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

atomisticparsers/gromos/parser.py

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+#
+# 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 re
+
+from nomad.units import ureg
+from simulationparsers.utils import BasicParser
+
+
+class GromosParser:
+    def __init__(self):
+        re_f = r'\-*\d+\.\d+E*e*\-*\+*\d*'
+
+        def get_positions(val):
+            try:
+                labels, positions = zip(
+                    *re.findall(
+                        rf'\d+ \w* +([A-Z])\w* +\d+ +({re_f} +{re_f} +{re_f})', val
+                    )
+                )
+                positions = [v.split() for v in positions]
+            except Exception:
+                labels, positions = [], []
+            return dict(atom_labels=labels, atom_positions=positions)
+
+        self._parser = BasicParser(
+            'Gromos',
+            units_mapping=dict(length=ureg.nm, energy=ureg.kJ / 6.02214076e23),
+            # include code name to distinguish gamess and firefly
+            program_version=r'version *\: *([\d\.]+)',
+            auxilliary_files=r'configuration read from\s*(\S+)',
+            atom_labels_atom_positions=(
+                rf'POSITION\s*(\d+ +[A-Z]+ +\w+ +\d+ +{re_f} +{re_f} +{re_f}[\s\S]+?)END',
+                get_positions,
+            ),
+            energy_total=rf'E\_Total +\:\ *({re_f})',
+            pressure=rf'pressure\: +({re_f})',
+            time_step=r'TIMESTEP\s+(\d+)',
+        )
+
+    def parse(self, mainfile, archive, logger=None):
+        self._parser.parse(mainfile, archive, logger=None)

atomisticparsers/gulp/__init__.py

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+#
+# 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 GulpParser

atomisticparsers/gulp/__main__.py

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+#
+# 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.gulp import GulpParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    GulpParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

atomisticparsers/gulp/metainfo/__init__.py

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+#
+# 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 gulp