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

atomisticparsers/h5md/__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 H5MDParser

atomisticparsers/h5md/__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.h5md import H5MDParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    H5MDParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

atomisticparsers/h5md/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 h5md

atomisticparsers/h5md/metainfo/h5md.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 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,
+)
+import runschema.run  # pylint: disable=unused-import
+import runschema.calculation  # pylint: disable=unused-import
+import runschema.method  # pylint: disable=unused-import
+import runschema.system  # pylint: disable=unused-import
+
+
+m_package = Package()
+
+
+class ParamEntry(MSection):
+    """
+    Generic section defining a parameter name and value
+    """
+
+    m_def = Section(validate=False)
+
+    kind = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Name of the parameter.
+        """,
+    )
+
+    value = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Value of the parameter as a string.
+        """,
+    )
+
+    unit = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Unit of the parameter as a string.
+        """,
+    )
+
+    # TODO add description quantity
+
+
+class CalcEntry(MSection):
+    """
+    Section describing a general type of calculation.
+    """
+
+    m_def = Section(validate=False)
+
+    kind = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Kind of the quantity.
+        """,
+    )
+
+    value = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Value of this contribution.
+        """,
+    )
+
+    unit = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Unit of the parameter as a string.
+        """,
+    )
+
+    # TODO add description quantity
+
+
+class ForceCalculations(runschema.method.ForceCalculations):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_h5md_parameters = SubSection(
+        sub_section=ParamEntry.m_def,
+        description="""
+        Contains non-normalized force calculation parameters.
+        """,
+        repeats=True,
+    )
+
+
+class NeighborSearching(runschema.method.NeighborSearching):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_h5md_parameters = SubSection(
+        sub_section=ParamEntry.m_def,
+        description="""
+        Contains non-normalized neighbor searching parameters.
+        """,
+        repeats=True,
+    )
+
+
+class AtomsGroup(runschema.system.AtomsGroup):
+    """
+    Describes a group of atoms which may constitute a sub system as in the case of a
+    molecule.
+    """
+
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_h5md_parameters = (
+        SubSection(  # TODO should this be called parameters or attributes or what?
+            sub_section=ParamEntry.m_def,
+            description="""
+        Contains additional information about the atom group .
+        """,
+            repeats=True,
+        )
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_h5md_custom_calculations = SubSection(
+        sub_section=ParamEntry.m_def,
+        description="""
+        Contains other generic custom calculations that are not already defined.
+        """,
+        repeats=True,
+    )
+
+
+class Energy(runschema.calculation.Energy):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_h5md_energy_contributions = SubSection(
+        sub_section=runschema.calculation.EnergyEntry.m_def,
+        description="""
+        Contains other custom energy contributions that are not already defined.
+        """,
+        repeats=True,
+    )
+
+
+class Author(MSection):
+    """
+    Contains the specifications of the program.
+    """
+
+    m_def = Section(validate=False)
+
+    name = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Specifies the name of the author who generated the h5md file.
+        """,
+    )
+
+    email = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Author's email.
+        """,
+    )
+
+
+class Program(runschema.run.Program):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+
+class Run(runschema.run.Run):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    # TODO Not sure how we are dealing with versioning with H5MD-NOMAD
+    x_h5md_version = Quantity(
+        type=np.int32,
+        shape=[2],
+        description="""
+        Specifies the version of the h5md schema being followed.
+        """,
+    )
+
+    x_h5md_author = SubSection(sub_section=Author.m_def)
+
+    x_h5md_creator = SubSection(sub_section=Program.m_def)