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Commit cf285c82 authored by Rosendo Valero Montero's avatar Rosendo Valero Montero
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Gaussian parser with ground and excited state energies

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parser/parser-gaussian/parser_gaussian.py
+ 298
− 97
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...@@ -64,33 +64,23 @@ mainFileDescription = SM( ...@@ -64,33 +64,23 @@ mainFileDescription = SM(
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_natoms', SM(name = 'charge_multiplicity_cell_natoms',
sections = ['section_system'], sections = ['section_system'],
startReStr = r"\s*Charge =", startReStr = r"\s*Charge =",
endReStr = r"\s*Leave Link 101\s*",
subFlags = SM.SubFlags.Unordered, subFlags = SM.SubFlags.Unordered,
forwardMatch = True, forwardMatch = True,
subMatchers = [ 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*Charge =\s*(?P<x_gaussian_total_charge>[-+0-9]*) Multiplicity =\s*(?P<x_gaussian_spin_target_multiplicity>[0-9]*)"),
SM(r"\s*NAtoms=\s*(?P<x_gaussian_natoms>[0-9]*)\s*NQM="), 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(name = 'atomic masses',
sections = ['x_gaussian_section_atomic_masses'],
startReStr = r"\s*AtmWgt=",
endReStr = r"\s*Leave Link 101",
forwardMatch = True,
subMatchers = [
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(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)
] ]
), ),
# this SimpleMatcher groups a single configuration calculation together with output after SCF convergence from relaxation
SM (name = 'SingleConfigurationCalculationWithSystemDescription', SM (name = 'SingleConfigurationCalculationWithSystemDescription',
startReStr = "\s*Standard orientation:", startReStr = "\s*Standard orientation:",
# endReStr = "\s*Link1: Proceeding to internal job step number",
repeats = False, repeats = False,
forwardMatch = True, forwardMatch = True,
subMatchers = [ subMatchers = [
# the actual section for a single configuration calculation starts here
SM (name = 'SingleConfigurationCalculation', SM (name = 'SingleConfigurationCalculation',
startReStr = "\s*Standard orientation:", startReStr = "\s*Standard orientation:",
repeats = True, repeats = True,
...@@ -99,7 +89,7 @@ mainFileDescription = SM( ...@@ -99,7 +89,7 @@ mainFileDescription = SM(
subMatchers = [ subMatchers = [
SM(name = 'geometry', SM(name = 'geometry',
sections = ['x_gaussian_section_geometry'], sections = ['x_gaussian_section_geometry'],
startReStr = r"\s*Standard orientation", startReStr = r"\s*Standard orientation:",
endReStr = r"\s*Rotational constants", endReStr = r"\s*Rotational constants",
subMatchers = [ 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+[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),
...@@ -109,19 +99,15 @@ mainFileDescription = SM( ...@@ -109,19 +99,15 @@ mainFileDescription = SM(
SM(name = 'TotalEnergyScfGaussian', SM(name = 'TotalEnergyScfGaussian',
sections = ['section_scf_iteration'], sections = ['section_scf_iteration'],
startReStr = r"\s*Cycle\s+[0-9]+", startReStr = r"\s*Cycle\s+[0-9]+",
endReStr = r"\s*Leave Link 502\s*",
forwardMatch = True, forwardMatch = True,
repeats = True, repeats = True,
subMatchers = [ subMatchers = [
SM(r"\s*Cycle\s+[0-9]+"), SM(r"\s*Cycle\s+[0-9]+"),
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*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*[(),A-Za-z0-9-]+\s*=\s*(?P<x_gaussian_energy_total__hartree>[-+0-9.]+)"),
), SM(r"\s*NFock=\s*[0-9]+\s*Conv=(?P<x_gaussian_energy_error__hartree>[-+0-9EeDd.]+)\s*"),
SM(name = 'TotalEnergyScfConverged', SM(r"\s*KE=\s*(?P<x_gaussian_electronic_kinetic_energy__hartree>[-+0-9EeDd.]+)\s*"),
sections = ['x_gaussian_section_total_scf_one_geometry'],
startReStr = r"\s*SCF Done",
forwardMatch = True,
subMatchers = [
SM(r"\s*(?P<x_gaussian_single_configuration_calculation_converged>SCF Done):\s*[(),A-Za-z0-9-]+\s*=\s*(?P<energy_total__hartree>[-+0-9.]+)")
] ]
), ),
SM(name = 'RealSpinValue', SM(name = 'RealSpinValue',
...@@ -134,20 +120,106 @@ mainFileDescription = SM( ...@@ -134,20 +120,106 @@ mainFileDescription = SM(
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-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(name = 'ForcesGaussian', SM(name = 'PerturbationEnergies',
sections = ['x_gaussian_section_atom_forces'], sections = ['x_gaussian_section_moller_plesset'],
startReStr = "\s*Center\s+Atomic\s+Forces ", startReStr = r"\s*E2 =\s*",
forwardMatch = True, forwardMatch = True,
subMatchers = [ subMatchers = [
SM(r"\s*Center\s+Atomic\s+Forces "), SM(r"\s*E2 =\s*(?P<x_gaussian_mp2_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P<x_gaussian_mp2_energy__hartree>[-+0-9EeDd.]+)"),
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*E3=\s*(?P<x_gaussian_mp3_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP3=\s*(?P<x_gaussian_mp3_energy__hartree>[-+0-9EeDd.]+)\s*"),
SM(r"\s*Cartesian Forces:\s+") SM(r"\s*E4\(DQ\)=\s*(?P<x_gaussian_mp4dq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(DQ\)=\s*(?P<x_gaussian_mp4dq_energy__hartree>[-+0-9EeDd.]+)\s*"),
SM(r"\s*E4\(SDQ\)=\s*(?P<x_gaussian_mp4sdq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(SDQ\)=\s*(?P<x_gaussian_mp4sdq_energy__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*E4\(SDTQ\)=\s*(?P<x_gaussian_mp4sdtq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(SDTQ\)=\s*(?P<x_gaussian_mp4sdtq_energy__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*DEMP5 =\s*(?P<x_gaussian_mp5_correction_energy__hartree>[-+0-9EeDd.]+)\s*MP5 =\s*(?P<x_gaussian_mp5_energy__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<x_gaussian_ccsd_energy__hartree>[-+0-9EeDd.]+)", repeats = True),
SM(r"\s*CCSD\(T\)=\s*(?P<x_gaussian_ccsdt_energy__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<x_gaussian_qcisd_energy__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<x_gaussian_qcisd_energy__hartree>[-+0-9EeDd.]+)", repeats = True),
SM(r"\s*QCISD\(T\)=\s*(?P<x_gaussian_qcisdt_energy__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*DE5\s*=\s*(?P<x_gaussian_qcisdtq_correction_energy__hartree>[-+0-9EeDd.]+)\s*QCISD\(TQ\)\s*=\s*(?P<x_gaussian_qcisdtq_energy__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<x_gaussian_ci_energy__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<x_gaussian_semiempirical_energy_converged>[-+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<x_gaussian_molmech_energy>[-+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\s*",
forwardMatch = True,
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', SM(name = 'Geometry_optimization',
sections = ['x_gaussian_section_geometry_optimization_info'],
startReStr = r"\s*Optimization completed.", startReStr = r"\s*Optimization completed.",
forwardMatch = True,
subMatchers = [ subMatchers = [
SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimized Parameters)"), 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*(?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+[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(r"\s*Distance matrix|\s*Rotational constants|\s*Stoichiometry")
...@@ -216,6 +288,16 @@ mainFileDescription = SM( ...@@ -216,6 +288,16 @@ mainFileDescription = SM(
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_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(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 = '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 = 'Frequencies', SM (name = 'Frequencies',
sections = ['x_gaussian_section_frequencies'], sections = ['x_gaussian_section_frequencies'],
...@@ -254,6 +336,26 @@ mainFileDescription = SM( ...@@ -254,6 +336,26 @@ mainFileDescription = SM(
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*[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(r"\s*Force constants in internal coordinates")
] ]
),
SM(name = 'CompositeModelEnergies',
sections = ['x_gaussian_section_models'],
startReStr = r"\s*Diagonal vibrational polarizability\s*",
forwardMatch = False,
repeats = True,
subMatchers = [
SM(r"\s*G1 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G2 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G2MP2 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G3 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G3MP2 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-4 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-q Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-Q Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-QB3 Energy=\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*W1U Electronic Energy\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*W1RO Electronic Energy\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
SM(r"\s*W1BD Electronic Energy\s*(?P<x_gaussian_model_energy__hartree>[-+0-9.]+)"),
]
), ),
SM(name = 'run times', SM(name = 'run times',
sections = ['x_gaussian_section_times'], sections = ['x_gaussian_section_times'],
...@@ -291,7 +393,9 @@ class GaussianParserContext(object): ...@@ -291,7 +393,9 @@ class GaussianParserContext(object):
def __init__(self): def __init__(self):
# dictionary of energy values, which are tracked between SCF iterations and written after convergence # dictionary of energy values, which are tracked between SCF iterations and written after convergence
self.totalEnergyList = { self.totalEnergyList = {
'energy_XC_potential': None 'x_gaussian_electronic_kinetic_energy': None,
'x_gaussian_energy_electrostatic': None,
'x_gaussian_energy_error': None,
} }
def initialize_values(self): def initialize_values(self):
...@@ -300,12 +404,17 @@ class GaussianParserContext(object): ...@@ -300,12 +404,17 @@ class GaussianParserContext(object):
This allows a consistent setting and resetting of the variables, This allows a consistent setting and resetting of the variables,
when the parsing starts and when a section_run closes. 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 # start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1 self.scfIterNr = -1
self.singleConfCalcs = []
self.scfConvergence = False self.scfConvergence = False
self.geoConvergence = None self.geoConvergence = False
self.geoCrashed = None
self.scfenergyconverged = 0.0 self.scfenergyconverged = 0.0
self.scfkineticenergyconverged = 0.0
self.scfelectrostaticenergy = 0.0
self.periodicCalc = False
def startedParsing(self, path, parser): def startedParsing(self, path, parser):
self.parser = parser self.parser = parser
...@@ -314,6 +423,34 @@ class GaussianParserContext(object): ...@@ -314,6 +423,34 @@ class GaussianParserContext(object):
# allows to reset values if the same superContext is used to parse different files # allows to reset values if the same superContext is used to parse different files
self.initialize_values() 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.
"""
# write geometry optimization convergence
sampling_method = None
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): def onClose_x_gaussian_section_geometry(self, backend, gIndex, section):
xCoord = section["x_gaussian_atom_x_coord"] xCoord = section["x_gaussian_atom_x_coord"]
yCoord = section["x_gaussian_atom_y_coord"] yCoord = section["x_gaussian_atom_y_coord"]
...@@ -345,41 +482,35 @@ class GaussianParserContext(object): ...@@ -345,41 +482,35 @@ class GaussianParserContext(object):
atom_forces[i,2] = zForce[i] atom_forces[i,2] = zForce[i]
backend.addArrayValues("atom_forces_raw", atom_forces) backend.addArrayValues("atom_forces_raw", atom_forces)
def onClose_section_run(self, backend, gIndex, section): def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
"""Trigger called when section_run is closed. self.singleConfCalcs.append(gIndex)
"""
# write geometry optimization convergence
gIndexTmp = backend.openSection('section_single_configuration_calculation')
if self.geoConvergence is not None:
backend.addValue('x_gaussian_geometry_optimization_converged', self.geoConvergence)
backend.closeSection('section_single_configuration_calculation', gIndexTmp)
def onClose_section_single_configuration_calculation(self, backend, gIndex, section): def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
"""Trigger called when section_single_configuration_calculation is closed. """Trigger called when section_single_configuration_calculation is closed.
Write number of SCF iterations and convergence. Write number of SCF iterations and convergence.
Check for convergence of geometry optimization. Check for convergence of geometry optimization.
""" """
# write number of SCF iterations
self.scfenergyconverged = section['energy_total']
backend.addValue('x_gaussian_number_of_scf_iterations', self.scfIterNr)
# write SCF convergence and reset # write SCF convergence and reset
<<<<<<< HEAD
backend.addValue('x_gaussian_single_configuration_calculation_converged', self.scfConvergence) backend.addValue('x_gaussian_single_configuration_calculation_converged', self.scfConvergence)
backend.addValue('energy_total', self.scfenergyconverged[-1]) backend.addValue('energy_total', self.scfenergyconverged[-1])
=======
backend.addValue('single_configuration_calculation_converged', self.scfConvergence)
>>>>>>> Gaussian parser with ground and excited state energies
self.scfConvergence = False 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 # check for geometry optimization convergence
if section['x_gaussian_geometry_optimization_converged'] is not None: if section['x_gaussian_geometry_optimization_converged'] is not None:
if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization completed': if section['x_gaussian_geometry_optimization_converged'] == ['Optimization completed']:
self.geoConvergence = True self.geoConvergence = True
else: elif section['x_gaussian_geometry_optimization_converged'] == ['Optimization stopped']:
if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization stopped':
self.geoConvergence = False self.geoConvergence = False
if section['x_gaussian_geometry_optimization_converged'] is not None:
if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization stopped':
self.geoCrashed = True
else:
self.geoCrashed = False
# start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1
def onClose_section_scf_iteration(self, backend, gIndex, section): def onClose_section_scf_iteration(self, backend, gIndex, section):
# count number of SCF iterations # count number of SCF iterations
...@@ -387,16 +518,11 @@ class GaussianParserContext(object): ...@@ -387,16 +518,11 @@ class GaussianParserContext(object):
# check for SCF convergence # check for SCF convergence
if section['x_gaussian_single_configuration_calculation_converged'] is not None: if section['x_gaussian_single_configuration_calculation_converged'] is not None:
self.scfConvergence = True self.scfConvergence = True
if section['x_gaussian_energy_total']:
def onClose_x_gaussian_section_atomic_masses(self, backend, gIndex, section): if section['x_gaussian_electronic_kinetic_energy']:
if(section["x_gaussian_atomic_masses"]): self.scfkineticenergyconverged = float(str(section['x_gaussian_electronic_kinetic_energy']).replace("[","").replace("]","").replace("D","E"))
atomicmasses = str(section["x_gaussian_atomic_masses"]) self.scfelectrostaticenergy = self.scfenergyconverged - self.scfkineticenergyconverged
atmass = [] backend.addValue('x_gaussian_energy_electrostatic', self.scfelectrostaticenergy)
mass = [float(f) for f in atomicmasses[1:].replace("'","").replace(",","").replace("]","").replace(" ."," 0.").replace(" -."," -0.").split()]
atmass = np.append(atmass, mass)
gIndexTmp = backend.openSection("section_system")
backend.addArrayValues("x_gaussian_masses", atmass)
backend.closeSection("section_system", gIndexTmp)
def onClose_x_gaussian_section_eigenvalues(self, backend, gIndex, section): def onClose_x_gaussian_section_eigenvalues(self, backend, gIndex, section):
eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"]) eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"])
...@@ -475,7 +601,6 @@ class GaussianParserContext(object): ...@@ -475,7 +601,6 @@ class GaussianParserContext(object):
char = str(section["charge"]) char = str(section["charge"])
cha = str([char]) cha = str([char])
charge = [float(f) for f in cha[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").replace('"','').split()] charge = [float(f) for f in cha[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").replace('"','').split()]
# charge = convert_unit
dipx = section["dipole_moment_x"] dipx = section["dipole_moment_x"]
dipy = section["dipole_moment_y"] dipy = section["dipole_moment_y"]
...@@ -538,10 +663,6 @@ class GaussianParserContext(object): ...@@ -538,10 +663,6 @@ class GaussianParserContext(object):
x_gaussian_molecular_multipole_values = np.resize(multipoles, (x_gaussian_number_of_lm_molecular_multipoles)) x_gaussian_molecular_multipole_values = np.resize(multipoles, (x_gaussian_number_of_lm_molecular_multipoles))
# x_gaussian_molecular_multipole_lm[0] = (0,0)
# x_gaussian_molecular_multipole_lm[1] = (1,0)
# x_gaussian_molecular_multipole_lm[2] = (1,1)
# x_gaussian_molecular_multipole_lm[3] = (1,2)
backend.addArrayValues("x_gaussian_molecular_multipole_values", x_gaussian_molecular_multipole_values) 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) backend.addValue("x_gaussian_molecular_multipole_m_kind", x_gaussian_molecular_multipole_m_kind)
...@@ -648,6 +769,10 @@ class GaussianParserContext(object): ...@@ -648,6 +769,10 @@ class GaussianParserContext(object):
backend.addArrayValues("x_gaussian_force_constant_values", cartforceconst) 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): def onClose_section_method(self, backend, gIndex, section):
# handling of xc functional # handling of xc functional
# two functions to convert hybrid_xc_coeff to the correct weight # two functions to convert hybrid_xc_coeff to the correct weight
...@@ -761,6 +886,7 @@ class GaussianParserContext(object): ...@@ -761,6 +886,7 @@ class GaussianParserContext(object):
'AM1': [{'name': 'AM1'}], 'AM1': [{'name': 'AM1'}],
'PM3': [{'name': 'PM3'}], 'PM3': [{'name': 'PM3'}],
'PM3MM': [{'name': 'PM3MM'}], 'PM3MM': [{'name': 'PM3MM'}],
'PM3D3': [{'name': 'PM3D3'}],
'PM6': [{'name': 'PM6'}], 'PM6': [{'name': 'PM6'}],
'PDDG': [{'name': 'PDDG'}], 'PDDG': [{'name': 'PDDG'}],
'CNDO': [{'name': 'CNDO'}], 'CNDO': [{'name': 'CNDO'}],
...@@ -768,6 +894,8 @@ class GaussianParserContext(object): ...@@ -768,6 +894,8 @@ class GaussianParserContext(object):
'MINDO': [{'name': 'MINDO'}], 'MINDO': [{'name': 'MINDO'}],
'MINDO3': [{'name': 'MINDO3'}], 'MINDO3': [{'name': 'MINDO3'}],
'ZINDO': [{'name': 'ZINDO'}], 'ZINDO': [{'name': 'ZINDO'}],
'HUCKEL': [{'name': 'HUCKEL'}],
'EXTENDEDHUCKEL': [{'name': 'HUCKEL'}],
'ONIOM': [{'name': 'ONIOM'}], 'ONIOM': [{'name': 'ONIOM'}],
'RHF': [{'name': 'RHF'}], 'RHF': [{'name': 'RHF'}],
'UHF': [{'name': 'UHF'}], 'UHF': [{'name': 'UHF'}],
...@@ -778,13 +906,23 @@ class GaussianParserContext(object): ...@@ -778,13 +906,23 @@ class GaussianParserContext(object):
'CISD': [{'name': 'CISD'}], 'CISD': [{'name': 'CISD'}],
'CIS': [{'name': 'CIS'}], 'CIS': [{'name': 'CIS'}],
'BD': [{'name': 'BD'}], 'BD': [{'name': 'BD'}],
'BD(T)': [{'name': 'BD(T)'}],
'CCD': [{'name': 'CCD'}], 'CCD': [{'name': 'CCD'}],
'CCSD': [{'name': 'CCSD'}], 'CCSD': [{'name': 'CCSD'}],
'EOMCCSD': [{'name': 'EOMCCSD'}], 'EOMCCSD': [{'name': 'EOMCCSD'}],
'QCISD': [{'name': 'QCISD'}], 'QCISD': [{'name': 'QCISD'}],
'CCSD(T)': [{'name': 'CCSD(T)'}],
'QCISD(T)': [{'name': 'QCISD(T)'}],
'QCISD(TQ)': [{'name': 'QCISD(TQ)'}],
'MP2': [{'name': 'MP2'}], 'MP2': [{'name': 'MP2'}],
'MP3': [{'name': 'MP3'}], 'MP3': [{'name': 'MP3'}],
'MP4': [{'name': 'MP4'}], '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'}], 'MP5': [{'name': 'MP5'}],
'CAS': [{'name': 'CASSCF'}], 'CAS': [{'name': 'CASSCF'}],
'CASSCF': [{'name': 'CASSCF'}], 'CASSCF': [{'name': 'CASSCF'}],
...@@ -797,8 +935,8 @@ class GaussianParserContext(object): ...@@ -797,8 +935,8 @@ class GaussianParserContext(object):
'G3MP2B3': [{'name': 'G3MP2B3'}], 'G3MP2B3': [{'name': 'G3MP2B3'}],
'G4': [{'name': 'G4'}], 'G4': [{'name': 'G4'}],
'G4MP2': [{'name': 'G4MP2'}], 'G4MP2': [{'name': 'G4MP2'}],
'CBSExtrap': [{'name': 'CBSExtrapolate'}], 'CBSEXTRAP': [{'name': 'CBSExtrapolate'}],
'CBSExtrapolate': [{'name': 'CBSExtrapolate'}], 'CBSEXTRAPOLATE': [{'name': 'CBSExtrapolate'}],
'CBS-4M': [{'name': 'CBS-4M'}], 'CBS-4M': [{'name': 'CBS-4M'}],
'CBS-4O': [{'name': 'CBS-4O'}], 'CBS-4O': [{'name': 'CBS-4O'}],
'CBS-QB3': [{'name': 'CBS-QB3'}], 'CBS-QB3': [{'name': 'CBS-QB3'}],
...@@ -866,6 +1004,8 @@ class GaussianParserContext(object): ...@@ -866,6 +1004,8 @@ class GaussianParserContext(object):
'TZVPFIT': [{'name': 'TZVPFit'}], 'TZVPFIT': [{'name': 'TZVPFit'}],
'W06': [{'name': 'W06'}], 'W06': [{'name': 'W06'}],
'CHF': [{'name': 'CHF'}], 'CHF': [{'name': 'CHF'}],
'FIT': [{'name': 'FIT'}],
'AUTO': [{'name': 'AUTO'}],
} }
global xc, method, basisset, xcWrite, methodWrite, basissetWrite, methodreal, basissetreal, exc, corr, exccorr, methodprefix global xc, method, basisset, xcWrite, methodWrite, basissetWrite, methodreal, basissetreal, exc, corr, exccorr, methodprefix
...@@ -881,6 +1021,7 @@ class GaussianParserContext(object): ...@@ -881,6 +1021,7 @@ class GaussianParserContext(object):
exc = None exc = None
corr = None corr = None
exccorr = None exccorr = None
settings = section["x_gaussian_settings"] settings = section["x_gaussian_settings"]
settings = map(str.strip, settings) settings = map(str.strip, settings)
settings = [''.join(map(str,settings))] settings = [''.join(map(str,settings))]
...@@ -896,7 +1037,7 @@ class GaussianParserContext(object): ...@@ -896,7 +1037,7 @@ class GaussianParserContext(object):
method1 = method1.upper() method1 = method1.upper()
for x in method1.split(): for x in method1.split():
method2 = str(x) method2 = str(x)
if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF': 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': if (method2[0] == 'R' and method2[0:2] != 'RO') or method2[0] == 'U':
methodprefix = method2[0] methodprefix = method2[0]
method2 = method2[1:] method2 = method2[1:]
...@@ -904,6 +1045,7 @@ class GaussianParserContext(object): ...@@ -904,6 +1045,7 @@ class GaussianParserContext(object):
methodprefix = method2[0:2] methodprefix = method2[0:2]
method2 = method2[2:] method2 = method2[2:]
if method2[0] == 'S' or method2[0] == 'B' or method2[0] == 'O': if method2[0] == 'S' or method2[0] == 'B' or method2[0] == 'O':
if method2[1] != '2' and method2[1] != '3':
exc = method2[0] exc = method2[0]
corr = method2[1:] corr = method2[1:]
if exc in xcDict.keys() and corr in xcDict.keys(): if exc in xcDict.keys() and corr in xcDict.keys():
...@@ -925,6 +1067,7 @@ class GaussianParserContext(object): ...@@ -925,6 +1067,7 @@ class GaussianParserContext(object):
if method2 in xcDict.keys(): if method2 in xcDict.keys():
xc = method2 xc = method2
xcWrite= True xcWrite= True
methodWrite = True
method = 'DFT' method = 'DFT'
if method2 in methodDict.keys(): if method2 in methodDict.keys():
method = method2 method = method2
...@@ -933,6 +1076,10 @@ class GaussianParserContext(object): ...@@ -933,6 +1076,10 @@ class GaussianParserContext(object):
else: else:
for n in range(2,9): for n in range(2,9):
if method2[0:n] in methodDict.keys(): if method2[0:n] in methodDict.keys():
if method2[0:n] in xcDict.keys():
method = 'DFT'
methodWrite = True
else:
method = method2[0:n] method = method2[0:n]
methodWrite = True methodWrite = True
methodreal = method2 methodreal = method2
...@@ -940,7 +1087,7 @@ class GaussianParserContext(object): ...@@ -940,7 +1087,7 @@ class GaussianParserContext(object):
method = method2[0:9] method = method2[0:9]
methodWrite = True methodWrite = True
methodreal = method2 methodreal = method2
rest = settings.split('/')[1] rest = settings.split('/')[1].replace("'","").replace("]","")
rest = rest.upper() rest = rest.upper()
for x in rest.split(): for x in rest.split():
if x in basissetDict.keys(): if x in basissetDict.keys():
...@@ -967,6 +1114,16 @@ class GaussianParserContext(object): ...@@ -967,6 +1114,16 @@ class GaussianParserContext(object):
basisset = method2[0:5] basisset = method2[0:5]
basissetWrite = True basissetWrite = True
basissetreal = method2 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: if '6-31' in x:
method2 = x method2 = x
if '6-311' in x: if '6-311' in x:
...@@ -977,12 +1134,21 @@ class GaussianParserContext(object): ...@@ -977,12 +1134,21 @@ class GaussianParserContext(object):
basisset = '6-31G' basisset = '6-31G'
basissetWrite = True basissetWrite = True
basissetreal = '6-31' + method2[4:] 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: else:
method1 = settings.split() method1 = settings.split()
for x in method1: for x in method1:
method2 = str(x) method2 = str(x)
method2 = method2.upper() method2 = method2.upper()
if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF': 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': if (method2[0] == 'R' and method2[0:2] != 'RO') or method2[0] == 'U':
methodprefix = method2[0] methodprefix = method2[0]
method2 = method2[1:] method2 = method2[1:]
...@@ -1069,7 +1235,7 @@ class GaussianParserContext(object): ...@@ -1069,7 +1235,7 @@ class GaussianParserContext(object):
# description for hybrid coefficient # description for hybrid coefficient
xcHybridCoeffDescr = 'hybrid coefficient $\\alpha$' xcHybridCoeffDescr = 'hybrid coefficient $\\alpha$'
hseFunc = 'HSEh1PBE' hseFunc = 'HSEH1PBE'
# functionals where hybrid_xc_coeff is written # functionals where hybrid_xc_coeff is written
writeHybridCoeff = ['B3LYP', 'OHSE2PBE', 'HSEh1PBE', 'PBE1PBE' ] writeHybridCoeff = ['B3LYP', 'OHSE2PBE', 'HSEh1PBE', 'PBE1PBE' ]
if xc is not None: if xc is not None:
...@@ -1138,9 +1304,9 @@ class GaussianParserContext(object): ...@@ -1138,9 +1304,9 @@ class GaussianParserContext(object):
if methodName is not None: if methodName is not None:
# write section and method name # write section and method name
gIndexTmp = backend.openSection('x_gaussian_section_elstruc_method') gIndexTmp = backend.openSection('x_gaussian_section_elstruc_method')
if methodprefix != None: if methodprefix != None and methodreal != None:
backend.addValue('x_gaussian_elstruc_method_name', str(methodprefix) + methodreal) backend.addValue('x_gaussian_elstruc_method_name', str(methodprefix) + methodreal)
else: elif methodreal != None:
backend.addValue('x_gaussian_elstruc_method_name', methodreal) backend.addValue('x_gaussian_elstruc_method_name', methodreal)
else: 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__))) 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__)))
...@@ -1162,7 +1328,7 @@ class GaussianParserContext(object): ...@@ -1162,7 +1328,7 @@ class GaussianParserContext(object):
for basissetItem in basissetList: for basissetItem in basissetList:
basissetName = basissetItem.get('name') basissetName = basissetItem.get('name')
if basissetName is not None: if basissetName is not None:
# write section and method name # write section and basis set name(s)
gIndexTmp = backend.openSection('section_basis_set_atom_centered') gIndexTmp = backend.openSection('section_basis_set_atom_centered')
backend.addValue('basis_set_atom_centered_short_name', basissetreal) backend.addValue('basis_set_atom_centered_short_name', basissetreal)
else: else:
...@@ -1170,6 +1336,42 @@ class GaussianParserContext(object): ...@@ -1170,6 +1336,42 @@ class GaussianParserContext(object):
else: 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__))) 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_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
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)
backend.addValue("x_gaussian_number_of_atoms",numberofatoms)
# which values to cache or forward (mapping meta name -> CachingLevel) # which values to cache or forward (mapping meta name -> CachingLevel)
...@@ -1179,17 +1381,16 @@ cachingLevelForMetaName = { ...@@ -1179,17 +1381,16 @@ cachingLevelForMetaName = {
"x_gaussian_atom_z_coord": CachingLevel.Cache, "x_gaussian_atom_z_coord": CachingLevel.Cache,
"x_gaussian_atomic_number": CachingLevel.Cache, "x_gaussian_atomic_number": CachingLevel.Cache,
"x_gaussian_section_geometry": CachingLevel.Ignore, "x_gaussian_section_geometry": CachingLevel.Ignore,
"x_gaussian_geometry_optimization_converged": CachingLevel.Cache,
"x_gaussian_single_configuration_calculation_converged": CachingLevel.Ignore,
"x_gaussian_atom_x_force": CachingLevel.Cache, "x_gaussian_atom_x_force": CachingLevel.Cache,
"x_gaussian_atom_y_force": CachingLevel.Cache, "x_gaussian_atom_y_force": CachingLevel.Cache,
"x_gaussian_atom_z_force": CachingLevel.Cache, "x_gaussian_atom_z_force": CachingLevel.Cache,
"x_gaussian_section_atom_forces": CachingLevel.Ignore,
"x_gaussian_section_frequencies": CachingLevel.Forward, "x_gaussian_section_frequencies": CachingLevel.Forward,
"x_gaussian_atomic_masses": CachingLevel.Cache, "x_gaussian_atomic_masses": CachingLevel.Cache,
"x_gaussian_section_eigenvalues": CachingLevel.Cache, "x_gaussian_section_eigenvalues": CachingLevel.Cache,
"x_gaussian_section_orbital_symmetries": CachingLevel.Cache, "x_gaussian_section_orbital_symmetries": CachingLevel.Cache,
"x_gaussian_section_molecular_multipoles": CachingLevel.Cache, "x_gaussian_section_molecular_multipoles": CachingLevel.Cache,
"x_gaussian_single_configuration_calculation_converged": CachingLevel.Cache,
"x_gaussian_geometry_optimization_converged": CachingLevel.Cache,
} }
if __name__ == "__main__": if __name__ == "__main__":
......
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