Merge pull request #71 from nomad-coe/49-add-support-for-h5md-files

49 add support for h5md files

atomisticparsers/h5md/README.md

@@ -0,0 +1,5 @@
+This is a NOMAD parser for the [H5MD](http://www.??.org/) schema for hdf5 files. It will read
+an hdf5 file and transform the content into NOMAD's unified Metainfo based Archive format according to the H5MD schema.
+
+
+

atomisticparsers/h5md/__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 H5MDParser

atomisticparsers/h5md/__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 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

@@ -0,0 +1,24 @@
+#
+# 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 nomad.metainfo import Environment
+
+from . import h5md
+
+m_env = Environment()
+m_env.m_add_sub_section(Environment.packages, h5md.m_package)

atomisticparsers/h5md/metainfo/h5md.py

@@ -0,0 +1,190 @@
+#
+# 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
+)
+from nomad.datamodel.metainfo import simulation
+
+
+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.dtype(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(simulation.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(simulation.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(simulation.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(simulation.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(simulation.calculation.Energy):
+
+    m_def = Section(validate=False, extends_base_section=True,)
+
+    x_h5md_energy_contributions = SubSection(
+        sub_section=simulation.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 Run(simulation.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.dtype(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=simulation.run.Program.m_def)

atomisticparsers/h5md/nomad_plugin.yaml

@@ -0,0 +1,19 @@
+code_category: Atomistic code
+# code_homepage: http://www.??.org/
+# TODO is this the correct category
+code_name: H5MD
+metadata:
+  codeCategory: Atomistic code
+  codeLabel: H5MD
+  codeLabelStyle: All in capitals
+  codeName: h5md
+  # codeUrl: http://www.??.org/
+  parserDirName: dependencies/parsers/atomistic/atomisticparsers/h5md/
+  parserGitUrl: https://github.com/nomad-coe/atomistic-parsers.git
+  parserSpecific: ''
+  preamble: ''
+  status: production
+  tableOfFiles: ''
+name: parsers/h5md
+parser_class_name: atomisticparsers.h5md.parser.H5MDParser
+python_package: atomisticparsers.h5md