nomad-parser-plugins-atomistic 1.0__py3-none-any.whl

atomisticparsers/__init__.py

@@ -0,0 +1,400 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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 pydantic import Field
+from typing import Optional
+
+from nomad.config.models.plugins import ParserEntryPoint
+
+
+class EntryPoint(ParserEntryPoint):
+    parser_class_name: str = Field(
+        description="""
+        The fully qualified name of the Python class that implements the parser.
+        This class must have a function `def parse(self, mainfile, archive, logger)`.
+    """
+    )
+    code_name: Optional[str]
+    code_homepage: Optional[str]
+    code_category: Optional[str]
+    metadata: Optional[dict] = Field(
+        description="""
+        Metadata passed to the UI. Deprecated. """
+    )
+
+    def load(self):
+        from nomad.parsing import MatchingParserInterface
+
+        return MatchingParserInterface(**self.dict())
+
+
+amber_parser_entry_point = EntryPoint(
+    name='parsers/amber',
+    aliases=['parsers/amber'],
+    description='NOMAD parser for AMBER.',
+    python_package='atomisticparsers.amber',
+    mainfile_contents_re=r'\s*Amber\s[0-9]+\s[A-Z]+\s*[0-9]+',
+    parser_class_name='atomisticparsers.amber.AmberParser',
+    code_name='Amber',
+    code_homepage='http://ambermd.org/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'Amber',
+        'codeLabelStyle': 'only first character in capitals',
+        'codeName': 'amber',
+        'codeUrl': 'http://ambermd.org/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/amber/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': 'The Amber parser supports the SANDER and PMEMD Molecular Dynamics codes.',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+asap_parser_entry_point = EntryPoint(
+    name='parsers/asap',
+    aliases=['parsers/asap'],
+    description='NOMAD parser for ASAP.',
+    python_package='atomisticparsers.asap',
+    mainfile_binary_header_re=b'AFFormatASE\\-Trajectory',
+    mainfile_mime_re='application/octet-stream',
+    mainfile_name_re=r'.*.traj$',
+    parser_class_name='atomisticparsers.asap.AsapParser',
+    code_name='ASAP',
+    code_homepage='https://wiki.fysik.dtu.dk/asap',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'ASAP',
+        'codeLabelStyle': 'all in capitals',
+        'codeName': 'asap',
+        'codeUrl': 'https://wiki.fysik.dtu.dk/asap',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/asap/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+bopfox_parser_entry_point = EntryPoint(
+    name='parsers/bopfox',
+    aliases=['parsers/bopfox'],
+    description='NOMAD parser for BOPFOX.',
+    python_package='atomisticparsers.bopfox',
+    mainfile_contents_re=r'\-+\s+BOPfox \(v',
+    parser_class_name='atomisticparsers.bopfox.BOPfoxParser',
+    code_name='BOPfox',
+    code_homepage='http://bopfox.de/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'BOPfox',
+        'codeLabelStyle': 'Capitals: B,O,P',
+        'codeName': 'bopfox',
+        'codeUrl': 'http://bopfox.de/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/bopfox/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+dftbplus_parser_entry_point = EntryPoint(
+    name='parsers/dftbplus',
+    aliases=['parsers/dftbplus'],
+    description='NOMAD parser for DFTBPLUS.',
+    python_package='atomisticparsers.dftbplus',
+    mainfile_contents_re=r'\|  DFTB\+',
+    mainfile_mime_re='text/.*',
+    parser_class_name='atomisticparsers.dftbplus.DFTBPlusParser',
+    code_name='DFTB+',
+    code_homepage='http://www.dftbplus.org/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'DFTB+',
+        'codeLabelStyle': 'all in capitals; use + instead of word',
+        'codeName': 'dftbplus',
+        'codeUrl': 'http://www.dftbplus.org/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/dftbplus/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+dlpoly_parser_entry_point = EntryPoint(
+    name='parsers/dl-poly',
+    aliases=['parsers/dl-poly'],
+    description='NOMAD parser for DLPOLY.',
+    python_package='atomisticparsers.dlpoly',
+    mainfile_contents_re=r'\*\*\s+DL_POLY.+\*\*',
+    parser_class_name='atomisticparsers.dlpoly.DLPolyParser',
+    code_name='DL_POLY',
+    code_homepage='https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'DL_POLY',
+        'codeLabelStyle': 'all capitals and underscore, not dash (minus)',
+        'codeName': 'dl-poly',
+        'codeUrl': 'https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/dl-poly/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+gromacs_parser_entry_point = EntryPoint(
+    name='parsers/gromacs',
+    aliases=['parsers/gromacs'],
+    description='NOMAD parser for GROMACS.',
+    python_package='atomisticparsers.gromacs',
+    mainfile_contents_re=r'gmx mdrun, (VERSION|version)[\s\S]*Input Parameters:',
+    parser_class_name='atomisticparsers.gromacs.GromacsParser',
+    code_name='GROMACS',
+    code_homepage='http://www.gromacs.org/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'GROMACS',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'gromacs',
+        'codeUrl': 'http://www.gromacs.org/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/gromacs/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+gromos_parser_entry_point = EntryPoint(
+    name='parsers/gromos',
+    aliases=['parsers/gromos'],
+    description='NOMAD parser for GROMOS.',
+    python_package='atomisticparsers.gromos',
+    mainfile_contents_re=r'Bugreports to http://www.gromos.net',
+    parser_class_name='atomisticparsers.gromos.GromosParser',
+    code_name='GROMOS',
+    code_homepage='http://www.gromos.net/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'GROMOS',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'gromos',
+        'codeUrl': 'http://www.gromos.net/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/gromos/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+gulp_parser_entry_point = EntryPoint(
+    name='parsers/gulp',
+    aliases=['parsers/gulp'],
+    description='NOMAD parser for GULP.',
+    python_package='atomisticparsers.gulp',
+    mainfile_contents_re=(
+        r'\s*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\s*\s*\*\s*GENERAL UTILITY '
+        r'LATTICE PROGRAM\s*\*\s*'
+    ),
+    parser_class_name='atomisticparsers.gulp.GulpParser',
+    code_name='GULP',
+    code_homepage='http://gulp.curtin.edu.au/gulp/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'GULP',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'gulp',
+        'codeUrl': 'http://gulp.curtin.edu.au/gulp/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/gulp/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+h5md_parser_entry_point = EntryPoint(
+    name='parsers/h5md',
+    aliases=['parsers/h5md'],
+    description='NOMAD parser for H5MD.',
+    python_package='atomisticparsers.h5md',
+    mainfile_binary_header_re=b'^\\x89HDF',
+    mainfile_contents_dict={'__has_all_keys': ['h5md']},
+    mainfile_mime_re='(application/x-hdf)',
+    mainfile_name_re=r'^.*\.(h5|hdf5)$',
+    parser_class_name='atomisticparsers.h5md.H5MDParser',
+    code_name='H5MD',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'H5MD',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'h5md',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/h5md/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+lammps_parser_entry_point = EntryPoint(
+    name='parsers/lammps',
+    aliases=['parsers/lammps'],
+    description='NOMAD parser for LAMMPS.',
+    python_package='atomisticparsers.lammps',
+    mainfile_contents_re=r'^LAMMPS\s+\(.+\)',
+    parser_class_name='atomisticparsers.lammps.LammpsParser',
+    code_name='LAMMPS',
+    code_homepage='https://lammps.sandia.gov/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'LAMMPS',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'lammps',
+        'codeUrl': 'https://lammps.sandia.gov/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/lammps/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+libatoms_parser_entry_point = EntryPoint(
+    name='parsers/lib-atoms',
+    aliases=['parsers/lib-atoms'],
+    description='NOMAD parser for LIBATOMS.',
+    python_package='atomisticparsers.libatoms',
+    mainfile_contents_re=r'\s*<GAP_params\s',
+    parser_class_name='atomisticparsers.libatoms.LibAtomsParser',
+    code_name='libAtoms',
+    code_homepage='http://libatoms.github.io/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'libAtoms',
+        'codeLabelStyle': 'Capitals: A',
+        'codeName': 'lib-atoms',
+        'codeUrl': 'http://libatoms.github.io/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/lib-atoms/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+namd_parser_entry_point = EntryPoint(
+    name='parsers/namd',
+    aliases=['parsers/namd'],
+    description='NOMAD parser for NAMD.',
+    python_package='atomisticparsers.namd',
+    mainfile_contents_re=r'\s*Info:\s*NAMD\s*[0-9.]+\s*for\s*',
+    mainfile_mime_re='text/.*',
+    parser_class_name='atomisticparsers.namd.NAMDParser',
+    code_name='NAMD',
+    code_homepage='http://www.ks.uiuc.edu/Research/namd/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'NAMD',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'namd',
+        'codeUrl': 'http://www.ks.uiuc.edu/Research/namd/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/namd/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+tinker_parser_entry_point = EntryPoint(
+    name='parsers/tinker',
+    aliases=['parsers/tinker'],
+    description='NOMAD parser for TINKER.',
+    python_package='atomisticparsers.tinker',
+    mainfile_contents_re=r'TINKER  ---  Software Tools for Molecular Design',
+    parser_class_name='atomisticparsers.tinker.TinkerParser',
+    code_name='Tinker',
+    code_homepage='https://dasher.wustl.edu/tinker/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'Tinker',
+        'codeLabelStyle': 'Capitals: T',
+        'codeName': 'tinker',
+        'codeUrl': 'https://dasher.wustl.edu/tinker/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/tinker/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+xtb_parser_entry_point = EntryPoint(
+    name='parsers/xtb',
+    aliases=['parsers/xtb'],
+    description='NOMAD parser for XTB.',
+    python_package='atomisticparsers.xtb',
+    mainfile_contents_re=r'x T B\s+\|\s+\|\s+=',
+    parser_class_name='atomisticparsers.xtb.XTBParser',
+    code_name='xTB',
+    code_homepage='https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'xTB',
+        'codeLabelStyle': 'Capitals: TB',
+        'codeName': 'xtb',
+        'codeUrl': 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/gromacs//xtb/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '|Input Filename| Description|\n|--- | --- |\n|`*.out` | **Mainfile:** a plain text file w/ **user-defined** name|\n|`*.coord`|plain text; structure file|\n|`*.xyz`| plain text, structure file|\n|`*xtbopt.log`|plain text, trajectory file of geometry optimization|\n|`*xtb.trj`|plain text, trajectory of molecular dynamics|\n|`*xtbtopo.mol`|plain text, topology file|\n|`*xtbrestart`|binary file, restart file|\n|`charges` |plain text, output charges|\n',
+    },
+)

atomisticparsers/amber/__init__.py

@@ -0,0 +1,19 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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 .parser import AmberParser

atomisticparsers/amber/__main__.py

@@ -0,0 +1,31 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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 json
+import logging
+
+from nomad.utils import configure_logging
+from nomad.datamodel import EntryArchive
+from atomisticparsers.amber import AmberParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    AmberParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

atomisticparsers/amber/metainfo/__init__.py

@@ -0,0 +1,19 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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 . import amber