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

workflowparsers/__init__.py

@@ -0,0 +1,314 @@
+#
+# 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())
+
+
+aflow_parser_entry_point = EntryPoint(
+    name='parsers/aflow',
+    aliases=['parsers/aflow'],
+    description='NOMAD parser for AFLOW.',
+    python_package='workflowparsers.aflow',
+    mainfile_contents_re=(
+        r'^\s*\[AFLOW\] \*+\s*\[AFLOW\]\s*\[AFLOW\]                     .o.        .o88o.'
+        r"oooo\s*\[AFLOW\]                    .888.       888 `` `888\s*\[AFLOW\]                   .8'888.     o888oo   888   .ooooo.  oooo"
+        r"oooo    ooo\s*\[AFLOW\]                  .8' `888.     888     888  d88' `88b  `88."
+        r"`88.  .8'\s*\[AFLOW\]                 .88ooo8888.    888     888  888   888   `88..]88..8'\s*\[AFLOW\]                .8'     `888.   888     888  888   888    `888'`888'\s*\[AFLOW\]               o88o     o8888o"
+        r"o888o   o888o `Y8bod8P'     `8'  `8'  .in|^\s*\{\"aurl\"\:\"aflowlib\.duke\.edu\:AFLOWDATA"
+    ),
+    mainfile_mime_re='(application/json)|(text/.*)',
+    mainfile_name_re=r'.*aflowlib\.json.*',
+    mainfile_alternative=True,
+    supported_compressions=['gz', 'bz2', 'xz'],
+    parser_class_name='workflowparsers.aflow.AFLOWParser',
+    code_name='AFLOW',
+    code_homepage='http://www.aflowlib.org/',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'AFLOW',
+        'codeLabelStyle': 'all capitals',
+        'codeName': 'aflow',
+        'codeUrl': 'http://www.aflowlib.org/',
+        'parserDirName': 'dependencies/workflow/workflowparsers/aflow/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '|Input Filename| Description|\n|--- | --- |\n|`aflowlib.json` | **Mainfile:** a json file containing the aflow output|\n|`aflow.ael.out`| plain text, elastic outputs|\n|`aflow.agl.out` | plain text, Debye model output|\n',
+    },
+)
+
+asr_parser_entry_point = EntryPoint(
+    name='parsers/asr',
+    aliases=['parsers/asr'],
+    description='NOMAD parser for ASR.',
+    python_package='workflowparsers.asr',
+    mainfile_contents_re='"name": "ASR"',
+    mainfile_mime_re='(application/json)|(text/.*)',
+    mainfile_name_re=r'.*archive_.*\.json',
+    parser_class_name='workflowparsers.asr.ASRParser',
+    code_name='ASR',
+    code_homepage='https://asr.readthedocs.io/en/latest/index.html',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'ASR',
+        'codeLabelStyle': 'all in capitals',
+        'codeName': 'asr',
+        'codeUrl': 'https://asr.readthedocs.io/en/latest/index.html',
+        'parserDirName': 'dependencies/workflow/workflowparsers/asr/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '|Input Filename| Description|\n|--- | --- |\n|`archive*.json` | **Mainfile:** a json file w/ **user-defined** name|\n',
+    },
+)
+
+atomate_parser_entry_point = EntryPoint(
+    name='parsers/atomate',
+    aliases=['parsers/atomate'],
+    description='NOMAD parser for ATOMATE.',
+    python_package='workflowparsers.atomate',
+    mainfile_contents_re='"pymatgen_version":',
+    mainfile_mime_re='(application/json)|(text/.*)',
+    mainfile_name_re=r'.*mp.+materials\.json',
+    parser_class_name='workflowparsers.atomate.AtomateParser',
+    code_name='Atomate',
+    code_homepage='https://www.atomate.org/',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'Atomate',
+        'codeLabelStyle': 'Capitals: A',
+        'codeName': 'atomate',
+        'codeUrl': 'https://www.atomate.org/',
+        'parserDirName': 'dependencies/workflow/workflowparsers/mp/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '|Input Filename| Description|\n|--- | --- |\n|`*materials.json` | **Mainfile:** a json file containing system info|\n|`*.json` | json files containing workflow results|\n',
+    },
+)
+
+elastic_parser_entry_point = EntryPoint(
+    name='parsers/elastic',
+    aliases=['parsers/elastic'],
+    description='NOMAD parser for ELASTIC.',
+    python_package='workflowparsers.elastic',
+    mainfile_contents_re=r'\s*Order of elastic constants\s*=\s*[0-9]+\s*',
+    mainfile_name_re='.*/INFO_ElaStic',
+    parser_class_name='workflowparsers.elastic.ElasticParser',
+    code_name='ElaStic',
+    code_homepage='http://exciting.wikidot.com/elastic',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'ElaStic',
+        'codeLabelStyle': 'capitals: E, S. This is part of the exciting project',
+        'codeName': 'elastic',
+        'codeUrl': 'http://exciting.wikidot.com/elastic',
+        'parserDirName': 'dependencies/workflow/workflowparsers/elastic/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+fhivibes_parser_entry_point = EntryPoint(
+    name='parsers/fhivibes',
+    aliases=['parsers/fhivibes'],
+    description='NOMAD parser for FHIVIBES.',
+    python_package='workflowparsers.fhivibes',
+    mainfile_binary_header_re=b'^\\x89HDF',
+    mainfile_contents_dict={'__has_all_keys': ['I', 'a', 'b']},
+    mainfile_mime_re='(application/x-hdf)',
+    mainfile_name_re=r'^.*\.(nc)$',
+    parser_class_name='workflowparsers.fhivibes.FHIVibesParser',
+    code_name='FHI-vibes',
+    code_homepage='https://vibes.fhi-berlin.mpg.de/',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'FHI-vibes',
+        'codeLabelStyle': 'Capitals: FHI, the rest in lowercase; use dash.',
+        'codeName': 'fhi-vibes',
+        'codeUrl': 'https://vibes.fhi-berlin.mpg.de/',
+        'parserDirName': 'dependencies/workflow/workflowparsers/fhi-vibes/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '|Input Filename| Description|\n|--- | --- |\n|`<hdf_file>` | **Mainfile**, binary hdf file w/ ext .nc` |\n',
+    },
+)
+
+lobster_parser_entry_point = EntryPoint(
+    name='parsers/lobster',
+    aliases=['parsers/lobster'],
+    description='NOMAD parser for LOBSTER.',
+    python_package='workflowparsers.lobster',
+    mainfile_contents_re=r'^LOBSTER\s*v[\d\.]+.*',
+    mainfile_name_re='.*lobsterout.*',
+    supported_compressions=['gz', 'bz2', 'xz'],
+    parser_class_name='workflowparsers.lobster.LobsterParser',
+    code_name='LOBSTER',
+    code_homepage='http://schmeling.ac.rwth-aachen.de/cohp/',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'LOBSTER',
+        'codeLabelStyle': 'All in capitals',
+        'codeName': 'lobster',
+        'codeUrl': 'http://schmeling.ac.rwth-aachen.de/cohp/',
+        'parserDirName': 'dependencies/workflow/workflowparsers/lobster/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '|Input Filename| Description|\n|--- | --- |\n|`lobsterout` | **Mainfile** in LOBSTER specific plain-text |\n',
+    },
+)
+
+phonopy_parser_entry_point = EntryPoint(
+    name='parsers/phonopy',
+    aliases=['parsers/phonopy'],
+    description='NOMAD parser for PHONOPY.',
+    python_package='workflowparsers.phonopy',
+    mainfile_name_re='(.*/phonopy-FHI-aims-displacement-0*1/control.in$)|(.*/phon[^/]+yaml)',
+    parser_class_name='workflowparsers.phonopy.PhonopyParser',
+    code_name='phonopy',
+    code_homepage='https://phonopy.github.io/phonopy/',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'phonopy',
+        'codeLabelStyle': 'all in lower case',
+        'codeName': 'phonopy',
+        'codeUrl': 'https://phonopy.github.io/phonopy/',
+        'parserDirName': 'dependencies/workflow/workflowparsers/phonopy/',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+quantum_espresso_epw_parser_entry_point = EntryPoint(
+    name='parsers/quantum_espresso_epw',
+    aliases=['parsers/quantum_espresso_epw'],
+    description='NOMAD parser for QUANTUM_ESPRESSO_EPW.',
+    python_package='workflowparsers.quantum_espresso_epw',
+    mainfile_contents_re=r'Program EPW.+\s*This program is part of the open-source Quantum ESPRESSO suite',
+    parser_class_name='workflowparsers.quantum_espresso_epw.QuantumEspressoEPWParser',
+    code_name='QuantumEspressoEPW',
+    code_homepage='https://www.quantum-espresso.org',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'QuantumEspressoEPW',
+        'codeLabelStyle': 'Capitals: Q, E, E, P, W',
+        'codeName': 'quantumespressoepw',
+        'codeUrl': 'https://www.quantum-espresso.org',
+        'parserDirName': 'dependencies/workflow/workflowparsers/quantum_espresso_epw',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+quantum_espresso_phonon_parser_entry_point = EntryPoint(
+    name='parsers/quantum_espresso_phonon',
+    aliases=['parsers/quantum_espresso_phonon'],
+    description='NOMAD parser for QUANTUM_ESPRESSO_PHONON.',
+    python_package='workflowparsers.quantum_espresso_phonon',
+    mainfile_contents_re=r'Program PHONON.+\s*This program is part of the open-source Quantum ESPRESSO suite',
+    parser_class_name='workflowparsers.quantum_espresso_phonon.QuantumEspressoPhononParser',
+    code_name='QuantumEspressPhonon',
+    code_homepage='https://www.quantum-espresso.org',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'QuantumEspressPhonon',
+        'codeLabelStyle': 'Capitals: Q, E, P',
+        'codeName': 'quantumespressophonon',
+        'codeUrl': 'https://www.quantum-espresso.org',
+        'parserDirName': 'dependencies/workflow/workflowparsers/quantumespressophonon',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
+quantum_espresso_xspectra_parser_entry_point = EntryPoint(
+    name='parsers/quantum_espresso_xspectra',
+    aliases=['parsers/quantum_espresso_xspectra'],
+    description='NOMAD parser for QUANTUM_ESPRESSO_XSPECTRA.',
+    python_package='workflowparsers.quantum_espresso_xspectra',
+    mainfile_contents_re=r'\s*Program XSpectra\s*',
+    mainfile_mime_re='(application/.*)|(text/.*)',
+    parser_class_name='workflowparsers.quantum_espresso_xspectra.QuantumEspressoXSpectraParser',
+    code_name='QuantumESPRESSOXSpectra',
+    code_homepage='https://www.quantum-espresso.org/Doc/INPUT_XSpectra.txt',
+    code_category='Workflow manager',
+    metadata={
+        'codeCategory': 'Workflow manager',
+        'codeLabel': 'QuantumESPRESSOXSpectra',
+        'codeLabelStyle': 'Capitals: Q, ESPRESSO, X, S',
+        'codeName': 'quantumespressoxspectra',
+        'codeUrl': 'https://www.quantum-espresso.org/Doc/INPUT_XSpectra.txt',
+        'parserDirName': 'dependencies/workflow/workflowparsers/quantumespressoxspectra',
+        'parserGitUrl': 'https://github.com/nomad-coe/workflow-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '| Input Filename | Description |\n| --- | --- |\n| `*.out` | **Mainfile:** text output file |\n| `*.dat` | output data file with the Absorption Spectra |\n',
+    },
+)

workflowparsers/aflow/__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 AFLOWParser

workflowparsers/aflow/__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 workflowparsers.aflow import AFLOWParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    AFLOWParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

workflowparsers/aflow/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 aflow