Commit bdc67791 authored by Daniel Speckhard's avatar Daniel Speckhard

Added Elk Parser.

parent c8966450
...@@ -9,6 +9,7 @@ syntax: glob ...@@ -9,6 +9,7 @@ syntax: glob
*.pyc *.pyc
*.bk *.bk
*.swp *.swp
*.egg-info
.DS_Store .DS_Store
# logging files # logging files
......
# Copyright 2015-2018 Lauri Himanen, Fawzi Mohamed, Ankit Kariryaa
#
# 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.
from elkparser.parser_elk import ElkParser
# Copyright 2017-2018 Lorenzo Pardini
#
# 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.
from builtins import object
# 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
from nomadcore.unit_conversion import unit_conversion
import os, sys, json, logging
class ElkContext(object):
"""context for elk parser"""
def startedParsing(self, path, parser):
"""called when parsing starts"""
self.parser = parser
self.secMethodIndex = None
self.secSystemIndex = None
self.enTot = []
self.atom_pos = []
self.atom_labels = []
self.spinTreat = None
def onOpen_section_system(self, backend, gIndex, section):
self.secSystemIndex = gIndex
def onOpen_section_method(self, backend, gIndex, section):
self.secMethodIndex = gIndex
def onClose_x_elk_section_lattice_vectors(self, backend, gIndex, section):
latticeX = section["x_elk_geometry_lattice_vector_x"]
latticeY = section["x_elk_geometry_lattice_vector_y"]
latticeZ = section["x_elk_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_x_elk_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
recLatticeX = section["x_elk_geometry_reciprocal_lattice_vector_x"]
recLatticeY = section["x_elk_geometry_reciprocal_lattice_vector_y"]
recLatticeZ = section["x_elk_geometry_reciprocal_lattice_vector_z"]
recCell = [[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
[recLatticeX[1],recLatticeY[1],recLatticeZ[1]],
[recLatticeX[2],recLatticeY[2],recLatticeZ[2]]]
backend.addValue("x_elk_simulation_reciprocal_cell", recCell)
def onClose_x_elk_section_xc(self, backend, gIndex, section):
xcNr = section["x_elk_xc_functional"][0]
xc_internal_map = {
2: ['LDA_C_PZ', 'LDA_X_PZ'],
3: ['LDA_C_PW', 'LDA_X_PZ'],
4: ['LDA_C_XALPHA'],
5: ['LDA_C_VBH'],
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")
backend.addValue("XC_functional_name", xcName)
backend.closeSection("section_XC_functionals", gi)
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex)
dirPath = os.path.dirname(self.parser.fIn.name)
dosFile = os.path.join(dirPath, "TDOS.OUT")
eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
if os.path.exists(dosFile):
dosGIndex=backend.openSection("section_dos")
with open(dosFile) as f:
dosE=[]
dosV=[]
fromH = unit_conversion.convert_unit_function("hartree", "J")
while True:
line = f.readline()
if not line: break
nrs = list(map(float,line.split()))
if len(nrs) == 2:
dosV.append(nrs[1])
dosE.append(fromH(nrs[0]))
elif len(nrs) != 0:
raise Exception("Found more than two values in dos file %s" % dosFile)
backend.addArrayValues("dos_values", np.asarray(dosV))
backend.addArrayValues("dos_energies", np.asarray(dosE))
backend.closeSection("section_dos", dosGIndex)
if os.path.exists(eigvalFile):
eigvalGIndex = backend.openSection("section_eigenvalues")
with open(eigvalFile) as g:
eigvalKpoint=[]
eigvalVal=[]
eigvalOcc=[]
eigvalValSpin = [[],[]]
eigvalOccSpin = [[],[]]
fromH = unit_conversion.convert_unit_function("hartree", "J")
while 1:
s = g.readline()
if not s: break
s = s.strip()
if len(s) < 20:
if "nstsv" in s.split():
nstsv = int(s.split()[0])
nstsv2=int(nstsv/2)
elif "nkpt" in s.split():
nkpt = int(s.split()[0])
continue
elif len(s) > 50:
eigvalVal.append([])
eigvalOcc.append([])
eigvalKpoint.append(list(map(float, s.split()[1:4])))
else:
try: int(s[0])
except ValueError:
continue
else:
n, e, occ = s.split()
eigvalVal[-1].append(fromH(float(e)))
eigvalOcc[-1].append(float(occ))
if not self.spinTreat:
backend.addArrayValues("eigenvalues_values", np.asarray([eigvalVal]))
backend.addArrayValues("eigenvalues_occupation", np.asarray([eigvalOcc]))
else:
for i in range(0,nkpt):
eigvalValSpin[0].append(eigvalVal[i][0:nstsv2])
eigvalOccSpin[0].append(eigvalOcc[i][0:nstsv2])
eigvalValSpin[1].append(eigvalVal[i][nstsv2:nstsv])
eigvalOccSpin[1].append(eigvalOcc[i][nstsv2:nstsv])
backend.addArrayValues("eigenvalues_values", np.asarray(eigvalValSpin))
backend.addArrayValues("eigenvalues_occupation", np.asarray(eigvalOccSpin))
backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint))
backend.closeSection("section_eigenvalues",eigvalGIndex)
# backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint))
# backend.addArrayValues("eigenvalues_values", np.asarray([eigvalVal]))
# backend.addArrayValues("eigenvalues_occupation", np.asarray([eigvalOcc]))
# backend.closeSection("section_eigenvalues",eigvalGIndex)
backend.addValue("energy_total", self.enTot[-1])
def onClose_x_elk_section_spin(self, backend, gIndex, section):
spin = section["x_elk_spin_treatment"][0]
spin = spin.strip()
if spin == "spin-polarised":
self.spinTreat = True
else:
self.spinTreat = False
def onClose_section_system(self, backend, gIndex, section):
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
self.secSystemDescriptionIndex = gIndex
self.secSystemDescriptionIndex = gIndex
if self.atom_pos:
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
self.atom_pos = []
if self.atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(self.atom_labels))
self.atom_labels = []
def onClose_x_elk_section_atoms_group(self, backend, gIndex, section):
pos = [section['x_elk_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
pl = [len(comp) for comp in pos]
natom = pl[0]
if pl[1] != natom or pl[2] != natom:
raise Exception("invalid number of atoms in various components %s" % pl)
for i in range(natom):
self.atom_pos.append([pos[0][i], pos[1][i], pos[2][i]])
self.atom_labels = self.atom_labels + (section['x_elk_geometry_atom_labels'] * natom)
def onClose_section_scf_iteration(self, backend, gIndex, section):
Etot = section["energy_total_scf_iteration"]
self.enTot.append(Etot[0])
# description of the input
mainFileDescription = \
SM(name = "root matcher",
startReStr = "",
weak = True,
subMatchers = [
SM(name = "header",
startReStr = r"\s*\|\s*Elk version\s*(?P<program_version>[-a-zA-Z0-9\.]+)\s*started\s*",
fixedStartValues={'program_name': 'elk', 'program_basis_set_type': '(L)APW+lo' },
sections = ["section_run", "section_method"],
subMatchers = [
SM(name = 'input',
startReStr = r"\|\sGround-state\s*[-a-zA-Z\s]+\s*\|\s",
endReStr = r"\|\sDensity and potential initialised from atomic data\s",
sections = ['section_system'],
subMatchers = [
SM(startReStr = r"\s*Lattice vectors :",
sections = ["x_elk_section_lattice_vectors"],
subMatchers = [
SM(startReStr = r"\s*(?P<x_elk_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_elk_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_elk_geometry_lattice_vector_z__bohr>[-+0-9.]+)", repeats = True)
]),
SM(startReStr = r"Reciprocal lattice vectors :",
sections = ["x_elk_section_reciprocal_lattice_vectors"],
subMatchers = [
SM(startReStr = r"\s*(?P<x_elk_geometry_reciprocal_lattice_vector_x__bohr_1>[-+0-9.]+)\s+(?P<x_elk_geometry_reciprocal_lattice_vector_y__bohr_1>[-+0-9.]+)\s+(?P<x_elk_geometry_reciprocal_lattice_vector_z__bohr_1>[-+0-9.]+)", repeats = True)
]),
SM(r"\s*Unit cell volume\s*:\s*(?P<x_elk_unit_cell_volume__bohr3>[-0-9.]+)"),
SM(r"\s*Brillouin zone volume\s*:\s*(?P<x_elk_brillouin_zone_volume__bohr_3>[-0-9.]+)"),
SM(r"\s*Species\s*:\s*[0-9]\s*\((?P<x_elk_geometry_atom_labels>[-a-zA-Z0-9]+)\)", repeats = True,
sections = ["x_elk_section_atoms_group"],
subMatchers = [
SM(r"\s*muffin-tin radius\s*:\s*(?P<x_elk_muffin_tin_radius__bohr>[-0-9.]+)", repeats = True),
SM(r"\s*number of radial points in muffin-tin\s*:\s*(?P<x_elk_muffin_tin_points>[-0-9.]+)", repeats = True),
SM(startReStr = r"\s*atomic positions\s*\(lattice\)\, magnetic fields \(Cartesian\)\s*:\s*",
subMatchers = [
SM(r"\s*(?P<x_elk_geometry_atom_number>[+0-9]+)\s*:\s*(?P<x_elk_geometry_atom_positions_x__bohr>[-+0-9.]+)\s*(?P<x_elk_geometry_atom_positions_y__bohr>[-+0-9.]+)\s*(?P<x_elk_geometry_atom_positions_z__bohr>[-+0-9.]+)", repeats = True)
])
]),
SM(startReStr = r"\s*Spin treatment\s*:\s*",
sections = ["x_elk_section_spin"],
subMatchers = [
SM(r"\s*(?P<x_elk_spin_treatment>[-a-zA-Z\s*]+)")
]),
SM(r"\s*k-point grid\s*:\s*(?P<x_elk_number_kpoint_x>[-0-9.]+)\s+(?P<x_elk_number_kpoint_y>[-0-9.]+)\s+(?P<x_elk_number_kpoint_z>[-0-9.]+)"),
SM(r"\s*k-point offset\s*:\s*(?P<x_elk_kpoint_offset_x>[-0-9.]+)\s+(?P<x_elk_kpoint_offset_y>[-0-9.]+)\s+(?P<x_elk_kpoint_offset_z>[-0-9.]+)"),
SM(r"\s*Total number of k-points\s*:\s*(?P<x_elk_number_kpoints>[-0-9.]+)"),
SM(r"\s*Muffin-tin radius times maximum \|G\+k\|\s*:\s*(?P<x_elk_rgkmax__bohr>[-0-9.]+)"),
SM(r"\s*Maximum \|G\+k\| for APW functions\s*:\s*(?P<x_elk_gkmax__bohr_1>[-0-9.]+)"),
SM(r"\s*Maximum \|G\| for potential and density\s*:\s*(?P<x_elk_gmaxvr__bohr_1>[-0-9.]+)"),
SM(r"\s*G-vector grid sizes\s*:\s*(?P<x_elk_gvector_size_x>[-0-9.]+)\s+(?P<x_elk_gvector_size_y>[-0-9.]+)\s+(?P<x_elk_gvector_size_z>[-0-9.]+)"),
SM(r"\s*Number of G-vectors\s*:\s*(?P<x_elk_gvector_total>[-0-9.]+)"),
SM(startReStr = r"\s*Maximum angular momentum used for\s*",
subMatchers = [
SM(r"\s*APW functions\s*:\s*(?P<x_elk_lmaxapw>[-0-9.]+)")
]),
SM(r"\s*Total nuclear charge\s*:\s*(?P<x_elk_nuclear_charge>[-0-9.]+)"),
SM(r"\s*Total core charge\s*:\s*(?P<x_elk_core_charge>[-0-9.]+)"),
SM(r"\s*Total valence charge\s*:\s*(?P<x_elk_valence_charge>[-0-9.]+)"),
SM(r"\s*Total electronic charge\s*:\s*(?P<x_elk_electronic_charge>[-0-9.]+)"),
SM(r"\s*Effective Wigner radius, r_s\s*:\s*(?P<x_elk_wigner_radius>[-0-9.]+)"),
SM(r"\s*Number of empty states\s*:\s*(?P<x_elk_empty_states>[-0-9.]+)"),
SM(r"\s*Total number of valence states\s*:\s*(?P<x_elk_valence_states>[-0-9.]+)"),
SM(r"\s*Total number of core states\s*:\s*(?P<x_elk_core_states>[-0-9.]+)"),
SM(r"\s*Total number of local-orbitals\s*:\s*(?P<x_elk_lo>[-0-9.]+)"),
SM(r"\s*Smearing width\s*:\s*(?P<x_elk_smearing_width__hartree>[-0-9.]+)"),
SM(startReStr = r"\s*Exchange-correlation functional\s*:\s*(?P<x_elk_xc_functional>[-0-9.]+)",
sections = ['x_elk_section_xc'])
]),
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*[-a-zA-Z]+ number\s*:",
sections = ["section_scf_iteration"],
repeats = True,
subMatchers = [
SM(r"\s*Fermi\s*:\s*(?P<x_elk_fermi_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*electron kinetic\s*:\s*(?P<electronic_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy_scf_iteration__hartree>[-0-9.]+([E]?[-]?[0-9]+))"),
SM(r"\s*total energy\s*:\s*(?P<energy_total_scf_iteration__hartree>[-0-9.]+([E]?[-]?[0-9]+))"),
SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi_scf_iteration__hartree_1>[-0-9.]+)"),
SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap_scf_iteration__hartree>[-0-9.]+)"),
SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap_scf_iteration__hartree>[-0-9.]+)"),
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.]+)"),
]) #,
]
)
])
])
parserInfo = {
"name": "Elk"
}
# metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/elk.nomadmetainfo.json"))
# metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
cachingLevelForMetaName = {
"x_elk_geometry_lattice_vector_x":CachingLevel.Cache,
"x_elk_geometry_lattice_vector_y":CachingLevel.Cache,
"x_elk_geometry_lattice_vector_z":CachingLevel.Cache,
"x_elk_section_lattice_vectors": CachingLevel.Ignore,
"x_elk_geometry_reciprocal_lattice_vector_x":CachingLevel.Cache,
"x_elk_geometry_reciprocal_lattice_vector_y":CachingLevel.Cache,
"x_elk_geometry_reciprocal_lattice_vector_z":CachingLevel.Cache,
"x_elk_section_reciprocal_lattice_vectors": CachingLevel.Ignore
}
import nomad_meta_info
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)), "elk.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
class ElkParser():
""" A proper class envolop for running this parser from within python. """
def __init__(self, backend, **kwargs):
self.backend_factory = backend
def parse(self, mainfile):
from unittest.mock import patch
logging.info('elk parser started')
logging.getLogger('nomadcore').setLevel(logging.WARNING)
backend = self.backend_factory(metaInfoEnv)
with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
mainFunction(
mainFileDescription=mainFileDescription,
metaInfoEnv=metaInfoEnv,
parserInfo = parserInfo,
cachingLevelForMetaName = cachingLevelForMetaName,
superContext=ElkContext(),
superBackend=backend,
defaultSectionCachingLevel = True)
return backend
if __name__ == "__main__":
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ElkContext())
# Copyright 2015-2018 Lorenzo Pardini
#
# 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.
from setuptools import setup, find_packages
def main():
setup(
name='elkparser',
version='0.1',
description='NOMAD parser implementation for Elk.',
license='APACHE 2.0',
package_dir={'': './'},
packages=find_packages(),
install_requires=[
'nomadcore'
],
)
if __name__ == '__main__':
main()
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