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 update_ff_jobs(s: Settings) -> None:
"""Update forcefield settings."""
if NANO_CAT is not None:
raise NANO_CAT
ff = Settings()
set_cp2k_param(ff, s.optional.forcefield)
optimize = s.optional.qd.optimize
if optimize and optimize.use_ff:
if optimize.job1 and str(optimize.job1) == str(Cp2kJob):
optimize.s1 = Settings() if optimize.s1 is None else optimize.s1
optimize.s1 += get_template('qd.yaml')['CP2K_CHARM_opt']
optimize.s1 += ff
if optimize.job2 and str(optimize.job1) == str(Cp2kJob):
optimize.s2 = Settings() if optimize.s2 is None else optimize.s2
optimize.s2 += get_template('qd.yaml')['CP2K_CHARM_opt']
optimize.s2 += ff
dissociate = s.optional.qd.dissociate
if dissociate and dissociate.use_ff:
if dissociate.job1 and str(dissociate.job1) == str(Cp2kJob):
dissociate.s1 = Settings(
) if dissociate.s1 is None else dissociate.s1
dissociate.s1 += get_template('qd.yaml')['CP2K_CHARM_opt']
dissociate.s1 += ff
activation_strain = s.optional.qd.activation_strain
if activation_strain and activation_strain.use_ff:
if activation_strain.job1 and str(
activation_strain.job1) == str(Cp2kJob):
key = 'CP2K_CHARM_singlepoint' if not activation_strain.md else 'CP2K_CHARM_md'
activation_strain.s1 = Settings(
) if activation_strain.s1 is None else activation_strain.s1 # noqa
activation_strain.s1 += get_template('qd.yaml')[key]
activation_strain.s1 += ff
def _get_logp(s: Settings, name: str, logger: logging.Logger) -> float:
logp_s = s.copy()
logp_s.update(get_template('qd.yaml')['COSMO-RS logp'])
for v in logp_s.input.compound:
v._h = v._h.format(os.environ["ADFRESOURCES"])
logp_job = CRSJob(settings=logp_s, name='LogP')
results = _crs_run(logp_job, name)
try:
logp = results.readkf('LOGP', 'logp')[0]
logger.info(f'{results.job.__class__.__name__}: {name} LogP '
f'calculation ({results.job.name}) is successful')
except Exception:
logger.error(f'{results.job.__class__.__name__}: {name} LogP '
f'calculation ({results.job.name}) has failed')
logp = np.nan
return logp
def _preoptimize(mol: Molecule) -> None:
"""Perform a constrained geometry optimization of **mol** with AMS UFF."""
s = get_template('qd.yaml')['UFF']
s.input.ams.constraints.atom = mol.properties.indices
s.input.ams.GeometryOptimization.coordinatetype = 'Cartesian'
mol.job_geometry_opt(AMSJob, s, name='E_XYn_preopt')
#: Print time for each log event
time: bool
#: Print date for each log event
date: bool
__all__ = [
"get_compkf",
"get_fast_sigma_properties",
"run_fast_sigma",
"read_csv",
"sanitize_smiles_df",
]
LOGP_SETTINGS = get_template('qd.yaml')['COSMO-RS logp']
LOGP_SETTINGS.runscript.nproc = 1
LOGP_SETTINGS.update(get_template('crs.yaml')['ADF combi2005'])
LOGP_SETTINGS.input.property.volumequotient = 6.766
GAMMA_E_SETTINGS = get_template('qd.yaml')['COSMO-RS activity coefficient']
GAMMA_E_SETTINGS.runscript.nproc = 1
GAMMA_E_SETTINGS.update(get_template('crs.yaml')['ADF combi2005'])
del GAMMA_E_SETTINGS.input.compound[0]
SOL_SETTINGS = copy.deepcopy(GAMMA_E_SETTINGS)
SOL_SETTINGS.input.property._h = "puresolubility"
SOL_SETTINGS.input.temperature = "298.15 298.15 1"
SOL_SETTINGS.input.pressure = "1.01325"
SOL_SETTINGS.input.compound = [Settings({"_h": None, "_1": "compkffile"})]