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

atomisticparsers/dftbplus/__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 DFTBPlusParser

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

atomisticparsers/dftbplus/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 dftbplus

atomisticparsers/dftbplus/metainfo/dftbplus.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
+
+from nomad.metainfo import (  # pylint: disable=unused-import
+    Package,
+    Quantity,
+    Section,
+    SubSection,
+    JSON,
+)
+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 AtomParameters(runschema.method.AtomParameters):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    atom = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_charge = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class System(runschema.system.System):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dftbp_atom_positions_X = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_atom_positions_Y = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_atom_positions_Z = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class BandEnergies(runschema.calculation.BandEnergies):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dftbp_eigenvalues_values = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_eigenvalues_occupation = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dftbp_atom_forces_X = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_atom_forces_Y = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_atom_forces_Z = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_force_max = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_force_max_mov = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class Energy(runschema.calculation.Energy):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dftbp_total_mermin = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_band = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_ts = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_band_free = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_band_t0 = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_scc = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_dispersion = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+    x_dftbp_force_related = SubSection(runschema.calculation.EnergyEntry.m_def)
+
+
+class TB(runschema.method.TB):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dftbp_input_parameters = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_dftbp_n_sk_files = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dftbp_sk_files = Quantity(
+        type=str,
+        shape=['x_dftbp_n_sk_files'],
+        description="""
+        """,
+    )
+
+
+class Run(runschema.run.Run):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dftbp_input_file = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dftbp_processed_input_file = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dftbp_parser_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        """,
+    )