parser_gaussian.py 87.2 KB
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# Copyright 2015-2018 Rosendo Valero, Fawzi Mohamed, Ankit Kariryaa, Rosendo Valero Montero
# 
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
# 
#     http://www.apache.org/licenses/LICENSE-2.0
# 
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.

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from __future__ import division
from builtins import str
from builtins import range
from builtins import object
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from functools import reduce
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import setup_paths
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from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
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from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
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from nomadcore.caching_backend import CachingLevel
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from nomadcore.unit_conversion.unit_conversion import convert_unit
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import os, sys, json, logging
import numpy as np
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import ase
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import re

############################################################
# This is the parser for the output file of Gaussian.
############################################################

logger = logging.getLogger("nomad.GaussianParser")
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# description of the output
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mainFileDescription = SM(
    name = 'root',
    weak = True,
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    forwardMatch = True, 
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    startReStr = "",
    subMatchers = [
        SM(name = 'newRun',
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           startReStr = r"\s*Cite this work as:",
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           repeats = True,
           required = True,
           forwardMatch = True,
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           fixedStartValues={ 'program_name': 'Gaussian', 'program_basis_set_type': 'gaussians' },
           sections   = ['section_run'],
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           subMatchers = [
               SM(name = 'header',
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                  startReStr = r"\s*Cite this work as:",
                  forwardMatch = True,
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                  subMatchers = [
                      SM(r"\s*Cite this work as:"),
                      SM(r"\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,"),
                      SM(r"\s\*\*\*\*\*\*\*\*\*\*\*\**"),
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                      SM(r"\s*Gaussian\s*(?P<program_version>[0-9]+):\s*(?P<x_gaussian_program_implementation>[A-Za-z0-9-.]+)\s*(?P<x_gaussian_program_release_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
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                      SM(r"\s*(?P<x_gaussian_program_execution_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
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                      ]
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             ),
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               SM(name = 'globalparams',
                  startReStr = r"\s*%\w*=",
                  subFlags = SM.SubFlags.Unordered,
                  forwardMatch = True,
                  subMatchers = [
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                      SM(r"\s*%[Cc]hk=(?P<x_gaussian_chk_file>[A-Za-z0-9.]*)"),
                      SM(r"\s*%[Mm]em=(?P<x_gaussian_memory>[A-Za-z0-9.]*)"),
                      SM(r"\s*%[Nn][Pp]roc=(?P<x_gaussian_number_of_processors>[A-Za-z0-9.]*)")
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                      ]
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             ),
               SM (name = 'SectionMethod',
               sections = ['section_method'],
                   startReStr = r"\s*#",
                   forwardMatch = True,
                   subMatchers = [
                       SM(r"\s*(?P<x_gaussian_settings>([a-zA-Z0-9-/=(),#*+:]*\s*)+)"),
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                       SM(r"\s*(?P<x_gaussian_settings>([a-zA-Z0-9-/=(),#*+:]*\s*)+)"),
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                       ]
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             ),
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               SM(name = 'charge_multiplicity_cell_masses',
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               sections = ['section_system'],
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		  startReStr = r"\s*Charge =",
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                  endReStr = r"\s*Leave Link  101\s*",
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                  subFlags = SM.SubFlags.Unordered,
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                  forwardMatch = True,
                  subMatchers = [
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                      SM(r"\s*Charge =\s*(?P<x_gaussian_total_charge>[-+0-9]*) Multiplicity =\s*(?P<x_gaussian_spin_target_multiplicity>[0-9]*)"),
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                      SM(r"\s*(Tv|Tv\s*[0]|TV|TV\s*[0])\s*(?P<x_gaussian_geometry_lattice_vector_x>[0-9.]+)\s+(?P<x_gaussian_geometry_lattice_vector_y>[0-9.]+)\s+(?P<x_gaussian_geometry_lattice_vector_z>[0-9.]+)", repeats = True),
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                      SM(r"\s*AtmWgt=\s+(?P<x_gaussian_atomic_masses>[0-9.]+(\s+[0-9.]+)(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?)", repeats = True)
                      ]
             ),
            SM (name = 'SingleConfigurationCalculationWithSystemDescription',
                startReStr = "\s*Standard orientation:",
                repeats = False,
                forwardMatch = True,
                subMatchers = [
                SM (name = 'SingleConfigurationCalculation',
                  startReStr = "\s*Standard orientation:",
                  repeats = True,
                  forwardMatch = True,
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                  sections = ['section_single_configuration_calculation'],
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                  subMatchers = [
                  SM(name = 'geometry',
                   sections  = ['x_gaussian_section_geometry'],
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                   startReStr = r"\s*Standard orientation:",
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                   endReStr = r"\s*Rotational constants",
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                      subMatchers = [
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                      SM(r"\s+[0-9]+\s+(?P<x_gaussian_atomic_number>[0-9]+)\s+[0-9]*\s+(?P<x_gaussian_atom_x_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_y_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_z_coord__angstrom>[-+0-9EeDd.]+)",repeats = True),
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                      SM(r"\s*Rotational constants")
                    ]
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                ),
                    SM(name = 'SectionHybridCoeffs',
                    sections = ['x_gaussian_section_hybrid_coeffs'],
                    startReStr = r"\s*IExCor=",
                    forwardMatch = True,
                    subMatchers = [
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                     SM(r"\s*IExCor=\s*[0-9-]+\s*DFT=[A-Z]\s*Ex\+Corr=[a-zA-Z0-9]+\s*ExCW=[0-9]\s*ScaHFX=\s*(?P<hybrid_xc_coeff1>[0-9.]+)"),
                     SM(r"\s*IExCor=\s*[0-9-]+\s*DFT=[A-Z]\s*Ex\=[a-zA-Z0-9+]+\s*Corr=[ a-zA-Z0-9]+\s*?ExCW=[0-9]\s*ScaHFX=\s*(?P<hybrid_xc_coeff1>[0-9.]+)"),
                     SM(r"\s*IExCor=\s*[0-9-]+\s*DFT=[A-Z]\s*Ex\=[a-zA-Z0-9+]+\s*Corr=[ a-zA-Z0-9]+\s*ScaHFX=\s*(?P<hybrid_xc_coeff1>[0-9.]+)"),
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                     SM(r"\s*ScaDFX=\s*(?P<hybrid_xc_coeff2>[0-9.]+\s*[0-9.]+\s*[0-9.]+\s*[0-9.]+)")
                    ]
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                ),
                    SM(name = 'TotalEnergyScfGaussian',
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                    sections  = ['section_scf_iteration'],
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                    startReStr = r"\s*Requested convergence on RMS",
                    forwardMatch = False,
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                    repeats = True,
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                    subMatchers = [
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                     SM(r"\s*Cycle\s+[0-9]+|\s*Initial guess <Sx>="),
                     SM(r"\s*E=\s*(?P<energy_total_scf_iteration__hartree>[-+0-9.]+)\s*Delta-E=\s*(?P<x_gaussian_delta_energy_total_scf_iteration__hartree>[-+0-9.]+)"),
                     SM(r"\s*(?P<x_gaussian_single_configuration_calculation_converged>SCF Done):\s*E\((?P<x_gaussian_hf_detect>[A-Z0-9]+)\)\s*=\s*(?P<x_gaussian_energy_scf__hartree>[-+0-9.]+)"),
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                     SM(r"\s*NFock=\s*[0-9]+\s*Conv=(?P<x_gaussian_energy_error__hartree>[-+0-9EeDd.]+)\s*"),
                     SM(r"\s*KE=\s*(?P<x_gaussian_electronic_kinetic_energy__hartree>[-+0-9EeDd.]+)\s*"),
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                     SM(r"\s*Annihilation of the first spin contaminant"),
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                     SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*(?P<spin_S2>[0-9.]+),\s*after\s*(?P<x_gaussian_after_annihilation_spin_S2>[0-9.]+)"),
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                     SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P<x_gaussian_perturbation_energy__hartree>[-+0-9D.]+)"),
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                    ]
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                ),
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                    SM(name = 'PerturbationEnergies',
                    sections = ['x_gaussian_section_moller_plesset'],
                    startReStr = r"\s*E2 =\s*",
                    forwardMatch = True,
                    subMatchers = [
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                     SM(r"\s*E2 =\s*(?P<x_gaussian_mp2_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
                     SM(r"\s*E3=\s*(?P<x_gaussian_mp3_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP3=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)\s*"),
                     SM(r"\s*E4\(DQ\)=\s*(?P<x_gaussian_mp4dq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(DQ\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)\s*"),
                     SM(r"\s*E4\(SDQ\)=\s*(?P<x_gaussian_mp4sdq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(SDQ\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
                     SM(r"\s*E4\(SDTQ\)=\s*(?P<x_gaussian_mp4sdtq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(SDTQ\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
                     SM(r"\s*DEMP5 =\s*(?P<x_gaussian_mp5_correction_energy__hartree>[-+0-9EeDd.]+)\s*MP5 =\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
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                     ]
                ),
                    SM(name = 'CoupledClusterEnergies',
                    sections = ['x_gaussian_section_coupled_cluster'],
                    startReStr = r"\s*CCSD\(T\)\s*",
                    endReStr = r"\s*Population analysis using the SCF density",
                    forwardMatch = True,
                    subMatchers = [
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                     SM(r"\s*DE\(Corr\)=\s*(?P<x_gaussian_ccsd_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
                     SM(r"\s*CCSD\(T\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
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                     ]
                ),
                    SM(name = 'QuadraticCIEnergies',
                    sections = ['x_gaussian_section_quadratic_ci'],
                    startReStr = r"\s*Quadratic Configuration Interaction\s*",
                    endReStr = r"\s*Population analysis using the SCF density",
                    forwardMatch = True,
                    subMatchers = [
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                     SM(r"\s*DE\(Z\)=\s*(?P<x_gaussian_qcisd_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(Z\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
                     SM(r"\s*DE\(Corr\)=\s*(?P<x_gaussian_qcisd_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
                     SM(r"\s*QCISD\(T\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
                     SM(r"\s*DE5\s*=\s*(?P<x_gaussian_qcisdtq_correction_energy__hartree>[-+0-9EeDd.]+)\s*QCISD\(TQ\)\s*=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
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                     ]
                ),
                    SM(name = 'CIEnergies',
                    sections = ['x_gaussian_section_ci'],
                    startReStr = r"\s*Configuration Interaction\s*",
                    endReStr = r"\s*Population analysis using the SCF density",
                    forwardMatch = True,
                    subMatchers = [
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                     SM(r"\s*DE\(CI\)=\s*(?P<x_gaussian_ci_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(CI\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
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                     ]
                ),
                    SM(name = 'SemiempiricalEnergies',
                    sections = ['x_gaussian_section_semiempirical'],
                    startReStr = r"\s*[-A-Z0-9]+\s*calculation of energy[a-zA-Z,. ]+\s*",
                    endReStr = r"\s*Population analysis using the SCF density",
                    forwardMatch = True,
                    subMatchers = [
                     SM(r"\s*(?P<x_gaussian_semiempirical_method>[-A-Z0-9]+\s*calculation of energy[a-zA-Z,. ]+)"),
                     SM(r"\s*It=\s*[0-9]+\s*PL=\s*[-+0-9EeDd.]+\s*DiagD=[A-Z]\s*ESCF=\s*(?P<x_gaussian_semiempirical_energy>[-+0-9.]+)\s*", repeats = True),
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                     SM(r"\s*Energy=\s*(?P<energy_total>[-+0-9EeDd.]+)"),
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                     ]
                ),
                    SM(name = 'MolecularMechanicsEnergies',
                    sections = ['x_gaussian_section_molmech'],
                    startReStr = r"\s*[-A-Z0-9]+\s*calculation of energy[a-zA-Z,. ]+\s*",
                    forwardMatch = False,
                    repeats = True,
                    subMatchers = [
                     SM(r"\s*(?P<x_gaussian_molmech_method>[a-zA-Z0-9]+\s*calculation of energy[a-z,. ]+)"),
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                     SM(r"\s*Energy=\s*(?P<energy_total>[-+0-9EeDd.]+)\s*NIter=\s*[0-9.]"),
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                     ]
                ),
                  SM(name = 'ExcitedStates',
                   sections  = ['x_gaussian_section_excited_initial'],
                   startReStr = r"\s*Excitation energies and oscillator strengths",
                   forwardMatch = False,
                   repeats = True,
                   subMatchers = [
                    SM(name = 'ExcitedStates',
                    sections = ['x_gaussian_section_excited'],
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                    startReStr = r"\s*Excited State",
                    forwardMatch = False,
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                    repeats = True,
                    subMatchers = [
                     SM(r"\s*Excited State\s*(?P<x_gaussian_excited_state_number>[0-9]+):\s*[-+0-9A-Za-z.\?]+\s*(?P<x_gaussian_excited_energy__eV>[0-9.]+)\s*eV\s*[0-9.]+\s*nm\s*f=(?P<x_gaussian_excited_oscstrength>[0-9.]+)\s*<[A-Z][*][*][0-9]>=(?P<x_gaussian_excited_spin_squared>[0-9.]+)"),
                     SM(r"\s*(?P<x_gaussian_excited_transition>[0-9A-Z]+\s*->\s*[0-9A-Z]+\s*[-+0-9.]+)", repeats = True),
                     SM(r"\s*This state for optimization|\r?\n"),
                     ]
                    )
                   ]
               ),  
                  SM(name = 'CASSCFStates',
                   sections = ['x_gaussian_section_casscf'],
                   startReStr = r"\s*EIGENVALUES AND\s*",
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                   forwardMatch = True,
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                   repeats = False,
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                   subMatchers = [
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                    SM(r"\s*EIGENVALUES AND\s*"),
                    SM(r"\s*\(\s*[0-9]+\)\s*EIGENVALUE\s*(?P<x_gaussian_casscf_energy__hartree>[-+0-9.]+)", repeats = True),
                   ]
               ),
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                  SM(name = 'Geometry_optimization',
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                  sections  = ['x_gaussian_section_geometry_optimization_info'],
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                  startReStr = r"\s*Optimization completed.",
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                  forwardMatch = True,
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                  subMatchers = [
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                  SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimization completed)"),
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                  SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimization stopped)"),
                  SM(r"\s+[0-9]+\s+[0-9]+\s+[0-9]+\s+[-+0-9EeDd.]+\s+[-+0-9EeDd.]+\s+[-+0-9EeDd.]+",repeats = True),
                  SM(r"\s*Distance matrix|\s*Rotational constants|\s*Stoichiometry")
                    ]
               ),
                SM(name = 'Orbital symmetries',
                sections = ['x_gaussian_section_orbital_symmetries'],
                startReStr = r"\s+Population analysis",
                subFlags = SM.SubFlags.Sequenced,
                subMatchers = [
                      SM(r"\s*Orbital symmetries"), 
                      SM(r"\s*Alpha Orbitals"),
                      SM(r"\s*Occupied\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\)?)", repeats = True),
                      SM(r"\s*Virtual\s+(?P<x_gaussian_alpha_vir_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_alpha_vir_symmetry_values>\((.+)\)?)", repeats = True),
                      SM(r"\s*Beta Orbitals"),
                      SM(r"\s*Occupied\s+(?P<x_gaussian_beta_occ_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_beta_occ_symmetry_values>\((.+)\)?)", repeats = True),
                      SM(r"\s*Virtual\s+(?P<x_gaussian_beta_vir_symmetry_values>\((.+)\))?"),
                      SM(r"\s+(?P<x_gaussian_beta_vir_symmetry_values>\((.+)\)?)", repeats = True),
                      ]
             ),
                SM(name = 'Electronicstatesymmetry',
                sections = ['x_gaussian_section_symmetry'],
                startReStr = r"\s*The electronic state is",
                forwardMatch = True,
                subMatchers = [
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                      SM(r"\s*The electronic state is\s*(?P<x_gaussian_elstate_symmetry>[A-Z0-9-']+)[.]")
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                      ]
             ),
                SM(name = 'Eigenvalues',
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                sections = ['section_eigenvalues'],
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                startReStr = r"\s*Alpha  occ. eigenvalues --",
                forwardMatch = True,
                subFlags = SM.SubFlags.Sequenced,
                subMatchers = [
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                      SM(r"\s*Alpha  occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True), 
                      SM(r"\s*Alpha virt. eigenvalues --\s+(?P<x_gaussian_alpha_vir_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
                      SM(r"\s*Beta  occ. eigenvalues --\s+(?P<x_gaussian_beta_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
                      SM(r"\s*Beta virt. eigenvalues --\s+(?P<x_gaussian_beta_vir_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
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                      SM(r"\s*- Condensed to atoms (all electrons)"),
                      ]
             ),
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                   SM(name = 'ForcesGaussian',
                   sections  = ['x_gaussian_section_atom_forces'],
                   startReStr = "\s*Center\s+Atomic\s+Forces ",
                   forwardMatch = True,
                   subMatchers = [
                    SM(r"\s*Center\s+Atomic\s+Forces "),
                    SM(r"\s+[0-9]+\s+[0-9]+\s+(?P<x_gaussian_atom_x_force__hartree_bohr_1>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_y_force__hartree_bohr_1>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_z_force__hartree_bohr_1>[-+0-9EeDd.]+)",repeats = True),
                    SM(r"\s*Cartesian Forces:\s+")
                    ]
                ),
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                SM(name = 'Multipoles',
                  sections = ['x_gaussian_section_molecular_multipoles'],
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                  startReStr = r"\s*Electronic spatial extent",
                  forwardMatch = False,
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                  subMatchers = [
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                      SM(r"\s*Charge=(?P<charge>\s*[-0-9.]+)"),
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                      SM(r"\s*Dipole moment "), 
                      SM(r"\s+\w+=\s+(?P<dipole_moment_x>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_y>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_z>[-+0-9EeDd.]+)"),
                      SM(r"\s*Quadrupole moment"), 
                      SM(r"\s+\w+=\s+(?P<quadrupole_moment_xx>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_zz>[0-9-.]+)"), 
                      SM(r"\s+\w+=\s+(?P<quadrupole_moment_xy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_xz>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yz>[0-9-.]+)"),
                      SM(r"\s*Traceless Quadrupole moment"),
                      SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
                      SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
                      SM(r"\s*Octapole moment"),
                      SM(r"\s+\w+=\s+(?P<octapole_moment_xxx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_yyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_zzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xyy>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<octapole_moment_xxy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_yzz>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<octapole_moment_yyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xyz>[-+0-9EeDd.]+)"),
                      SM(r"\s*Hexadecapole moment"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxxx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxxy>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzzx>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_zzzy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyzz>[-+0-9EeDd.]+)"),
                      SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzxy>[-+0-9EeDd.]+)")
                      ]
             ),    
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                SM (name = 'Frequencies',
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                     sections = ['x_gaussian_section_frequencies'],
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                     startReStr = r"\s*Frequencies --\s+(?:(?:[-]?[0-9]+\.\d*)\s*(?:[-]?[-0-9]+\.\d*)?\s*(?:[-]?[-0-9]+\.\d*)?)",
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                     endReStr = r"\s*- Thermochemistry -",
                     forwardMatch = True,
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                     repeats = False,
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                     subMatchers = [
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                       SM (name = 'Frequencies',
                         startReStr = r"\s*Frequencies --\s+(?:(?:[-]?[0-9]+\.\d*)\s*(?:[-]?[-0-9]+\.\d*)?\s*(?:[-]?[-0-9]+\.\d*)?)",
                         forwardMatch = True,
                         repeats = True,
                         subFlags = SM.SubFlags.Unordered,
                         subMatchers = [
                           SM(r"\s*Frequencies --\s+(?P<x_gaussian_frequency_values>([-]?[0-9]+\.\d*)\s*([-]?[-0-9]+\.\d*)?\s*([-]?[-0-9]+\.\d*)?)", repeats = True),
                           SM(r"\s*Red. masses --\s+(?P<x_gaussian_reduced_masses>(.+))", repeats = True),
                           SM(r"\s*[0-9]+\s*[0-9]+\s*(?P<x_gaussian_normal_modes>([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+)\s*([-0-9.]+))", repeats = True),
                           SM(r"\s*[0-9]+\s*([0-9]+)?\s*([0-9]+)?"),
                         ])
                     ]
                ),
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                SM(name = 'Thermochemistry',
                sections = ['x_gaussian_section_thermochem'],
                startReStr = r"\s*Temperature",
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                forwardMatch = True,
                subMatchers = [
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                      SM(r"\s*Temperature\s*(?P<x_gaussian_temperature>[0-9.]+)\s*Kelvin.\s*Pressure\s*(?P<x_gaussian_pressure__atmosphere>[0-9.]+)\s*Atm."),
                      SM(r"\s*Principal axes and moments of inertia in atomic units:"),
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                      SM(r"\s*Eigenvalues --\s*(?P<x_gaussian_moment_of_inertia_X__amu_angstrom_angstrom>(\d+\.\d{5}))\s*?(?P<x_gaussian_moment_of_inertia_Y__amu_angstrom_angstrom>(\d+\.\d{5}))\s*?(?P<x_gaussian_moment_of_inertia_Z__amu_angstrom_angstrom>(\d+\.\d{5}))"),
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                      SM(r"\s*Zero-point correction=\s*(?P<x_gaussian_zero_point_energy__hartree>[0-9.]+)"),
                      SM(r"\s*Thermal correction to Energy=\s*(?P<x_gaussian_thermal_correction_energy__hartree>[0-9.]+)"),
                      SM(r"\s*Thermal correction to Enthalpy=\s*(?P<x_gaussian_thermal_correction_enthalpy__hartree>[0-9.]+)"),
                      SM(r"\s*Thermal correction to Gibbs Free Energy=\s*(?P<x_gaussian_thermal_correction_free_energy__hartree>[0-9.]+)"), 
                      ]
             ),       
                SM(name = 'Forceconstantmatrix',
                sections = ['x_gaussian_section_force_constant_matrix'],
                startReStr = r"\s*Force constants in Cartesian coordinates",
                forwardMatch = True,
                subMatchers = [
                      SM(r"\s*Force constants in Cartesian coordinates"),
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                      SM(r"\s*[0-9]+\s*(?P<x_gaussian_force_constants>(-?\d*\.\d*D?\+?\-?\d+)|(\-?\d*\.\d*[-+DE0-9]+)\s*(\-?\d*\.\d*[-+DE0-9]+)?\s*(\-?\d*\.\d*[-+DE0-9]+)?\s*(\-?\d*\.\d*[-+DE0-9]+)?\s*(\-?\d*\.\d*[-+DE0-9]+)?)", repeats = True),
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                      SM(r"\s*Force constants in internal coordinates")
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                      ]
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             ),
                SM(name = 'CompositeModelEnergies',
                sections = ['x_gaussian_section_models'],
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                startReStr = r"\s*Temperature=\s*",
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                forwardMatch = False,
                repeats = True,
                subMatchers = [
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                 SM(r"\s*G1\(0 K\)=\s*[-+0-9.]+\s*G1 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*G2\(0 K\)=\s*[-+0-9.]+\s*G2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*G2MP2\(0 K\)=\s*[-+0-9.]+\s*G2MP2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*G3\(0 K\)=\s*[-+0-9.]+\s*G3 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*G3MP2\(0 K\)=\s*[-+0-9.]+\s*G3MP2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*G4\(0 K\)=\s*[-+0-9.]+\s*G4 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*G4MP2\(0 K\)=\s*[-+0-9.]+\s*G4MP2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*CBS-4 \(0 K\)=\s*[-+0-9.]+\s*CBS-4 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*CBS-q \(0 K\)=\s*[-+0-9.]+\s*CBS-q Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*CBS-Q \(0 K\)=\s*[-+0-9.]+\s*CBS-Q Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*CBS-QB3 \(0 K\)=\s*[-+0-9.]+\s*CBS-QB3 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*W1U  \(0 K\)=\s*[-+0-9.]+\s*W1U   Electronic Energy\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*W1RO  \(0 K\)=\s*[-+0-9.]+\s*W1RO  Electronic Energy\s*(?P<energy_total__hartree>[-+0-9.]+)"),
                 SM(r"\s*W1BD  \(0 K\)=\s*[-+0-9.]+\s*W1BD  Electronic Energy\s*(?P<energy_total__hartree>[-+0-9.]+)"),
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                       ]
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             ),
                SM(name = 'run times',
                  sections = ['x_gaussian_section_times'],
                  startReStr = r"\s*Job cpu time:",
                  forwardMatch = True,
                  subMatchers = [
                      SM(r"\s*Job cpu time:\s*(?P<x_gaussian_program_cpu_time>\s*[0-9]+\s*[a-z]+\s*[0-9]+\s*[a-z]+\s*[0-9]+\s*[a-z]+\s*[0-9.]+\s*[a-z]+)"),
                      SM(r"\s*Normal termination of Gaussian\s*[0-9]+\s* at \s*(?P<x_gaussian_program_termination_date>[A-Za-z]+\s*[A-Za-z]+\s*[0-9]+\s*[0-9:]+\s*[0-9]+)"),
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                      ]
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             )
          ])
        ])
      ])
    ])

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# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/gaussian.nomadmetainfo.json
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/gaussian.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)

parserInfo = {
  "name": "parser_gaussian",
  "version": "1.0"
}

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class GaussianParserContext(object):
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      """Context for parsing Gaussian output file.

        This class keeps tracks of several Gaussian settings to adjust the parsing to them.
        The onClose_ functions allow processing and writing of cached values after a section is closed.
        They take the following arguments:
        backend: Class that takes care of writing and caching of metadata.
        gIndex: Index of the section that is closed.
        section: The cached values and sections that were found in the section that is closed.
      """
      def __init__(self):
        # dictionary of energy values, which are tracked between SCF iterations and written after convergence
        self.totalEnergyList = {
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                                'x_gaussian_hf_detect': None,
                                'x_gaussian_energy_scf': None,
                                'x_gaussian_perturbation_energy': None,
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                                'x_gaussian_electronic_kinetic_energy': None,
                                'x_gaussian_energy_electrostatic': None,
                                'x_gaussian_energy_error': None,
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                               }
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      def initialize_values(self):
        """Initializes the values of certain variables.

        This allows a consistent setting and resetting of the variables,
        when the parsing starts and when a section_run closes.
        """
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        self.secMethodIndex = None
        self.secSystemDescriptionIndex = None
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        # start with -1 since zeroth iteration is the initialization
        self.scfIterNr = -1
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        self.singleConfCalcs = []
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        self.scfConvergence = False
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        self.geoConvergence = False
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        self.scfenergyconverged = 0.0
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        self.scfkineticenergyconverged = 0.0
        self.scfelectrostaticenergy = 0.0
        self.periodicCalc = False
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      def startedParsing(self, path, parser):
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        self.parser = parser
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        # save metadata
        self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
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        # allows to reset values if the same superContext is used to parse different files
        self.initialize_values()
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      def onClose_section_run(self, backend, gIndex, section):
          """Trigger called when section_run is closed.

          Write convergence of geometry optimization.
          Variables are reset to ensure clean start for new run.
          """
Rosendo Valero Montero's avatar
Rosendo Valero Montero committed
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          global sampling_method
          sampling_method = ""
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          # write geometry optimization convergence
          gIndexTmp = backend.openSection('section_frame_sequence')
          backend.addValue('geometry_optimization_converged', self.geoConvergence)
          backend.closeSection('section_frame_sequence', gIndexTmp)
          # frame sequence
          if self.geoConvergence:
              sampling_method = "geometry_optimization"
          elif len(self.singleConfCalcs) > 1:
              pass # to do
          else:
              return
          samplingGIndex = backend.openSection("section_sampling_method")
          backend.addValue("sampling_method", sampling_method)
          backend.closeSection("section_sampling_method", samplingGIndex)
          frameSequenceGIndex = backend.openSection("section_frame_sequence")
          backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex)
          backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
          backend.closeSection("section_frame_sequence", frameSequenceGIndex)
          # reset all variables
          self.initialize_values()

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      def onClose_x_gaussian_section_geometry(self, backend, gIndex, section):
        xCoord = section["x_gaussian_atom_x_coord"]
        yCoord = section["x_gaussian_atom_y_coord"]
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        zCoord = section["x_gaussian_atom_z_coord"]
        numbers = section["x_gaussian_atomic_number"]
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        atom_coords = np.zeros((len(xCoord),3), dtype=float)
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        atom_numbers = np.zeros(len(xCoord), dtype=int)
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        atomic_symbols = np.empty((len(xCoord)), dtype=object)
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        for i in range(len(xCoord)):
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           atom_coords[i,0] = xCoord[i]
           atom_coords[i,1] = yCoord[i]
           atom_coords[i,2] = zCoord[i]
        for i in range(len(xCoord)):
          atom_numbers[i] = numbers[i]
          atomic_symbols[i] = ase.data.chemical_symbols[atom_numbers[i]]
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        gIndexTmp = backend.openSection("section_system")
        backend.addArrayValues("atom_labels", atomic_symbols)
        backend.addArrayValues("atom_positions", atom_coords)
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        backend.addValue("x_gaussian_number_of_atoms",len(atomic_symbols))
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        backend.closeSection("section_system", gIndexTmp)
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      def onClose_x_gaussian_section_atom_forces(self, backend, gIndex, section):
        xForce = section["x_gaussian_atom_x_force"]
        yForce = section["x_gaussian_atom_y_force"]
        zForce = section["x_gaussian_atom_z_force"]
        atom_forces = np.zeros((len(xForce),3), dtype=float)
        for i in range(len(xForce)):
           atom_forces[i,0] = xForce[i]
           atom_forces[i,1] = yForce[i]
           atom_forces[i,2] = zForce[i]
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        backend.addArrayValues("atom_forces_raw", atom_forces)
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      def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
          self.singleConfCalcs.append(gIndex)
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      def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
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        """Trigger called when section_single_configuration_calculation is closed.
         Write number of SCF iterations and convergence.
         Check for convergence of geometry optimization.
        """
        # write SCF convergence and reset
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        backend.addValue('single_configuration_calculation_converged', self.scfConvergence)
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        self.scfConvergence = False
        # start with -1 since zeroth iteration is the initialization
        self.scfIterNr = -1
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        # write the references to section_method and section_system
        backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
        backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)

      def onClose_x_gaussian_section_geometry_optimization_info(self, backend, gIndex, section):
        # check for geometry optimization convergence
        if section['x_gaussian_geometry_optimization_converged'] is not None:
           if section['x_gaussian_geometry_optimization_converged'] == ['Optimization completed']:
              self.geoConvergence = True
           elif section['x_gaussian_geometry_optimization_converged'] == ['Optimization stopped']:
              self.geoConvergence = False
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      def onClose_section_scf_iteration(self, backend, gIndex, section):
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        # count number of SCF iterations
        self.scfIterNr += 1
        # check for SCF convergence
        if section['x_gaussian_single_configuration_calculation_converged'] is not None:
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           self.scfConvergence = True
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           if section['x_gaussian_energy_scf']:
               self.scfenergyconverged = float(str(section['x_gaussian_energy_scf']).replace("[","").replace("]","").replace("D","E"))
               self.scfcharacter = section['x_gaussian_hf_detect']
               if (self.scfcharacter != ['RHF'] and self.scfcharacter != ['ROHF'] and self.scfcharacter != ['UHF']):
                  self.energytotal = self.scfenergyconverged
                  backend.addValue('energy_total', self.energytotal)
               else:
                  pass
               if section['x_gaussian_electronic_kinetic_energy']:
                  self.scfkineticenergyconverged = float(str(section['x_gaussian_electronic_kinetic_energy']).replace("[","").replace("]","").replace("D","E"))
                  self.scfelectrostaticenergy = self.scfenergyconverged - self.scfkineticenergyconverged
                  backend.addValue('x_gaussian_energy_electrostatic', self.scfelectrostaticenergy)

      def onClose_section_eigenvalues(self, backend, gIndex, section):
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          eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"])
          eigenen1 = []
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          if('*' in eigenenergies):
             energy = [0.0]
          else:
             energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
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          eigenen1 = np.append(eigenen1, energy)
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          if(section["x_gaussian_beta_occ_eigenvalues_values"]):
             occoccupationsalp = np.ones(len(eigenen1), dtype=float)
          else:
             occoccupationsalp = 2.0 * np.ones(len(eigenen1), dtype=float)

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          eigenenergies = str(section["x_gaussian_alpha_vir_eigenvalues_values"])
          eigenen2 = []
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          if('*' in eigenenergies):
             energy = [0.0]
          else:
             energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
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          eigenen2 = np.append(eigenen2, energy)
          viroccupationsalp = np.zeros(len(eigenen2), dtype=float)
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          leneigenenconalp = len(eigenen1) + len(eigenen2)
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          eigenenconalp = np.concatenate((eigenen1,eigenen2), axis=0)
          eigenenconalp = convert_unit(eigenenconalp, "hartree", "J")
          occupconalp = np.concatenate((occoccupationsalp, viroccupationsalp), axis=0)
          eigenenconalpnew = np.reshape(eigenenconalp,(1, 1, len(eigenenconalp)))
          occupconalpnew = np.reshape(occupconalp,(1, 1, len(occupconalp)))
          if(section["x_gaussian_beta_occ_eigenvalues_values"]):
             pass
          else:
             backend.addArrayValues("eigenvalues_values", eigenenconalpnew)
             backend.addArrayValues("eigenvalues_occupation", occupconalpnew)
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          if(section["x_gaussian_beta_occ_eigenvalues_values"]):
             eigenenergies = str(section["x_gaussian_beta_occ_eigenvalues_values"])
             eigenen1 = []
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             if('*' in eigenenergies):
                energy = [0.0]
             else:
                energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
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             eigenen1 = np.append(eigenen1, energy)
             occoccupationsbet = np.ones(len(eigenen1), dtype=float)
             eigenenergies = str(section["x_gaussian_beta_vir_eigenvalues_values"])
             eigenen2 = []
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             if('*' in eigenenergies):
                energy = [0.0]
             else:
                energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
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             eigenen2 = np.append(eigenen2, energy)
             viroccupationsbet = np.zeros(len(eigenen2), dtype=float)
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             leneigenenconbet = len(eigenen1) + len(eigenen2)
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             eigenenconbet = np.concatenate((eigenen1,eigenen2), axis=0)
             eigenenconbet = convert_unit(eigenenconbet, "hartree", "J")
             occupconbet = np.concatenate((occoccupationsbet, viroccupationsbet), axis=0)
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             if(leneigenenconalp >= leneigenenconbet):
                 eigenenall = np.zeros(2*leneigenenconalp)
                 occupall = np.zeros(2*leneigenenconalp)
             else:
                 eigenenall = np.zeros(2*leneigenenconbet)
                 occupall = np.zeros(2*leneigenenconbet)
             eigenenall[:len(eigenenconalp) + len(eigenenconbet)] = np.concatenate((eigenenconalp,eigenenconbet), axis=0)
             occupall[:len(occupconalp) + len(occupconbet)] = np.concatenate((occupconalp,occupconbet), axis=0)
             eigenenall = np.reshape(eigenenall,(2, 1, max(len(eigenenconalp),len(eigenenconbet))))
             occupall = np.reshape(occupall,(2, 1, max(len(occupconalp),len(occupconbet))))
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             backend.addArrayValues("eigenvalues_values", eigenenall)
             backend.addArrayValues("eigenvalues_occupation", occupall)
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      def onClose_x_gaussian_section_orbital_symmetries(self, backend, gIndex, section):
          symoccalpha = str(section["x_gaussian_alpha_occ_symmetry_values"])
          symviralpha = str(section["x_gaussian_alpha_vir_symmetry_values"])
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          if(section["x_gaussian_beta_occ_symmetry_values"]):
             symoccbeta = str(section["x_gaussian_beta_occ_symmetry_values"])
             symvirbeta = str(section["x_gaussian_beta_vir_symmetry_values"])

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          symmetry = [str(f) for f in symoccalpha[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("'E","E").replace("G'","G").replace("\"A'\"","A'").split()]
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          sym1 = []
          sym1 = np.append(sym1, symmetry)  
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          symmetry = [str(f) for f in symviralpha[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("\"A'\"","A'").replace("'E","E").replace("G'","G").split()]
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          sym2 = []
          sym2 = np.append(sym2, symmetry)
          symmetrycon = np.concatenate((sym1, sym2), axis=0)
          backend.addArrayValues("x_gaussian_alpha_symmetries", symmetrycon) 
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          if(section["x_gaussian_beta_occ_symmetry_values"]):
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             symmetry = [str(f) for f in symoccbeta[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("\"A'\"","A'").replace("'E","E").replace("G'","G").split()]
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             sym1 = []
             sym1 = np.append(sym1, symmetry)
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             symmetry = [str(f) for f in symvirbeta[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("\"A'\"","A'").replace("'E","E").replace("G'","G").split()]
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             sym2 = []
             sym2 = np.append(sym2, symmetry)
             symmetrycon = np.concatenate((sym1, sym2), axis=0)
             backend.addArrayValues("x_gaussian_beta_symmetries", symmetrycon)

      def onClose_x_gaussian_section_molecular_multipoles(self, backend, gIndex, section):
          if(section["quadrupole_moment_xx"]):
             x_gaussian_number_of_lm_molecular_multipoles = 35
          else:
             x_gaussian_number_of_lm_molecular_multipoles = 4

          x_gaussian_molecular_multipole_m_kind = 'polynomial'

          char = str(section["charge"])
          cha = str([char])
          charge = [float(f) for f in cha[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").replace('"','').split()]

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          if(section["dipole_moment_x"]):
            dipx = section["dipole_moment_x"]
            dipy = section["dipole_moment_y"]
            dipz = section["dipole_moment_z"]
            dip = str([dipx, dipy, dipz])
            dipoles = [float(f) for f in dip[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").split()]
            dipoles = convert_unit(dipoles, "debye", "coulomb * meter")
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          if(section["quadrupole_moment_xx"]):
            quadxx = section["quadrupole_moment_xx"]
            quadxy = section["quadrupole_moment_xy"]
            quadyy = section["quadrupole_moment_yy"]
            quadxz = section["quadrupole_moment_xz"]
            quadyz = section["quadrupole_moment_yz"]
            quadzz = section["quadrupole_moment_zz"]
            quad = str([quadxx, quadxy, quadyy, quadxz, quadyz, quadzz])
            quadrupoles = [float(f) for f in quad[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").split()] 
            quadrupoles = convert_unit(quadrupoles, "debye * angstrom", "coulomb * meter**2")
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          if(section["octapole_moment_xxx"]):
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            octaxxx = section["octapole_moment_xxx"]
            octayyy = section["octapole_moment_yyy"]
            octazzz = section["octapole_moment_zzz"]
            octaxyy = section["octapole_moment_xyy"]
            octaxxy = section["octapole_moment_xxy"]
            octaxxz = section["octapole_moment_xxz"]
            octaxzz = section["octapole_moment_xzz"]
            octayzz = section["octapole_moment_yzz"]
            octayyz = section["octapole_moment_yyz"]
            octaxyz = section["octapole_moment_xyz"]
            octa = str([octaxxx, octayyy, octazzz, octaxyy, octaxxy, octaxxz, octaxzz, octayzz, octayyz, octaxyz])
            octapoles = [float(f) for f in octa[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").split()]
            octapoles = convert_unit(octapoles, "debye * angstrom**2", "coulomb * meter**3")
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          if(section["hexadecapole_moment_xxxx"]):
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            hexadecaxxxx = section["hexadecapole_moment_xxxx"]
            hexadecayyyy = section["hexadecapole_moment_yyyy"]
            hexadecazzzz = section["hexadecapole_moment_zzzz"]
            hexadecaxxxy = section["hexadecapole_moment_xxxy"]
            hexadecaxxxz = section["hexadecapole_moment_xxxz"]
            hexadecayyyx = section["hexadecapole_moment_yyyx"]
            hexadecayyyz = section["hexadecapole_moment_yyyz"]
            hexadecazzzx = section["hexadecapole_moment_zzzx"]
            hexadecazzzy = section["hexadecapole_moment_zzzy"]
            hexadecaxxyy = section["hexadecapole_moment_xxyy"]
            hexadecaxxzz = section["hexadecapole_moment_xxzz"]
            hexadecayyzz = section["hexadecapole_moment_yyzz"]
            hexadecaxxyz = section["hexadecapole_moment_xxyz"]
            hexadecayyxz = section["hexadecapole_moment_yyxz"]
            hexadecazzxy = section["hexadecapole_moment_zzxy"]
            hexa = str([hexadecaxxxx, hexadecayyyy, hexadecazzzz, hexadecaxxxy, hexadecaxxxz, hexadecayyyx, hexadecayyyz,
            hexadecazzzx, hexadecazzzy, hexadecaxxyy, hexadecaxxzz, hexadecayyzz, hexadecaxxyz, hexadecayyxz, hexadecazzxy])
            hexadecapoles = [float(f) for f in hexa[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").split()]
            hexadecapoles = convert_unit(hexadecapoles, "debye * angstrom**3", "coulomb * meter**4")
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          if(section["quadrupole_moment_xx"]):
             multipoles = np.hstack((charge, dipoles, quadrupoles, octapoles, hexadecapoles))
          else:
             multipoles = np.hstack((charge, dipoles)) 

          x_gaussian_molecular_multipole_values = np.resize(multipoles, (x_gaussian_number_of_lm_molecular_multipoles))

          backend.addArrayValues("x_gaussian_molecular_multipole_values", x_gaussian_molecular_multipole_values)
          backend.addValue("x_gaussian_molecular_multipole_m_kind", x_gaussian_molecular_multipole_m_kind)

      def onClose_x_gaussian_section_frequencies(self, backend, gIndex, section):
          frequencies = str(section["x_gaussian_frequency_values"])
          vibfreqs = []
          freqs = [float(f) for f in frequencies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace("\\n","").replace(" ."," 0.").replace(" -."," -0.").split()]
          vibfreqs = np.append(vibfreqs, freqs)
          vibfreqs = convert_unit(vibfreqs, "inversecm", "J")
          backend.addArrayValues("x_gaussian_frequencies", vibfreqs)

          masses = str(section["x_gaussian_reduced_masses"])
          vibreducedmasses = []
          reduced = [float(f) for f in masses[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").split()]
          vibreducedmasses = np.append(vibreducedmasses, reduced)
          vibreducedmasses = convert_unit(vibreducedmasses, "amu", "kilogram")
          backend.addArrayValues("x_gaussian_red_masses", vibreducedmasses)

          vibnormalmodes = []
          vibdisps = str(section["x_gaussian_normal_modes"])
          disps = [float(s) for s in vibdisps[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace("\\n","").replace(" ."," 0.").replace(" -."," -0.").split()]
          dispsnew = np.zeros(len(disps), dtype = float)

#  Reorder disps 

          if len(vibfreqs) % 3 == 0:
             k = 0
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             for p in range(0,len(vibfreqs) // 3):
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                M = int(len(disps)/len(vibfreqs)) * (p+1) 
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                for m in range(3):
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                  for n in range(M - int(len(disps) / len(vibfreqs)),M,3):
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                    for l in range(3):
                      dispsnew[k] = disps[3*(n + m) + l]
                      k = k + 1
          elif len(vibfreqs) % 3 != 0:
             k = 0
             for p in range(len(vibfreqs)-1,0,-3):
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                M = (len(disps) - int(len(disps) / len(vibfreqs))) // p
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                for m in range(3):
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                  for n in range(M - int(len(disps) / len(vibfreqs)),M,3):
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                    for l in range(3):
                      dispsnew[k] = disps[3*(n + m) + l]
                      k = k + 1
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             for m in range(int(len(disps) / len(vibfreqs))):
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                   dispsnew[k] = disps[k]
                   k = k + 1

          vibnormalmodes = np.append(vibnormalmodes, dispsnew)
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          if len(vibfreqs) != 0:
            natoms = int(len(disps) / len(vibfreqs) / 3)
            vibnormalmodes = np.reshape(vibnormalmodes,(len(vibfreqs),natoms,3))
            backend.addArrayValues("x_gaussian_normal_mode_values", vibnormalmodes)
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      def onClose_x_gaussian_section_force_constant_matrix(self, backend, gIndex, section):

          forcecnstvalues = []
          forceconst = str(section["x_gaussian_force_constants"])
          numbers = [float(s) for s in forceconst[1:].replace("'","").replace(",","").replace("]","").replace("\\n","").replace("D","E").replace(" ."," 0.").replace(" -."," -0.").split()]
          length = len(numbers)
          dim = int(((1 + 8 * length)**0.5 - 1) / 2) 
          cartforceconst = np.zeros([dim, dim])
          forcecnstvalues = np.append(forcecnstvalues, numbers) 
          if dim > 6:
             l = 0
             for i in range(0,5):
                for k in range(0,i+1):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
             for i in range(5,dim):
                for k in range(0,5):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
             for i in range(5,dim-2): 
                for k in range(5,i+1):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
             for i in range(dim-2,dim):
                for k in range(5,dim-2):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
             for i in range(dim-2,dim):
                for k in range(i,dim):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
          elif dim == 6:
             l = 0
             for i in range(0,5):
                for k in range(0,i+1):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
             for i in range(5,dim):
                for k in range(0,5):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
             for i in range(dim,dim):
                for k in range(i,dim):
                   l = l + 1
                   cartforceconst[i,k] = forcecnstvalues[l-1]
 
          for i in range(0,dim):
             for k in range(i+1,dim):
                 cartforceconst[i,k] = cartforceconst[k,i]

          cartforceconst = convert_unit(cartforceconst, "forceAu / bohr", "J / (meter**2)")

          backend.addArrayValues("x_gaussian_force_constant_values", cartforceconst) 
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      def onOpen_section_method(self, backend, gIndex, section):
        # keep track of the latest method section
        self.secMethodIndex = gIndex

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      def onClose_section_method(self, backend, gIndex, section):
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       # handling of xc functional
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       # Dictionary for conversion of xc functional name in Gaussian to metadata format.
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       # The individual x and c components of the functional are given as dictionaries.
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       # Possible key of such a dictionary is 'name'.
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        xcDict = {
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              'S':          [{'name': 'LDA_X'}],
              'XA':	    [{'name': 'X_ALPHA'}],
              'VWN':        [{'name': 'LDA_C_VWN'}],
              'VWN3':       [{'name': 'LDA_C_VWN_3'}],
              'LSDA':       [{'name': 'LDA_X'}, {'name': 'LDA_C_VWN'}], 
              'B':          [{'name': 'GGA_X_B88'}],
              'BLYP':       [{'name': 'GGA_C_LYP'}, {'name': 'GGA_X_B88'}],
              'PBEPBE':     [{'name': 'GGA_C_PBE'}, {'name': 'GGA_X_PBE'}],
              'PBEH':       [{'name': 'GGA_X_PBEH'}],
              'WPBEH':      [{'name': 'GGA_X_WPBEH'}],
              'PW91PW91':   [{'name': 'GGA_C_PW91'}, {'name': 'GGA_X_PW91'}],
              'M06L':       [{'name': 'MGGA_C_M06_L'}, {'name': 'MGGA_X_M06_L'}],
              'M11L':       [{'name': 'MGGA_C_M11_L'}, {'name': 'MGGA_X_M11_L'}],
              'SOGGA11':    [{'name': 'GGA_XC_SOGGA11'}],
              'MN12L':      [{'name': 'GGA_XC_MN12L'}],
              'N12':        [{'name': 'GGA_C_N12'}, {'name': 'GGA_X_N12'}],
              'VSXC':       [{'name': 'MGGA_XC_VSXC'}],
              'HCTH93':     [{'name': 'GGA_XC_HCTH_93'}],
              'HCTH147':    [{'name': 'GGA_XC_HCTH_147'}],
              'HCTH407':    [{'name': 'GGA_XC_HCTH_407'}],
              'HCTH':       [{'name': 'GGA_XC_HCTH_407'}],
              'B97D':       [{'name': 'GGA_XC_B97D'}],
              'B97D3':      [{'name': 'GGA_XC_B97D3'}],
              'MPW':        [{'name': 'GGA_X_MPW'}],
              'G96':        [{'name': 'GGA_X_G96'}],
              'O':          [{'name': 'GGA_X_O'}],
              'BRX':        [{'name': 'GGA_X_BRX'}],
              'PKZB':       [{'name': 'GGA_C_PKZB'}, {'name': 'GGA_X_PKZB'}],
              'PL':         [{'name': 'C_PL'}],
              'P86':        [{'name': 'GGA_C_P86'}],
              'B95':        [{'name': 'MGGA_C_B95'}],
              'KCIS':       [{'name': 'GGA_C_KCIS'}],
              'BRC':        [{'name': 'GGA_C_BRC'}],
              'VP86':       [{'name': 'GGA_C_VP86'}],
              'V5LYP':      [{'name': 'GGA_C_V5LYP'}],
              'THCTH':      [{'name': 'MGGA_XC_TAU_HCTH'}],
              'TPSSTPSS':   [{'name': 'MGGA_C_TPSS'}, {'name': 'MGGA_X_TPSS'}],
              'B3LYP':      [{'name': 'HYB_GGA_XC_B3LYP'}], 
              'B3PW91':     [{'name': 'HYB_GGA_XC_B3PW91'}],
              'B3P86':      [{'name': 'HYB_GGA_XC_B3P86'}], 
              'B1B95':      [{'name': 'HYB_GGA_XC_B1B95'}],
              'MPW1PW91':   [{'name': 'HYB_GGA_XC_MPW1PW91'}],
              'MPW1LYP':    [{'name': 'HYB_GGA_XC_MPW1LYP'}],
              'MPW1PBE':    [{'name': 'HYB_GGA_XC_MPW1PBE'}],
              'MPW3PBE':    [{'name': 'HYB_GGA_XC_MPW3PBE'}],
              'B98':        [{'name': 'HYB_GGA_XC_B98'}],
              'B971':       [{'name': 'HYB_GGA_XC_B971'}],
              'B972':       [{'name': 'HYB_GGA_XC_B972'}],
              'O3LYP':      [{'name': 'HYB_GGA_XC_O3LYP'}], 
              'TPSSH':      [{'name': 'HYB_GGA_XC_TPSSh'}],
              'BMK':        [{'name': 'HYB_MGGA_XC_BMK'}],
              'X3LYP':      [{'name': 'HYB_GGA_XC_X3LYP'}],
              'THCTHHYB':   [{'name': 'HYB_MGGA_XC_THCTHHYB'}],
              'BHANDH':     [{'name': 'HYB_GGA_XC_BHANDH'}],
              'BHANDHLYP':  [{'name': 'HYB_GGA_XC_BHANDHLYP'}],
              'APF':        [{'name': 'HYB_GGA_XC_APF'}],
              'APFD':       [{'name': 'HYB_GGA_XC_APFD'}],
              'B97D':       [{'name': 'HYB_GGA_XC_B97D'}],
              'RHF':        [{'name': 'RHF_X'}],
              'UHF':        [{'name': 'UHF_X'}],
              'ROHF':       [{'name': 'ROHF_X'}],
              'OHSE2PBE':   [{'name': 'HYB_GGA_XC_HSE03'}],
              'HSEH1PBE':   [{'name': 'HYB_GGA_XC_HSE06'}],
              'OHSE1PBE':   [{'name': 'HYB_GGA_XC_HSEOLD'}],
              'PBEH1PBE':   [{'name': 'HYB_GGA_XC_PBEH1PBE'}],
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              'PBE1PBE':    [{'name': 'HYB_GGA_XC_PBE1PBE'}],
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              'M05':        [{'name': 'HYB_MGGA_XC_M05'}],
              'M052X':      [{'name': 'HYB_MGGA_XC_M05_2X'}],
              'M06':        [{'name': 'HYB_MGGA_XC_M06'}],
              'M062X':      [{'name': 'HYB_MGGA_XC_M06_2X'}],
              'M06HF':      [{'name': 'HYB_MGGA_XC_M06_HF'}],
              'M11':        [{'name': 'HYB_MGGA_XC_M11'}],
              'SOGGAX11':   [{'name': 'HYB_MGGA_XC_SOGGA11_X'}],
              'MN12SX':     [{'name': 'HYB_MGGA_XC_MN12_SX'}],
              'N12SX':      [{'name': 'HYB_MGGA_XC_N12_SX'}],
              'LC-WPBE':    [{'name': 'LC-WPBE'}],
              'CAM-B3LYP':  [{'name': 'CAM-B3LYP'}],
              'WB97':       [{'name': 'WB97'}],
              'WB97X':      [{'name': 'WB97X'}],
              'WB97XD':     [{'name': 'WB97XD'}],
              'HISSBPBE':   [{'name': 'HISSBPBE'}],
              'B2PLYP':     [{'name': 'B2PLYP'}],
              'MPW2PLYP':   [{'name': 'MPW2PLYP'}],
              'B2PLYPD':    [{'name': 'B2PLYPD'}],
              'MPW2PLYPD':  [{'name': 'MPW2PLYPD'}],
              'B97D3':      [{'name': 'B97D3'}], 
              'B2PLYPD3':   [{'name': 'B2PLYPD3'}],
              'MPW2PLYPD3': [{'name': 'MPW2PLYPD3'}],
              'LC-':        [{'name': 'LONG-RANGE CORRECTED'}],
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             }

        methodDict = {
              'AMBER':     [{'name': 'Amber'}],
              'DREIDING':  [{'name': 'Dreiding'}],
              'UFF':       [{'name': 'UFF'}],
              'AM1':       [{'name': 'AM1'}],
              'PM3':       [{'name': 'PM3'}],
              'PM3MM':     [{'name': 'PM3MM'}],
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              'PM3D3':     [{'name': 'PM3D3'}],
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              'PM6':       [{'name': 'PM6'}],
              'PDDG':      [{'name': 'PDDG'}],
              'CNDO':      [{'name': 'CNDO'}],
              'INDO':      [{'name': 'INDO'}],
              'MINDO':     [{'name': 'MINDO'}],
              'MINDO3':    [{'name': 'MINDO3'}],
              'ZINDO':     [{'name': 'ZINDO'}],
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              'HUCKEL':    [{'name': 'HUCKEL'}],
              'EXTENDEDHUCKEL':    [{'name': 'HUCKEL'}],
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              'ONIOM':     [{'name': 'ONIOM'}],
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              'HF':        [{'name': 'HF'}],
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              'RHF':       [{'name': 'RHF'}],
              'UHF':       [{'name': 'UHF'}],
              'ROHF':      [{'name': 'ROHF'}],
              'GVB':       [{'name': 'GVB'}],
              'DFT':       [{'name': 'DFT'}],
              'CID':       [{'name': 'CID'}],
              'CISD':      [{'name': 'CISD'}],
              'CIS':       [{'name': 'CIS'}],
              'BD':        [{'name': 'BD'}],
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              'BD(T)':     [{'name': 'BD(T)'}],
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              'CCD':       [{'name': 'CCD'}],
              'CCSD':      [{'name': 'CCSD'}],
              'EOMCCSD':   [{'name': 'EOMCCSD'}],
              'QCISD':     [{'name': 'QCISD'}],
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              'CCSD(T)':   [{'name': 'CCSD(T)'}],
              'QCISD(T)':  [{'name': 'QCISD(T)'}],
              'QCISD(TQ)': [{'name': 'QCISD(TQ)'}],
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              'MP2':       [{'name': 'MP2'}],
              'MP3':       [{'name': 'MP3'}],
              'MP4':       [{'name': 'MP4'}],
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              'MP4DQ':     [{'name': 'MP4DQ'}],
              'MP4(DQ)':   [{'name': 'MP4DQ'}],
              'MP4SDQ':    [{'name': 'MP4SDQ'}],
              'MP4(SDQ)':  [{'name': 'MP4SDQ'}],
              'MP4SDTQ':   [{'name': 'MP4SDTQ'}],
              'MP4(SDTQ)': [{'name': 'MP4SDTQ'}],
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              'MP5':       [{'name': 'MP5'}],
              'CAS':       [{'name': 'CASSCF'}],
              'CASSCF':    [{'name': 'CASSCF'}],
              'G1':        [{'name': 'G1'}],
              'G2':        [{'name': 'G2'}],
              'G2MP2':     [{'name': 'G2MP2'}],
              'G3':        [{'name': 'G3'}],
              'G3MP2':     [{'name': 'G3MP2'}],
              'G3B3':      [{'name': 'G3B3'}],
              'G3MP2B3':   [{'name': 'G3MP2B3'}],
              'G4':        [{'name': 'G4'}],
              'G4MP2':     [{'name': 'G4MP2'}],
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              'CBSEXTRAP':   [{'name': 'CBSExtrapolate'}],
              'CBSEXTRAPOLATE':   [{'name': 'CBSExtrapolate'}],
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              'CBS-4M':    [{'name': 'CBS-4M'}],
              'CBS-4O':    [{'name': 'CBS-4O'}],
              'CBS-QB3':   [{'name': 'CBS-QB3'}],
              'CBS-QB3O':  [{'name': 'CBS-QB3O'}],
              'CBS-APNO':  [{'name': 'CBS-APNO'}],
              'W1U':       [{'name': 'W1U'}],
              'W1BD':      [{'name': 'W1BD'}],
              'W1RO':      [{'name': 'W1RO'}],
             }

        basissetDict = {
              'STO-3G':      [{'name': 'STO-3G'}],
              '3-21G':       [{'name': '3-21G'}],
              '6-21G':       [{'name': '6-21G'}],
              '4-31G':       [{'name': '4-31G'}],
              '6-31G':       [{'name': '6-31G'}],
              '6-311G':      [{'name': '6-311G'}],
              'D95V':        [{'name': 'D95V'}],
              'D95':         [{'name': 'D95'}],
              'CC-PVDZ':     [{'name': 'cc-pVDZ'}],
              'CC-PVTZ':     [{'name': 'cc-pVTZ'}],
              'CC-PVQZ':     [{'name': 'cc-pVQZ'}],
              'CC-PV5Z':     [{'name': 'cc-pV5Z'}],
              'CC-PV6Z':     [{'name': 'cc-pV6Z'}],
              'SV':          [{'name': 'SV'}],
              'SVP':         [{'name': 'SVP'}],
              'TZV':         [{'name': 'TZV'}],
              'TZVP':        [{'name': 'TZVP'}],              
              'DEF2SV':      [{'name': 'Def2SV'}],
              'DEF2SVP':     [{'name': 'Def2SVP'}],
              'DEF2SVPP':    [{'name': 'Def2SVPP'}],
              'DEF2TZV':     [{'name': 'Def2TZV'}],
              'DEF2TZVP':    [{'name': 'Def2TZVP'}],
              'DEF2TZVPP':   [{'name': 'Def2TZVPP'}],
              'DEF2QZV':     [{'name': 'Def2QZV'}],
              'DEF2QZVP':    [{'name': 'Def2QZVP'}],
              'DEF2QZVPP':   [{'name': 'Def2QZVPP'}],
              'QZVP':        [{'name': 'QZVP'}],
              'MIDIX':       [{'name': 'MidiX'}],
              'EPR-II':      [{'name': 'EPR-II'}],
              'EPR-III':     [{'name': 'EPR-III'}],
              'UGBS':        [{'name': 'UGBS'}],     
              'MTSMALL':     [{'name': 'MTSmall'}],
              'DGDZVP':      [{'name': 'DGDZVP'}],
              'DGDZVP2':     [{'name': 'DGDZVP2'}],
              'DGTZVP':      [{'name': 'DGTZVP'}],
              'CBSB3':       [{'name': 'CBSB3'}],  
              'CBSB7':       [{'name': 'CBSB7'}],
              'SHC':         [{'name': 'SHC'}],
              'SEC':         [{'name': 'SHC'}],
              'CEP-4G':      [{'name': 'CEP-4G'}],
              'CEP-31G':     [{'name': 'CEP-31G'}],
              'CEP-121G':    [{'name': 'CEP-121G'}],
              'LANL1':       [{'name': 'LANL1'}],
              'LANL2':       [{'name': 'LANL2'}],
              'SDD':         [{'name': 'SDD'}],
              'OLDSDD':      [{'name': 'OldSDD'}], 
              'SDDALL':      [{'name': 'SDDAll'}],
              'GEN':         [{'name': 'General'}],
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              'GENECP':      [{'name': 'General ECP'}],
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              'CHKBAS':      [{'name': 'CHKBAS'}],
              'EXTRABASIS':  [{'name': 'ExtraBasis'}],
              'DGA1':        [{'name': 'DGA1'}],
              'DGA2':        [{'name': 'DGA2'}],
              'SVPFIT':      [{'name': 'SVPFit'}],
              'TZVPFIT':     [{'name': 'TZVPFit'}],
              'W06':         [{'name': 'W06'}],
              'CHF':         [{'name': 'CHF'}],
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              'FIT':         [{'name': 'FIT'}],
              'AUTO':        [{'name': 'AUTO'}],
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             }

        global xc, method, basisset, xcWrite, methodWrite, basissetWrite, methodreal, basissetreal, exc, corr, exccorr, methodprefix
        xc = None
        method = None
        basisset = None
        xcWrite = False
        methodWrite = False
        basissetWrite = False
        methodreal = None
        basissetreal = None 
        methodprefix = None
        exc = None
        corr = None
        exccorr = None
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        settings = section["x_gaussian_settings"]
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        settings1 = str(settings[0]).strip()
        settings2 = str(settings[1]).strip()
        settings = [settings1, settings2]
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        settings = [''.join(map(str,settings))]
        settings = str(settings)
        settings = re.sub('[-]{2,}', '', settings)
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        backend.addValue("x_gaussian_settings_corrected", settings)
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        method1 = settings.replace("['#p ","").replace("['#P ","").replace("['#","")
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        method1 = method1.upper()

        if 'ONIOM' not in method1: 
          if settings.find("/") >= 0:
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               method1 = settings.split('/')[0].replace("['#p ","").replace("['#P ","").replace("['#","")
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               method1 = method1.upper()
               for x in method1.split():
                  method2 = str(x)
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                  if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF' and method2 != 'UFF':
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                     if (method2[0] == 'R' and method2[0:2] != 'RO') or method2[0] == 'U':
                        methodprefix = method2[0] 
                        method2 = method2[1:]
                     elif method2[0:2] == 'RO':
                        methodprefix = method2[0:2]
                        method2 = method2[2:]
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                  if method2[0:2] == 'SV' or method2[0] == 'B' or method2[0] == 'O':
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                     if method2[1] != '2' and method2[1] != '3':
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                       if method2[0] in xcDict.keys() and method2[1:] in xcDict.keys():
                         exc = method2[0]
                         corr = method2[1:]
                         excfunc = xcDict[exc][0]['name']
                         corrfunc = xcDict[corr][0]['name']
                         xc = str(excfunc) + "_" + str(corrfunc)
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                  if method2[0:3] == 'BRX' or method2[0:3] == 'G96':
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                    exc = method2[0:3]
                    corr = method2[3:]
                    if exc in xcDict.keys() and corr in xcDict.keys():
                      excfunc = xcDict[exc][0]['name']
                      corrfunc = xcDict[corr][0]['name']
                      xc = str(excfunc) + "_" + str(corrfunc)
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                  if method2[0:5] == 'WPBEH':
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                    exc = method2[0:5]
                    corr = method2[6:]
                    if exc in xcDict.keys() and corr in xcDict.keys():
                      excfunc = xcDict[exc][0]['name']
                      corrfunc = xcDict[corr][0]['name']
                      xc = str(excfunc) + "_" + str(corrfunc)
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                  if method2[0:3] == 'LC-':
                     exccorr = method2[3:]
                     if exccorr in xcDict.keys():
                        xc = 'LC-' + xcDict.get([exccorr][-1])
                  if method2 in xcDict.keys():
                     xc = method2
                     xcWrite= True
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                     methodWrite = True 
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                     method = 'DFT'
                  if method2 in methodDict.keys():
                     method = method2
                     methodWrite = True
                     methodreal = method2
                  else:
                     for n in range(2,9):
                        if method2[0:n] in methodDict.keys():
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                          method = method2[0:n]
                          methodWrite = True
                          methodreal = method2
                        if method2[0:n] in xcDict.keys():
                          xc = method2[0:n]
                          xcWrite = True
                          methodWrite = True
                          method = 'DFT'
                        if method2[0:9] == 'CBSEXTRAP':
                          method = method2[0:9]
                          methodWrite = True
                          methodreal = method2
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               rest = settings.split('/')[1].replace("'","").replace("]","")
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               rest = rest.upper() 
               for x in rest.split():
                  if x in basissetDict.keys():
                     basisset = x
                     basissetWrite = True
                     basissetreal = x
                  if 'D95' in x:
                     method2 = x
                     basisset = method2[0:3]
                     basissetWrite = True
                     basissetreal = method2
                  if 'AUG-' in x:
                     method2 = x
                     basisset = method2[4:]
                     basissetWrite = True
                     basissetreal = method2
                  if 'UGBS' in x:
                     method2 = x
                     basisset = method2[0:4]
                     basissetWrite = True
                     basissetreal = method2
                  if 'CBSB7' in x:
                     method2 = x
                     basisset = method2[0:5]
                     basissetWrite = True
                     basissetreal = method2
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                  if 'LANL1' in x:
                     method2 = x
                     basisset = method2[0:5]
                     basissetWrite = True
                     basissetreal = method2
                  if 'LANL2' in x:
                     method2 = x
                     basisset = method2[0:5]
                     basissetWrite = True
                     basissetreal = method2
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                  if '6-31' in x:
                     method2 = x
                     if '6-311' in x:
                        basisset = '6-311G'
                        basissetWrite = True
                        basissetreal = '6-311' + method2[5:]
                     else:
                        basisset = '6-31G'
                        basissetWrite = True
                        basissetreal = '6-31' + method2[4:]
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                  slashes = settings.count('/')
                  if slashes > 1:
                    rest2 = settings.split()[1]
                    rest2 = rest2.upper()
                    for z in rest2.split('/'):
                       if z in basissetDict.keys():
                         basisset = z
                    basissetWrite = True
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                    if (len(rest2.split('/')) == 2): 
                       if(basisset is not None):
                          basissetreal = rest2.s