from __future__ import division
from builtins import str
from builtins import range
from builtins import object
from functools import reduce
import setup_paths
from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel
from nomadcore.unit_conversion.unit_conversion import convert_unit
import os, sys, json, logging
import numpy as np
import ase
import re
############################################################
# This is the parser for the output file of Gaussian.
############################################################
logger = logging.getLogger("nomad.GaussianParser")
# description of the output
mainFileDescription = SM(
name = 'root',
weak = True,
forwardMatch = True,
startReStr = "",
subMatchers = [
SM(name = 'newRun',
startReStr = r"\s*Cite this work as:",
repeats = True,
required = True,
forwardMatch = True,
fixedStartValues={ 'program_name': 'Gaussian', 'program_basis_set_type': 'gaussians' },
sections = ['section_run'],
subMatchers = [
SM(name = 'header',
startReStr = r"\s*Cite this work as:",
forwardMatch = True,
subMatchers = [
SM(r"\s*Cite this work as:"),
SM(r"\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,"),
SM(r"\s\*\*\*\*\*\*\*\*\*\*\*\**"),
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]+)"),
SM(r"\s*(?P<x_gaussian_program_execution_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
]
),
SM(name = 'globalparams',
startReStr = r"\s*%\w*=",
subFlags = SM.SubFlags.Unordered,
forwardMatch = True,
subMatchers = [
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.]*)")
]
),
SM (name = 'SectionMethod',
sections = ['section_method'],
startReStr = r"\s*#",
forwardMatch = True,
subMatchers = [
SM(r"\s*(?P<x_gaussian_settings>([a-zA-Z0-9-/=(),#*+:]*\s*)+)"),
SM(r"\s*(?P<x_gaussian_settings>([a-zA-Z0-9-/=(),#*+:]*\s*)+)"),
]
),
SM(name = 'charge_multiplicity_cell_masses',
sections = ['section_system'],
startReStr = r"\s*Charge =",
endReStr = r"\s*Leave Link 101\s*",
subFlags = SM.SubFlags.Unordered,
forwardMatch = True,
subMatchers = [
SM(r"\s*Charge =\s*(?P<x_gaussian_total_charge>[-+0-9]*) Multiplicity =\s*(?P<x_gaussian_spin_target_multiplicity>[0-9]*)"),
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),
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,
sections = ['section_single_configuration_calculation'],
subMatchers = [
SM(name = 'geometry',
sections = ['x_gaussian_section_geometry'],
startReStr = r"\s*Standard orientation:",
endReStr = r"\s*Rotational constants",
subMatchers = [
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),
SM(r"\s*Rotational constants")
]
),
SM(name = 'SectionHybridCoeffs',
sections = ['x_gaussian_section_hybrid_coeffs'],
startReStr = r"\s*IExCor=",
forwardMatch = True,
subMatchers = [
SM(r"\s*IExCor=\s*[0-9]+\s*DFT=[A-Z]\s*Ex\+Corr=[A-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-Z0-9]+\s*Corr=[a-zA-Z0-9]+\s*ExCW=[0-9]\s*ScaHFX=\s*(?P<hybrid_xc_coeff1>[0-9.]+)"),
SM(r"\s*ScaDFX=\s*(?P<hybrid_xc_coeff2>[0-9.]+\s*[0-9.]+\s*[0-9.]+\s*[0-9.]+)")
]
),
SM(name = 'TotalEnergyScfGaussian',
sections = ['section_scf_iteration'],
startReStr = r"\s*Requested convergence on RMS",
forwardMatch = False,
repeats = True,
subMatchers = [
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.]+)"),
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*"),
SM(r"\s*Annihilation of the first spin contaminant"),
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.]+)"),
SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P<x_gaussian_perturbation_energy__hartree>[-+0-9D.]+)"),
]
),
SM(name = 'PerturbationEnergies',
sections = ['x_gaussian_section_moller_plesset'],
startReStr = r"\s*E2 =\s*",
forwardMatch = True,
subMatchers = [
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.]+)"),
]
),
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 = [
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.]+)"),
]
),
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 = [
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),
]
),
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 = [
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),
]
),
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),
SM(r"\s*Energy=\s*(?P<energy_total>[-+0-9EeDd.]+)"),
]
),
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,. ]+)"),
SM(r"\s*Energy=\s*(?P<energy_total>[-+0-9EeDd.]+)\s*NIter=\s*[0-9.]"),
]
),
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'],
startReStr = r"\s*Excited State",
forwardMatch = False,
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*",
forwardMatch = True,
repeats = False,
subMatchers = [
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),
]
),
SM(name = 'Geometry_optimization',
sections = ['x_gaussian_section_geometry_optimization_info'],
startReStr = r"\s*Optimization completed.",
forwardMatch = True,
subMatchers = [
SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimization completed)"),
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 = [
SM(r"\s*The electronic state is\s*(?P<x_gaussian_elstate_symmetry>[A-Z0-9-']+)[.]")
]
),
SM(name = 'Eigenvalues',
sections = ['section_eigenvalues'],
startReStr = r"\s*Alpha occ. eigenvalues --",
forwardMatch = True,
subFlags = SM.SubFlags.Sequenced,
subMatchers = [
SM(r"\s*Alpha occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*Alpha virt. eigenvalues --\s+(?P<x_gaussian_alpha_vir_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*Beta occ. eigenvalues --\s+(?P<x_gaussian_beta_occ_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*Beta virt. eigenvalues --\s+(?P<x_gaussian_beta_vir_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*- Condensed to atoms (all electrons)"),
]
),
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+")
]
),
SM(name = 'Multipoles',
sections = ['x_gaussian_section_molecular_multipoles'],
startReStr = r"\s*Electronic spatial extent",
forwardMatch = False,
subMatchers = [
SM(r"\s*Charge=(?P<charge>\s*[-0-9.]+)"),
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.]+)")
]
),
SM (name = 'Frequencies',
sections = ['x_gaussian_section_frequencies'],
startReStr = r"\s*Frequencies --\s+(?:(?:[-]?[0-9]+\.\d*)\s*(?:[-]?[-0-9]+\.\d*)?\s*(?:[-]?[-0-9]+\.\d*)?)",
endReStr = r"\s*- Thermochemistry -",
forwardMatch = True,
repeats = False,
subMatchers = [
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]+)?"),
])
]
),
SM(name = 'Thermochemistry',
sections = ['x_gaussian_section_thermochem'],
startReStr = r"\s*Temperature",
forwardMatch = True,
subMatchers = [
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:"),
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}))"),
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"),
SM(r"\s*[0-9]+\s*(?P<x_gaussian_force_constants>(\-?\d+\.\d*[-+D0-9]+)\s*(\-?\d+\.\d*[-+D0-9]+)?\s*(\-?\d+\.\d*[-+D0-9]+)?\s*(\-?\d+\.\d*[-+D0-9]+)?\s*(\-?\d+\.\d*[-+D0-9]+)?)", repeats = True),
SM(r"\s*Force constants in internal coordinates")
]
),
SM(name = 'CompositeModelEnergies',
sections = ['x_gaussian_section_models'],
startReStr = r"\s*Temperature=\s*",
forwardMatch = False,
repeats = True,
subMatchers = [
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.]+)"),
]
),
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]+)"),
]
)
])
])
])
])
# 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"
}
class GaussianParserContext(object):
"""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 = {
'x_gaussian_hf_detect': None,
'x_gaussian_energy_scf': None,
'x_gaussian_perturbation_energy': None,
'x_gaussian_electronic_kinetic_energy': None,
'x_gaussian_energy_electrostatic': None,
'x_gaussian_energy_error': None,
}
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.
"""
self.secMethodIndex = None
self.secSystemDescriptionIndex = None
# start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1
self.singleConfCalcs = []
self.scfConvergence = False
self.geoConvergence = False
self.scfenergyconverged = 0.0
self.scfkineticenergyconverged = 0.0
self.scfelectrostaticenergy = 0.0
self.periodicCalc = False
def startedParsing(self, path, parser):
self.parser = parser
# save metadata
self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
# allows to reset values if the same superContext is used to parse different files
self.initialize_values()
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.
"""
global sampling_method
sampling_method = ""
# 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()
def onClose_x_gaussian_section_geometry(self, backend, gIndex, section):
xCoord = section["x_gaussian_atom_x_coord"]
yCoord = section["x_gaussian_atom_y_coord"]
zCoord = section["x_gaussian_atom_z_coord"]
numbers = section["x_gaussian_atomic_number"]
atom_coords = np.zeros((len(xCoord),3), dtype=float)
atom_numbers = np.zeros(len(xCoord), dtype=int)
atomic_symbols = np.empty((len(xCoord)), dtype=object)
for i in range(len(xCoord)):
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]]
gIndexTmp = backend.openSection("section_system")
backend.addArrayValues("atom_labels", atomic_symbols)
backend.addArrayValues("atom_positions", atom_coords)
backend.addValue("x_gaussian_number_of_atoms",len(atomic_symbols))
backend.closeSection("section_system", gIndexTmp)
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]
backend.addArrayValues("atom_forces_raw", atom_forces)
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
self.singleConfCalcs.append(gIndex)
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
"""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
backend.addValue('single_configuration_calculation_converged', self.scfConvergence)
self.scfConvergence = False
# start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1
# 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
def onClose_section_scf_iteration(self, backend, gIndex, section):
# count number of SCF iterations
self.scfIterNr += 1
# check for SCF convergence
if section['x_gaussian_single_configuration_calculation_converged'] is not None:
self.scfConvergence = True
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):
eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"])
eigenen1 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen1 = np.append(eigenen1, energy)
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)
eigenenergies = str(section["x_gaussian_alpha_vir_eigenvalues_values"])
eigenen2 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen2 = np.append(eigenen2, energy)
viroccupationsalp = np.zeros(len(eigenen2), dtype=float)
eigenenconalp = np.zeros(len(eigenen1) + len(eigenen2))
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)
if(section["x_gaussian_beta_occ_eigenvalues_values"]):
eigenenergies = str(section["x_gaussian_beta_occ_eigenvalues_values"])
eigenen1 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen1 = np.append(eigenen1, energy)
occoccupationsbet = np.ones(len(eigenen1), dtype=float)
eigenenergies = str(section["x_gaussian_beta_vir_eigenvalues_values"])
eigenen2 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen2 = np.append(eigenen2, energy)
viroccupationsbet = np.zeros(len(eigenen2), dtype=float)
eigenenconbet = np.zeros(len(eigenen1) + len(eigenen2))
eigenenconbet = np.concatenate((eigenen1,eigenen2), axis=0)
eigenenconbet = convert_unit(eigenenconbet, "hartree", "J")
occupconbet = np.concatenate((occoccupationsbet, viroccupationsbet), axis=0)
eigenenall = np.concatenate((eigenenconalp,eigenenconbet), axis=0)
occupall = np.concatenate((occupconalp,occupconbet), axis=0)
eigenenall = np.reshape(eigenenall,(2, 1, len(eigenenconalp)))
occupall = np.reshape(occupall,(2, 1, len(occupconalp)))
backend.addArrayValues("eigenvalues_values", eigenenall)
backend.addArrayValues("eigenvalues_occupation", occupall)
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"])
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"])
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()]
sym1 = []
sym1 = np.append(sym1, symmetry)
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()]
sym2 = []
sym2 = np.append(sym2, symmetry)
symmetrycon = np.concatenate((sym1, sym2), axis=0)
backend.addArrayValues("x_gaussian_alpha_symmetries", symmetrycon)
if(section["x_gaussian_beta_occ_symmetry_values"]):
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()]
sym1 = []
sym1 = np.append(sym1, symmetry)
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()]
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()]
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")
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")
if(section["octapole_moment_xxx"]):
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")
if(section["hexadecapole_moment_xxxx"]):
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")
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
for p in range(0,len(vibfreqs) // 3):
M = int(len(disps)/len(vibfreqs)) * (p+1)
for m in range(3):
for n in range(M - int(len(disps) / len(vibfreqs)),M,3):
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):
M = (len(disps) - int(len(disps) / len(vibfreqs))) // p
for m in range(3):
for n in range(M - int(len(disps) / len(vibfreqs)),M,3):
for l in range(3):
dispsnew[k] = disps[3*(n + m) + l]
k = k + 1
for m in range(int(len(disps) / len(vibfreqs))):
dispsnew[k] = disps[k]
k = k + 1
vibnormalmodes = np.append(vibnormalmodes, dispsnew)
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)
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)
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
self.secMethodIndex = gIndex
def onClose_section_method(self, backend, gIndex, section):
# handling of xc functional
# Dictionary for conversion of xc functional name in Gaussian to metadata format.
# The individual x and c components of the functional are given as dictionaries.
# Possible key of such a dictionary is 'name'.
xcDict = {
'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'}],
'PBE1PBE': [{'name': 'HYB_GGA_XC_PBE1PBE'}],
'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'}],
}
methodDict = {
'AMBER': [{'name': 'Amber'}],
'DREIDING': [{'name': 'Dreiding'}],
'UFF': [{'name': 'UFF'}],
'AM1': [{'name': 'AM1'}],
'PM3': [{'name': 'PM3'}],
'PM3MM': [{'name': 'PM3MM'}],
'PM3D3': [{'name': 'PM3D3'}],
'PM6': [{'name': 'PM6'}],
'PDDG': [{'name': 'PDDG'}],
'CNDO': [{'name': 'CNDO'}],
'INDO': [{'name': 'INDO'}],
'MINDO': [{'name': 'MINDO'}],
'MINDO3': [{'name': 'MINDO3'}],
'ZINDO': [{'name': 'ZINDO'}],
'HUCKEL': [{'name': 'HUCKEL'}],
'EXTENDEDHUCKEL': [{'name': 'HUCKEL'}],
'ONIOM': [{'name': 'ONIOM'}],
'HF': [{'name': 'HF'}],
'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'}],
'BD(T)': [{'name': 'BD(T)'}],
'CCD': [{'name': 'CCD'}],
'CCSD': [{'name': 'CCSD'}],
'EOMCCSD': [{'name': 'EOMCCSD'}],
'QCISD': [{'name': 'QCISD'}],
'CCSD(T)': [{'name': 'CCSD(T)'}],
'QCISD(T)': [{'name': 'QCISD(T)'}],
'QCISD(TQ)': [{'name': 'QCISD(TQ)'}],
'MP2': [{'name': 'MP2'}],
'MP3': [{'name': 'MP3'}],
'MP4': [{'name': 'MP4'}],
'MP4DQ': [{'name': 'MP4DQ'}],
'MP4(DQ)': [{'name': 'MP4DQ'}],
'MP4SDQ': [{'name': 'MP4SDQ'}],
'MP4(SDQ)': [{'name': 'MP4SDQ'}],
'MP4SDTQ': [{'name': 'MP4SDTQ'}],
'MP4(SDTQ)': [{'name': 'MP4SDTQ'}],
'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'}],
'CBSEXTRAP': [{'name': 'CBSExtrapolate'}],
'CBSEXTRAPOLATE': [{'name': 'CBSExtrapolate'}],
'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'}],
'CHKBAS': [{'name': 'CHKBAS'}],
'EXTRABASIS': [{'name': 'ExtraBasis'}],
'DGA1': [{'name': 'DGA1'}],
'DGA2': [{'name': 'DGA2'}],
'SVPFIT': [{'name': 'SVPFit'}],
'TZVPFIT': [{'name': 'TZVPFit'}],
'W06': [{'name': 'W06'}],
'CHF': [{'name': 'CHF'}],
'FIT': [{'name': 'FIT'}],
'AUTO': [{'name': 'AUTO'}],
}
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
settings = section["x_gaussian_settings"]
settings1 = str(settings[0]).strip()
settings2 = str(settings[1]).strip()
settings = [settings1, settings2]
settings = [''.join(map(str,settings))]
settings = str(settings)
settings = re.sub('[-]{2,}', '', settings)
backend.addValue("x_gaussian_settings_corrected", settings)
method1 = settings.replace("['#p ","").replace("['#P ","").replace("['#","")
method1 = method1.upper()
if 'ONIOM' not in method1:
if settings.find("/") >= 0:
method1 = settings.split('/')[0].replace("['#p ","").replace("['#P ","").replace("['#","")
method1 = method1.upper()
for x in method1.split():
method2 = str(x)
if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF' and method2 != 'UFF':
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:]
if method2[0:2] == 'SV' or method2[0] == 'B' or method2[0] == 'O':
if method2[1] != '2' and method2[1] != '3':
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)
if method2[0:3] == 'BRX' or method2[0:3] == 'G96':
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)
if method2[0:5] == 'WPBEH':
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)
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
methodWrite = True
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():
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
rest = settings.split('/')[1].replace("'","").replace("]","")
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
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
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:]
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
basissetreal = rest2.split('/')[1] + '/' + basisset
else:
method1 = settings.split()
for x in method1:
method2 = str(x)
method2 = method2.upper()
if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF' and method2 != 'UFF':
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:]
if method2[0:2] == 'SV' or method2[0] == 'B' or method2[0] == 'O':
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)
if method2[0:3] == 'BRX' or method2[0:3] == 'G96':
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)
if method2[0:5] == 'WPBEH':
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)
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
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():
method = method2[0:n]
methodWrite = True
methodreal = method2
if method2[0:9] == 'CBSEXTRAP':
method = method2[0:9]
methodWrite = True
methodreal = method2
if method2 in basissetDict.keys():
basisset = method2
basissetWrite = True
basissetreal = method2
if 'D95' in method2:
basisset = method2[0:3]
basissetWrite = True
basissetreal = method2
if 'AUG-' in method2:
basisset = method2[4:]
basissetWrite = True
basissetreal = method2
if 'UGBS' in method2:
basisset = method2[0:4]
basissetWrite = True
basissetreal = method2
if 'CBSB7' in method2:
basisset = method2[0:5]
basissetWrite = True
basissetreal = method2
if '6-31' in method2:
if '6-311' in method2:
basisset = '6-311G'
basissetWrite = True
basissetreal = '6-311' + method2[5:]
else:
basisset = '6-31G'
basissetWrite = True
basissetreal = '6-31' + method2[4:]
# special options for ONIOM calculations
else:
method = 'ONIOM'
methodWrite = True
method1 = settings.split()
for x in method1:
method2 = str(x)
method2 = method2.upper()
if 'ONIOM' in method2:
methodreal = method2
# functionals where hybrid_xc_coeff are written
if xc is not None:
# check if only one xc keyword was found in output
if len([xc]) > 1:
logger.error("Found %d settings for the xc functional: %s. This leads to an undefined behavior of the calculation and no metadata can be written for xc." % (len(xc), xc))
else:
backend.superBackend.addValue('x_gaussian_xc', [xc][-1])
if xcWrite:
# get list of xc components according to parsed value
xcList = xcDict.get([xc][-1])
if xcList is not None:
# loop over the xc components
for xcItem in xcList:
xcName = xcItem.get('name')
if xcName is not None:
# write section and XC_functional_name
gIndexTmp = backend.openSection('section_XC_functionals')
backend.addValue('XC_functional_name', xcName)
# write hybrid_xc_coeff for PBE1PBE into XC_functional_parameters
backend.closeSection('section_XC_functionals', gIndexTmp)
else:
logger.error("The dictionary for xc functional '%s' does not have the key 'name'. Please correct the dictionary xcDict in %s." % (xc[-1], os.path.basename(__file__)))
else:
logger.error("The xc functional '%s' could not be converted for the metadata. Please add it to the dictionary xcDict in %s." % (xc[-1], os.path.basename(__file__)))
# Write electronic structure method to metadata
if method is not None:
# check if only one method keyword was found in output
if len([method]) > 1:
logger.error("Found %d settings for the method: %s. This leads to an undefined behavior of the calculation and no metadata can be written for the method." % (len(method), method))
else:
backend.superBackend.addValue('x_gaussian_method', [method][-1])
methodList = methodDict.get([method][-1])
if methodWrite:
if methodList is not None:
# loop over the method components
for methodItem in methodList:
methodName = methodItem.get('name')
if methodName is not None:
# write section and method name
if methodprefix != None and methodreal != None:
gIndexTmp = backend.openSection('x_gaussian_section_elstruc_method')
backend.addValue('x_gaussian_electronic_structure_method', str(methodprefix) + methodreal)
backend.closeSection('x_gaussian_section_elstruc_method', gIndexTmp)
elif methodreal != None:
gIndexTmp = backend.openSection('x_gaussian_section_elstruc_method')
backend.addValue('x_gaussian_electronic_structure_method', methodreal)
backend.closeSection('x_gaussian_section_elstruc_method', gIndexTmp)
else:
logger.error("The dictionary for method '%s' does not have the key 'name'. Please correct the dictionary methodDict in %s." % (method[-1], os.path.basename(__file__)))
else:
logger.error("The method '%s' could not be converted for the metadata. Please add it to the dictionary methodDict in %s." % (method[-1], os.path.basename(__file__)))
#Write basis sets to metadata
if basisset is not None:
# check if only one method keyword was found in output
if len([basisset]) > 1:
logger.error("Found %d settings for the basis set: %s. This leads to an undefined behavior of the calculation and no metadata can be written for the basis set." % (len(method), method))
else:
backend.superBackend.addValue('basis_set', basisset)
basissetList = basissetDict.get([basisset][-1])
if basissetWrite:
if basissetList is not None:
# loop over the basis set components
for basissetItem in basissetList:
basissetName = basissetItem.get('name')
if basissetName is not None:
# write section and basis set name(s)
gIndexTmp = backend.openSection('section_basis_set_atom_centered')
backend.addValue('basis_set_atom_centered_short_name', basissetreal)
backend.closeSection('section_basis_set_atom_centered', gIndexTmp)
else:
logger.error("The dictionary for basis set '%s' does not have the key 'name'. Please correct the dictionary basissetDict in %s." % (basisset[-1], os.path.basename(__file__)))
else:
logger.error("The basis set '%s' could not be converted for the metadata. Please add it to the dictionary basissetDict in %s." % (basisset[-1], os.path.basename(__file__)))
def onOpen_section_system(self, backend, gIndex, section):
# keep track of the latest system description section
self.secSystemDescriptionIndex = gIndex
def onClose_x_gaussian_section_hybrid_coeffs(self, backend, gIndex, section):
# assign the coefficients to the hybrid functionals
hybrid_xc_coeffsa = ()
hybrid_xc_coeffsb = ()
hybrid_xc_coeffsa = float(str(section['hybrid_xc_coeff1']).replace("[","").replace("]",""))
backend.addValue('x_gaussian_hybrid_xc_hfx', hybrid_xc_coeffsa)
hybrid_xc_coeffs = str(section['hybrid_xc_coeff2'])
hybrid_xc_coeffsb = [float(f) for f in hybrid_xc_coeffs[1:].replace("'","").replace("]","").replace("]","").split()]
backend.addValue('x_gaussian_hybrid_xc_slater', hybrid_xc_coeffsb[0])
backend.addValue('x_gaussian_hybrid_xc_nonlocalex', hybrid_xc_coeffsb[1])
backend.addValue('x_gaussian_hybrid_xc_localcorr', hybrid_xc_coeffsb[2])
backend.addValue('x_gaussian_hybrid_xc_nonlocalcorr', hybrid_xc_coeffsb[3])
def onClose_section_system(self, backend, gIndex, section):
# write/store unit cell if present and set flag self.periodicCalc
if(section['x_gaussian_geometry_lattice_vector_x']):
unit_cell = []
for i in ['x', 'y', 'z']:
uci = str(section['x_gaussian_geometry_lattice_vector_' + i])
uci = uci.split()
for i in range(len(uci)):
uci[i] = str(uci[i]).replace("[","").replace("'","").replace("]","").replace("\"","").replace(",","")
uci[i] = float(uci[i])
if uci is not None:
uci = convert_unit(uci, "angstrom", "m")
unit_cell.append(uci)
if unit_cell:
# from metadata: "The first index is x,y,z and the second index the lattice vector."
# => unit_cell has already the right format
backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
if np.shape(unit_cell) == (3, 1):
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, False, False]))
if np.shape(unit_cell) == (3, 2):
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, False]))
if np.shape(unit_cell) == (3, 3):
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
self.periodicCalc = True
else:
unit_cell = [[0.0,0.0,0.0],[0.0,0.0,0.0],[0.0,0.0,0.0]]
backend.addArrayValues('simulation_cell', np.asarray(unit_cell))
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([False, False, False]))
if(section["x_gaussian_atomic_masses"]):
atomicmasses = str(section["x_gaussian_atomic_masses"])
atmass = []
mass = [float(f) for f in atomicmasses[1:].replace("'","").replace(",","").replace("]","").replace(" ."," 0.").replace(" -."," -0.").split()]
atmass = np.append(atmass, mass)
numberofatoms = len(atmass)
backend.addArrayValues("x_gaussian_masses", atmass)
# which values to cache or forward (mapping meta name -> CachingLevel)
cachingLevelForMetaName = {
"x_gaussian_atom_x_coord": CachingLevel.Cache,
"x_gaussian_atom_y_coord": CachingLevel.Cache,
"x_gaussian_atom_z_coord": CachingLevel.Cache,
"x_gaussian_atomic_number": CachingLevel.Cache,
"x_gaussian_section_geometry": CachingLevel.Forward,
"x_gaussian_atom_x_force": CachingLevel.Cache,
"x_gaussian_atom_y_force": CachingLevel.Cache,
"x_gaussian_atom_z_force": CachingLevel.Cache,
"x_gaussian_number_of_atoms": CachingLevel.ForwardAndCache,
"section_scf_iteration": CachingLevel.Forward,
"energy_total_scf_iteration": CachingLevel.ForwardAndCache,
"x_gaussian_delta_energy_total_scf_iteration": CachingLevel.ForwardAndCache,
"energy_total": CachingLevel.ForwardAndCache,
"x_gaussian_energy_error": CachingLevel.ForwardAndCache,
"x_gaussian_electronic_kinetic_energy": CachingLevel.ForwardAndCache,
"x_gaussian_energy_electrostatic": CachingLevel.ForwardAndCache,
"x_gaussian_section_frequencies": CachingLevel.Forward,
"x_gaussian_frequency_values": CachingLevel.Cache,
"x_gaussian_frequencies": CachingLevel.ForwardAndCache,
"x_gaussian_reduced_masses": CachingLevel.Cache,
"x_gaussian_red_masses": CachingLevel.ForwardAndCache,
"x_gaussian_normal_modes": CachingLevel.Cache,
"x_gaussian_normal_mode_values": CachingLevel.ForwardAndCache,
"x_gaussian_atomic_masses": CachingLevel.ForwardAndCache,
"x_gaussian_section_force_constant_matrix": CachingLevel.Forward,
"x_gaussian_force_constant_values": CachingLevel.ForwardAndCache,
"x_gaussian_force_constants": CachingLevel.Cache,
"section_eigenvalues": CachingLevel.Forward,
"eigenvalues_values": CachingLevel.ForwardAndCache,
"eigenvalues_occupation": CachingLevel.ForwardAndCache,
"x_gaussian_section_orbital_symmetries": CachingLevel.Forward,
"x_gaussian_alpha_occ_symmetry_values":CachingLevel.Cache,
"x_gaussian_alpha_vir_symmetry_values":CachingLevel.Cache,
"x_gaussian_beta_occ_symmetry_values":CachingLevel.Cache,
"x_gaussian_beta_vir_symmetry_values":CachingLevel.Cache,
"x_gaussian_alpha_symmetries": CachingLevel.ForwardAndCache,
"x_gaussian_beta_symmetries": CachingLevel.ForwardAndCache,
"x_gaussian_section_molecular_multipoles": CachingLevel.Forward,
"dipole_moment_x": CachingLevel.Cache,
"dipole_moment_y": CachingLevel.Cache,
"dipole_moment_z": CachingLevel.Cache,
"quadrupole_moment_xx": CachingLevel.Cache,
"quadrupole_moment_yy": CachingLevel.Cache,
"quadrupole_moment_zz": CachingLevel.Cache,
"quadrupole_moment_xy": CachingLevel.Cache,
"quadrupole_moment_xz": CachingLevel.Cache,
"quadrupole_moment_yz": CachingLevel.Cache,
"octapole_moment_xxx": CachingLevel.Cache,
"octapole_moment_yyy": CachingLevel.Cache,
"octapole_moment_zzz": CachingLevel.Cache,
"octapole_moment_xyy": CachingLevel.Cache,
"octapole_moment_xxy": CachingLevel.Cache,
"octapole_moment_xxz": CachingLevel.Cache,
"octapole_moment_xzz": CachingLevel.Cache,
"octapole_moment_yzz": CachingLevel.Cache,
"octapole_moment_yyz": CachingLevel.Cache,
"octapole_moment_xyz": CachingLevel.Cache,
"hexadecapole_moment_xxxx": CachingLevel.Cache,
"hexadecapole_moment_yyyy": CachingLevel.Cache,
"hexadecapole_moment_zzzz": CachingLevel.Cache,
"hexadecapole_moment_xxxy": CachingLevel.Cache,
"hexadecapole_moment_xxxz": CachingLevel.Cache,
"hexadecapole_moment_yyyx": CachingLevel.Cache,
"hexadecapole_moment_yyyz": CachingLevel.Cache,
"hexadecapole_moment_zzzx": CachingLevel.Cache,
"hexadecapole_moment_zzzy": CachingLevel.Cache,
"hexadecapole_moment_xxyy": CachingLevel.Cache,
"hexadecapole_moment_xxzz": CachingLevel.Cache,
"hexadecapole_moment_yyzz": CachingLevel.Cache,
"hexadecapole_moment_xxyz": CachingLevel.Cache,
"hexadecapole_moment_yyxz": CachingLevel.Cache,
"hexadecapole_moment_zzxy": CachingLevel.Cache,
"x_gaussian_molecular_multipole_values": CachingLevel.ForwardAndCache,
"single_configuration_calculation_converged": CachingLevel.ForwardAndCache,
"x_gaussian_single_configuration_calculation_converged": CachingLevel.ForwardAndCache,
"x_gaussian_section_geometry_optimization_info": CachingLevel.Forward,
"x_gaussian_geometry_optimization_converged": CachingLevel.ForwardAndCache,
"x_gaussian_hf_detect": CachingLevel.ForwardAndCache,
"x_gaussian_section_hybrid_coeffs": CachingLevel.Forward,
"section_method": CachingLevel.Forward,
"x_gaussian_section_elstruc_method": CachingLevel.Forward,
"x_gaussian_electronic_structure_method": CachingLevel.ForwardAndCache,
"XC_functional_name": CachingLevel.ForwardAndCache,
"basis_set_atom_centered_short_name": CachingLevel.Forward,
"x_gaussian_settings": CachingLevel.Cache,
"x_gaussian_settings_corrected": CachingLevel.ForwardAndCache,
"section_system": CachingLevel.Forward,
"x_gaussian_atomic_masses": CachingLevel.ForwardAndCache,
"x_gaussian_masses": CachingLevel.ForwardAndCache,
}
if __name__ == "__main__":
mainFunction(mainFileDescription, metaInfoEnv, parserInfo,
cachingLevelForMetaName = cachingLevelForMetaName,
superContext = GaussianParserContext())