#
#@BEGIN LICENSE
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# 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
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# GNU General Public License for more details.
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# with this program; if not, write to the Free Software Foundation, Inc.,
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import math
from collections import defaultdict
from exceptions import *
import qcformat
import molpro_basissets
import options
[docs]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 or 'mp2c' 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 muster_basis_options(self):
text = ''
lowername = self.method.lower()
options = defaultdict(lambda: defaultdict(dict))
options['BASIS']['ORBITAL']['value'] = self.basis
if self.method in ['ccsd(t)-f12-optri']:
if self.basis == 'cc-pvdz-f12':
options['BASIS']['JKFIT']['value'] = 'aug-cc-pvtz/jkfit'
options['BASIS']['JKFITC']['value'] = self.basis + '/optri'
options['BASIS']['MP2FIT']['value'] = 'aug-cc-pvtz/mp2fit'
elif ('df-' in self.method) or ('f12' in self.method) or (self.method in ['mp2c', 'dft-sapt', 'dft-sapt-pbe0acalda']):
if self.unaugbasis and self.auxbasis:
options['BASIS']['JKFIT']['value'] = self.auxbasis + '/jkfit'
options['BASIS']['JKFITB']['value'] = self.unaugbasis + '/jkfit'
options['BASIS']['MP2FIT']['value'] = self.auxbasis + '/mp2fit'
options['BASIS']['DFLHF']['value'] = self.auxbasis + '/jkfit'
else:
raise ValidationError("""Auxiliary basis not predictable from orbital basis '%s'""" % (self.basis))
return text, options
def prepare_basis_for_molpro(self):
text = ''
for opt, val in self.options['BASIS'].items():
#print opt, val['value']
#print molpro_basissets.altbasis.keys()
if not text:
text += """basis={\n"""
try:
# jaxz, maxz, etc.
for line in molpro_basissets.altbasis[val['value']]:
text += """%s\n""" % (line)
text += '\n'
except KeyError:
# haxz
if val['value'].startswith('heavy-aug-'):
text += """set,%s; default,%s,H=%s\n""" % (opt.lower(), self.augbasis, self.unaugbasis)
# xz, axz, 6-31g*
else:
text += """set,%s; default,%s\n""" % (opt.lower(), val['value'])
if text:
text += """}\n\n"""
return text
def format_infile_string(self):
"""
"""
# Handle memory and comment
memcmd, _memkw = """***, %s\nmemory,%d,m\n""" % (self.molecule.tagline, int(math.ceil(self.memory / 8.0))), {}
# Handle molecule and basis set
molcmd, _molkw = self.molecule.format_molecule_for_molpro(), {}
# format global convergence directions
# text += self.format_global_parameters()
_cdscmd, cdskw = muster_cdsgroup_options(self.method)
# Handle calc type and quantum chemical method
mdccmd, mdckw, mdcls = procedures['energy'][self.method](self.method, self.dertype, self.molecule)
_bascmd, baskw = self.muster_basis_options()
# # 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 = options.reconcile_options2(userkw, cdskw)
userkw = options.reconcile_options2(userkw, baskw)
#userkw = qcdb.options.reconcile_options(userkw, psikw)
userkw = options.reconcile_options2(userkw, mdckw)
# Handle conversion of psi4 keyword structure into cfour format
#optcmdB = options.prepare_options_for_psi4(userkw)
optcmd = prepare_options_for_molpro(userkw, mdcls)
bascmd, _baskw = self.prepare_basis_for_molpro(), {} #self.options['BASIS']), {}
# Handle text to be passed untouched
litcmd = """\nshow[1,20f20.12],ee*,ce*,te*\nshow[1,60f20.12],_E*\n\n"""
# Assemble infile pieces
return memcmd + molcmd + bascmd + optcmd + mdccmd + litcmd
[docs]def muster_cdsgroup_options(name):
text = ''
lowername = name.lower()
options = defaultdict(lambda: defaultdict(dict))
options['GTHRESH']['ZERO']['value'] = 1.0e-14
options['GTHRESH']['ONEINT']['value'] = 1.0e-14
options['GTHRESH']['TWOINT']['value'] = 1.0e-14
options['GTHRESH']['ENERGY']['value'] = 1.0e-9
if name in ['mp2c', 'dft-sapt-shift', 'dft-sapt', 'dft-sapt-pbe0ac', 'dft-sapt-pbe0acalda']:
options['GTHRESH']['ENERGY']['value'] = 1.0e-8
options['GTHRESH']['ORBITAL']['value'] = 1.0e-8
options['GTHRESH']['GRID']['value'] = 1.0e-8
elif name in ['b3lyp', 'b3lyp-d', 'df-b3lyp', 'df-b3lyp-d']:
options['GTHRESH']['ENERGY']['value'] = 1.0e-8
options['GTHRESH']['ORBITAL']['value'] = 1.0e-7
options['GTHRESH']['GRID']['value'] = 1.0e-8
else:
pass
return text, options
[docs]def prepare_options_for_molpro(options, proc):
"""Function to take the full snapshot of the liboptions object
encoded in dictionary *options*, find the options directable toward
Cfour (options['CFOUR']['CFOUR_**']) that aren't default, then write
a CFOUR deck with those options.
Note that unlike the cfour version, this uses complete options deck.
"""
text = ''
if len(options['GTHRESH']) > 0:
text += 'gthresh'
for opt, val in options['GTHRESH'].items():
text += """,%s=%s""" % (opt, val['value'])
text += '\n\n'
for item in proc:
if len(options[item.upper()]) > 0:
text += """{%s%s}\n""" % (item, options[item.upper()]['OPTIONS']['value'])
else:
text += """%s\n""" % (item)
if text:
text += '\n'
return text
[docs]def muster_modelchem(name, dertype, mol):
"""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))
proc = []
if dertype == 0:
pass
else:
raise ValidationError("""Requested Psi4 dertype %d is not available.""" % (dertype))
if lowername == 'mp2':
pass
options['GLOBALS']['FREEZE_CORE']['value'] = True
options['SCF']['SCF_TYPE']['value'] = 'direct'
options['MP2']['MP2_TYPE']['value'] = 'conv'
text += """mp2')\n\n"""
elif lowername == 'ccsd(t)-f12':
proc.append('rhf')
proc.append('ccsd(t)-f12')
options['CCSD(T)-F12']['OPTIONS']['value'] = ',df_basis=mp2fit,df_basis_exch=jkfitb,ri_basis=jkfitb'
elif lowername == 'ccsd(t)-f12-optri':
proc.append('rhf')
proc.append('ccsd(t)-f12')
options['CCSD(T)-F12']['OPTIONS']['value'] = ',df_basis=mp2fit,df_basis_exch=jkfit,ri_basis=jkfitc'
elif lowername == 'mp2c':
proc.append('gdirect')
proc.append(mol.extract_fragments(1, 2).format_molecule_for_molpro())
proc.append('df-hf,')
proc.append('df-ks,')
proc.append('sapt; monomerA')
options['DF-HF,']['OPTIONS']['value'] = """basis=jkfit,locorb=0; start,atdens; save,1101.2"""
options['DF-KS,']['OPTIONS']['value'] = """lhf,df_basis=dflhf,basis_coul=jkfitb,basis_exch=jkfitb; dftfac,1.0; start,1101.2; save,2101.2"""
proc.append(mol.extract_fragments(2, 1).format_molecule_for_molpro())
proc.append('df-hf')
proc.append('df-ks')
proc.append('sapt; monomerB')
options['DF-HF']['OPTIONS']['value'] = """,basis=jkfit,locorb=0; start,atdens; save,1102.2"""
options['DF-KS']['OPTIONS']['value'] = """,lhf,df_basis=dflhf,basis_coul=jkfitb,basis_exch=jkfitb; dftfac,1.0; start,1102.2; save,2102.2"""
proc.append(mol.format_molecule_for_molpro())
proc.append('sapt; intermol')
options['SAPT; INTERMOL']['OPTIONS']['value'] = """,saptlevel=3,ca=2101.2,cb=2102.2,icpks=0,fitlevel=3,nlexfac=0.0,cfac=0.0; dfit,basis_coul=jkfit,basis_exch=jkfit,cfit_scf=3"""
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, proc
procedures = {
'energy': {
'mp2c' : muster_modelchem,
'ccsd(t)-f12' : muster_modelchem,
'ccsd(t)-f12-optri' : muster_modelchem,
#'sapt0' : muster_modelchem,
#'sapt2+' : muster_modelchem,
#'sapt2+(3)' : muster_modelchem,
#'sapt2+3(ccd)' : muster_modelchem,
}
}
qcmtdIN = procedures['energy']
[docs]def psi4_list():
"""Return an array of Psi4 methods with energies.
"""
return procedures['energy'].keys()