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[0-9]+):\s*(?P[A-Za-z0-9-.]+)\s*(?P[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"), SM(r"\s*(?P[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[A-Za-z0-9.]*)"), SM(r"\s*%[Mm]em=(?P[A-Za-z0-9.]*)"), SM(r"\s*%[Nn][Pp]roc=(?P[A-Za-z0-9.]*)") ] ), SM (name = 'SectionMethod', sections = ['section_method'], startReStr = r"\s*#", forwardMatch = True, subMatchers = [ SM(r"\s*(?P([a-zA-Z0-9-/=(),#*+:]*\s*)+)"), SM(r"\s*(?P([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[-+0-9]*) Multiplicity =\s*(?P[0-9]*)"), SM(r"\s*(Tv|Tv\s*[0]|TV|TV\s*[0])\s*(?P[0-9.]*)\s+(?P[0-9.]*)\s+(?P[0-9.]*)", repeats = True), SM(r"\s*AtmWgt=\s+(?P[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[0-9]+)\s+[0-9]+\s+(?P[-+0-9EeDd.]+)\s+(?P[-+0-9EeDd.]+)\s+(?P[-+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[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[0-9.]+)"), SM(r"\s*ScaDFX=\s*(?P[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 ="), SM(r"\s*E=\s*(?P[-+0-9.]+)\s*Delta-E=\s*(?P[-+0-9.]+)"), SM(r"\s*(?PSCF Done):\s*E\((?P[A-Z0-9]+)\)\s*=\s*(?P[-+0-9.]+)"), SM(r"\s*NFock=\s*[0-9]+\s*Conv=(?P[-+0-9EeDd.]+)\s*"), SM(r"\s*KE=\s*(?P[-+0-9EeDd.]+)\s*"), SM(r"\s*Annihilation of the first spin contaminant"), SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*(?P[0-9.]+),\s*after\s*(?P[0-9.]+)"), SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P[-+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[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P[-+0-9EeDd.]+)"), SM(r"\s*E3=\s*(?P[-+0-9EeDd.]+)\s*EUMP3=\s*(?P[-+0-9EeDd.]+)\s*"), SM(r"\s*E4\(DQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(DQ\)=\s*(?P[-+0-9EeDd.]+)\s*"), SM(r"\s*E4\(SDQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(SDQ\)=\s*(?P[-+0-9EeDd.]+)"), SM(r"\s*E4\(SDTQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(SDTQ\)=\s*(?P[-+0-9EeDd.]+)"), SM(r"\s*DEMP5 =\s*(?P[-+0-9EeDd.]+)\s*MP5 =\s*(?P[-+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[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), SM(r"\s*CCSD\(T\)=\s*(?P[-+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[-+0-9EeDd.]+)\s*E\(Z\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), SM(r"\s*DE\(Corr\)=\s*(?P[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), SM(r"\s*QCISD\(T\)=\s*(?P[-+0-9EeDd.]+)"), SM(r"\s*DE5\s*=\s*(?P[-+0-9EeDd.]+)\s*QCISD\(TQ\)\s*=\s*(?P[-+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[-+0-9EeDd.]+)\s*E\(CI\)=\s*(?P[-+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[-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[-+0-9.]+)\s*", repeats = True), SM(r"\s*Energy=\s*(?P[-+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[a-zA-Z0-9]+\s*calculation of energy[a-z,. ]+)"), SM(r"\s*Energy=\s*(?P[-+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[0-9]+):\s*[-+0-9A-Za-z.\?]+\s*(?P[0-9.]+)\s*eV\s*[0-9.]+\s*nm\s*f=(?P[0-9.]+)\s*<[A-Z][*][*][0-9]>=(?P[0-9.]+)"), SM(r"\s*(?P[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[-+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*(?POptimization completed)"), SM(r"\s*(?POptimization 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\((.+)\))?"), SM(r"\s+(?P\((.+)\)?)", repeats = True), SM(r"\s*Virtual\s+(?P\((.+)\))?"), SM(r"\s+(?P\((.+)\)?)", repeats = True), SM(r"\s*Beta Orbitals"), SM(r"\s*Occupied\s+(?P\((.+)\))?"), SM(r"\s+(?P\((.+)\)?)", repeats = True), SM(r"\s*Virtual\s+(?P\((.+)\))?"), SM(r"\s+(?P\((.+)\)?)", 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[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(.+)?)", repeats = True), SM(r"\s*Alpha virt. eigenvalues --\s+(?P(.+)?)", repeats = True), SM(r"\s*Beta occ. eigenvalues --\s+(?P(.+)?)", repeats = True), SM(r"\s*Beta virt. eigenvalues --\s+(?P(.+)?)", 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[-+0-9EeDd.]+)\s+(?P[-+0-9EeDd.]+)\s+(?P[-+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\s*[-0-9.]+)"), SM(r"\s*Dipole moment "), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s*Quadrupole moment"), SM(r"\s+\w+=\s+(?P[0-9-.]+)\s+\w+=\s+(?P[0-9-.]+)\s+\w+=\s+(?P[0-9-.]+)"), SM(r"\s+\w+=\s+(?P[0-9-.]+)\s+\w+=\s+(?P[0-9-.]+)\s+\w+=\s+(?P[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[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s*Hexadecapole moment"), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)"), SM(r"\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+0-9EeDd.]+)\s+\w+=\s+(?P[-+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([-]?[0-9]+\.\d*)\s*([-]?[-0-9]+\.\d*)?\s*([-]?[-0-9]+\.\d*)?)", repeats = True), SM(r"\s*Red. masses --\s+(?P(.+))", repeats = True), SM(r"\s*[0-9]+\s*[0-9]+\s*(?P([-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[0-9.]+)\s*Kelvin.\s*Pressure\s*(?P[0-9.]+)\s*Atm."), SM(r"\s*Principal axes and moments of inertia in atomic units:"), SM(r"\s*Eigenvalues --\s*(?P(\d+\.\d{5}))\s*?(?P(\d+\.\d{5}))\s*?(?P(\d+\.\d{5}))"), SM(r"\s*Zero-point correction=\s*(?P[0-9.]+)"), SM(r"\s*Thermal correction to Energy=\s*(?P[0-9.]+)"), SM(r"\s*Thermal correction to Enthalpy=\s*(?P[0-9.]+)"), SM(r"\s*Thermal correction to Gibbs Free Energy=\s*(?P[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(\-?\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[-+0-9.]+)"), SM(r"\s*G2\(0 K\)=\s*[-+0-9.]+\s*G2 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*G2MP2\(0 K\)=\s*[-+0-9.]+\s*G2MP2 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*G3\(0 K\)=\s*[-+0-9.]+\s*G3 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*G3MP2\(0 K\)=\s*[-+0-9.]+\s*G3MP2 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*G4\(0 K\)=\s*[-+0-9.]+\s*G4 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*G4MP2\(0 K\)=\s*[-+0-9.]+\s*G4MP2 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*CBS-4 \(0 K\)=\s*[-+0-9.]+\s*CBS-4 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*CBS-q \(0 K\)=\s*[-+0-9.]+\s*CBS-q Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*CBS-Q \(0 K\)=\s*[-+0-9.]+\s*CBS-Q Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*CBS-QB3 \(0 K\)=\s*[-+0-9.]+\s*CBS-QB3 Energy=\s*(?P[-+0-9.]+)"), SM(r"\s*W1U \(0 K\)=\s*[-+0-9.]+\s*W1U Electronic Energy\s*(?P[-+0-9.]+)"), SM(r"\s*W1RO \(0 K\)=\s*[-+0-9.]+\s*W1RO Electronic Energy\s*(?P[-+0-9.]+)"), SM(r"\s*W1BD \(0 K\)=\s*[-+0-9.]+\s*W1BD Electronic Energy\s*(?P[-+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\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[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())