Commit 05e5f608 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Added minimar OUTCAR parser that can be used in absence of .xml to create repository meta data.

parent 3670915d
......@@ -20,6 +20,7 @@ import nomadcore.baseclasses
from vaspparser.parser_vasprun import parserInfo
from vaspparser.parser_vasprun import VasprunContext, XmlParser, parserInfo
from vaspparser.parser_outcar import VaspOutcarParser
class VASPRunParser:
......
# Copyright 2019-2018 Markus Scheidgen
#
# 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.
import sys
import numpy as np
from ase.io import read as ase_read
from nomadcore.simple_parser import SimpleMatcher
from nomadcore.baseclasses import ParserInterface, MainHierarchicalParser
from nomad.parsing import LocalBackend
"""
A very basic VASP OUTCAR parser. It is only used to get nomad repository
metadata in absence of the VASP .xml file.
"""
class VaspOutcarParser(ParserInterface):
def get_metainfo_filename(self):
return 'vasp.nomadmetainfo.json'
def get_parser_info(self):
return {
'name': 'vaspoutcar_parser',
'version': '1.0.0'
}
def setup_version(self):
self.setup_main_parser(None)
def setup_main_parser(self, _):
self.main_parser = MainParser(self.parser_context)
class MainParser(MainHierarchicalParser):
def __init__(self, parser_context, *args, **kwargs):
super().__init__(parser_context, *args, **kwargs)
self.lattice_vectors = []
self.root_matcher = SimpleMatcher(
name='root',
startReStr=r'vasp.',
weak=True,
sections=['section_run', 'section_system', 'section_method'],
subMatchers=[
SimpleMatcher(r'\svasp.(?P<program_version>\d+.\d+.\d+)\s.*')
]
)
def parse(self, mainfile, *args, **kwargs):
self.ase = ase_read(mainfile, format='vasp-out')
super().parse(mainfile, *args, **kwargs)
def add_lattice_vector(self, backend, data):
self.lattice_vectors.append(list(float(x.strip()) for x in data[1].split(',')))
def onClose_section_method(self, backend, *args, **kwargs):
backend.openNonOverlappingSection('section_XC_functionals')
backend.addValue('XC_functional_name', 'GGA_X_PBE')
backend.closeNonOverlappingSection('section_XC_functionals')
backend.addValue('electronic_structure_method', 'DFT')
def onClose_section_system(self, backend, *args, **kwargs):
backend.addArrayValues('atom_labels', np.array(self.ase.get_chemical_symbols()))
backend.addArrayValues('atom_positions', self.ase.get_positions())
backend.addArrayValues('lattice_vectors', self.ase.get_cell())
backend.addArrayValues('configuration_periodic_dimensions', self.ase.get_pbc())
def onClose_section_run(self, backend, *args, **kwargs):
backend.addValue('program_name', 'vasp')
backend.addValue('program_basis_set_type', 'plane waves')
if __name__ == "__main__":
parser = VaspOutcarParser(backend=LocalBackend)
parser.parse(sys.argv[1])
print(parser.parser_context.super_backend)
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