/usr/share/psi/python/qcdb/psi4.py is in psi4-data 1:0.3-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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
#
import re
import math
from collections import defaultdict
from exceptions import *
import qcformat
#import molpro_basissets
import options
from pdict import PreservingDict
def harvest_output(outtext):
"""Function to separate portions of a PSI4 output file *outtext*.
"""
psivar = PreservingDict()
psivar_coord = None
psivar_grad = None
NUMBER = "((?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?))"
# Process PsiVariables
mobj = re.search(r'^(?: Variable Map:)\s*' +
r'^\s*(?:-+)\s*' +
r'^(.*?)' +
r'^(?:\s*?)$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
for pv in mobj.group(1).split('\n'):
submobj = re.search(r'^\s+' + r'"(.+?)"' + r'\s+=>\s+' + NUMBER + r'\s*$', pv)
if submobj:
psivar['%s' % (submobj.group(1))] = submobj.group(2)
# Process Completion
mobj = re.search(r'PSI4 exiting successfully. Buy a developer a beer!',
outtext, re.MULTILINE)
if mobj:
psivar['SUCCESS'] = True
return psivar, psivar_coord, psivar_grad
class Infile(qcformat.InputFormat2):
def __init__(self, mem, mol, mtd, der, opt):
qcformat.InputFormat2.__init__(self, mem, mol, mtd, der, opt)
print self.method, self.molecule.nactive_fragments()
if 'sapt' in self.method and self.molecule.nactive_fragments() != 2:
raise FragmentCountError("""Requested molecule has %d, not 2, fragments.""" % (self.molecule.nactive_fragments()))
# # memory in MB --> MW
# self.memory = int(math.ceil(mem / 8.0))
# # auxiliary basis sets
# [self.unaugbasis, self.augbasis, self.auxbasis] = self.corresponding_aux_basis()
def format_infile_string(self):
"""
"""
# Handle memory and comment
memcmd, memkw = """# %s\n\nmemory %d mb\n\n""" % (self.molecule.tagline, self.memory), {}
# Handle molecule and basis set
molcmd, molkw = self.molecule.format_molecule_for_psi4(), {}
# format global convergence directions
# text += self.format_global_parameters()
_cdscmd, cdskw = muster_cdsgroup_options()
# Handle calc type and quantum chemical method
mdccmd, mdckw = procedures['energy'][self.method](self.method, self.dertype)
# # format options
# optcmd = qcdb.options.prepare_options_for_psi4(mdckw)
# make options from imdb only user options (currently non-existent). set basis and castup from here.
# Handle driver vs input/default keyword reconciliation
userkw = self.options
# userkw = p4util.prepare_options_for_modules()
#userkw = qcdb.options.reconcile_options(userkw, memkw)
#userkw = qcdb.options.reconcile_options(userkw, molkw)
#userkw = qcdb.options.reconcile_options(userkw, baskw)
#userkw = qcdb.options.reconcile_options(userkw, psikw)
userkw = options.reconcile_options2(userkw, cdskw)
userkw = options.reconcile_options2(userkw, mdckw)
# Handle conversion of psi4 keyword structure into cfour format
optcmd = options.prepare_options_for_psi4(userkw)
# Handle text to be passed untouched to psi4
litcmd = """\nprint_variables()\n\n"""
# Assemble infile pieces
return memcmd + molcmd + optcmd + mdccmd + litcmd
#'hf'
#'df-hf'
#'b3lyp'
#'blyp'
#'bp86'
#'fno-ccsd(t)'
#'df-ccsd(t)'
#'fno-df-ccsd(t)'
#'df-b97-d'
#'df-b97-d3'
#'pbe0-2'
#'dsd-pbep86'
#'wb97x-2'
#'DLdf+d'
#'DLdf+d09'
#'df-b3lyp'
#'df-b3lyp-d'
#'df-b3lyp-d3'
#'df-wb97x-d'
def muster_cdsgroup_options():
text = ''
options = defaultdict(lambda: defaultdict(dict))
options['GLOBALS']['E_CONVERGENCE']['value'] = 8
options['SCF']['GUESS']['value'] = 'sad'
options['SCF']['MAXITER']['value'] = 200
return text, options
def muster_modelchem(name, dertype):
"""Transform calculation method *name* and derivative level *dertype*
into options for cfour. While deliberately requested pieces,
generally |cfour__cfour_deriv_level| and |cfour__cfour_calc_level|,
are set to complain if contradicted ('clobber' set to True), other
'recommended' settings, like |cfour__cfour_cc_program|, can be
countermanded by keywords in input file ('clobber' set to False).
Occasionally, want these pieces to actually overcome keywords in
input file ('superclobber' set to True).
"""
text = ''
lowername = name.lower()
options = defaultdict(lambda: defaultdict(dict))
if dertype == 0:
text += """energy('"""
else:
raise ValidationError("""Requested Psi4 dertype %d is not available.""" % (dertype))
if lowername == 'mp2':
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'direct'
options['MP2']['MP2_TYPE']['value'] = 'conv'
text += """mp2')\n\n"""
elif lowername == 'df-mp2':
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'df'
options['MP2']['MP2_TYPE']['value'] = 'df'
text += """mp2')\n\n"""
elif lowername == 'sapt0':
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'df'
text += """sapt0')\n\n"""
elif lowername == 'sapt2+':
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'df'
options['SAPT']['NAT_ORBS_T2']['value'] = True
options['SAPT']['NAT_ORBS_T3']['value'] = True
options['SAPT']['NAT_ORBS_V4']['value'] = True
options['SAPT']['OCC_TOLERANCE']['value'] = 1.0e-6
text += """sapt2+')\n\n"""
elif lowername == 'sapt2+(3)':
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'df'
options['SAPT']['NAT_ORBS_T2']['value'] = True
options['SAPT']['NAT_ORBS_T3']['value'] = True
options['SAPT']['NAT_ORBS_V4']['value'] = True
options['SAPT']['OCC_TOLERANCE']['value'] = 1.0e-6
text += """sapt2+(3)')\n\n"""
elif lowername == 'sapt2+3(ccd)':
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'df'
options['SAPT']['NAT_ORBS_T2']['value'] = True
options['SAPT']['NAT_ORBS_T3']['value'] = True
options['SAPT']['NAT_ORBS_V4']['value'] = True
options['SAPT']['OCC_TOLERANCE']['value'] = 1.0e-6
options['SAPT']['DO_MBPT_DISP']['value'] = True
text += """sapt2+3(ccd)')\n\n"""
elif lowername == 'df-b97-d3':
options['SCF']['SCF_TYPE']['value'] = 'df'
options['SCF']['DFT_SPHERICAL_POINTS']['value'] = 302
options['SCF']['DFT_RADIAL_POINTS']['value'] = 100
text += """b97-d3')\n\n"""
elif lowername == 'df-wb97x-d':
options['SCF']['SCF_TYPE']['value'] = 'df'
options['SCF']['DFT_SPHERICAL_POINTS']['value'] = 302
options['SCF']['DFT_RADIAL_POINTS']['value'] = 100
text += """wb97x-d')\n\n"""
elif lowername == 'df-b3lyp-d3':
options['SCF']['SCF_TYPE']['value'] = 'df'
options['SCF']['DFT_SPHERICAL_POINTS']['value'] = 302
options['SCF']['DFT_RADIAL_POINTS']['value'] = 100
text += """b3lyp-d3')\n\n"""
elif lowername == 'ccsd-polarizability':
options['GLOBALS']['FREEZE_CORE']['value'] = True
text = """property('ccsd', properties=['polarizability'])\n\n"""
else:
raise ValidationError("""Requested Cfour computational methods %d is not available.""" % (lowername))
# # Set clobbering
# if 'CFOUR_DERIV_LEVEL' in options['CFOUR']:
# options['CFOUR']['CFOUR_DERIV_LEVEL']['clobber'] = True
# options['CFOUR']['CFOUR_DERIV_LEVEL']['superclobber'] = True
# if 'CFOUR_CALC_LEVEL' in options['CFOUR']:
# options['CFOUR']['CFOUR_CALC_LEVEL']['clobber'] = True
# options['CFOUR']['CFOUR_CALC_LEVEL']['superclobber'] = True
# if 'CFOUR_CC_PROGRAM' in options['CFOUR']:
# options['CFOUR']['CFOUR_CC_PROGRAM']['clobber'] = False
return text, options
procedures = {
'energy': {
'df-b97-d3' : muster_modelchem,
'df-wb97x-d' : muster_modelchem,
'df-b3lyp-d3' : muster_modelchem,
'mp2' : muster_modelchem,
'df-mp2' : muster_modelchem,
'sapt0' : muster_modelchem,
'sapt2+' : muster_modelchem,
'sapt2+(3)' : muster_modelchem,
'sapt2+3(ccd)' : muster_modelchem,
'ccsd-polarizability' : muster_modelchem,
}
}
qcmtdIN = procedures['energy']
def psi4_list():
"""Return an array of Psi4 methods with energies.
"""
return sorted(procedures['energy'].keys())
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