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parser-gaussian
Commit 319583f0 authored by Rosendo Valero Montero's avatar Rosendo Valero Montero
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Improved Gaussian parser with alternative parsing for eigenvalues and hybrid coefficients

parent 11486bc2
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Showing with 52 additions and 22 deletions
parser/parser-gaussian/parser_gaussian.py
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......@@ -72,7 +72,7 @@ mainFileDescription = SM(
forwardMatch = True,
subMatchers = [
SM(r"\s*Charge =\s*(?P<x_gaussian_total_charge>[-+0-9]*) Multiplicity =\s*(?P<x_gaussian_spin_target_multiplicity>[0-9]*)"),
SM(r"\s*(Tv|Tv\s*[0]|TV|TV\s*[0])\s*(?P<x_gaussian_geometry_lattice_vector_x>[0-9.]*)\s+(?P<x_gaussian_geometry_lattice_vector_y>[0-9.]*)\s+(?P<x_gaussian_geometry_lattice_vector_z>[0-9.]*)", repeats = True),
SM(r"\s*(Tv|Tv\s*[0]|TV|TV\s*[0])\s*(?P<x_gaussian_geometry_lattice_vector_x>[0-9.]+)\s+(?P<x_gaussian_geometry_lattice_vector_y>[0-9.]+)\s+(?P<x_gaussian_geometry_lattice_vector_z>[0-9.]+)", repeats = True),
SM(r"\s*AtmWgt=\s+(?P<x_gaussian_atomic_masses>[0-9.]+(\s+[0-9.]+)(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?(\s+[0-9.]+)?)", repeats = True)
]
),
......@@ -92,7 +92,7 @@ mainFileDescription = SM(
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+[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")
]
),
......@@ -101,8 +101,9 @@ mainFileDescription = SM(
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*IExCor=\s*[0-9-]+\s*DFT=[A-Z]\s*Ex\+Corr=[a-zA-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-zA-Z0-9+]+\s*Corr=[ a-zA-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-zA-Z0-9+]+\s*Corr=[ a-zA-Z0-9]+\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.]+)")
]
),
......@@ -259,10 +260,10 @@ mainFileDescription = SM(
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*Alpha occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*Alpha virt. eigenvalues --\s+(?P<x_gaussian_alpha_vir_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*Beta occ. eigenvalues --\s+(?P<x_gaussian_beta_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*Beta virt. eigenvalues --\s+(?P<x_gaussian_beta_vir_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*- Condensed to atoms (all electrons)"),
]
),
......@@ -341,7 +342,7 @@ mainFileDescription = SM(
forwardMatch = True,
subMatchers = [
SM(r"\s*Force constants in Cartesian coordinates"),
SM(r"\s*[0-9]+\s*(?P<x_gaussian_force_constants>(\-?\d+\.\d*[-+D0-9]+)\s*(\-?\d+\.\d*[-+D0-9]+)?\s*(\-?\d+\.\d*[-+D0-9]+)?\s*(\-?\d+\.\d*[-+D0-9]+)?\s*(\-?\d+\.\d*[-+D0-9]+)?)", repeats = True),
SM(r"\s*[0-9]+\s*(?P<x_gaussian_force_constants>(-?\d*\.\d*D?\+?\-?\d+)|(\-?\d*\.\d*[-+DE0-9]+)\s*(\-?\d*\.\d*[-+DE0-9]+)?\s*(\-?\d*\.\d*[-+DE0-9]+)?\s*(\-?\d*\.\d*[-+DE0-9]+)?\s*(\-?\d*\.\d*[-+DE0-9]+)?)", repeats = True),
SM(r"\s*Force constants in internal coordinates")
]
),
......@@ -544,7 +545,10 @@ class GaussianParserContext(object):
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()]
if('*' in eigenenergies):
energy = [0.0]
else:
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
eigenen1 = np.append(eigenen1, energy)
if(section["x_gaussian_beta_occ_eigenvalues_values"]):
occoccupationsalp = np.ones(len(eigenen1), dtype=float)
......@@ -553,10 +557,13 @@ class GaussianParserContext(object):
eigenenergies = str(section["x_gaussian_alpha_vir_eigenvalues_values"])
eigenen2 = []
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
if('*' in eigenenergies):
energy = [0.0]
else:
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)
eigenenconalp = np.zeros(len(eigenen1) + len(eigenen2))
leneigenenconalp = len(eigenen1) + len(eigenen2)
eigenenconalp = np.concatenate((eigenen1,eigenen2), axis=0)
eigenenconalp = convert_unit(eigenenconalp, "hartree", "J")
occupconalp = np.concatenate((occoccupationsalp, viroccupationsalp), axis=0)
......@@ -571,22 +578,34 @@ class GaussianParserContext(object):
if(section["x_gaussian_beta_occ_eigenvalues_values"]):
eigenenergies = str(section["x_gaussian_beta_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()]
if('*' in eigenenergies):
energy = [0.0]
else:
energy = [float(f) for f in eigenenergies[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").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("]","").replace("one","").replace(" ."," 0.").replace(" -."," -0.").replace("\\n","").replace("-"," -").split()]
if('*' in eigenenergies):
energy = [0.0]
else:
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)
eigenenconbet = np.zeros(len(eigenen1) + len(eigenen2))
leneigenenconbet = 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)))
if(leneigenenconalp >= leneigenenconbet):
eigenenall = np.zeros(2*leneigenenconalp)
occupall = np.zeros(2*leneigenenconalp)
else:
eigenenall = np.zeros(2*leneigenenconbet)
occupall = np.zeros(2*leneigenenconbet)
eigenenall[:len(eigenenconalp) + len(eigenenconbet)] = np.concatenate((eigenenconalp,eigenenconbet), axis=0)
occupall[:len(occupconalp) + len(occupconbet)] = np.concatenate((occupconalp,occupconbet), axis=0)
eigenenall = np.reshape(eigenenall,(2, 1, max(len(eigenenconalp),len(eigenenconbet))))
occupall = np.reshape(occupall,(2, 1, max(len(occupconalp),len(occupconbet))))
backend.addArrayValues("eigenvalues_values", eigenenall)
backend.addArrayValues("eigenvalues_occupation", occupall)
......@@ -1016,6 +1035,7 @@ class GaussianParserContext(object):
'OLDSDD': [{'name': 'OldSDD'}],
'SDDALL': [{'name': 'SDDAll'}],
'GEN': [{'name': 'General'}],
'GENECP': [{'name': 'General ECP'}],
'CHKBAS': [{'name': 'CHKBAS'}],
'EXTRABASIS': [{'name': 'ExtraBasis'}],
'DGA1': [{'name': 'DGA1'}],
......@@ -1172,7 +1192,13 @@ class GaussianParserContext(object):
if z in basissetDict.keys():
basisset = z
basissetWrite = True
basissetreal = rest2.split('/')[1] + '/' + basisset
if (len(rest2.split('/')) == 2):
if(basisset is not None):
basissetreal = rest2.split('/')[1] + '/' + basisset
else:
basissetreal = rest2.split('/')[1]
else:
pass
else:
method1 = settings.split()
for x in method1:
......@@ -1357,7 +1383,10 @@ class GaussianParserContext(object):
hybrid_xc_coeffsa = ()
hybrid_xc_coeffsb = ()
hybrid_xc_coeffsa = float(str(section['hybrid_xc_coeff1']).replace("[","").replace("]",""))
if(str(section['hybrid_xc_coeff1']) != 'None'):
hybrid_xc_coeffsa = float(str(section['hybrid_xc_coeff1']).replace("[","").replace("]",""))
else:
hybrid_xc_coeffsa = 0.0
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()]
......@@ -1375,7 +1404,8 @@ class GaussianParserContext(object):
uci = uci.split()
for i in range(len(uci)):
uci[i] = str(uci[i]).replace("[","").replace("'","").replace("]","").replace("\"","").replace(",","")
uci[i] = float(uci[i])
if uci[i] is not None:
uci[i] = float(uci[i])
if uci is not None:
uci = convert_unit(uci, "angstrom", "m")
unit_cell.append(uci)
......
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