/usr/share/psi/python/qmmm.py is in psi4-data 1:0.3-5.
This file is owned by root:root, with mode 0o644.
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#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
#@END LICENSE
#
"""Module with classes to integrate MM charges into
a QM calculation.
"""
#CUimport psi4
import re
import os
import math
#CUimport p4const
#CUfrom molutil import *
from 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 = psi4.has_option_changed("BASIS")
ribasisChanged = psi4.has_option_changed("DF_BASIS_SCF")
scftypeChanged = psi4.has_option_changed("SCF_TYPE")
basis = psi4.get_option("BASIS")
ribasis = psi4.get_option("DF_BASIS_SCF")
scftype = psi4.get_option("SCF_TYPE")
psi4.print_out(" => Diffuse SCF (Determines Da) <=\n\n")
activate(self.molecule)
psi4.set_global_option("BASIS", self.basisname)
psi4.set_global_option("DF_BASIS_SCF", self.ribasisname)
psi4.set_global_option("SCF_TYPE", "DF")
energy('scf')
psi4.print_out("\n")
self.fitGeneral()
psi4.clean()
psi4.set_global_option("BASIS", basis)
psi4.set_global_option("DF_BASIS_SCF", ribasis)
psi4.set_global_option("SCF_TYPE", scftype)
if not basisChanged:
psi4.revoke_option_changed("BASIS")
if not ribasisChanged:
psi4.revoke_option_changed("DF_BASIS_SCF")
if not scftypeChanged:
psi4.revoke_option_changed("SCF_TYPE")
def fitGeneral(self):
"""Function to perform a general fit of diffuse charges
to wavefunction density.
"""
psi4.print_out(" => Diffuse Charge Fitting (Determines da) <=\n\n")
self.wfn = psi4.wavefunction()
self.Da = self.wfn.Da()
self.basis = self.wfn.basisset()
parser = psi4.Gaussian94BasisSetParser()
self.ribasis = psi4.BasisSet.construct(parser, self.molecule, "DF_BASIS_SCF")
fitter = psi4.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))
class QMMM(object):
def __init__(self):
self.charges = []
self.diffuses = []
self.extern = psi4.ExternalPotential()
def addDiffuse(self, diffuse):
"""Function to add a diffuse charge field *diffuse*."""
self.diffuses.append(diffuse)
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])
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 / p4const.psi_bohr2angstroms, y / p4const.psi_bohr2angstroms, z / p4const.psi_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
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)
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