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# Psi4: an open-source quantum chemistry software package
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"""Module with classes to integrate MM charges into
a QM calculation.
"""
from psi4.driver import *
class Diffuse(object):
def __init__(self, molecule, basisname, ribasisname):
self.molecule = molecule
self.basisname = basisname
self.ribasisname = ribasisname
self.basis = None
self.ribasis = None
self.da = None
self.Da = None
self.wfn = None
def __str__(self):
s = ' => Diffuse <=\n\n'
s = s + ' ' + str(self.molecule) + '\n'
s = s + ' ' + self.basisname + '\n'
s = s + ' ' + self.ribasisname + '\n'
s = s + '\n'
return s
def fitScf(self):
"""Function to run scf and fit a system of diffuse charges to
resulting density.
"""
basisChanged = core.has_option_changed("BASIS")
ribasisChanged = core.has_option_changed("DF_BASIS_SCF")
scftypeChanged = core.has_option_changed("SCF_TYPE")
basis = core.get_option("BASIS")
ribasis = core.get_option("DF_BASIS_SCF")
scftype = core.get_global_option("SCF_TYPE")
core.print_out(" => Diffuse SCF (Determines Da) <=\n\n")
core.set_global_option("BASIS", self.basisname)
core.set_global_option("DF_BASIS_SCF", self.ribasisname)
core.set_global_option("SCF_TYPE", "DF")
E, ref = energy('scf', return_wfn=True, molecule=self.molecule)
self.wfn = ref
core.print_out("\n")
self.fitGeneral()
core.clean()
core.set_global_option("BASIS", basis)
core.set_global_option("DF_BASIS_SCF", ribasis)
core.set_global_option("SCF_TYPE", scftype)
if not basisChanged:
core.revoke_option_changed("BASIS")
if not ribasisChanged:
core.revoke_option_changed("DF_BASIS_SCF")
if not scftypeChanged:
core.revoke_option_changed("SCF_TYPE")
def fitGeneral(self):
"""Function to perform a general fit of diffuse charges
to wavefunction density.
"""
core.print_out(" => Diffuse Charge Fitting (Determines da) <=\n\n")
self.Da = self.wfn.Da()
self.basis = self.wfn.basisset()
parser = core.Gaussian94BasisSetParser()
self.ribasis = core.BasisSet.construct(parser, self.molecule, "DF_BASIS_SCF")
fitter = core.DFChargeFitter()
fitter.setPrimary(self.basis)
fitter.setAuxiliary(self.ribasis)
fitter.setD(self.Da)
self.da = fitter.fit()
self.da.scale(2.0)
def populateExtern(self, extern):
# Electronic Part
extern.addBasis(self.ribasis, self.da)
# Nuclear Part
for A in range(0, self.molecule.natom()):
extern.addCharge(self.molecule.Z(A), self.molecule.x(A), self.molecule.y(A), self.molecule.z(A))
[docs]class QMMM():
"""Hold charges and :py:class:`psi4.core.ExternalPotential`. Use :py:class:`psi4.driver.QMMMbohr` instead."""
def __init__(self):
raise UpgradeHelper(self.__class__.__name__, "QMMMbohr", 1.6, ' Replace object with a list of charges and locations in Bohr passed as keyword argument, e.g., `energy(..., external_potentials=[[0.5, [0, 0, 1]], [-0.5, [0, 0, -1]]])`.')
[docs]class QMMMbohr():
"""Hold charges and :py:class:`psi4.core.ExternalPotential`. To add external charges to a calculation, prefer
passing the array of charges with kwarg ``external_potentials``, as in extern2 example."""
def __init__(self):
self.charges = []
self.diffuses = []
self.extern = core.ExternalPotential()
[docs] def addDiffuse(self, diffuse):
"""Function to add a diffuse charge field *diffuse*."""
self.diffuses.append(diffuse)
[docs] def addChargeBohr(self, Q, x, y, z):
"""Function to add a point charge of magnitude *Q* at
position (*x*, *y*, *z*) Bohr.
"""
self.charges.append([Q, x, y, z])
[docs] def addChargeAngstrom(self, Q, x, y, z):
"""Function to add a point charge of magnitude *Q* at
position (*x*, *y*, *z*) Angstroms.
"""
self.charges.append([Q, x / constants.bohr2angstroms, y / constants.bohr2angstroms, z / constants.bohr2angstroms])
def __str__(self):
s = ' ==> QMMM <==\n\n'
s = s + ' => Charges (a.u.) <=\n\n'
s = s + ' %11s %11s %11s %11s\n' % ('Z', 'x', 'y', 'z')
for k in range(0, len(self.charges)):
s = s + ' %11.7f %11.3E %11.3E %11.3E\n' % (self.charges[k][0], self.charges[k][1], self.charges[k][2], self.charges[k][3])
s = s + '\n'
s = s + ' => Diffuses <=\n\n'
for k in range(0, len(self.diffuses)):
s = s + str(self.diffuses[k])
return s
[docs] def populateExtern(self):
"""Function to define a charge field external to the
molecule through point and diffuse charges.
"""
# Charges
for charge in self.charges:
self.extern.addCharge(charge[0], charge[1], charge[2], charge[3])
# Diffuses
for diffuse in self.diffuses:
diffuse.populateExtern(self.extern)
