def allign_axis(mol: Molecule, anchor: Atom):
"""Allign a molecule with the Cartesian X-axis; setting **anchor** as the origin."""
try:
idx = mol.atoms.index(anchor)
except ValueError as ex:
raise MoleculeError("The passed anchor is not in mol") from ex
xyz = mol.as_array() # Allign the molecule with the X-axis
rotmat = optimize_rotmat(xyz, idx)
xyz[:] = xyz @ rotmat.T
xyz -= xyz[idx]
xyz[:] = xyz.round(decimals=3)
mol.from_array(xyz)
def __exit__(self, exc_type, exc_value, traceback) -> None:
"""Exit the context manager; update the Cartesian coordinates of :attr:`AsArray.mol`."""
Molecule.from_array(None, self._xyz, atom_subset=self.mol)
self._xyz = None
def retrieve_results(mol: Molecule, results: Results, job_preset: str) -> None:
"""Unpack the :class:`results` from a PLAMS-facilitated calculation.
Performs an inplace update of **results**:
* The Cartesian coordinates of :attr:`Results.job.molecule` are updated.
* Energies and frequencies are added to :attr:`Results.job.molecule.properties`.
*
Paramaters
----------
mol : |plams.Molecule|_
A PLAMS molecule.
results : |plams.Results|_
A PLAMS :class:`Results` instance.
job_preset : str
The name of a job preset from :mod:`CAT.jobs`.
Accepted values are ``"single point"``, ``"geometry optimization"`` or
``"frequency analysis"``.
"""
if job_preset not in JOB_PRESETS:
raise ValueError(f'Invalid value for job_preset: {job_preset!r}')
# Unpack arguments
job = results.job
name = job.name
# Define more arguments
freq = np.empty(1)
nan_dict = {
'frequencies': np.nan,
'energy': {
'E': np.nan,
'H': np.nan,
'S': np.nan,
'G': np.nan
}
}
try:
if job.status in {'failed', 'crashed'}:
raise _get_results_error(results)
# Read all relevant results
energy = mol.properties.energy.E = results.get_energy(unit='kcal/mol')
if job_preset in ('geometry optimization', 'frequency analysis'):
mol_new = results.get_main_molecule() or Molecule()
mol.from_array(mol_new)
if job_preset == 'frequency analysis':
freq = mol.properties.frequencies = results.get_frequencies()
energy = mol.properties.energy = get_thermo(mol, freq, energy)
# Evaluate all results
if not (energy and isinstance(freq, np.ndarray)):
raise _get_results_error(results)
log_succes(job, mol, job_preset, name)
except Exception as ex: # Failed to retrieve results
if job_preset == 'geometry optimization':
mol.properties.is_opt = False
mol.properties.soft_update(nan_dict)
log_fail(job, mol, job_preset, name)
logger.debug(f'{ex.__class__.__name__}: {ex}', exc_info=True)
else:
if job_preset == 'geometry optimization':
mol.properties.is_opt = True
if job.status != 'copied':
return None
# results.job is a copy from a previously run job.
# Exchange the attributes of results.job wth those of the revious job
job_old = config.default_jobmanager.hashes[job._hash]()
log_copy(job, mol, job_preset, name, job_old)
rmtree(job.path)
for key, value in vars(job_old).items():
if key != 'molecule':
setattr(job, key, value)
return None
