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Reinsert get_chemical_symbols
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ndaelman committed Oct 15, 2024
1 parent ad29fa0 commit 4887cb4
Showing 1 changed file with 20 additions and 0 deletions.
20 changes: 20 additions & 0 deletions src/nomad_simulations/schema_packages/model_system.py
Original file line number Diff line number Diff line change
Expand Up @@ -454,6 +454,26 @@ def _generate_comparer(obj: 'AtomicCell') -> 'Generator[Any, None, None]':
except AttributeError:
raise NotImplementedError

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 []

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]':
"""
Generates an ASE Atoms object with the most basic information from the parsed `AtomicCell`
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Coverage

Coverage Report
FileStmtsMissCoverMissing
src/nomad_simulations
   __init__.py4250%3–4
   _version.py11282%5–6
src/nomad_simulations/schema_packages
   __init__.py15287%39–41
   atoms_state.py1902189%13–15, 201–204, 228, 283–284, 352–353, 355, 537, 549–550, 611–615, 630–634, 641
   basis_set.py2402888%8–9, 122–133, 172–185, 208, 391–395, 417–418, 462–465, 584, 615, 617
   general.py89891%4–7, 121, 185, 295–296, 306
   model_method.py2697871%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.py3483789%45–51, 235, 254, 258, 261, 264, 290, 376–377, 454–455, 472–473, 686–689, 736–743, 917–918, 1139–1143, 1149–1150, 1158–1159, 1164, 1187
   numerical_settings.py2596176%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.py1201092%9–10, 252–255, 295–298, 323, 325, 362, 381
   physical_property.py102793%20–22, 202, 331–333
   variables.py861286%8–10, 98, 121, 145, 167, 189, 211, 233, 256, 276
src/nomad_simulations/schema_packages/properties
   band_gap.py51590%8–10, 135–136
   band_structure.py1232580%9–11, 232–265, 278, 285, 321–322, 325, 372–373, 378
   energies.py42979%7–9, 36, 57, 82, 103, 119, 134
   fermi_surface.py17476%7–9, 40
   forces.py22673%7–9, 36, 56, 79
   greens_function.py991387%7–9, 210–211, 214, 235–236, 239, 260–261, 264, 400
   hopping_matrix.py29583%7–9, 58, 94
   permittivity.py48883%7–9, 97–105
   spectral_profile.py26012851%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.py752764%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.py791680%8–11, 65–74, 83–84, 89, 92, 169–170
TOTAL258951480% 

Tests Skipped Failures Errors Time
402 0 💤 0 ❌ 0 🔥 5.940s ⏱️

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