28 add md relevant outputs

properties/__init__.py

@@ -0,0 +1,32 @@
+#
+# 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 .energies import FermiLevel, ChemicalPotential
+from .band_gap import ElectronicBandGap
+from .spectral_profile import (
+    SpectralProfile,
+    DOSProfile,
+    ElectronicDensityOfStates,
+    AbsorptionSpectrum,
+    XASSpectrum,
+)
+from .hopping_matrix import HoppingMatrix, CrystalFieldSplitting
+from .permittivity import Permittivity
+from .fermi_surface import FermiSurface
+from .band_structure import ElectronicEigenvalues, ElectronicBandStructure
+

properties/band_gap.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
+from structlog.stdlib import BoundLogger
+import pint
+from typing import Optional
+
+from nomad.metainfo import Quantity, MEnum, Section, Context
+
+from nomad_simulations.physical_property import PhysicalProperty
+
+
+class ElectronicBandGap(PhysicalProperty):
+    """
+    Energy difference between the highest occupied electronic state and the lowest unoccupied electronic state.
+    """
+
+    # ! implement `iri` and `rank` as part of `m_def = Section()`
+
+    iri = 'http://fairmat-nfdi.eu/taxonomy/ElectronicBandGap'
+
+    type = Quantity(
+        type=MEnum('direct', 'indirect'),
+        description="""
+        Type categorization of the electronic band gap. This quantity is directly related with `momentum_transfer` as by
+        definition, the electronic band gap is `'direct'` for zero momentum transfer (or if `momentum_transfer` is `None`) and `'indirect'`
+        for finite momentum transfer.
+
+        Note: in the case of finite `variables`, this quantity refers to all of the `value` in the array.
+        """,
+    )
+
+    momentum_transfer = Quantity(
+        type=np.float64,
+        shape=[2, 3],
+        description="""
+        If the electronic band gap is `'indirect'`, the reciprocal momentum transfer for which the band gap is defined
+        in units of the `reciprocal_lattice_vectors`. The initial and final momentum 3D vectors are given in the first
+        and second element. Example, the momentum transfer in bulk Si2 happens between the Γ and the (approximately)
+        X points in the Brillouin zone; thus:
+            `momentum_transfer = [[0, 0, 0], [0.5, 0.5, 0]]`.
+
+        Note: this quantity only refers to scalar `value`, not to arrays of `value`.
+        """,
+    )
+
+    spin_channel = Quantity(
+        type=np.int32,
+        description="""
+        Spin channel of the corresponding electronic band gap. It can take values of 0 or 1.
+        """,
+    )
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        The value of the electronic band gap. This value has to be positive, otherwise it will
+        prop an error and be set to None by the `normalize()` function.
+        """,
+    )
+
+    def __init__(
+        self, m_def: Section = None, m_context: Context = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        self.name = self.m_def.name
+        self.rank = []
+
+    def validate_values(self, logger: BoundLogger) -> Optional[pint.Quantity]:
+        """
+        Validate the electronic band gap `value` by checking if they are negative and sets them to None if they are.
+
+        Args:
+            logger (BoundLogger): The logger to log messages.
+        """
+        value = self.value.magnitude
+        if not isinstance(self.value.magnitude, np.ndarray):  # for scalars
+            value = np.array(
+                [value]
+            )  # ! check this when talking with Lauri and Theodore
+
+        # Set the value to 0 when it is negative
+        if (value < 0).any():
+            logger.error('The electronic band gap cannot be defined negative.')
+            return None
+
+        if not isinstance(self.value.magnitude, np.ndarray):  # for scalars
+            value = value[0]
+        return value * self.value.u
+
+    def resolve_type(self, logger: BoundLogger) -> Optional[str]:
+        """
+        Resolves the `type` of the electronic band gap based on the stored `momentum_transfer` values.
+
+        Args:
+            logger (BoundLogger): The logger to log messages.
+
+        Returns:
+            (Optional[str]): The resolved `type` of the electronic band gap.
+        """
+        mtr = self.momentum_transfer if self.momentum_transfer is not None else []
+
+        # Check if the `momentum_transfer` is [], and return the type and a warning in the log for `indirect` band gaps
+        if len(mtr) == 0:
+            if self.type == 'indirect':
+                logger.warning(
+                    'The `momentum_transfer` is not stored for an `indirect` band gap.'
+                )
+            return self.type
+
+        # Check if the `momentum_transfer` has at least two elements, and return None if it does not
+        if len(mtr) == 1:
+            logger.warning(
+                'The `momentum_transfer` should have at least two elements so that the difference can be calculated and the type of electronic band gap can be resolved.'
+            )
+            return None
+
+        # Resolve `type` from the difference between the initial and final momentum transfer
+        momentum_difference = np.diff(mtr, axis=0)
+        if (np.isclose(momentum_difference, np.zeros(3))).all():
+            return 'direct'
+        else:
+            return 'indirect'
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+        # Checks if the `value` is negative and sets it to None if it is.
+        self.value = self.validate_values(logger)
+        if self.value is None:
+            # ? What about deleting the class if `value` is None?
+            logger.error('The `value` of the electronic band gap is not stored.')
+            return
+
+        # Resolve the `type` of the electronic band gap from `momentum_transfer`, ONLY for scalar `value`
+        if isinstance(self.value.magnitude, np.ndarray):
+            logger.info(
+                'We do not support `type` which describe individual elements in an array `value`.'
+            )
+        else:
+            self.type = self.resolve_type(logger)
+