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"""
Module to provide lightweight definitions of emperical dispersion terms.
"""
from psi4 import core
from psi4.driver.qcdb import interface_dftd3 as dftd3
from psi4.driver.qcdb import interface_gcp as gcp
[docs]class EmpericalDispersion(object):
def __init__(self, alias, dtype, **kwargs):
self.alias = alias.upper() # Functional Alias
# Figure out dispersion type
if dtype[0] != "-":
dtype = "-" + dtype
tuple_params = kwargs.pop('tuple_params', None)
if dtype.lower() in dftd3.dash_alias.keys():
self.dtype = dftd3.dash_alias[dtype.lower()].upper()
else:
self.dtype = dtype.upper() # Dispersion type
if dtype.replace('-', '') in dftd3.dashcoeff.keys():
self.dash_params = dftd3.dash_server(alias, dtype.replace('-', ''))
else:
self.dash_params = {'s6': 1.0}
# Build coefficients
if self.dtype in ["-D2GR", "-D3ZERO", "-D3BJ", "-D3MZERO", "-D3MBJ"]:
self.dtype = self.dtype.replace('-D2GR', '-D2')
self.disp_type = 'gr'
# Odd tuple syntax favored by psi
if (tuple_params is not None):
self.tuple_params = None
self.dash_params['s6'] = tuple_params[0]
if len(tuple_params) > 1:
if "D2" in self.dtype:
self.dash_params["alpha6"] = tuple_params[1]
elif ("ZERO" in self.dtype) or ("BJ" in self.dtype):
self.dash_params["s8"] = tuple_params[1]
if len(tuple_params) > 2:
if "ZERO" in self.dtype:
self.dash_params["sr6"] = tuple_params[2]
elif "BJ" in self.dtype:
self.dash_params["a1"] = tuple_params[2]
if len(tuple_params) > 3:
if "ZERO" in self.dtype:
self.dash_params["alpha6"] = tuple_params[3]
elif "BJ" in self.dtype:
self.dash_params["a2"] = tuple_params[3]
if len(tuple_params) > 4:
raise Exception("Too many parameter in input tuple param.")
else: # Only other case at the moment
self.dtype = self.dtype.replace('-D2P4', '-D2')
self.disp_type = 'p4'
if tuple_params is not None:
self.dash_params = {}
for k, v in zip(['s6', 'p1', 'p2', 'p3'], tuple_params):
self.dash_params[k] = v
# Build the C++ dispersion class
if self.disp_type == 'p4':
self.disp = core.Dispersion.build(self.dtype, **self.dash_params)
else:
self.disp = None
# Set user input
for k, v in kwargs.keys():
if k in self.dash_params.keys():
self.dash_params[k] = kwargs.pop(k)
if len(kwargs):
raise Exception("The following DFTD3 parameters were not understood for %s dispersion type: %s" %
(dtype, ', '.join(kwargs.keys())))
if self.dtype == "-D1":
self.description = " Grimme's -D1 Dispersion Correction"
self.citation = " Grimme, S. (2004), J. Comp. Chem., 25: 1463-1473"
self.bibtex = "Grimme:2004:1463"
elif self.dtype == "-D2":
self.description = " Grimme's -D2 Dispersion Correction"
self.citation = " Grimme, S. (2006), J. Comp. Chem., 27: 1787-1799"
self.bibtex = "Grimme:2006:1787"
elif self.dtype == "-CHG":
self.description = " Chai and Head-Gordon Dispersion Correction"
self.citation = " Chai, J.-D.; Head-Gordon, M. (2010), J. Chem. Phys., 132: 6615-6620"
self.bibtex = "Chai:2010:6615"
elif self.dtype == "-DAS2009":
self.description = " Podeszwa and Szalewicz Dispersion Correction"
self.citation = " Pernal, K.; Podeszwa, R.; Patkowski, K.; Szalewicz, K. (2009), Phys. Rev. Lett., 103: 263201"
self.bibtex = "Pernal:2009:263201"
elif self.dtype == "-DAS2010":
self.description = " Podeszwa and Szalewicz Dispersion Correction"
self.citation = " Podeszwa, R.; Pernal, K.; Patkowski, K.; Szalewicz, K. (2010), J. Phys. Chem. Lett., 1: 550"
self.bibtex = "Podeszwa:2010:550"
elif self.dtype == "-D2GR":
self.description = " Grimme's -D2 Dispersion Correction"
self.citation = " Grimme, S. (2006), J. Comp. Chem., 27: 1787-1799"
self.bibtex = "Grimme:2006:1787"
elif self.dtype == "-D3ZERO":
self.description = " Grimme's -D3 (zero-damping) Dispersion Correction"
self.citation = " Grimme S.; Antony J.; Ehrlich S.; Krieg H. (2010), J. Chem. Phys., 132: 154104"
self.bibtex = "Grimme:2010:154104"
elif self.dtype == "-D3BJ":
self.description = " Grimme's -D3 (BJ-damping) Dispersion Correction"
self.citation = " Grimme S.; Ehrlich S.; Goerigk L. (2011), J. Comput. Chem., 32: 1456"
self.bibtex = "Grimme:2011:1456"
elif self.dtype == "-D3MZERO":
self.description = " Grimme's -D3 (zero-damping, short-range refitted) Dispersion Correction"
self.citation = " Grimme S.; Antony J.; Ehrlich S.; Krieg H. (2010), J. Chem. Phys., 132: 154104\n"
self.citation += " Smith, D. G. A.; Burns, L. A.; Patkowski, K.; Sherrill, C. D. (2016), J. Phys. Chem. Lett.; 7: 2197"
self.bibtex = "Grimme:2010:154104"
elif self.dtype == "-D3MBJ":
self.description = " Grimme's -D3 (BJ-damping, short-range refitted) Dispersion Correction"
self.citation = " Grimme S.; Ehrlich S.; Goerigk L. (2011), J. Comput. Chem., 32: 1456\n"
self.citation += " Smith, D. G. A.; Burns, L. A.; Patkowski, K.; Sherrill, C. D. (2016), J. Phys. Chem. Lett.; 7: 2197"
self.bibtex = "Grimme:2011:1456"
else:
raise Exception("Emperical Dispersion type %s not understood." % self.dtype)
[docs] def print_out(self, level=1):
core.print_out(" => %s: Empirical Dispersion <=\n\n" % self.dtype)
core.print_out(self.description + "\n")
core.print_out(self.citation + "\n\n")
core.print_out(" S6 = %14.6E\n" % self.dash_params["s6"]);
if "s8" in self.dash_params.keys():
core.print_out(" S8 = %14.6E\n" % self.dash_params["s8"]);
for k, v in self.dash_params.items():
if k in ["s6", "s8"]: continue
core.print_out(" %6s = %14.6E\n" % (k.upper(), v));
# Psi auto sets this with no change of deviation
if (self.disp_type == 'p4') and (self.dtype == "-D2"):
core.print_out(" %6s = %14.6E\n" % ("A6", 20.0))
core.print_out("\n");
[docs] def compute_energy(self, molecule):
if self.disp_type == 'gr':
if self.alias in ['HF3C', 'PBEH3C']:
dashd_part = dftd3.run_dftd3(molecule, dashlvl=self.dtype.lower().replace('-', ''),
dashparam=self.dash_params, verbose=False, dertype=0)
gcp_part = gcp.run_gcp(molecule, self.alias.lower(), verbose=False, dertype=0)
return dashd_part + gcp_part
else:
return dftd3.run_dftd3(molecule, dashlvl=self.dtype.lower().replace('-', ''),
dashparam=self.dash_params, verbose=False, dertype=0)
else:
return self.disp.compute_energy(molecule)
[docs] def compute_gradient(self, molecule):
if self.disp_type == 'gr':
if self.alias in ['HF3C', 'PBEH3C']:
dashd_part = dftd3.run_dftd3(molecule, dashlvl=self.dtype.lower().replace('-', ''),
dashparam=self.dash_params, verbose=False, dertype=1)
gcp_part = gcp.run_gcp(molecule, self.alias.lower(), verbose=False, dertype=1)
dashd_part.add(gcp_part)
return dashd_part
else:
return dftd3.run_dftd3(molecule, dashlvl=self.dtype.lower().replace('-', ''),
dashparam=self.dash_params, verbose=False, dertype=1)
else:
return self.disp.compute_gradient(molecule)
