def _overlay_s_plams(self, lj: Iterable[Mapping],
sigma_dict: MutableMapping,
epsilon_dict: MutableMapping) -> None:
"""Extract PLAMS-style settings from **lj** and put them in **sigma_dict** and **epsilon_dict**.""" # noqa: E501
for block in lj:
with Settings.suppress_missing():
atoms = tuple(block['atoms'].split())
try:
unit_sigma, sigma = block['sigma'].split()
except ValueError:
unit_sigma, sigma = '[angstrom]', block['sigma']
except (TypeError, KeyError):
unit_sigma = sigma = None
try:
unit_eps, epsilon = block['epsilon'].split()
except ValueError:
unit_eps, epsilon = '[kcalmol]', block['sigma']
except (TypeError, KeyError):
unit_eps = epsilon = None
if sigma is not None:
unit_sigma = unit_sigma[1:-1]
unit_sigma = self.UNIT_MAPPING.get(unit_sigma, unit_sigma)
sigma_dict[unit_sigma][atoms] = float(sigma)
if epsilon is not None:
unit_eps = unit_eps[1:-1]
unit_eps = self.UNIT_MAPPING.get(unit_eps, unit_eps)
epsilon_dict[unit_eps][atoms] = float(epsilon)
def from_template(cls, settings: Union[Settings, SettingsDataFrame], name: str) -> 'WorkFlow':
"""Construct a :class:`WorkFlow` instance from a |plams.Settings| object.
Parameters
----------
settings : |plams.Settings|
A Settings instance with all CAT settings.
Certain values are extracted from **settings** based on the supplied template
(see **name**).
name : :class:`str`
The name of the settings template.
See Also
--------
:attr:`WorkFlow._WORKFLOW_TEMPLATES`
A dictionary with all available template names (*i.e.* its keys).
"""
# Extract the settings object from the SettingsDataFrame
if isinstance(settings, SettingsDataFrame):
settings = settings.settings
kwargs: Dict[str, Any] = {'name': name}
# Raise a KeyError if a key cannot be found
with Settings.suppress_missing():
try: # Extract the correct template
template = cls._WORKFLOW_TEMPLATES[name]['template']
except KeyError as ex:
err = (f"Invalid value for the 'name' parameter: {name!r}\n"
f"Allowed values: {', '.join(repr(k) for k in cls._WORKFLOW_TEMPLATES)}")
raise ValueError(err) from ex
# Create a dictionary with keyword arguments
for k, v in template.items():
kwargs[k] = settings.get_nested(v)
# Post process all jobs and job settings
kwargs['jobs'] = pop_and_concatenate(kwargs, 'job')
kwargs['settings'] = pop_and_concatenate(kwargs, 's')
return cls.from_dict(kwargs)
