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Commit d20ec712 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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fixed bugs with atomic structure, total energy, xc functional

parent 4820d09d
Pipeline #7795 passed with stage
in 12 minutes and 11 seconds
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parser/parser-elk/parser_elk.py
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......@@ -30,6 +30,7 @@ class ElkContext(object):
cell = [[latticeX[0],latticeY[0],latticeZ[0]],
[latticeX[1],latticeY[1],latticeZ[1]],
[latticeX[2],latticeY[2],latticeZ[2]]]
# print ("celll= ", cell)
backend.addValue("simulation_cell", cell)
def onClose_x_elk_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
......@@ -45,14 +46,14 @@ class ElkContext(object):
xcNr = section["x_elk_xc_functional"][0]
xc_internal_map = {
2: ['LDA_C_PZ', 'LDA_X_PZ'],
3: ['LDA_C_PW'],
3: ['LDA_C_PW', 'LDA_X_PZ'],
4: ['LDA_C_XALPHA'],
5: ['LDA_C_VBH'],
20: ['GGA_C_PBE'],
21: ['GGA_X_PBE_R'],
22: ['GGA_C_PBE_SOL'],
26: ['GGA_X_WC'],
30: ['GGA_C_AM05']
20: ['GGA_C_PBE', 'GGA_X_PBE'],
21: ['GGA_C_PBE', 'GGA_X_PBE_R'],
22: ['GGA_C_PBE_SOL', 'GGA_X_PBE_SOL'],
26: ['GGA_C_PBE', 'GGA_X_WC'],
30: ['GGA_C_AM05', 'GGA_X_AM05']
}
for xcName in xc_internal_map[xcNr]:
gi = backend.openSection("section_XC_functionals")
......@@ -87,26 +88,17 @@ class ElkContext(object):
eigvalKpoint=[]
eigvalVal=[]
eigvalOcc=[]
# eigvalVal=[[],[]]
# eigvalOcc=[[],[]]
fromH = unit_conversion.convert_unit_function("hartree", "J")
while 1:
s = g.readline()
if not s: break
s = s.strip()
# print ("s= ", s)
# print ("len(s)= ", len(s))
if len(s) < 20:
continue
elif len(s) > 50:
eigvalVal.append([])
eigvalOcc.append([])
# eigvalVal[0].append([])
# eigvalVal[1].append([])
# eigvalOcc[0].append([])
# eigvalOcc[1].append([])
eigvalKpoint.append(list(map(float, s.split()[1:4])))
# print ("eigvalKpoint= ", eigvalKpoint)
else:
try: int(s[0])
except ValueError:
......@@ -115,17 +107,28 @@ class ElkContext(object):
n, e, occ = s.split()
eigvalVal[-1].append(fromH(float(e)))
eigvalOcc[-1].append(float(occ))
# eigvalVal[0][-1].append(int(n))
# eigvalVal[1][-1].append(fromH(float(e)))
# eigvalOcc[0][-1].append(int(n))
# eigvalOcc[1][-1].append(float(occ))
# print ("eigvalOcc= ", eigvalOcc)
backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint))
backend.addArrayValues("eigenvalues_values", np.asarray(eigvalVal))
backend.addArrayValues("eigenvalues_occupation", np.asarray(eigvalOcc))
def onClose_section_system(self, backend, gIndex, section):
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
self.secSystemDescriptionIndex = gIndex
atom_pos = []
for i in ['x', 'y', 'z']:
api = section['x_elk_geometry_atom_positions_' + i]
if api is not None:
atom_pos.append(api)
if atom_pos:
backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
atom_labels = section['x_elk_geometry_atom_labels']
if atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
def onClose_section_scf_iteration(self, backend, gIndex, section):
Etot = section["energy_total_scf_iteration"]
backend.addValue("energy_total", Etot)
# description of the input
mainFileDescription = \
......@@ -222,33 +225,33 @@ mainFileDescription = \
SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_scf_iteration>[-0-9.]+)"),
]),
SM(name="final_quantities",
startReStr = r"\sConvergence targets achieved\s*\+",
endReStr = r"\| Self-consistent loop stopped\s*\|\+",
subMatchers = [
SM(r"\s*Fermi\s*:\s*(?P<x_elk_fermi_energy__hartree>[-0-9.]+)"),
SM(r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
SM(r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy__hartree>[-0-9.]+)"),
SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy__hartree>[-0-9.]+)"),
SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy__hartree>[-0-9.]+)"),
SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy__hartree>[-0-9.]+)"),
SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy__hartree>[-0-9.]+)"),
SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy__hartree>[-0-9.]+)"),
SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy__hartree>[-0-9.]+)"),
SM(r"\s*total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi__hartree_1>[-0-9.]+)"),
SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap__hartree>[-0-9.]+)"),
SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap__hartree>[-0-9.]+)"),
SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_final>[-0-9.]+)"),
SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_final>[-0-9.]+)"),
SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_final>[-0-9.]+)")
])
]) #,
# SM(name="final_quantities",
# startReStr = r"\sConvergence targets achieved\s*\+",
# endReStr = r"\| Self-consistent loop stopped\s*\|\+",
# subMatchers = [
# SM(r"\s*Fermi\s*:\s*(?P<x_elk_fermi_energy__hartree>[-0-9.]+)"),
# SM(r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
# SM(r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
# SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy__hartree>[-0-9.]+)"),
# SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
# SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy__hartree>[-0-9.]+)"),
# SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
# SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy__hartree>[-0-9.]+)"),
# SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy__hartree>[-0-9.]+)"),
# SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy__hartree>[-0-9.]+)"),
# SM(r"\s*total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
# SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi__hartree_1>[-0-9.]+)"),
# SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap__hartree>[-0-9.]+)"),
# SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap__hartree>[-0-9.]+)"),
# SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_final>[-0-9.]+)"),
# SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_final>[-0-9.]+)"),
# SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_final>[-0-9.]+)")
# ])
]
)
])
......
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