Skip to content

GitLab

P
parser-gaussian
Commit beb2cbbe authored by Rosendo Valero Montero's avatar Rosendo Valero Montero
Browse files
Options

Several new sections added

parent 16a72f9e
Hide whitespace changes
Inline Side-by-side
Showing with 360 additions and 38 deletions
parser/parser-gaussian/parser_gaussian.py
View file @ beb2cbbe
......@@ -10,25 +10,29 @@ import ase
mainFileDescription = SM(
name = 'root',
weak = True,
forwardMatch = True,
startReStr = "",
subMatchers = [
SM(name = 'newRun',
startReStr = r"\s*Entering Link 1 ",
startReStr = r"\s*Cite this work as:",
# endReStr = r"\s*Normal termination of Gaussian",
repeats = True,
required = True,
forwardMatch = True,
fixedStartValues={ 'program_basis_set_type': 'gaussians' },
sections = ['section_run','section_method'],
fixedStartValues={ 'program_name': 'Gaussian', 'program_basis_set_type': 'gaussians' },
sections = ['section_run'],
subMatchers = [
SM(name = 'header',
startReStr = r"\s*Entering Link 1 ",
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*(?P<program_name>Gaussian)\s*(?P<program_version>[0-9]*:\s.*)")
SM(r"\s*(?P<program_name>Gaussian)\s*(?P<program_version>[0-9]+):\s*(?P<x_gaussian_program_implementation>[A-Za-z0-9-.]+)\s*(?P<x_gaussian_program_release_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
SM(r"\s*(?P<x_gaussian_program_execution_date>[0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)"),
]
),
),
SM(name = 'globalparams',
startReStr = r"\s*%\w*=",
subFlags = SM.SubFlags.Unordered,
......@@ -38,27 +42,183 @@ mainFileDescription = SM(
SM(r"\s*%[Mm]em=(?P<x_gaussian_memory>[A-Za-z0-9.]*)"),
SM(r"\s*%[Nn][Pp]roc=(?P<x_gaussian_number_of_processors>[A-Za-z0-9.]*)")
]
),
SM(name = 'charge_multiplicity',
sections = ['section_system','x_gaussian_section_chargemult'],
),
SM(name = 'charge_multiplicity_natoms',
sections = ['x_gaussian_section_system'],
startReStr = r"\s*Charge =",
subFlags = SM.SubFlags.Sequenced,
forwardMatch = True,
subMatchers = [
SM(r"\s*Charge =\s*(?P<total_charge>[-+0-9]+) Multiplicity =\s*(?P<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=(?P<x_gaussian_natoms>[0-9]+)"),
]
),
SM(name = 'geometry',
sections = ['section_system','x_gaussian_section_geometry'],
startReStr = r"\s*Input orientation:|\s*Z-Matrix orientation:|\s*Standard orientation:",
subFlags = SM.SubFlags.Sequenced,
),
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)
]
),
# 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,
forwardMatch = True,
sections = ['x_gaussian_section_single_configuration_calculation'],
subMatchers = [
SM(name = 'geometry',
sections = ['x_gaussian_section_geometry'],
startReStr = r"\s*Standard orientation",
endReStr = r"\s*Rotational constants",
subMatchers = [
SM(r"\s+[0-9]+\s+(?P<x_gaussian_atomic_number>[0-9]+)\s+[0-9]+\s+(?P<x_gaussian_atom_x_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_y_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<x_gaussian_atom_z_coord__angstrom>[-+0-9EeDd.]+)",repeats = True),
SM(r"\s*Distance matrix|\s*Rotational constants|\s*Stoichiometry")
SM(r"\s*Rotational constants")
]
),
SM(name = 'TotalEnergyScfGaussian',
sections = ['x_gaussian_section_scf_iteration'],
startReStr = r"\s*Cycle\s+[0-9]+",
forwardMatch = True,
repeats = True,
subMatchers = [
SM(r"\s*Cycle\s+[0-9]+"),
SM(r"\s*E=\s*(?P<x_gaussian_energy_total_scf_iteration__hartree>[-+0-9.]+)\s*Delta-E=\s*(?P<x_gaussian_delta_energy_total_scf_iteration__hartree>[-+0-9.]+)")
]
),
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<x_gaussian_energy_total_scf_converged__hartree>[-+0-9.]+)")
]
),
SM(name = 'RealSpinValue',
sections = ['x_gaussian_section_real_spin_squared'],
startReStr = r"\s*Convg\s*=",
forwardMatch = True,
subMatchers = [
SM(r"\s*[A-Z][*][*][0-9]\s*=\s*(?P<x_gaussian_spin_S2>[0-9.]+)"),
SM(r"\s*Annihilation of the first spin contaminant"),
SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*[0-9.,]+\s*after\s*(?P<x_gaussian_after_annihilation_spin_S2>[0-9.]+)")
]
),
SM(name = 'ForcesScfGaussian',
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 = 'Geometry_optimization',
startReStr = r"\s*Optimization completed.",
subMatchers = [
SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimized Parameters)"),
SM(r"\s*(?P<x_gaussian_geometry_optimization_converged>Optimization stopped)"),
SM(r"\s+[0-9]+\s+[0-9]+\s+[0-9]+\s+[-+0-9EeDd.]+\s+[-+0-9EeDd.]+\s+[-+0-9EeDd.]+",repeats = True),
SM(r"\s*Distance matrix|\s*Rotational constants|\s*Stoichiometry")
]
),
SM(name = 'Orbital symmetries',
sections = ['x_gaussian_section_orbital_symmetries'],
startReStr = r"\s+Population analysis",
subFlags = SM.SubFlags.Sequenced,
subMatchers = [
SM(r"\s*Orbital symmetries"),
SM(r"\s*Alpha Orbitals"),
SM(r"\s*Occupied\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\))?"),
SM(r"\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\)?)", repeats = True),
SM(r"\s*Virtual\s+(?P<x_gaussian_alpha_vir_symmetry_values>\((.+)\))?"),
SM(r"\s+(?P<x_gaussian_alpha_vir_symmetry_values>\((.+)\)?)", repeats = True),
SM(r"\s*Beta Orbitals"),
SM(r"\s*Occupied\s+(?P<x_gaussian_beta_occ_symmetry_values>\((.+)\))?"),
SM(r"\s+(?P<x_gaussian_beta_occ_symmetry_values>\((.+)\)?)", repeats = True),
SM(r"\s*Virtual\s+(?P<x_gaussian_beta_vir_symmetry_values>\((.+)\))?"),
SM(r"\s+(?P<x_gaussian_beta_vir_symmetry_values>\((.+)\)?)", repeats = True),
]
),
SM(name = 'Electronicstatesymmetry',
sections = ['x_gaussian_section_symmetry'],
startReStr = r"\s*The electronic state is",
forwardMatch = True,
subMatchers = [
SM(r"\s*The electronic state is\s*(?P<x_gaussian_elstate_symmetry>[A-Z0-9-]+)[.]")
]
),
SM(name = 'Eigenvalues',
sections = ['x_gaussian_section_eigenvalues'],
startReStr = r"\s*Alpha occ. eigenvalues --",
forwardMatch = True,
subFlags = SM.SubFlags.Sequenced,
subMatchers = [
SM(r"\s*Alpha occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*Alpha virt. eigenvalues --\s+(?P<x_gaussian_alpha_vir_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*Beta occ. eigenvalues --\s+(?P<x_gaussian_beta_occ_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*Beta virt. eigenvalues --\s+(?P<x_gaussian_beta_vir_eigenvalues_values>(.+)?)", repeats = True),
SM(r"\s*- Condensed to atoms (all electrons)"),
]
),
SM(name = 'Multipoles',
sections = ['x_gaussian_section_molecular_multipoles'],
startReStr = r"\s*Charge=",
forwardMatch = True,
subMatchers = [
SM(r"\s*Dipole moment "),
SM(r"\s+\w+=\s+(?P<dipole_moment_x>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_y>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_z>[-+0-9EeDd.]+)"),
SM(r"\s*Quadrupole moment"),
SM(r"\s+\w+=\s+(?P<quadrupole_moment_xx>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_zz>[0-9-.]+)"),
SM(r"\s+\w+=\s+(?P<quadrupole_moment_xy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_xz>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yz>[0-9-.]+)"),
SM(r"\s*Traceless Quadrupole moment"),
SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
SM(r"\s*Octapole moment"),
SM(r"\s+\w+=\s+(?P<octapole_moment_xxx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_yyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_zzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xyy>[-+0-9EeDd.]+)"),
SM(r"\s+\w+=\s+(?P<octapole_moment_xxy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_yzz>[-+0-9EeDd.]+)"),
SM(r"\s+\w+=\s+(?P<octapole_moment_yyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<octapole_moment_xyz>[-+0-9EeDd.]+)"),
SM(r"\s*Hexadecapole moment"),
SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxxx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxxy>[-+0-9EeDd.]+)"),
SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyx>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzzx>[-+0-9EeDd.]+)"),
SM(r"\s+\w+=\s+(?P<hexadecapole_moment_zzzy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyzz>[-+0-9EeDd.]+)"),
SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzxy>[-+0-9EeDd.]+)")
]
),
SM(name = 'Frequencies',
sections = ['x_gaussian_section_frequencies'],
startReStr = r"\s*Frequencies --",
forwardMatch = True,
subFlags = SM.SubFlags.Sequenced,
subMatchers = [
SM(r"\s*Frequencies --\s*(?P<x_gaussian_frequency_values>(.+)?)", repeats = True),
SM(r"\s*- Thermochemistry -"),
]
),
SM(name = 'run times',
sections = ['x_gaussian_section_times'],
startReStr = r"\s*Job cpu time:",
forwardMatch = True,
subMatchers = [
SM(r"\s*Job cpu time:\s*(?P<x_gaussian_program_cpu_time>\s*[0-9]+\s*[a-z]+\s*[0-9]+\s*[a-z]+\s*[0-9]+\s*[a-z]+\s*[0-9.]+\s*[a-z]+)"),
SM(r"\s*Normal termination of Gaussian\s*[0-9]+\s* at \s*(?P<x_gaussian_program_termination_date>[A-Za-z]+\s*[A-Za-z]+\s*[0-9]+\s*[0-9:]+\s*[0-9]+)"),
]
),
])
])
)
])
])
])
])
# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/gaussian.nomadmetainfo.json
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/gaussian.nomadmetainfo.json"))
......@@ -70,38 +230,200 @@ parserInfo = {
}
class GaussianParserContext(object):
"""main place to keep the parser status, open ancillary files,..."""
def __init__(self):
pass
"""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 = {
'energy_XC_potential': None
}
def startedParsing(self, path, parser):
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.
"""
# start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1
self.scfConvergence = False
self.geoConvergence = None
self.geoCrashed = None
self.scfenergyconverged = 0.0
def startedParsing(self, path, parser):
self.parser = parser
# allows to reset values if the same superContext is used to parse different files
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"]
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_positions = np.zeros((len(xCoord),3), dtype=float)
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_positions[i,0] = xCoord[i]
atom_positions[i,1] = yCoord[i]
atom_positions[i,2] = zCoord[i]
atomic_symbols = np.empty((len(xCoord)), dtype=object)
for i in range(len(xCoord)):
atom_numbers[i] = numbers[i]
atomic_symbols[i] = ase.data.chemical_symbols[atom_numbers[i]]
backend.addArrayValues("atom_positions", atom_positions)
backend.addArrayValues("atom_labels", atomic_symbols)
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]]
backend.addArrayValues("x_gaussian_atom_labels", atomic_symbols)
backend.addArrayValues("x_gaussian_atom_positions", atom_coords)
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("x_gaussian_atom_forces", atom_forces)
def onClose_section_run(self, backend, gIndex, section):
"""Trigger called when section_run is closed.
"""
# write geometry optimization convergence
gIndexTmp = backend.openSection('x_gaussian_section_single_configuration_calculation')
if self.geoConvergence is not None:
backend.addValue('x_gaussian_geometry_optimization_converged', self.geoConvergence)
# use values of control.in which was parsed in section_method
backend.closeSection('x_gaussian_section_single_configuration_calculation', gIndexTmp)
def onClose_x_gaussian_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['x_gaussian_energy_total_scf_converged']
backend.addValue('x_gaussian_number_of_scf_iterations', self.scfIterNr)
# write SCF convergence and reset
backend.addValue('x_gaussian_single_configuration_calculation_converged', self.scfConvergence)
backend.addValue('x_gaussian_energy_total_scf_converged', self.scfenergyconverged)
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
def onClose_x_gaussian_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
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("]","").split()]
vibfreqs = np.append(vibfreqs, freqs)
backend.addArrayValues("x_gaussian_frequencies", vibfreqs)
def onClose_x_gaussian_section_atomic_masses(self, backend, gIndex, section):
atomicmasses = str(section["x_gaussian_atomic_masses"])
atmass = []
mass = [float(f) for f in atomicmasses[1:].replace("'","").replace(",","").replace("]","").split()]
atmass = np.append(atmass, mass)
backend.addArrayValues("x_gaussian_masses", atmass)
def onClose_x_gaussian_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("]","").split()]
eigenen1 = np.append(eigenen1, energy)
occoccupationsalp = 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("]","").split()]
eigenen2 = np.append(eigenen2, energy)
viroccupationsalp = np.zeros(len(eigenen2), dtype=float)
eigenencon = np.zeros(len(eigenen1) + len(eigenen2))
eigenencon = np.concatenate((eigenen1,eigenen2), axis=0)
occupcon = np.concatenate((occoccupationsalp, viroccupationsalp), axis=0)
backend.addArrayValues("x_gaussian_alpha_eigenvalues", eigenencon)
backend.addArrayValues("x_gaussian_alpha_occupations", occupcon)
eigenenergies = str(section["x_gaussian_beta_occ_eigenvalues_values"])
eigenen1 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").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("]","").split()]
eigenen2 = np.append(eigenen2, energy)
viroccupationsbet = np.zeros(len(eigenen2), dtype=float)
eigenencon = np.zeros(len(eigenen1) + len(eigenen2))
eigenencon = np.concatenate((eigenen1,eigenen2), axis=0)
occupcon = np.concatenate((occoccupationsbet, viroccupationsbet), axis=0)
backend.addArrayValues("x_gaussian_beta_eigenvalues", eigenencon)
backend.addArrayValues("x_gaussian_beta_occupations", occupcon)
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"])
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("]","").split()]
sym1 = []
sym1 = np.append(sym1, symmetry)
symmetry = [str(f) for f in symviralpha[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
sym2 = []
sym2 = np.append(sym2, symmetry)
symmetrycon = np.concatenate((sym1, sym2), axis=0)
backend.addArrayValues("x_gaussian_alpha_symmetries", symmetrycon)
symmetry = [str(f) for f in symoccbeta[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
sym1 = []
sym1 = np.append(sym1, symmetry)
symmetry = [str(f) for f in symvirbeta[1:].replace("'","").replace(",","").replace("(","").replace(")","").replace("]","").split()]
sym2 = []
sym2 = np.append(sym2, symmetry)
symmetrycon = np.concatenate((sym1, sym2), axis=0)
backend.addArrayValues("x_gaussian_beta_symmetries", symmetrycon)
# which values to cache or forward (mapping meta name -> CachingLevel)
cachingLevelForMetaName = {
"x_gaussian_atom_x_coord": CachingLevel.Cache,
"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.Ignore,
"x_gaussian_section_geometry": CachingLevel.Ignore,
"x_gaussian_section_total_scf_one_geometry": CachingLevel.Cache,
"x_gaussian_geometry_optimization_converged": CachingLevel.Cache,
"x_gaussian_section_scf_iteration": CachingLevel.Cache,
"x_gaussian_single_configuration_calculation_converged": CachingLevel.Ignore,
"x_gaussian_atom_x_force": CachingLevel.Cache,
"x_gaussian_atom_y_force": CachingLevel.Cache,
"x_gaussian_atom_z_force": CachingLevel.Cache,
"x_gaussian_section_atom_forces": CachingLevel.Ignore,
"x_gaussian_section_frequencies": CachingLevel.Cache,
"x_gaussian_atomic_masses": CachingLevel.Cache,
"x_gaussian_section_eigenvalues": CachingLevel.Cache,
"x_gaussian_section_orbital_symmetries": CachingLevel.Cache,
}
if __name__ == "__main__":
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment