Fix HoppingMatrix with new schema (#61)

* Added HoppingMatrix, CrystalFieldSplitting to properties

Added WignerSeitz to variables

Removed common.py module

* Added HoppingMatrix and CrystalFieldSplittings to Outputs list of properties

* Added testing

* Added todo in HoppingMatrix

src/nomad_simulations/outputs.py

@@ -27,9 +27,11 @@
 from .physical_property import PhysicalProperty
 from .numerical_settings import SelfConsistency
 from .properties import (
-    ElectronicBandGap,
     FermiLevel,
     ChemicalPotential,
+    CrystalFieldSplitting,
+    HoppingMatrix,
+    ElectronicBandGap,
     ElectronicDensityOfStates,
     XASSpectra,
 )
@@ -65,6 +67,12 @@ class Outputs(ArchiveSection):
 
     chemical_potential = SubSection(sub_section=ChemicalPotential.m_def, repeats=True)
 
+    crystal_field_splitting = SubSection(
+        sub_section=CrystalFieldSplitting.m_def, repeats=True
+    )
+
+    hopping_matrix = SubSection(sub_section=HoppingMatrix.m_def, repeats=True)
+
     electronic_band_gap = SubSection(sub_section=ElectronicBandGap.m_def, repeats=True)
 
     electronic_dos = SubSection(

src/nomad_simulations/properties/__init__.py

@@ -24,3 +24,4 @@
     ElectronicDensityOfStates,
     XASSpectra,
 )
+from .hopping_matrix import HoppingMatrix, CrystalFieldSplitting

src/nomad_simulations/properties/hopping_matrix.py

@@ -0,0 +1,106 @@
+#
+# 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 nomad.metainfo import Quantity, Section, Context
+
+from ..physical_property import PhysicalProperty
+
+
+class HoppingMatrix(PhysicalProperty):
+    """
+    Transition probability between two atomic orbitals in a tight-binding model.
+    """
+
+    iri = 'http://fairmat-nfdi.eu/taxonomy/HoppingMatrix'
+
+    n_orbitals = Quantity(
+        type=np.int32,
+        description="""
+        Number of orbitals in the tight-binding model.
+        """,
+    )
+
+    degeneracy_factors = Quantity(
+        type=np.int32,
+        shape=['*'],
+        description="""
+        Degeneracy of each Wigner-Seitz point.
+        """,
+    )
+
+    value = Quantity(
+        type=np.complex128,
+        unit='joule',
+        description="""
+        Value of the hopping matrix in joules. The elements are complex numbers defined for each Wigner-Seitz point and
+        each pair of orbitals; thus, `rank = [n_orbitals, n_orbitals]`. Note this contains also the onsite values, i.e.,
+        it includes the Wigner-Seitz point (0, 0, 0), hence the `CrystalFieldSplitting` values.
+        """,
+    )
+
+    def __init__(
+        self, m_def: Section = None, m_context: Context = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        # ! n_orbitals need to be set up during initialization of the class
+        self.rank = (
+            [] if self.n_orbitals is None else [self.n_orbitals, self.n_orbitals]
+        )
+        self.name = self.m_def.name
+
+    # TODO add normalization to extract DOS, band structure, etc, properties from `HoppingMatrix`
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+class CrystalFieldSplitting(PhysicalProperty):
+    """
+    Energy difference between the degenerated orbitals of an ion in a crystal field environment.
+    """
+
+    iri = 'http://fairmat-nfdi.eu/taxonomy/CrystalFieldSplitting'
+
+    n_orbitals = Quantity(
+        type=np.int32,
+        description="""
+        Number of orbitals in the tight-binding model.
+        """,
+    )
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        Value of the crystal field splittings in joules. This is the intra-orbital local contribution, i.e., the same orbital
+        at the same Wigner-Seitz point (0, 0, 0).
+        """,
+    )
+
+    def __init__(
+        self, m_def: Section = None, m_context: Context = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        # ! n_orbitals need to be set up during initialization of the class
+        self.rank = [] if self.n_orbitals is None else [self.n_orbitals]
+        self.name = self.m_def.name
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)

src/nomad_simulations/variables.py

@@ -129,3 +129,27 @@ def __init__(
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
+
+
+class WignerSeitz(Variables):
+    """
+    Wigner-Seitz points in which the real space is discretized. This variable is used to define `HoppingMatrix(PhysicalProperty)` and
+    other inter-cell properties. See, e.g., https://en.wikipedia.org/wiki/Wigner–Seitz_cell.
+    """
+
+    grid_points = Quantity(
+        type=np.float64,
+        shape=['n_grid_points', 3],
+        description="""
+        Wigner-Seitz points with respect to the origin cell, (0, 0, 0). These are 3D arrays stored in fractional coordinates.
+        """,
+    )
+
+    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
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)

tests/test_hopping_matrix.py

@@ -0,0 +1,70 @@
+#
+# 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 pytest
+import numpy as np
+
+from nomad_simulations.properties import HoppingMatrix, CrystalFieldSplitting
+
+
+class TestHoppingMatrix:
+    """
+    Test the `HoppingMatrix` class defined in `properties/hopping_matrix.py`.
+    """
+
+    # ! Include this initial `test_default_quantities` method when testing your PhysicalProperty classes
+    @pytest.mark.parametrize(
+        'n_orbitals, rank',
+        [
+            (None, []),
+            (3, [3, 3]),
+        ],
+    )
+    def test_default_quantities(self, n_orbitals: int, rank: list):
+        """
+        Test the default quantities assigned when creating an instance of the `HoppingMatrix` class.
+        """
+        hopping_matrix = HoppingMatrix(n_orbitals=n_orbitals)
+        assert hopping_matrix.iri == 'http://fairmat-nfdi.eu/taxonomy/HoppingMatrix'
+        assert hopping_matrix.name == 'HoppingMatrix'
+        assert hopping_matrix.rank == rank
+
+
+class TestCrystalFieldSplitting:
+    """
+    Test the `CrystalFieldSplitting` class defined in `properties/hopping_matrix.py`.
+    """
+
+    # ! Include this initial `test_default_quantities` method when testing your PhysicalProperty classes
+    @pytest.mark.parametrize(
+        'n_orbitals, rank',
+        [
+            (None, []),
+            (3, [3]),
+        ],
+    )
+    def test_default_quantities(self, n_orbitals: int, rank: list):
+        """
+        Test the default quantities assigned when creating an instance of the `CrystalFieldSplitting` class.
+        """
+        crystal_field = CrystalFieldSplitting(n_orbitals=n_orbitals)
+        assert (
+            crystal_field.iri == 'http://fairmat-nfdi.eu/taxonomy/CrystalFieldSplitting'
+        )
+        assert crystal_field.name == 'CrystalFieldSplitting'
+        assert crystal_field.rank == rank