From beb2cbbef344f19ee3080d948319690d7ddb3fb1 Mon Sep 17 00:00:00 2001
From: rosendo <rosendo.valero@gmail.com>
Date: Fri, 10 Jun 2016 16:54:42 +0200
Subject: [PATCH] Several new sections added
---
parser/parser-gaussian/parser_gaussian.py | 398 +++++++++++++++++++---
1 file changed, 360 insertions(+), 38 deletions(-)
diff --git a/parser/parser-gaussian/parser_gaussian.py b/parser/parser-gaussian/parser_gaussian.py
index e4ce3eb..1f0903a 100644
--- a/parser/parser-gaussian/parser_gaussian.py
+++ b/parser/parser-gaussian/parser_gaussian.py
@@ -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__":
--
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