Skip to content

GitLab

P
parser-gaussian

Planned maintenance on Wednesday, 2021-01-20, 17:00-18:00. Expect some interruptions during that time

Commit a6cc5928 authored by Rosendo Valero Montero's avatar Rosendo Valero Montero
Browse files
Options

Updated version with all metadata

parent cab51190
Hide whitespace changes
Inline Side-by-side
Showing with 123 additions and 117 deletions
parser/parser-gaussian/parser_gaussian.py
View file @ a6cc5928
......@@ -61,7 +61,7 @@ mainFileDescription = SM(
forwardMatch = True,
subMatchers = [
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(r"\s*(?P<x_gaussian_settings>([a-zA-Z0-9-/=(),#*+:]*\s*)+)"),
]
),
SM(name = 'charge_multiplicity_cell_masses',
......@@ -95,21 +95,31 @@ mainFileDescription = SM(
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*Rotational constants")
]
),
SM(name = 'SectionHybridCoeffs',
sections = ['x_gaussian_section_hybrid_coeffs'],
startReStr = r"\s*IExCor=",
forwardMatch = True,
subMatchers = [
SM(r"\s*IExCor=\s*[0-9]+\s*DFT=[A-Z]\s*Ex\+Corr=[A-Z0-9]+\s*ExCW=[0-9]\s*ScaHFX=\s*(?P<hybrid_xc_coeff1>[0-9.]+)"),
SM(r"\s*IExCor=\s*[0-9]+\s*DFT=[A-Z]\s*Ex\=[A-Z0-9]+\s*Corr=[a-zA-Z0-9]+\s*ExCW=[0-9]\s*ScaHFX=\s*(?P<hybrid_xc_coeff1>[0-9.]+)"),
SM(r"\s*ScaDFX=\s*(?P<hybrid_xc_coeff2>[0-9.]+\s*[0-9.]+\s*[0-9.]+\s*[0-9.]+)")
]
),
SM(name = 'TotalEnergyScfGaussian',
sections = ['section_scf_iteration'],
startReStr = r"\s*Cycle\s+[0-9]+|\s*Initial guess <Sx>=",
forwardMatch = True,
startReStr = r"\s*Requested convergence on RMS",
forwardMatch = False,
repeats = True,
subMatchers = [
SM(r"\s*Cycle\s+[0-9]+|\s*Initial guess <Sx>="),
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*Cycle\s+[0-9]+|\s*Initial guess <Sx>="),
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*E\((?P<x_gaussian_hf_detect>[A-Z0-9]+)\)\s*=\s*(?P<x_gaussian_energy_scf__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(r"\s*Annihilation of the first spin contaminant"),
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-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P<x_gaussian_energy_total_perturbative__hartree>[-+0-9D.]+)"),
SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P<x_gaussian_perturbation_energy__hartree>[-+0-9D.]+)"),
]
),
SM(name = 'PerturbationEnergies',
......@@ -117,12 +127,12 @@ mainFileDescription = SM(
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(r"\s*E2 =\s*(?P<x_gaussian_mp2_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*E3=\s*(?P<x_gaussian_mp3_correction_energy__hartree>[-+0-9EeDd.]+)\s*EUMP3=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)\s*"),
SM(r"\s*E4\(DQ\)=\s*(?P<x_gaussian_mp4dq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(DQ\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)\s*"),
SM(r"\s*E4\(SDQ\)=\s*(?P<x_gaussian_mp4sdq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(SDQ\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*E4\(SDTQ\)=\s*(?P<x_gaussian_mp4sdtq_correction_energy__hartree>[-+0-9EeDd.]+)\s*UMP4\(SDTQ\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*DEMP5 =\s*(?P<x_gaussian_mp5_correction_energy__hartree>[-+0-9EeDd.]+)\s*MP5 =\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
]
),
SM(name = 'CoupledClusterEnergies',
......@@ -131,8 +141,8 @@ mainFileDescription = SM(
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(r"\s*DE\(Corr\)=\s*(?P<x_gaussian_ccsd_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
SM(r"\s*CCSD\(T\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
]
),
SM(name = 'QuadraticCIEnergies',
......@@ -141,10 +151,10 @@ mainFileDescription = SM(
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(r"\s*DE\(Z\)=\s*(?P<x_gaussian_qcisd_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(Z\)=\s*(?P<energy_total__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<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
SM(r"\s*QCISD\(T\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)"),
SM(r"\s*DE5\s*=\s*(?P<x_gaussian_qcisdtq_correction_energy__hartree>[-+0-9EeDd.]+)\s*QCISD\(TQ\)\s*=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
]
),
SM(name = 'CIEnergies',
......@@ -153,7 +163,7 @@ mainFileDescription = SM(
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(r"\s*DE\(CI\)=\s*(?P<x_gaussian_ci_correction_energy__hartree>[-+0-9EeDd.]+)\s*E\(CI\)=\s*(?P<energy_total__hartree>[-+0-9EeDd.]+)", repeats = True),
]
),
SM(name = 'SemiempiricalEnergies',
......@@ -164,7 +174,7 @@ mainFileDescription = SM(
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(r"\s*Energy=\s*(?P<energy_total>[-+0-9EeDd.]+)"),
]
),
SM(name = 'MolecularMechanicsEnergies',
......@@ -174,7 +184,7 @@ mainFileDescription = SM(
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(r"\s*Energy=\s*(?P<energy_total>[-+0-9EeDd.]+)\s*NIter=\s*[0-9.]"),
]
),
SM(name = 'ExcitedStates',
......@@ -185,8 +195,8 @@ mainFileDescription = SM(
subMatchers = [
SM(name = 'ExcitedStates',
sections = ['x_gaussian_section_excited'],
startReStr = r"\s*Excited State\s*",
forwardMatch = True,
startReStr = r"\s*Excited State",
forwardMatch = False,
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.]+)"),
......@@ -244,7 +254,7 @@ mainFileDescription = SM(
]
),
SM(name = 'Eigenvalues',
sections = ['x_gaussian_section_eigenvalues'],
sections = ['section_eigenvalues'],
startReStr = r"\s*Alpha occ. eigenvalues --",
forwardMatch = True,
subFlags = SM.SubFlags.Sequenced,
......@@ -335,20 +345,20 @@ mainFileDescription = SM(
forwardMatch = False,
repeats = True,
subMatchers = [
SM(r"\s*G1\(0 K\)=\s*[-+0-9.]+\s*G1 Energy=\s*(?P<x_gaussian_G1_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G2\(0 K\)=\s*[-+0-9.]+\s*G2 Energy=\s*(?P<x_gaussian_G2_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G2MP2\(0 K\)=\s*[-+0-9.]+\s*G2MP2 Energy=\s*(?P<x_gaussian_G2MP2_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G3\(0 K\)=\s*[-+0-9.]+\s*G3 Energy=\s*(?P<x_gaussian_G3_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G3MP2\(0 K\)=\s*[-+0-9.]+\s*G3MP2 Energy=\s*(?P<x_gaussian_G3MP2_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G4\(0 K\)=\s*[-+0-9.]+\s*G4 Energy=\s*(?P<x_gaussian_G4_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G4MP2\(0 K\)=\s*[-+0-9.]+\s*G4MP2 Energy=\s*(?P<x_gaussian_G4MP2_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-4 \(0 K\)=\s*[-+0-9.]+\s*CBS-4 Energy=\s*(?P<x_gaussian_CBS4_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-q \(0 K\)=\s*[-+0-9.]+\s*CBS-q Energy=\s*(?P<x_gaussian_CBSq_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-Q \(0 K\)=\s*[-+0-9.]+\s*CBS-Q Energy=\s*(?P<x_gaussian_CBSQ_energy__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-QB3 \(0 K\)=\s*[-+0-9.]+\s*CBS-QB3 Energy=\s*(?P<x_gaussian_CBSQB3_energy__hartree>[-+0-9.]+)"),
SM(r"\s*W1U \(0 K\)=\s*[-+0-9.]+\s*W1U Electronic Energy\s*(?P<x_gaussian_W1U_energy__hartree>[-+0-9.]+)"),
SM(r"\s*W1RO \(0 K\)=\s*[-+0-9.]+\s*W1RO Electronic Energy\s*(?P<x_gaussian_W1RO_energy__hartree>[-+0-9.]+)"),
SM(r"\s*W1BD \(0 K\)=\s*[-+0-9.]+\s*W1BD Electronic Energy\s*(?P<x_gaussian_W1BD_energy__hartree>[-+0-9.]+)"),
SM(r"\s*G1\(0 K\)=\s*[-+0-9.]+\s*G1 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*G2\(0 K\)=\s*[-+0-9.]+\s*G2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*G2MP2\(0 K\)=\s*[-+0-9.]+\s*G2MP2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*G3\(0 K\)=\s*[-+0-9.]+\s*G3 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*G3MP2\(0 K\)=\s*[-+0-9.]+\s*G3MP2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*G4\(0 K\)=\s*[-+0-9.]+\s*G4 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*G4MP2\(0 K\)=\s*[-+0-9.]+\s*G4MP2 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-4 \(0 K\)=\s*[-+0-9.]+\s*CBS-4 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-q \(0 K\)=\s*[-+0-9.]+\s*CBS-q Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-Q \(0 K\)=\s*[-+0-9.]+\s*CBS-Q Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*CBS-QB3 \(0 K\)=\s*[-+0-9.]+\s*CBS-QB3 Energy=\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*W1U \(0 K\)=\s*[-+0-9.]+\s*W1U Electronic Energy\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*W1RO \(0 K\)=\s*[-+0-9.]+\s*W1RO Electronic Energy\s*(?P<energy_total__hartree>[-+0-9.]+)"),
SM(r"\s*W1BD \(0 K\)=\s*[-+0-9.]+\s*W1BD Electronic Energy\s*(?P<energy_total__hartree>[-+0-9.]+)"),
]
),
SM(name = 'run times',
......@@ -387,8 +397,9 @@ class GaussianParserContext(object):
def __init__(self):
# dictionary of energy values, which are tracked between SCF iterations and written after convergence
self.totalEnergyList = {
'x_gaussian_energy_total': None,
'x_gaussian_energy_total_perturbative': None,
'x_gaussian_hf_detect': None,
'x_gaussian_energy_scf': None,
'x_gaussian_perturbation_energy': None,
'x_gaussian_electronic_kinetic_energy': None,
'x_gaussian_energy_electrostatic': None,
'x_gaussian_energy_error': None,
......@@ -511,14 +522,20 @@ class GaussianParserContext(object):
# check for SCF convergence
if section['x_gaussian_single_configuration_calculation_converged'] is not None:
self.scfConvergence = True
if section['x_gaussian_energy_total']:
if section['x_gaussian_electronic_kinetic_energy']:
self.scfenergyconverged = float(str(section['x_gaussian_energy_total']).replace("[","").replace("]","").replace("D","E"))
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_eigenvalues(self, backend, gIndex, section):
if section['x_gaussian_energy_scf']:
self.scfenergyconverged = float(str(section['x_gaussian_energy_scf']).replace("[","").replace("]","").replace("D","E"))
self.scfcharacter = section['x_gaussian_hf_detect']
if (self.scfcharacter != ['RHF'] and self.scfcharacter != ['ROHF'] and self.scfcharacter != ['UHF']):
self.energytotal = self.scfenergyconverged
backend.addValue('energy_total', self.energytotal)
else:
pass
if section['x_gaussian_electronic_kinetic_energy']:
self.scfkineticenergyconverged = float(str(section['x_gaussian_electronic_kinetic_energy']).replace("[","").replace("]","").replace("D","E"))
self.scfelectrostaticenergy = self.scfenergyconverged - self.scfkineticenergyconverged
backend.addValue('x_gaussian_energy_electrostatic', self.scfelectrostaticenergy)
def onClose_section_eigenvalues(self, backend, gIndex, section):
eigenenergies = str(section["x_gaussian_alpha_occ_eigenvalues_values"])
eigenen1 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
......@@ -533,12 +550,17 @@ class GaussianParserContext(object):
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen2 = np.append(eigenen2, energy)
viroccupationsalp = np.zeros(len(eigenen2), dtype=float)
eigenencon = np.zeros(len(eigenen1) + len(eigenen2))
eigenencon = np.concatenate((eigenen1,eigenen2), axis=0)
eigenencon = convert_unit(eigenencon, "hartree", "J")
occupcon = np.concatenate((occoccupationsalp, viroccupationsalp), axis=0)
backend.addArrayValues("x_gaussian_alpha_eigenvalues", eigenencon)
backend.addArrayValues("x_gaussian_alpha_occupations", occupcon)
eigenenconalp = np.zeros(len(eigenen1) + len(eigenen2))
eigenenconalp = np.concatenate((eigenen1,eigenen2), axis=0)
eigenenconalp = convert_unit(eigenenconalp, "hartree", "J")
occupconalp = np.concatenate((occoccupationsalp, viroccupationsalp), axis=0)
eigenenconalpnew = np.reshape(eigenenconalp,(1, 1, len(eigenenconalp)))
occupconalpnew = np.reshape(occupconalp,(1, 1, len(occupconalp)))
if(section["x_gaussian_beta_occ_eigenvalues_values"]):
pass
else:
backend.addArrayValues("eigenvalues_values", eigenenconalpnew)
backend.addArrayValues("eigenvalues_occupation", occupconalpnew)
if(section["x_gaussian_beta_occ_eigenvalues_values"]):
eigenenergies = str(section["x_gaussian_beta_occ_eigenvalues_values"])
......@@ -551,12 +573,16 @@ class GaussianParserContext(object):
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen2 = np.append(eigenen2, energy)
viroccupationsbet = np.zeros(len(eigenen2), dtype=float)
eigenencon = np.zeros(len(eigenen1) + len(eigenen2))
eigenencon = np.concatenate((eigenen1,eigenen2), axis=0)
eigenencon = convert_unit(eigenencon, "hartree", "J")
occupcon = np.concatenate((occoccupationsbet, viroccupationsbet), axis=0)
backend.addArrayValues("x_gaussian_beta_eigenvalues", eigenencon)
backend.addArrayValues("x_gaussian_beta_occupations", occupcon)
eigenenconbet = np.zeros(len(eigenen1) + len(eigenen2))
eigenenconbet = np.concatenate((eigenen1,eigenen2), axis=0)
eigenenconbet = convert_unit(eigenenconbet, "hartree", "J")
occupconbet = np.concatenate((occoccupationsbet, viroccupationsbet), axis=0)
eigenenall = np.concatenate((eigenenconalp,eigenenconbet), axis=0)
occupall = np.concatenate((occupconalp,occupconbet), axis=0)
eigenenall = np.reshape(eigenenall,(2, 1, len(eigenenconalp)))
occupall = np.reshape(occupall,(2, 1, len(occupconalp)))
backend.addArrayValues("eigenvalues_values", eigenenall)
backend.addArrayValues("eigenvalues_occupation", occupall)
def onClose_x_gaussian_section_orbital_symmetries(self, backend, gIndex, section):
symoccalpha = str(section["x_gaussian_alpha_occ_symmetry_values"])
......@@ -770,12 +796,8 @@ class GaussianParserContext(object):
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
def GGA_weight(x):
return 1.0 - x
def HF_weight(x):
return x
# handling of xc functional
# two functions to convert hybrid_xc_coeff to the correct weight
# TODO vdW functionals and double-hybrid functionals
# Dictionary for conversion of xc functional name in aims to metadata format.
# The individual x and c components of the functional are given as dictionaries.
......@@ -848,7 +870,7 @@ class GaussianParserContext(object):
'HSEH1PBE': [{'name': 'HYB_GGA_XC_HSE06'}],
'OHSE1PBE': [{'name': 'HYB_GGA_XC_HSEOLD'}],
'PBEH1PBE': [{'name': 'HYB_GGA_XC_PBEH1PBE'}],
'PBE1PBE': [{'name': 'GGA_C_PBE'}, {'name': 'GGA_X_PBE', 'weight': 0.75, 'convert': GGA_weight}, {'name': 'HF_X', 'weight': 0.25, 'convert': HF_weight}],
'PBE1PBE': [{'name': 'HYB_GGA_XC_PBE1PBE'}],
'M05': [{'name': 'HYB_MGGA_XC_M05'}],
'M052X': [{'name': 'HYB_MGGA_XC_M05_2X'}],
'M06': [{'name': 'HYB_MGGA_XC_M06'}],
......@@ -1243,56 +1265,31 @@ class GaussianParserContext(object):
if 'ONIOM' in method2:
methodreal = method2
# description for hybrid coefficient
xcHybridCoeffDescr = 'hybrid coefficient $\\alpha$'
hseFunc = 'HSEH1PBE'
# functionals where hybrid_xc_coeff is written
writeHybridCoeff = ['B3LYP', 'OHSE2PBE', 'HSEh1PBE', 'PBE1PBE' ]
# functionals where hybrid_xc_coeff are written
# writeHybridCoeff = ['PBE1PBE']
if xc is not None:
# check if only one xc keyword was found in output
if len([xc]) > 1:
logger.error("Found %d settings for the xc functional: %s. This leads to an undefined behavior of the calculation and no metadata can be written for xc." % (len(xc), xc))
else:
backend.superBackend.addValue('x_gaussian_xc', [xc][-1])
# check for hybrid_xc_coeff
# hybridCoeff = valuesDict.get('hybrid_xc_coeff')
# write hybrid_xc_coeff for certain functionals
# if hybridCoeff is not None and xc[-1] in writeHybridCoeff:
# backend.superBackend.addValue('hybrid_xc_coeff', hybridCoeff[-1])
# convert xc functional for metadata
if xcWrite:
# get list of xc components according to parsed value
xcList = xcDict.get([xc][-1])
if xcList is not None:
# loop over the xc components
# loop over the xc components
for xcItem in xcList:
xcName = xcItem.get('name')
if xcName is not None:
# write section and XC_functional_name
gIndexTmp = backend.openSection('section_XC_functionals')
backend.addValue('XC_functional_name', xcName)
# write hybrid_xc_coeff for B3LYP and HSE03 into XC_functional_parameters
# if hybridCoeff is not None and xc[-1] in ['B3LYP', 'OHSE2PBE']:
# backend.addValue('XC_functional_parameters', {xcHybridCoeffDescr: hybridCoeff[-1]})
# write hybrid_xc_coeff for HSE06
# elif xc[-1] == hseFunc:
# add hybrid_xc_coeff
# if hybridCoeff is not None:
# hybrid = hybridCoeff[-1]
# else:
# hybrid = 0.25
# parameters[xcHybridCoeffDescr] = hybrid
# backend.addValue('XC_functional_parameters', parameters)
# adjust weight of functionals that are affected by hybrid_xc_coeff
# elif hybridCoeff is not None and 'convert' in xcItem:
# backend.addValue('XC_functional_weight', xcItem['convert'](hybridCoeff[-1]))
# write weight if present for current xcItem
# else:
# xcWeight = xcItem.get('weight')
# if xcWeight is not None:
# backend.addValue('XC_functional_weight', xcWeight)
backend.closeSection('section_XC_functionals', gIndexTmp)
# write hybrid_xc_coeff for PBE1PBE into XC_functional_parameters
# if hybridCoeff is not None and 'convert' in xcItem:
# backend.addValue('XC_functional_parameters', xcItem['convert'](hybridCoeff[-1]))
else:
backend.closeSection('section_XC_functionals', gIndexTmp)
logger.error("The dictionary for xc functional '%s' does not have the key 'name'. Please correct the dictionary xcDict in %s." % (xc[-1], os.path.basename(__file__)))
else:
logger.error("The xc functional '%s' could not be converted for the metadata. Please add it to the dictionary xcDict in %s." % (xc[-1], os.path.basename(__file__)))
......@@ -1315,10 +1312,10 @@ class GaussianParserContext(object):
# write section and method name
gIndexTmp = backend.openSection('x_gaussian_section_elstruc_method')
if methodprefix != None and methodreal != None:
backend.addValue('x_gaussian_elstruc_method_name', str(methodprefix) + methodreal)
backend.addValue('x_gaussian_electronic_structure_method', str(methodprefix) + methodreal)
backend.closeSection('x_gaussian_section_elstruc_method', gIndexTmp)
elif methodreal != None:
backend.addValue('x_gaussian_elstruc_method_name', methodreal)
backend.addValue('x_gaussian_electronic_structure_method', methodreal)
backend.closeSection('x_gaussian_section_elstruc_method', gIndexTmp)
else:
logger.error("The dictionary for method '%s' does not have the key 'name'. Please correct the dictionary methodDict in %s." % (method[-1], os.path.basename(__file__)))
......@@ -1353,6 +1350,20 @@ class GaussianParserContext(object):
# keep track of the latest system description section
self.secSystemDescriptionIndex = gIndex
def onClose_x_gaussian_section_hybrid_coeffs(self, backend, gIndex, section):
# assign the coefficients to the hybrid functionals
hybrid_xc_coeffsa = ()
hybrid_xc_coeffsb = ()
hybrid_xc_coeffsa = float(str(section['hybrid_xc_coeff1']).replace("[","").replace("]",""))
backend.addValue('x_gaussian_hybrid_xc_hfx', hybrid_xc_coeffsa)
hybrid_xc_coeffs = str(section['hybrid_xc_coeff2'])
hybrid_xc_coeffsb = [float(f) for f in hybrid_xc_coeffs[1:].replace("'","").replace("]","").replace("]","").split()]
backend.addValue('x_gaussian_hybrid_xc_slater', hybrid_xc_coeffsb[0])
backend.addValue('x_gaussian_hybrid_xc_nonlocalex', hybrid_xc_coeffsb[1])
backend.addValue('x_gaussian_hybrid_xc_localcorr', hybrid_xc_coeffsb[2])
backend.addValue('x_gaussian_hybrid_xc_nonlocalcorr', hybrid_xc_coeffsb[3])
def onClose_section_system(self, backend, gIndex, section):
# write/store unit cell if present and set flag self.periodicCalc
if(section['x_gaussian_geometry_lattice_vector_x']):
......@@ -1400,11 +1411,10 @@ cachingLevelForMetaName = {
"section_scf_iteration": CachingLevel.Forward,
"energy_total_scf_iteration": CachingLevel.ForwardAndCache,
"x_gaussian_delta_energy_total_scf_iteration": CachingLevel.ForwardAndCache,
"x_gaussian_energy_total": CachingLevel.ForwardAndCache,
"energy_total": CachingLevel.ForwardAndCache,
"x_gaussian_energy_error": CachingLevel.ForwardAndCache,
"x_gaussian_electronic_kinetic_energy": CachingLevel.ForwardAndCache,
"x_gaussian_energy_electrostatic": CachingLevel.ForwardAndCache,
"x_gaussian_energy_total_perturbative": CachingLevel.ForwardAndCache,
"x_gaussian_section_frequencies": CachingLevel.Forward,
"x_gaussian_frequency_values": CachingLevel.Cache,
"x_gaussian_frequencies": CachingLevel.ForwardAndCache,
......@@ -1416,15 +1426,9 @@ cachingLevelForMetaName = {
"x_gaussian_section_force_constant_matrix": CachingLevel.Forward,
"x_gaussian_force_constant_values": CachingLevel.ForwardAndCache,
"x_gaussian_force_constants": CachingLevel.Cache,
"x_gaussian_section_eigenvalues": CachingLevel.Forward,
"x_gaussian_alpha_occ_eigenvalues_values":CachingLevel.Cache,
"x_gaussian_alpha_vir_eigenvalues_values":CachingLevel.Cache,
"x_gaussian_alpha_eigenvalues": CachingLevel.ForwardAndCache,
"x_gaussian_alpha_occupations": CachingLevel.ForwardAndCache,
"x_gaussian_beta_occ_eigenvalues_values":CachingLevel.Cache,
"x_gaussian_beta_vir_eigenvalues_values":CachingLevel.Cache,
"x_gaussian_beta_eigenvalues": CachingLevel.ForwardAndCache,
"x_gaussian_beta_occupations": CachingLevel.ForwardAndCache,
"section_eigenvalues": CachingLevel.Forward,
"eigenvalues_values": CachingLevel.ForwardAndCache,
"eigenvalues_occupation": CachingLevel.ForwardAndCache,
"x_gaussian_section_orbital_symmetries": CachingLevel.Forward,
"x_gaussian_alpha_occ_symmetry_values":CachingLevel.Cache,
"x_gaussian_alpha_vir_symmetry_values":CachingLevel.Cache,
......@@ -1472,11 +1476,13 @@ cachingLevelForMetaName = {
"x_gaussian_single_configuration_calculation_converged": CachingLevel.ForwardAndCache,
"x_gaussian_section_geometry_optimization_info": CachingLevel.Forward,
"x_gaussian_geometry_optimization_converged": CachingLevel.ForwardAndCache,
"x_gaussian_hf_detect": CachingLevel.ForwardAndCache,
"x_gaussian_section_hybrid_coeffs": CachingLevel.Forward,
"section_method": CachingLevel.Forward,
"x_gaussian_section_elstruc_method": CachingLevel.ForwardAndCache,
"x_gaussian_elstruc_method_name": CachingLevel.ForwardAndCache,
"x_gaussian_section_elstruc_method": CachingLevel.Forward,
"x_gaussian_electronic_structure_method": CachingLevel.ForwardAndCache,
"XC_functional_name": CachingLevel.ForwardAndCache,
"basis_set_atom_centered_short_name": CachingLevel.ForwardAndCache,
"basis_set_atom_centered_short_name": CachingLevel.Forward,
"x_gaussian_settings": CachingLevel.Cache,
"x_gaussian_settings_corrected": CachingLevel.ForwardAndCache,
"section_system": CachingLevel.Forward,
......
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