Source code for qcdb.molpro2

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# PSI4: an ab initio quantum chemistry software package
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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()