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

atomisticparsers/libatoms/__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 LibAtomsParser

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

atomisticparsers/libatoms/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 lib_atoms

atomisticparsers/libatoms/metainfo/lib_atoms.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 x_lib_atoms_section_gap(MSection):
+    """
+    Description of Gaussian Approximation Potentials (GAPs).
+    """
+
+    m_def = Section(validate=False)
+
+    x_lib_atoms_training_config_refs = Quantity(
+        type=runschema.calculation.Calculation,
+        shape=['n_sparseX'],
+        description="""
+        References to frames in training configuration.
+        """,
+    )
+
+    x_lib_atoms_GAP_params_label = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_GAP_params_svn_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_GAP_data_do_core = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_GAP_data_e0 = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_command_line_command_line = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpSparse_n_coordinate = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_n_permutations = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_sparsified = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_signal_variance = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_label = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_n_sparseX = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_covariance_type = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_signal_mean = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_sparseX_filename = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_dimensions = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_theta = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_descriptor = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_perm_permutation = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_perm_i = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_alpha = Quantity(
+        type=np.float64,
+        shape=['n_sparseX', 2],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+    x_lib_atoms_gpCoordinates_sparseX = Quantity(
+        type=np.float64,
+        shape=['n_sparseX', 'dimensions'],
+        description="""
+        GAP classifier.
+        """,
+    )
+
+
+class Run(runschema.run.Run):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_lib_atoms_section_gap = SubSection(
+        sub_section=SectionProxy('x_lib_atoms_section_gap'), repeats=False
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_lib_atoms_virial_tensor = Quantity(
+        type=np.float64,
+        shape=[3, 3],
+        unit='pascal',
+        description="""
+        Virial tensor for this frame.
+        """,
+    )
+
+    x_lib_atoms_config_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Configuration type, e.g. = dislocation_quadrupole.
+        """,
+    )

atomisticparsers/libatoms/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.
+#
+
+from simulationparsers.utils import BasicParser
+from nomad.units import ureg
+
+
+class LibAtomsParser:
+    def __init__(self):
+        re_f = r'\-*\d+\.\d+E*e*\-*\+*\d*'
+
+        self._parser = BasicParser(
+            'libAtoms',
+            units_mapping=dict(length=ureg.angstrom, energy=ureg.eV),
+            # necessary to include version due to auto type conversion
+            program_version=r'(svn\_version\=\"\d+\")',
+            atom_labels_atom_positions_atom_forces=r'(\<\!\[CDATA\[[A-Z][a-z]* +[\s\S]+?)(?:\<\!\[CDATA\[\d+\]\]\>|\Z)',
+            energy_total=rf'slice\_sample energy\=({re_f})',
+        )
+
+    def parse(self, mainfile, archive, logger=None):
+        self._parser.parse(mainfile, archive, logger=None)

atomisticparsers/namd/__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 NAMDParser

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

atomisticparsers/namd/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 namd