diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..f8a741c2a8ce3f971ee76c289fc6eaf67f0c7f6c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+*parser.egg-info/
\ No newline at end of file
diff --git a/openkimparser/__init__.py b/openkimparser/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e79d95f7821222c40037b374e9f5dafbd8aea5bb
--- /dev/null
+++ b/openkimparser/__init__.py
@@ -0,0 +1 @@
+from .parser_openkim import OpenKIMParser
\ No newline at end of file
diff --git a/openkimparser/__pycache__/__init__.cpython-36.pyc b/openkimparser/__pycache__/__init__.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..afac27cc12e18943d3d21a233a0a3104db5bc557
Binary files /dev/null and b/openkimparser/__pycache__/__init__.cpython-36.pyc differ
diff --git a/openkimparser/__pycache__/parser_openkim.cpython-36.pyc b/openkimparser/__pycache__/parser_openkim.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..bdc360c9e13533a789ea5cbb447689e7d21c00d8
Binary files /dev/null and b/openkimparser/__pycache__/parser_openkim.cpython-36.pyc differ
diff --git a/openkimparser/metainfo/__init__.py b/openkimparser/metainfo/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..4991a626815853e6d7b76d14a402e4c596c552bf
--- /dev/null
+++ b/openkimparser/metainfo/__init__.py
@@ -0,0 +1,13 @@
+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import openkimparser.metainfo.openkim
+import nomad.datamodel.metainfo.common
+import nomad.datamodel.metainfo.public
+import nomad.datamodel.metainfo.general
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['openkimparser.metainfo.openkim'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package) # type: ignore
diff --git a/openkimparser/metainfo/__pycache__/__init__.cpython-36.pyc b/openkimparser/metainfo/__pycache__/__init__.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..83bdcafc28e6ef4a0522f65167dc907c0d06055b
Binary files /dev/null and b/openkimparser/metainfo/__pycache__/__init__.cpython-36.pyc differ
diff --git a/openkimparser/metainfo/__pycache__/openkim.cpython-36.pyc b/openkimparser/metainfo/__pycache__/openkim.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..4c8737249232ec897c3e526fa0907f38eef8c921
Binary files /dev/null and b/openkimparser/metainfo/__pycache__/openkim.cpython-36.pyc differ
diff --git a/openkimparser/metainfo/openkim.py b/openkimparser/metainfo/openkim.py
new file mode 100644
index 0000000000000000000000000000000000000000..d2d3c196ca986967140b8590ce8d474e4d6d5e20
--- /dev/null
+++ b/openkimparser/metainfo/openkim.py
@@ -0,0 +1,53 @@
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+
+m_package = Package(
+ name='openkim_nomadmetainfo_json',
+ description='None',
+ a_legacy=LegacyDefinition(name='openkim.nomadmetainfo.json'))
+
+
+class section_run(public.section_run):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
+
+ openkim_build_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ build date as string
+ ''',
+ categories=[public.accessory_info, public.program_info],
+ a_legacy=LegacyDefinition(name='openkim_build_date'))
+
+ openkim_src_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ date of last modification of the source as string
+ ''',
+ categories=[public.accessory_info, public.program_info],
+ a_legacy=LegacyDefinition(name='openkim_src_date'))
+
+
+class section_method(public.section_method):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+ x_openkim_atom_kind_refs = Quantity(
+ type=public.section_method_atom_kind,
+ shape=['number_of_atoms'],
+ description='''
+ reference to the atom kinds of each atom
+ ''',
+ a_legacy=LegacyDefinition(name='x_openkim_atom_kind_refs'))
+
+
+m_package.__init_metainfo__()
diff --git a/parser/parser-openkim/openkim_tool.py b/openkimparser/openkim_tool.py
similarity index 100%
rename from parser/parser-openkim/openkim_tool.py
rename to openkimparser/openkim_tool.py
diff --git a/parser/parser-openkim/parser_openkim.py b/openkimparser/parser_openkim.py
similarity index 94%
rename from parser/parser-openkim/parser_openkim.py
rename to openkimparser/parser_openkim.py
index 4707a8c4bb2fd6bd07db62431f2e720eab59d29e..6927d8eaf7f8497519aa04cfb4a8671221733214 100644
--- a/parser/parser-openkim/parser_openkim.py
+++ b/openkimparser/parser_openkim.py
@@ -4,10 +4,8 @@ from builtins import map
from builtins import range
from builtins import object
import logging, sys, bisect
-import setup_paths
from datetime import datetime
-import os, logging, re, traceback
-from nomadcore.parser_backend import JsonParseEventsWriterBackend
+import re, traceback
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
import numpy as np
from nomadcore.unit_conversion.unit_conversion import convert_unit_function
@@ -138,7 +136,7 @@ class OpenkimContext(object):
self.cell = None
self.labels = None
celltype = None
- if('basis-atom-coordinates.source-value' in querydict and
+ if('basis-atom-coordinates.source-value' in querydict and
('a.si-value' in querydict) or
('b.si-value' in querydict) or
('c.si-value' in querydict) or
@@ -164,9 +162,9 @@ class OpenkimContext(object):
else:
lat_a = float(a_si_val)
si_conv = convert_unit_function("m", "angstrom")
- cellAtoms = Atoms(
- positions=basis,
- cell=[si_conv(lat_a),
+ cellAtoms = Atoms(
+ positions=basis,
+ cell=[si_conv(lat_a),
si_conv(lat_a),
si_conv(lat_a)],
pbc=True)
@@ -293,7 +291,8 @@ class KIMParser(object):
backend.startedParsingSession(
mainFileUri = mainFileUri,
parserInfo = self.parserInfo)
- self.superContext.startedParsing(self)
+ superContext = self.superContext
+ superContext.startedParsing(self)
QueryList = KIMQueryReader(self.fIn)
try:
for qi, qdict in enumerate(QueryList):
@@ -338,13 +337,19 @@ parserInfo = {
"version": "1.0"
}
-if __name__ == "__main__":
- """
- This code is modified from parser-vasprun to work for OpenKIM
- """
- metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/openkim.nomadmetainfo.json"))
- metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
- superContext = OpenkimContext()
- parser = KIMParser(parserInfo, superContext)
- backend = JsonParseEventsWriterBackend(metaInfoEnv, sys.stdout)
- parser.parse(sys.argv[1], sys.argv[2], backend)
+
+class OpenKIMParser():
+ """ A proper class envolop for running this parser from within python. """
+ def __init__(self, backend, **kwargs):
+ self.backend_factory = backend
+
+ def parse(self, mainfile):
+ logging.info('turbomole parser started')
+ logging.getLogger('nomadcore').setLevel(logging.WARNING)
+ backend = self.backend_factory("openkim.nomadmetainfo.json")
+ parserInfo = {'name': 'parser_openkim', 'version': '1.0'}
+ context = OpenkimContext()
+ parser = KIMParser(parserInfo, context)
+ parser.parse('nmd://uri', mainfile, backend)
+
+ return backend
diff --git a/parser/parser-openkim/setup_paths.py b/parser/parser-openkim/setup_paths.py
deleted file mode 100644
index f823d43b987767343f5ab8b64bb085113066f391..0000000000000000000000000000000000000000
--- a/parser/parser-openkim/setup_paths.py
+++ /dev/null
@@ -1,12 +0,0 @@
-import sys
-import os
-import os.path
-
-basedir = os.path.dirname(os.path.abspath(__file__))
-commondir = os.path.normpath(os.path.join(basedir,"../../../../python-common/common/python"))
-parserdir = os.path.normpath(os.path.join(basedir, ".."))
-
-if commondir not in sys.path:
- sys.path.insert(1, commondir)
-if parserdir not in sys.path:
- sys.path.insert(1, parserdir)
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..e0af2ae5bc616bb3ae8b4d1e1b1cad18e563bc71
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,34 @@
+# Copyright 2015-2018 Berk Onat
+#
+# 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='openkimparser',
+ version='0.1',
+ description='NOMAD parser implementation for OpenKIM.',
+ license='MIT',
+ package_dir={'': './'},
+ packages=find_packages(),
+ install_requires=[
+ 'nomadcore',
+ 'nomad'
+ ],
+ )
+
+
+if __name__ == '__main__':
+ main()
diff --git a/src/main/scala/eu/nomad_lab/parsers/OpenkimParser.scala b/src/main/scala/eu/nomad_lab/parsers/OpenkimParser.scala
deleted file mode 100644
index 27698c686f583e2f7e3708077da4ae290a3b7887..0000000000000000000000000000000000000000
--- a/src/main/scala/eu/nomad_lab/parsers/OpenkimParser.scala
+++ /dev/null
@@ -1,43 +0,0 @@
-package eu.nomad_lab.parsers
-
-import eu.nomad_lab
-import eu.nomad_lab.DefaultPythonInterpreter
-import org.{ json4s => jn }
-import eu.{ nomad_lab => lab }
-import scala.collection.breakOut
-
-object OpenkimParser extends SimpleExternalParserGenerator(
- name = "OpenkimParser",
- parserInfo = jn.JObject(
- ("name" -> jn.JString("OpenkimParser")) ::
- ("parserId" -> jn.JString("OpenkimParser" + lab.OpenkimVersionInfo.version)) ::
- ("versionInfo" -> jn.JObject(
- ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
- case (k, v) => k -> jn.JString(v.toString)
- }(breakOut): List[(String, jn.JString)])) ::
- (lab.OpenkimVersionInfo.toMap.map {
- case (key, value) =>
- (key -> jn.JString(value.toString))
- }(breakOut): List[(String, jn.JString)])
- )) :: Nil
- ),
- mainFileTypes = Seq("text/.*"),
- mainFileRe = """\s*OPENKIM_QUERY_OUTPUT\s*""".r,
- cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/openkim/parser/parser-openkim/parser-openkim.py",
- "${mainFilePath}", "${mainFilePath}/data.json"),
- resList = Seq(
- "parser-openkim/parser-openkim.py",
- "parser-openkim/setup_paths.py",
- "nomad_meta_info/public.nomadmetainfo.json",
- "nomad_meta_info/common.nomadmetainfo.json",
- "nomad_meta_info/meta_types.nomadmetainfo.json",
- "nomad_meta_info/openkim.nomadmetainfo.json"
- ) ++ DefaultPythonInterpreter.commonFiles(),
- dirMap = Map(
- "parser-openkim" -> "parsers/openkim/parser/parser-openkim",
- "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
- "python" -> "python-common/common/python/nomadcore"
- ) ++ DefaultPythonInterpreter.commonDirMapping(),
- metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.openkim)
-)
-
diff --git a/src/test/scala/eu/nomad_lab/parsers/OpenkimParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/OpenkimParserSpec.scala
deleted file mode 100644
index b74f1e4b86528a4313bd467e9617072f7dcb73a4..0000000000000000000000000000000000000000
--- a/src/test/scala/eu/nomad_lab/parsers/OpenkimParserSpec.scala
+++ /dev/null
@@ -1,14 +0,0 @@
-package eu.nomad_lab.parsers
-
-import org.specs2.mutable.Specification
-
-object OpenkimParserTests extends Specification {
- "OpenkimParserTest" >> {
- "[OpenKIM Query with 3767 entries] test with json-events" >> {
- ParserRun.parse(OpenkimParser, "parsers/openkim/test/examples/data.json", "json-events") must_== ParseResult.ParseSuccess
- }
- "[OpenKIM Query with 3767 entries] test with json" >> {
- ParserRun.parse(OpenkimParser, "parsers/openkim/test/examples/data.json", "json") must_== ParseResult.ParseSuccess
- }
- }
-}