diff --git a/parser/parser-gaussian/parser_gaussian.py b/parser/parser-gaussian/parser_gaussian.py index ed2738539a438812c866b0a9bc270ca23a067112..027bb77c9fa0ee042436aaaec1c1a8bd10bb4929 100644 --- a/parser/parser-gaussian/parser_gaussian.py +++ b/parser/parser-gaussian/parser_gaussian.py @@ -61,7 +61,7 @@ mainFileDescription = SM( forwardMatch = True, subMatchers = [ SM(r"\s*(?P([a-zA-Z0-9-/=(),#*+:]*\s*)+)"), - SM(r"\s*(?P([a-zA-Z0-9-/=(),#*+:]*\s*)+)") + SM(r"\s*(?P([a-zA-Z0-9-/=(),#*+:]*\s*)+)"), ] ), SM(name = 'charge_multiplicity_cell_masses', @@ -95,21 +95,31 @@ mainFileDescription = SM( SM(r"\s+[0-9]+\s+(?P[0-9]+)\s+[0-9]+\s+(?P[-+0-9EeDd.]+)\s+(?P[-+0-9EeDd.]+)\s+(?P[-+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[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[0-9.]+)"), + SM(r"\s*ScaDFX=\s*(?P[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 =", - forwardMatch = True, + startReStr = r"\s*Requested convergence on RMS", + forwardMatch = False, repeats = True, subMatchers = [ - SM(r"\s*Cycle\s+[0-9]+|\s*Initial guess ="), - SM(r"\s*E=\s*(?P[-+0-9.]+)\s*Delta-E=\s*(?P[-+0-9.]+)"), - SM(r"\s*(?PSCF Done):\s*[(),A-Za-z0-9-]+\s*=\s*(?P[-+0-9.]+)"), + SM(r"\s*Cycle\s+[0-9]+|\s*Initial guess ="), + SM(r"\s*E=\s*(?P[-+0-9.]+)\s*Delta-E=\s*(?P[-+0-9.]+)"), + SM(r"\s*(?PSCF Done):\s*E\((?P[A-Z0-9]+)\)\s*=\s*(?P[-+0-9.]+)"), SM(r"\s*NFock=\s*[0-9]+\s*Conv=(?P[-+0-9EeDd.]+)\s*"), SM(r"\s*KE=\s*(?P[-+0-9EeDd.]+)\s*"), SM(r"\s*Annihilation of the first spin contaminant"), SM(r"\s*[A-Z][*][*][0-9]\s*before annihilation\s*(?P[0-9.]+),\s*after\s*(?P[0-9.]+)"), - SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P[-+0-9D.]+)"), + SM(r"\s*[()A-Z0-9]+\s*=\s*[-+0-9D.]+\s*[()A-Z0-9]+\s*=\s*(?P[-+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[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P[-+0-9EeDd.]+)"), - SM(r"\s*E3=\s*(?P[-+0-9EeDd.]+)\s*EUMP3=\s*(?P[-+0-9EeDd.]+)\s*"), - SM(r"\s*E4\(DQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(DQ\)=\s*(?P[-+0-9EeDd.]+)\s*"), - SM(r"\s*E4\(SDQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(SDQ\)=\s*(?P[-+0-9EeDd.]+)"), - SM(r"\s*E4\(SDTQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(SDTQ\)=\s*(?P[-+0-9EeDd.]+)"), - SM(r"\s*DEMP5 =\s*(?P[-+0-9EeDd.]+)\s*MP5 =\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*E2 =\s*(?P[-+0-9EeDd.]+)\s*EUMP2 =\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*E3=\s*(?P[-+0-9EeDd.]+)\s*EUMP3=\s*(?P[-+0-9EeDd.]+)\s*"), + SM(r"\s*E4\(DQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(DQ\)=\s*(?P[-+0-9EeDd.]+)\s*"), + SM(r"\s*E4\(SDQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(SDQ\)=\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*E4\(SDTQ\)=\s*(?P[-+0-9EeDd.]+)\s*UMP4\(SDTQ\)=\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*DEMP5 =\s*(?P[-+0-9EeDd.]+)\s*MP5 =\s*(?P[-+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[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), - SM(r"\s*CCSD\(T\)=\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*DE\(Corr\)=\s*(?P[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), + SM(r"\s*CCSD\(T\)=\s*(?P[-+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[-+0-9EeDd.]+)\s*E\(Z\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), - SM(r"\s*DE\(Corr\)=\s*(?P[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), - SM(r"\s*QCISD\(T\)=\s*(?P[-+0-9EeDd.]+)"), - SM(r"\s*DE5\s*=\s*(?P[-+0-9EeDd.]+)\s*QCISD\(TQ\)\s*=\s*(?P[-+0-9EeDd.]+)", repeats = True), + SM(r"\s*DE\(Z\)=\s*(?P[-+0-9EeDd.]+)\s*E\(Z\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), + SM(r"\s*DE\(Corr\)=\s*(?P[-+0-9EeDd.]+)\s*E\(CORR\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), + SM(r"\s*QCISD\(T\)=\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*DE5\s*=\s*(?P[-+0-9EeDd.]+)\s*QCISD\(TQ\)\s*=\s*(?P[-+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[-+0-9EeDd.]+)\s*E\(CI\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), + SM(r"\s*DE\(CI\)=\s*(?P[-+0-9EeDd.]+)\s*E\(CI\)=\s*(?P[-+0-9EeDd.]+)", repeats = True), ] ), SM(name = 'SemiempiricalEnergies', @@ -164,7 +174,7 @@ mainFileDescription = SM( subMatchers = [ SM(r"\s*(?P[-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[-+0-9.]+)\s*", repeats = True), - SM(r"\s*Energy=\s*(?P[-+0-9EeDd.]+)"), + SM(r"\s*Energy=\s*(?P[-+0-9EeDd.]+)"), ] ), SM(name = 'MolecularMechanicsEnergies', @@ -174,7 +184,7 @@ mainFileDescription = SM( repeats = True, subMatchers = [ SM(r"\s*(?P[a-zA-Z0-9]+\s*calculation of energy[a-z,. ]+)"), - SM(r"\s*Energy=\s*(?P[-+0-9EeDd.]+)\s*NIter=\s*[0-9.]"), + SM(r"\s*Energy=\s*(?P[-+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[0-9]+):\s*[-+0-9A-Za-z.\?]+\s*(?P[0-9.]+)\s*eV\s*[0-9.]+\s*nm\s*f=(?P[0-9.]+)\s*<[A-Z][*][*][0-9]>=(?P[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[-+0-9.]+)"), - SM(r"\s*G2\(0 K\)=\s*[-+0-9.]+\s*G2 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*G2MP2\(0 K\)=\s*[-+0-9.]+\s*G2MP2 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*G3\(0 K\)=\s*[-+0-9.]+\s*G3 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*G3MP2\(0 K\)=\s*[-+0-9.]+\s*G3MP2 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*G4\(0 K\)=\s*[-+0-9.]+\s*G4 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*G4MP2\(0 K\)=\s*[-+0-9.]+\s*G4MP2 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*CBS-4 \(0 K\)=\s*[-+0-9.]+\s*CBS-4 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*CBS-q \(0 K\)=\s*[-+0-9.]+\s*CBS-q Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*CBS-Q \(0 K\)=\s*[-+0-9.]+\s*CBS-Q Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*CBS-QB3 \(0 K\)=\s*[-+0-9.]+\s*CBS-QB3 Energy=\s*(?P[-+0-9.]+)"), - SM(r"\s*W1U \(0 K\)=\s*[-+0-9.]+\s*W1U Electronic Energy\s*(?P[-+0-9.]+)"), - SM(r"\s*W1RO \(0 K\)=\s*[-+0-9.]+\s*W1RO Electronic Energy\s*(?P[-+0-9.]+)"), - SM(r"\s*W1BD \(0 K\)=\s*[-+0-9.]+\s*W1BD Electronic Energy\s*(?P[-+0-9.]+)"), + SM(r"\s*G1\(0 K\)=\s*[-+0-9.]+\s*G1 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*G2\(0 K\)=\s*[-+0-9.]+\s*G2 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*G2MP2\(0 K\)=\s*[-+0-9.]+\s*G2MP2 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*G3\(0 K\)=\s*[-+0-9.]+\s*G3 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*G3MP2\(0 K\)=\s*[-+0-9.]+\s*G3MP2 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*G4\(0 K\)=\s*[-+0-9.]+\s*G4 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*G4MP2\(0 K\)=\s*[-+0-9.]+\s*G4MP2 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*CBS-4 \(0 K\)=\s*[-+0-9.]+\s*CBS-4 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*CBS-q \(0 K\)=\s*[-+0-9.]+\s*CBS-q Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*CBS-Q \(0 K\)=\s*[-+0-9.]+\s*CBS-Q Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*CBS-QB3 \(0 K\)=\s*[-+0-9.]+\s*CBS-QB3 Energy=\s*(?P[-+0-9.]+)"), + SM(r"\s*W1U \(0 K\)=\s*[-+0-9.]+\s*W1U Electronic Energy\s*(?P[-+0-9.]+)"), + SM(r"\s*W1RO \(0 K\)=\s*[-+0-9.]+\s*W1RO Electronic Energy\s*(?P[-+0-9.]+)"), + SM(r"\s*W1BD \(0 K\)=\s*[-+0-9.]+\s*W1BD Electronic Energy\s*(?P[-+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,