Merge pull request #338 from pyiron/atoms_order

Consistent atoms order
pyiron · Sep 18, 2021 · 97a1d0b · 97a1d0b
2 parents 3b7f9b6 + 45d6571
commit 97a1d0b
Show file tree

Hide file tree

Showing 3 changed files with 24 additions and 2 deletions.
diff --git a/pyiron_atomistics/atomistics/structure/atoms.py b/pyiron_atomistics/atomistics/structure/atoms.py
@@ -165,8 +165,8 @@ def __init__(
             if el_object_list is None:
                 el_object_list = [self.convert_element(el) for el in element_list]
 
-            self.set_species(list(set(el_object_list)))
-            # species_to_index_dict = {el: i for i, el in enumerate(self.species)}
+            # Create a list from a set but always preserve order
+            self.set_species(list(dict.fromkeys(el_object_list)))
             el_index_lst = [self._species_to_index_dict[el] for el in el_object_list]
 
         elif indices is not None:

diff --git a/tests/static/vasp_test_files/poscar_samples/POSCAR_diff_species b/tests/static/vasp_test_files/poscar_samples/POSCAR_diff_species
@@ -0,0 +1,11 @@
+POSCAR file written by Ovito Basic 3.0.0
+    1.00000000000000
+        12.4524250200999997    0.0000000000000000    0.0000157408058710
+        -3.1131062549999999    5.3920451819000004   -0.0000039352014677
+         0.0000530996979940    0.0000000000000000   40.4697188976000035
+Ca   Mg   Al
+1    1    1
+Cartesian
+6.2262054545 8.8300000128e-06  1.9039669849
+0.3113441054 0.5391959194  18.3309003343
+3.1131124744 5.3920363513  12.0213927741
diff --git a/tests/vasp/test_structure.py b/tests/vasp/test_structure.py
@@ -48,6 +48,17 @@ def test_atoms_from_string(self):
                     self.assertRaises(AssertionError, atoms_from_string, string=lines)
                 else:
                     atoms = atoms_from_string(string=lines)
+                    if "diff_species" in poscar_file:
+                        for _ in range(10):
+                            atoms = atoms_from_string(string=lines)
+                            self.assertEqual(atoms.indices.tolist(), [0, 1, 2])
+                            self.assertEqual(" ".join(atoms.get_chemical_symbols()), " ".join(["Ca", "Mg", "Al"]))
+                            self.assertTrue(np.allclose(atoms.positions[atoms.select_index("Ca")],
+                                                        np.array([6.2262054545, 8.8300000128e-06,  1.9039669849])))
+                            self.assertTrue(np.allclose(atoms.positions[atoms.select_index("Mg")],
+                                                        np.array([0.3113441054, 0.5391959194,  18.3309003343])))
+                            self.assertTrue(np.allclose(atoms.positions[atoms.select_index("Al")],
+                                                        np.array([3.1131124744, 5.3920363513,  12.0213927741])))
                     self.assertIsInstance(atoms, Atoms)
 
     def test_read_atoms(self):