Ensure sorted defect supercell structure returned

SMTG-Bham · Oct 11, 2023 · 6da183b · 6da183b
1 parent dbeb6a9
commit 6da183b
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Showing 3 changed files with 17 additions and 8 deletions.
diff --git a/doped/core.py b/doped/core.py
@@ -602,14 +602,16 @@ def _remove_site_oxi_state(site):
         if dummy_species is not None:
             sc_defect_struct.insert(len(self.structure * sc_mat), dummy_species, sc_site.frac_coords)
 
+        sorted_sc_defect_struct = sc_defect_struct.get_sorted_structure()  # ensure proper sorting
+
         return (
             (
-                sc_defect_struct,
+                sorted_sc_defect_struct,
                 sc_site,
                 equiv_sites,
             )
             if return_sites
-            else sc_defect_struct
+            else sorted_sc_defect_struct
         )
 
     def as_dict(self):

diff --git a/doped/vasp.py b/doped/vasp.py
@@ -257,7 +257,14 @@ def poscar(self) -> Poscar:
         """
         Return Poscar object with comment.
         """
-        return Poscar(self.structure, comment=self.poscar_comment)
+        unsorted_poscar = Poscar(self.structure, comment=self.poscar_comment)
+
+        # check if POSCAR should be sorted:
+        if len(unsorted_poscar.site_symbols) == len(set(unsorted_poscar.site_symbols)):
+            # no duplicates, return poscar as is
+            return unsorted_poscar
+
+        return Poscar(self.structure, comment=self.poscar_comment, sort_structure=True)
 
     @property
     def kpoints(self):
@@ -1891,9 +1898,9 @@ def _format_defect_entries_input(
 
     @staticmethod
     def _write_defect(args):
-        defect_species, defect_entry, output_dir, unperturbed_poscar, vasp_gam, bulk, kwargs = args
+        defect_species, defect_relax_set, output_dir, unperturbed_poscar, vasp_gam, bulk, kwargs = args
         defect_dir = os.path.join(output_dir, defect_species)
-        defect_entry.write_all(
+        defect_relax_set.write_all(
             defect_dir=defect_dir,
             unperturbed_poscar=unperturbed_poscar,
             vasp_gam=vasp_gam,
@@ -2022,14 +2029,14 @@ def write_files(
         args_list = [
             (
                 defect_species,
-                defect_entry,
+                defect_relax_set,
                 output_dir,
                 unperturbed_poscar,
                 vasp_gam,
                 bulk if i == 0 else False,  # only write bulk folder(s) for first defect
                 kwargs,
             )
-            for i, (defect_species, defect_entry) in enumerate(self.defect_sets.items())
+            for i, (defect_species, defect_relax_set) in enumerate(self.defect_sets.items())
         ]
         with Pool(processes=processes or cpu_count() - 1) as pool:
             for _ in tqdm(

diff --git a/pyproject.toml b/pyproject.toml
@@ -21,7 +21,7 @@ dependencies = [
     "tabulate",
     "matplotlib>=3.5.2",
     "numpy>=1.21.0",
-    "pymatgen>=2023.5.8",  # imposed by pymatgen-analysis-defects
+    "pymatgen>=2023.8.10",
     "pymatgen-analysis-defects>=2023.8.22",
     "shakenbreak>=3.2.0",
     "pandas",