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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
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    Showing with 50 additions and 47 deletions
    parser/parser-elk/parser_elk.py
    View file @ d20ec712
    ......@@ -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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