Version 1.8.1

Improvements to readcif, added atomic form factors and classes_orbitals, among other changes.

Author: DanPorter

Dans_Diffraction/__init__.py

@@ -4,9 +4,9 @@
 
 Usage:
     ***In Python***
-    from Dans_Diffraction import Crystal
+    import Dans_Diffraction as dif
     f = '/location/of/file.cif'
-    xtl = Crystal(f)
+    xtl = dif.Crystal(f)
     
 Usage:
     ***From Terminal***
@@ -17,8 +17,8 @@
 Diamond
 2017
 
-Version 1.8
-Last updated: 05/05/20
+Version 1.8.1
+Last updated: 12/05/20
 
 Version History:
 02/03/18 1.0    Version History started.
@@ -31,6 +31,7 @@
 31/03/20 1.7    Refactored multicrystal methods, other minor changes, improved powder diffraction
 19/04/20 1.7.1  Added writecif + spacegroup file + functions
 02/05/20 1.8    Updated readcif, added heavy atom properties, added magnetic spacegroups
+12/05/20 1.8.1  Updated readcif, added atomic_scattering_factors and classes_orbitals
 
 -----------------------------------------------------------------------------
    Copyright 2020 Diamond Light Source Ltd.
@@ -53,6 +54,7 @@
     classes_plotting.py
     classes_properties.py
     classes_multicrystal.py
+    classes_orbitals.py
     functions_general.py
     functions_plotting.py
     functions_crystallography.py
@@ -83,8 +85,8 @@
     from .classes_fdmnes import Fdmnes, FdmnesAnalysis
 
 
-__version__ = '1.8'
-__date__ = '05/05/20'
+__version__ = '1.8.1'
+__date__ = '12/05/20'
 
 
 # Build

Dans_Diffraction/__main__.py

@@ -10,6 +10,9 @@
 For GUI use:
     ipython -m Dans_Diffraction gui
 
+To Parse a cif:
+    ipython -m Dans_Diffraction 'somefile.cif'
+
 By Dan Porter, PhD
 Diamond
 2017
@@ -28,6 +31,7 @@
     for arg in sys.argv:
         if 'cif' in arg.lower():
             xtl = dif.Crystal(arg)
+            print(xtl.info())
         elif 'gui' in arg.lower():
             xtl.start_gui()
 

Dans_Diffraction/classes_crystal.py

@@ -51,6 +51,7 @@
 from . import functions_general as fg, functions_crystallography as fc
 from . import functions_crystallography as fc
 from .classes_properties import Properties
+#from .classes_orbitals import CrystalOrbitals
 from .classes_scattering import Scattering
 from .classes_multicrystal import MultiCrystal
 from .classes_plotting import Plotting, PlottingSuperstructure
@@ -127,6 +128,7 @@ def __init__(self, filename=None):
         self.Plot = Plotting(self)
         self.Scatter = Scattering(self)
         self.Properties = Properties(self)
+        #self.Orbitals = CrystalOrbitals(self) # slows down cif parsing a lot!
         # self.Fdmnes = Fdmnes(self)
 
     def generate_structure(self):
@@ -823,9 +825,14 @@ def fromcif(self, cifvals):
         label = cifvals['_atom_site_label']
 
         if '_atom_site_type_symbol' in keys:
-            element = [x.strip('+-.0123456789()') for x in cifvals['_atom_site_type_symbol']]
+            element = [fc.str2element(x) for x in cifvals['_atom_site_type_symbol']]
         else:
-            element = [x.strip('+-.0123456789()') for x in cifvals['_atom_site_label']]
+            element = [fc.str2element(x) for x in cifvals['_atom_site_label']]
+
+        while False in element:
+            fidx = element.index(False)
+            warn('%s is not a valid element, replacing with H' % cifvals['_atom_site_label'][fidx])
+            element[fidx] = 'H'
 
         # Replace Deuterium with Hydrogen
         if 'D' in element:
@@ -1187,17 +1194,22 @@ def info(self, idx=None, type=None):
 
         out = ''
         if np.any(fg.mag(self.mxmymz()) > 0):
-            out += '  n Atom  u       v       w        Occ  Uiso      mx      my      mz      \n'
-            fmt = '%3.0f %4s %7.4f %7.4f %7.4f   %4.2f %6.4f   %7.4f %7.4f %7.4f\n'
+            out += '  n Label Atom  u       v       w        Occ  Uiso      mx      my      mz      \n'
+            fmt = '%3.0f %5s %4s %7.4f %7.4f %7.4f   %4.2f %6.4f   %7.4f %7.4f %7.4f\n'
             for n in disprange:
                 out += fmt % (
-                    n, self.type[n], self.u[n], self.v[n], self.w[n], self.occupancy[n], self.uiso[n], self.mx[n],
-                    self.my[n], self.mz[n])
+                    n, self.label[n], self.type[n], self.u[n], self.v[n], self.w[n],
+                    self.occupancy[n], self.uiso[n],
+                    self.mx[n], self.my[n], self.mz[n]
+                )
         else:
-            out += '  n Atom  u       v       w        Occ  Uiso\n'
-            fmt = '%3.0f %4s %7.4f %7.4f %7.4f   %4.2f %6.4f\n'
+            out += '  n Label Atom  u       v       w        Occ  Uiso\n'
+            fmt = '%3.0f %5s %4s %7.4f %7.4f %7.4f   %4.2f %6.4f\n'
             for n in disprange:
-                out += fmt % (n, self.type[n], self.u[n], self.v[n], self.w[n], self.occupancy[n], self.uiso[n])
+                out += fmt % (
+                    n, self.label[n], self.type[n], self.u[n], self.v[n], self.w[n],
+                    self.occupancy[n], self.uiso[n]
+                )
         return out
 
     def __repr__(self):
@@ -1887,8 +1899,8 @@ class Superstructure(Crystal):
     superstructure Crystal class
     """
 
-    Parent = Crystal()
-    P = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+    #Parent = Crystal()
+    #P = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
 
     def __init__(self, Parent, P):
         """Initialise"""

Dans_Diffraction/classes_fdmnes.py

@@ -256,7 +256,8 @@ def generate_parameters_string(self):
         param_string += '%s Quadrupole                   ! Allows quadrupolar E1E2 terms\n' % quadrupole
         param_string += '! magnetism                    ! performs magnetic calculations\n'
         param_string += ' Density                      ! Outputs the density of states as _sd1.txt\n'
-        param_string += ' Spherical                    ! Outputs the spherical tensors as _sph_.txt\n'
+        param_string += ' Sphere_all                   ! Outputs the spherical tensors as _sph_.txt\n'
+        param_string += ' Cartesian                    ! Outputs the cartesian tensors as _car_.txt\n'
         param_string += ' energpho                     ! output the energies in real terms\n'
         param_string += ' Convolution                  ! Performs the convolution\n\n'