added mechanics and molecular

src/nomad_simulations/mechanics.py

@@ -0,0 +1,129 @@
+#
+# 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.
+#
+#
+# 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
+import numpy as np
+
+from nomad.units import ureg
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum
+from nomad.metainfo.metainfo import DirectQuantity, Dimension
+from nomad.datamodel.metainfo.annotations import ELNAnnotation
+
+from .outputs import Outputs, SCFOutputs, WorkflowOutputs, TrajectoryOutputs
+from .atoms_state import AtomsState
+from .physical_property import PhysicalProperty
+
+
+from nomad.datamodel.metainfo.common import (
+    FastAccess,
+    PropertySection,
+    ProvenanceTracker,
+)
+from nomad.metainfo import (
+    Category,
+    HDF5Reference,
+    MCategory,
+    MEnum,
+    MSection,
+    Package,
+    Quantity,
+    Reference,
+    Section,
+    SectionProxy,
+    SubSection,
+)
+
+from .model_system import ModelSystem
+
+
+class StressEntry(Atomic):
+    """
+    Section describing a contribution to or a type of stress.
+    """
+
+    m_def = Section(validate=False)
+
+    value = Quantity(
+        type=np.dtype(np.float64),
+        shape=[3, 3],
+        unit='joule/meter**3',
+        description="""
+        Value of the stress on the simulation cell. It is given as the functional
+        derivative of the corresponding energy with respect to the deformation tensor.
+        """,
+    )
+
+    values_per_atom = Quantity(
+        type=np.dtype(np.float64),
+        shape=['number_of_atoms', 3, 3],
+        unit='joule/meter**3',
+        description="""
+        Value of the atom-resolved stresses.
+        """,
+    )
+
+
+class Stress(MSection):
+    """
+    Section containing all stress types and contributions.
+    """
+
+    m_def = Section(validate=False)
+
+    total = SubSection(
+        sub_section=StressEntry.m_def,
+        description="""
+        Contains the value and information regarding the stress on the simulation cell
+        and the atomic stresses corresponding to energy_total.
+        """,
+    )
+
+    contributions = SubSection(
+        sub_section=StressEntry.m_def,
+        description="""
+        Contains contributions for the total stress.
+        """,
+        repeats=True,
+    )
+
+    types = SubSection(
+        sub_section=StressEntry.m_def,
+        description="""
+        Contains other types of stress.
+        """,
+        repeats=True,
+    )

src/nomad_simulations/molecular.py

@@ -0,0 +1,109 @@
+#
+# 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.
+#
+#
+# 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
+import numpy as np
+
+from nomad.units import ureg
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum
+from nomad.metainfo.metainfo import DirectQuantity, Dimension
+from nomad.datamodel.metainfo.annotations import ELNAnnotation
+
+from .outputs import Outputs, SCFOutputs, WorkflowOutputs, TrajectoryOutputs
+from .atoms_state import AtomsState
+from .physical_property import PhysicalProperty
+
+
+class RadiusOfGyration(PhysicalProperty):
+
+    value = Quantity(
+        type=np.float64,
+        unit='m',
+    )
+
+class Hessian(TrajectoryOutputs):
+    """
+    Section containing the Hessian matrix, i.e., 2nd derivatives with respect to atomic displacements,
+    of the potential energy of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.dtype(np.float64),
+        shape=['n_atoms', 'n_atoms', 3, 3],
+        unit='joule / m ** 2',
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+        self.value_unit = 'joule / m ** 2'
+        self.name = 'hessian'
+        self.variables = [['atom_index'], ['atom_index'], ['x', 'y', 'z'], ['x', 'y', 'z']]
+        self.bins = [np.range(self.n_atoms), np.range(self.n_atoms)]
+
+
+class RadialDistributionFunction(TrajectoryOutputs):
+    """
+    Section containing information about the calculation of
+    radial distribution functions (rdfs).
+    """
+
+    value = Quantity(
+        type=np.dtype(np.float64),
+        shape=['*'],
+    )
+
+    variables = Quantity(
+        type=str,
+        shape=[1],
+        description="""
+        Name/description of the variables along which the property is defined.
+        """,
+    )
+
+    bins = Quantity(
+        type=np.float64,
+        shape=['*'],
+        unit='m',
+        description="""
+        Distances along which the rdf was calculated.
+        """,
+    )
+
+    def normalize(self, archive, logger):
+        super().normalize(archive, logger)
+        self.variables = ['distance']
+        assert len(self.bins) == len(self.value)