Source code for qcdb.psi4

#
#@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.
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# 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.
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# with this program; if not, write to the Free Software Foundation, Inc.,
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from __future__ import absolute_import
from __future__ import print_function
import re
import math
from collections import defaultdict

from .exceptions import *
from . import qcformat
#import molpro_basissets
from . import options
from .pdict import PreservingDict
from .psivarrosetta import useme2psivar


[docs]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 SAPT mobj = re.search( r'^\s+' + r'SAPT Results' + r'\s*' + r'^\s*(?:-+)\s*' + r'^\s+' + r'Electrostatics' + r'(?:.*?)' + r'^\s+' + r'Exchange' + r'(?:.*?)' + r'^\s+' + r'Induction' + r'(?:.*?)' + r'^\s+' + r'Dispersion' + r'(?:.*?)' + r'^\s+' + r'Total' + r'(?:.*?)' + r'^(?:\s*?)$', outtext, re.MULTILINE | re.DOTALL) if mobj: print('matched sapt') for pv in mobj.group(0).split('\n'): submobj = re.search(r'^\s+' + r'(.+?)' + r'\s+' + NUMBER + r'\s+' + r'[mEh]' + r'\s+' + NUMBER + r'\s+' + r'[kcal/mol]' + r'\s*$', pv) if submobj: try: key = ''.join(submobj.group(1).split()) useme = useme2psivar[key] except KeyError: #print '%30s' % (''), pass else: #print '%30s' % (useme), psivar['%s' % (useme)] = submobj.group(2) #print '*', submobj.group(1), submobj.group(2), submobj.group(3) # 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
[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 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()
[docs] 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'
[docs]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
[docs]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 == 'dfdf-b2plyp-d3': options['GLOBALS']['FREEZE_CORE']['value'] = True options['SCF']['SCF_TYPE']['value'] = 'df' options['DFMP2']['MP2_TYPE']['value'] = 'df' options['SCF']['DFT_SPHERICAL_POINTS']['value'] = 302 options['SCF']['DFT_RADIAL_POINTS']['value'] = 100 text += """b2plyp-d3')\n\n""" elif lowername == 'df-wpbe': options['SCF']['SCF_TYPE']['value'] = 'df' options['SCF']['DFT_SPHERICAL_POINTS']['value'] = 302 options['SCF']['DFT_RADIAL_POINTS']['value'] = 100 text += """wpbe')\n\n""" elif lowername == 'ccsd-polarizability': options['GLOBALS']['FREEZE_CORE']['value'] = True text = """property('ccsd', properties=['polarizability'])\n\n""" elif lowername == 'mrccsdt(q)': options['SCF']['SCF_TYPE']['value'] = 'pk' options['GLOBALS']['FREEZE_CORE']['value'] = True options['GLOBALS']['NAT_ORBS']['value'] = True # needed by mrcc but not recognized by mrcc options['FNOCC']['OCC_TOLERANCE']['value'] = 6 text += """mrccsdt(q)')\n\n""" elif lowername == 'c4-ccsdt(q)': options['CFOUR']['CFOUR_SCF_CONV']['value'] = 11 options['CFOUR']['CFOUR_CC_CONV']['value'] = 10 options['CFOUR']['CFOUR_FROZEN_CORE']['value'] = True text += """c4-ccsdt(q)')\n\n""" elif lowername == 'df-m05-2x': options['SCF']['SCF_TYPE']['value'] = 'df' options['SCF']['DFT_SPHERICAL_POINTS']['value'] = 302 options['SCF']['DFT_RADIAL_POINTS']['value'] = 100 text += """m05-2x')\n\n""" else: raise ValidationError("""Requested Psi4 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, 'mrccsdt(q)' : muster_modelchem, 'c4-ccsdt(q)' : muster_modelchem, 'ccsd-polarizability' : muster_modelchem, 'dfdf-b2plyp-d3': muster_modelchem, 'df-wpbe' : muster_modelchem, 'df-m05-2x' : muster_modelchem, } } qcmtdIN = procedures['energy']
[docs]def psi4_list(): """Return an array of Psi4 methods with energies. """ return sorted(procedures['energy'].keys())