From 05e5f608178df11fe5563dcb88c3e475d51cd230 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Mon, 4 Feb 2019 20:16:07 +0100
Subject: [PATCH] Added minimar OUTCAR parser that can be used in absence of
.xml to create repository meta data.
---
vaspparser/__init__.py | 1 +
vaspparser/parser_outcar.py | 92 +++++++++++++++++++++++++++++++++++++
2 files changed, 93 insertions(+)
create mode 100644 vaspparser/parser_outcar.py
diff --git a/vaspparser/__init__.py b/vaspparser/__init__.py
index 7380dc0..9b0f6bc 100644
--- a/vaspparser/__init__.py
+++ b/vaspparser/__init__.py
@@ -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:
diff --git a/vaspparser/parser_outcar.py b/vaspparser/parser_outcar.py
new file mode 100644
index 0000000..2e3776d
--- /dev/null
+++ b/vaspparser/parser_outcar.py
@@ -0,0 +1,92 @@
+# 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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