5.3.1. ADF and COSMO-RS workflow¶
(contributed by Bas van Beek)
-
run_crs_adf(settings_adf, settings_crs, solvents, solutes=None, return_adfresults=False, **kwargs)[source]¶ A workflow for running COSMO-RS calculations with ADF (i.e. DFT) COSMO surface charges.
The workflow consists of three distinct steps:
- Perform gas-phase
ADFJobcalculations on the solvents and solutes (see settings_adf). - Perform COSMO
ADFJobcalculations using the .t21 file from step 1. as molecular fragment (see settings_adf). This ensures that zero-point is defined by the gas-phase molecule than the gas-phase atomic fragments. - Perform a COSMO-RS calculations with the COSMO surface charges produced in step 2 (see settings_crs). This calculation is conducted for all possible solvent/solute pairs, assuming solutes have been specified by the user.
The adf solvation block (adf_settings.input.solvation) is soft updated with suitable settings for constructing COSMO-RS compatible surface charges (see
add_solvation_block()). No user-specified values are overwritten during this process.Examples
An example value for settings_adf:
>>> from scm.plams import Settings >>> settings_adf = Settings() >>> settings_adf.input.basis.type = 'TZ2P' >>> settings_adf.input.xc.gga = 'BP86' >>> settings_adf.input.scf.converge = '1.0e-06'
An example value for settings_crs (activity coefficient calculation):
>>> settings_crs = Settings() >>> settings_crs.input.temperature = 298.15 >>> settings_crs.input.property._h = 'activitycoef'
And finally the actual calculation with methanol, ethanol and propanol as solvents and acetic acid as solute:
>>> solvents = [Molecule('methanol.xyz'), Molecule('ethanol.xyz'), Molecule('propanol.xyz')] >>> solutes = Molecule('acetic_acid.xyz') >>> crs_dict = run_crs_adf(settings_adf, settings_crs, solvents, solutes) >>> print(crs_dict) {'CRSJob.methanol.acetic_acid': <scm.plams.interfaces.adfsuite.crs.CRSResults object at 0x7f89b0355668>, 'CRSJob.ethanol.acetic_acid': <scm.plams.interfaces.adfsuite.crs.CRSResults object at 0x7f89b0355f60>, 'CRSJob.propanol.acetic_acid': <scm.plams.interfaces.adfsuite.crs.CRSResults object at 0x7f89b0355b00>}
Parameters: - settings_adf (
Settings) – A Settings instance with settings forADFJob(see Examples). - settings_crs (
Settings) – A Settings instance with settings forCRSJob(see Examples). - solvents (
Moleculeorlist[Molecule]) – A Molecule or list of one or more Molecules representing solvents. - solutes (
Moleculeorlist[Molecule], optional) – An optional Molecule or list of one or more Molecules representing solutes. - return_adfresults (
bool) – IfTrue, return both the solvent and solute ADF results in addition to the final COSMO-RS. - optional (**kwargs,) – Optional keyword arguments that will be passed to all calls of
Job.run(). For example, one could consider passing a custom Job runners or Job manager.
Returns: A dictionary with the resulting COSMO-RS output. The name of each
CRSResultsinstance is used as key. Ifreturn_adfresults=True, return both the COSMO-RS and ADF solvent and solute results.Return type: - Perform gas-phase
The source code:
from scm.plams import Settings, JobError, ADFJob, CRSJob, Molecule, ADFResults, ig, CRSResults
__all__ = ['run_crs_adf']
def run_crs_adf(settings_adf, settings_crs,
solvents, solutes=None,
return_adfresults=False, **kwargs):
"""A workflow for running COSMO-RS calculations with ADF (*i.e.* DFT) COSMO surface charges.
The workflow consists of three distinct steps:
1. Perform gas-phase |ADFJob| calculations on the solvents and solutes (see *settings_adf*).
2. Perform COSMO |ADFJob| calculations using the .t21 file from step 1. as molecular
fragment (see *settings_adf*).
This ensures that zero-point is defined by the gas-phase molecule than the gas-phase
atomic fragments.
3. Perform a COSMO-RS calculations with the COSMO surface charges produced in step 2
(see *settings_crs*).
This calculation is conducted for all possible solvent/solute pairs,
assuming solutes have been specified by the user.
The adf solvation block (*adf_settings.input.solvation*) is soft updated with suitable
settings for constructing COSMO-RS compatible surface charges
(see :func:`.add_solvation_block`).
No user-specified values are overwritten during this process.
.. admonition:: Examples
An example value for *settings_adf*:
.. code:: python
>>> from scm.plams import Settings
>>> settings_adf = Settings()
>>> settings_adf.input.basis.type = 'TZ2P'
>>> settings_adf.input.xc.gga = 'BP86'
>>> settings_adf.input.scf.converge = '1.0e-06'
An example value for *settings_crs* (`activity coefficient`_ calculation):
.. code:: python
>>> settings_crs = Settings()
>>> settings_crs.input.temperature = 298.15
>>> settings_crs.input.property._h = 'activitycoef'
And finally the actual calculation with methanol, ethanol and propanol as solvents and
acetic acid as solute:
.. code:: python
>>> solvents = [Molecule('methanol.xyz'), Molecule('ethanol.xyz'), Molecule('propanol.xyz')]
>>> solutes = Molecule('acetic_acid.xyz')
>>> crs_dict = run_crs_adf(settings_adf, settings_crs, solvents, solutes)
>>> print(crs_dict)
{'CRSJob.methanol.acetic_acid': <scm.plams.interfaces.adfsuite.crs.CRSResults object at 0x7f89b0355668>,
'CRSJob.ethanol.acetic_acid': <scm.plams.interfaces.adfsuite.crs.CRSResults object at 0x7f89b0355f60>,
'CRSJob.propanol.acetic_acid': <scm.plams.interfaces.adfsuite.crs.CRSResults object at 0x7f89b0355b00>}
:type settings_adf: :class:`.Settings`
:parameter settings_adf:
A Settings instance with settings for :class:`.ADFJob` (see Examples).
:type settings_crs: :class:`.Settings`
:parameter settings_crs:
A Settings instance with settings for :class:`.CRSJob` (see Examples).
:type solvents: |Molecule| or :class:`list` [|Molecule|]
:parameter solvents: A Molecule or list of one or more Molecules representing solvents.
:type solutes: |Molecule| or :class:`list` [|Molecule|], optional
:parameter solutes: An optional Molecule or list of one or more Molecules representing solutes.
:type return_adfresults: :class:`bool`
:parameter return_adfresults: If ``True``, return both the solvent and solute ADF results in addition to the final COSMO-RS.
:parameter \**kwargs, optional:
Optional keyword arguments that will be passed to all calls of :meth:`.Job.run`.
For example, one could consider passing a custom :ref:`job_runners` or :ref:`job_manager`.
:returns: A dictionary with the resulting COSMO-RS output.
The `name` of each :class:`.CRSResults` instance is used as key.
If ``return_adfresults=True``, return both the COSMO-RS and ADF solvent and solute results.
:rtype: :class:`dict` or :class:`tuple` [:class:`dict`, :class:`list`, :class:`list`]
.. _`activity coefficient`: ../../COSMO-RS/Properties.html#activity-coefficients-solvent-and-solute
""" # noqa
solvents = [solvents] if isinstance(solvents, Molecule) else solvents
solutes = [solutes] if isinstance(solutes, Molecule) else solutes
# Validate arguments
_settings_adf = add_solvation_block(settings_adf)
_validate_settings_adf(_settings_adf)
# Decapitalize the "solvation" and "allpoints" keys
if ig('solvation') in _settings_adf.settings.input:
_settings_adf.input.solvation = _settings_adf.settings.input.pop(ig('solvation'))
if ig('allpoints') in _settings_adf.settings.input:
_settings_adf.input.allpoints = _settings_adf.settings.input.pop(ig('allpoints'))
# Create the COSMO surfaces for the solute
solvent_list = [run_adfjob(mol, _settings_adf, **kwargs) for mol in solvents]
solute_list = [run_adfjob(mol, _settings_adf, **kwargs) for mol in solutes]
if not solutes:
solute_list = [None]
# Start the and return the COSMO-RS job
crs = {}
for solvent in solvent_list:
for solute in solute_list:
results = run_crsjob(solvent, settings_crs, solute=solute, **kwargs)
crs[results.job.name] = results
if not return_adfresults:
return crs
else:
return crs, solvent_list, solute_list
def run_adfjob(mol: Molecule, s: Settings, **kwargs) -> ADFResults:
"""Run an :class:`.ADFJob` on *mol* using the settings provided in *s*."""
name = 'ADFJob.' + mol.properties.name if 'name' in mol.properties else 'ADFJob.mol'
# Create the gas-phase molecular fragment
job1 = ADFJob(molecule=mol, settings=s, name=name+'.gas')
job1.settings.input.allpoints = ''
del job1.settings.input.solvation
results1 = job1.run(**kwargs)
restart1 = results1['$JN.t21']
# Construct the ADF COSMO surface
job2 = ADFJob(molecule=mol, settings=s, depend=[job1], name=name)
job2.settings.input.allpoints = ''
job2.settings.input.fragments.gas = restart1
for at in job2.molecule:
at.properties.adf.fragment = 'gas'
return job2.run(**kwargs)
def run_crsjob(solvent: ADFResults, s: Settings, solute: ADFResults = None, **kwargs) -> CRSResults:
"""Run an :class:`.CRSJob` on with *solvent* and, optionally, *solute* using the settings provided in *s*."""
name = 'CRSJob.' + solvent.job.name.split('.')[1]
if solute is not None:
name += '.' + solute.job.name.split('.')[1]
job = CRSJob(settings=s, depend=[solvent.job, solute.job], name=name)
set_header(job.settings, solvent['$JN.t21'], solute['$JN.t21'])
else:
job = CRSJob(settings=s, depend=[solvent.job], name=name)
set_header(job.settings, solvent['$JN.t21'])
return job.run(**kwargs)
def set_header(s: Settings, *values: str) -> None:
"""Assign *value* to the ``["_h"]`` key in *s.input.compound*."""
s.input.compound = []
for item in values:
s.input.compound.append(Settings({'_h': item}))
s.input.compound[0].frac1 = 1.0 # The first item in *values should be the solvent
def add_solvation_block(adf_settings: Settings) -> None:
"""Add the solvation block to *adf_settings*, returning a copy of the new settings.
The solvation block (*adf_settings.input.solvation*) is soft updated
with the following Settings:
.. code::
c-mat: Exact
charged: method=Conj
radii:
Br: 2.16
C: 2.0
Cl: 2.05
F: 1.72
H: 1.3
I: 2.32
N: 1.83
O: 1.72
P: 2.13
S: 2.16
Si: 2.48
scf: Var All
solv: name=CRS cav0=0.0 cav1=0.0
surf: Delley
"""
# Find the solvation key
solvation = adf_settings.input.find_case('solvation')
solvation_block = adf_settings.input[solvation]
# Find all keys for within the solvation block
keys = ('surf', 'solv', 'charged', 'c-mat', 'scf', 'radii')
surf, solv, charged, cmat, scf, radii = [solvation_block.find_case(item) for item in keys]
# Construct the default solvation block
solvation_block_new = {
surf: 'Delley',
solv: 'name=CRS cav0=0.0 cav1=0.0',
charged: 'method=Conj',
cmat: 'Exact',
scf: 'Var All',
radii: {
'H': 1.30,
'C': 2.00,
'N': 1.83,
'O': 1.72,
'F': 1.72,
'Si': 2.48,
'P': 2.13,
'S': 2.16,
'Cl': 2.05,
'Br': 2.16,
'I': 2.32
}
}
# Copy adf_settings and perform a soft update
ret = adf_settings.copy()
ret.input[solvation].soft_update(solvation_block_new)
return ret
def _validate_settings_adf(s: Settings) -> None:
"""Validate the *settings_adf* argument in :func:`run_crs_adf`."""
solvation = s.input.find_case('solvation')
solv = s.input[solvation].find_case('solv')
if solvation not in s.input:
raise JobError("run_crs_adf: The 'solvation' key is absent"
" from settings_adf.input'")
if solv not in s.input[solvation]:
raise JobError("run_crs_adf: The 'solv' key is absent"
" from settings_adf.input.solvation")
if 'name=crs' not in s.input[solvation][solv].lower():
raise JobError("run_crs_adf: The 'name=CRS' value is absent"
" from settings_adf.input.solvation.solv")