Commit bb2f7205 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
Browse files

convergence criteria

parent a59650b2
import setup_paths
import numpy as np
from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure
class ExcitingParserContext(object):
def startedParsing(self, path, parser):
self.parser=parser
def onClose_exciting_section_lattice_vectors(self, backend, gIndex, section):
latticeX = section["exciting_geometry_lattice_vector_x"]
latticeY = section["exciting_geometry_lattice_vector_y"]
latticeZ = section["exciting_geometry_lattice_vector_z"]
cell = [[latticeX[0],latticeY[0],latticeZ[0]],
[latticeX[1],latticeY[1],latticeZ[1]],
[latticeX[2],latticeY[2],latticeZ[2]]]
backend.addValue("simulation_cell", cell)
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
dirPath = os.path.dirname(self.parser.fIn.name)
dosFile = os.path.join(dirPath, "dos.xml")
bandFile = os.path.join(dirPath, "bandstructure.xml")
if os.path.exists(dosFile):
with open(dosFile) as f:
exciting_parser_dos.parseDos(f, backend)
if os.path.exists(bandFile):
with open(bandFile) as g:
exciting_parser_bandstructure.parseBand(g, backend)
mainFileDescription = \
SM(name = "root matcher",
startReStr = "",
weak = True,
subMatchers = [
SM(name = "header",
startReStr = r"\s*\|\s*EXCITING\s*(?P<program_version>[-a-zA-Z0-9]+)\s*started\s*=",
fixedStartValues={'program_name': 'exciting', 'program_basis_set_type': '(L)APW+lo' },
sections = ["section_run"],
subMatchers = [
SM(name = 'input',
startReStr = r"\|\sStarting initialization",
endReStr = r"\|\sEnding initialization",
sections = ['section_system'],
subMatchers = [
SM(startReStr = r"\sLattice vectors \(cartesian\) :",
sections = ["exciting_section_lattice_vectors"],
subMatchers = [
SM(startReStr = r"\s*(?P<exciting_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<exciting_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<exciting_geometry_lattice_vector_z__bohr>[-+0-9.]+)", repeats = True)
]),
SM(startReStr = r"\sReciprocal lattice vectors \(cartesian\) :",
sections = ["exciting_section_reciprocal_lattice_vectors"],
subMatchers = [
SM(startReStr = r"\s*(?P<exciting_geometry_reciprocal_lattice_vector_x__bohr_1>[-+0-9.]+)\s+(?P<exciting_geometry_reciprocal_lattice_vector_y__bohr_1>[-+0-9.]+)\s+(?P<exciting_geometry_reciprocal_lattice_vector_z__bohr_1>[-+0-9.]+)", repeats = True)
]),
SM(r"\s*Unit cell volume\s*:\s*(?P<exciting_unit_cell_volume__bohr3>[-0-9.]+)"),
SM(r"\s*Brillouin zone volume\s*:\s*(?P<exciting_brillouin_zone_volume__bohr_3>[-0-9.]+)"),
SM(r"\s*Species\s*:\s*[0-9]\s*\((?P<exciting_geometry_atom_labels>[-a-zA-Z0-9]+)\)", repeats = True,
subMatchers = [
SM(r"\s*muffin-tin radius\s*:\s*(?P<exciting_muffin_tin_radius__bohr>[-0-9.]+)"),
SM(r"\s*# of radial points in muffin-tin\s*:\s*(?P<exciting_muffin_tin_points>[-0-9.]+)"),
SM(startReStr = r"\s*atomic positions\s*\(lattice\)\s*:\s*",
subMatchers = [
SM(r"\s*[0-9]\s*:\s*(?P<exciting_geometry_atom_positions_x__bohr>[-+0-9.]+)\s*(?P<exciting_geometry_atom_positions_y__bohr>[-+0-9.]+)\s*(?P<exciting_geometry_atom_positions_z__bohr>[-+0-9.]+)", repeats = True)
])
]),
SM(r"\s*k-point grid\s*:\s*(?P<exciting_number_kpoint_x>[-0-9.]+)\s+(?P<exciting_number_kpoint_y>[-0-9.]+)\s+(?P<exciting_number_kpoint_z>[-0-9.]+)"),
SM(r"\s*k-point offset\s*:\s*(?P<exciting_kpoint_offset_x>[-0-9.]+)\s+(?P<exciting_kpoint_offset_y>[-0-9.]+)\s+(?P<exciting_kpoint_offset_z>[-0-9.]+)"),
SM(r"\s*Total number of k-points\s*:\s*(?P<exciting_number_kpoints>[-0-9.]+)"),
SM(r"\s*R\^MT_min \* \|G\+k\|_max \(rgkmax\)\s*:\s*(?P<exciting_rgkmax__bohr>[-0-9.]+)"),
SM(r"\s*Maximum \|G\| for potential and density\s*:\s*(?P<exciting_gmaxvr__bohr_1>[-0-9.]+)"),
SM(r"\s*G-vector grid sizes\s*:\s*(?P<exciting_gvector_size_x>[-0-9.]+)\s+(?P<exciting_gvector_size_y>[-0-9.]+)\s+(?P<exciting_gvector_size_z>[-0-9.]+)"),
SM(r"\s*Total number of G-vectors\s*:\s*(?P<exciting_gvector_total>[-0-9.]+)"),
SM(startReStr = r"\s*Maximum angular momentum used for\s*",
subMatchers = [
SM(r"\s*APW functions\s*:\s*(?P<exciting_lmaxapw>[-0-9.]+)")
]),
SM(r"\s*Total nuclear charge\s*:\s*(?P<exciting_nuclear_charge>[-0-9.]+)"),
SM(r"\s*Total electronic charge\s*:\s*(?P<exciting_electronic_charge>[-0-9.]+)"),
SM(r"\s*Total core charge\s*:\s*(?P<exciting_core_charge>[-0-9.]+)"),
SM(r"\s*Total valence charge\s*:\s*(?P<exciting_valence_charge>[-0-9.]+)"),
SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<exciting_wigner_radius>[-0-9.]+)"),
SM(r"\s*Number of empty states\s*:\s*(?P<exciting_empty_states>[-0-9.]+)"),
SM(r"\s*Total number of valence states\s*:\s*(?P<exciting_valence_states>[-0-9.]+)"),
SM(r"\s*Maximum Hamiltonian size\s*:\s*(?P<exciting_hamiltonian_size>[-0-9.]+)"),
SM(r"\s*Maximum number of plane-waves\s*:\s*(?P<exciting_pw>[-0-9.]+)"),
SM(r"\s*Total number of local-orbitals\s*:\s*(?P<exciting_lo>[-0-9.]+)"),
SM(r"\s*Smearing scheme\s*:\s*(?P<exciting_smearing_type>[-a-zA-Z0-9]+)"),
SM(r"\s*Smearing width\s*:\s*(?P<exciting_smearing_width__hartree>[-0-9.]+)"),
SM(r"\s*Using\s*(?P<exciting_potential_mixing>[-a-zA-Z\s*]+)\s*potential mixing")
]),
# SM(name = "functionals", sections = ['section_method'],
# subMatchers = [
# SM(startReStr = r"\s*Exchange-correlation type\s*:\s*(?P<exciting_xc_functional>[-0-9.]+)"),
# sections = ['section_XC_functionals']),
# xc_internal_map = {
# 2: 'LDA_C_PZ',
# 3: 'LDA_C_PW',
# 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',
# 300: 'GGA_C_BGCP',
# 406: 'HYB_GGA_C_PBEH',
# }
# self.XC_functional_name = ExcitingParserContext.xc_internal_map.get('exciting_xc_functional'))
# ]),
SM(name = "single configuration iteration",
startReStr = r"\|\s*Self-consistent loop started\s*\+",
sections = ["section_single_configuration_calculation"],
repeats = True,
subMatchers = [
SM(name = "scfi totE",
startReStr =r"\|\s*SCF iteration number\s*:",
sections = ["section_scf_iteration"],
repeats = True,
subMatchers = [
SM(r"\s*Total energy\s*:\s*(?P<energy_total_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Fermi energy\s*:\s*(?P<exciting_fermi_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Kinetic energy\s*:\s*(?P<electronic_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb energy\s*:\s*(?P<exciting_coulomb_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Exchange energy\s*:\s*(?P<exciting_exchange_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Correlation energy\s*:\s*(?P<exciting_correlation_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Effective potential energy\s*:\s*(?P<exciting_effective_potential_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb potential energy\s*:\s*(?P<exciting_coulomb_potential_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*xc potential energy\s*:\s*(?P<energy_XC_potential_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Hartree energy\s*:\s*(?P<exciting_hartree_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Electron-nuclear energy\s*:\s*(?P<exciting_electron_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Nuclear-nuclear energy\s*:\s*(?P<exciting_nuclear_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Madelung energy\s*:\s*(?P<exciting_madelung_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Core-electron kinetic energy\s*:\s*(?P<exciting_core_electron_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Absolute change in total energy (target)\s*:\s*(?P<energy_change_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*DOS at Fermi energy \(states\/Ha\/cell\)\s*:\s*(?P<exciting_dos_fermi_scf_iteration__hartree_1>[-0-9.]+)"),
SM(r"\s*core leakage\s*:\s*(?P<exciting_core_leakage_scf_iteration>[-0-9.]+)"),
SM(r"\s*interstitial\s*:\s*(?P<exciting_interstitial_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*total charge in muffin-tins\s*:\s*(?P<exciting_total_MT_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*Estimated fundamental gap\s*:\s*(?P<exciting_gap_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Wall time \(seconds\)\s*:\s*(?P<exciting_time_scf_iteration>[-0-9.]+)"),
SM(r"\s*RMS change in effective potential \(target\)\s*:\s*(?P<exciting_effective_potential_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))"),
SM(r"\s*Absolute change in total energy\s*\(target\)\s*:\s*(?P<exciting_energy_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))"),
SM(r"\s*Charge distance\s*\(target\)\s*:\s*(?P<exciting_charge_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))")
]),
SM(name="final_quantities",
startReStr = r"\| Convergence targets achieved. Performing final SCF iteration\s*\+",
endReStr = r"\| Self-consistent loop stopped\s*\+",
subMatchers = [
SM(r"\s*Total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
SM(r"\s*Fermi energy\s*:\s*(?P<exciting_fermi_energy__hartree>[-0-9.]+)"),
SM(r"\s*Kinetic energy\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb energy\s*:\s*(?P<exciting_coulomb_energy__hartree>[-0-9.]+)"),
SM(r"\s*Exchange energy\s*:\s*(?P<exciting_exchange_energy__hartree>[-0-9.]+)"),
SM(r"\s*Correlation energy\s*:\s*(?P<exciting_correlation_energy__hartree>[-0-9.]+)"),
SM(r"\s*Sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
SM(r"\s*Effective potential energy\s*:\s*(?P<exciting_effective_potential_energy__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb potential energy\s*:\s*(?P<exciting_coulomb_potential_energy__hartree>[-0-9.]+)"),
SM(r"\s*xc potential energy\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
SM(r"\s*Hartree energy\s*:\s*(?P<exciting_hartree_energy__hartree>[-0-9.]+)"),
SM(r"\s*Electron-nuclear energy\s*:\s*(?P<exciting_electron_nuclear_energy__hartree>[-0-9.]+)"),
SM(r"\s*Nuclear-nuclear energy\s*:\s*(?P<exciting_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
SM(r"\s*Madelung energy\s*:\s*(?P<exciting_madelung_energy__hartree>[-0-9.]+)"),
SM(r"\s*Core-electron kinetic energy\s*:\s*(?P<exciting_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
SM(r"\s*DOS at Fermi energy \(states\/Ha\/cell\)\s*:\s*(?P<exciting_dos_fermi__hartree_1>[-0-9.]+)"),
SM(r"\s*core leakage\s*:\s*(?P<exciting_core_leakage>[-0-9.]+)"),
SM(r"\s*interstitial\s*:\s*(?P<exciting_interstitial_charge>[-0-9.]+)"),
SM(r"\s*total charge in muffin-tins\s*:\s*(?P<exciting_total_MT_charge>[-0-9.]+)"),
SM(r"\s*Estimated fundamental gap\s*:\s*(?P<exciting_gap__hartree>[-0-9.]+)")
])
]
)
])
])
parserInfo = {
"name": "exciting_parser",
"version": "1.0"
}
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/exciting.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
cachingLevelForMetaName = {
"exciting_geometry_lattice_vector_x":CachingLevel.Cache,
"exciting_geometry_lattice_vector_y":CachingLevel.Cache,
"exciting_geometry_lattice_vector_z":CachingLevel.Cache,
"exciting_section_lattice_vectors": CachingLevel.Ignore
}
if __name__ == "__main__":
# for name in metaInfoEnv.infoKinds:
# print 'nameo', name
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext())
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<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
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<basevect> 0.0 0.5 0.5 </basevect>
</crystal>
<species speciesfile="Ag.xml">
<atom coord="0.00 0.00 0.00" />
</species>
</structure>
<groundstate
ngridk="8 8 8"
swidth="0.01"
rgkmax="7.5">
</groundstate>
</input>
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/home1/pardini/Boron10/exciting/bin/excitingser
<?xml version='1.0' encoding='UTF-8'?>
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<title>Silver</title>
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</crystal>
<species speciesfile="Ag.xml">
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<groundstate ngridk="8 8 8" swidth="0.01" rgkmax="7.5">
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 7.4198400000">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
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<species speciesfile="Ag.xml">
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
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<basevect> 0.5 0.5 0.0 </basevect>
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
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<basevect> 0.0 0.5 0.5 </basevect>
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 7.7290077290">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
<basevect> 0.0 0.5 0.5 </basevect>
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 7.8062900000">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
<basevect> 0.0 0.5 0.5 </basevect>
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<species speciesfile="Ag.xml">
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<groundstate ngridk="8 8 8" swidth="0.01" rgkmax="7.5">
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 7.8835800000">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
<basevect> 0.0 0.5 0.5 </basevect>
</crystal>
<species speciesfile="Ag.xml">
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<groundstate ngridk="8 8 8" swidth="0.01" rgkmax="7.5">
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 7.9608700000">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
<basevect> 0.0 0.5 0.5 </basevect>
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<species speciesfile="Ag.xml">
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</structure>
<groundstate ngridk="8 8 8" swidth="0.01" rgkmax="7.5">
</groundstate>
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 8.0381600000">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
<basevect> 0.0 0.5 0.5 </basevect>
</crystal>
<species speciesfile="Ag.xml">
<atom coord="0.00 0.00 0.00"/>
</species>
</structure>
<groundstate ngridk="8 8 8" swidth="0.01" rgkmax="7.5">
</groundstate>
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<?xml version='1.0' encoding='UTF-8'?>
<input>
<title>Silver</title>
<structure speciespath="/home1/pardini/Boron10/exciting/species">
<crystal scale=" 8.1154500000">
<basevect> 0.5 0.5 0.0 </basevect>
<basevect> 0.5 0.0 0.5 </basevect>
<basevect> 0.0 0.5 0.5 </basevect>
</crystal>
<species speciesfile="Ag.xml">
<atom coord="0.00 0.00 0.00"/>
</species>
</structure>
<groundstate ngridk="8 8 8" swidth="0.01" rgkmax="7.5">
</groundstate>
</input>
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