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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

parent 49bc2765
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parser/parser-gaussian/parser_gaussian.py
View file @ cf285c82
......@@ -64,33 +64,23 @@ mainFileDescription = SM(
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'],
startReStr = r"\s*Charge =",
endReStr = r"\s*Leave Link 101\s*",
subFlags = SM.SubFlags.Unordered,
forwardMatch = True,
subMatchers = [
SM(r"\s*Charge =\s*(?P<x_gaussian_total_charge>[-+0-9]*) Multiplicity =\s*(?P<x_gaussian_spin_target_multiplicity>[0-9]*)"),
SM(r"\s*NAtoms=\s*(?P<x_gaussian_natoms>[0-9]*)\s*NQM="),
]
),
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*(Tv|Tv\s*[0]|TV|TV\s*[0])\s*(?P<x_gaussian_geometry_lattice_vector_x>[0-9.]*)\s+(?P<x_gaussian_geometry_lattice_vector_y>[0-9.]*)\s+(?P<x_gaussian_geometry_lattice_vector_z>[0-9.]*)", repeats = True),
SM(r"\s*AtmWgt=\s+(?P<x_gaussian_atomic_masses>[0-9.]+(\s+[0-9.]+)(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?)", repeats = True)
]
),
# this SimpleMatcher groups a single configuration calculation together with output after SCF convergence from relaxation
SM (name = 'SingleConfigurationCalculationWithSystemDescription',
startReStr = "\s*Standard orientation:",
# endReStr = "\s*Link1: Proceeding to internal job step number",
repeats = False,
forwardMatch = True,
subMatchers = [
# the actual section for a single configuration calculation starts here
SM (name = 'SingleConfigurationCalculation',
startReStr = "\s*Standard orientation:",
repeats = True,
......@@ -99,7 +89,7 @@ mainFileDescription = SM(
subMatchers = [
SM(name = 'geometry',
sections = ['x_gaussian_section_geometry'],
startReStr = r"\s*Standard orientation",
startReStr = r"\s*Standard orientation:",
endReStr = r"\s*Rotational constants",
subMatchers = [
SM(r"\s+[0-9]+\s+(?P<x_gaussian_atomic_number>[0-9]+)\s+[0-9]+\s+(?P<x_gaussian_atom_x_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_y_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_z_coord__angstrom>[-+0-9EeDd.]+)",repeats = True),
......@@ -109,21 +99,17 @@ mainFileDescription = SM(
SM(name = 'TotalEnergyScfGaussian',
sections = ['section_scf_iteration'],
startReStr = r"\s*Cycle\s+[0-9]+",
endReStr = r"\s*Leave Link 502\s*",
forwardMatch = True,
repeats = True,
subMatchers = [
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(r"\s*KE=\s*(?P<x_gaussian_electronic_kinetic_energy__hartree>[-+0-9EeDd.]+)\s*"),
]
),
SM(name = 'TotalEnergyScfConverged',
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',
sections = ['x_gaussian_section_real_spin_squared'],
startReStr = r"\s*Annihilation of the first spin contaminant",
......@@ -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(name = 'ForcesGaussian',
sections = ['x_gaussian_section_atom_forces'],
startReStr = "\s*Center\s+Atomic\s+Forces ",
SM(name = 'PerturbationEnergies',
sections = ['x_gaussian_section_moller_plesset'],
startReStr = r"\s*E2 =\s*",
forwardMatch = True,
subMatchers = [
SM(r"\s*E2 =\s*(?P<x_gaussian_mp2_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P<x_gaussian_mp2_energy__hartree>[-+0-9EeDd.]+)"),
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*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*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(r"\s*EIGENVALUES AND\s*"),
SM(r"\s*\(\s*[0-9]+\)\s*EIGENVALUE\s*(?P<x_gaussian_casscf_energy__hartree>[-+0-9.]+)", repeats = True),
]
),
SM(name = 'Geometry_optimization',
sections = ['x_gaussian_section_geometry_optimization_info'],
startReStr = r"\s*Optimization completed.",
forwardMatch = True,
subMatchers = [
SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>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+[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")
......@@ -217,6 +289,16 @@ mainFileDescription = SM(
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',
sections = ['x_gaussian_section_frequencies'],
startReStr = r"\s*Frequencies --",
......@@ -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*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',
sections = ['x_gaussian_section_times'],
......@@ -291,7 +393,9 @@ class GaussianParserContext(object):
def __init__(self):
# dictionary of energy values, which are tracked between SCF iterations and written after convergence
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):
......@@ -300,12 +404,17 @@ class GaussianParserContext(object):
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 = None
self.geoCrashed = None
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
......@@ -314,6 +423,34 @@ class GaussianParserContext(object):
# 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.
"""
# 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):
xCoord = section["x_gaussian_atom_x_coord"]
yCoord = section["x_gaussian_atom_y_coord"]
......@@ -345,59 +482,48 @@ class GaussianParserContext(object):
atom_forces[i,2] = zForce[i]
backend.addArrayValues("atom_forces_raw", atom_forces)
def onClose_section_run(self, backend, gIndex, section):
"""Trigger called when section_run is closed.
"""
# 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 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 number of SCF iterations
self.scfenergyconverged = section['energy_total']
backend.addValue('x_gaussian_number_of_scf_iterations', self.scfIterNr)
# write SCF convergence and reset
<<<<<<< HEAD
backend.addValue('x_gaussian_single_configuration_calculation_converged', self.scfConvergence)
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
# check for geometry optimization convergence
if section['x_gaussian_geometry_optimization_converged'] is not None:
if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization completed':
self.geoConvergence = True
else:
if section['x_gaussian_geometry_optimization_converged'][-1] == 'Optimization stopped':
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
# 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
self.scfConvergence = True
if section['x_gaussian_energy_total']:
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_x_gaussian_section_atomic_masses(self, backend, gIndex, section):
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)
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):
eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"])
eigenen1 = []
......@@ -475,7 +601,6 @@ class GaussianParserContext(object):
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()]
# charge = convert_unit
dipx = section["dipole_moment_x"]
dipy = section["dipole_moment_y"]
......@@ -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_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.addValue("x_gaussian_molecular_multipole_m_kind", x_gaussian_molecular_multipole_m_kind)
......@@ -648,6 +769,10 @@ class GaussianParserContext(object):
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
# two functions to convert hybrid_xc_coeff to the correct weight
......@@ -761,6 +886,7 @@ class GaussianParserContext(object):
'AM1': [{'name': 'AM1'}],
'PM3': [{'name': 'PM3'}],
'PM3MM': [{'name': 'PM3MM'}],
'PM3D3': [{'name': 'PM3D3'}],
'PM6': [{'name': 'PM6'}],
'PDDG': [{'name': 'PDDG'}],
'CNDO': [{'name': 'CNDO'}],
......@@ -768,6 +894,8 @@ class GaussianParserContext(object):
'MINDO': [{'name': 'MINDO'}],
'MINDO3': [{'name': 'MINDO3'}],
'ZINDO': [{'name': 'ZINDO'}],
'HUCKEL': [{'name': 'HUCKEL'}],
'EXTENDEDHUCKEL': [{'name': 'HUCKEL'}],
'ONIOM': [{'name': 'ONIOM'}],
'RHF': [{'name': 'RHF'}],
'UHF': [{'name': 'UHF'}],
......@@ -778,13 +906,23 @@ class GaussianParserContext(object):
'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'}],
......@@ -797,8 +935,8 @@ class GaussianParserContext(object):
'G3MP2B3': [{'name': 'G3MP2B3'}],
'G4': [{'name': 'G4'}],
'G4MP2': [{'name': 'G4MP2'}],
'CBSExtrap': [{'name': 'CBSExtrapolate'}],
'CBSExtrapolate': [{'name': 'CBSExtrapolate'}],
'CBSEXTRAP': [{'name': 'CBSExtrapolate'}],
'CBSEXTRAPOLATE': [{'name': 'CBSExtrapolate'}],
'CBS-4M': [{'name': 'CBS-4M'}],
'CBS-4O': [{'name': 'CBS-4O'}],
'CBS-QB3': [{'name': 'CBS-QB3'}],
......@@ -866,6 +1004,8 @@ class GaussianParserContext(object):
'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
......@@ -881,6 +1021,7 @@ class GaussianParserContext(object):
exc = None
corr = None
exccorr = None
settings = section["x_gaussian_settings"]
settings = map(str.strip, settings)
settings = [''.join(map(str,settings))]
......@@ -896,7 +1037,7 @@ class GaussianParserContext(object):
method1 = method1.upper()
for x in method1.split():
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':
methodprefix = method2[0]
method2 = method2[1:]
......@@ -904,10 +1045,11 @@ class GaussianParserContext(object):
methodprefix = method2[0:2]
method2 = method2[2:]
if method2[0] == 'S' or method2[0] == 'B' or method2[0] == 'O':
exc = method2[0]
corr = method2[1:]
if exc in xcDict.keys() and corr in xcDict.keys():
xc = xcDict.get([exc][-1]) + xcDict.get([corr][-1])
if method2[1] != '2' and method2[1] != '3':
exc = method2[0]
corr = method2[1:]
if exc in xcDict.keys() and corr in xcDict.keys():
xc = xcDict.get([exc][-1]) + xcDict.get([corr][-1])
if method2[0:3] == 'BRX' or method2[0:3] == 'G96':
exc = method2[0:3]
corr = method2[3:]
......@@ -925,6 +1067,7 @@ class GaussianParserContext(object):
if method2 in xcDict.keys():
xc = method2
xcWrite= True
methodWrite = True
method = 'DFT'
if method2 in methodDict.keys():
method = method2
......@@ -933,14 +1076,18 @@ class GaussianParserContext(object):
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
rest = settings.split('/')[1]
if method2[0:n] in xcDict.keys():
method = 'DFT'
methodWrite = True
else:
method = method2[0:n]
methodWrite = True
methodreal = method2
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():
......@@ -967,6 +1114,16 @@ class GaussianParserContext(object):
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:
......@@ -977,12 +1134,21 @@ class GaussianParserContext(object):
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':
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:]
......@@ -1069,7 +1235,7 @@ class GaussianParserContext(object):
# description for hybrid coefficient
xcHybridCoeffDescr = 'hybrid coefficient $\\alpha$'
hseFunc = 'HSEh1PBE'
hseFunc = 'HSEH1PBE'
# functionals where hybrid_xc_coeff is written
writeHybridCoeff = ['B3LYP', 'OHSE2PBE', 'HSEh1PBE', 'PBE1PBE' ]
if xc is not None:
......@@ -1138,9 +1304,9 @@ class GaussianParserContext(object):
if methodName is not None:
# write section and method name
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)
else:
elif methodreal != None:
backend.addValue('x_gaussian_elstruc_method_name', methodreal)
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__)))
......@@ -1162,7 +1328,7 @@ class GaussianParserContext(object):
for basissetItem in basissetList:
basissetName = basissetItem.get('name')
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')
backend.addValue('basis_set_atom_centered_short_name', basissetreal)
else: