Fixed bug in volume calculation done by DOS normalizer, added the possibility...

Fixed bug in volume calculation done by DOS normalizer, added the possibility of using the fermi energy as BS energy reference for band gap calculation.

nomad/atomutils.py

@@ -41,6 +41,19 @@ def get_summed_atomic_mass(atomic_numbers: np.ndarray) -> float:
     return mass
 
 
+def get_volume(parallelepiped: np.ndarray) -> float:
+    """Calculates a volume of the given parallelepiped.
+
+    Args:
+        cell: The parallellepiped as 3x3 matrix with cell basis vectors as
+        rows.
+
+    Returns:
+        The cell volume.
+    """
+    return np.abs(np.linalg.det(parallelepiped))
+
+
 def find_match(pos: np.array, positions: np.array, eps: float) -> Union[int, None]:
     """Attempts to find a position within a larger list of positions.
 

nomad/normalizing/band_structure.py

@@ -41,8 +41,11 @@ class BandStructureNormalizer(Normalizer):
         for scc in self.section_run.section_single_configuration_calculation:
 
             # In order to resolve band gaps, we need a reference to the highest
-            # occupied energy.
-            valence_band_maximum = scc.energy_reference_highest_occupied
+            # occupied energy (semiconductors/insulators) or the Fermi energy
+            # (metals)
+            e_valence = scc.energy_reference_highest_occupied
+            e_fermi = scc.energy_reference_fermi
+            energy_reference = e_fermi if e_valence is None else e_valence
 
             # In order to resolve the special points and the reciprocal cell,
             # we need information about the system.
@@ -52,7 +55,7 @@ class BandStructureNormalizer(Normalizer):
                 if band.band_structure_kind != "vibrational":
                     self.add_reciprocal_cell(band, system)
                     self.add_brillouin_zone(band)
-                    self.add_band_gaps(band, valence_band_maximum)
+                    self.add_band_gaps(band, energy_reference)
                     self.add_path_labels(band, system)
 
     def add_reciprocal_cell(self, band: section_k_band, system: section_system):
@@ -90,10 +93,9 @@ class BandStructureNormalizer(Normalizer):
         band.reciprocal_cell = recip_cell
 
     def add_brillouin_zone(self, band: section_k_band) -> None:
-        """Adds a dictionary containing the information needed to display
-        the Brillouin zone for this material. This functionality could be put
-        into the GUI directly, with the Brillouin zone construction performed
-        from the reciprocal cell.
+        """Adds the information needed to display the Brillouin zone for this
+        material. This functionality could be put into the GUI directly, with
+        the Brillouin zone construction performed from the reciprocal cell.
 
         The Brillouin Zone is a Wigner-Seitz cell, and is thus uniquely
         defined. It's shape does not depend on the used primitive cell.
@@ -125,12 +127,11 @@ class BandStructureNormalizer(Normalizer):
 
         return k_point_distance
 
-    def add_band_gaps(self, band: section_k_band, valence_band_maximum: np.array) -> None:
-        """Given the band structure and fermi level, calculates the band gap
-        for spin channels and also reports the total band gap as the minum gap
-        found.
+    def add_band_gaps(self, band: section_k_band, energy_reference: np.array) -> None:
+        """Given the band structure and an energy reference, calculates the band gap
+        separately for all spin channels.
         """
-        if valence_band_maximum is None:
+        if energy_reference is None:
             self.logger.info("Could not resolve band gaps as the energy reference is missing.")
             return
 
@@ -142,7 +143,7 @@ class BandStructureNormalizer(Normalizer):
         # Gather the energies and k points from each segment into one big
         # array
         reciprocal_cell = reciprocal_cell.magnitude
-        valence_band_maximum = valence_band_maximum.magnitude
+        valence_band_maximum = energy_reference.magnitude
         path: np.array = []
         energies: np.array = []
         for segment in band.section_k_band_segment:

nomad/normalizing/dos.py

@@ -13,6 +13,7 @@
 # limitations under the License.
 
 from .normalizer import Normalizer
+from nomad.atomutils import get_volume
 import numpy as np
 
 
@@ -58,7 +59,7 @@ class DosNormalizer(Normalizer):
                     return
 
                 number_of_atoms = np.shape(atom_positions)[0]
-                unit_cell_volume = np.linalg.det(lattice_vectors.magnitude)
+                unit_cell_volume = get_volume(lattice_vectors.magnitude)
 
                 # Final quantities
                 dos_normed = dos_values / (number_of_atoms * unit_cell_volume)