Added exception handling when reference from scc to system is missing, added...

Added exception handling when reference from scc to system is missing, added bravais_lattice to Encyclopedia.material.

nomad/metainfo/encyclopedia.py

@@ -50,6 +50,31 @@ class Material(MSection):
         Position of each atom, given in relative coordinates.
         """
     )
+    bravais_lattice = Quantity(
+        type=str,
+        description="""
+        The Bravais lattice type in the Pearson notation, where the first
+        lowercase letter indicates the crystal system, and the second uppercase
+        letter indicates the lattice type.
+
+        Crystal system letters:
+
+        a = Triclinic
+        m = Monoclinic
+        o = Orthorhombic
+        t = Tetragonal
+        h = Hexagonal and Trigonal
+        c = Cubic
+
+        Lattice type letters:
+
+        P = Primitive
+        S (A, B, C) = One side/face centred
+        I = Body centered
+        R = Rhombohedral centring
+        F = All faces centred
+        """
+    )
 
 
 class Calculation(MSection):

nomad/normalizing/encyclopedia.py

@@ -75,8 +75,9 @@ class EncyclopediaNormalizer(Normalizer):
         pass
 
     # NOTE: System normalizer
-    def get_bravais_lattice(self) -> None:
-        pass
+    def get_bravais_lattice(self, material: Material, section_system: Dict) -> None:
+        bravais_lattice = section_system["section_symmetry"][0]["bravais_lattice"]
+        material.bravais_lattice = bravais_lattice
 
     # NOTE: Band structure normalizer
     def get_brillouin_zone(self) -> None:
@@ -502,6 +503,7 @@ class EncyclopediaNormalizer(Normalizer):
         self.get_number_of_atoms(material, std_atoms)
         self.get_atom_labels(material, std_atoms)
         self.get_atomic_density(calculation, repr_atoms)
+        self.get_bravais_lattice(material, system)
 
         # Put the encyclopedia section into backend
         self._backend.add_mi2_section(sec_enc)

nomad/normalizing/normalizer.py

@@ -112,7 +112,7 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
                 else:
                     sequences.append(frames)
 
-        # If no frames exist, consider all existing sccs
+        # If no frame_sequences exist, consider all existing sccs
         if len(sequences) == 0:
             try:
                 sccs = self._backend.get_sections(s_scc)
@@ -132,9 +132,15 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
                 indices = [0, -2, -1]
             else:
                 break
-            for scc_idx in [seq[idx] for idx in indices]:
-                system_idx = sccs[scc_idx][r_scc_to_system]
-                systems.append(system_idx)
+            for idx in indices:
+                scc_idx = seq[idx]
+                scc = sccs[scc_idx]
+                try:
+                    system_idx = scc[r_scc_to_system]
+                except KeyError:
+                    self.logger.info("section_single_configuration_calculation is missing a reference into a system.")
+                else:
+                    systems.append(system_idx)
 
         if len(systems) == 0:
             self.logger.error('no "representative" section system found')

tests/normalizing/test_encyclopedia.py

@@ -54,3 +54,4 @@ def test_bulk_information(geometry_optimization: Encyclopedia):
     assert go.material.number_of_atoms == 4
     assert go.material.atom_labels == ["Na", "Na", "Na", "Na"]
     assert go.calculation.atomic_density == pytest.approx(4.0e+30, rel=0.000001, abs=None)
+    assert go.material.bravais_lattice == "cF"