def sample_record() -> MoleculeData:
md = MoleculeData.from_identifier('O')
result = OptimizationResult.parse_file(
_my_path.joinpath('records/xtb-neutral.json'))
md.add_geometry(result, "xtb")
md.subsets.append('pytest')
return md
def test_add_data():
md = MoleculeData.from_identifier("O")
# Load the xtb geometry
xtb_geom = OptimizationResult.parse_file(
_my_path.joinpath('records/xtb-neutral.json'))
md.add_geometry(xtb_geom)
assert "xtb" in md.data
assert "neutral" in md.data["xtb"]
assert isclose(md.data["xtb"][
OxidationState.NEUTRAL].atomization_energy["xtb-no_zpe"],
-0.515,
abs_tol=1e-2)
assert ("xtb", "neutral") == md.match_geometry(xtb_geom.final_molecule)
# Load in a relaxed oxidized geometry
xtb_geom_ox = OptimizationResult.parse_file(
_my_path.joinpath('records/xtb-oxidized.json'))
md.add_geometry(xtb_geom_ox)
assert "xtb" in md.data
assert "oxidized" in md.data["xtb"]
assert ("xtb",
"neutral") == md.match_geometry(xtb_geom_ox.initial_molecule)
assert ("xtb", "oxidized") == md.match_geometry(xtb_geom_ox.final_molecule)
assert md.data['xtb'][OxidationState.OXIDIZED].total_energy[OxidationState.OXIDIZED]['xtb'] != \
md.data['xtb'][OxidationState.NEUTRAL].total_energy[OxidationState.OXIDIZED]['xtb']
# Load in a oxidized energy for the neutral structure
xtb_energy = AtomicResult.parse_file(
_my_path.joinpath('records/xtb-neutral_xtb-oxidized-energy.json'))
md.add_single_point(xtb_energy)
# Add in solvation energies
xtb_energy = AtomicResult.parse_file(
_my_path.joinpath('records/xtb-neutral_acn.json'))
md.add_single_point(xtb_energy)
assert "acetonitrile" in md.data['xtb']['neutral'].solvation_energy[
'neutral']
xtb_energy = AtomicResult.parse_file(
_my_path.joinpath('records/xtb-oxidized_acn.json'))
md.add_single_point(xtb_energy)
assert "acetonitrile" in md.data['xtb']['oxidized'].solvation_energy[
'oxidized']
# Show that we can compute a redox potential
recipe = RedoxEnergyRecipe(name="xtb-vertical",
geometry_level="xtb",
energy_level="xtb",
adiabatic=False)
result = recipe.compute_redox_potential(md, OxidationState.OXIDIZED)
assert md.oxidation_potential['xtb-vertical'] == result
recipe = RedoxEnergyRecipe(name="xtb",
geometry_level="xtb",
energy_level="xtb",
adiabatic=True)
result = recipe.compute_redox_potential(md, OxidationState.OXIDIZED)
assert md.oxidation_potential['xtb'] == result
assert md.oxidation_potential['xtb'] < md.oxidation_potential[
'xtb-vertical']
recipe = RedoxEnergyRecipe(name="xtb-acn",
geometry_level="xtb",
energy_level="xtb",
adiabatic=True,
solvent='acetonitrile',
solvation_level='xtb')
result = recipe.compute_redox_potential(md, OxidationState.OXIDIZED)
assert md.oxidation_potential['xtb-acn'] == result
assert md.oxidation_potential['xtb-acn'] != md.oxidation_potential['xtb']
# Add a single point small_basis computation
smb_hessian = AtomicResult.parse_file(
_my_path.joinpath('records/xtb-neutral_smb-neutral-hessian.json'))
md.add_single_point(smb_hessian)
assert isclose(md.data["xtb"][OxidationState.NEUTRAL].zpe[
OxidationState.NEUTRAL]['small_basis'],
0.02155,
abs_tol=1e-3)
# Add an NWChem with solvent
smb_solvent = AtomicResult.parse_file(
_my_path.joinpath('records/xtb-neutral_smb-neutral_water.json'))
md.add_single_point(smb_solvent)
assert 'small_basis' in md.data['xtb']['neutral'].total_energy_in_solvent[
'neutral']['water']