def get_surface_charge_adf(mol: Molecule, job: Type[Job],
s: Settings) -> Settings:
"""Perform a gas-phase ADF single point and return settings for a COSMO-ADF single point.
The previous gas-phase calculation as moleculair fragment.
Parameters
----------
mol : |plams.Molecule|_
A PLAMS Molecule.
job : |Callable|_
A type Callable of a class derived from :class:`Job`, e.g. :class:`AMSJob`
or :class:`Cp2kJob`.
s : |plams.Settings|_
The settings for **job**.
Returns
-------
|plams.Settings|_
A new Settings intance, constructed from **s**, suitable for DFT COSMO-RS calculations.
"""
s.input.allpoints = ''
results = mol.job_single_point(job, s, ret_results=True)
coskf = get_coskf(results)
for at in mol:
at.properties.adf.fragment = 'gas'
s.update(get_template('qd.yaml')['COSMO-ADF'])
s.input.fragments.gas = coskf
return s
def pre_process_settings(mol: Molecule, s: Settings, job_type: Type[Job],
template_name: str) -> Settings:
"""Update all :class:`Settings`, **s**, with those from a QMFlows template (see **job**)."""
ret = Settings()
type_key = type_to_string(job_type)
ret.input = getattr(qmflows, template_name)['specific'][type_key].copy()
ret.update(s)
if job_type is AMSJob:
mol.properties.pop('charge', None)
# ret.input.ams.system.BondOrders._1 = adf_connectivity(mol)
if 'uff' not in s.input:
ret.input.ams.system.charge = int(
sum(at.properties.get('charge', 0) for at in mol))
elif job_type is ADFJob:
mol.properties.pop('charge', None)
if not ret.input.charge:
ret.input.charge = int(
sum(at.properties.get('charge', 0) for at in mol))
return ret
