Fix get_chemical_symbols

nomad-coe · Sep 30, 2024 · 6772df4 · 6772df4 · github-actions · Sep 30, 2024
1 parent 8f65497
commit 6772df4
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Showing 2 changed files with 16 additions and 7 deletions.
diff --git a/src/nomad_simulations/schema_packages/model_system.py b/src/nomad_simulations/schema_packages/model_system.py
@@ -391,16 +391,26 @@ def is_equal_cell(self, other) -> bool:
             return False
         return True
 
-    def get_chemical_symbols(self) -> list:
+    def get_chemical_symbols(self, logger: 'BoundLogger') -> list[str]:
         """
         Get the chemical symbols of the atoms in the atomic cell. These are defined on `atoms_state[*].chemical_symbol`.
 
+        Args:
+            logger (BoundLogger): The logger to log messages.
+
         Returns:
             list: The list of chemical symbols of the atoms in the atomic cell.
         """
         if not self.atoms_state:
             return []
-        return [atom_state.chemical_symbol for atom_state in self.atoms_state]
+
+        chemical_symbols = []
+        for atom_state in self.atoms_state:
+            if not atom_state.chemical_symbol:
+                logger.warning('Could not find `AtomsState[*].chemical_symbol`.')
+                return []
+            chemical_symbols.append(atom_state.chemical_symbol)
+        return chemical_symbols
 
     def to_ase_atoms(self, logger: 'BoundLogger') -> Optional[ase.Atoms]:
         """
@@ -414,7 +424,7 @@ def to_ase_atoms(self, logger: 'BoundLogger') -> Optional[ase.Atoms]:
             (Optional[ase.Atoms]): The ASE Atoms object with the basic information from the `AtomicCell`.
         """
         # Initialize ase.Atoms object with labels
-        atoms_labels = self.get_chemical_symbols()
+        atoms_labels = self.get_chemical_symbols(logger=logger)
         ase_atoms = ase.Atoms(symbols=atoms_labels)
 
         # PBC
@@ -456,8 +466,7 @@ def from_ase_atoms(self, ase_atoms: ase.Atoms, logger: 'BoundLogger') -> None:
             logger (BoundLogger): The logger to log messages.
         """
         # `AtomsState[*].chemical_symbol`
-        chemical_symbols = ase_atoms.get_chemical_symbols()
-        for symbol in chemical_symbols:
+        for symbol in ase_atoms.get_chemical_symbols():
             atom_state = AtomsState(chemical_symbol=symbol)
             self.atoms_state.append(atom_state)
 

diff --git a/tests/test_model_system.py b/tests/test_model_system.py
@@ -193,7 +193,7 @@ def test_get_chemical_symbols(self, atomic_cell: AtomicCell, result: list[str]):
         """
         Test the `get_chemical_symbols` method of `AtomicCell`.
         """
-        assert atomic_cell.get_chemical_symbols() == result
+        assert atomic_cell.get_chemical_symbols(logger=logger) == result
 
     @pytest.mark.parametrize(
         'chemical_symbols, atomic_numbers, formula, lattice_vectors, positions, periodic_boundary_conditions',
@@ -334,7 +334,7 @@ def test_from_ase_atoms(
     ):
         atomic_cell = AtomicCell()
         atomic_cell.from_ase_atoms(ase_atoms=ase_atoms, logger=logger)
-        assert atomic_cell.get_chemical_symbols() == chemical_symbols
+        assert atomic_cell.get_chemical_symbols(logger=logger) == chemical_symbols
         assert atomic_cell.periodic_boundary_conditions == pbc
         assert (
             atomic_cell.lattice_vectors.to('angstrom').magnitude
File	Stmts	Miss	Cover	Missing
src/nomad_simulations
__init__.py	4	2	50%	3–4
_version.py	11	2	82%	5–6
src/nomad_simulations/schema_packages
__init__.py	15	2	87%	39–41
atoms_state.py	190	21	89%	13–15, 201–204, 228, 283–284, 352–353, 355, 537, 549–550, 611–615, 630–634, 641
basis_set.py	240	28	88%	8–9, 122–133, 172–185, 208, 391–395, 417–418, 462–465, 584, 615, 617
general.py	89	8	91%	4–7, 121, 185, 295–296, 306
model_method.py	269	78	71%	10–12, 171–174, 177–184, 276–277, 297, 318–339, 355–381, 384–401, 587, 780, 791, 833–840, 878, 897, 977, 1034, 1109, 1223
model_system.py	317	25	92%	25–27, 378, 410–411, 621–624, 671–678, 852–853, 1074–1078, 1084–1085, 1093–1094, 1099, 1122
numerical_settings.py	259	61	76%	12–14, 217, 219–220, 223–226, 230–231, 238–241, 250–253, 257–260, 262–265, 270–273, 279–282, 469–496, 571, 606–609, 633, 636, 681, 683–686, 690, 694, 741, 745–766, 821–822, 889
outputs.py	120	10	92%	9–10, 252–255, 295–298, 323, 325, 362, 381
physical_property.py	102	7	93%	20–22, 202, 331–333
variables.py	86	12	86%	8–10, 98, 121, 145, 167, 189, 211, 233, 256, 276
src/nomad_simulations/schema_packages/properties
band_gap.py	51	5	90%	8–10, 135–136
band_structure.py	123	25	80%	9–11, 232–265, 278, 285, 321–322, 325, 372–373, 378
energies.py	42	9	79%	7–9, 36, 57, 82, 103, 119, 134
fermi_surface.py	17	4	76%	7–9, 40
forces.py	22	6	73%	7–9, 36, 56, 79
greens_function.py	99	13	87%	7–9, 210–211, 214, 235–236, 239, 260–261, 264, 400
hopping_matrix.py	29	5	83%	7–9, 58, 94
permittivity.py	48	8	83%	7–9, 97–105
spectral_profile.py	260	128	51%	9–11, 57–60, 95–98, 199–300, 356–368, 393–396, 416, 421–424, 466–502, 526, 573–576, 592–593, 598–604
thermodynamics.py	75	27	64%	7–9, 35, 56, 72, 81, 90, 101, 110, 137, 147, 157, 172–174, 177, 193, 213–215, 218, 234, 254–256, 259
src/nomad_simulations/schema_packages/utils
utils.py	70	14	80%	8–11, 65–74, 83–84, 89, 92
TOTAL	2549	500	80%