ADF: Task COSMO-RS Compound¶
The ADFCOSMORSCompound class mimics the “Task COSMO-RS Compound” in the AMS ADF graphical user interface.
It is used to generate .coskf files for use with COSMO-RS.
For an example, see ADF and COSMO-RS workflow.
import os
import shutil
from scm.plams import Settings, JobError, AMSJob, CRSJob, Molecule, AMSResults, CRSResults, KFFile
from collections import OrderedDict
from ..core.functions import add_to_instance
from ..core.basejob import MultiJob
from ..core.results import Results
from ..core.settings import Settings
from ..mol.molecule import Molecule
from ..mol.atom import Atom
from ..interfaces.adfsuite.ams import AMSJob
from ..tools.units import Units
from ..interfaces.adfsuite.quickjobs import model_to_settings
from typing import List
import numpy as np
__all__ = ['ADFCOSMORSCompoundJob', 'ADFCOSMORSCompoundResults']
class ADFCOSMORSCompoundResults(Results):
"""Results class for ADFCOSMORSCompoundJob
"""
def coskfpath(self):
"""
Returns the path to the resulting .coskf
"""
return os.path.join(self.job.path, self.job.name+".coskf")
def get_main_molecule(self):
"""
Returns the optimized molecule
"""
return self.job.children['solv'].results.get_main_molecule()
def get_input_molecule(self):
"""
Returns the input molecule
"""
for job in self.job.children.values():
return job.results.get_input_molecule()
def get_sigma_profile(self, subsection: str = 'profil'):
"""
Returns the sigma profile of the molecule. For more details see `CRSResults.get_sigma_profile`.
"""
return self.job.children['crs'].results.get_sigma_profile(subsection = subsection)
class ADFCOSMORSCompoundJob(MultiJob):
"""A class for performing the equivalent of Task COSMO-RS Compound in the AMS GUI
"""
_result_type = ADFCOSMORSCompoundResults
def __init__(self, molecule:Molecule, preoptimization=None, singlepoint=False, settings=None, **kwargs):
"""
Class for running the equivalent of "COSMO-RS Compound" in the AMS
GUI. Note that these are ADF calculations, not COSMO-RS
calculations!
Initialize two or three jobs:
(optional): Preoptimization with force field or semi-empirical method
1. Gasphase optimization (BP86, DZP)
2. Gasphase optimization (BP86, TZP, BeckeGrid Quality Good)
3. Take optimized structure and run singlepoint with implicit solvation
Access the result .coskf file with ``job.results.coskfpath()``.
Note: this file will be called jobname.coskf, where jobname is the
name of the ADFCOSMORSCompoundJob.
molecule : Molecule
The initial structure
preoptimization : str or None
If None, do not preoptimize with a fast engine (then initial optimization is done with ADF). Otherwise, can be one of 'UFF', 'GAFF', 'GFNFF', 'GFN1-xTB', 'ANI-2x'. Note that you need valid licenses for ForceField or DFTB or MLPotential to use these preoptimizers.
singlepoint : bool
Only run a singlepoint with solvation to generate the .coskf file on the given Molecule. (no geometry optimization)
settings : settings
settings.runscript.nproc, settings.input.adf.custom_options. If 'adf' is in settings.input it should be provided without the solvation block.
Usage:
.. code-block:: python
mol = from_smiles('O')
job = ADFCOSMORSCompoundJob(name='water', molecule=mol, preoptimization='UFF')
job.run()
print(job.results.coskfpath())
print(job.results.get_sigma_profile())
"""
MultiJob.__init__(self, children=OrderedDict(), **kwargs)
self.input_molecule = molecule
self.settings = settings or Settings()
if not singlepoint:
if preoptimization:
preoptimization_s = Settings()
preoptimization_s.runscript.nproc = 1
preoptimization_s.input.ams.Task = 'GeometryOptimization'
preoptimization_s += model_to_settings(preoptimization)
preoptimization_job = AMSJob(settings=preoptimization_s, name='preoptimization', molecule=molecule)
self.children['preoptimization'] = preoptimization_job
gas_s = Settings()
gas_s.input.ams.Task = 'GeometryOptimization'
gas_s += self.adf_settings(solvation=False, settings=self.settings)
gas_job = AMSJob(settings=gas_s, name='gas')
if preoptimization:
@add_to_instance(gas_job)
def prerun(self):
self.molecule = self.parent.children['preoptimization'].results.get_main_molecule()
else:
gas_job.molecule = molecule
self.children['gas'] = gas_job
solv_s = Settings()
solv_s.input.ams.Task = 'SinglePoint'
solv_job = AMSJob(settings=solv_s, name='solv')
if singlepoint:
@add_to_instance(solv_job)
def prerun(self):
self.molecule = self.parent.input_molecule
self.settings += self.parent.adf_settings(solvation=True, settings=self.parent.settings, elements=list(set(at.symbol for at in self.parent.input_molecule)))
else:
@add_to_instance(solv_job)
def prerun(self):
gas_job.results.wait()
self.settings.input.ams.EngineRestart = "../gas/adf.rkf"
self.settings.input.ams.LoadSystem.File = "../gas/ams.rkf"
self.settings += self.parent.adf_settings(solvation=True, settings=self.parent.settings, elements=list(set(at.symbol for at in self.parent.input_molecule)))
#self.settings.input.ams.EngineRestart = self.parent.children['gas'].results.rkfpath(file='adf') # this doesn't work with PLAMS restart since the file will refer to the .res directory (so the job is rerun needlessly)
#self.settings.input.ams.LoadSystem.File = self.parent.children['gas'].results.rkfpath(file='ams')
# cannot copy to gasphase-ams.rkf etc. because that conflicts with PLAMS restarts
#shutil.copyfile(gas_job.results.rkfpath(file='ams'), os.path.join(self.path, 'gasphase-ams.rkf'))
#shutil.copyfile(gas_job.results.rkfpath(file='adf'), os.path.join(self.path, 'gasphase-adf.rkf'))
@add_to_instance(solv_job)
def postrun(self):
self.parent.convert_to_coskf(self.results.rkfpath(file='adf'), os.path.join(self.parent.path, self.parent.name+'.coskf'))
self.children['solv'] = solv_job
sigma_s = Settings()
sigma_s.input.property._h = 'PURESIGMAPROFILE'
compounds = [Settings()]
sigma_s.input.compound = compounds
crsjob = CRSJob(settings=sigma_s, name = 'sigma')
@add_to_instance(crsjob)
def prerun(self):
self.parent.children['solv'].results.wait()
self.settings.input.compound[0]._h = os.path.join(self.parent.path, self.parent.name+'.coskf')
self.children['crs'] = crsjob
@staticmethod
def _get_radii() -> dict:
""" Method to get the atomic radii from solvent.txt (for some elements the radii are instead the Klamt radii) """
with open(os.path.expandvars('$AMSHOME/data/gui/solvent.txt'), 'r') as f:
mod_allinger_radii = [float(x) for i,x in enumerate(f) if i > 0]
radii = { PeriodicTable.get_symbol(i) : r for i,r in enumerate(mod_allinger_radii, 1) if i<= 118 }
klamt_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
}
radii.update(klamt_radii)
return radii
@staticmethod
def solvation_settings(elements:List[str]=None) -> Settings:
sett = Settings()
radii = {'H': 1.3, 'He': 1.275, 'Li': 2.125, 'Be': 1.858, 'B': 1.792, 'C': 2.0, 'N': 1.83, 'O': 1.72, 'F': 1.72, 'Ne': 1.333, 'Na': 2.25, 'Mg': 2.025, 'Al': 1.967, 'Si': 2.48, 'P': 2.13, 'S': 2.16, 'Cl': 2.05, 'Ar': 1.658, 'K': 2.575, 'Ca': 2.342, 'Sc': 2.175, 'Ti': 1.992, 'V': 1.908, 'Cr': 1.875, 'Mn': 1.867, 'Fe': 1.858, 'Co': 1.858, 'Ni': 1.85, 'Cu': 1.883, 'Zn': 1.908, 'Ga': 2.05, 'Ge': 2.033, 'As': 1.967, 'Se': 1.908, 'Br': 2.16, 'Kr': 1.792, 'Rb': 2.708, 'Sr': 2.5, 'Y': 2.258, 'Zr': 2.117, 'Nb': 2.025, 'Mo': 1.992, 'Tc': 1.967, 'Ru': 1.95, 'Rh': 1.95, 'Pd': 1.975, 'Ag': 2.025, 'Cd': 2.083, 'In': 2.2, 'Sn': 2.158, 'Sb': 2.1, 'Te': 2.033, 'I': 2.32, 'Xe': 1.9, 'Cs': 2.867, 'Ba': 2.558, 'La': 2.317, 'Ce': 2.283, 'Pr': 2.275, 'Nd': 2.275, 'Pm': 2.267, 'Sm': 2.258, 'Eu': 2.45, 'Gd': 2.258, 'Tb': 2.25, 'Dy': 2.242, 'Ho': 2.225, 'Er': 2.225, 'Tm': 2.225, 'Yb': 2.325, 'Lu': 2.208, 'Hf': 2.108, 'Ta': 2.025, 'W': 1.992, 'Re': 1.975, 'Os': 1.958, 'Ir': 1.967, 'Pt': 1.992, 'Au': 2.025, 'Hg': 2.108, 'Tl': 2.158, 'Pb': 2.283, 'Bi': 2.217, 'Po': 2.158, 'At': 2.092, 'Rn': 2.025, 'Fr': 3.033, 'Ra': 2.725, 'Ac': 2.567, 'Th': 2.283, 'Pa': 2.2, 'U': 2.1, 'Np': 2.1, 'Pu': 2.1, 'Am': 2.1, 'Cm': 2.1, 'Bk': 2.1, 'Cf': 2.1, 'Es': 2.1, 'Fm': 2.1, 'Md': 2.1, 'No': 2.1, 'Lr': 2.1, 'Rf': 2.1, 'Db': 2.1, 'Sg': 2.1, 'Bh': 2.1, 'Hs': 2.1, 'Mt': 2.1, 'Ds': 2.1, 'Rg': 2.1, 'Cn': 2.1, 'Nh': 2.1, 'Fl': 2.1, 'Mc': 2.1, 'Lv': 2.1, 'Ts': 2.1, 'Og': 2.1} # from _get_radii()
if elements:
radii = {k:radii[k] for k in sorted(elements)}
sett.input.adf.solvation = {
'surf': 'Delley',
'solv': 'name=CRS cav0=0.0 cav1=0.0',
'charged': 'method=Conj corr',
'c-mat': 'Exact',
'scf': 'Var All',
'radii': radii,
}
return sett
@staticmethod
def adf_settings(solvation:bool, settings=None, elements:List[str]=None) -> Settings:
"""
Returns ADF settings with or without solvation
If solvation == True, then also include the solvation block.
"""
s = Settings()
if settings:
s = settings.copy()
if 'basis' not in s.input.adf and 'xc' not in s.input.adf:
s.input.adf.Basis.Type = 'TZP'
s.input.adf.Basis.Core = 'Small'
s.input.adf.XC.GGA = 'BP86'
s.input.adf.Symmetry = 'NOSYM'
s.input.adf.BeckeGrid.Quality = 'Good'
if solvation:
s += ADFCOSMORSCompoundJob.solvation_settings(elements=elements)
return s
@staticmethod
def convert_to_coskf(rkf: str, coskf: str):
""" rkf: absolute path to adf.rkf, coskf: path to write out the resulting .coskf file """
f = KFFile(rkf)
cosmo = f.read_section("COSMO")
coskf = KFFile(coskf)
for k,v in cosmo.items():
coskf.write("COSMO",k,v)