Fixed issue with API, refactored BZ information into proper metainfo.

nomad/app/api/encyclopedia.py

@@ -789,16 +789,16 @@ statistics = api.model("statistics", {
     "histogram": fields.Nested(histogram)
 })
 statistics_result = api.model("statistics_result", {
-    "cell_volume": fields.Nested(statistics),
-    "atomic_density": fields.Nested(statistics),
-    "mass_density": fields.Nested(statistics),
-    "lattice_a": fields.Nested(statistics),
-    "lattice_b": fields.Nested(statistics),
-    "lattice_c": fields.Nested(statistics),
-    "alpha": fields.Nested(statistics),
-    "beta": fields.Nested(statistics),
-    "gamma": fields.Nested(statistics),
-    "band_gap": fields.Nested(statistics),
+    "cell_volume": fields.Nested(statistics, skip_none=True),
+    "atomic_density": fields.Nested(statistics, skip_none=True),
+    "mass_density": fields.Nested(statistics, skip_none=True),
+    "lattice_a": fields.Nested(statistics, skip_none=True),
+    "lattice_b": fields.Nested(statistics, skip_none=True),
+    "lattice_c": fields.Nested(statistics, skip_none=True),
+    "alpha": fields.Nested(statistics, skip_none=True),
+    "beta": fields.Nested(statistics, skip_none=True),
+    "gamma": fields.Nested(statistics, skip_none=True),
+    "band_gap": fields.Nested(statistics, skip_none=True),
 })
 property_map = {
     "cell_volume": "encyclopedia.material.idealized_structure.cell_volume",
@@ -827,7 +827,6 @@ class EncStatisticsResource(Resource):
         calculations.
         """
         # Get query parameters as json
-        print(request.get_json())
         try:
             data = marshal(request.get_json(), statistics_query)
         except Exception as e:
@@ -908,7 +907,7 @@ wyckoff_set_result = api.model("wyckoff_set_result", {
     "wyckoff_letter": fields.String,
     "indices": fields.List(fields.Integer),
     "element": fields.String,
-    "variables": fields.List(fields.Nested(wyckoff_variables_result)),
+    "variables": fields.List(fields.Nested(wyckoff_variables_result, skip_none=True)),
 })
 lattice_parameters = api.model("lattice_parameters", {
     "a": fields.Float,
@@ -1033,21 +1032,22 @@ electronic_band_structure = api.model("electronic_band_structure", {
     "reciprocal_cell": fields.List(fields.List(fields.Float)),
     "brillouin_zone": fields.Raw,
     "section_k_band_segment": fields.Raw,
+    "section_band_gap": fields.Raw,
 })
 electronic_dos = api.model("electronic_dos", {
     "dos_energies": fields.List(fields.Float),
-    "dos_values": fields.List(fields.Float),
+    "dos_values": fields.List(fields.List(fields.Float)),
 })
-calculation_property_result = api.model("calculation_query", {
-    "lattice_parameters": fields.Nested(lattice_parameters),
-    "energies": fields.Nested(energies),
+calculation_property_result = api.model("calculation_property_result", {
+    "lattice_parameters": fields.Nested(lattice_parameters, skip_none=True),
+    "energies": fields.Nested(energies, skip_none=True),
     "mass_density": fields.Float,
     "atomic_density": fields.Float,
     "cell_volume": fields.Float,
-    "wyckoff_sets": fields.Nested(wyckoff_set_result),
-    "band_gap": fields.Float(wyckoff_set_result),
-    "electronic_band_structure": fields.Nested(electronic_band_structure),
-    "electronic_dos": fields.Nested(electronic_dos),
+    "wyckoff_sets": fields.Nested(wyckoff_set_result, skip_none=True),
+    "band_gap": fields.Float,
+    "electronic_band_structure": fields.Nested(electronic_band_structure, skip_none=True),
+    "electronic_dos": fields.Nested(electronic_dos, skip_none=True),
 })
 
 
@@ -1057,7 +1057,7 @@ class EncCalculationResource(Resource):
     @api.response(400, "Bad request")
     @api.response(200, "Metadata send", fields.Raw)
     @api.expect(calculation_property_query, validate=False)
-    # @api.marshal_with(calculation_property_result, skip_none=True)
+    @api.marshal_with(calculation_property_result, skip_none=True)
     @api.doc("enc_calculation")
     def post(self, material_id, calc_id):
         """Used to return calculation details. Some properties are not

nomad/datamodel/metainfo/public.py

@@ -2269,6 +2269,28 @@ class section_band_gap(MSection):
     )
 
 
+class section_brillouin_zone(MSection):
+    '''Defines a polyhedra for the Brillouin zone in reciprocal space.
+    '''
+    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_brillouin_zone'))
+
+    vertices = Quantity(
+        type=np.dtype(np.float64),
+        shape=[3, "1..*"],
+        description='''
+        The vertices of the Brillouin zone corners as 3D coordinates in reciprocal space.
+        ''',
+        a_legacy=LegacyDefinition(name='vertices'))
+    faces = Quantity(
+        type=np.dtype(np.int32),
+        shape=["1..*", "3..*"],
+        description='''
+        The faces of the Brillouin zone polyhedron as vertex indices. The
+        surface normal is determined by a right-hand ordering of the points.
+        ''',
+        a_legacy=LegacyDefinition(name='faces'))
+
+
 class section_k_band(MSection):
     '''
     This section stores information on a $k$-band (electronic or vibrational band
@@ -2297,22 +2319,10 @@ class section_k_band(MSection):
         a_legacy=LegacyDefinition(name='reciprocal_cell')
     )
 
-    brillouin_zone = Quantity(
-        type=str,
-        description="""
-        The Brillouin zone that corresponds to the reciprocal cell used in the
-        band calculation. The Brillouin Zone is defined as a list of vertices
-        and facets that are encoded with JSON. The vertices are 3D points in
-        the reciprocal space, and facets are determined by a chain of vertice
-        indices, with a right-hand ordering determining the surface normal
-        direction.
-        {
-          "vertices": [[3, 2, 1], ...]
-          "faces":  [[0, 1, 2, 3], ...]
-        }
-        """,
-        a_legacy=LegacyDefinition(name='brillouin_zone')
-    )
+    brillouin_zone = SubSection(
+        sub_section=SectionProxy('section_brillouin_zone'),
+        repeats=False,
+        a_legacy=LegacyDefinition(name='section_k_band_segment'))
 
     section_band_gap = SubSection(
         sub_section=section_band_gap.m_def,

nomad/normalizing/band_structure.py

@@ -12,11 +12,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import json
 import numpy as np
 import ase
 
-from nomad.datamodel.metainfo.public import section_k_band, section_band_gap, section_system
+from nomad.datamodel.metainfo.public import section_k_band, section_band_gap, section_system, section_brillouin_zone
 from nomad.normalizing.normalizer import Normalizer
 from nomad import config, atomutils
 from nomad.constants import pi
@@ -104,9 +103,10 @@ class BandStructureNormalizer(Normalizer):
             self.logger.info("Could not resolve Brillouin zone as reciprocal cell is missing.")
             return
 
-        brillouin_zone = atomutils.get_brillouin_zone(recip_cell.magnitude)
-        bz_json = json.dumps(brillouin_zone)
-        band.brillouin_zone = bz_json
+        brillouin_zone_data = atomutils.get_brillouin_zone(recip_cell.magnitude)
+        section_bz = band.m_create(section_brillouin_zone)
+        section_bz.vertices = brillouin_zone_data["vertices"]
+        section_bz.faces = brillouin_zone_data["faces"]
 
     def get_k_space_distance(self, reciprocal_cell: np.array, point1: np.array, point2: np.array) -> float:
         """Used to calculate the Euclidean distance of two points in k-space,