ASE supercell generation (#22)

* ase sc

* fixed tests

Author: jmmshn

pymatgen/analysis/defects/supercells.py

@@ -126,12 +126,15 @@ def _ase_cubic(base_struture, min_atoms: int = 80, max_atoms: int = 240):
     from ase.build import find_optimal_cell_shape, get_deviation_from_optimal_cell_shape
     from pymatgen.io.ase import AseAtomsAdaptor
 
+    _logger.info("ASE cubic supercell generation.")
+
     aaa = AseAtomsAdaptor()
     ase_atoms = aaa.get_atoms(base_struture)
     lower = math.ceil(min_atoms / base_struture.num_sites)
     upper = math.floor(max_atoms / base_struture.num_sites)
     min_dev = (float("inf"), None)
     for size in range(lower, upper + 1):
+        _logger.info(f"Trying size {size} out of {upper}.")
         sc = find_optimal_cell_shape(
             ase_atoms.cell, target_size=size, target_shape="sc"
         )

tests/test_supercells.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from pymatgen.analysis.defects.supercells import (
+    _ase_cubic,
     get_matched_structure_mapping,
     get_sc_fromstruct,
 )
@@ -18,3 +19,10 @@ def test_supercells(gan_struct):
     np.testing.assert_allclose(
         sc.lattice.abc, sc2.lattice.abc
     )  # the sc_mat can be reconstructed from the sc
+
+
+def test_ase_supercells(gan_struct):
+    sc_mat = _ase_cubic(gan_struct, min_atoms=4, max_atoms=8)
+    sc = gan_struct * sc_mat
+    assert 4 <= sc.num_sites <= 8
+    assert False