Skip to content

GitLab

P
parser-elk
Commit d820a7fd authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
Browse files
Options

dos + tests

parent 53870bbf
Pipeline #6710 passed with stage
    in 5 minutes and 9 seconds
    Hide whitespace changes
    Inline Side-by-side
    Showing with 24791 additions and 2735 deletions
    parser/parser-elk/elk_parser_dos.py deleted 100644 → 0
    View file @ 53870bbf
    import xml.sax
    import logging
    class DosHandler(xml.sax.handler.ContentHandler):
    def __init__(self, backend):
    self.backend = backend
    self.dosSectionGIndex = -1
    self.inDos = False
    def endDocument(self):
    pass
    def startElement(self, name, attrs):
    if name == "dos":
    self.dosSectionGIndex = self.backend.openSection("x_exciting_section_dos")
    self.inDos = True
    elif name == "point" and self.inDos:
    self.backend.addValue("x_exciting_dos_value",float(attrs.getValue('dos')))
    self.backend.addValue("x_exciting_dos_energy",float(attrs.getValue('e')))
    # attrDict={}
    # for name in attrs.getNames():
    # attrDict[name] = attrs.getValue(name)
    # logging.error("start element %s attr %s", name, attrDict)
    def endElement(self, name):
    if name == 'dos':
    self.inDos = False
    self.backend.closeSection("x_exciting_section_dos",self.dosSectionGIndex)
    self.dosSectionGIndex = -1
    # logging.error("end element %s", name)
    def startElementNS(self, name, qname, attrs):
    attrDict={}
    for name in attrs.getNames():
    attrDict[name] = attrs.getValue(name)
    logging.error("start element %s ns %s attr %s", name, qname, attrDict)
    def endElementNS(self, name, qname):
    logging.error("end element %s ns %s", name, qname)
    def characters(self, content):
    pass
    def parseDos(inF, backend):
    handler = DosHandler(backend)
    logging.error("will parse")
    xml.sax.parse(inF, handler)
    logging.error("did parse")
    parser/parser-elk/out deleted 100644 → 0
    View file @ 53870bbf
    [{
    "type": "nomad_parse_events_1_0",
    "mainFileUri": "file://../../test/examples/GaAs/INFO.OUT",
    "parserInfo": {
    "name":"Elk"
    },
    "events": [{
    "event":"openSection",
    "gIndex":0,
    "metaName":"section_run"
    }, {
    "event":"openSection",
    "gIndex":0,
    "metaName":"section_method"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"program_version",
    "value":"4.0.15"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"program_basis_set_type",
    "value":"(L)APW+lo"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"program_name",
    "value":"elk"
    }, {
    "event":"openSection",
    "gIndex":0,
    "metaName":"section_system"
    }, {
    "event":"openSection",
    "gIndex":0,
    "metaName":"x_elk_section_lattice_vectors"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_x",
    "value":2.827658425215145e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_y",
    "value":2.827658425215145e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_z",
    "value":0.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_x",
    "value":2.827658425215145e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_y",
    "value":0.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_z",
    "value":2.827658425215145e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_x",
    "value":0.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_y",
    "value":2.827658425215145e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_lattice_vector_z",
    "value":2.827658425215145e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"simulation_cell",
    "value":[
    [
    2.827658425215145e-10,
    2.827658425215145e-10,
    0.0
    ],
    [
    2.827658425215145e-10,
    0.0,
    2.827658425215145e-10
    ],
    [
    0.0,
    2.827658425215145e-10,
    2.827658425215145e-10
    ]
    ]
    }, {
    "event":"closeSection",
    "gIndex":0,
    "metaName":"x_elk_section_lattice_vectors"
    }, {
    "event":"openSection",
    "gIndex":0,
    "metaName":"x_elk_section_reciprocal_lattice_vectors"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_x",
    "value":11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_y",
    "value":11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_z",
    "value":-11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_x",
    "value":11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_y",
    "value":-11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_z",
    "value":11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_x",
    "value":-11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_y",
    "value":11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_reciprocal_lattice_vector_z",
    "value":11110226841.696657
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_simulation_reciprocal_cell",
    "value":[
    [
    11110226841.696657,
    11110226841.696657,
    -11110226841.696657
    ],
    [
    11110226841.696657,
    -11110226841.696657,
    11110226841.696657
    ],
    [
    -11110226841.696657,
    11110226841.696657,
    11110226841.696657
    ]
    ]
    }, {
    "event":"closeSection",
    "gIndex":0,
    "metaName":"x_elk_section_reciprocal_lattice_vectors"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_unit_cell_volume",
    "value":4.521794644902194e-29
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_brillouin_zone_volume",
    "value":5.485658525754647e+30
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_labels",
    "value":"Ga"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_muffin_tin_radius",
    "value":1.2111825846962275e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_muffin_tin_points",
    "value":497
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_number",
    "value":"1"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_positions_x",
    "value":0.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_positions_y",
    "value":0.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_positions_z",
    "value":0.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_labels",
    "value":"As"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_muffin_tin_radius",
    "value":1.2111825846962275e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_muffin_tin_points",
    "value":497
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_number",
    "value":"1"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_positions_x",
    "value":1.322943026675e-11
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_positions_y",
    "value":1.322943026675e-11
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_geometry_atom_positions_z",
    "value":1.322943026675e-11
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_number_kpoint_x",
    "value":4
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_number_kpoint_y",
    "value":4
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_number_kpoint_z",
    "value":4
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_kpoint_offset_x",
    "value":0.5
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_kpoint_offset_y",
    "value":0.5
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_kpoint_offset_z",
    "value":0.5
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_number_kpoints",
    "value":20
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_rgkmax",
    "value":3.70424047469e-10
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_gkmax",
    "value":57794754391.024345
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_gmaxvr",
    "value":226767135054.9394
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_gvector_size_x",
    "value":30
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_gvector_size_y",
    "value":30
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_gvector_size_z",
    "value":30
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_gvector_total",
    "value":8873
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_lmaxapw",
    "value":8
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_nuclear_charge",
    "value":-64.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_core_charge",
    "value":36.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_valence_charge",
    "value":28.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_electronic_charge",
    "value":64.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_wigner_radius",
    "value":1.04411007
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_empty_states",
    "value":8
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_valence_states",
    "value":23
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_core_states",
    "value":36
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_lo",
    "value":29
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_smearing_width",
    "value":4.359743940000001e-19
    }, {
    "event":"addArrayValues",
    "flatValues":[
    true,
    true,
    true
    ],
    "gIndex":-1,
    "metaName":"configuration_periodic_dimensions",
    "valuesShape":[
    3
    ]
    }, {
    "event":"closeSection",
    "gIndex":0,
    "metaName":"section_system"
    }, {
    "event":"openSection",
    "gIndex":0,
    "metaName":"section_single_configuration_calculation"
    }, {
    "event":"openSection",
    "gIndex":0,
    "metaName":"section_scf_iteration"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_fermi_energy_scf_iteration",
    "value":4.530334567465577e-19
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"energy_sum_eigenvalues_scf_iteration",
    "value":-1.0587324815035128e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"electronic_kinetic_energy_scf_iteration",
    "value":1.8699206079776878e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_core_electron_kinetic_energy_scf_iteration",
    "value":1.7344928741100222e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_coulomb_energy_scf_iteration",
    "value":-3.636366408302897e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_coulomb_potential_energy_scf_iteration",
    "value":-2.8381471017426835e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_nuclear_nuclear_energy_scf_iteration",
    "value":-1.9015940652939077e-15
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_electron_nuclear_energy_scf_iteration",
    "value":-4.054266901804329e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_hartree_energy_scf_iteration",
    "value":6.080599000286431e-15
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_madelung_energy_scf_iteration",
    "value":-2.2172928574315558e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"energy_XC_potential_scf_iteration",
    "value":-9.05059877402612e-16
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_exchange_energy_scf_iteration",
    "value":-6.822152812135417e-16
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_correlation_energy_scf_iteration",
    "value":-1.361718537796743e-17
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_electron_entropic_energy_scf_iteration",
    "value":-1.8633973037575367e-18
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"energy_total_scf_iteration",
    "value":-1.8360290469851233e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_dos_fermi_scf_iteration",
    "value":3.402698455267535e+16
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_indirect_gap_scf_iteration",
    "value":2.424591884340468e-18
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_direct_gap_scf_iteration",
    "value":3.0857173812961615e-18
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_core_charge_scf_iteration",
    "value":36.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_valence_charge_scf_iteration",
    "value":28.0
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_interstitial_charge_scf_iteration",
    "value":3.216153569
    }, {
    "event":"closeSection",
    "gIndex":0,
    "metaName":"section_scf_iteration"
    }, {
    "event":"openSection",
    "gIndex":1,
    "metaName":"section_scf_iteration"
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_fermi_energy_scf_iteration",
    "value":4.928703345174187e-19
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"energy_sum_eigenvalues_scf_iteration",
    "value":-1.0584670671110853e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"electronic_kinetic_energy_scf_iteration",
    "value":1.8701675091883265e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_core_electron_kinetic_energy_scf_iteration",
    "value":1.7344196042228485e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_coulomb_energy_scf_iteration",
    "value":-3.636354965117308e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_coulomb_potential_energy_scf_iteration",
    "value":-2.8381277044048237e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_nuclear_nuclear_energy_scf_iteration",
    "value":-1.9015940652939077e-15
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_electron_nuclear_energy_scf_iteration",
    "value":-4.05426341277101e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_hartree_energy_scf_iteration",
    "value":6.0806785418091345e-15
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_madelung_energy_scf_iteration",
    "value":-2.2172911129148958e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"energy_XC_potential_scf_iteration",
    "value":-9.050687189240846e-16
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_exchange_energy_scf_iteration",
    "value":-6.82219764172565e-16
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_correlation_energy_scf_iteration",
    "value":-1.3618003209253903e-17
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_electron_entropic_energy_scf_iteration",
    "value":-4.001825220412249e-18
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"energy_total_scf_iteration",
    "value":-1.835771232668362e-14
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_dos_fermi_scf_iteration",
    "value":7.516134653999886e+16
    }, {
    "event":"addValue",
    "gIndex":-1,
    "metaName":"x_elk_indirect_gap_scf_iteration",
    "value":2.355470350202202e-18