperature=temperature,

From ff3c44029b5660c5fbb9bd7897420735e7f8a680 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Mon, 20 Mar 2023 18:41:45 -0700
Subject: [PATCH 167/207] renormalization works

---
 atomate/vasp/firetasks/lattice_dynamics.py      | 4 ++--
 atomate/vasp/workflows/base/lattice_dynamics.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index be8b4b48c..ad301b192 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -405,7 +405,7 @@ def run_task(self, fw_spec):
 
         else:
             T = renorm_temperature
-            renorm_thermal_data = loadfn("renorm_thermal_data_{}.json".format(T))
+            renorm_thermal_data = loadfn("renorm_thermal_data_{}K.json".format(T))
             fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
             
             dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
@@ -433,7 +433,7 @@ def run_task(self, fw_spec):
             fitting_id = _get_fc_fitting_id(mmdb)
             metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
             data_at_T.update(metadata)
-            data_at_T = jsanitize(data,strict=True,allow_bson=True)
+            data_at_T = jsanitize(data_at_T,strict=True,allow_bson=True)
             
             mmdb.db.renormalized_lattice_dynamics.insert_one(data_at_T)
             
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index b73f59fc2..a42bb962b 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -208,7 +208,7 @@ def get_lattice_dynamics_wf(
     # 3. Renormalization FW (pass_inputs like bulk modulus)
     if renormalize:
         for temperature in renormalize_temperature:
-            nconfig = renormalize_nconfig*(1+np.mod(temperature,100))
+            nconfig = renormalize_nconfig*(1+temperature//100)
             fw_renormalization = RenormalizationFW(
                 db_file=db_file,
                 temperature=temperature,

From 95e2b23626092c09a798c09ae74981bfe09e53ee Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Tue, 21 Mar 2023 08:47:45 -0700
Subject: [PATCH 168/207] anything?

---
 atomate/vasp/analysis/lattice_dynamics.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index ab0f2bc25..69bafa131 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -63,7 +63,7 @@
 RENORM_CONV_THRESH = 0.1 # meV/atom
 RENORM_MAX_ITER = 30
 
-eV2J = 1.602e-19
+eV2J = sp.constants.elementary_charge
 hbar = sp.constants.hbar # J-s
 kB = sp.constants.Boltzmann # J/K
 
@@ -864,6 +864,7 @@ def run_renormalization(
     """
 
     nconfig = int(nconfig)
+    nconfig *= 8
     renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
     fcp, fcs, param = renorm.renormalize(nconfig,conv_tresh)
 

From 7cfbba78db6da2c248194fed1c58e3db72719939 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Tue, 21 Mar 2023 12:26:27 -0700
Subject: [PATCH 169/207] renorm data push

---
 atomate/vasp/analysis/lattice_dynamics.py  |  1 -
 atomate/vasp/firetasks/lattice_dynamics.py | 29 +++++++++-------------
 2 files changed, 12 insertions(+), 18 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 69bafa131..02f4dc409 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -864,7 +864,6 @@ def run_renormalization(
     """
 
     nconfig = int(nconfig)
-    nconfig *= 8
     renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
     fcp, fcs, param = renorm.renormalize(nconfig,conv_tresh)
 
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index ad301b192..2286f7d87 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -301,16 +301,7 @@ def run_task(self, fw_spec):
                         
         # write results
         logger.info("Writing renormalized results")
-        thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
-                        "gruneisen","thermal_expansion","expansion_ratio",
-                        "free_energy_correction_S","free_energy_correction_SC"]
-        renorm_thermal_data = {key: [] for key in thermal_keys}
         logger.info("DEBUG: ",renorm_data)
-        fcs = renorm_data["fcs"]
-        fcs.write("force_constants_{}K.fcs".format(temperature))
-        np.savetxt('parameters_{}K.txt'.format(temperature),renorm_data["param"])
-        for key in thermal_keys:
-            renorm_thermal_data[key].append(renorm_data[key])
         if renorm_data["n_imaginary"] > 0:
             logger.warning('Imaginary modes remain for {} K!'.format(temperature))
             logger.warning('ShengBTE files not written')
@@ -320,7 +311,7 @@ def run_task(self, fw_spec):
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(temperature), format="text")
 
         dumpfn(structure_data, "structure_data_{}K.json".format(temperature))
-        dumpfn(renorm_thermal_data, "renorm_thermal_data_{}K.json".format(temperature))
+        dumpfn(renorm_thermal_data, "renorm_data_{}K.json".format(temperature))
 
         
 @explicit_serialize
@@ -395,7 +386,7 @@ def run_task(self, fw_spec):
 
             # Get an id for the force constants
             fitting_id = _get_fc_fitting_id(mmdb)
-            metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
+            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
             data.update(metadata)
             data = jsanitize(data,strict=True,allow_bson=True)
             
@@ -405,9 +396,15 @@ def run_task(self, fw_spec):
 
         else:
             T = renorm_temperature
-            renorm_thermal_data = loadfn("renorm_thermal_data_{}K.json".format(T))
-            fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
-            
+            renorm_data = loadfn("renorm_data_{}K.json".format(T))
+            fcs = renorm_data["fcs"]
+            thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
+                            "gruneisen","thermal_expansion","expansion_ratio",
+                            "free_energy_correction_S","free_energy_correction_SC"]
+            renorm_thermal_data = {key: [] for key in thermal_keys}
+            for key in thermal_keys:
+                renorm_thermal_data[key].append(renorm_data[key])
+
             dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
                 structure, supercell_matrix, fcs, mesh_density, mmdb
             )
@@ -419,8 +416,6 @@ def run_task(self, fw_spec):
                 "structure": structure.as_dict(),
                 "supercell_matrix": supercell_matrix,
                 "supercell_structure": supercell_structure.as_dict(),
-                "renormalized": renormalized,
-                "temperature": T,
                 "thermal_data": renorm_thermal_data,
                 "force_constants_fs_id": fc_fsid,
                 "phonon_dos_fs_id": dos_fsid,
@@ -431,7 +426,7 @@ def run_task(self, fw_spec):
         
             # Get an id for the force constants
             fitting_id = _get_fc_fitting_id(mmdb)
-            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+            metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
             data_at_T.update(metadata)
             data_at_T = jsanitize(data_at_T,strict=True,allow_bson=True)
             

From f97213e973176da695c33bfe30f57b7c6cc48e04 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Wed, 22 Mar 2023 20:36:15 -0700
Subject: [PATCH 170/207] renorm_thermal_data

---
 atomate/vasp/firetasks/lattice_dynamics.py | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 2286f7d87..4ee629ad4 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -301,6 +301,16 @@ def run_task(self, fw_spec):
                         
         # write results
         logger.info("Writing renormalized results")
+        renorm_thermal_data = dict()
+        fcs = renorm_data['fcs']
+        fcs.write("force_constants_{}K.fcs".format(temperature))
+        thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
+                        "gruneisen","thermal_expansion","expansion_ratio",
+                        "free_energy_correction_S","free_energy_correction_SC"]
+        renorm_thermal_data = {key: [] for key in thermal_keys}
+        for key in thermal_keys:
+            renorm_thermal_data[key].append(renorm_data[key])
+        
         logger.info("DEBUG: ",renorm_data)
         if renorm_data["n_imaginary"] > 0:
             logger.warning('Imaginary modes remain for {} K!'.format(temperature))
@@ -311,7 +321,7 @@ def run_task(self, fw_spec):
             fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(temperature), format="text")
 
         dumpfn(structure_data, "structure_data_{}K.json".format(temperature))
-        dumpfn(renorm_thermal_data, "renorm_data_{}K.json".format(temperature))
+        dumpfn(renorm_thermal_data, "renorm_thermal_data_{}K.json".format(temperature))
 
         
 @explicit_serialize
@@ -396,14 +406,8 @@ def run_task(self, fw_spec):
 
         else:
             T = renorm_temperature
-            renorm_data = loadfn("renorm_data_{}K.json".format(T))
-            fcs = renorm_data["fcs"]
-            thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
-                            "gruneisen","thermal_expansion","expansion_ratio",
-                            "free_energy_correction_S","free_energy_correction_SC"]
-            renorm_thermal_data = {key: [] for key in thermal_keys}
-            for key in thermal_keys:
-                renorm_thermal_data[key].append(renorm_data[key])
+            renorm_thermal_data = loadfn("renorm_thermal_data_{}K.json".format(T))
+            fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
 
             dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
                 structure, supercell_matrix, fcs, mesh_density, mmdb

From 940bae9b7ae6d42f19574758ad589a9b774ccfd9 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Thu, 23 Mar 2023 00:24:39 -0400
Subject: [PATCH 171/207] dependencies

---
 atomate/vasp/firetasks/lattice_dynamics.py    | 14 ++---
 atomate/vasp/fireworks/lattice_dynamics.py    | 40 ++++--------
 .../vasp/workflows/base/lattice_dynamics.py   | 62 ++++++++++++-------
 3 files changed, 59 insertions(+), 57 deletions(-)

diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 4ee629ad4..4a571b51f 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -303,7 +303,7 @@ def run_task(self, fw_spec):
         logger.info("Writing renormalized results")
         renorm_thermal_data = dict()
         fcs = renorm_data['fcs']
-        fcs.write("force_constants_{}K.fcs".format(temperature))
+        fcs.write("force_constants.fcs")
         thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
                         "gruneisen","thermal_expansion","expansion_ratio",
                         "free_energy_correction_S","free_energy_correction_SC"]
@@ -318,10 +318,10 @@ def run_task(self, fw_spec):
             logger.warning('No renormalization with thermal expansion')
         else:
             logger.info("No imaginary modes! Writing ShengBTE files")
-            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND_{}K".format(temperature), format="text")
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND".format(temperature), format="text")
 
-        dumpfn(structure_data, "structure_data_{}K.json".format(temperature))
-        dumpfn(renorm_thermal_data, "renorm_thermal_data_{}K.json".format(temperature))
+        dumpfn(structure_data, "structure_data.json".format(temperature))
+        dumpfn(renorm_thermal_data, "renorm_thermal_data.json".format(temperature))
 
         
 @explicit_serialize
@@ -405,9 +405,9 @@ def run_task(self, fw_spec):
             logger.info("Finished inserting force constants and phonon data")
 
         else:
-            T = renorm_temperature
-            renorm_thermal_data = loadfn("renorm_thermal_data_{}K.json".format(T))
-            fcs = ForceConstants.read("force_constants_{}K.fcs".format(T))
+            renorm_thermal_data = loadfn("renorm_thermal_data.json")
+            fcs = ForceConstants.read("force_constants.fcs")
+            T = renorm_thermal_data["temperature"]
 
             dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
                 structure, supercell_matrix, fcs, mesh_density, mmdb
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 827f495f2..4adb1b157 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -122,34 +122,22 @@ def __init__(
         ):
 
         # files needed to run ShengBTE
-        if renormalized: # must check if FORCE_CONSTANTS_2ND_{T}K can be copied individually
+        
+        files = [
+            "structure_data.json",
+            "FORCE_CONSTANTS_2ND",
+            "FORCE_CONSTANTS_3RD"
+        ]
+        
+        if renormalized: 
             assert type(temperature) in [float,int]
-            files = [
-                "structure_data.json",
-                "FORCE_CONSTANTS_2ND_{}K".format(temperature),
-                "FORCE_CONSTANTS_3RD"
-            ]
-#            temperature_copy = temperature[:]
-#            for t,T in enumerate(temperature_copy):
-#                try:
-#                    files = files.append("FORCE_CONSTANTS_2ND_{}K".format(T))
-#                except:
-#                    logger.info("FORCE_CONSTANTS_2ND_{}K is missing".format(T))
-#                    logger.info("Renormalization must have failed at {} K".format(T))
-#                    logger.info("Cannot calculate thermal conductivity at {} K".format(T))
-#                    temperature.remove(T)
+            name = '{} at {}K'.format(name,temperature)
             if prev_calc_dir:
                 copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
                 copy_files = CopyFilesFromCalcLoc(calc_loc='Renormalization_{}K'.format(temperature), filenames=files)
-            os.system('mv FORCE_CONSTANTS_2ND_{}K FORCE_CONSTANTS_2ND'.format(temperature))
-
-        else: # only the default files are needed
-            files = [
-                "structure_data.json",
-                "FORCE_CONSTANTS_2ND",
-                "FORCE_CONSTANTS_3RD",
-            ]
+
+        else:
             if prev_calc_dir:
                 copy_files = CopyFiles(from_dir=prev_calc_dir, filenames=files)
             else:
@@ -165,10 +153,8 @@ def __init__(
         shengbte_to_db = ShengBTEToDb(db_file=db_file, additional_fields={})
 
         tasks = [copy_files, run_shengbte, shengbte_to_db]
-        if renormalized:
-            super().__init__(tasks, name=name+' at {}K'.format(temperature), **kwargs)
-        else:
-            super().__init__(tasks, name=name, **kwargs)
+
+        super().__init__(tasks, name=name, **kwargs)
 
 
 
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a42bb962b..8dd9f6c4c 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -171,10 +171,13 @@ def get_lattice_dynamics_wf(
                 )
         supercell_matrix_kwargs["force_diagonal"] = True
 
+    logger.debug('Transforming supercell!')
+    logger.debug('KWARGS: \n {}'.format(supercell_matrix_kwargs))
     st = CubicSupercellTransformation(**supercell_matrix_kwargs)
     supercell = st.apply_transformation(structure)
     supercell_matrix = st.transformation_matrix
-
+    logger.debug('SUPERCELL MATRIX: \n {}'.format(supercell_matrix))
+    
     if "n_configs_per_std" not in perturbed_structure_kwargs:
         n_supercells = get_num_supercells(supercell, **num_supercell_kwargs)
         perturbed_structure_kwargs["n_configs_per_std"] = n_supercells
@@ -204,7 +207,8 @@ def get_lattice_dynamics_wf(
         imaginary_tol=IMAGINARY_TOL,
         )
     wf.append_wf(Workflow.from_Firework(fw_fit_force_constant), wf.leaf_fw_ids)
-
+    fitting_fw_id = wf.fws[-1].fw_id
+    
     # 3. Renormalization FW (pass_inputs like bulk modulus)
     if renormalize:
         for temperature in renormalize_temperature:
@@ -221,40 +225,52 @@ def get_lattice_dynamics_wf(
                 mesh_density=mesh_density,
             )
             wf.append_wf(
-                Workflow.from_Firework(fw_renormalization), [wf.fws[-1].fw_id]
+                Workflow.from_Firework(fw_renormalization), [fitting_fw_id]
             )
 
     # 4. Lattice thermal conductivity calculation
     if calculate_lattice_thermal_conductivity:
         if renormalize:
-            # Because of the way ShengBTE works, a temperature array that is not
-            # equally spaced out (T_step) requires submission for each temperature
-            for t,T in enumerate(renormalize_temperature):
+            temperatures = renormalize_temperature
+        else:
+            temperatures = thermal_conductivity_temperature
+        # Because of the way ShengBTE works, a temperature array that is not
+        # evenly spaced out (T_step) requires submission for each temperature
+        even_spacing = all(np.diff(temperatures)==np.diff(temperatures)[0])
+        if even_spacing and not renormalize:
+            fw_lattice_conductivity = LatticeThermalConductivityFW(
+                db_file=db_file,
+                shengbte_cmd=shengbte_cmd,
+                renormalized=renormalize,
+                temperature=temperatures
+            )
+            if shengbte_fworker:
+                fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
+            wf.append_wf(
+                Workflow.from_Firework(fw_lattice_conductivity), [fitting_fw_id]
+            )
+        else:
+            push = 1
+            for t,T in enumerate(temperatures):
                 if T == 0:
+                    push = 0
                     continue
                 fw_lattice_conductivity = LatticeThermalConductivityFW(
                     db_file=db_file,
                     shengbte_cmd=shengbte_cmd,
-                    renormalized=True,
+                    renormalized=renormalize,
                     temperature=T
-                    )
+                )
                 if shengbte_fworker:
                     fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
-                wf.append_wf(
-                    Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-(t+1)].fw_id]
+                if renormalize:
+                    wf.append_wf(
+                        Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-(len(temperatures)+push)].fw_id]
                     )
-        else:
-            fw_lattice_conductivity = LatticeThermalConductivityFW(
-                db_file=db_file,
-                shengbte_cmd=shengbte_cmd,
-                renormalized=False,
-                temperature=thermal_conductivity_temperature,
-                )
-            if shengbte_fworker:
-                fw_lattice_conductivity.spec["_fworker"] = shengbte_fworker
-            wf.append_wf(
-                Workflow.from_Firework(fw_lattice_conductivity), [wf.fws[-1].fw_id]
-                )
+                else:
+                    wf.append_wf(
+                        Workflow.from_Firework(fw_lattice_conductivity), [fitting_fw_id]
+                    )                    
                 
     formula = structure.composition.reduced_formula
     wf.name = "{} - lattice dynamics".format(formula)
@@ -318,7 +334,7 @@ def get_perturbed_structure_wf(
     natoms = len(structure * supercell_matrix)
 
     if rattle_stds is None:
-        rattle_stds = np.linspace(0.008, 0.08, 5)
+        rattle_stds = np.linspace(0.005, 0.1, 5)
 
     if vasp_input_set is None:
         vasp_input_set = MPStaticSet(structure)

From dfc7d7d7b2228bf3ecfb7e12950e26fd8e8972a5 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Thu, 23 Mar 2023 07:10:45 -0700
Subject: [PATCH 172/207] len(temperature)=1

---
 atomate/vasp/analysis/lattice_dynamics.py | 52 ++++++++++++++---------
 1 file changed, 32 insertions(+), 20 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 02f4dc409..5b43d9211 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -605,7 +605,7 @@ def harmonic_properties(
     structure: Structure,
     supercell_matrix: np.ndarray,
     fcs: ForceConstants,
-    T: List,
+    temperature: List,
     imaginary_tol: float = IMAGINARY_TOL
 ) -> Tuple[Dict,Phonopy]:
     """
@@ -634,13 +634,13 @@ def harmonic_properties(
     
     phonopy.set_force_constants(fcs2)
     phonopy.set_mesh(mesh,is_eigenvectors=True,is_mesh_symmetry=False) #run_mesh(is_gamma_center=True)
-    phonopy.run_thermal_properties(temperatures=T)
+    phonopy.run_thermal_properties(temperatures=temperature)
     logger.info('Thermal properties successfully run!')
 
-    _, free_energy, entropy, Cv = phonopy.get_thermal_properties()
+    _, free_energy, entropy, heat_capacity = phonopy.get_thermal_properties()
     free_energy *= 1000/sp.constants.Avogadro/eV2J/natom # kJ/mol to eV/atom
     entropy *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
-    Cv *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
+    heat_capacity *= 1/sp.constants.Avogadro/eV2J/natom # J/K/mol to eV/K/atom
 
     freq = phonopy.mesh.frequencies # in THz
     # find imaginary modes at gamma
@@ -654,11 +654,17 @@ def harmonic_properties(
     else: # do not calculate these if imaginary modes exist
         logger.warning('Imaginary modes found!')
 
+    if len(temperature)==1:
+        temperature = temperature[0]
+        free_energy = free_energy[0]
+        entropy = entropy[0]
+        heat_capacity = heat_capacity[0]
+        
     return {
-        "temperature": T,
+        "temperature": temperature,
         "free_energy": free_energy,
         "entropy": entropy,
-        "heat_capacity": Cv,
+        "heat_capacity": heat_capacity,
         "n_imaginary": n_imaginary
         }, phonopy
 
@@ -666,8 +672,8 @@ def harmonic_properties(
 def anharmonic_properties(
     phonopy: Phonopy,
     fcs: ForceConstants,
-    T: List,
-    Cv: np.ndarray,
+    temperature: List,
+    heat_capacity: np.ndarray,
     n_imaginary: float,
     bulk_modulus: float = None
 ) -> Dict:
@@ -676,21 +682,27 @@ def anharmonic_properties(
         logger.info('Evaluating anharmonic properties...')
         fcs2 = fcs.get_fc_array(2)
         fcs3 = fcs.get_fc_array(3)
-        grun, cte = gruneisen(phonopy,fcs2,fcs3,T,Cv,bulk_modulus=bulk_modulus)
+        grun, cte = gruneisen(phonopy,fcs2,fcs3,temperature,heat_capacity,bulk_modulus=bulk_modulus)
         if type(bulk_modulus) is float or int:
-            dLfrac = thermal_expansion(T,cte)
+            dLfrac = thermal_expansion(temperature,cte)
         else:
             logger.warning('Thermal expansion cannot be calculated without bulk modulus input. Set to 0.')
-            cte = np.zeros((len(T),3))
-            dLfrac = np.zeros((len(T),3))
+            cte = np.zeros((len(temperature),3))
+            dLfrac = np.zeros((len(temperature),3))
     else: # do not calculate these if imaginary modes exist
         logger.warning('Gruneisen and thermal expansion cannot be calculated with imaginary modes. All set to 0.')
-        grun = np.zeros((len(T),3))
-        cte = np.zeros((len(T),3))
-        dLfrac = np.zeros((len(T),3))
-
+        grun = np.zeros((len(temperature),3))
+        cte = np.zeros((len(temperature),3))
+        dLfrac = np.zeros((len(temperature),3))
+
+    if len(temperature)==1:
+        temperature = temperature[0]
+        grun = grun[0]
+        cte = cte[0]
+        dLfrac = dLfrac[0]
+        
     return {
-        "temperature": T,
+        "temperature": temperature,
         "gruneisen": grun,
         "thermal_expansion": cte,
         "expansion_ratio": dLfrac,
@@ -879,9 +891,9 @@ def run_renormalization(
     else:
         anharmonic_data = dict()
         anharmonic_data["temperature"] = T
-        anharmonic_data["gruneisen"] = np.array([[0,0,0]])
-        anharmonic_data["thermal_expansion"] = np.array([[0,0,0]])
-        anharmonic_data["expansion_ratio"] = np.array([[0,0,0]])
+        anharmonic_data["gruneisen"] = np.array([0,0,0])
+        anharmonic_data["thermal_expansion"] = np.array([0,0,0])
+        anharmonic_data["expansion_ratio"] = np.array([0,0,0])
     renorm_data.update(anharmonic_data)
 
     phonopy_orig.run_mesh()

From d28e087e9179270bd37b5d46472b565a9552ea19 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Tue, 4 Apr 2023 09:32:46 -0700
Subject: [PATCH 173/207]  everything works?

---
 atomate/vasp/analysis/lattice_dynamics.py  | 57 ++++++++++------------
 atomate/vasp/firetasks/lattice_dynamics.py |  4 +-
 2 files changed, 27 insertions(+), 34 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 5b43d9211..15b17beec 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -630,7 +630,7 @@ def harmonic_properties(
     parent_phonopy = get_phonopy_structure(structure)
     phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
     natom = phonopy.primitive.get_number_of_atoms()
-    mesh = supercell_matrix.diagonal()*4
+    mesh = supercell_matrix.diagonal()*2
     
     phonopy.set_force_constants(fcs2)
     phonopy.set_mesh(mesh,is_eigenvectors=True,is_mesh_symmetry=False) #run_mesh(is_gamma_center=True)
@@ -682,30 +682,17 @@ def anharmonic_properties(
         logger.info('Evaluating anharmonic properties...')
         fcs2 = fcs.get_fc_array(2)
         fcs3 = fcs.get_fc_array(3)
-        grun, cte = gruneisen(phonopy,fcs2,fcs3,temperature,heat_capacity,bulk_modulus=bulk_modulus)
-        if type(bulk_modulus) is float or int:
-            dLfrac = thermal_expansion(temperature,cte)
-        else:
-            logger.warning('Thermal expansion cannot be calculated without bulk modulus input. Set to 0.')
-            cte = np.zeros((len(temperature),3))
-            dLfrac = np.zeros((len(temperature),3))
+        grun, cte, dLfrac = gruneisen(phonopy,fcs2,fcs3,temperature,heat_capacity,bulk_modulus=bulk_modulus)
     else: # do not calculate these if imaginary modes exist
         logger.warning('Gruneisen and thermal expansion cannot be calculated with imaginary modes. All set to 0.')
         grun = np.zeros((len(temperature),3))
         cte = np.zeros((len(temperature),3))
         dLfrac = np.zeros((len(temperature),3))
 
-    if len(temperature)==1:
-        temperature = temperature[0]
-        grun = grun[0]
-        cte = cte[0]
-        dLfrac = dLfrac[0]
-        
     return {
-        "temperature": temperature,
         "gruneisen": grun,
         "thermal_expansion": cte,
-        "expansion_ratio": dLfrac,
+        "expansion_fraction": dLfrac,
         }
 
 
@@ -781,7 +768,7 @@ def gruneisen(
         fcs2: np.ndarray,
         fcs3: np.ndarray,
         temperature: List,
-        Cv: np.ndarray, # in eV/K/atom
+        heat_capacity: np.ndarray, # in eV/K/atom
         bulk_modulus: float = None # in GPa
 ) -> Tuple[List,List]:
 
@@ -797,17 +784,21 @@ def gruneisen(
         grun_tot.append(get_total_grun(omega,grun,kweight,temp))
     grun_tot = np.nan_to_num(np.array(grun_tot))
     
-    # linear thermal expansion coefficient
+    # linear thermal expansion coefficeint and fraction
     if bulk_modulus is None:
         cte = None
+        dLfrac = None
     else:
-        Cv *= eV2J*phonopy.primitive.get_number_of_atoms() # eV/K/atom to J/K 
+        heat_capacity *= eV2J*phonopy.primitive.get_number_of_atoms() # eV/K/atom to J/K 
         vol = phonopy.primitive.get_volume()
-        cte = grun_tot*(Cv.repeat(3).reshape((len(Cv),3)))/(vol/10**30)/(bulk_modulus*10**9)/3
-        cte = np.nan_to_num(cte)    
+        cte = grun_tot*heat_capacity.repeat(3)/(vol/10**30)/(bulk_modulus*10**9)/3
+        cte = np.nan_to_num(cte)
+        dLfrac = thermal_expansion(temperature,list(cte))
         logger.info('Gruneisen: \n {}'.format(grun_tot))
-        logger.info('CTE: \n {}'.format(cte))    
-    return grun_tot, cte
+        logger.info('Coefficient of Thermal Expansion: \n {}'.format(cte))
+        logger.info('Linear Expansion Fraction: \n {}'.format(dLfrac))        
+        
+    return grun_tot, cte, dLfrac
 
 
 def thermal_expansion(
@@ -819,6 +810,8 @@ def thermal_expansion(
     if 0 not in temperature:
         temperature = [0] + temperature
         cte = [[0,0,0]] + cte
+    logger.info('CTE: {}'.format(cte))
+    logger.info('T_array: {}'.format(temperature))
     temperature = np.array(temperature)
     ind = np.argsort(temperature)
     temperature = temperature[ind]
@@ -885,15 +878,15 @@ def run_renormalization(
 
     if renorm_data["n_imaginary"] == 0:
         logger.info('Renormalized phonon is completely real at T = {} K!'.format(T))
-        anharmonic_data = anharmonic_properties(
-            phonopy, fcs, [T], thermal_data["heat_capacity"], n_imaginary, bulk_modulus=bulk_modulus
-	)
-    else:
-        anharmonic_data = dict()
-        anharmonic_data["temperature"] = T
-        anharmonic_data["gruneisen"] = np.array([0,0,0])
-        anharmonic_data["thermal_expansion"] = np.array([0,0,0])
-        anharmonic_data["expansion_ratio"] = np.array([0,0,0])
+    anharmonic_data = anharmonic_properties(
+        phonopy, fcs, [T], renorm_data["heat_capacity"], renorm_data["n_imaginary"], bulk_modulus=bulk_modulus
+    )
+#    else:
+#        anharmonic_data = dict()
+#        anharmonic_data["temperature"] = T
+#        anharmonic_data["gruneisen"] = np.array([0,0,0])
+#        anharmonic_data["thermal_expansion"] = np.array([0,0,0])
+#        anharmonic_data["expansion_fraction"] = np.array([0,0,0])
     renorm_data.update(anharmonic_data)
 
     phonopy_orig.run_mesh()
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 4a571b51f..789073c3b 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -284,7 +284,7 @@ def run_task(self, fw_spec):
                 else:
                     logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
 
-                dLfrac = renorm_data["expansion_ratio"]  
+                dLfrac = renorm_data["expansion_fraction"]  
                 param = renorm_data["param"]
 
                 parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,temperature,dLfrac)
@@ -305,7 +305,7 @@ def run_task(self, fw_spec):
         fcs = renorm_data['fcs']
         fcs.write("force_constants.fcs")
         thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
-                        "gruneisen","thermal_expansion","expansion_ratio",
+                        "gruneisen","thermal_expansion","expansion_fraction",
                         "free_energy_correction_S","free_energy_correction_SC"]
         renorm_thermal_data = {key: [] for key in thermal_keys}
         for key in thermal_keys:

From dbef4f7915eff480c33e7cfafd18ed01298e372b Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Tue, 4 Apr 2023 09:50:19 -0700
Subject: [PATCH 174/207] cleanup

---
 atomate/vasp/analysis/lattice_dynamics.py | 21 ++++++---------------
 1 file changed, 6 insertions(+), 15 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 15b17beec..c78655a5b 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -793,7 +793,9 @@ def gruneisen(
         vol = phonopy.primitive.get_volume()
         cte = grun_tot*heat_capacity.repeat(3)/(vol/10**30)/(bulk_modulus*10**9)/3
         cte = np.nan_to_num(cte)
-        dLfrac = thermal_expansion(temperature,list(cte))
+        dLfrac = thermal_expansion(temperature,cte)
+        if len(temperature)==1:
+            dLfrac = dLfrac[-1]
         logger.info('Gruneisen: \n {}'.format(grun_tot))
         logger.info('Coefficient of Thermal Expansion: \n {}'.format(cte))
         logger.info('Linear Expansion Fraction: \n {}'.format(dLfrac))        
@@ -803,15 +805,12 @@ def gruneisen(
 
 def thermal_expansion(
         temperature: List,
-        cte: List,
-        T: Optional[float]=None
+        cte: np.array,
 ) -> np.ndarray:
     assert len(temperature)==len(cte)
     if 0 not in temperature:
         temperature = [0] + temperature
-        cte = [[0,0,0]] + cte
-    logger.info('CTE: {}'.format(cte))
-    logger.info('T_array: {}'.format(temperature))
+        cte = np.array([np.array([0,0,0])] + list(cte))
     temperature = np.array(temperature)
     ind = np.argsort(temperature)
     temperature = temperature[ind]
@@ -821,15 +820,7 @@ def thermal_expansion(
     for t in range(len(temperature)):
         dLfrac[t,:] = np.trapz(cte[:t+1,:],temperature[:t+1],axis=0)
     dLfrac = np.nan_to_num(dLfrac)
-    logger.info('dLfrac: \n {}'.format(dLfrac))
-    if T is None:
-        return dLfrac
-    else:
-        try:
-            T_ind = np.where(temperature==T)[0][0]
-            return np.array([dLfrac[T_ind]])
-        except:
-            raise ValueError('Designated T does not exist in the temperature array!')
+    return dLfrac
 
 
 def run_renormalization(

From 7b002554414c228f9266b8aa1436b86414c51a18 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Fri, 19 May 2023 13:02:38 -0400
Subject: [PATCH 175/207] fixed random displacements

---
 atomate/vasp/analysis/lattice_dynamics.py       |  4 ++--
 atomate/vasp/workflows/base/lattice_dynamics.py | 16 ++++++++++++----
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index c78655a5b..5e9163eba 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -26,7 +26,7 @@
 from hiphive.fitting import Optimizer
 from hiphive.renormalization import Renormalization
 from hiphive.utilities import get_displacements
-from hiphive.run_tools import _clean_data, FE_correction, construct_fit_data
+from hiphive.run_tools import _clean_data, free_energy_correction, construct_fit_data
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
@@ -886,7 +886,7 @@ def run_renormalization(
     omega_TD = phonopy.mesh.frequencies # THz
     evec = phonopy.mesh.eigenvectors
 #    natom = phonopy.primitive.get_number_of_atoms()
-    correction_S, correction_SC = FE_correction(omega0,omega_TD,evec,[T]) # eV/atom
+    correction_S, correction_SC = free_energy_correction(omega0,omega_TD,evec,[T]) # eV/atom
 
     renorm_data["free_energy_correction_S"] = correction_S[0]
     renorm_data["free_energy_correction_SC"] = correction_SC[0]
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 8dd9f6c4c..a094fdc78 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -186,6 +186,7 @@ def get_lattice_dynamics_wf(
     wf = get_perturbed_structure_wf(
         structure,
         supercell_matrix=supercell_matrix,
+        separate_fit=separate_fit,
         vasp_input_set=vasp_input_set,
         common_settings=common_settings,
         copy_vasp_outputs=copy_vasp_outputs,
@@ -288,6 +289,7 @@ def get_lattice_dynamics_wf(
 def get_perturbed_structure_wf(
     structure: Structure,
     supercell_matrix: Optional[np.ndarray],
+    separate_fit: bool = False,
     name: str = "perturbed structure",
     vasp_input_set: Optional[VaspInputSet] = None,
     common_settings: Optional[Dict] = None,
@@ -363,10 +365,16 @@ def get_perturbed_structure_wf(
         rattle_min_distance = min_distance - 2 * rattle_std
         rattle_min_distance = min(scaled_min_distance, rattle_min_distance)
 
-        transformations = [
-            "SupercellTransformation",
-            "MonteCarloRattleTransformation",
-        ]
+        if separate_fit:
+            transformations = [
+                "SupercellTransformation",
+                "FixedRandomDisplacementTransformation",
+            ]            
+        else:
+            transformations = [
+                "SupercellTransformation",
+                "MonteCarloRattleTransformation",
+            ]
         transformation_params = [
             {"scaling_matrix": supercell_matrix},
             {"rattle_std": rattle_std, "min_distance": rattle_min_distance},

From 32768217ee71b2fafa256ecafffc3b85ae1868ec Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Wed, 24 May 2023 10:42:27 -0400
Subject: [PATCH 176/207] T diff

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a094fdc78..a75151da8 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -237,8 +237,11 @@ def get_lattice_dynamics_wf(
             temperatures = thermal_conductivity_temperature
         # Because of the way ShengBTE works, a temperature array that is not
         # evenly spaced out (T_step) requires submission for each temperature
-        even_spacing = all(np.diff(temperatures)==np.diff(temperatures)[0])
-        if even_spacing and not renormalize:
+        if not renormalize:
+            if type(temperatures)==dict:
+                pass
+            elif type(temperatures) in [list,np.ndarray]:
+                assert all(np.diff(temperatures)==np.diff(temperatures)[0])
             fw_lattice_conductivity = LatticeThermalConductivityFW(
                 db_file=db_file,
                 shengbte_cmd=shengbte_cmd,

From 0ccc13f87304a8868a9ce467818a45d507645383 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Thu, 25 May 2023 12:59:29 -0400
Subject: [PATCH 177/207] syntax errors

---
 atomate/vasp/analysis/lattice_dynamics.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 5e9163eba..6ed62a0e6 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -791,7 +791,8 @@ def gruneisen(
     else:
         heat_capacity *= eV2J*phonopy.primitive.get_number_of_atoms() # eV/K/atom to J/K 
         vol = phonopy.primitive.get_volume()
-        cte = grun_tot*heat_capacity.repeat(3)/(vol/10**30)/(bulk_modulus*10**9)/3
+#        cte = grun_tot*heat_capacity.repeat(3)/(vol/10**30)/(bulk_modulus*10**9)/3
+        cte = grun_tot*heat_capacity.repeat(3).reshape(len(heat_capacity),3)/(vol/10**30)/(bulk_modulus*10**9)/3
         cte = np.nan_to_num(cte)
         dLfrac = thermal_expansion(temperature,cte)
         if len(temperature)==1:
@@ -861,7 +862,7 @@ def run_renormalization(
 
     nconfig = int(nconfig)
     renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
-    fcp, fcs, param = renorm.renormalize(nconfig,conv_tresh)
+    fcp, fcs, param = renorm.renormalize(nconfig)#,conv_tresh)
 
     renorm_data, phonopy = harmonic_properties(
         structure, supercell_matrix, fcs, [T], imaginary_tol

From bfcfdbb257d3f8b98aa44b31661a9f8f059dc98d Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Fri, 9 Jun 2023 15:14:05 -0400
Subject: [PATCH 178/207] remove separate_fit

---
 atomate/vasp/analysis/lattice_dynamics.py  | 57 +++++++++++++++-------
 atomate/vasp/firetasks/lattice_dynamics.py |  8 +--
 atomate/vasp/fireworks/lattice_dynamics.py |  6 +--
 atomate/vasp/workflows/presets/core.py     |  5 +-
 4 files changed, 46 insertions(+), 30 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 6ed62a0e6..e8422a4e8 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -172,8 +172,7 @@ def fit_force_constants(
     supercell_matrix: np.ndarray,
     structures: List["Atoms"],
     all_cutoffs: List[List[float]],
-    separate_fit: bool,
-    disp_cut: float = None,
+    disp_cut: float = 0.055,
     imaginary_tol: float = IMAGINARY_TOL,
     fit_method: str = FIT_METHOD,
 <<<<<<< HEAD
@@ -203,9 +202,7 @@ def fit_force_constants(
         all_cutoffs: A nested list of cutoff values to trial. Each set of
             cutoffs contains the radii for different orders starting with second
             order.
-        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
-            are to be done separately (True) or in one shot (False)
-        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+        disp_cut: determines the mean displacement of perturbed
             structure to be included in harmonic (<) or anharmonic (>) fitting
         imaginary_tol: Tolerance used to decide if a phonon mode is imaginary,
             in THz.
@@ -235,14 +232,7 @@ def fit_force_constants(
     fitting_data = {
         "cutoffs": [],
         "rmse_test": [],
-#        "n_imaginary": [],
-#        "min_frequency": [],
-#        "temperature": [],
-#        "free_energy": [],
-#        "entropy": [],
-#        "heat_capacity": [],
         "fit_method": fit_method,
-        "separate_fit": separate_fit,
         "disp_cut": disp_cut,
         "imaginary_tol": imaginary_tol,
 #        "max_n_imaginary": max_n_imaginary,
@@ -273,7 +263,7 @@ def fit_force_constants(
 
     cutoff_results = Parallel(n_jobs=min(os.cpu_count(),len(all_cutoffs)), backend="multiprocessing")(delayed(_run_cutoffs)(
         i, cutoffs, n_cutoffs, parent_structure, structures, supercell_matrix, fit_method,
-        separate_fit, disp_cut, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
+        disp_cut, imaginary_tol, fit_kwargs) for i, cutoffs in enumerate(all_cutoffs))
 
     logger.info('CUTOFF RESULTS \n {}'.format(cutoff_results))
     
@@ -343,10 +333,10 @@ def get_fit_data(
             saved_structures.append(structure)
         else: # fit separately
             if param2 is None: # for harmonic fitting
-                if mean_displacements < disp_cut:
+                if mean_displacements <= disp_cut:
                     saved_structures.append(structure)
             else: # for anharmonic fitting
-                if mean_displacements >= disp_cut:
+                if mean_displacements > disp_cut:
                     saved_structures.append(structure)
 
     fit_data_tmp = Parallel(n_jobs=min(os.cpu_count(),max(1,len(saved_structures))))(#,prefer="threads")(
@@ -373,7 +363,6 @@ def _run_cutoffs(
     structures,
     supercell_matrix,
     fit_method,
-    separate_fit,
     disp_cut,
     imaginary_tol,
     fit_kwargs
@@ -405,6 +394,7 @@ def _run_cutoffs(
     logger.debug(cs.__repr__())
     n2nd = cs.get_n_dofs_by_order(2)
     nall = cs.n_dofs
+<<<<<<< HEAD
     
     if separate_fit:
         logger.info('Fitting harmonic force constants separately')
@@ -425,6 +415,38 @@ def _run_cutoffs(
         param_harmonic = opt.parameters # harmonic force constant parameters
         
         logger.info('Fitting anharmonic force constants separately')
+=======
+
+    logger.info('Fitting harmonic force constants separately')
+    separate_fit = True
+#    fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
+#                            disp_cut, ncut=n2nd, param2=None)
+    sc = get_structure_container(cs, structures, separate_fit, disp_cut,
+                                 ncut=n2nd, param2=None)
+    opt = Optimizer(sc.get_fit_data(),
+                    fit_method,
+                    [0,n2nd],
+                    **fit_kwargs)
+    opt.train()
+    param_harmonic = opt.parameters # harmonic force constant parameters
+    param_tmp = np.concatenate((param2,np.zeros(cs.n_dofs-len(param_harmonic))))
+    fcp = ForceConstantPotential(cs, param_tmp)
+    fcs = fcp.get_force_constants(supercell_atoms)
+
+    parent_phonopy = get_phonopy_structure(parent_structure)
+    phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
+    natom = phonopy.primitive.get_number_of_atoms()
+    mesh = supercell_matrix.diagonal()*2
+    phonopy.set_force_constants(fcs2)
+    phonopy.set_mesh(mesh,is_eigenvectors=False,is_mesh_symmetry=False) #run_mesh(is_gamma_center=True)
+    phonopy.run_mesh(mesh, with_eigenvectors=False, is_mesh_symmetry=False)
+    omega = phonopy.mesh.frequencies  # THz
+    omega = np.sort(omega.flatten())
+    imaginary = np.any(omega<-1e-3)
+
+    if imaginary:
+        logger.info('Imaginary modes found! Fitting anharmonic force constants separately')
+>>>>>>> 2e30eb4a (remove separate_fit)
 #        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
 #                                disp_cut, ncut=n2nd, param2=param_harmonic)
         sc = get_structure_container(cs, structures, separate_fit, disp_cut,
@@ -509,7 +531,8 @@ def get_structure_container(
         logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
         
     else:
-        logger.info('Fitting all force constants in one shot')
+        logger.info('No imaginary modes! Fitting all force constants in one shot')
+        separate_fit = False
 #        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
 #                                disp_cut=None, ncut=None, param2=None)
         sc = get_structure_container(cs, structures, separate_fit, disp_cut=None,
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 789073c3b..2c24c55bd 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -126,10 +126,7 @@ class RunHiPhive(FiretaskBase):
         cutoffs (Optional[list[list]]): A list of cutoffs to trial. If None,
             a set of trial cutoffs will be generated based on the structure
             (default).
-        separate_fit: If True, harmonic and anharmonic force constants are fit
-            separately and sequentially, harmonic first then anharmonic. If
-            False, then they are all fit in one go. Default is False.
-        disp_cut: if separate_fit=True, determines the mean displacement of perturbed
+        disp_cut: determines the mean displacement of perturbed
             structure to be included in harmonic (<) or anharmonic (>) fitting  
         imaginary_tol (float): Tolerance used to decide if a phonon mode
             is imaginary, in THz.
@@ -139,7 +136,6 @@ class RunHiPhive(FiretaskBase):
 
     optional_params = [
         "cutoffs",
-        "separate_fit",
         "disp_cut",
         "temperature_qha",
         "bulk_modulus",
@@ -157,7 +153,6 @@ def run_task(self, fw_spec):
         supercell_structure = structure_data["supercell_structure"]
         supercell_matrix = np.array(structure_data["supercell_matrix"])
 
-        separate_fit = self.get('separate_fit', False)
         disp_cut = self.get('disp_cut', None)
         cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
         T_qha = self.get("temperature_qha", T_QHA)
@@ -181,7 +176,6 @@ def run_task(self, fw_spec):
             supercell_matrix,
             structures,
             cutoffs,
-            separate_fit,
             disp_cut,
             imaginary_tol,
             fit_method
diff --git a/atomate/vasp/fireworks/lattice_dynamics.py b/atomate/vasp/fireworks/lattice_dynamics.py
index 4adb1b157..db6aed82a 100644
--- a/atomate/vasp/fireworks/lattice_dynamics.py
+++ b/atomate/vasp/fireworks/lattice_dynamics.py
@@ -37,9 +37,7 @@ class FitForceConstantsFW(Firework):
         db_file: Path to a db file.
         cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
             will be generated based on the structure (default).
-        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
-            are to be done separately (True) or in one shot (False)
-        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+        disp_cut: determines the mean displacement of perturbed
             structure to be included in harmonic (<) or anharmonic (>) fitting  
         bulk_modulus: in GPa, necessary for thermal expansion
         imaginary_tol: Tolerance used to decide if a phonon mode is
@@ -55,7 +53,6 @@ class FitForceConstantsFW(Firework):
     def __init__(
         self,
         fit_method: str,
-        separate_fit: bool,
         disp_cut: float,
         bulk_modulus: float,
         imaginary_tol: float,
@@ -71,7 +68,6 @@ def __init__(
         
         fit_force_constants = RunHiPhive(
             cutoffs=cutoffs,
-            separate_fit=separate_fit,
             fit_method=fit_method,
             disp_cut=disp_cut,
             bulk_modulus=bulk_modulus,
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 6f206ef52..e56f0dd98 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -854,8 +854,12 @@ def wf_nudged_elastic_band(structures, parent, c=None):
 
 def wf_lattice_dynamics(
     structure: Structure,
+<<<<<<< HEAD
     separate_fit: bool = False,
     fit_method: str = FIT_METHOD,
+=======
+    fit_method: str = False,
+>>>>>>> 2e30eb4a (remove separate_fit)
     disp_cut: float = None,
     bulk_modulus: float = None,
     c: Optional[dict] = None,
@@ -918,7 +922,6 @@ def wf_lattice_dynamics(
     wf_ld = get_lattice_dynamics_wf(
         structure,
         fit_method=fit_method,
-        separate_fit=separate_fit,
         disp_cut=disp_cut,
         bulk_modulus=bulk_modulus,
         common_settings=c,

From 09664c0c4673b489c1356baa64021cea56bdff9a Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 9 Jun 2023 12:54:46 -0700
Subject: [PATCH 179/207] remove separate_fit

---
 .../vasp/workflows/base/lattice_dynamics.py   | 31 ++++++-------------
 1 file changed, 10 insertions(+), 21 deletions(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index a75151da8..7d85ea7bf 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -70,7 +70,6 @@
 def get_lattice_dynamics_wf(
     structure: Structure,
     fit_method:str = FIT_METHOD,
-    separate_fit: bool = False,
     disp_cut: float = None,
     bulk_modulus: float = None,
     common_settings: Dict = None,
@@ -119,9 +118,7 @@ def get_lattice_dynamics_wf(
 
     Args:
         structure: Initial structure.
-        separate_fit: Boolean to determine whether harmonic and anharmonic fitting
-            are to be done separately (True) or in one shot (False)
-        disp_cut: if separate_fit true, determines the mean displacement of perturbed
+        disp_cut: determines the mean displacement of perturbed
             structure to be included in harmonic (<) or anharmonic (>) fitting  
         bulk_modulus: bulk modulus in GPa, necessary for thermal expansion
         common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
@@ -186,7 +183,6 @@ def get_lattice_dynamics_wf(
     wf = get_perturbed_structure_wf(
         structure,
         supercell_matrix=supercell_matrix,
-        separate_fit=separate_fit,
         vasp_input_set=vasp_input_set,
         common_settings=common_settings,
         copy_vasp_outputs=copy_vasp_outputs,
@@ -199,7 +195,6 @@ def get_lattice_dynamics_wf(
     fw_fit_force_constant = FitForceConstantsFW(
         db_file=db_file,
         spec=allow_fizzled,
-        separate_fit=separate_fit,
         fit_method=fit_method,
         disp_cut=disp_cut,
         bulk_modulus=bulk_modulus, 
@@ -292,7 +287,6 @@ def get_lattice_dynamics_wf(
 def get_perturbed_structure_wf(
     structure: Structure,
     supercell_matrix: Optional[np.ndarray],
-    separate_fit: bool = False,
     name: str = "perturbed structure",
     vasp_input_set: Optional[VaspInputSet] = None,
     common_settings: Optional[Dict] = None,
@@ -365,22 +359,17 @@ def get_perturbed_structure_wf(
 
         # make sure the minimum distance is at least min_dist - 2 * rattle_std
         # as a sanity check
-        rattle_min_distance = min_distance - 2 * rattle_std
-        rattle_min_distance = min(scaled_min_distance, rattle_min_distance)
-
-        if separate_fit:
-            transformations = [
-                "SupercellTransformation",
-                "FixedRandomDisplacementTransformation",
-            ]            
-        else:
-            transformations = [
-                "SupercellTransformation",
-                "MonteCarloRattleTransformation",
-            ]
+#        rattle_min_distance = min_distance - 2 * rattle_std
+#        rattle_min_distance = min(scaled_min_distance, rattle_min_distance)
+
+        transformations = [
+            "SupercellTransformation",
+            "FixedRandomDisplacementTransformation",
+        ]            
+
         transformation_params = [
             {"scaling_matrix": supercell_matrix},
-            {"rattle_std": rattle_std, "min_distance": rattle_min_distance},
+            {"rattle_std": rattle_std}#, "min_distance": rattle_min_distance},
         ]
 
         fw = TransmuterFW(

From 16b22d09ba154dad0336321d9e501ffef49c09f6 Mon Sep 17 00:00:00 2001
From: Junsoo Park <Glasperlenspiel@Glasperlenspiel.vpn-dhcp.lbl.gov>
Date: Wed, 14 Jun 2023 13:32:30 -0400
Subject: [PATCH 180/207] separate harmonic

---
 atomate/vasp/analysis/lattice_dynamics.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index e8422a4e8..5dc1b7d57 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -429,7 +429,7 @@ def _run_cutoffs(
                     **fit_kwargs)
     opt.train()
     param_harmonic = opt.parameters # harmonic force constant parameters
-    param_tmp = np.concatenate((param2,np.zeros(cs.n_dofs-len(param_harmonic))))
+    param_tmp = np.concatenate((param_harmonic,np.zeros(cs.n_dofs-len(param_harmonic))))
     fcp = ForceConstantPotential(cs, param_tmp)
     fcs = fcp.get_force_constants(supercell_atoms)
 
@@ -437,7 +437,7 @@ def _run_cutoffs(
     phonopy = Phonopy(parent_phonopy, supercell_matrix=supercell_matrix)
     natom = phonopy.primitive.get_number_of_atoms()
     mesh = supercell_matrix.diagonal()*2
-    phonopy.set_force_constants(fcs2)
+    phonopy.set_force_constants(fcs.get_fc_array(2))
     phonopy.set_mesh(mesh,is_eigenvectors=False,is_mesh_symmetry=False) #run_mesh(is_gamma_center=True)
     phonopy.run_mesh(mesh, with_eigenvectors=False, is_mesh_symmetry=False)
     omega = phonopy.mesh.frequencies  # THz

From 5df072422f12f9d294ec8a1950e4891b1a6480a5 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Wed, 21 Jun 2023 16:55:17 -0700
Subject: [PATCH 181/207] clean-up

---
 atomate/vasp/workflows/presets/core.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index e56f0dd98..8d898d141 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -854,12 +854,13 @@ def wf_nudged_elastic_band(structures, parent, c=None):
 
 def wf_lattice_dynamics(
     structure: Structure,
-<<<<<<< HEAD
-    separate_fit: bool = False,
     fit_method: str = FIT_METHOD,
+<<<<<<< HEAD
 =======
     fit_method: str = False,
 >>>>>>> 2e30eb4a (remove separate_fit)
+=======
+>>>>>>> ac887694 (clean-up)
     disp_cut: float = None,
     bulk_modulus: float = None,
     c: Optional[dict] = None,

From db53650e129b16e488fe12b844140b953e4bd915 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Fri, 5 Jan 2024 11:23:57 -0800
Subject: [PATCH 182/207] PhonopySupercellTransformation

---
 atomate/vasp/workflows/base/lattice_dynamics.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index 7d85ea7bf..c105ca4b4 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -363,7 +363,8 @@ def get_perturbed_structure_wf(
 #        rattle_min_distance = min(scaled_min_distance, rattle_min_distance)
 
         transformations = [
-            "SupercellTransformation",
+#            "SupercellTransformation",
+            "PhonopySupercellTransformation",
             "FixedRandomDisplacementTransformation",
         ]            
 

From 8c272be16fd149daaf18c06cf027db86a3a1e24c Mon Sep 17 00:00:00 2001
From: Junsoo Park <cpark21@swansong37.mynetworksettings.com>
Date: Fri, 12 Jan 2024 15:49:03 -0500
Subject: [PATCH 183/207] ARC AIMD

---
 atomate/vasp/analysis/lattice_dynamics.py     |   4 +
 atomate/vasp/firetasks/aimd.py                | 501 ++++++++++++++++++
 atomate/vasp/firetasks/lattice_dynamics.py    |   3 +-
 atomate/vasp/firetasks/run_calc.py            |   7 +
 atomate/vasp/fireworks/aimd.py                | 193 +++++++
 atomate/vasp/fireworks/core.py                |   8 +
 atomate/vasp/workflows/base/aimd.py           | 162 ++++++
 .../vasp/workflows/base/lattice_dynamics.py   |   2 +-
 atomate/vasp/workflows/presets/core.py        |  82 +++
 9 files changed, 960 insertions(+), 2 deletions(-)
 create mode 100644 atomate/vasp/firetasks/aimd.py
 create mode 100644 atomate/vasp/fireworks/aimd.py
 create mode 100644 atomate/vasp/workflows/base/aimd.py

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 5dc1b7d57..938575ce1 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -912,8 +912,12 @@ def run_renormalization(
 #    natom = phonopy.primitive.get_number_of_atoms()
     correction_S, correction_SC = free_energy_correction(omega0,omega_TD,evec,[T]) # eV/atom
 
+    lambda_array = np.array([0,0.1,0.3,0.5,0.7,0.9,1])
+    correction_TI = renorm.thermodynamic_integration(lambda_array,param,fcs,TI_nconfig=3)
+
     renorm_data["free_energy_correction_S"] = correction_S[0]
     renorm_data["free_energy_correction_SC"] = correction_SC[0]
+    renorm_data["free_energy_correction_TI"] = correction_TI
     renorm_data["fcp"] = fcp
     renorm_data["fcs"] = fcs
     renorm_data["param"] = param
diff --git a/atomate/vasp/firetasks/aimd.py b/atomate/vasp/firetasks/aimd.py
new file mode 100644
index 000000000..83a2ff286
--- /dev/null
+++ b/atomate/vasp/firetasks/aimd.py
@@ -0,0 +1,501 @@
+import json
+import os
+import subprocess
+import shlex
+from datetime import datetime
+from pathlib import Path
+
+import numpy as np
+from copy import copy, deepcopy
+
+from monty.dev import requires
+from monty.serialization import dumpfn, loadfn
+from monty.json import jsanitize
+from pymongo import ReturnDocument
+
+from atomate.utils.utils import env_chk, get_logger
+from atomate.vasp.database import VaspCalcDb
+from atomate.vasp.drones import VaspDrone
+
+from fireworks import FiretaskBase, FWAction, explicit_serialize
+
+from pymatgen.core.structure import Structure
+from pymatgen.transformations.standard_transformations import (
+    SupercellTransformation,
+)
+
+
+__author__ = "Junsoo Park"
+__email__ = "junsoo.park@nasa.gov"
+
+logger = get_logger(__name__)
+
+
+@explicit_serialize
+class CollectMDSegments(FiretaskBase):
+    """
+    Aggregate the structures and forces of perturbed supercells.
+
+    Requires a ``perturbed_tasks`` key to be set in the fw_spec, containing a
+    list of dictionaries, each with the keys:
+
+    - "parent_structure": The original structure.
+    - "supercell_matrix": The supercell transformation matrix.
+    - "structure": The perturbed supercell structure.
+    - "forces": The forces on each site in the supercell.
+    """
+
+    def run_task(self, fw_spec):
+        results = fw_spec.get("aimd", [])
+        logger.info("Found {} AIMD segments".format(len(results)))
+
+        structures = [r["structure"] for r in results]
+        forces = [np.asarray(r["forces"][i]) for i in range(len(r)) for r in results]
+        stress = [np.asarray(r["stress"][i]) for i in range(len(r)) for r in results]
+        configs = [r["configurations"][i] for i in range(len(r)) for r in results]
+
+        # if relaxation, get original structure from that calculation
+        calc_locs = fw_spec.get("calc_locs", [])
+        opt_calc_locs = [c for c in calc_locs if "optimiz" in c["name"]]
+        if opt_calc_locs:
+            opt_loc = opt_calc_locs[-1]["path"]
+            logger.info("Parsing optimization directory: {}".format(opt_loc))
+            opt_doc = VaspDrone(
+                parse_dos=False, parse_locpot=False,
+                parse_bader=False, store_volumetric_data=[],
+            ).assimilate(opt_loc)
+            opt_output = opt_doc["calcs_reversed"][0]["output"]
+            structure = Structure.from_dict(opt_output["structure"])
+        else:
+            structure = results[0]["parent_structure"]
+        supercell_matrix = results[0]["supercell_matrix"]
+
+        # regenerate pure supercell structure
+        st = SupercellTransformation(supercell_matrix)
+        supercell_structure = st.apply_transformation(structure)
+
+        structure_data = {
+            "structure": structure,
+            "supercell_structure": supercell_structure,
+            "supercell_matrix": supercell_matrix,
+        }
+
+        logger.info("Writing structure and forces data.")
+        dumpfn(structures, "perturbed_structures.json")
+        dumpfn(forces, "perturbed_forces.json")
+        dumpfn(structure_data, "structure_data.json")
+
+
+@explicit_serialize
+class MDToDB(FiretaskBase):
+    required_params = ["db_file"]
+    optional_params = ["renormalized","renorm_temperature","mesh_density", "additional_fields"]
+
+    def run_task(self, fw_spec):
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+
+        # Get an id for the force constants
+        fitting_id = _get_fc_fitting_id(mmdb)
+        metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
+        data = {
+            "created_at": datetime.utcnow(),
+            "tags": fw_spec.get("tags", None),
+            "formula_pretty": structure.composition.reduced_formula,
+            "structure": structure.as_dict(),
+            "supercell_matrix": supercell_matrix,
+            "supercell_structure": supercell_structure.as_dict(),
+            "perturbed_structures": [s.as_dict() for s in perturbed_structures],
+            "perturbed_forces": [f.tolist() for f in forces],
+            "fitting_data": fitting_data,
+            "thermal_data": thermal_data,
+            "force_constants_fs_id": fc_fsid,
+            "phonon_dos_fs_id": dos_fsid,
+            "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+            "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+        }
+        data.update(self.get("additional_fields", {}))
+        data.update(metadata)
+        data = jsanitize(data, strict=True, allow_bson=True)
+        mmdb.db.aimd_for_potential_fitting.insert_one(data)
+
+        logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
+
+        return FWAction(update_spec=metadata)
+
+
+@explicit_serialize
+class RunHiPhive(FiretaskBase):
+    """
+    Fit force constants using hiPhive.
+
+    Requires "perturbed_structures.json", "perturbed_forces.json", and
+    "structure_data.json" files to be present in the current working directory.
+
+    Optional parameters:
+        cutoffs (Optional[list[list]]): A list of cutoffs to trial. If None,
+            a set of trial cutoffs will be generated based on the structure
+            (default).
+        disp_cut: determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting  
+        imaginary_tol (float): Tolerance used to decide if a phonon mode
+            is imaginary, in THz.
+        fit_method (str): Method used for fitting force constants. This can
+            be any of the values allowed by the hiphive ``Optimizer`` class.
+    """
+
+    optional_params = [
+        "cutoffs",
+        "disp_cut",
+        "temperature_qha",
+        "bulk_modulus",
+        "imaginary_tol",
+        "fit_method",
+    ]
+
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
+    def run_task(self, fw_spec):
+
+        all_structures = loadfn("perturbed_structures.json")
+        all_forces = loadfn("perturbed_forces.json")
+        structure_data = loadfn("structure_data.json")
+        parent_structure = structure_data["structure"]
+        supercell_structure = structure_data["supercell_structure"]
+        supercell_matrix = np.array(structure_data["supercell_matrix"])
+
+        disp_cut = self.get('disp_cut', None)
+        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
+        T_qha = self.get("temperature_qha", T_QHA)
+        T_qha.sort()
+        imaginary_tol = self.get("imaginary_tol")
+        bulk_modulus = self.get("bulk_modulus")
+        fit_method = self.get("fit_method")
+
+        structures = []
+        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+        for structure, forces in zip(all_structures, all_forces):
+            atoms = AseAtomsAdaptor.get_atoms(structure)
+            displacements = get_displacements(atoms, supercell_atoms)
+            atoms.new_array("displacements", displacements)
+            atoms.new_array("forces", forces)
+            atoms.positions = supercell_atoms.get_positions()
+            structures.append(atoms)
+
+        fcs, param, cs, fitting_data = fit_force_constants(
+            parent_structure,
+            supercell_matrix,
+            structures,
+            cutoffs,
+            disp_cut,
+            imaginary_tol,
+            fit_method
+        )
+
+        if fcs is None:
+            # fitting failed for some reason
+            raise RuntimeError(
+                "Could not find a force constant solution"
+            )
+        
+        thermal_data, phonopy = harmonic_properties(
+            parent_structure, supercell_matrix, fcs, T_qha, imaginary_tol
+        )
+        anharmonic_data = anharmonic_properties(
+            phonopy, fcs, T_qha, thermal_data["heat_capacity"],
+            thermal_data["n_imaginary"], bulk_modulus
+        )
+
+        phonopy.save("phonopy_orig.yaml")
+        fitting_data["n_imaginary"] = thermal_data.pop("n_imaginary")
+        thermal_data.update(anharmonic_data)
+        dumpfn(fitting_data, "fitting_data.json")
+        dumpfn(thermal_data, "thermal_data.json")
+
+        logger.info("Writing cluster space and force_constants")
+        logger.info("{}".format(type(fcs)))
+        fcs.write("force_constants.fcs")
+        np.savetxt('parameters.txt',param)
+        cs.write('cluster_space.cs')
+
+        if fitting_data["n_imaginary"] == 0:
+            logger.info("No imaginary modes! Writing ShengBTE files")
+            atoms = AseAtomsAdaptor.get_atoms(parent_structure)
+            fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms, order=3)
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
+        else:
+            logger.info("ShengBTE files not written due to imaginary modes.")
+            logger.info("You may want to perform phonon renormalization.")
+
+
+
+@explicit_serialize
+class RunHiPhiveRenorm(FiretaskBase):
+    """
+    Perform phonon renormalization to obtain dependent-temperature force constants
+    using hiPhive. Requires "structure_data.json" to be present in the current working
+    directory.
+
+    Required parameters:
+   
+    Optional parameter:
+        temperature (float): temperature to perform renormalization
+        renorm_TE_iter (bool): if True, perform outer iteration over thermally expanded volumes
+        bulk_modulus (float): input bulk modulus - required for thermal expansion iterations
+    """
+
+    optional_params = ["renorm_method","temperature","nconfig","conv_thresh","max_iter",
+                       "renorm_TE_iter","bulk_modulus","imaginary_tol"]
+
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
+    def run_task(self, fw_spec):
+
+        cs = ClusterSpace.read('cluster_space.cs')
+        fcs = ForceConstants.read('force_constants.fcs')
+        param = np.loadtxt('parameters.txt')
+        fitting_data = loadfn("fitting_data.json")
+        structure_data = loadfn("structure_data.json")
+        phonopy_orig = phpy.load("phonopy_orig.yaml")
+
+        cutoffs = fitting_data["cutoffs"]
+        fit_method = fitting_data["fit_method"]
+        imaginary_tol = fitting_data["imaginary_tol"]
+
+        parent_structure = structure_data["structure"]
+        supercell_structure = structure_data["supercell_structure"]
+        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+        supercell_matrix = np.array(structure_data["supercell_matrix"])
+
+        temperature = self.get("temperature")
+        renorm_method = self.get("renorm_method")
+        nconfig = self.get("nconfig")
+        conv_thresh = self.get("conv_thresh")
+        max_iter = self.get("max_iter")
+        renorm_TE_iter = self.get("renorm_TE_iter")
+        bulk_modulus = self.get("bulk_modulus")
+
+        # Renormalization with DFT lattice
+        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, temperature,
+                                          nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
+
+        # Additional renormalization with thermal expansion - optional - just single "iteration" for now
+        if renorm_TE_iter:
+            n_TE_iter = 1
+            for i in range(n_TE_iter):
+                if renorm_data is None: # failed or incomplete 
+                    break
+                elif result["n_imaginary"] < 0: # still imaginary
+                    break
+                else:
+                    logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
+
+                dLfrac = renorm_data["expansion_fraction"]  
+                param = renorm_data["param"]
+
+                parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,temperature,dLfrac)
+                prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
+                prim_TE_phonopy = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
+                                               scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
+                phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
+                
+                renorm_data = run_renormalization(parent_structure_TE, supercell_atoms_TE, supercell_matrix, 
+                                                  cs_TE, fcs_TE, param, temperature, nconfig, max_iter,
+                                                  conv_thresh,  renorm_method, fit_method, bulk_modulus, phonopy_TE)
+            structure_data["structure"] = parent_structure_TE
+            structure_data["supercell_structure"] = AseAtomsAdaptor.get_structure(supercell_atoms_TE)
+                        
+        # write results
+        logger.info("Writing renormalized results")
+        renorm_thermal_data = dict()
+        fcs = renorm_data['fcs']
+        fcs.write("force_constants.fcs")
+        thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
+                        "gruneisen","thermal_expansion","expansion_fraction",
+                        "free_energy_correction_S","free_energy_correction_SC"]
+        renorm_thermal_data = {key: [] for key in thermal_keys}
+        for key in thermal_keys:
+            renorm_thermal_data[key].append(renorm_data[key])
+        
+        logger.info("DEBUG: ",renorm_data)
+        if renorm_data["n_imaginary"] > 0:
+            logger.warning('Imaginary modes remain for {} K!'.format(temperature))
+            logger.warning('ShengBTE files not written')
+            logger.warning('No renormalization with thermal expansion')
+        else:
+            logger.info("No imaginary modes! Writing ShengBTE files")
+            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND".format(temperature), format="text")
+
+        dumpfn(structure_data, "structure_data.json".format(temperature))
+        dumpfn(renorm_thermal_data, "renorm_thermal_data.json".format(temperature))
+
+        
+@explicit_serialize
+class ForceConstantsToDb(FiretaskBase):
+    """
+    Add force constants, phonon band structure and density of states
+    to the database.
+
+    Assumes you are in a directory with the force constants, fitting
+    data, and structure data written to files.
+
+    Required parameters:
+        db_file (str): Path to DB file for the database that contains the
+            perturbed structure calculations.
+
+    Optional parameters:
+        renormalized (bool): Whether FC resulted from original fitting (False)
+            or renormalization process (True) determines how data are stored. 
+            Default is False.
+        mesh_density (float): The density of the q-point mesh used to calculate
+            the phonon density of states. See the docstring for the ``mesh``
+            argument in Phonopy.init_mesh() for more details.
+        additional_fields (dict): Additional fields added to the document, such
+            as user-defined tags, name, ids, etc.
+    """
+
+    required_params = ["db_file"]
+    optional_params = ["renormalized","renorm_temperature","mesh_density", "additional_fields"]
+
+    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
+    def run_task(self, fw_spec):
+
+        db_file = env_chk(self.get("db_file"), fw_spec)
+        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
+        renormalized = self.get("renormalized", False)
+        renorm_temperature = self.get("renorm_temperature", None)
+        mesh_density = self.get("mesh_density", 100.0)
+
+        structure_data = loadfn("structure_data.json")        
+        structure = structure_data["structure"]
+        supercell_structure = structure_data["supercell_structure"]
+        supercell_matrix = structure_data["supercell_matrix"]
+
+        if not renormalized:
+            perturbed_structures = loadfn("perturbed_structures.json")
+            forces = loadfn("perturbed_forces.json")
+            fitting_data = loadfn("fitting_data.json")
+            thermal_data = loadfn("thermal_data.json")
+            fcs = ForceConstants.read("force_constants.fcs")
+            
+            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                structure, supercell_matrix, fcs, mesh_density, mmdb
+                )
+        
+            data = {
+                "created_at": datetime.utcnow(),            
+                "tags": fw_spec.get("tags", None),
+                "formula_pretty": structure.composition.reduced_formula,            
+                "structure": structure.as_dict(),
+                "supercell_matrix": supercell_matrix,
+                "supercell_structure": supercell_structure.as_dict(),
+                "perturbed_structures": [s.as_dict() for s in perturbed_structures],
+                "perturbed_forces": [f.tolist() for f in forces],
+                "fitting_data": fitting_data,
+                "thermal_data": thermal_data,
+                "force_constants_fs_id": fc_fsid,
+                "phonon_dos_fs_id": dos_fsid,
+                "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+                "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+                }
+            data.update(self.get("additional_fields", {}))
+
+            # Get an id for the force constants
+            fitting_id = _get_fc_fitting_id(mmdb)
+            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
+            data.update(metadata)
+            data = jsanitize(data,strict=True,allow_bson=True)
+            
+            mmdb.db.lattice_dynamics.insert_one(data)
+            
+            logger.info("Finished inserting force constants and phonon data")
+
+        else:
+            renorm_thermal_data = loadfn("renorm_thermal_data.json")
+            fcs = ForceConstants.read("force_constants.fcs")
+            T = renorm_thermal_data["temperature"]
+
+            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
+                structure, supercell_matrix, fcs, mesh_density, mmdb
+            )
+                
+            data_at_T = {
+                "created_at": datetime.utcnow(),
+                "tags": fw_spec.get("tags", None),
+                "formula_pretty": structure.composition.reduced_formula,
+                "structure": structure.as_dict(),
+                "supercell_matrix": supercell_matrix,
+                "supercell_structure": supercell_structure.as_dict(),
+                "thermal_data": renorm_thermal_data,
+                "force_constants_fs_id": fc_fsid,
+                "phonon_dos_fs_id": dos_fsid,
+                "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
+                "phonon_bandstructure_line_fs_id": lm_bs_fsid,
+            }
+            data_at_T.update(self.get("additional_fields", {}))
+        
+            # Get an id for the force constants
+            fitting_id = _get_fc_fitting_id(mmdb)
+            metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
+            data_at_T.update(metadata)
+            data_at_T = jsanitize(data_at_T,strict=True,allow_bson=True)
+            
+            mmdb.db.renormalized_lattice_dynamics.insert_one(data_at_T)
+            
+            logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
+            
+        return FWAction(update_spec=metadata)        
+
+
+def _get_fc_fitting_id(mmdb: VaspCalcDb) -> int:
+    """Helper method to get a force constant fitting id."""
+    fc_id = mmdb.db.counter.find_one_and_update(
+        {"_id": "fc_fitting_id"},
+        {"$inc": {"c": 1}},
+        return_document=ReturnDocument.AFTER,
+    )
+    if fc_id is None:
+        mmdb.db.counter.insert({"_id": "fc_fitting_id", "c": 1})
+        fc_id = 1
+    else:
+        fc_id = fc_id["c"]
+
+    return fc_id
+
+
+def _get_fc_fsid(structure, supercell_matrix, fcs, mesh_density, mmdb):
+    phonopy_fc = fcs.get_fc_array(order=2)
+    
+    logger.info("Getting uniform phonon band structure.")
+    uniform_bs = get_phonon_band_structure_from_fc(
+        structure, supercell_matrix, phonopy_fc
+    )
+    
+    logger.info("Getting line mode phonon band structure.")
+    lm_bs = get_phonon_band_structure_symm_line_from_fc(
+        structure, supercell_matrix, phonopy_fc
+    )
+    
+    logger.info("Getting phonon density of states.")
+    dos = get_phonon_dos_from_fc(
+        structure, supercell_matrix, phonopy_fc, mesh_density=mesh_density
+    )
+    
+    logger.info("Inserting phonon objects into database.")
+    dos_fsid, _ = mmdb.insert_gridfs(
+        dos.to_json(), collection="phonon_dos_fs"
+    )
+    uniform_bs_fsid, _ = mmdb.insert_gridfs(
+        uniform_bs.to_json(), collection="phonon_bandstructure_fs"
+    )
+    lm_bs_fsid, _ = mmdb.insert_gridfs(
+        lm_bs.to_json(), collection="phonon_bandstructure_fs"
+    )
+    
+    logger.info("Inserting force constants into database.")
+    fc_json = json.dumps(
+        {str(k): v.tolist() for k, v in fcs.get_fc_dict().items()}
+    )
+    fc_fsid, _ = mmdb.insert_gridfs(
+        fc_json, collection="phonon_force_constants_fs"
+    )
+
+    return dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index 2c24c55bd..ca2b886f7 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -300,7 +300,8 @@ def run_task(self, fw_spec):
         fcs.write("force_constants.fcs")
         thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
                         "gruneisen","thermal_expansion","expansion_fraction",
-                        "free_energy_correction_S","free_energy_correction_SC"]
+                        "free_energy_correction_S","free_energy_correction_SC",
+                        "free_energy_correction_TI"]
         renorm_thermal_data = {key: [] for key in thermal_keys}
         for key in thermal_keys:
             renorm_thermal_data[key].append(renorm_data[key])
diff --git a/atomate/vasp/firetasks/run_calc.py b/atomate/vasp/firetasks/run_calc.py
index 9b771c221..1eb017431 100644
--- a/atomate/vasp/firetasks/run_calc.py
+++ b/atomate/vasp/firetasks/run_calc.py
@@ -10,7 +10,14 @@
 from custodian import Custodian
 from custodian.vasp.handlers import (
     AliasingErrorHandler,
+<<<<<<< HEAD
     DriftErrorHandler,
+=======
+    MeshSymmetryErrorHandler,
+    UnconvergedErrorHandler,
+#    MaxForceErrorHandler,
+    PotimErrorHandler,
+>>>>>>> c012f5fb (ARC AIMD)
     FrozenJobErrorHandler,
     IncorrectSmearingHandler,
     LargeSigmaHandler,
diff --git a/atomate/vasp/fireworks/aimd.py b/atomate/vasp/fireworks/aimd.py
new file mode 100644
index 000000000..40a0251b2
--- /dev/null
+++ b/atomate/vasp/fireworks/aimd.py
@@ -0,0 +1,193 @@
+from typing import List, Optional, Union, Dict
+
+import os
+
+from atomate.common.firetasks.glue_tasks import (
+    CopyFiles,
+    CopyFilesFromCalcLoc,
+    PassCalcLocs,
+)
+
+from atomate.vasp.firetasks.aimd import (
+    CollectMDSegments,
+    MDToDB
+    )
+
+from fireworks import Firework
+
+__author__ = "Junsoo Park"
+__email__ = "junsoo.park@nasa.gov"
+
+
+class ARCMDFW(Firework):
+    def __init__(
+        self,
+        structure,
+        start_temp,
+        end_temp,
+        nsteps,
+        name="AIMD",
+        vasp_input_set=None,
+        vasp_cmd=VASP_CMD,
+        override_default_vasp_params=None,
+        wall_time=19200,
+        db_file=DB_FILE,
+        parents=None,
+        **kwargs,
+    ):
+        """
+        Standard firework for a single MD run.
+
+        Args:
+            structure (Structure): Input structure.
+            start_temp (float): Start temperature of MD run.
+            end_temp (float): End temperature of MD run.
+            nsteps (int): Number of MD steps
+            name (string): Name for the Firework.
+            vasp_input_set (string): string name for the VASP input set (e.g.,
+                "MITMDVaspInputSet").
+            vasp_cmd (string): Command to run vasp.
+            override_default_vasp_params (dict): If this is not None,
+                these params are passed to the default vasp_input_set, i.e.,
+                MITMDSet. This allows one to easily override some
+                settings, e.g., user_incar_settings, etc. Particular to MD,
+                one can control time_step and all other settings of the input set.
+            wall_time (int): Total wall time in seconds before writing STOPCAR.
+            copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True.
+            db_file (string): Path to file specifying db credentials.
+            parents (Firework): Parents of this particular Firework. FW or list of FWS.
+            **kwargs: Other kwargs that are passed to Firework.__init__.
+        """
+        override_default_vasp_params = override_default_vasp_params or {}
+        vasp_input_set = vasp_input_set or ARCMDSet(
+            structure,
+            start_temp=start_temp,
+            end_temp=end_temp,
+            nsteps=nsteps,
+            **override_default_vasp_params,
+        )
+        prev_runs = fw_spec.get("aimd", [])
+        last_run = prev_runs[-1]
+        last_config = last_run["final_configuration"]
+        t = []
+        t.append(WriteVaspFromIOSet(structure=last_config, vasp_input_set=vasp_input_set))
+        t.append(
+            RunVaspCustodian(
+                vasp_cmd=vasp_cmd,
+                gamma_vasp_cmd=">>vasp_cmd<<",#">>gamma_vasp_cmd<<",
+                handler_group="md",
+                wall_time=wall_time,
+            )
+        )
+        t.append(PassCalcLocs(name=name))
+        t.append(
+            VaspToDb(
+                db_file=db_file,
+                additional_fields={"task_label": name},
+                defuse_unsuccessful=False,
+            )
+        )
+        super().__init__(
+            t,
+            parents=parents,
+            name=f"{structure.composition.reduced_formula}-{name}",
+            **kwargs,
+        )
+
+
+class CollectMDSegmentsFW(Firework):
+    """
+    Compile serial AIMD runs segmented into multiple Fireworks
+
+    Args:
+        parents: Parent(s) of this Firework.
+        name: Name of this FW.
+        db_file: Path to a db file.
+        cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
+            will be generated based on the structure (default).
+        disp_cut: determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting  
+        bulk_modulus: in GPa, necessary for thermal expansion
+        imaginary_tol: Tolerance used to decide if a phonon mode is
+            imaginary, in THz.
+        fit_method: Method used for fitting force constants. This can be
+            any of the values allowed by the hiphive ``Optimizer`` class.
+        mesh_density: The density of the q-point mesh used to calculate the
+            phonon density of states. See the docstring for the ``mesh``
+            argument in Phonopy.init_mesh() for more details.
+        **kwargs: Other kwargs that are passed to Firework.__init__.
+    """
+
+    def __init__(
+        self,
+        name="Collect MD Runs",
+        parents: Optional[Union[Firework, List[Firework]]] = None,
+        db_file: str = None,
+        **kwargs
+    ):
+        collect = CollectMDSegments()
+
+        to_db = AIMDToDB(
+            db_file=db_file, additional_fields={}
+        )
+        pass_locs = PassCalcLocs(name=name)
+
+        tasks = [collect, to_db, pass_locs]
+        super().__init__(tasks, parents=parents, name=name, **kwargs)
+
+
+class FitForceConstantsFW(Firework):
+    """
+    Compile perturbed supercell calculations and fit force constants
+    using hiPhive.
+
+    Args:
+        parents: Parent(s) of this Firework.
+        name: Name of this FW.
+        db_file: Path to a db file.
+        cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
+            will be generated based on the structure (default).
+        disp_cut: determines the mean displacement of perturbed
+            structure to be included in harmonic (<) or anharmonic (>) fitting
+        bulk_modulus: in GPa, necessary for thermal expansion
+        imaginary_tol: Tolerance used to decide if a phonon mode is
+            imaginary, in THz.
+        fit_method: Method used for fitting force constants. This can be
+            any of the values allowed by the hiphive ``Optimizer`` class.
+        mesh_density: The density of the q-point mesh used to calculate the
+            phonon density of states. See the docstring for the ``mesh``
+            argument in Phonopy.init_mesh() for more details.
+        **kwargs: Other kwargs that are passed to Firework.__init__.
+    """
+
+    def __init__(
+            self,
+            fit_method: str,
+            disp_cut: float,
+            bulk_modulus: float,
+            imaginary_tol: float,
+            mesh_density: float,
+            temperature_qha: float,
+            cutoffs: Optional[List[List[float]]] = None,
+            name="Fit Force Constants",
+            parents: Optional[Union[Firework, List[Firework]]] = None,
+            db_file: str = None,
+            **kwargs
+    ):
+        collect_structures = CollectPerturbedStructures()
+
+        fit_force_constants = RunHiPhive(
+            cutoffs=cutoffs,
+            fit_method=fit_method,
+            disp_cut=disp_cut,
+            bulk_modulus=bulk_modulus,
+            temperature_qha=temperature_qha,
+            imaginary_tol=imaginary_tol,
+        )
+        to_db = ForceConstantsToDb(
+            db_file=db_file, renormalized=False, mesh_density=mesh_density, additional_fields={}
+        )
+        pass_locs = PassCalcLocs(name=name)
+
+        tasks = [collect_structures, fit_force_constants, to_db, pass_locs]
+        super().__init__(tasks, parents=parents, name=name, **kwargs)
diff --git a/atomate/vasp/fireworks/core.py b/atomate/vasp/fireworks/core.py
index e99d18925..373635e30 100644
--- a/atomate/vasp/fireworks/core.py
+++ b/atomate/vasp/fireworks/core.py
@@ -64,6 +64,10 @@ def __init__(
         db_file=DB_FILE,
         force_gamma=True,
         job_type="double_relaxation_run",
+<<<<<<< HEAD
+=======
+#        max_force_threshold=RELAX_MAX_FORCE,
+>>>>>>> c012f5fb (ARC AIMD)
         auto_npar=">>auto_npar<<",
         half_kpts_first_relax=HALF_KPOINTS_FIRST_RELAX,
         parents=None,
@@ -113,6 +117,10 @@ def __init__(
             RunVaspCustodian(
                 vasp_cmd=vasp_cmd,
                 job_type=job_type,
+<<<<<<< HEAD
+=======
+#                max_force_threshold=max_force_threshold,
+>>>>>>> c012f5fb (ARC AIMD)
                 ediffg=ediffg,
                 auto_npar=auto_npar,
                 half_kpts_first_relax=half_kpts_first_relax,
diff --git a/atomate/vasp/workflows/base/aimd.py b/atomate/vasp/workflows/base/aimd.py
new file mode 100644
index 000000000..096aea5e6
--- /dev/null
+++ b/atomate/vasp/workflows/base/aimd.py
@@ -0,0 +1,162 @@
+import math
+import warnings
+from copy import deepcopy
+from typing import Dict, List, Optional, Union
+import numpy as np
+from monty.serialization import loadfn, dumpfn
+
+from atomate.utils.utils import get_logger
+from atomate.vasp.config import DB_FILE, VASP_CMD
+from atomate.vasp.firetasks import pass_vasp_result
+from atomate.vasp.analysis.lattice_dynamics import (
+    FIT_METHOD,
+    MESH_DENSITY,
+)
+from atomate.vasp.fireworks.core import TransmuterFW, OptimizeFW
+from atomate.vasp.fireworks.aimd import ARCMDFW, CollectMDSegmentsFW
+from atomate.common.powerups import add_additional_fields_to_taskdocs
+from fireworks import Workflow
+from pymatgen.core.structure import Structure
+from pymatgen.io.vasp.sets import ARCMDSet, VaspInputSet
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from pymatgen.transformations.advanced_transformations import (
+    CubicSupercellTransformation,
+)
+
+__author__ = "Junsoo Park"
+__email__ = "junsoo.park@nasa.gov"
+__date__ = "December 2023"
+
+logger = get_logger(__name__)
+
+vasp_to_db_params = {
+    "store_volumetric_data": tuple(),
+    "vasp_drone_params": {"parse_bader": False, "parse_locpot": False}
+}
+
+_DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
+_WF_VERSION = 0.1
+
+
+def get_aimd_wf(
+    structure: Structure,
+    common_settings: Dict = None,
+    ensemble='NVT',
+    start_temp=start_temp,
+    end_temp=end_temp,
+    simulation_time = simulation_time,
+    time_step = time_step,
+    copy_vasp_outputs = True,
+    supercell_matrix_kwargs: Optional[dict] = None
+):
+    """
+    This workflow will perform AIMD on VASP,
+
+    Args:
+        structure: Initial structure.
+        common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
+            and "user_incar_settings" keys.
+        vasp_input_set: Vasp input set for perturbed structure calculations.
+        copy_vasp_outputs: Whether or not to copy previous vasp outputs.
+        supercell_matrix_kwargs: Options that control the size of the supercell.
+            Will be passed directly to CubicSupercellTransformation in
+            pymatgen.transformations.advanced_transformations. Note, a diagonal
+            supercell is required to calculate lattice thermal conductivity.
+        ensemble: NVT, NPT, etc.
+   """
+
+    parent_structure = structure.as_dict()
+    supercell_matrix_kwargs = supercell_matrix_kwargs or {}
+    common_settings = _get_common_settings(common_settings)
+    db_file = common_settings["DB_FILE"]
+
+    logger.debug('Transforming supercell!')
+    logger.debug('KWARGS: \n {}'.format(supercell_matrix_kwargs))
+    st = CubicSupercellTransformation(**supercell_matrix_kwargs)
+    supercell = st.apply_transformation(structure)
+    supercell_matrix = st.transformation_matrix
+    logger.debug('SUPERCELL MATRIX: \n {}'.format(supercell_matrix))
+
+    nsteps_total = ceil(simulation_time/time_step)
+    nsteps_each = 500
+    nfws = ceil(nsteps_total/nsteps_each)
+    parents=None
+
+    vasp_input_set = ARCMDSet(
+        structure=supercell,
+        ensemble=ensemble,
+        start_temp=start_temp,
+        end_temp=end_temp,
+        nsteps=nsteps_each,
+        time_step=time_step,
+        reciprocal_density=1,
+        small_gap_multiply=None
+    )
+    for ifw in range(nfws):
+        if ifw>0:
+            vasp_input_set.update()
+            parents = aimd_wf.fws[-1]
+            start_temp = end_temp
+
+        aimd_fw = ARCMDFW( start_structure,
+                        start_temp,
+                        end_temp,
+                        nsteps_fw,
+                        name="AIMD_segment_{}".format(ifw+1),
+                        vasp_input_set=vasp_input_set,
+                        vasp_cmd=VASP_CMD,
+                        wall_time=1080000,
+                        db_file=DB_FILE,
+                        parents=parents,
+                        copy_vasp_outputs=copy_vasp_outputs,
+                        override_default_vasp_params=None,
+                        **kwargs,)
+        pass_task = pass_vasp_result(
+            pass_dict={
+            "parent_structure": parent_structure,
+            "supercell_matrix": supercell_matrix,
+            "forces": ">>output.ionic_steps.:-1.forces",
+            "stress": ">>output.ionic_steps.:-1.stress",
+            "configurations": ">>output.ionic_steps.:-1.structure",
+            "final_configuration": ">>output.ionic_steps.-1.structure"
+            },
+            mod_spec_cmd="_push",
+            mod_spec_key="aimd",
+        )
+        aimd_fw.tasks.append(pass_task)
+        if ifw==0:
+            wf = Workflow.from_Firework(aimd_fw)
+        else:
+            wf.append_wf(Workflow.from_Firework(aimd_fw), wf.fws[-1].fw_id)
+
+    collect_fw = CollectMDSegmentsFW(
+        db_file=db_file,
+        parents=wf.fws[-nfws:]
+    )
+    wf.append_wf(
+            Workflow.from_Firework(collect_fw), [fw.fw_id for fw in wf.fws[-nfws:]]
+        )
+
+    # Add workflow metadata to all relevant *ToDb tasks.
+    wf_meta = {"wf_name": "AIMDWF", "wf_version": _WF_VERSION}
+    for task_name in ["VaspToDb"]:
+        wf = add_additional_fields_to_taskdocs(
+            wf, {"wf_meta": wf_meta}, task_name_constraint=task_name
+        )
+
+    return wf
+
+
+def _get_common_settings(common_settings: Optional[Dict]):
+    common_settings = common_settings or {}
+    for k, v in _DEFAULT_SETTINGS.items():
+        if k not in common_settings:
+            common_settings[k] = v
+
+    user_incar_settings = deepcopy(_aimd_user_incar_settings)
+    user_incar_settings.update(common_settings.get("user_incar_settings", {}))
+    common_settings["user_incar_settings"] = user_incar_settings
+
+    return common_settings
+
+
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index c105ca4b4..dab868dc6 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -190,7 +190,7 @@ def get_lattice_dynamics_wf(
         **perturbed_structure_kwargs,
         )
 
-    # 2. Fit interatomic force constants from pertrubed structures
+    # 2. Fit interatomic force constants from perturbed structures
     allow_fizzled = {"_allow_fizzled_parents": True}
     fw_fit_force_constant = FitForceConstantsFW(
         db_file=db_file,
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 8d898d141..21c5ad522 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -950,3 +950,85 @@ def wf_lattice_dynamics(
 
     return wf
 
+
+def wf_aimd(
+    structure: Structure,
+    c: Optional[dict] = None,
+    supercell_matrix_kwargs: Optional[dict] = None,
+    num_supercell_kwargs: Optional[dict] = None,
+    ensemble='NVT',
+    simulation_time=10000,
+    time_step=2,
+    **aimd_kwargs
+) -> Workflow:
+    """
+    Get a workflow to run AIMD on vasp, preceded by a structure optimization.
+
+    Args:
+        structure: The input structure.
+        c: Workflow common settings dict. Supports the keys: "VASP_CMD",
+            "DB_FILE", and "user_incar_settings", "ADD_WF_METADATA", and the
+            options supported by "add_common_powerups".
+        **aimd_kwargs: Keyword arguments to be passed directly to the AIMD base workflow.
+
+    Returns:
+        A workflow to perform AIMD.
+    """
+
+    # start with defining the relaxation workflow
+    optimize_uis = {
+        "LAECHG": False,
+        'ENCUT': 600,
+        'ADDGRID': True,
+        'EDIFF': 1e-8,
+        'EDIFFG': -5e-4,
+        'PREC': 'Accurate',
+        "LREAL": False,
+        'LASPH': True,
+        'ISPIN': 2,
+        'ISMEAR': 0,
+        'SIGMA': 0.1,
+        'LCHARG': False,
+        'LWAVE': False
+    }
+    c = c if c is not None else {}
+    if "USER_INCAR_SETTINGS" not in c:
+        c["USER_INCAR_SETTINGS"] = {}
+
+    # wf_structure_optimization expects user incar settings in capitals
+    c["USER_INCAR_SETTINGS"].update(optimize_uis)
+    c["USER_INCAR_SETTINGS"].update(c.get("user_incar_settings", {}))
+    wf = wf_structure_optimization(structure, c=c)
+
+    # don't store CHGCAR and other volumetric data in the VASP drone
+    for task in wf.fws[0].tasks:
+        if "VaspToDb" in str(task):
+            task.update(vasp_to_db_params)
+
+    # Define AIMD workflow
+    wf_aimd = get_aimd_wf(
+        structure,
+        common_settings=c,
+        ensemble=ensemble,
+        start_temp=start_temp,
+        end_temp=end_temp,
+        simulation_time=simulation_time,
+        time_step=time_step,
+        copy_vasp_outputs = True,
+        supercell_matrix_kwargs=supercell_matrix_kwargs,
+        **aimd_kwargs
+    )
+
+    # join the workflows
+    wf.append_wf(wf_aimd, wf.leaf_fw_ids)
+
+    formula = structure.composition.reduced_formula
+    wf_name = "{} AIMD - {} - {}K".format(formula,ensemble,end_temp)
+    wf.name = wf_name
+
+    wf = add_common_powerups(wf, c)
+    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
+        wf = add_wf_metadata(wf, structure)
+
+    return wf
+

From 75e4846b230cbaf5a89b706d9c09f6d6ad741542 Mon Sep 17 00:00:00 2001
From: jsyony37 <qkwnstn@gmail.com>
Date: Sat, 2 Mar 2024 01:05:41 -0500
Subject: [PATCH 184/207] TI_IFC + clean-up

---
 atomate/vasp/analysis/lattice_dynamics.py     | 124 ++++++++++++------
 atomate/vasp/firetasks/lattice_dynamics.py    |  91 +++++++------
 .../vasp/workflows/base/lattice_dynamics.py   |   8 +-
 3 files changed, 133 insertions(+), 90 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index 938575ce1..fce785f11 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -747,7 +747,7 @@ def percent_diff(a,b):
             return abs((a-b)/b)
         # This process preserves cell symmetry upon thermal expansion, i.e., it prevents
         # symmetry-identical directions from inadvertently expanding by different ratios
-        # when the Gruneisen routine returns slighlty different ratios for those directions
+        # when/if the Gruneisen routine returns slightly different ratios for those directions
         avg012 = np.mean((grun_total_diag[0],grun_total_diag[1],grun_total_diag[2]))
         avg01 = np.mean((grun_total_diag[0],grun_total_diag[1]))
         avg02 = np.mean((grun_total_diag[0],grun_total_diag[2]))
@@ -817,9 +817,10 @@ def gruneisen(
 #        cte = grun_tot*heat_capacity.repeat(3)/(vol/10**30)/(bulk_modulus*10**9)/3
         cte = grun_tot*heat_capacity.repeat(3).reshape(len(heat_capacity),3)/(vol/10**30)/(bulk_modulus*10**9)/3
         cte = np.nan_to_num(cte)
-        dLfrac = thermal_expansion(temperature,cte)
         if len(temperature)==1:
-            dLfrac = dLfrac[-1]
+            dLfrac = cte*temperature
+        else:
+            dLfrac = thermal_expansion(temperature, cte)
         logger.info('Gruneisen: \n {}'.format(grun_tot))
         logger.info('Coefficient of Thermal Expansion: \n {}'.format(cte))
         logger.info('Linear Expansion Fraction: \n {}'.format(dLfrac))        
@@ -849,19 +850,19 @@ def thermal_expansion(
 
 def run_renormalization(
         structure: Structure,
-        supercell: Atoms,
+        supercell_structure: Structure,
         supercell_matrix: np.ndarray,
         cs: ClusterSpace,
         fcs: ForceConstants,
         param: np.ndarray,
         T: float,
         nconfig: int,
-        max_iter: int,
-        conv_tresh: float,
         renorm_method: str,
         fit_method: str,
         bulk_modulus: float = None,
         phonopy_orig: Phonopy = None,
+        param_TD: np.ndarray = None,
+        fcs_TD: ForceConstants = None,
         imaginary_tol: float = IMAGINARY_TOL,
 ) -> Dict:
     """
@@ -884,63 +885,100 @@ def run_renormalization(
     """
 
     nconfig = int(nconfig)
-    renorm = Renormalization(cs,supercell,fcs,param,T,renorm_method,fit_method)
-    fcp, fcs, param = renorm.renormalize(nconfig)#,conv_tresh)
+    supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+    renorm = Renormalization(cs,supercell_atoms,param,fcs,T,renorm_method,fit_method,param_TD=param_TD,fcs_TD=fcs_TD)
+    fcp_TD, fcs_TD, param_TD = renorm.renormalize(nconfig)#,conv_tresh)
 
-    renorm_data, phonopy = harmonic_properties(
-        structure, supercell_matrix, fcs, [T], imaginary_tol
+    TD_data, phonopy_TD = harmonic_properties(
+        structure, supercell_matrix, fcs_TD, [T], imaginary_tol
     )
 
-    if renorm_data["n_imaginary"] == 0:
+    if TD_data["n_imaginary"] == 0:
         logger.info('Renormalized phonon is completely real at T = {} K!'.format(T))
-    anharmonic_data = anharmonic_properties(
-        phonopy, fcs, [T], renorm_data["heat_capacity"], renorm_data["n_imaginary"], bulk_modulus=bulk_modulus
-    )
+        anharmonic_data = anharmonic_properties(
+            phonopy_TD, fcs_TD, [T], TD_data["heat_capacity"], TD_data["n_imaginary"], bulk_modulus=bulk_modulus
+        )
+        TD_data.update(anharmonic_data)
 #    else:
 #        anharmonic_data = dict()
 #        anharmonic_data["temperature"] = T
 #        anharmonic_data["gruneisen"] = np.array([0,0,0])
 #        anharmonic_data["thermal_expansion"] = np.array([0,0,0])
 #        anharmonic_data["expansion_fraction"] = np.array([0,0,0])
-    renorm_data.update(anharmonic_data)
 
     phonopy_orig.run_mesh()
     phonopy.run_mesh()
-    omega0 = phonopy_orig.mesh.frequencies # THz
+    omega_h = phonopy_orig.mesh.frequencies # THz
+    evec_h = phonopy_orig.mesh.eigenvectors
     omega_TD = phonopy.mesh.frequencies # THz
-    evec = phonopy.mesh.eigenvectors
-#    natom = phonopy.primitive.get_number_of_atoms()
-    correction_S, correction_SC = free_energy_correction(omega0,omega_TD,evec,[T]) # eV/atom
-
-    lambda_array = np.array([0,0.1,0.3,0.5,0.7,0.9,1])
-    correction_TI = renorm.thermodynamic_integration(lambda_array,param,fcs,TI_nconfig=3)
-
-    renorm_data["free_energy_correction_S"] = correction_S[0]
-    renorm_data["free_energy_correction_SC"] = correction_SC[0]
-    renorm_data["free_energy_correction_TI"] = correction_TI
-    renorm_data["fcp"] = fcp
-    renorm_data["fcs"] = fcs
-    renorm_data["param"] = param
+    evec_TD = phonopy.mesh.eigenvectors
+    correction_S, correction_SC = free_energy_correction(omega_h,omega_TD,evec_h,evec_TD,[T]) # eV/atom
+
+    TD_data["free_energy_correction_S"] = correction_S   # S = -(dF/dT)_V quasiparticle correction
+    TD_data["free_energy_correction_SC"] = correction_SC # SCPH 4th-order correction (perturbation theory)
+    TD_data["fcp"] = fcp_TD
+    TD_data["fcs"] = fcs_TD
+    TD_data["param"] = param_TD
+    TD_data['cs'] = cs
     
-    return renorm_data
+    return TD_data
 
 
+def thermodynamic_integration_ifc(
+        TD_data: Dict,
+        fcs: ForceConstants,
+        param: np.ndarray,
+        lambda_array: np.ndarray = np.array([0, 0.1, 0.3, 0.5, 0.7, 0.9, 1]),
+        TI_nconfig=3,
+) -> Dict:
 
-def setup_TE_iter(cs,cutoffs,parent_structure,param,temperatures,dLfrac):
-    new_atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-    new_cell = Cell(np.transpose([new_atoms.get_cell()[:,i]*(1+dLfrac[0,i]) for i in range(3)]))
-    new_atoms.set_cell(new_cell,scale_atoms=True)
-    parent_structure_TE = AseAtomsAdaptor.get_structure(new_atoms)
-    supercell_atoms_TE = AseAtomsAdaptor.get_atoms(parent_structure_TE*supercell_matrix)
-    new_cutoffs = [i*(1+np.linalg.norm(dLfrac)) for i in cutoffs]
+    supercell_structure = TD_data["supercell_structure"]
+    cs = TD_data['cs']
+    fcs_TD = TD_data["fcs"]
+    param_TD = TD_data["param"]
+    T = TD_data['temperature']
+    supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+    renorm = Renormalization(cs, supercell_atoms, param, fcs, T, 'least_squares', 'rfe', param_TD, fcs_TD)
+    matcov_TD, matcov_BO, matcov_TDBO = renorm.born_oppenheimer_qcv(TI_nconfig)
+    correction_TI = renorm.thermodynamic_integration(lambda_array, matcov_TD, matcov_BO, matcov_TDBO, TI_nconfig)
+    TD_data["free_energy_correction_TI"] = correction_TI
+    return TD_data
+
+
+def setup_TE_renorm(cs,cutoffs,parent_atoms,supercell_atoms,param,dLfrac):
+    parent_atoms_TE = copy(parent_atoms)
+    new_cell = Cell(np.transpose([parent_atoms_TE.get_cell()[:,i]*(1+dLfrac[0,i]) for i in range(3)]))
+    parent_atoms_TE.set_cell(new_cell,scale_atoms=True)
+    parent_structure_TE = AseAtomsAdaptor.get_structure(parent_atoms_TE)
+    supercell_atoms_TE = copy(supercell_atoms)
+    new_supercell = Cell(np.transpose([supercell_atoms_TE.get_cell()[:,i]*(1+dLfrac[0,i]) for i in range(3)]))
+    supercell_atoms_TE.set_cell(new_supercell,scale_atoms=True)
+    supercell_structure_TE = AseAtomsAdaptor.get_structure(supercell_atoms_TE)
+    count = 0
+    failed = False
+    cs_TE = ClusterSpace(parent_atoms_TE,cutoffs,symprec=1e-2,acoustic_sum_rules=True)
     while True:
-        cs_TE = ClusterSpace(atoms,new_cutoffs,1e-3,acoustic_sum_rules=True)
+        count += 1
         if cs_TE.n_dofs == cs.n_dofs:
             break
+        elif count>10:
+            logger.warning("Could not find ClusterSpace for expanded cell identical to the original cluster space!")
+            failed = True
+            break
+        elif count==1:
+            cutoffs_TE = [i*(1+np.linalg.norm(dLfrac)) for i in cutoffs]
         elif cs_TE.n_dofs > cs.n_dofs:
-            new_cutoffs = [i*0.999 for i in new_cutoffs]
+            cutoffs_TE = [i*0.999 for i in cutoffs_TE]
         elif cs_TE.n_dofs < cs.n_dofs:
-            new_cutoffs = [i*1.001 for i in new_cutoffs]
-        new_fcp = ForceConstantsPotential(cs_TE,param)
-        fcs_TE.append(new_fcp.get_force_constants(supercell_atoms_TE))
-    return parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE
+            cutoffs_TE = [i*1.001 for i in cutoffs_TE]
+        cs_TE = ClusterSpace(parent_atoms_TE,cutoffs_TE,symprec=1e-2,acoustic_sum_rules=True)
+    if failed:
+        return None, None, None, None, None, failed
+    else:
+        fcp_TE = ForceConstantPotential(cs_TE, param)
+        fcs_TE = fcp_TE.get_force_constants(supercell_atoms_TE)
+        prim_TE_phonopy = PhonopyAtoms(symbols=parent_atoms_TE.get_chemical_symbols(),
+                                       scaled_positions=parent_atoms_TE.get_scaled_positions(),
+                                       cell=parent_atoms_TE.cell)
+        phonopy_TE = Phonopy(prim_TE_phonopy, supercell_matrix=scmat, primitive_matrix=None)
+        return parent_structure_TE, supercell_structure_TE, cs_TE, phonopy_TE, fcs_TE, failed
diff --git a/atomate/vasp/firetasks/lattice_dynamics.py b/atomate/vasp/firetasks/lattice_dynamics.py
index ca2b886f7..84a572a60 100644
--- a/atomate/vasp/firetasks/lattice_dynamics.py
+++ b/atomate/vasp/firetasks/lattice_dynamics.py
@@ -26,7 +26,7 @@
     harmonic_properties,
     anharmonic_properties,
     run_renormalization,
-    setup_TE_iter,
+    setup_TE_renorm,
     get_cutoffs
 )
 
@@ -233,7 +233,7 @@ class RunHiPhiveRenorm(FiretaskBase):
         bulk_modulus (float): input bulk modulus - required for thermal expansion iterations
     """
 
-    optional_params = ["renorm_method","temperature","nconfig","conv_thresh","max_iter",
+    optional_params = ["renorm_method","temperature","nconfig",
                        "renorm_TE_iter","bulk_modulus","imaginary_tol"]
 
     @requires(hiphive, "hiphive is required for lattice dynamics workflow")
@@ -248,82 +248,88 @@ def run_task(self, fw_spec):
 
         cutoffs = fitting_data["cutoffs"]
         fit_method = fitting_data["fit_method"]
-        imaginary_tol = fitting_data["imaginary_tol"]
 
         parent_structure = structure_data["structure"]
         supercell_structure = structure_data["supercell_structure"]
-        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
         supercell_matrix = np.array(structure_data["supercell_matrix"])
 
         temperature = self.get("temperature")
         renorm_method = self.get("renorm_method")
         nconfig = self.get("nconfig")
-        conv_thresh = self.get("conv_thresh")
-        max_iter = self.get("max_iter")
         renorm_TE_iter = self.get("renorm_TE_iter")
         bulk_modulus = self.get("bulk_modulus")
 
+        parent_atoms = AseAtomsAdaptor.get_atoms(parent_structure)
+        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
+
         # Renormalization with DFT lattice
-        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, temperature,
-                                          nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
+        TD_data = run_renormalization(parent_structure, supercell_structure, supercell_matrix,
+                                      cs, fcs, param, temperature, nconfig, renorm_method,
+                                      fit_method, bulk_modulus, phonopy_orig)
+        TD_structure_data = copy(structure_data)
+        TD_structure_data["structure"] = parent_structure
+        TD_structure_data["supercell_structure"] = supercell_structure
 
         # Additional renormalization with thermal expansion - optional - just single "iteration" for now
         if renorm_TE_iter:
             n_TE_iter = 1
             for i in range(n_TE_iter):
-                if renorm_data is None: # failed or incomplete 
+                if TD_data is None: # failed or incomplete
                     break
                 elif result["n_imaginary"] < 0: # still imaginary
                     break
                 else:
                     logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
+                dLfrac = TD_data["expansion_fraction"]
+                param_TD = TD_data["param"]
+                a, b, c, d, e, failed = setup_TE_renorm(
+                    cs,cutoffs,parent_atoms,supercell_atoms,param_TD,temperature,dLfrac
+                )
+                if not failed:
+                    parent_structure_TD, supercell_structure_TD, cs_TD, phonopy_TD, fcs_TD  = a, b, c, d, e
+                    TD_data = run_renormalization(parent_structure_TD, supercell_structure_TD, supercell_matrix,
+                                                  cs_TD, fcs, param, temperature, nconfig,
+                                                  renorm_method, fit_method, bulk_modulus,
+                                                  phonopy_TD, param_TD, fcs_TD
+                                                  )
+                    TD_structure_data["structure"] = parent_structure_TD
+                    TD_structure_data["supercell_structure"] = supercell_structure_TD
+
+        # Thermodynamic integration for anharmonic free energy
+        TD_data = thermodynamic_integration_ifc(TD_data, # everything TD
+                                                    fcs, # original
+                                                    param, # original
+                                                    )
 
-                dLfrac = renorm_data["expansion_fraction"]  
-                param = renorm_data["param"]
-
-                parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,temperature,dLfrac)
-                prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
-                prim_TE_phonopy = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
-                                               scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
-                phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
-                
-                renorm_data = run_renormalization(parent_structure_TE, supercell_atoms_TE, supercell_matrix, 
-                                                  cs_TE, fcs_TE, param, temperature, nconfig, max_iter,
-                                                  conv_thresh,  renorm_method, fit_method, bulk_modulus, phonopy_TE)
-            structure_data["structure"] = parent_structure_TE
-            structure_data["supercell_structure"] = AseAtomsAdaptor.get_structure(supercell_atoms_TE)
-                        
         # write results
         logger.info("Writing renormalized results")
-        renorm_thermal_data = dict()
-        fcs = renorm_data['fcs']
-        fcs.write("force_constants.fcs")
+        fcs_TD = TD_data['fcs']
+        fcs_TD.write("force_constants.fcs")
         thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
                         "gruneisen","thermal_expansion","expansion_fraction",
                         "free_energy_correction_S","free_energy_correction_SC",
                         "free_energy_correction_TI"]
-        renorm_thermal_data = {key: [] for key in thermal_keys}
+        TD_thermal_data = {key: [] for key in thermal_keys}
         for key in thermal_keys:
-            renorm_thermal_data[key].append(renorm_data[key])
+            TD_thermal_data[key].append(TD_data[key])
         
-        logger.info("DEBUG: ",renorm_data)
-        if renorm_data["n_imaginary"] > 0:
-            logger.warning('Imaginary modes remain for {} K!'.format(temperature))
-            logger.warning('ShengBTE files not written')
-            logger.warning('No renormalization with thermal expansion')
+        logger.info("DEBUG: ",TD_data)
+        if TD_data["n_imaginary"] > 0:
+            logger.warning('Imaginary modes remain still exist')
+            logger.warning('ShengBTE FORCE_CONSTANTS_2ND not written')
         else:
-            logger.info("No imaginary modes! Writing ShengBTE files")
-            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND".format(temperature), format="text")
+            logger.info("No imaginary modes! Writing ShengBTE FORCE_CONSTANTS_2ND...")
+            fcs_TD.write_to_phonopy("FORCE_CONSTANTS_2ND".format(temperature), format="text")
 
-        dumpfn(structure_data, "structure_data.json".format(temperature))
-        dumpfn(renorm_thermal_data, "renorm_thermal_data.json".format(temperature))
+        dumpfn(TD_structure_data, "structure_data.json")
+        dumpfn(TD_thermal_data, "thermal_data.json")
 
         
 @explicit_serialize
 class ForceConstantsToDb(FiretaskBase):
     """
     Add force constants, phonon band structure and density of states
-    to the database.
+    and thermal properties to the database.
 
     Assumes you are in a directory with the force constants, fitting
     data, and structure data written to files.
@@ -352,7 +358,6 @@ def run_task(self, fw_spec):
         db_file = env_chk(self.get("db_file"), fw_spec)
         mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
         renormalized = self.get("renormalized", False)
-        renorm_temperature = self.get("renorm_temperature", None)
         mesh_density = self.get("mesh_density", 100.0)
 
         structure_data = loadfn("structure_data.json")        
@@ -400,9 +405,9 @@ def run_task(self, fw_spec):
             logger.info("Finished inserting force constants and phonon data")
 
         else:
-            renorm_thermal_data = loadfn("renorm_thermal_data.json")
+            TD_thermal_data = loadfn("thermal_data.json")
             fcs = ForceConstants.read("force_constants.fcs")
-            T = renorm_thermal_data["temperature"]
+            T = TD_thermal_data["temperature"]
 
             dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
                 structure, supercell_matrix, fcs, mesh_density, mmdb
@@ -415,7 +420,7 @@ def run_task(self, fw_spec):
                 "structure": structure.as_dict(),
                 "supercell_matrix": supercell_matrix,
                 "supercell_structure": supercell_structure.as_dict(),
-                "thermal_data": renorm_thermal_data,
+                "thermal_data": TD_thermal_data,
                 "force_constants_fs_id": fc_fsid,
                 "phonon_dos_fs_id": dos_fsid,
                 "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
diff --git a/atomate/vasp/workflows/base/lattice_dynamics.py b/atomate/vasp/workflows/base/lattice_dynamics.py
index dab868dc6..1aa1568a4 100644
--- a/atomate/vasp/workflows/base/lattice_dynamics.py
+++ b/atomate/vasp/workflows/base/lattice_dynamics.py
@@ -339,10 +339,10 @@ def get_perturbed_structure_wf(
         vasp_input_set = MPStaticSet(structure)
 
     # find the smallest nearest neighbor distance taking into account PBC
-    min_distance = np.min(
-        [n.nn_distance for d in structure.get_all_neighbors(10) for n in d]
-    )
-    scaled_min_distance = min_distance * min_nn_scale
+#    min_distance = np.min(
+#        [n.nn_distance for d in structure.get_all_neighbors(10) for n in d]
+#    )
+#    scaled_min_distance = min_distance * min_nn_scale
     all_rattle_stds = np.repeat(rattle_stds, n_configs_per_std)
 
     logger.debug("Using supercell_matrix of: {}".format(supercell_matrix))

From 72c74cac6566c175d3c3c056362b6234691bfa25 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 4 Mar 2024 20:35:05 -0800
Subject: [PATCH 185/207] parse_output (fix conflicts and cleanup)

---
 atomate/vasp/firetasks/parse_outputs.py | 71 +------------------------
 1 file changed, 1 insertion(+), 70 deletions(-)

diff --git a/atomate/vasp/firetasks/parse_outputs.py b/atomate/vasp/firetasks/parse_outputs.py
index 1efb2b28c..a8b423401 100644
--- a/atomate/vasp/firetasks/parse_outputs.py
+++ b/atomate/vasp/firetasks/parse_outputs.py
@@ -1,8 +1,3 @@
-<<<<<<< HEAD
-=======
-# coding: utf-8
-
->>>>>>> 7a7f01df (Remove old firetasks)
 import json
 import os
 import re
@@ -10,28 +5,11 @@
 from datetime import datetime
 
 import numpy as np
-<<<<<<< HEAD
-=======
-
-from monty.json import MontyEncoder, jsanitize
-from pydash.objects import has, get
-
-from atomate.vasp.config import DEFUSE_UNSUCCESSFUL
->>>>>>> 816883c7 (Cleaned up code (made functions for CSLD firetask, adhered to PEP guidelines, etc.))
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 from fireworks.utilities.fw_serializers import DATETIME_HANDLER
-<<<<<<< HEAD
-<<<<<<< HEAD
 from monty.json import MontyEncoder, jsanitize
 from monty.os.path import zpath
 from pydash.objects import get, has
-=======
-from fireworks import Firework
-=======
->>>>>>> 7a7f01df (Remove old firetasks)
-
-from pymatgen import Structure
->>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
 from pymatgen.analysis.elasticity.elastic import ElasticTensor, ElasticTensorExpansion
 from pymatgen.analysis.elasticity.strain import Deformation, Strain
 from pymatgen.analysis.elasticity.stress import Stress
@@ -50,36 +28,12 @@
 from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer
 from pymatgen.io.vasp.sets import get_vasprun_outcar
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-<<<<<<< HEAD
-=======
-from pymatgen.analysis.ferroelectricity.polarization import Polarization, get_total_ionic_dipole, \
-    EnergyTrend
-from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering, magnetic_deformation
-from pymatgen.command_line.bader_caller import bader_analysis_from_path
-<<<<<<< HEAD
-from pymatgen.io.vasp.sets import MPStaticSet
->>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
-=======
->>>>>>> 7a7f01df (Remove old firetasks)
 
 from atomate.common.firetasks.glue_tasks import get_calc_loc
 from atomate.utils.utils import env_chk, get_logger, get_meta_from_structure
-from atomate.vasp.config import DEFUSE_UNSUCCESSFUL, STORE_VOLUMETRIC_DATA
+from atomate.vasp.config import DEFUSE_UNSUCCESSFUL, STORE_VOLUMETRIC_DATA, STORE_BADER
 from atomate.vasp.database import VaspCalcDb
-<<<<<<< HEAD
-<<<<<<< HEAD
 from atomate.vasp.drones import BADER_EXE_EXISTS, VaspDrone
-=======
-from atomate.vasp.drones import VaspDrone
-<<<<<<< HEAD
-from atomate.vasp.fireworks.core import StaticFW
->>>>>>> 9a28c322 (Added dynamic fireworks for possible error handling (i.e. larger displacement values))
-=======
->>>>>>> fd3cc888 (Added fw_spec updates to all dynamically added fireworks and wrote a ShengBTE firetask)
-=======
-from atomate.vasp.drones import VaspDrone, BADER_EXE_EXISTS
-from atomate.vasp.config import STORE_VOLUMETRIC_DATA, STORE_BADER
->>>>>>> 13ec960c (VASP runs successfully)
 
 __author__ = "Anubhav Jain, Kiran Mathew, Shyam Dwaraknath"
 __email__ = "ajain@lbl.gov, kmathew@lbl.gov, shyamd@lbl.gov"
@@ -123,7 +77,6 @@ class VaspToDb(FiretaskBase):
             Format: {key : path} -> fw.spec[key] = task_doc[path]
             The path is a full mongo-style path so subdocuments can be referenced
             using dot notation and array keys can be referenced using the index.
-<<<<<<< HEAD
             E.g "calcs_reversed.0.output.outcar.run_stats"
     """
 
@@ -143,17 +96,6 @@ class VaspToDb(FiretaskBase):
         "parse_bader",
         "store_volumetric_data",
     ]
-=======
-            E.g "calcs_reversed.0.output.outar.run_stats"
-        vasp_drone_params (dict): Additional keyword arguments to pass to the
-            VaspDrone.
-    """
-    optional_params = ["calc_dir", "calc_loc", "parse_dos", "bandstructure_mode",
-                       "additional_fields", "db_file", "fw_spec_field", "defuse_unsuccessful",
-                       "task_fields_to_push", "parse_chgcar", "parse_aeccar",
-                       "parse_potcar_file",
-                       "store_volumetric_data", "vasp_drone_params"]
->>>>>>> cf160919 (Tweak VaspToDb params)
 
     def run_task(self, fw_spec):
         # get the directory that contains the VASP dir to parse
@@ -166,7 +108,6 @@ def run_task(self, fw_spec):
         # parse the VASP directory
         logger.info(f"PARSING DIRECTORY: {calc_dir}")
 
-<<<<<<< HEAD
         drone = VaspDrone(
             additional_fields=self.get("additional_fields"),
             parse_dos=self.get("parse_dos", False),
@@ -179,16 +120,6 @@ def run_task(self, fw_spec):
                 "store_volumetric_data", STORE_VOLUMETRIC_DATA
             ),
         )
-=======
-        drone = VaspDrone(additional_fields=self.get("additional_fields"),
-                          parse_dos=self.get("parse_dos", False),
-                          parse_potcar_file=self.get("parse_potcar_file", True),
-                          bandstructure_mode=self.get("bandstructure_mode", False),
-                          parse_chgcar=self.get("parse_chgcar", False),  # deprecated
-                          parse_aeccar=self.get("parse_aeccar", False),  # deprecated
-                          store_volumetric_data=self.get("store_volumetric_data", STORE_VOLUMETRIC_DATA),
-                          **self.get("vasp_drone_params", {}))
->>>>>>> cf160919 (Tweak VaspToDb params)
 
         # assimilate (i.e., parse)
         task_doc = drone.assimilate(calc_dir)

From 2b733377b7b7cf326638a6d7691e5c4908d3a513 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 4 Mar 2024 21:05:44 -0800
Subject: [PATCH 186/207] cleanup imports

---
 atomate/vasp/firetasks/run_calc.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/atomate/vasp/firetasks/run_calc.py b/atomate/vasp/firetasks/run_calc.py
index 1eb017431..9b771c221 100644
--- a/atomate/vasp/firetasks/run_calc.py
+++ b/atomate/vasp/firetasks/run_calc.py
@@ -10,14 +10,7 @@
 from custodian import Custodian
 from custodian.vasp.handlers import (
     AliasingErrorHandler,
-<<<<<<< HEAD
     DriftErrorHandler,
-=======
-    MeshSymmetryErrorHandler,
-    UnconvergedErrorHandler,
-#    MaxForceErrorHandler,
-    PotimErrorHandler,
->>>>>>> c012f5fb (ARC AIMD)
     FrozenJobErrorHandler,
     IncorrectSmearingHandler,
     LargeSigmaHandler,

From b8d024668deba812c39f0eaeb641931075778404 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 16:19:28 -0800
Subject: [PATCH 187/207] remove aimd wf

---
 atomate/common/powerups.py             |  38 ------
 atomate/vasp/fireworks/core.py         |  82 -------------
 atomate/vasp/workflows/base/aimd.py    | 162 -------------------------
 atomate/vasp/workflows/presets/core.py | 110 +----------------
 4 files changed, 2 insertions(+), 390 deletions(-)
 delete mode 100644 atomate/vasp/workflows/base/aimd.py

diff --git a/atomate/common/powerups.py b/atomate/common/powerups.py
index f9658f89f..d76db63b5 100644
--- a/atomate/common/powerups.py
+++ b/atomate/common/powerups.py
@@ -1,4 +1,3 @@
-<<<<<<< HEAD
 """
 This module defines general powerups that can be used for all workflows
 """
@@ -319,40 +318,3 @@ def powerup_by_kwargs(
         if not found:
             raise RuntimeError(f"Could not find powerup {name}.")
     return original_wf
-=======
-from typing import Dict, Any, Optional
-
-from fireworks import Workflow
-from atomate.utils.utils import get_fws_and_tasks
-
-
-def update_firetask(
-    original_wf: Workflow,
-    update_params: Dict[str, Any],
-    task_name_constraint: str,
-    fw_name_constraint: Optional[str] = None,
-) -> Workflow:
-    """
-    General powerup for arbitrary updates to a Firetask.
-
-    Args:
-        original_wf: The original workflow.
-        update_params: A dictionary of the keyword arguments to update.
-        task_name_constraint: Only apply changes to the Firetasks where the
-            Firetask class name contains this string.
-        fw_name_constraint: Only apply changes to Fireworks where the Firework
-            name contains this substring.
-
-    Returns:
-       Workflow
-    """
-    idx_list = get_fws_and_tasks(
-        original_wf,
-        fw_name_constraint=fw_name_constraint,
-        task_name_constraint=task_name_constraint,
-    )
-    for idx_fw, idx_t in idx_list:
-        original_wf.fws[idx_fw].tasks[idx_t].update(update_params)
-
-    return original_wf
->>>>>>> bd235a73 (Add powerup for updating any firetask)
diff --git a/atomate/vasp/fireworks/core.py b/atomate/vasp/fireworks/core.py
index 373635e30..7292a64dc 100644
--- a/atomate/vasp/fireworks/core.py
+++ b/atomate/vasp/fireworks/core.py
@@ -64,10 +64,6 @@ def __init__(
         db_file=DB_FILE,
         force_gamma=True,
         job_type="double_relaxation_run",
-<<<<<<< HEAD
-=======
-#        max_force_threshold=RELAX_MAX_FORCE,
->>>>>>> c012f5fb (ARC AIMD)
         auto_npar=">>auto_npar<<",
         half_kpts_first_relax=HALF_KPOINTS_FIRST_RELAX,
         parents=None,
@@ -103,13 +99,8 @@ def __init__(
             and job_type == "double_relaxation"
         ):
             warnings.warn(
-<<<<<<< HEAD
                 f"A double relaxation run might not be appropriate with ISIF {vasp_input_set.incar['ISIF']}"
             )
-=======
-                "A double relaxation run might not be appropriate with ISIF {}".format(
-                    vasp_input_set.incar["ISIF"]))
->>>>>>> 23b88a18 (Tidy docstrings)
 
         t = []
         t.append(WriteVaspFromIOSet(structure=structure, vasp_input_set=vasp_input_set))
@@ -117,10 +108,6 @@ def __init__(
             RunVaspCustodian(
                 vasp_cmd=vasp_cmd,
                 job_type=job_type,
-<<<<<<< HEAD
-=======
-#                max_force_threshold=max_force_threshold,
->>>>>>> c012f5fb (ARC AIMD)
                 ediffg=ediffg,
                 auto_npar=auto_npar,
                 half_kpts_first_relax=half_kpts_first_relax,
@@ -153,26 +140,11 @@ def __init__(
         **kwargs,
     ):
         """
-<<<<<<< HEAD
         Structure optimization using the SCAN metaGGA functional. If this Firework is
         initialized with no parents, it will perform a GGA optimization of the provided
         structure using the PBESol functional. This GGA-relaxed structure is intended
         to be passed to a second instance of this Firework for optimization with SCAN.
         (see workflow definition in metagga_optimization.yaml)
-=======
-        Structure optimization using the SCAN metaGGA functional.
-
-        This workflow performs a 3-step optmization. The first step ('relax1')
-        is a conventional GGA run relaxation that initializes the geometry and
-        calculates the bandgap of the structure. The bandgap is used to update
-        the KSPACING parameter, which sets the appropriate number of k-points
-        for the structure. The second step ('.relax2') is a static GGA
-        calculation that computes wavefunctions using the updated number of
-        k-points. The third step ('relax3') is a SCAN relaxation.
-
-        By default, .relax1 and .relax2 are force converged with
-        EDIFFG = -0.05, and .relax3 is force converged with EDIFFG=-0.02.
->>>>>>> 23b88a18 (Tidy docstrings)
 
         Args:
             structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
@@ -216,7 +188,6 @@ def __init__(
                  is not supported by this InputSet."
             )
 
-<<<<<<< HEAD
         if prev_calc_dir:
             has_previous_calc = True
             # Copy the CHGCAR from previous calc directory (usually PBE)
@@ -247,59 +218,6 @@ def __init__(
             raise UserWarning(
                 "You specified prev_calc_loc but did not provide a parent Firework. Set "
                 "parents and try again."
-=======
-        t = []
-        # write the VASP input files based on MPScanRelaxSet
-        t.append(WriteVaspFromIOSet(structure=structure,
-                                    vasp_input_set=orig_input_set
-                                    )
-                 )
-
-        # pass the CalcLoc so that CopyFilesFromCalcLoc can find the directory
-        t.append(PassCalcLocs(name=name))
-
-        # Copy the pre-compiled VdW kernel for VASP, if required
-        if orig_input_set.vdw is not None:
-            t.append(CopyFiles(from_dir=vdw_kernel_dir))
-
-        # Copy original inputs with the ".orig" suffix
-        t.append(
-            CopyFilesFromCalcLoc(
-                calc_loc=True,
-                name_append=".orig",
-                exclude_files=["vdw_kernel.bindat", "FW.json", "FW--*"],
-            )
-        )
-
-        # Update the INCAR for the GGA preconditioning step
-        # Disable writing the WAVECAR because the no. of k-points will likely
-        # change before the next step in the calculation
-        pre_opt_settings = {"_set": {"METAGGA": None,
-                                     "EDIFFG": -0.05,
-                                     "LWAVE": False}}
-
-        # Disable vdW for the precondition step
-        if orig_input_set.incar.get("LUSE_VDW", None):
-            pre_opt_settings.update({"_unset": {"LUSE_VDW": True,
-                                                "BPARAM": 15.7}})
-
-        t.append(ModifyIncar(incar_dictmod=pre_opt_settings))
-
-        # Run the GGA .relax1 step
-        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
-                                  job_type="normal_no_backup",
-                                  gzip_output=False
-                                  )
-                 )
-
-        # Copy GGA outputs with '.relax1' suffix
-        # by the subsequent UpdateScanRelaxBandgap Firetask
-        t.append(
-            CopyFilesFromCalcLoc(
-                calc_loc=True,
-                name_append=".relax1",
-                exclude_files=["vdw_kernel.bindat", "FW.json", "FW--*", "*.orig"],
->>>>>>> 23b88a18 (Tidy docstrings)
             )
 
         if has_previous_calc:
diff --git a/atomate/vasp/workflows/base/aimd.py b/atomate/vasp/workflows/base/aimd.py
deleted file mode 100644
index 096aea5e6..000000000
--- a/atomate/vasp/workflows/base/aimd.py
+++ /dev/null
@@ -1,162 +0,0 @@
-import math
-import warnings
-from copy import deepcopy
-from typing import Dict, List, Optional, Union
-import numpy as np
-from monty.serialization import loadfn, dumpfn
-
-from atomate.utils.utils import get_logger
-from atomate.vasp.config import DB_FILE, VASP_CMD
-from atomate.vasp.firetasks import pass_vasp_result
-from atomate.vasp.analysis.lattice_dynamics import (
-    FIT_METHOD,
-    MESH_DENSITY,
-)
-from atomate.vasp.fireworks.core import TransmuterFW, OptimizeFW
-from atomate.vasp.fireworks.aimd import ARCMDFW, CollectMDSegmentsFW
-from atomate.common.powerups import add_additional_fields_to_taskdocs
-from fireworks import Workflow
-from pymatgen.core.structure import Structure
-from pymatgen.io.vasp.sets import ARCMDSet, VaspInputSet
-from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.transformations.advanced_transformations import (
-    CubicSupercellTransformation,
-)
-
-__author__ = "Junsoo Park"
-__email__ = "junsoo.park@nasa.gov"
-__date__ = "December 2023"
-
-logger = get_logger(__name__)
-
-vasp_to_db_params = {
-    "store_volumetric_data": tuple(),
-    "vasp_drone_params": {"parse_bader": False, "parse_locpot": False}
-}
-
-_DEFAULT_SETTINGS = {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
-_WF_VERSION = 0.1
-
-
-def get_aimd_wf(
-    structure: Structure,
-    common_settings: Dict = None,
-    ensemble='NVT',
-    start_temp=start_temp,
-    end_temp=end_temp,
-    simulation_time = simulation_time,
-    time_step = time_step,
-    copy_vasp_outputs = True,
-    supercell_matrix_kwargs: Optional[dict] = None
-):
-    """
-    This workflow will perform AIMD on VASP,
-
-    Args:
-        structure: Initial structure.
-        common_settings: Common settings dict. Supports "VASP_CMD", "DB_FILE",
-            and "user_incar_settings" keys.
-        vasp_input_set: Vasp input set for perturbed structure calculations.
-        copy_vasp_outputs: Whether or not to copy previous vasp outputs.
-        supercell_matrix_kwargs: Options that control the size of the supercell.
-            Will be passed directly to CubicSupercellTransformation in
-            pymatgen.transformations.advanced_transformations. Note, a diagonal
-            supercell is required to calculate lattice thermal conductivity.
-        ensemble: NVT, NPT, etc.
-   """
-
-    parent_structure = structure.as_dict()
-    supercell_matrix_kwargs = supercell_matrix_kwargs or {}
-    common_settings = _get_common_settings(common_settings)
-    db_file = common_settings["DB_FILE"]
-
-    logger.debug('Transforming supercell!')
-    logger.debug('KWARGS: \n {}'.format(supercell_matrix_kwargs))
-    st = CubicSupercellTransformation(**supercell_matrix_kwargs)
-    supercell = st.apply_transformation(structure)
-    supercell_matrix = st.transformation_matrix
-    logger.debug('SUPERCELL MATRIX: \n {}'.format(supercell_matrix))
-
-    nsteps_total = ceil(simulation_time/time_step)
-    nsteps_each = 500
-    nfws = ceil(nsteps_total/nsteps_each)
-    parents=None
-
-    vasp_input_set = ARCMDSet(
-        structure=supercell,
-        ensemble=ensemble,
-        start_temp=start_temp,
-        end_temp=end_temp,
-        nsteps=nsteps_each,
-        time_step=time_step,
-        reciprocal_density=1,
-        small_gap_multiply=None
-    )
-    for ifw in range(nfws):
-        if ifw>0:
-            vasp_input_set.update()
-            parents = aimd_wf.fws[-1]
-            start_temp = end_temp
-
-        aimd_fw = ARCMDFW( start_structure,
-                        start_temp,
-                        end_temp,
-                        nsteps_fw,
-                        name="AIMD_segment_{}".format(ifw+1),
-                        vasp_input_set=vasp_input_set,
-                        vasp_cmd=VASP_CMD,
-                        wall_time=1080000,
-                        db_file=DB_FILE,
-                        parents=parents,
-                        copy_vasp_outputs=copy_vasp_outputs,
-                        override_default_vasp_params=None,
-                        **kwargs,)
-        pass_task = pass_vasp_result(
-            pass_dict={
-            "parent_structure": parent_structure,
-            "supercell_matrix": supercell_matrix,
-            "forces": ">>output.ionic_steps.:-1.forces",
-            "stress": ">>output.ionic_steps.:-1.stress",
-            "configurations": ">>output.ionic_steps.:-1.structure",
-            "final_configuration": ">>output.ionic_steps.-1.structure"
-            },
-            mod_spec_cmd="_push",
-            mod_spec_key="aimd",
-        )
-        aimd_fw.tasks.append(pass_task)
-        if ifw==0:
-            wf = Workflow.from_Firework(aimd_fw)
-        else:
-            wf.append_wf(Workflow.from_Firework(aimd_fw), wf.fws[-1].fw_id)
-
-    collect_fw = CollectMDSegmentsFW(
-        db_file=db_file,
-        parents=wf.fws[-nfws:]
-    )
-    wf.append_wf(
-            Workflow.from_Firework(collect_fw), [fw.fw_id for fw in wf.fws[-nfws:]]
-        )
-
-    # Add workflow metadata to all relevant *ToDb tasks.
-    wf_meta = {"wf_name": "AIMDWF", "wf_version": _WF_VERSION}
-    for task_name in ["VaspToDb"]:
-        wf = add_additional_fields_to_taskdocs(
-            wf, {"wf_meta": wf_meta}, task_name_constraint=task_name
-        )
-
-    return wf
-
-
-def _get_common_settings(common_settings: Optional[Dict]):
-    common_settings = common_settings or {}
-    for k, v in _DEFAULT_SETTINGS.items():
-        if k not in common_settings:
-            common_settings[k] = v
-
-    user_incar_settings = deepcopy(_aimd_user_incar_settings)
-    user_incar_settings.update(common_settings.get("user_incar_settings", {}))
-    common_settings["user_incar_settings"] = user_incar_settings
-
-    return common_settings
-
-
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 21c5ad522..0f8b5ec3b 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -1,23 +1,14 @@
-<<<<<<< HEAD
-from uuid import uuid4
-
-import numpy as np
-=======
-# coding: utf-8
 from typing import Optional
-
 from uuid import uuid4
-
 import numpy as np
 
 from atomate.vasp.workflows.base.lattice_dynamics import \
-    get_lattice_dynamics_wf, vasp_to_db_params
+    get_lattice_dynamics_wf, vasp_to_db_params 
+
 from fireworks import Workflow
 from pymatgen import Structure
 from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPHSERelaxSet
->>>>>>> 7cb526cb (Rewrite preset workflow)
 from pymatgen.io.vasp.inputs import Kpoints
-from pymatgen.io.vasp.sets import MPHSERelaxSet, MPRelaxSet, MPStaticSet
 
 from atomate.vasp.config import (
     ADD_WF_METADATA,
@@ -33,11 +24,8 @@
     add_stability_check,
     add_wf_metadata,
 )
-<<<<<<< HEAD
 from atomate.vasp.workflows.base.bulk_modulus import get_wf_bulk_modulus
-=======
 from atomate.vasp.analysis.lattice_dynamics import FIT_METHOD
->>>>>>> 0da85957 (small fix for cutoffs and fit_method)
 from atomate.vasp.workflows.base.core import get_wf
 from atomate.vasp.workflows.base.elastic import get_wf_elastic_constant
 from atomate.vasp.workflows.base.gibbs import get_wf_gibbs_free_energy
@@ -337,7 +325,6 @@ def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False):
 
     uis_optimize = {"ENCUT": 700, "EDIFF": 1e-6, "LAECHG": False, "LREAL": False}
     if order > 2:
-<<<<<<< HEAD
         uis_optimize.update(
             {
                 "EDIFF": 1e-10,
@@ -347,10 +334,6 @@ def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False):
                 "ISYM": 0,
             }
         )
-=======
-        uis_optimize.update({"EDIFF": 1e-8, "EDIFFG": -0.001,
-                             "ADDGRID": True, "LREAL": False, "ISYM": 0})
->>>>>>> 16220e12 (Tweak lattice dynamics settings)
         # This ensures a consistent k-point mesh across all calculations
         # We also turn off symmetry to prevent VASP from changing the
         # mesh internally
@@ -855,12 +838,6 @@ def wf_nudged_elastic_band(structures, parent, c=None):
 def wf_lattice_dynamics(
     structure: Structure,
     fit_method: str = FIT_METHOD,
-<<<<<<< HEAD
-=======
-    fit_method: str = False,
->>>>>>> 2e30eb4a (remove separate_fit)
-=======
->>>>>>> ac887694 (clean-up)
     disp_cut: float = None,
     bulk_modulus: float = None,
     c: Optional[dict] = None,
@@ -949,86 +926,3 @@ def wf_lattice_dynamics(
         wf = add_wf_metadata(wf, structure)
 
     return wf
-
-
-def wf_aimd(
-    structure: Structure,
-    c: Optional[dict] = None,
-    supercell_matrix_kwargs: Optional[dict] = None,
-    num_supercell_kwargs: Optional[dict] = None,
-    ensemble='NVT',
-    simulation_time=10000,
-    time_step=2,
-    **aimd_kwargs
-) -> Workflow:
-    """
-    Get a workflow to run AIMD on vasp, preceded by a structure optimization.
-
-    Args:
-        structure: The input structure.
-        c: Workflow common settings dict. Supports the keys: "VASP_CMD",
-            "DB_FILE", and "user_incar_settings", "ADD_WF_METADATA", and the
-            options supported by "add_common_powerups".
-        **aimd_kwargs: Keyword arguments to be passed directly to the AIMD base workflow.
-
-    Returns:
-        A workflow to perform AIMD.
-    """
-
-    # start with defining the relaxation workflow
-    optimize_uis = {
-        "LAECHG": False,
-        'ENCUT': 600,
-        'ADDGRID': True,
-        'EDIFF': 1e-8,
-        'EDIFFG': -5e-4,
-        'PREC': 'Accurate',
-        "LREAL": False,
-        'LASPH': True,
-        'ISPIN': 2,
-        'ISMEAR': 0,
-        'SIGMA': 0.1,
-        'LCHARG': False,
-        'LWAVE': False
-    }
-    c = c if c is not None else {}
-    if "USER_INCAR_SETTINGS" not in c:
-        c["USER_INCAR_SETTINGS"] = {}
-
-    # wf_structure_optimization expects user incar settings in capitals
-    c["USER_INCAR_SETTINGS"].update(optimize_uis)
-    c["USER_INCAR_SETTINGS"].update(c.get("user_incar_settings", {}))
-    wf = wf_structure_optimization(structure, c=c)
-
-    # don't store CHGCAR and other volumetric data in the VASP drone
-    for task in wf.fws[0].tasks:
-        if "VaspToDb" in str(task):
-            task.update(vasp_to_db_params)
-
-    # Define AIMD workflow
-    wf_aimd = get_aimd_wf(
-        structure,
-        common_settings=c,
-        ensemble=ensemble,
-        start_temp=start_temp,
-        end_temp=end_temp,
-        simulation_time=simulation_time,
-        time_step=time_step,
-        copy_vasp_outputs = True,
-        supercell_matrix_kwargs=supercell_matrix_kwargs,
-        **aimd_kwargs
-    )
-
-    # join the workflows
-    wf.append_wf(wf_aimd, wf.leaf_fw_ids)
-
-    formula = structure.composition.reduced_formula
-    wf_name = "{} AIMD - {} - {}K".format(formula,ensemble,end_temp)
-    wf.name = wf_name
-
-    wf = add_common_powerups(wf, c)
-    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
-        wf = add_wf_metadata(wf, structure)
-
-    return wf
-

From 743666efa77dfeb6a03d31b440d2e1f2bbb5b56e Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 18:05:45 -0800
Subject: [PATCH 188/207] Update fixes

---
 atomate/vasp/analysis/lattice_dynamics.py | 173 +---------------------
 1 file changed, 6 insertions(+), 167 deletions(-)

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index fce785f11..c86dbe9fb 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -1,5 +1,6 @@
 from itertools import product
-from typing import Dict, List, Tuple
+from joblib import Parallel, delayed
+from typing import Dict, List, Tuple, Optional
 
 import numpy as np
 import scipy as sp
@@ -8,20 +9,11 @@
 from copy import copy
 
 from atomate.utils.utils import get_logger
-<<<<<<< HEAD
-<<<<<<< HEAD
-from pymatgen import Structure
-=======
-=======
 
 from hiphive import (ForceConstants, ForceConstantPotential,
                      enforce_rotational_sum_rules, ClusterSpace,
                      StructureContainer)
-<<<<<<< HEAD
->>>>>>> 1e75a82a (imports)
-=======
 from hiphive.force_constant_model import ForceConstantModel
->>>>>>> 0d613579 (revert to structure container for fitting)
 from hiphive.cutoffs import is_cutoff_allowed, estimate_maximum_cutoff
 from hiphive.fitting import Optimizer
 from hiphive.renormalization import Renormalization
@@ -30,7 +22,6 @@
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.ase import AseAtomsAdaptor
->>>>>>> 8f4f7e37 (gruneisen and CTE)
 from pymatgen.io.phonopy import get_phonopy_structure
 
 from ase.atoms import Atoms
@@ -40,8 +31,8 @@
 from phono3py.phonon3.gruneisen import Gruneisen
 
 
-__author__ = "Alex Ganose, Rees Chang, Junsoo Park"
-__email__ = "aganose@lbl.gov, rc564@cornell.edu, jsyony37@lbl.gov"
+__author__ = "Alex Ganose, Rees Chang, Junsoo Park, Zhuoying Zhu"
+__email__ = "aganose@lbl.gov, rc564@cornell.edu, jsyony37@lbl.gov, zyzhu@lbl.gov"
 
 logger = get_logger(__name__)
 
@@ -69,11 +60,7 @@
 
 def get_cutoffs(structure: Structure):
     """
-<<<<<<< HEAD
-    Get a list of trial cutoffs based on a structure.
-=======
     Get a list of trial cutoffs based on a supercell structure for grid search.
->>>>>>> b637d9a8 (update)
 
     An initial guess for the lower bound of the cutoffs is made based on the
     average period (row) of the elements in the structure, according to:
@@ -99,15 +86,9 @@ def get_cutoffs(structure: Structure):
     ====== ==== =====
     Cutoff Max  Step
     ====== ==== =====
-<<<<<<< HEAD
-    2ND    +3.0 0.5
-    3RD    +1.5 0.25
-    4TH    +1.0 0.25
-=======
     2ND    +2.0 1.0
     3RD    +1.5 0.75
     4TH    +0.6 0.6
->>>>>>> b637d9a8 (update)
     ====== ==== =====
 
     Args:
@@ -123,28 +104,11 @@ def get_cutoffs(structure: Structure):
         3: {1: 3.0, 2: 3.5, 3: 4.5, 4: 5.5, 5: 6.0, 6: 6.5, 7: 7.0},
         4: {1: 2.5, 2: 3.0, 3: 3.5, 4: 4.0, 5: 4.5, 6: 5.0, 7: 5.5},
     }
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-    inc = {2: 3, 3: 1.5, 4: 1}
-    steps = {2: 0.5, 3: 0.25, 4: 0.25}
-
-    row = min([s.row for s in structure.species])
-=======
-    inc = {2: 2, 3: 1, 4: 0.5}
-    steps = {2: 1, 3: 0.5, 4: 0.5}
-=======
-    inc = {2: 2, 3: 1.5, 4: 0.5}
-    steps = {2: 1, 3: 0.75, 4: 0.5}
->>>>>>> c69d0316 (fixed cutoff)
-=======
     inc = {2: 2, 3: 1.5, 4: 0.6}
     steps = {2: 1, 3: 0.75, 4: 0.6}
->>>>>>> b637d9a8 (update)
 
     row = int(np.around(np.array([s.row for s in supercell_structure.species]).mean(),0))
     factor = row/4
->>>>>>> cc7520c5 (separate fitting)
     mins = {
         2: min_cutoffs[2][row], 3: min_cutoffs[3][row], 4: min_cutoffs[4][row]
     }
@@ -153,9 +117,6 @@ def get_cutoffs(structure: Structure):
     range_three = np.arange(mins[3], mins[3] + factor*(inc[3]+steps[3]), factor*steps[3])
     range_four = np.arange(mins[4], mins[4] + factor*(inc[4]+steps[4]), factor*steps[4])
 
-<<<<<<< HEAD
-    return list(map(list, product(range_two, range_three, range_four)))
-=======
     cutoffs = np.array(list(map(list, product(range_two, range_three, range_four))))
     max_cutoff = estimate_maximum_cutoff(AseAtomsAdaptor.get_atoms(supercell_structure))
     cutoffs[cutoffs>max_cutoff] = max_cutoff-0.2
@@ -164,7 +125,6 @@ def get_cutoffs(structure: Structure):
     good_cutoffs = np.all(cutoffs < max_cutoff-0.1, axis=1)
     logger.info('GOOD CUTOFFS \n{}'.format(good_cutoffs))
     return cutoffs[good_cutoffs].tolist()
->>>>>>> c094a175 (cutoff vs cell_size)
 
 
 def fit_force_constants(
@@ -175,13 +135,9 @@ def fit_force_constants(
     disp_cut: float = 0.055,
     imaginary_tol: float = IMAGINARY_TOL,
     fit_method: str = FIT_METHOD,
-<<<<<<< HEAD
-) -> Tuple["SortedForceConstants", Dict]:
-=======
     n_jobs: int = -1,
     fit_kwargs: Optional[Dict] = None
 ) -> Tuple["SortedForceConstants", np.ndarray, ClusterSpace, Dict]:
->>>>>>> fddd9681 (get_cutoffs)
     """
     Fit force constants using hiphive and select the optimum cutoff values.
 
@@ -220,14 +176,7 @@ def fit_force_constants(
         ``SortedForceConstants`` object, array of parameters, cluster space,
         and a dictionary of information on the fitting results.
     """
-<<<<<<< HEAD
-    from hiphive.fitting import Optimizer
-    from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
-
-    logger.info("Starting fitting force constants.")
-=======
     logger.info("Starting force constant fitting.")
->>>>>>> 8f4f7e37 (gruneisen and CTE)
 
     fitting_data = {
         "cutoffs": [],
@@ -242,20 +191,13 @@ def fit_force_constants(
 
     best_fit = {
         "n_imaginary": np.inf,
-<<<<<<< HEAD
-        "free_energy": np.inf,
-=======
         "rmse_test": np.inf,
         "cluster_space": None,
->>>>>>> cd00c732 (cluster_space to best_fit)
         "force_constants": None,
         "parameters":None,
         "cutoffs": None,
     }
     n_cutoffs = len(all_cutoffs)
-<<<<<<< HEAD
-    for i, cutoffs in enumerate(all_cutoffs):
-=======
 
     fit_kwargs = fit_kwargs if fit_kwargs else {}
     if fit_method == "rfe" and n_jobs == -1:
@@ -374,48 +316,15 @@ def _run_cutoffs(
     supercell_atoms = structures[0]
 
     if not is_cutoff_allowed(supercell_atoms, max(cutoffs)):
->>>>>>> 8f4f7e37 (gruneisen and CTE)
         logger.info(
-            "Testing cutoffs {} out of {}: {}".format(i, n_cutoffs, cutoffs)
+            "Skipping cutoff due as it is not commensurate with supercell size"
         )
-<<<<<<< HEAD
-        sc = get_structure_container(cutoffs, structures)
-<<<<<<< HEAD
-        opt = Optimizer(sc.get_fit_data(), fit_method)
-=======
-        logger.info('{}, {}: FINE UNTIL SC'.format(i,cutoffs))
-        opt = Optimizer(sc.get_fit_data(), fit_method, **fit_kwargs)
-        logger.info('{}, {}: FINE UNTIL OPT'.format(i,cutoffs))
->>>>>>> fddd9681 (get_cutoffs)
-=======
         return None
 
     cs = ClusterSpace(supercell_atoms, cutoffs, symprec=1e-3, acoustic_sum_rules=True)
     logger.debug(cs.__repr__())
     n2nd = cs.get_n_dofs_by_order(2)
     nall = cs.n_dofs
-<<<<<<< HEAD
-    
-    if separate_fit:
-        logger.info('Fitting harmonic force constants separately')
-#        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
-#                                disp_cut, ncut=n2nd, param2=None)
-        sc = get_structure_container(cs, structures, separate_fit, disp_cut,
-                                     ncut=n2nd, param2=None)
-        opt = Optimizer(sc.get_fit_data(),
-                        fit_method,
-                        [0,n2nd],
-                        **fit_kwargs)
-<<<<<<< HEAD
-        logger.info('Optimizer set up for cutoff: {}, {}'.format(i,cutoffs))
->>>>>>> 79348b89 (bulk_mod input)
-=======
->>>>>>> cc7520c5 (separate fitting)
-        opt.train()
-        param_harmonic = opt.parameters # harmonic force constant parameters
-        
-        logger.info('Fitting anharmonic force constants separately')
-=======
 
     logger.info('Fitting harmonic force constants separately')
     separate_fit = True
@@ -446,7 +355,6 @@ def _run_cutoffs(
 
     if imaginary:
         logger.info('Imaginary modes found! Fitting anharmonic force constants separately')
->>>>>>> 2e30eb4a (remove separate_fit)
 #        fit_data = get_fit_data(cs, supercell_atoms, structures, separate_fit,
 #                                disp_cut, ncut=n2nd, param2=param_harmonic)
         sc = get_structure_container(cs, structures, separate_fit, disp_cut,
@@ -457,75 +365,7 @@ def _run_cutoffs(
                         **fit_kwargs)
         opt.train()
         param_anharmonic = opt.parameters # anharmonic force constant parameters
-
-<<<<<<< HEAD
-        parameters = enforce_rotational_sum_rules(
-            sc.cluster_space, opt.parameters, ["Huang", "Born-Huang"]
-        )
-        fcp = ForceConstantPotential(sc.cluster_space, parameters)
-        fcs = fcp.get_force_constants(supercell_atoms)
-        logger.info('FCS generated for cutoff {}, {}'.format(i,cutoffs))
-        n_imaginary, min_freq, free_energy, entropy, Cv, grun, cte, dLfrac = evaluate_force_constants(
-            parent_structure, supercell_matrix, fcs, bulk_modulus, T_QHA, imaginary_tol
-        )
-<<<<<<< HEAD
-<<<<<<< HEAD
-<<<<<<< HEAD
-
-        fitting_data["cutoffs"].append(cutoffs)
-        fitting_data["rmse_test"].append(opt.rmse_test)
-        fitting_data["n_imaginary"].append(n_imaginary)
-        fitting_data["min_frequency"].append(min_freq)
-        fitting_data["300K_free_energy"].append(free_energy)
-
-        if (
-            min_freq > -np.abs(max_imaginary_freq)
-            and n_imaginary <= max_n_imaginary
-            and n_imaginary < best_fit["n_imaginary"]
-            and free_energy < best_fit["free_energy"]
-        ):
-            best_fit.update(
-                {
-                    "n_imaginary": n_imaginary,
-                    "free_energy": free_energy,
-                    "force_constants": fcs,
-                    "cutoffs": cutoffs,
-                }
-            )
-            fitting_data["best"] = cutoffs
-
-    logger.info("Finished fitting force constants.")
-
-    return best_fit["force_constants"], fitting_data
-=======
-=======
-        logger.info('evaluate_force_constants success!')
->>>>>>> fddd9681 (get_cutoffs)
-=======
-        logger.info('evaluate_force_constants success: {}, {}'.format(i,cutoffs))
->>>>>>> 79348b89 (bulk_mod input)
-        return {
-            "cutoffs": cutoffs,
-            "rmse_test": opt.rmse_test,
-            "n_imaginary": n_imaginary,
-            "min_frequency": min_freq,
-            "temperature": T_QHA,
-            "free_energy": free_energy,
-            "entropy": entropy,
-            "heat_capacity": Cv,
-            "thermal_expansion": cte,
-            "cluster_space": sc.cluster_space,
-            "parameters": parameters,
-            "force_constants": fcs
-        }
-    except Exception:
-        return None
->>>>>>> 8f4f7e37 (gruneisen and CTE)
-
-
-def get_structure_container(
-    cutoffs: List[float], structures: List["Atoms"]
-=======
+        
         parameters = np.concatenate((param_harmonic,param_anharmonic)) # combine 
         assert(nall==len(parameters))
         logger.info('Training complete for cutoff: {}, {}'.format(i,cutoffs))
@@ -572,7 +412,6 @@ def get_structure_container(
         disp_cut: float,
         ncut: int,
         param2: np.ndarray
->>>>>>> cc7520c5 (separate fitting)
 ) -> "StructureContainer":
     """
     Get a hiPhive StructureContainer from cutoffs and a list of atoms objects.

From 78bec862424dae83d2b40c5e07c77de366ea9f77 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 18:42:57 -0800
Subject: [PATCH 189/207] remove requirements.txt

---
 atomate/vasp/analysis/lattice_dynamics.py |  3 +--
 requirements-optional.txt                 |  2 --
 requirements.txt                          | 16 ----------------
 setup.py                                  |  1 +
 4 files changed, 2 insertions(+), 20 deletions(-)
 delete mode 100644 requirements-optional.txt
 delete mode 100644 requirements.txt

diff --git a/atomate/vasp/analysis/lattice_dynamics.py b/atomate/vasp/analysis/lattice_dynamics.py
index c86dbe9fb..9489d3a0c 100644
--- a/atomate/vasp/analysis/lattice_dynamics.py
+++ b/atomate/vasp/analysis/lattice_dynamics.py
@@ -404,7 +404,6 @@ def _run_cutoffs(
     except Exception:
         return None
 
-
 def get_structure_container(
         cs: ClusterSpace,
         structures: List["Atoms"],
@@ -820,4 +819,4 @@ def setup_TE_renorm(cs,cutoffs,parent_atoms,supercell_atoms,param,dLfrac):
                                        scaled_positions=parent_atoms_TE.get_scaled_positions(),
                                        cell=parent_atoms_TE.cell)
         phonopy_TE = Phonopy(prim_TE_phonopy, supercell_matrix=scmat, primitive_matrix=None)
-        return parent_structure_TE, supercell_structure_TE, cs_TE, phonopy_TE, fcs_TE, failed
+        return parent_structure_TE, supercell_structure_TE, cs_TE, phonopy_TE, fcs_TE, failed
\ No newline at end of file
diff --git a/requirements-optional.txt b/requirements-optional.txt
deleted file mode 100644
index 8218f9e81..000000000
--- a/requirements-optional.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-f90nml==1.1.2
-ase==3.19.0
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index a8b26d3e4..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-numpy==1.16.4
-scipy==1.2.0
-FireWorks==1.9.0
-pymatgen_diffusion==2019.2.28
-monty==2.0.4
-paramiko==2.4.2
-tqdm==4.32.1
-six==1.12.0
-pybtex==0.22.2
-ruamel.yaml==0.15.96
-pandas==0.24.2
-pymatgen==2019.5.8
-custodian==2019.2.10
-networkx==2.2
-pydash==4.7.4
-pymongo==3.10.1
diff --git a/setup.py b/setup.py
index 1f028bae2..5b050a0ce 100644
--- a/setup.py
+++ b/setup.py
@@ -46,6 +46,7 @@
             "phonons": ["phonopy>=1.10.8"],
             "qchem": ["openbabel-wheel"],
             "defects": ["pymatgen-analysis-defects"],
+            "hiphive": ["hiphive","phono3py","ase>=3.19.0"]
             "complete": [
                 "matplotlib>=1.5.2",
                 "phonopy>=1.10.8",

From affcb2650f28409bec6eee4809ea020a268f7e03 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 18:48:12 -0800
Subject: [PATCH 190/207] install dependencies

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 5b050a0ce..f1a95da42 100644
--- a/setup.py
+++ b/setup.py
@@ -46,7 +46,7 @@
             "phonons": ["phonopy>=1.10.8"],
             "qchem": ["openbabel-wheel"],
             "defects": ["pymatgen-analysis-defects"],
-            "hiphive": ["hiphive","phono3py","ase>=3.19.0"]
+            "hiphive": ["hiphive","phono3py","ase>=3.19.0"],
             "complete": [
                 "matplotlib>=1.5.2",
                 "phonopy>=1.10.8",

From c5432bfcc93044b8a1e7ee0fc56e0d0b23a67ec6 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 18:59:23 -0800
Subject: [PATCH 191/207] add setup

---
 setup.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index f1a95da42..77acc3e54 100644
--- a/setup.py
+++ b/setup.py
@@ -46,11 +46,14 @@
             "phonons": ["phonopy>=1.10.8"],
             "qchem": ["openbabel-wheel"],
             "defects": ["pymatgen-analysis-defects"],
-            "hiphive": ["hiphive","phono3py","ase>=3.19.0"],
+            "hiphive": ["hiphive>=1.1","phono3py","ase>=3.19.0"],
             "complete": [
                 "matplotlib>=1.5.2",
                 "phonopy>=1.10.8",
                 "openbabel-wheel",
+                "hiphive>=1.1",
+                "phono3py",
+                "ase>=3.19.0",
                 "boto3>=1.28.15",
                 "Flask>=2.3.2",
                 "coverage>=7.2.7",

From 2026f42b51590bded18589f9d569ce53d8976fe6 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 19:26:12 -0800
Subject: [PATCH 192/207] update phono3py dependencies

---
 setup.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 77acc3e54..2d9b4c011 100644
--- a/setup.py
+++ b/setup.py
@@ -46,13 +46,15 @@
             "phonons": ["phonopy>=1.10.8"],
             "qchem": ["openbabel-wheel"],
             "defects": ["pymatgen-analysis-defects"],
-            "hiphive": ["hiphive>=1.1","phono3py","ase>=3.19.0"],
+            "hiphive": ["hiphive>=1.1","phono3py==2.3.2","ase>=3.19.0"],
             "complete": [
                 "matplotlib>=1.5.2",
                 "phonopy>=1.10.8",
                 "openbabel-wheel",
                 "hiphive>=1.1",
-                "phono3py",
+                "phono3py==2.3.2",
+                "cmake==3.22.4",
+                "spglib==1.16.5",
                 "ase>=3.19.0",
                 "boto3>=1.28.15",
                 "Flask>=2.3.2",

From 68124f647e27410509b3941cd218cbd069ed7408 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 20:04:54 -0800
Subject: [PATCH 193/207] install f90nml

---
 setup.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 2d9b4c011..a92256448 100644
--- a/setup.py
+++ b/setup.py
@@ -46,12 +46,13 @@
             "phonons": ["phonopy>=1.10.8"],
             "qchem": ["openbabel-wheel"],
             "defects": ["pymatgen-analysis-defects"],
-            "hiphive": ["hiphive>=1.1","phono3py==2.3.2","ase>=3.19.0"],
+            "hiphive": ["hiphive>=1.1","phono3py==2.3.2","f90nml==1.3.1","ase>=3.19.0"],
             "complete": [
                 "matplotlib>=1.5.2",
                 "phonopy>=1.10.8",
                 "openbabel-wheel",
                 "hiphive>=1.1",
+                "f90nml==1.3.1",
                 "phono3py==2.3.2",
                 "cmake==3.22.4",
                 "spglib==1.16.5",
@@ -77,5 +78,5 @@
             "Topic :: Other/Nonlisted Topic",
             "Topic :: Scientific/Engineering",
         ],
-        scripts=[join("scripts", f) for f in os.listdir(join(module_dir, "scripts"))],
+        scripts=[join("scripts", f) for f in os.listdir(join(module_dir, "scripts"))]
     )

From c6a5747523d143789b6c35b55bfcb95510f1b47d Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Tue, 5 Mar 2024 22:31:56 -0800
Subject: [PATCH 194/207] Update requirements

---
 .github/workflows/test.yml |  4 ++++
 setup.py                   | 20 +++++++++-----------
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ce22bba3f..5bc02192e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -34,6 +34,10 @@ jobs:
           sudo apt-get install libopenbabel-dev
           # https://github.com/openbabel/openbabel/issues/2408#issuecomment-1014466193
           sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+      
+      - name: Install phono3py
+        run: |
+          conda install -c conda-forge phono3py
 
       - name: Install dependencies
         run: |
diff --git a/setup.py b/setup.py
index a92256448..957e8dc5c 100644
--- a/setup.py
+++ b/setup.py
@@ -33,8 +33,8 @@
             "paramiko",
             "pydash>=7.0.6",
             "pymatgen-analysis-diffusion>=2023.8.15",
-            "pymatgen-analysis-defects>=2023.7.24",
-            "pymatgen>=2023.7.20",
+            "pymatgen-analysis-defects==2023.7.24",
+            "pymatgen==2023.7.20",
             "pymongo",
             "pyyaml>=5.1.2",
             "ruamel.yaml",
@@ -43,20 +43,18 @@
         ],
         extras_require={
             "plotting": ["matplotlib>=1.5.2"],
-            "phonons": ["phonopy>=1.10.8"],
+            "phonons": ["phonopy>=2.21.0"],
             "qchem": ["openbabel-wheel"],
             "defects": ["pymatgen-analysis-defects"],
-            "hiphive": ["hiphive>=1.1","phono3py==2.3.2","f90nml==1.3.1","ase>=3.19.0"],
+            "hiphive": ["hiphive @ git+https://gitlab.com/jsyony37/hiphive.git@personal#egg=hiphive","f90nml==1.3.1","ase>=3.22.1"],
             "complete": [
                 "matplotlib>=1.5.2",
-                "phonopy>=1.10.8",
+                "phonopy>=2.21.0",
                 "openbabel-wheel",
-                "hiphive>=1.1",
-                "f90nml==1.3.1",
-                "phono3py==2.3.2",
-                "cmake==3.22.4",
-                "spglib==1.16.5",
-                "ase>=3.19.0",
+                "hiphive @ git+https://gitlab.com/jsyony37/hiphive.git@personal#egg=hiphive",
+                "f90nml==1.4.4",
+                "spglib>=2.2.0",
+                "ase>=3.22.1",
                 "boto3>=1.28.15",
                 "Flask>=2.3.2",
                 "coverage>=7.2.7",

From dce7e2de365d9e3eb94daeef904dec57388a506f Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Wed, 6 Mar 2024 11:20:48 -0800
Subject: [PATCH 195/207] fix tests file

---
 .../tests/test_polarization_to_db.py          | 35 +++----------------
 1 file changed, 4 insertions(+), 31 deletions(-)

diff --git a/atomate/vasp/firetasks/tests/test_polarization_to_db.py b/atomate/vasp/firetasks/tests/test_polarization_to_db.py
index b85b0da70..23cb62d58 100644
--- a/atomate/vasp/firetasks/tests/test_polarization_to_db.py
+++ b/atomate/vasp/firetasks/tests/test_polarization_to_db.py
@@ -1,11 +1,7 @@
-<<<<<<< HEAD
 import os
-=======
 import bson
 import gzip
-
 from pathlib import Path
->>>>>>> 45fcce62 (Tidy polarization tests)
 
 from atomate.utils.testing import AtomateTest
 from atomate.vasp.firetasks.parse_outputs import PolarizationToDb
@@ -13,10 +9,9 @@
 __author__ = "Tess Smidt"
 __email__ = "blondegeek@gmail.com"
 
-<<<<<<< HEAD
-module_dir = os.path.dirname(os.path.abspath(__file__))
-db_dir = os.path.join(module_dir, "..", "..", "..", "common", "test_files")
-ref_dir = os.path.join(module_dir, "..", "..", "test_files")
+module_dir = Path(__file__).resolve().parent
+db_dir = module_dir / "../../../common/test_files"
+ref_dir = module_dir / "../../test_files"
 
 
 DEBUG_MODE = (
@@ -24,32 +19,14 @@
 )
 # If None, runs a "fake" VASP. Otherwise, runs VASP with this command...
 VASP_CMD = None
-=======
-module_dir = Path(__file__).resolve().parent
-db_dir = module_dir / "../../../common/test_files"
-<<<<<<< HEAD
-ref_dir = module_dir / "../..//test_files"
->>>>>>> 45fcce62 (Tidy polarization tests)
-=======
-ref_dir = module_dir / "../../test_files"
->>>>>>> fcdf2e63 (Finish tidying polarization tests)
+
 
 
 class TestPolarizationFiretasks(AtomateTest):
     def test_polarizationtodb(self):
-<<<<<<< HEAD
-        import gzip
-
-        import bson
-
-        reference_dir = os.path.abspath(os.path.join(ref_dir, "ferroelectric_wf"))
-
-        with gzip.open(os.path.join(reference_dir, "tasks.bson.gz")) as f:
-=======
         wf_dir = ref_dir / "ferroelectric_wf"
 
         with gzip.open(wf_dir / "tasks.bson.gz") as f:
->>>>>>> 45fcce62 (Tidy polarization tests)
             coll_raw = f.read()
 
         coll = bson.decode_all(coll_raw)
@@ -69,8 +46,4 @@ def test_polarizationtodb(self):
         # Check recovered change in polarization
         coll = self.get_task_collection("polarization_tasks")
         d = coll.find_one()
-<<<<<<< HEAD
-        self.assertAlmostEqual(d["polarization_change_norm"], 46.288752795325244, 5)
-=======
         self.assertAlmostEqual(d["polarization_change_norm"], 46.28875279532, 5)
->>>>>>> 45fcce62 (Tidy polarization tests)

From 4d835dd6d672192508852ebd6141e6e7f5dbfea4 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Wed, 6 Mar 2024 14:18:42 -0800
Subject: [PATCH 196/207] delate aimd and csld related codes

---
 atomate/utils/tests/test_database.py          |  10 +-
 atomate/vasp/firetasks/aimd.py                | 501 ------------------
 atomate/vasp/fireworks/aimd.py                | 193 -------
 atomate/vasp/workflows/presets/core.py        |   2 +-
 .../workflows/tests/test_csld_workflow.py     | 175 ------
 .../tests/test_lattice_dynamics_workflow.py   |   2 +-
 .../workflows/tests/test_vasp_workflows.py    |   4 +-
 7 files changed, 9 insertions(+), 878 deletions(-)
 delete mode 100644 atomate/vasp/firetasks/aimd.py
 delete mode 100644 atomate/vasp/fireworks/aimd.py
 delete mode 100644 atomate/vasp/workflows/tests/test_csld_workflow.py

diff --git a/atomate/utils/tests/test_database.py b/atomate/utils/tests/test_database.py
index 0d1555f0f..03ce4879d 100644
--- a/atomate/utils/tests/test_database.py
+++ b/atomate/utils/tests/test_database.py
@@ -6,7 +6,7 @@
 
 import boto3
 from maggma.stores import MemoryStore
-from moto import mock_s3
+from moto import mock_aws
 
 __author__ = "Jimmy Shen <jmmshn@gmail.com>"
 
@@ -37,7 +37,7 @@ def tearDownClass(cls):
         cls.testdb.connection.drop_database(cls.testdb.db_name)
 
     def test_s3_valid(self):
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket")
             index_store = MemoryStore()
@@ -50,7 +50,7 @@ def test_s3_valid(self):
             self.assertEqual(res["data"], "111111111110111111")
 
     def test_s3_not_valid(self):
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket_2")
             index_store = MemoryStore()
@@ -61,7 +61,7 @@ def test_s3_not_valid(self):
                 store.connect()
 
     def test_maggma_store_names(self):
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket")
             index_store = MemoryStore()
@@ -84,7 +84,7 @@ def test_uri(self):
         calc_db.collection.insert_one({"task_id": "mp-1", "data": "12345"})
         self.assertEqual(calc_db.collection.find_one()["data"], "12345")
 
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket")
             uri_db = TestToDb.from_db_file(db_dir + "/db_aws_uri.json")
diff --git a/atomate/vasp/firetasks/aimd.py b/atomate/vasp/firetasks/aimd.py
deleted file mode 100644
index 83a2ff286..000000000
--- a/atomate/vasp/firetasks/aimd.py
+++ /dev/null
@@ -1,501 +0,0 @@
-import json
-import os
-import subprocess
-import shlex
-from datetime import datetime
-from pathlib import Path
-
-import numpy as np
-from copy import copy, deepcopy
-
-from monty.dev import requires
-from monty.serialization import dumpfn, loadfn
-from monty.json import jsanitize
-from pymongo import ReturnDocument
-
-from atomate.utils.utils import env_chk, get_logger
-from atomate.vasp.database import VaspCalcDb
-from atomate.vasp.drones import VaspDrone
-
-from fireworks import FiretaskBase, FWAction, explicit_serialize
-
-from pymatgen.core.structure import Structure
-from pymatgen.transformations.standard_transformations import (
-    SupercellTransformation,
-)
-
-
-__author__ = "Junsoo Park"
-__email__ = "junsoo.park@nasa.gov"
-
-logger = get_logger(__name__)
-
-
-@explicit_serialize
-class CollectMDSegments(FiretaskBase):
-    """
-    Aggregate the structures and forces of perturbed supercells.
-
-    Requires a ``perturbed_tasks`` key to be set in the fw_spec, containing a
-    list of dictionaries, each with the keys:
-
-    - "parent_structure": The original structure.
-    - "supercell_matrix": The supercell transformation matrix.
-    - "structure": The perturbed supercell structure.
-    - "forces": The forces on each site in the supercell.
-    """
-
-    def run_task(self, fw_spec):
-        results = fw_spec.get("aimd", [])
-        logger.info("Found {} AIMD segments".format(len(results)))
-
-        structures = [r["structure"] for r in results]
-        forces = [np.asarray(r["forces"][i]) for i in range(len(r)) for r in results]
-        stress = [np.asarray(r["stress"][i]) for i in range(len(r)) for r in results]
-        configs = [r["configurations"][i] for i in range(len(r)) for r in results]
-
-        # if relaxation, get original structure from that calculation
-        calc_locs = fw_spec.get("calc_locs", [])
-        opt_calc_locs = [c for c in calc_locs if "optimiz" in c["name"]]
-        if opt_calc_locs:
-            opt_loc = opt_calc_locs[-1]["path"]
-            logger.info("Parsing optimization directory: {}".format(opt_loc))
-            opt_doc = VaspDrone(
-                parse_dos=False, parse_locpot=False,
-                parse_bader=False, store_volumetric_data=[],
-            ).assimilate(opt_loc)
-            opt_output = opt_doc["calcs_reversed"][0]["output"]
-            structure = Structure.from_dict(opt_output["structure"])
-        else:
-            structure = results[0]["parent_structure"]
-        supercell_matrix = results[0]["supercell_matrix"]
-
-        # regenerate pure supercell structure
-        st = SupercellTransformation(supercell_matrix)
-        supercell_structure = st.apply_transformation(structure)
-
-        structure_data = {
-            "structure": structure,
-            "supercell_structure": supercell_structure,
-            "supercell_matrix": supercell_matrix,
-        }
-
-        logger.info("Writing structure and forces data.")
-        dumpfn(structures, "perturbed_structures.json")
-        dumpfn(forces, "perturbed_forces.json")
-        dumpfn(structure_data, "structure_data.json")
-
-
-@explicit_serialize
-class MDToDB(FiretaskBase):
-    required_params = ["db_file"]
-    optional_params = ["renormalized","renorm_temperature","mesh_density", "additional_fields"]
-
-    def run_task(self, fw_spec):
-        db_file = env_chk(self.get("db_file"), fw_spec)
-        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-
-        # Get an id for the force constants
-        fitting_id = _get_fc_fitting_id(mmdb)
-        metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
-        data = {
-            "created_at": datetime.utcnow(),
-            "tags": fw_spec.get("tags", None),
-            "formula_pretty": structure.composition.reduced_formula,
-            "structure": structure.as_dict(),
-            "supercell_matrix": supercell_matrix,
-            "supercell_structure": supercell_structure.as_dict(),
-            "perturbed_structures": [s.as_dict() for s in perturbed_structures],
-            "perturbed_forces": [f.tolist() for f in forces],
-            "fitting_data": fitting_data,
-            "thermal_data": thermal_data,
-            "force_constants_fs_id": fc_fsid,
-            "phonon_dos_fs_id": dos_fsid,
-            "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-            "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-        }
-        data.update(self.get("additional_fields", {}))
-        data.update(metadata)
-        data = jsanitize(data, strict=True, allow_bson=True)
-        mmdb.db.aimd_for_potential_fitting.insert_one(data)
-
-        logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
-
-        return FWAction(update_spec=metadata)
-
-
-@explicit_serialize
-class RunHiPhive(FiretaskBase):
-    """
-    Fit force constants using hiPhive.
-
-    Requires "perturbed_structures.json", "perturbed_forces.json", and
-    "structure_data.json" files to be present in the current working directory.
-
-    Optional parameters:
-        cutoffs (Optional[list[list]]): A list of cutoffs to trial. If None,
-            a set of trial cutoffs will be generated based on the structure
-            (default).
-        disp_cut: determines the mean displacement of perturbed
-            structure to be included in harmonic (<) or anharmonic (>) fitting  
-        imaginary_tol (float): Tolerance used to decide if a phonon mode
-            is imaginary, in THz.
-        fit_method (str): Method used for fitting force constants. This can
-            be any of the values allowed by the hiphive ``Optimizer`` class.
-    """
-
-    optional_params = [
-        "cutoffs",
-        "disp_cut",
-        "temperature_qha",
-        "bulk_modulus",
-        "imaginary_tol",
-        "fit_method",
-    ]
-
-    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
-    def run_task(self, fw_spec):
-
-        all_structures = loadfn("perturbed_structures.json")
-        all_forces = loadfn("perturbed_forces.json")
-        structure_data = loadfn("structure_data.json")
-        parent_structure = structure_data["structure"]
-        supercell_structure = structure_data["supercell_structure"]
-        supercell_matrix = np.array(structure_data["supercell_matrix"])
-
-        disp_cut = self.get('disp_cut', None)
-        cutoffs = self.get("cutoffs") or get_cutoffs(supercell_structure)
-        T_qha = self.get("temperature_qha", T_QHA)
-        T_qha.sort()
-        imaginary_tol = self.get("imaginary_tol")
-        bulk_modulus = self.get("bulk_modulus")
-        fit_method = self.get("fit_method")
-
-        structures = []
-        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
-        for structure, forces in zip(all_structures, all_forces):
-            atoms = AseAtomsAdaptor.get_atoms(structure)
-            displacements = get_displacements(atoms, supercell_atoms)
-            atoms.new_array("displacements", displacements)
-            atoms.new_array("forces", forces)
-            atoms.positions = supercell_atoms.get_positions()
-            structures.append(atoms)
-
-        fcs, param, cs, fitting_data = fit_force_constants(
-            parent_structure,
-            supercell_matrix,
-            structures,
-            cutoffs,
-            disp_cut,
-            imaginary_tol,
-            fit_method
-        )
-
-        if fcs is None:
-            # fitting failed for some reason
-            raise RuntimeError(
-                "Could not find a force constant solution"
-            )
-        
-        thermal_data, phonopy = harmonic_properties(
-            parent_structure, supercell_matrix, fcs, T_qha, imaginary_tol
-        )
-        anharmonic_data = anharmonic_properties(
-            phonopy, fcs, T_qha, thermal_data["heat_capacity"],
-            thermal_data["n_imaginary"], bulk_modulus
-        )
-
-        phonopy.save("phonopy_orig.yaml")
-        fitting_data["n_imaginary"] = thermal_data.pop("n_imaginary")
-        thermal_data.update(anharmonic_data)
-        dumpfn(fitting_data, "fitting_data.json")
-        dumpfn(thermal_data, "thermal_data.json")
-
-        logger.info("Writing cluster space and force_constants")
-        logger.info("{}".format(type(fcs)))
-        fcs.write("force_constants.fcs")
-        np.savetxt('parameters.txt',param)
-        cs.write('cluster_space.cs')
-
-        if fitting_data["n_imaginary"] == 0:
-            logger.info("No imaginary modes! Writing ShengBTE files")
-            atoms = AseAtomsAdaptor.get_atoms(parent_structure)
-            fcs.write_to_shengBTE("FORCE_CONSTANTS_3RD", atoms, order=3)
-            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND", format="text")
-        else:
-            logger.info("ShengBTE files not written due to imaginary modes.")
-            logger.info("You may want to perform phonon renormalization.")
-
-
-
-@explicit_serialize
-class RunHiPhiveRenorm(FiretaskBase):
-    """
-    Perform phonon renormalization to obtain dependent-temperature force constants
-    using hiPhive. Requires "structure_data.json" to be present in the current working
-    directory.
-
-    Required parameters:
-   
-    Optional parameter:
-        temperature (float): temperature to perform renormalization
-        renorm_TE_iter (bool): if True, perform outer iteration over thermally expanded volumes
-        bulk_modulus (float): input bulk modulus - required for thermal expansion iterations
-    """
-
-    optional_params = ["renorm_method","temperature","nconfig","conv_thresh","max_iter",
-                       "renorm_TE_iter","bulk_modulus","imaginary_tol"]
-
-    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
-    def run_task(self, fw_spec):
-
-        cs = ClusterSpace.read('cluster_space.cs')
-        fcs = ForceConstants.read('force_constants.fcs')
-        param = np.loadtxt('parameters.txt')
-        fitting_data = loadfn("fitting_data.json")
-        structure_data = loadfn("structure_data.json")
-        phonopy_orig = phpy.load("phonopy_orig.yaml")
-
-        cutoffs = fitting_data["cutoffs"]
-        fit_method = fitting_data["fit_method"]
-        imaginary_tol = fitting_data["imaginary_tol"]
-
-        parent_structure = structure_data["structure"]
-        supercell_structure = structure_data["supercell_structure"]
-        supercell_atoms = AseAtomsAdaptor.get_atoms(supercell_structure)
-        supercell_matrix = np.array(structure_data["supercell_matrix"])
-
-        temperature = self.get("temperature")
-        renorm_method = self.get("renorm_method")
-        nconfig = self.get("nconfig")
-        conv_thresh = self.get("conv_thresh")
-        max_iter = self.get("max_iter")
-        renorm_TE_iter = self.get("renorm_TE_iter")
-        bulk_modulus = self.get("bulk_modulus")
-
-        # Renormalization with DFT lattice
-        renorm_data = run_renormalization(parent_structure, supercell_atoms, supercell_matrix, cs, fcs, param, temperature,
-                                          nconfig, max_iter, conv_thresh, renorm_method, fit_method, bulk_modulus, phonopy_orig)
-
-        # Additional renormalization with thermal expansion - optional - just single "iteration" for now
-        if renorm_TE_iter:
-            n_TE_iter = 1
-            for i in range(n_TE_iter):
-                if renorm_data is None: # failed or incomplete 
-                    break
-                elif result["n_imaginary"] < 0: # still imaginary
-                    break
-                else:
-                    logger.info("Renormalizing with thermally expanded lattice - iteration {}".format(i))
-
-                dLfrac = renorm_data["expansion_fraction"]  
-                param = renorm_data["param"]
-
-                parent_structure_TE, supercell_atoms_TE, cs_TE, fcs_TE = setup_TE_iter(cs,cutoffs,parent_structure,param,temperature,dLfrac)
-                prim_TE_atoms = AseAtomsAdaptor.get_atoms(parent_structure_TE)
-                prim_TE_phonopy = PhonopyAtoms(symbols=prim_TE_atoms.get_chemical_symbols(), 
-                                               scaled_positions=prim_TE_atoms.get_scaled_positions(), cell=prim_TE_atoms.cell)
-                phonopy_TE = Phonopy(prim_phonopy_TE, supercell_matrix=scmat, primitive_matrix=None)
-                
-                renorm_data = run_renormalization(parent_structure_TE, supercell_atoms_TE, supercell_matrix, 
-                                                  cs_TE, fcs_TE, param, temperature, nconfig, max_iter,
-                                                  conv_thresh,  renorm_method, fit_method, bulk_modulus, phonopy_TE)
-            structure_data["structure"] = parent_structure_TE
-            structure_data["supercell_structure"] = AseAtomsAdaptor.get_structure(supercell_atoms_TE)
-                        
-        # write results
-        logger.info("Writing renormalized results")
-        renorm_thermal_data = dict()
-        fcs = renorm_data['fcs']
-        fcs.write("force_constants.fcs")
-        thermal_keys = ["temperature","free_energy","entropy","heat_capacity",
-                        "gruneisen","thermal_expansion","expansion_fraction",
-                        "free_energy_correction_S","free_energy_correction_SC"]
-        renorm_thermal_data = {key: [] for key in thermal_keys}
-        for key in thermal_keys:
-            renorm_thermal_data[key].append(renorm_data[key])
-        
-        logger.info("DEBUG: ",renorm_data)
-        if renorm_data["n_imaginary"] > 0:
-            logger.warning('Imaginary modes remain for {} K!'.format(temperature))
-            logger.warning('ShengBTE files not written')
-            logger.warning('No renormalization with thermal expansion')
-        else:
-            logger.info("No imaginary modes! Writing ShengBTE files")
-            fcs.write_to_phonopy("FORCE_CONSTANTS_2ND".format(temperature), format="text")
-
-        dumpfn(structure_data, "structure_data.json".format(temperature))
-        dumpfn(renorm_thermal_data, "renorm_thermal_data.json".format(temperature))
-
-        
-@explicit_serialize
-class ForceConstantsToDb(FiretaskBase):
-    """
-    Add force constants, phonon band structure and density of states
-    to the database.
-
-    Assumes you are in a directory with the force constants, fitting
-    data, and structure data written to files.
-
-    Required parameters:
-        db_file (str): Path to DB file for the database that contains the
-            perturbed structure calculations.
-
-    Optional parameters:
-        renormalized (bool): Whether FC resulted from original fitting (False)
-            or renormalization process (True) determines how data are stored. 
-            Default is False.
-        mesh_density (float): The density of the q-point mesh used to calculate
-            the phonon density of states. See the docstring for the ``mesh``
-            argument in Phonopy.init_mesh() for more details.
-        additional_fields (dict): Additional fields added to the document, such
-            as user-defined tags, name, ids, etc.
-    """
-
-    required_params = ["db_file"]
-    optional_params = ["renormalized","renorm_temperature","mesh_density", "additional_fields"]
-
-    @requires(hiphive, "hiphive is required for lattice dynamics workflow")
-    def run_task(self, fw_spec):
-
-        db_file = env_chk(self.get("db_file"), fw_spec)
-        mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
-        renormalized = self.get("renormalized", False)
-        renorm_temperature = self.get("renorm_temperature", None)
-        mesh_density = self.get("mesh_density", 100.0)
-
-        structure_data = loadfn("structure_data.json")        
-        structure = structure_data["structure"]
-        supercell_structure = structure_data["supercell_structure"]
-        supercell_matrix = structure_data["supercell_matrix"]
-
-        if not renormalized:
-            perturbed_structures = loadfn("perturbed_structures.json")
-            forces = loadfn("perturbed_forces.json")
-            fitting_data = loadfn("fitting_data.json")
-            thermal_data = loadfn("thermal_data.json")
-            fcs = ForceConstants.read("force_constants.fcs")
-            
-            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-                structure, supercell_matrix, fcs, mesh_density, mmdb
-                )
-        
-            data = {
-                "created_at": datetime.utcnow(),            
-                "tags": fw_spec.get("tags", None),
-                "formula_pretty": structure.composition.reduced_formula,            
-                "structure": structure.as_dict(),
-                "supercell_matrix": supercell_matrix,
-                "supercell_structure": supercell_structure.as_dict(),
-                "perturbed_structures": [s.as_dict() for s in perturbed_structures],
-                "perturbed_forces": [f.tolist() for f in forces],
-                "fitting_data": fitting_data,
-                "thermal_data": thermal_data,
-                "force_constants_fs_id": fc_fsid,
-                "phonon_dos_fs_id": dos_fsid,
-                "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-                "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-                }
-            data.update(self.get("additional_fields", {}))
-
-            # Get an id for the force constants
-            fitting_id = _get_fc_fitting_id(mmdb)
-            metadata = {"fc_fitting_id": fitting_id, "fc_fitting_dir": os.getcwd()}
-            data.update(metadata)
-            data = jsanitize(data,strict=True,allow_bson=True)
-            
-            mmdb.db.lattice_dynamics.insert_one(data)
-            
-            logger.info("Finished inserting force constants and phonon data")
-
-        else:
-            renorm_thermal_data = loadfn("renorm_thermal_data.json")
-            fcs = ForceConstants.read("force_constants.fcs")
-            T = renorm_thermal_data["temperature"]
-
-            dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid = _get_fc_fsid(
-                structure, supercell_matrix, fcs, mesh_density, mmdb
-            )
-                
-            data_at_T = {
-                "created_at": datetime.utcnow(),
-                "tags": fw_spec.get("tags", None),
-                "formula_pretty": structure.composition.reduced_formula,
-                "structure": structure.as_dict(),
-                "supercell_matrix": supercell_matrix,
-                "supercell_structure": supercell_structure.as_dict(),
-                "thermal_data": renorm_thermal_data,
-                "force_constants_fs_id": fc_fsid,
-                "phonon_dos_fs_id": dos_fsid,
-                "phonon_bandstructure_uniform_fs_id": uniform_bs_fsid,
-                "phonon_bandstructure_line_fs_id": lm_bs_fsid,
-            }
-            data_at_T.update(self.get("additional_fields", {}))
-        
-            # Get an id for the force constants
-            fitting_id = _get_fc_fitting_id(mmdb)
-            metadata = {"fc_fitting_id": fitting_id, "renormalization_dir": os.getcwd()}
-            data_at_T.update(metadata)
-            data_at_T = jsanitize(data_at_T,strict=True,allow_bson=True)
-            
-            mmdb.db.renormalized_lattice_dynamics.insert_one(data_at_T)
-            
-            logger.info("Finished inserting renormalized force constants and phonon data at {} K".format(T))
-            
-        return FWAction(update_spec=metadata)        
-
-
-def _get_fc_fitting_id(mmdb: VaspCalcDb) -> int:
-    """Helper method to get a force constant fitting id."""
-    fc_id = mmdb.db.counter.find_one_and_update(
-        {"_id": "fc_fitting_id"},
-        {"$inc": {"c": 1}},
-        return_document=ReturnDocument.AFTER,
-    )
-    if fc_id is None:
-        mmdb.db.counter.insert({"_id": "fc_fitting_id", "c": 1})
-        fc_id = 1
-    else:
-        fc_id = fc_id["c"]
-
-    return fc_id
-
-
-def _get_fc_fsid(structure, supercell_matrix, fcs, mesh_density, mmdb):
-    phonopy_fc = fcs.get_fc_array(order=2)
-    
-    logger.info("Getting uniform phonon band structure.")
-    uniform_bs = get_phonon_band_structure_from_fc(
-        structure, supercell_matrix, phonopy_fc
-    )
-    
-    logger.info("Getting line mode phonon band structure.")
-    lm_bs = get_phonon_band_structure_symm_line_from_fc(
-        structure, supercell_matrix, phonopy_fc
-    )
-    
-    logger.info("Getting phonon density of states.")
-    dos = get_phonon_dos_from_fc(
-        structure, supercell_matrix, phonopy_fc, mesh_density=mesh_density
-    )
-    
-    logger.info("Inserting phonon objects into database.")
-    dos_fsid, _ = mmdb.insert_gridfs(
-        dos.to_json(), collection="phonon_dos_fs"
-    )
-    uniform_bs_fsid, _ = mmdb.insert_gridfs(
-        uniform_bs.to_json(), collection="phonon_bandstructure_fs"
-    )
-    lm_bs_fsid, _ = mmdb.insert_gridfs(
-        lm_bs.to_json(), collection="phonon_bandstructure_fs"
-    )
-    
-    logger.info("Inserting force constants into database.")
-    fc_json = json.dumps(
-        {str(k): v.tolist() for k, v in fcs.get_fc_dict().items()}
-    )
-    fc_fsid, _ = mmdb.insert_gridfs(
-        fc_json, collection="phonon_force_constants_fs"
-    )
-
-    return dos_fsid, uniform_bs_fsid, lm_bs_fsid, fc_fsid
diff --git a/atomate/vasp/fireworks/aimd.py b/atomate/vasp/fireworks/aimd.py
deleted file mode 100644
index 40a0251b2..000000000
--- a/atomate/vasp/fireworks/aimd.py
+++ /dev/null
@@ -1,193 +0,0 @@
-from typing import List, Optional, Union, Dict
-
-import os
-
-from atomate.common.firetasks.glue_tasks import (
-    CopyFiles,
-    CopyFilesFromCalcLoc,
-    PassCalcLocs,
-)
-
-from atomate.vasp.firetasks.aimd import (
-    CollectMDSegments,
-    MDToDB
-    )
-
-from fireworks import Firework
-
-__author__ = "Junsoo Park"
-__email__ = "junsoo.park@nasa.gov"
-
-
-class ARCMDFW(Firework):
-    def __init__(
-        self,
-        structure,
-        start_temp,
-        end_temp,
-        nsteps,
-        name="AIMD",
-        vasp_input_set=None,
-        vasp_cmd=VASP_CMD,
-        override_default_vasp_params=None,
-        wall_time=19200,
-        db_file=DB_FILE,
-        parents=None,
-        **kwargs,
-    ):
-        """
-        Standard firework for a single MD run.
-
-        Args:
-            structure (Structure): Input structure.
-            start_temp (float): Start temperature of MD run.
-            end_temp (float): End temperature of MD run.
-            nsteps (int): Number of MD steps
-            name (string): Name for the Firework.
-            vasp_input_set (string): string name for the VASP input set (e.g.,
-                "MITMDVaspInputSet").
-            vasp_cmd (string): Command to run vasp.
-            override_default_vasp_params (dict): If this is not None,
-                these params are passed to the default vasp_input_set, i.e.,
-                MITMDSet. This allows one to easily override some
-                settings, e.g., user_incar_settings, etc. Particular to MD,
-                one can control time_step and all other settings of the input set.
-            wall_time (int): Total wall time in seconds before writing STOPCAR.
-            copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True.
-            db_file (string): Path to file specifying db credentials.
-            parents (Firework): Parents of this particular Firework. FW or list of FWS.
-            **kwargs: Other kwargs that are passed to Firework.__init__.
-        """
-        override_default_vasp_params = override_default_vasp_params or {}
-        vasp_input_set = vasp_input_set or ARCMDSet(
-            structure,
-            start_temp=start_temp,
-            end_temp=end_temp,
-            nsteps=nsteps,
-            **override_default_vasp_params,
-        )
-        prev_runs = fw_spec.get("aimd", [])
-        last_run = prev_runs[-1]
-        last_config = last_run["final_configuration"]
-        t = []
-        t.append(WriteVaspFromIOSet(structure=last_config, vasp_input_set=vasp_input_set))
-        t.append(
-            RunVaspCustodian(
-                vasp_cmd=vasp_cmd,
-                gamma_vasp_cmd=">>vasp_cmd<<",#">>gamma_vasp_cmd<<",
-                handler_group="md",
-                wall_time=wall_time,
-            )
-        )
-        t.append(PassCalcLocs(name=name))
-        t.append(
-            VaspToDb(
-                db_file=db_file,
-                additional_fields={"task_label": name},
-                defuse_unsuccessful=False,
-            )
-        )
-        super().__init__(
-            t,
-            parents=parents,
-            name=f"{structure.composition.reduced_formula}-{name}",
-            **kwargs,
-        )
-
-
-class CollectMDSegmentsFW(Firework):
-    """
-    Compile serial AIMD runs segmented into multiple Fireworks
-
-    Args:
-        parents: Parent(s) of this Firework.
-        name: Name of this FW.
-        db_file: Path to a db file.
-        cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
-            will be generated based on the structure (default).
-        disp_cut: determines the mean displacement of perturbed
-            structure to be included in harmonic (<) or anharmonic (>) fitting  
-        bulk_modulus: in GPa, necessary for thermal expansion
-        imaginary_tol: Tolerance used to decide if a phonon mode is
-            imaginary, in THz.
-        fit_method: Method used for fitting force constants. This can be
-            any of the values allowed by the hiphive ``Optimizer`` class.
-        mesh_density: The density of the q-point mesh used to calculate the
-            phonon density of states. See the docstring for the ``mesh``
-            argument in Phonopy.init_mesh() for more details.
-        **kwargs: Other kwargs that are passed to Firework.__init__.
-    """
-
-    def __init__(
-        self,
-        name="Collect MD Runs",
-        parents: Optional[Union[Firework, List[Firework]]] = None,
-        db_file: str = None,
-        **kwargs
-    ):
-        collect = CollectMDSegments()
-
-        to_db = AIMDToDB(
-            db_file=db_file, additional_fields={}
-        )
-        pass_locs = PassCalcLocs(name=name)
-
-        tasks = [collect, to_db, pass_locs]
-        super().__init__(tasks, parents=parents, name=name, **kwargs)
-
-
-class FitForceConstantsFW(Firework):
-    """
-    Compile perturbed supercell calculations and fit force constants
-    using hiPhive.
-
-    Args:
-        parents: Parent(s) of this Firework.
-        name: Name of this FW.
-        db_file: Path to a db file.
-        cutoffs: A list of cutoffs to trial. If None, a set of trial cutoffs
-            will be generated based on the structure (default).
-        disp_cut: determines the mean displacement of perturbed
-            structure to be included in harmonic (<) or anharmonic (>) fitting
-        bulk_modulus: in GPa, necessary for thermal expansion
-        imaginary_tol: Tolerance used to decide if a phonon mode is
-            imaginary, in THz.
-        fit_method: Method used for fitting force constants. This can be
-            any of the values allowed by the hiphive ``Optimizer`` class.
-        mesh_density: The density of the q-point mesh used to calculate the
-            phonon density of states. See the docstring for the ``mesh``
-            argument in Phonopy.init_mesh() for more details.
-        **kwargs: Other kwargs that are passed to Firework.__init__.
-    """
-
-    def __init__(
-            self,
-            fit_method: str,
-            disp_cut: float,
-            bulk_modulus: float,
-            imaginary_tol: float,
-            mesh_density: float,
-            temperature_qha: float,
-            cutoffs: Optional[List[List[float]]] = None,
-            name="Fit Force Constants",
-            parents: Optional[Union[Firework, List[Firework]]] = None,
-            db_file: str = None,
-            **kwargs
-    ):
-        collect_structures = CollectPerturbedStructures()
-
-        fit_force_constants = RunHiPhive(
-            cutoffs=cutoffs,
-            fit_method=fit_method,
-            disp_cut=disp_cut,
-            bulk_modulus=bulk_modulus,
-            temperature_qha=temperature_qha,
-            imaginary_tol=imaginary_tol,
-        )
-        to_db = ForceConstantsToDb(
-            db_file=db_file, renormalized=False, mesh_density=mesh_density, additional_fields={}
-        )
-        pass_locs = PassCalcLocs(name=name)
-
-        tasks = [collect_structures, fit_force_constants, to_db, pass_locs]
-        super().__init__(tasks, parents=parents, name=name, **kwargs)
diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 0f8b5ec3b..10fa8632c 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -6,7 +6,7 @@
     get_lattice_dynamics_wf, vasp_to_db_params 
 
 from fireworks import Workflow
-from pymatgen import Structure
+from pymatgen.core import Structure
 from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPHSERelaxSet
 from pymatgen.io.vasp.inputs import Kpoints
 
diff --git a/atomate/vasp/workflows/tests/test_csld_workflow.py b/atomate/vasp/workflows/tests/test_csld_workflow.py
deleted file mode 100644
index 07471c7ab..000000000
--- a/atomate/vasp/workflows/tests/test_csld_workflow.py
+++ /dev/null
@@ -1,175 +0,0 @@
-# coding: utf-8
-
-from __future__ import division, print_function, unicode_literals, absolute_import
-
-import os
-from monty.os.path import which
-import unittest
-import numpy as np
-import shutil
-
-from pymatgen import Structure
-from atomate.vasp.workflows.base.csld import CompressedSensingLatticeDynamicsWF
-from atomate.vasp.firetasks.parse_outputs import (
-    CSLDForceConstantsToDB,
-    ShengBTEToDB,
-)
-from atomate.utils.testing import AtomateTest, DB_DIR
-
-import json
-
-module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
-db_dir = os.path.join(module_dir, "..", "..", "..", "common", "test_files")
-ref_dir = os.path.join(module_dir, "..", "..", "test_files", "csld_wf")
-
-__author__ = "Rees Chang"
-__email__ = "rc564@cornell.edu"
-
-csld_present = which("csld_main")
-
-class TestCompressedSensingLatticeDynamicsWorkflow(AtomateTest):
-
-    @staticmethod
-    def init():
-        with open(os.path.join(ref_dir, "FW.json"),
-                  "r") as f:
-            sample_task = json.load(f)[0]
-        wf_uuid = sample_task["spec"]["_tasks"][0]["wf_uuid"]
-        parent_structure = Structure.from_dict(
-            sample_task["spec"]["_tasks"][0]["parent_structure"])
-        trans_mat = sample_task["spec"]["_tasks"][0]["trans_mat"]
-        supercell_structure = Structure.from_dict(
-            sample_task["spec"]["_tasks"][0]["supercell_structure"])
-        supercell_smallest_dim = sample_task["spec"]["_tasks"][0]["supercell_smallest_dim"]
-        perturbed_supercells = sample_task["spec"]["_tasks"][0]["perturbed_supercells"]
-        for i in range(len(perturbed_supercells)):
-            perturbed_supercells[i] = Structure.from_dict(
-                perturbed_supercells[i])
-        disps = sample_task["spec"]["_tasks"][0]["disps"]
-        first_pass = sample_task["spec"]["_tasks"][0]["first_pass"]
-        static_user_incar_settings = sample_task["spec"]["_tasks"][0]["static_user_incar_settings"]
-        env_vars = sample_task["spec"]["_tasks"][0]["env_vars"]
-        shengbte_t_range = sample_task["spec"]["_tasks"][0]["shengbte_t_range"]
-        shengbte_fworker = sample_task["spec"]["_tasks"][0]["shengbte_fworker"]
-
-        csld_firetask = CSLDForceConstantsToDB(
-            db_file=os.path.join(DB_DIR, "db.json"),
-            wf_uuid=wf_uuid,
-            parent_structure=parent_structure,
-            trans_mat=trans_mat,
-            supercell_structure=supercell_structure,
-            supercell_smallest_dim=supercell_smallest_dim,
-            perturbed_supercells=perturbed_supercells,
-            disps=disps,
-            first_pass=first_pass,
-            static_user_incar_settings=static_user_incar_settings,
-            env_vars=env_vars,
-            shengbte_t_range=shengbte_t_range,
-            shengbte_fworker=shengbte_fworker,
-            force_diagonal_transformation=True,
-        )
-
-        return csld_firetask
-
-    def test_collect_successful_static_calcs_results(self):
-        tasks = self.get_task_collection()
-        csld_firetask = self.init()
-        with open(os.path.join(ref_dir, "FW.json"),
-                  "r") as f:
-            sample_task = json.load(f)[1]
-        tasks.insert_one(sample_task)
-
-        supercells_forces, successful_disps = csld_firetask.collect_successful_static_calcs_results(
-            tasks)
-
-        self.assertEqual(
-            float(successful_disps[0]),
-            0.1
-        )
-        self.assertTrue(
-            isinstance(supercells_forces, list)
-        )
-        self.assertEqual(
-            supercells_forces[0][0][0],
-            0.07831190000000000373
-        )
-        self.assertEqual(
-            supercells_forces[0][0][1],
-            0.13348752999999999314
-        )
-        self.assertEqual(
-            supercells_forces[0][0][2],
-            -0.7885310199999999714
-        )
-        self.assertEqual(
-            len(supercells_forces[0]),
-            216
-        )
-
-    def test_set_params(self):
-
-        csld_firetask = self.init()
-        csld_firetask.set_params(
-            iteration_number=0,
-            disps=[0.1],
-            cluster_diam='11 6.5 5.0',
-            max_order=3,
-            submodel1='anh 0 1 2 3',
-            export_sbte='5 5 5 2 3',
-            supercells_forces=[np.eye(3)]
-        )
-
-        self.assertEqual(
-            csld_firetask["csld_settings"]["structure"]["prim"],
-            "Si_supercell_iter0/POSCAR")
-        self.assertEqual(
-            csld_firetask["csld_settings"]["model"]["max_order"],
-            '3'
-        )
-        self.assertEqual(
-            csld_firetask["csld_settings"]["model"]["cluster_diameter"],
-            '11 6.5 5.0'
-        )
-        self.assertEqual(
-            csld_firetask["csld_settings"]["model"]["cluster_filter"],
-            r"lambda cls: ((cls.order_uniq <= 2) or (cls.bond_counts(2.9) "
-            r">= 2)) and cls.is_small_in('" + "Si_supercell_iter0" + "/sc.txt')"
-        )
-        self.assertEqual(
-            csld_firetask["csld_settings"]["training"]["traindat1"],
-            'Si_supercell_iter0/SPOSCAR Si_supercell_iter0/disp0.10'
-        )
-        self.assertEqual(
-            csld_firetask["csld_settings"]["fitting"]["submodel1"],
-            'anh 0 1 2 3'
-        )
-        self.assertEqual(
-            csld_firetask["csld_settings"]["export_potential"]["export_shengbte"],
-            '5 5 5 2 3'
-        )
-        self.assertEqual(
-            csld_firetask["forces_paths"],
-            ['Si_supercell_iter0/disp0.10']
-        )
-        self.assertTrue(
-            os.path.isfile(csld_firetask["forces_paths"][0] + "/force.txt")
-        )
-        self.assertTrue(
-            os.path.isfile('Si_supercell_iter0/POSCAR')
-        )
-        self.assertTrue(
-            os.path.isfile('Si_supercell_iter0/SPOSCAR')
-        )
-        self.assertTrue(
-            os.path.isfile('Si_supercell_iter0/sc.txt')
-        )
-        shutil.rmtree('Si_supercell_iter0')
-
-    @unittest.skipIf(not csld_present, "CSLD not present")
-    def test_run_csld(self):
-        print('hi')
-
-
-
-
-
diff --git a/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py b/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
index 55da5cde4..2c04847db 100644
--- a/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
+++ b/atomate/vasp/workflows/tests/test_lattice_dynamics_workflow.py
@@ -1,7 +1,7 @@
 
 from pathlib import Path
 
-from atomate.vasp.workflows import get_lattice_dynamics_wf
+from atomate.vasp.workflows.base.lattice_dynamics import get_lattice_dynamics_wf
 from fireworks import FWorker
 from fireworks.core.rocket_launcher import rapidfire
 
diff --git a/atomate/vasp/workflows/tests/test_vasp_workflows.py b/atomate/vasp/workflows/tests/test_vasp_workflows.py
index b5d5fc0db..fbdbab5c4 100644
--- a/atomate/vasp/workflows/tests/test_vasp_workflows.py
+++ b/atomate/vasp/workflows/tests/test_vasp_workflows.py
@@ -7,7 +7,7 @@
 from fireworks import FWorker
 from fireworks.core.rocket_launcher import rapidfire
 from monty.json import MontyDecoder
-from moto import mock_s3
+from moto import mock_aws
 from pymatgen.core import Structure
 from pymatgen.electronic_structure.bandstructure import BandStructure
 from pymatgen.electronic_structure.dos import CompleteDos
@@ -403,7 +403,7 @@ def test_insert_maggma_store(self):
         # generate a doc from the test folder
         doc = {"a": 1, "b": 2}
 
-        with mock_s3():
+        with mock_aws():
             conn = boto3.client("s3")
             conn.create_bucket(Bucket="test_bucket")
             mmdb = VaspCalcDb.from_db_file(os.path.join(db_dir, "db_aws.json"))

From a156d310e503594dd0754c182d09d0e987b10efb Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Wed, 6 Mar 2024 14:29:14 -0800
Subject: [PATCH 197/207] remove __init__ for pytest

---
 atomate/vasp/workflows/tests/__init__.py | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 atomate/vasp/workflows/tests/__init__.py

diff --git a/atomate/vasp/workflows/tests/__init__.py b/atomate/vasp/workflows/tests/__init__.py
deleted file mode 100644
index b06452a32..000000000
--- a/atomate/vasp/workflows/tests/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__author__ = "Anubhav Jain <ajain@lbl.gov>"

From 16957fbf3dafdebbd22e0e1b558dd83f79f29704 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Wed, 6 Mar 2024 19:15:04 -0800
Subject: [PATCH 198/207] remove __init__ for pytest 2

---
 atomate/common/tests/__init__.py | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 atomate/common/tests/__init__.py

diff --git a/atomate/common/tests/__init__.py b/atomate/common/tests/__init__.py
deleted file mode 100644
index 982614220..000000000
--- a/atomate/common/tests/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__author__ = "Janine George (janine.george@uclouvain.be), Guido Petretto (guido.petretto@uclouvain.be)"

From 17929f463ddd574c010ce920f2a8e2cd43ed1e52 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 11:54:26 -0700
Subject: [PATCH 199/207] pytest fix

---
 atomate/common/firetasks/tests/test_parse_outputs.py | 3 ++-
 atomate/common/tests/__init__.py                     | 1 +
 atomate/vasp/workflows/tests/__init__.py             | 1 +
 3 files changed, 4 insertions(+), 1 deletion(-)
 create mode 100644 atomate/common/tests/__init__.py
 create mode 100644 atomate/vasp/workflows/tests/__init__.py

diff --git a/atomate/common/firetasks/tests/test_parse_outputs.py b/atomate/common/firetasks/tests/test_parse_outputs.py
index 09c7f5101..c2dc9ca89 100644
--- a/atomate/common/firetasks/tests/test_parse_outputs.py
+++ b/atomate/common/firetasks/tests/test_parse_outputs.py
@@ -14,7 +14,8 @@
 
 
 class TestDrone(AbstractDrone):
-    def __init__(self):
+    @classmethod
+    def setUpClass(cls):
         pass
 
     def assimilate(self, path):
diff --git a/atomate/common/tests/__init__.py b/atomate/common/tests/__init__.py
new file mode 100644
index 000000000..982614220
--- /dev/null
+++ b/atomate/common/tests/__init__.py
@@ -0,0 +1 @@
+__author__ = "Janine George (janine.george@uclouvain.be), Guido Petretto (guido.petretto@uclouvain.be)"
diff --git a/atomate/vasp/workflows/tests/__init__.py b/atomate/vasp/workflows/tests/__init__.py
new file mode 100644
index 000000000..b06452a32
--- /dev/null
+++ b/atomate/vasp/workflows/tests/__init__.py
@@ -0,0 +1 @@
+__author__ = "Anubhav Jain <ajain@lbl.gov>"

From f53134d09db882ea0e3b192a8d303e4ebce293a8 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 14:23:55 -0700
Subject: [PATCH 200/207] fix pytest

---
 atomate/utils/tests/test_database.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/atomate/utils/tests/test_database.py b/atomate/utils/tests/test_database.py
index 03ce4879d..636f2197b 100644
--- a/atomate/utils/tests/test_database.py
+++ b/atomate/utils/tests/test_database.py
@@ -3,7 +3,6 @@
 """
 import os
 import unittest
-
 import boto3
 from maggma.stores import MemoryStore
 from moto import mock_aws
@@ -19,7 +18,14 @@
 logger = get_logger(__name__)
 
 
+
+
 class TestToDb(CalcDb):
+    def setup_method(self,method):
+        self.reset()
+    
+    def teardown_method(self,method):
+
     def build_indexes(self, indexes=None, background=True):
         pass
 

From 9506c2799ddd2a5d472dc3941226e36a60de28b7 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 14:49:34 -0700
Subject: [PATCH 201/207] small fix

---
 atomate/utils/tests/test_database.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/atomate/utils/tests/test_database.py b/atomate/utils/tests/test_database.py
index 636f2197b..38718c874 100644
--- a/atomate/utils/tests/test_database.py
+++ b/atomate/utils/tests/test_database.py
@@ -25,7 +25,8 @@ def setup_method(self,method):
         self.reset()
     
     def teardown_method(self,method):
-
+        pass
+        
     def build_indexes(self, indexes=None, background=True):
         pass
 

From 18dd9b4d104bc200cbf57b7786a78ee04615aa5d Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 15:11:38 -0700
Subject: [PATCH 202/207] remove tests/__init__.py

---
 atomate/common/tests/__init__.py         | 1 -
 atomate/vasp/workflows/tests/__init__.py | 1 -
 2 files changed, 2 deletions(-)
 delete mode 100644 atomate/common/tests/__init__.py
 delete mode 100644 atomate/vasp/workflows/tests/__init__.py

diff --git a/atomate/common/tests/__init__.py b/atomate/common/tests/__init__.py
deleted file mode 100644
index 982614220..000000000
--- a/atomate/common/tests/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__author__ = "Janine George (janine.george@uclouvain.be), Guido Petretto (guido.petretto@uclouvain.be)"
diff --git a/atomate/vasp/workflows/tests/__init__.py b/atomate/vasp/workflows/tests/__init__.py
deleted file mode 100644
index b06452a32..000000000
--- a/atomate/vasp/workflows/tests/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__author__ = "Anubhav Jain <ajain@lbl.gov>"

From 461c5a934144821e9eb1d61bbd880f25a0134c56 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 16:17:17 -0700
Subject: [PATCH 203/207] add path in presets/core

---
 atomate/vasp/workflows/presets/core.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/atomate/vasp/workflows/presets/core.py b/atomate/vasp/workflows/presets/core.py
index 10fa8632c..00d2ef427 100644
--- a/atomate/vasp/workflows/presets/core.py
+++ b/atomate/vasp/workflows/presets/core.py
@@ -1,6 +1,8 @@
 from typing import Optional
 from uuid import uuid4
 import numpy as np
+import os
+import logging
 
 from atomate.vasp.workflows.base.lattice_dynamics import \
     get_lattice_dynamics_wf, vasp_to_db_params 
@@ -44,6 +46,8 @@
 # TODO: @computron: Clarify the config dict -computron
 # TODO: @computron: Allow default config dict to be loaded from file -computron
 
+module_dir = os.path.dirname(os.path.abspath(__file__))
+logger = logging.getLogger(__name__)
 
 def wf_bandstructure(structure, c=None):
 

From fa41428830b57b60caaf662a3dcd405886975c9c Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 16:27:09 -0700
Subject: [PATCH 204/207] test phono3py install

---
 atomate/vasp/workflows/tests/test_adsorbate_workflow.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/atomate/vasp/workflows/tests/test_adsorbate_workflow.py b/atomate/vasp/workflows/tests/test_adsorbate_workflow.py
index 644c2572a..f9170e5e3 100644
--- a/atomate/vasp/workflows/tests/test_adsorbate_workflow.py
+++ b/atomate/vasp/workflows/tests/test_adsorbate_workflow.py
@@ -16,6 +16,7 @@
     get_slab_trans_params,
     get_wf_slab,
 )
+from phono3py.phonon3.gruneisen import Gruneisen
 
 __author__ = "Kiran Mathew, Joseph Montoya"
 __email__ = "montoyjh@lbl.gov"

From 93a422fe9f48cc53ec56b6f65344a3485afdd1ae Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 16:37:30 -0700
Subject: [PATCH 205/207] add phono3y into complete

---
 atomate/vasp/workflows/tests/test_adsorbate_workflow.py | 1 -
 setup.py                                                | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/atomate/vasp/workflows/tests/test_adsorbate_workflow.py b/atomate/vasp/workflows/tests/test_adsorbate_workflow.py
index f9170e5e3..644c2572a 100644
--- a/atomate/vasp/workflows/tests/test_adsorbate_workflow.py
+++ b/atomate/vasp/workflows/tests/test_adsorbate_workflow.py
@@ -16,7 +16,6 @@
     get_slab_trans_params,
     get_wf_slab,
 )
-from phono3py.phonon3.gruneisen import Gruneisen
 
 __author__ = "Kiran Mathew, Joseph Montoya"
 __email__ = "montoyjh@lbl.gov"
diff --git a/setup.py b/setup.py
index 957e8dc5c..1c2b086b3 100644
--- a/setup.py
+++ b/setup.py
@@ -51,6 +51,7 @@
                 "matplotlib>=1.5.2",
                 "phonopy>=2.21.0",
                 "openbabel-wheel",
+                "phono3py",
                 "hiphive @ git+https://gitlab.com/jsyony37/hiphive.git@personal#egg=hiphive",
                 "f90nml==1.4.4",
                 "spglib>=2.2.0",

From 52ef78bb4eda56578b9f0a9dd61fa15fcf6ae826 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 16:50:24 -0700
Subject: [PATCH 206/207] install h5py

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1c2b086b3..2f2e8396b 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
             "pymatgen-analysis-defects==2023.7.24",
             "pymatgen==2023.7.20",
             "pymongo",
-            "pyyaml>=5.1.2",
+            "pyyaml>=5.3",
             "ruamel.yaml",
             "scipy",
             "tqdm>=4.65.0",
@@ -51,6 +51,7 @@
                 "matplotlib>=1.5.2",
                 "phonopy>=2.21.0",
                 "openbabel-wheel",
+                "h5py>=3.0",
                 "phono3py",
                 "hiphive @ git+https://gitlab.com/jsyony37/hiphive.git@personal#egg=hiphive",
                 "f90nml==1.4.4",

From a291b5d9bdabcbb714fc3187e0a90ed2145796a1 Mon Sep 17 00:00:00 2001
From: Zhuoying <zhz004@eng.ucsd.edu>
Date: Mon, 11 Mar 2024 17:06:49 -0700
Subject: [PATCH 207/207] revert back

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index 2f2e8396b..1cc4e6a2f 100644
--- a/setup.py
+++ b/setup.py
@@ -52,7 +52,6 @@
                 "phonopy>=2.21.0",
                 "openbabel-wheel",
                 "h5py>=3.0",
-                "phono3py",
                 "hiphive @ git+https://gitlab.com/jsyony37/hiphive.git@personal#egg=hiphive",
                 "f90nml==1.4.4",
                 "spglib>=2.2.0",