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Markus Scheidgen authoredMarkus Scheidgen authored
wien2k_parser.py 15.45 KiB
from builtins import object
from wien2kparser import setup_paths
import numpy as np
from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
import os, sys, json, logging
from wien2kparser import wien2k_parser_struct, wien2k_parser_in0, wien2k_parser_in1c, wien2k_parser_in2c, wien2k_parser_in1, wien2k_parser_in2
################################################################
# This is the parser for the main output file (.scf) of WIEN2k.
################################################################
# Copyright 2016-2018 Daria M. Tomecka, Fawzi Mohamed
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
__author__ = "Daria M. Tomecka"
__maintainer__ = "Daria M. Tomecka"
__email__ = "tomeckadm@gmail.com;"
__date__ = "15/05/2017"
class Wien2kContext(object):
"""context for wien2k parser"""
def __init__(self):
self.parser = None
def initialize_values(self):
"""allows to reset values if the same superContext is used to parse different files"""
self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
self.rootSecMethodIndex = None
self.secMethodIndex = None
self.secSystemIndex = None
self.scfIterNr = 0
def startedParsing(self, path, parser):
"""called when parsing starts"""
self.parser = parser
# allows to reset values if the same superContext is used to parse different files
self.initialize_values()
def onClose_x_wien2k_header(self, backend, gIndex, section):
version_check = section["x_wien2k_version"]
# riprova = section["x_wien2k_release_date"][0]
# print("prova=",prova," riprova=",riprova)
if version_check:
backend.addValue("program_version",
section["x_wien2k_version"][0] + " " +
section["x_wien2k_release_date"][0])
else:
backend.addValue("program_version", "Before_wien2k11")
def onOpen_section_system(self, backend, gIndex, section):
self.secSystemIndex = gIndex
def onOpen_section_method(self, backend, gIndex, section):
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".in0"
if os.path.exists(fName):
subSuperContext = wien2k_parser_in0.Wien2kIn0Context()
subParser = AncillaryParser(
fileDescription = wien2k_parser_in0.buildIn0Matchers(),
parser = self.parser,
cachingLevelForMetaName = wien2k_parser_in0.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = subSuperContext)
with open(fName) as fIn:
subParser.parseFile(fIn)
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".in1c"
if os.path.exists(fName):
subSuperContext = wien2k_parser_in1c.Wien2kIn1cContext()
subParser = AncillaryParser(
fileDescription = wien2k_parser_in1c.buildIn1cMatchers(),
parser = self.parser,
cachingLevelForMetaName = wien2k_parser_in1c.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = subSuperContext)
with open(fName) as fIn:
subParser.parseFile(fIn)
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".in2c"
if os.path.exists(fName):
subSuperContext = wien2k_parser_in2c.Wien2kIn2cContext()
subParser = AncillaryParser(
fileDescription = wien2k_parser_in2c.buildIn2cMatchers(),
parser = self.parser,
cachingLevelForMetaName = wien2k_parser_in2c.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = subSuperContext)
with open(fName) as fIn:
subParser.parseFile(fIn)
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".in1"
if os.path.exists(fName):
subSuperContext = wien2k_parser_in1.Wien2kIn1Context()
subParser = AncillaryParser(
fileDescription = wien2k_parser_in1.buildIn1Matchers(),
parser = self.parser,
cachingLevelForMetaName = wien2k_parser_in1.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = subSuperContext)
with open(fName) as fIn:
subParser.parseFile(fIn)
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".in2"
if os.path.exists(fName):
subSuperContext = wien2k_parser_in2.Wien2kIn2Context()
subParser = AncillaryParser(
fileDescription = wien2k_parser_in2.buildIn2Matchers(),
parser = self.parser,
cachingLevelForMetaName = wien2k_parser_in2.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = subSuperContext)
with open(fName) as fIn:
subParser.parseFile(fIn)
#if self.secMethodIndex is None:
if self.rootSecMethodIndex is None:
self.rootSecMethodIndex = gIndex
self.secMethodIndex = gIndex
# self.secMethodIndex["single_configuration_to_calculation_method_ref"] = gIndex
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
# write number of SCF iterations
backend.addValue('number_of_scf_iterations', self.scfIterNr)
# write the references to section_method and section_system
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex)
def onClose_section_system(self, backend, gIndex, section):
#backend.addValue("smearing_kind", x_fleur_smearing_kind)
smearing_kind = section['x_wien2k_smearing_kind']
if smearing_kind is not None:
# value = ''
backend.addValue('x_wien2k_smearing_kind', value)
smearing_width = section['x_wien2k_smearing_width']
if smearing_width is not None:
# value = ''
backend.addValue('x_wien2k_smearing_width', value)
# atom labels
atom_labels = section['x_wien2k_atom_name']
if atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
# atom force
atom_force = []
for i in ['x', 'y', 'z']:
api = section['x_wien2k_for_' + i]
if api is not None:
atom_force.append(api)
if atom_force:
# need to transpose array since its shape is [number_of_atoms,3] in\the metadata
backend.addArrayValues('atom_forces', np.transpose(np.asarray(atom_force)))
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".struct"
if os.path.exists(fName):
structSuperContext = wien2k_parser_struct.Wien2kStructContext()
structParser = AncillaryParser(
fileDescription = wien2k_parser_struct.buildStructureMatchers(),
parser = self.parser,
cachingLevelForMetaName = wien2k_parser_struct.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = structSuperContext)
with open(fName) as fIn:
structParser.parseFile(fIn)
def onClose_section_scf_iteration(self, backend, gIndex, section):
#Trigger called when section_scf_iteration is closed.
# count number of SCF iterations
self.scfIterNr += 1
# description of the input
mainFileDescription = SM(
name = 'root',
weak = True,
startReStr = "",
sections = ['section_run','x_wien2k_header'],
subMatchers = [
SM(r"\s*:LABEL[0-9]+: using WIEN2k_(?P<x_wien2k_version>[0-9.]+) \(Release (?P<x_wien2k_release_date>[0-9/.]+)\) in "),
SM(name = 'newRun',
# subMatchers=[
# SM(r"\s*:LABEL[0-9]+: using WIEN2k_(?P<x_wien2k_version>[0-9.]+) \(Release (?P<x_wien2k_release_date>[0-9/.]+)\) in ")
# ],
startReStr = r"\s*:ITE[0-9]+:\s*[0-9]+.\s*ITERATION",
repeats = True,
required = True,
forwardMatch = True,
sections = ['section_method', 'section_system', 'section_single_configuration_calculation'],
fixedStartValues={'program_name': 'WIEN2k', 'program_basis_set_type': '(L)APW+lo' }, #, 'program_version': 'Before WIEN2k_11'},
subMatchers = [
SM(
name = "scf iteration",
startReStr = r"\s*:ITE(?P<x_wien2k_iteration_number>[0-9]+):\s*[0-9]*. ITERATION",
sections=["section_scf_iteration"],
repeats = True,
subMatchers=[
SM(r":NATO\s*:\s*(?P<x_wien2k_nr_of_independent_atoms>[0-9]+)\s*INDEPENDENT AND\s*(?P<x_wien2k_total_atoms>[0-9]+)\s*TOTAL ATOMS IN UNITCELL"),
SM(r"\s*SUBSTANCE: (?P<x_wien2k_system_name>.*)"),
SM(r":POT\s*:\s*POTENTIAL OPTION\s*(?P<x_wien2k_potential_option>[0-9]+)"),
SM(r":LAT\s*:\s*LATTICE CONSTANTS=\s*(?P<x_wien2k_lattice_const_a>[0-9.]+)\s*(?P<x_wien2k_lattice_const_b>[0-9.]+)\s*(?P<x_wien2k_lattice_const_c>[0-9.]+)"),
SM(r":VOL\s*:\s*UNIT CELL VOLUME\s*=\s*(?P<x_wien2k_unit_cell_volume_bohr3>[0-9.]+)"),
SM(r":RKM : MATRIX SIZE (?P<x_wien2k_matrix_size>[0-9]+)\s*LOs:\s*(?P<x_wien2k_LOs>[0-9.]+)\s*RKM=\s*(?P<x_wien2k_rkm>[0-9.]+)\s*WEIGHT=\s*[0-9.]*\s*\w*:"),
SM(r":KPT\s*:\s*NUMBER\s*OF\s*K-POINTS:\s*(?P<x_wien2k_nr_kpts>[-+0-9.]+)"),
#SM(r":GMA\s*:\s*POTENTIAL\sAND\sCHARGE\sCUT-OFF\s*(?P<x_wien2k_cutoff>[0-9.]+)\s*Ry\*\*[0-9.]+"),
SM(r":GMA\s*:\s*POTENTIAL\sAND\sCHARGE\sCUT-OFF\s*(?P<x_wien2k_cutoff>[0-9.]+)\s*Ry\W\W[0-9.]+"),
SM(r":GAP\s*:\s*(?P<x_wien2k_ene_gap__rydberg>[-+0-9.]+)\s*Ry\s*=\s*(?P<x_wien2k_ene_gap_eV>[-+0-9.]+)\s*eV\s*.*"),
SM(r":NOE\s*:\s*NUMBER\sOF\sELECTRONS\s*=\s*(?P<x_wien2k_noe>[0-9.]+)"),
SM(r":FER\s*:\s(\w*\s*)*-\s\w*\W\w*\WM\W*=\s*(?P<x_wien2k_fermi_ene__rydberg>[-+0-9.]+)"),
SM(r":GMA\s*:\s*POTENTIAL\sAND\sCHARGE\sCUT-OFF\s*[0-9.]+\s*Ry\W\W[0-9.]+"),
SM(r":CHA(?P<x_wien2k_atom_nr>[-+0-9]+):\s*TOTAL\s*\w*\s*CHARGE INSIDE SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_val_charge_sphere>[0-9.]+)",repeats = True),
SM(r":CHA\s*:\s*TOTAL\s*\w*\s*CHARGE INSIDE\s*\w*\s*CELL\s=\s*(?P<x_wien2k_tot_val_charge_cell>[-+0-9.]+)"),
SM(r":MMTOT: TOTAL MAGNETIC MOMENT IN CELL =\s*(?P<x_wien2k_mmtot>[-+0-9.]+)"),
SM(r":MMINT: MAGNETIC MOMENT IN INTERSTITIAL =\s*(?P<x_wien2k_mmint>[-+0-9.]+)"),
SM(r":MMI001: MAGNETIC MOMENT IN SPHERE 1 =\s*(?P<x_wien2k_mmi001>[-+0-9.]+)"),
SM(r":RTO(?P<x_wien2k_atom_nr>[-+0-9]+)\s*:\s*[0-9]+\s*(?P<x_wien2k_density_at_nucleus_valence>[-+0-9.]+)\s*(?P<x_wien2k_density_at_nucleus_semicore>[-+0-9.]+)\s*(?P<x_wien2k_density_at_nucleus_core>[-+0-9.]+)\s*(?P<x_wien2k_density_at_nucleus_tot>[0-9.]+)",repeats = True),
SM(r":NTO\s*:\s*\sTOTAL\s*INTERSTITIAL\s*CHARGE=\s*(?P<x_wien2k_tot_int_charge_nm>[-+0-9.]+)"),
SM(r":NTO(?P<x_wien2k_atom_nr>[-+0-9]+)[0-9]*:\s*\sTOTAL\s*CHARGE\s*IN\s*SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_charge_in_sphere_nm>[-+0-9.]+)",repeats = True),
SM(r":DTO(?P<x_wien2k_atom_nr>[-+0-9]+)[0-9]*:\sTOTAL\s*DIFFERENCE\s*CHARGE\W*\w*\s*IN\s*SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_diff_charge>[-+0-9.]+)", repeats = True),
SM(r":DIS\s*:\s*CHARGE\sDISTANCE\s*\W*[0-9.]+\sfor\satom\s*[0-9]*\sspin\s[0-9]*\W\s*(?P<x_wien2k_charge_distance>[0-9.]+)"),
SM(r":CTO\s*:\s*\sTOTAL\s*INTERSTITIAL\s*CHARGE=\s*(?P<x_wien2k_tot_int_charge>[-+0-9.]+)"),
SM(r":CTO(?P<x_wien2k_atom_nr>[-+0-9]+)[0-9]*:\s*\sTOTAL\s*CHARGE\s*IN\s*SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_charge_in_sphere>[-+0-9.]+)",repeats = True),
# SM(r":NEC(?P<x_wien2k_necnr>[-+0-9]+)\s*:\s*NUCLEAR AND ELECTRONIC CHARGE\s*(?P<x_wien2k_nuclear_charge>[-+0-9.]+)\s*(?P<x_wien2k_electronic_charge>[0-9.]+)",repeats = True),
SM(r":ENE\s*:\s*\W*\w*\W*\s*TOTAL\s*ENERGY\s*IN\s*Ry\s*=\s*(?P<x_wien2k_energy_total__rydberg>[-+0-9.]+)"),
SM(r":FOR[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_abs>[0-9.]+)\s*(?P<x_wien2k_for_x>[-++0-9.]+)\s*(?P<x_wien2k_for_y>[-+0-9.]+)\s*(?P<x_wien2k_for_z>[-+0-9.]+)\s*partial\sforces", repeats = True),
SM(r":FGL[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_x_gl>[-+0-9.]+)\s*(?P<x_wien2k_for_y_gl>[-+0-9.]+)\s*(?P<x_wien2k_for_z_gl>[-+0-9.]+)\s*partial\sforces", repeats = True)
]
)
]
)
])
# which values to cache or forward (mapping meta name -> CachingLevel)
cachingLevelForMetaName = {
"XC_functional_name": CachingLevel.ForwardAndCache,
"energy_total": CachingLevel.ForwardAndCache
}
# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
parserInfo = {
"name": "Wien2k",
"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/wien2k.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
class Wien2kParser:
""" A proper class envolop for running this parser from within python. """
def __init__(self, backend, **kwargs):
self.backend_factory = backend
logging.warn('something is wrong')
logger = logging.getLogger(__name__)
logger.warn(...)
def parse(self, mainfile):
from unittest.mock import patch
# _logging.getLogger('nomadcore').setLevel(_logging.WARNING)
backend = self.backend_factory(metaInfoEnv)
with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
mainFunction(
mainFileDescription,
metaInfoEnv,
parserInfo,
superContext=Wien2kContext(),
superBackend=backend)
return backend
def setup_logger(self, new_logger):
if hasattr(new_logger, 'bind'):
# tell tests about received logger
new_logger.debug('received logger')
if __name__ == "__main__":
superContext = Wien2kContext()
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)