added physicalproperty

src/nomad_simulations/property.py

@@ -0,0 +1,188 @@
+#
+# 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, Reference
+from nomad.metainfo.metainfo import DirectQuantity, Dimension
+from nomad.datamodel.metainfo.annotations import ELNAnnotation
+
+from .model_system import ModelSystem
+from .outputs import Outputs
+
+class Errors(ArchiveSection):
+    """
+    A base section used to define errors.
+    """
+
+    type = Quantity(
+        type=str,
+        description="""
+        Type of error.
+        """,
+        a_eln=ELNAnnotation(component='StringEditQuantity'),
+    )
+
+    value = Quantity(
+        type=np.float64,
+        shape=['*'],
+        description="""
+        Value/s of the error.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+class Smoothing(ArchiveSection):
+    """
+    A base section used to define data smoothing procedures.
+    """
+
+    type = Quantity(
+        type=str,
+        description="""
+        Type of smoothing, e.g., "running_average".
+        """,
+        a_eln=ELNAnnotation(component='StringEditQuantity'),
+    )
+
+    parameters = SubSection(sub_section=ParameterEntry.m_def, repeats=True)
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+class PhysicalPropery(ArchiveSection):
+    """
+    A base section used to define properties.
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+    name = Quantity(
+        type=str,
+        description="""
+        Name of the Property section. This will be set by the individual subclasses.
+        """,
+        a_eln=ELNAnnotation(component='StringEditQuantity'),
+    )
+
+    type = Quantity(
+        type=str,
+        description="""
+        Categorization of the property.
+        """,
+        a_eln=ELNAnnotation(component='StringEditQuantity'),
+    )
+
+    label = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Additional descriptive label for the property.
+        """,
+    )
+
+    description = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Detailed description of the property.
+        """,
+    )
+
+    # ? Just copied this from Quantity, not sure what I am doing
+    # shape/fullshape = DirectQuantity(type=Dimension, shape=['0..*'], name='shape', default=[])
+
+    variables = Quantity(
+        type=str,
+        shape=['*'],
+        description="""
+        Name/description of the variables along which the property is defined.
+        """,
+    )
+
+    bins = Quantity(
+        type=np.float64,
+        shape=['*'],
+        description="""
+        Values of the variable along which the property is stored.
+        """,
+    )
+
+    # TODO Add a check in normalization to ensure that value and bins have the same first dimension
+    value = Quantity(
+        type=np.float64,
+        shape=['*'],
+        description="""
+        Values of the property with units defined within the individual subclass.
+        """,
+    )
+
+    # TODO Add value_per_particle?
+
+    # ! Probably not needed, already in Quantity
+    is_scalar = Quantity(
+        type=bool,
+        default=False,
+        description="""
+        Flag indicating whether the output property is a scalar. If yes, variable and bin quantities
+        are ensured to not be populated.
+        """,
+    )
+
+    errors = SubSection(sub_section=Errors.m_def, repeats=True)
+    smoothing = SubSection(sub_section=Smoothing.m_def, repeats=True)
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+        # ! Use is scalar under value instead?
+        if self.is_scalar:
+            if self.variables is not None:
+                self.variables = None
+                # TODO throw warning/error
+            if self.bins is not None:
+                self.bins = None
+                # TODO throw warning/error
+                # TODO ...
+