Added infrastructure config for materials index, added initial function for...

Added infrastructure config for materials index, added initial function for pushing calculation info to that index.

encyclopedia-gui @ f19b84de

-Subproject commit bdffb455f21577435477daa9c871205e6c118efd
+Subproject commit f19b84de11b1004548e8e5a324df78bb356e7896

phonopy @ bc9be212

-Subproject commit 59ecd6cddb2bbf75000a1454fe40ceace2d2c207
+Subproject commit bc9be2124405b87987e04d286e385f23b7b5712f

nomad/app/api/repo.py

@@ -26,7 +26,6 @@ import elasticsearch.helpers
 from datetime import datetime
 
 from nomad import search, utils, datamodel, processing as proc, infrastructure, files
-from nomad.metainfo import search_extension
 from nomad.datamodel import Dataset, User, EditableUserMetadata
 from nomad.app import common
 from nomad.app.common import RFC3339DateTime, DotKeyNested
@@ -88,13 +87,13 @@ _search_request_parser.add_argument(
 _search_request_parser.add_argument(
     'metrics', type=str, action='append', help=(
         'Metrics to aggregate over all quantities and their values as comma separated list. '
-        'Possible values are %s.' % ', '.join(search_extension.metrics.keys())))
+        'Possible values are %s.' % ', '.join(search.metrics.keys())))
 _search_request_parser.add_argument(
     'statistics', type=str, action='append', help=(
         'Quantities for which to aggregate values and their metrics.'))
 _search_request_parser.add_argument(
     'exclude', type=str, action='split', help='Excludes the given keys in the returned data.')
-for group_name in search_extension.groups:
+for group_name in search.groups:
     _search_request_parser.add_argument(
         group_name, type=bool, help=('Return %s group data.' % group_name))
     _search_request_parser.add_argument(
@@ -106,15 +105,15 @@ _repo_calcs_model_fields = {
         'A dict with all statistics. Each statistic is dictionary with a metrics dict as '
         'value and quantity value as key. The possible metrics are code runs(calcs), %s. '
         'There is a pseudo quantity "total" with a single value "all" that contains the '
-        ' metrics over all results. ' % ', '.join(search_extension.metrics.keys())))}
+        ' metrics over all results. ' % ', '.join(search.metrics.keys())))}
 
-for group_name in search_extension.groups:
+for group_name in search.groups:
     _repo_calcs_model_fields[group_name] = (DotKeyNested if '.' in group_name else fields.Nested)(api.model('RepoGroup', {
         'after': fields.String(description='The after value that can be used to retrieve the next %s.' % group_name),
         'values': fields.Raw(description='A dict with %s as key. The values are dicts with "total" and "examples" keys.' % group_name)
     }), skip_none=True)
 
-for qualified_name, quantity in search_extension.search_quantities.items():
+for qualified_name, quantity in search.search_quantities.items():
     _repo_calcs_model_fields[qualified_name] = fields.Raw(
         description=quantity.description, allow_null=True, skip_none=True)
 
@@ -123,7 +122,7 @@ _repo_calcs_model_fields.update(**{
     'interval': fields.String(description='Interval to use for upload time aggregation.', allow_null=True, skip_none=True),
     'metrics': fields.List(fields.String, description=(
         'Metrics to aggregate over all quantities and their values as comma separated list. '
-        'Possible values are %s.' % ', '.join(search_extension.metrics.keys())), allow_null=True, skip_none=True),
+        'Possible values are %s.' % ', '.join(search.metrics.keys())), allow_null=True, skip_none=True),
     'statistics_required': fields.List(fields.String, description='Quantities for which to aggregate values and their metrics.', allow_null=True, skip_none=True),
     'exclude': fields.List(fields.String, description='Excludes the given keys in the returned data.', allow_null=True, skip_none=True)
 })
@@ -192,7 +191,7 @@ class RepoCalcsResource(Resource):
             abort(400, message='bad parameters: %s' % str(e))
 
         for metric in metrics:
-            if metric not in search_extension.metrics:
+            if metric not in search.metrics:
                 abort(400, message='there is no metric %s' % metric)
 
         search_request = search.SearchRequest()
@@ -214,7 +213,7 @@ class RepoCalcsResource(Resource):
 
         group_metrics = [
             group_quantity.metric_name
-            for group_name, group_quantity in search_extension.groups.items()
+            for group_name, group_quantity in search.groups.items()
             if args.get(group_name, False)]
         total_metrics = metrics + group_metrics
         if len(total_metrics) > 0:
@@ -230,7 +229,7 @@ class RepoCalcsResource(Resource):
                 results = search_request.execute_scrolled(scroll_id=scroll_id, size=per_page)
 
             else:
-                for group_name, group_quantity in search_extension.groups.items():
+                for group_name, group_quantity in search.groups.items():
                     if args.get(group_name, False):
                         kwargs: Dict[str, Any] = {}
                         if group_name == 'uploads_grouped':
@@ -252,7 +251,7 @@ class RepoCalcsResource(Resource):
                 if 'quantities' in results:
                     quantities = results.pop('quantities')
 
-                for group_name, group_quantity in search_extension.groups.items():
+                for group_name, group_quantity in search.groups.items():
                     if args.get(group_name, False):
                         results[group_name] = quantities[group_quantity.qualified_name]
 
@@ -335,7 +334,7 @@ class RepoCalcsResource(Resource):
             abort(400, message='bad parameters: %s' % str(e))
 
         for metric in metrics:
-            if metric not in search_extension.metrics:
+            if metric not in search.metrics:
                 abort(400, message='there is no metric %s' % metric)
 
         search_request = search.SearchRequest()
@@ -363,7 +362,7 @@ class RepoCalcsResource(Resource):
 
         group_metrics = [
             group_quantity.metric_name
-            for group_name, group_quantity in search_extension.groups.items()
+            for group_name, group_quantity in search.groups.items()
             if group_name in data_in]
         total_metrics = metrics + group_metrics
         if len(total_metrics) > 0:
@@ -379,7 +378,7 @@ class RepoCalcsResource(Resource):
                 results = search_request.execute_scrolled(scroll_id=scroll_id, size=per_page)
 
             else:
-                for group_name, group_quantity in search_extension.groups.items():
+                for group_name, group_quantity in search.groups.items():
                     if group_name in data_in:
                         kwargs: Dict[str, Any] = {}
                         if group_name == 'uploads_grouped':
@@ -401,7 +400,7 @@ class RepoCalcsResource(Resource):
                 if 'quantities' in results:
                     quantities = results.pop('quantities')
 
-                for group_name, group_quantity in search_extension.groups.items():
+                for group_name, group_quantity in search.groups.items():
                     if group_name in data_in:
                         results[group_name] = quantities[group_quantity.qualified_name]
 
@@ -865,7 +864,7 @@ _repo_quantities_search_request_parser.add_argument(
 _repo_quantities_model = api.model('RepoQuantitiesResponse', {
     'quantities': fields.Nested(api.model('RepoQuantities', {
         quantity: fields.List(fields.Nested(_repo_quantity_model))
-        for quantity in search_extension.search_quantities
+        for quantity in search.search_quantities
     }))
 })
 

nomad/cli/admin/admin.py

@@ -21,6 +21,10 @@ import threading
 
 from nomad import processing as proc, search, datamodel, infrastructure, utils, config
 from nomad.cli.cli import cli
+from nomad.datamodel.material import Material, Calculation
+from nomad.datamodel.encyclopedia import EncyclopediaMetadata
+from nomad.search import material_document
+from nomad.datamodel.material import Material, Calculation, Method, Properties, IdealizedStructure, Energies, Workflow, Bulk
 
 
 def __run_parallel(
@@ -209,16 +213,367 @@ def index(threads, dry):
     if dry:
         for _ in elastic_updates():
             pass
-    if threads > 1:
-        print('  use %d threads' % threads)
-        for _ in elasticsearch.helpers.parallel_bulk(
-                infrastructure.elastic_client, elastic_updates(), chunk_size=500,
-                thread_count=threads):
+    else:
+        if threads > 1:
+            print('  use %d threads' % threads)
+            for _ in elasticsearch.helpers.parallel_bulk(
+                    infrastructure.elastic_client, elastic_updates(), chunk_size=500,
+                    thread_count=threads):
+                pass
+        else:
+            elasticsearch.helpers.bulk(
+                infrastructure.elastic_client, elastic_updates())
+        search.refresh()
+
+    print('')
+    print('indexing completed')
+
+
+@admin.command()
+@click.option('--threads', type=int, default=1, help='Number of threads to use.')
+@click.option('--code', multiple=True, type=str, help='Index only calculcations of given codes.')
+@click.option('--dry', is_flag=True, help='Do not index, just compute entries.')
+@click.option('--in-place', is_flag=True, default=False, help='Perform indexing in the current elastic search index. Meant only for small reindex operations.')
+@click.option('-n', type=int, default=None, help='Number of calculations to process. Leave undefined to process all calculations.')
+@click.option('--source',
+              type=click.Choice(['mongo', 'es'], case_sensitive=True))
+def index_materials(threads, code, dry, in_place, n, source):
+    """(Re-)index all materials.
+
+    This command will completely rebuild the materials index. The index is
+    built from the material metainfo stored in MongoDB. The materials index can
+    be used normally during the reindexing.
+    """
+    chunk_size = 500
+    infrastructure.setup_mongo()
+    client = infrastructure.setup_elastic()
+
+    # In order to do the reindexing with zero downtime, two different indices
+    # are rotated and an alias is used
+    old_index_name = list(client.indices.get(config.elastic.materials_index_name).keys())[0]
+    if in_place:
+        target_index_name = old_index_name
+    else:
+        if old_index_name == config.elastic.materials_index_name + "_a":
+            target_index_name = config.elastic.materials_index_name + "_b"
+        elif old_index_name == config.elastic.materials_index_name + "_b":
+            target_index_name = config.elastic.materials_index_name + "_a"
+        else:
+            raise ValueError(
+                "Unrecognized index name accociated with the alias {}"
+                .format(config.elastic.materials_index_name)
+            )
+
+    if source == "mongo":
+        all_calcs = proc.Calc.objects().count()
+        print('indexing materials from %d calculations ...' % all_calcs)
+
+        # Bulk update
+        def elastic_updates():
+            with utils.ETA(all_calcs, '   index %10d of %10d calcs, ETA %s') as eta:
+                mongo_db = infrastructure.mongo_client[config.mongo.db_name]
+                mongo_collection = mongo_db['archive']
+                i_calc = 0
+                for mongo_archive in mongo_collection.find():
+                    i_calc += 1
+                    if n is not None:
+                        if i_calc > n:
+                            return
+                    eta.add()
+
+                    # Do not process entries that do not have the material
+                    # information
+                    try:
+                        status = mongo_archive["section_metadata"]["encyclopedia"]["status"]
+                        if status != EncyclopediaMetadata.status.type.success:
+                            raise AttributeError
+                    except (KeyError, AttributeError, IndexError):
+                        continue
+
+                    # Create material information
+                    metadata = mongo_archive["section_metadata"]
+                    encyclopedia = EncyclopediaMetadata.m_from_dict(metadata["encyclopedia"])
+                    dft = metadata["dft"]
+                    material: Material = Material()
+                    material.material_id = encyclopedia.material.material_id
+                    material.material_type = encyclopedia.material.material_type
+                    material.material_name = encyclopedia.material.material_name
+                    material.material_classification = encyclopedia.material.material_classification
+                    material.formula = encyclopedia.material.formula
+                    material.formula_reduced = encyclopedia.material.formula_reduced
+                    material.species_and_counts = encyclopedia.material.species_and_counts
+                    material.species = encyclopedia.material.species
+                    enc_bulk = encyclopedia.material.bulk
+                    if enc_bulk:
+                        bulk = Bulk.m_from_dict(enc_bulk.m_to_dict())
+                        material.m_add_sub_section(Material.bulk, bulk)
+
+                    # Create calculation info for this entry
+                    calc = Calculation()
+                    calc.calc_id = metadata["calc_id"]
+                    calc.upload_id = metadata["upload_id"]
+                    mongo_calc = proc.Calc.get(calc.calc_id)
+                    calc.published = mongo_calc["metadata"]["published"]
+                    calc.with_embargo = mongo_calc["metadata"]["with_embargo"]
+                    calc.owners = [mongo_calc["metadata"]["uploader"]] + mongo_calc["metadata"]["shared_with"]
+                    enc_idealized_structure = encyclopedia.material.idealized_structure
+                    idealized_structure = IdealizedStructure()
+                    cell_volume = enc_idealized_structure.cell_volume
+                    if cell_volume is not None:
+                        idealized_structure.cell_volume = cell_volume
+                    idealized_structure.lattice_parameters = enc_idealized_structure.lattice_parameters
+                    calc.m_add_sub_section(Calculation.idealized_structure, idealized_structure)
+                    enc_method = encyclopedia.method
+                    method = Method.m_from_dict(enc_method.m_to_dict())
+                    method.program_name = dft["code_name"]
+                    method.program_version = dft["code_version"]
+                    method.basis_set = dft["basis_set"]
+                    calc.m_add_sub_section(Calculation.method, method)
+                    enc_props = encyclopedia.properties
+
+                    # Properties may not exist at all
+                    if enc_props is not None:
+                        properties = Properties()
+
+                        # Energies may not be present in all calculations
+                        try:
+                            energies = Energies.m_from_dict(enc_props.energies.m_to_dict())
+                            properties.m_add_sub_section(Properties.energies, energies)
+                        except AttributeError:
+                            pass
+
+                        properties.has_electronic_dos = enc_props.electronic_dos is not None
+                        properties.has_electronic_band_structure = enc_props.electronic_band_structure is not None
+                        properties.has_thermodynamical_properties = enc_props.thermodynamical_properties is not None
+                        atomic_density = enc_props.atomic_density
+                        if atomic_density is not None:
+                            properties.atomic_density = atomic_density
+                        mass_density = enc_props.mass_density
+                        if mass_density is not None:
+                            properties.mass_density = mass_density
+                        band_gap = enc_props.band_gap
+                        if band_gap is not None:
+                            properties.band_gap = band_gap
+                        band_gap_direct = enc_props.band_gap_direct
+                        if band_gap_direct is not None:
+                            properties.band_gap_direct = band_gap_direct
+                        calc.m_add_sub_section(Calculation.properties, properties)
+
+                    workflow = Workflow()
+                    workflow.workflow_type = encyclopedia.calculation.calculation_type
+                    calc.m_add_sub_section(Calculation.workflow, workflow)
+                    material.m_add_sub_section(Material.calculations, calc)
+
+                    # Update entry that inserts the full material info if entry
+                    # does not exists, otherwise only adds the calculation into the
+                    # nested subdocument
+                    entry = {}
+                    entry['_op_type'] = 'update'
+                    entry['_index'] = target_index_name
+                    entry['_id'] = material.material_id
+                    entry['_type'] = 'doc'
+                    entry['_source'] = {
+                        "upsert": material.m_to_dict(include_defaults=False, partial="es"),
+                        "doc_as_upsert": False,
+                        "script": {
+                            "source": "ctx._source.calculations.add(params.calc)",
+                            "params": {
+                                "calc": calc.m_to_dict(include_defaults=False, partial="es")
+                            },
+                        }
+                    }
+                    yield entry
+    elif source == "es":
+        s = elasticsearch_dsl.Search(index=config.elastic.index_name)
+        filters = [elasticsearch_dsl.Q("term", encyclopedia__status="success")]
+        if code:
+            filters.append(elasticsearch_dsl.Q("terms", dft__code_name=code))
+        query = elasticsearch_dsl.Q(
+            "bool",
+            filter=filters,
+        )
+        s = s.query(query)
+        s = s.extra(**{
+            "size": 0,
+        })
+        all_calcs = s.execute().hits.total
+        print('indexing materials from %d calculations ...' % all_calcs)
+
+        def elastic_updates():
+            with utils.ETA(all_calcs, '   index %10d of %10d calcs, ETA %s', chunk_size) as eta:
+
+                s = elasticsearch_dsl.Search(index=config.elastic.index_name)
+                filters = [elasticsearch_dsl.Q("term", encyclopedia__status="success")]
+                if code:
+                    filters.append(elasticsearch_dsl.Q("terms", dft__code_name=code))
+                query = elasticsearch_dsl.Q(
+                    "bool",
+                    filter=filters,
+                )
+                s = s.query(query)
+                s = s.extra(**{
+                    "size": chunk_size,
+                })
+                i_calc = 0
+                for hit in s.scan():
+                    i_calc += 1
+                    if n is not None:
+                        if i_calc > n:
+                            return
+                    eta.add()
+
+                    material: Material = Material()
+                    calc = Calculation()
+
+                    # Check that all required information exists. If not, the
+                    # calculation is skipped.
+                    try:
+                        material.material_id = hit.encyclopedia.material.material_id
+                        material.material_type = hit.encyclopedia.material.material_type
+                        material.formula = hit.encyclopedia.material.formula
+                        material.formula_reduced = hit.encyclopedia.material.formula_reduced
+                        material.species_and_counts = hit.encyclopedia.material.species_and_counts
+                        material.species = hit.encyclopedia.material.species
+                        calc.calc_id = hit.calc_id
+                        calc.upload_id = hit.upload_id
+                        calc.published = hit.published
+                        calc.with_embargo = hit.with_embargo
+                        calc.owners = [x.user_id for x in hit.owners]
+                        idealized_structure = IdealizedStructure.m_from_dict(hit.encyclopedia.material.idealized_structure.to_dict())
+                        calc.m_add_sub_section(Calculation.idealized_structure, idealized_structure)
+
+                        method = Method.m_from_dict(hit.encyclopedia.method.to_dict())
+                        method.program_name = hit.dft.code_name
+                        method.program_version = hit.dft.code_version
+                        method.basis_set = hit.dft.basis_set
+                        calc.m_add_sub_section(Calculation.method, method)
+
+                        workflow = Workflow()
+                        workflow.workflow_type = hit.encyclopedia.calculation.calculation_type
+                        calc.m_add_sub_section(Calculation.workflow, workflow)
+                    except AttributeError:
+                        continue
+
+                    # Not all materials have a name
+                    try:
+                        material.material_name = hit.encyclopedia.material.material_name
+                    except AttributeError:
+                        pass
+
+                    # Not all materials have a bulk section
+                    try:
+                        bulk = Bulk.m_from_dict(hit.encyclopedia.material.bulk)
+                        material.m_add_sub_section(Material.bulk, bulk)
+                    except AttributeError:
+                        pass
+
+                    # Properties may not exist at all
+                    try:
+                        enc_properties = hit.encyclopedia.properties
+                    except AttributeError:
+                        pass
+                    else:
+                        properties = Properties()
+
+                        # Energies may not be present in all calculations
+                        try:
+                            energies = Energies.m_from_dict(enc_properties.energies.to_dict())
+                            properties.m_add_sub_section(Properties.energies, energies)
+                        except AttributeError:
+                            pass
+
+                        # Gather the boolean flags that indicate the presence of
+                        # certain properties
+                        try:
+                            properties.has_electronic_dos = enc_properties.electronic_dos is not None
+                        except AttributeError:
+                            properties.has_electronic_dos = False
+                        try:
+                            properties.has_electronic_band_structure = enc_properties.electronic_band_structure is not None
+                        except AttributeError:
+                            properties.has_electronic_band_structure = False
+                        try:
+                            properties.has_thermodynamical_properties = enc_properties.thermodynamical_properties is not None
+                        except AttributeError:
+                            properties.has_thermodynamical_properties = False
+
+                        # Not all materials have an atomic density
+                        try:
+                            properties.atomic_density = enc_properties.atomic_density
+                        except AttributeError:
+                            pass
+
+                        # Not all materials have a mass density
+                        try:
+                            properties.mass_density = enc_properties.mass_density
+                        except AttributeError:
+                            pass
+
+                        # Not all materials have band gaps
+                        try:
+                            properties.band_gap = enc_properties.band_gap
+                        except AttributeError:
+                            pass
+
+                        # Not all materials have band gap type
+                        try:
+                            properties.band_gap_direct = enc_properties.band_gap_direct
+                        except AttributeError:
+                            pass
+
+                        calc.m_add_sub_section(Calculation.properties, properties)
+
+                    material.m_add_sub_section(Material.calculations, calc)
+
+                    # Update entry that inserts the full material info if entry
+                    # does not exists, otherwise only adds the calculation into
+                    # the nested subdocument
+                    entry = {}
+                    entry['_op_type'] = 'update'
+                    entry['_index'] = target_index_name
+                    entry['_id'] = material.material_id
+                    entry['_type'] = 'doc'
+                    entry['_source'] = {
+                        "upsert": material.m_to_dict(include_defaults=False, partial="es"),
+                        "doc_as_upsert": False,
+                        "script": {
+                            "params": {
+                                "calc": calc.m_to_dict(include_defaults=False, partial="es")
+                            },
+                        }
+                    }
+                    if in_place:
+                        entry['_source']["script"]["source"] = "ctx._source.calculations.removeIf(x -> x.calc_id == params.calc.calc_id); ctx._source.calculations.add(params.calc)"
+                    else:
+                        entry['_source']["script"]["source"] = "ctx._source.calculations.add(params.calc)"
+                    yield entry
+
+    if dry:
+        for _ in elastic_updates():
             pass
     else:
-        elasticsearch.helpers.bulk(
-            infrastructure.elastic_client, elastic_updates())
-    search.refresh()
+        # Create new index into which the data will be inserted. The old index will
+        # keep working while the new index is being built
+        material_document.init(index=target_index_name)
+
+        if threads > 1:
+            print('  use %d threads' % threads)
+            for _ in elasticsearch.helpers.parallel_bulk(
+                    infrastructure.elastic_client, elastic_updates(), chunk_size=chunk_size,
+                    thread_count=threads):
+                pass
+        else:
+            elasticsearch.helpers.bulk(
+                infrastructure.elastic_client, elastic_updates())
+            search.refresh()
+
+        # Changes materials index alias to point to the new index and remove the
+        # old index.
+        if not in_place:
+            new_index = elasticsearch_dsl.Index(target_index_name)
+            new_index.put_alias(name=config.elastic.materials_index_name)
+            old_index = elasticsearch_dsl.Index(old_index_name)
+            old_index.delete()
 
     print('')
     print('indexing completed')

nomad/config.py

@@ -116,7 +116,8 @@ fs = NomadConfig(
 elastic = NomadConfig(
     host='localhost',
     port=9200,
-    index_name='nomad_fairdi_calcs'
+    index_name='nomad_fairdi_calcs',
+    materials_index_name='nomad_fairdi_materials'
 )
 
 keycloak = NomadConfig(

nomad/datamodel/datamodel.py

@@ -536,7 +536,7 @@ class EntryMetadata(metainfo.MSection):
     ems = metainfo.SubSection(sub_section=EMSMetadata, a_search='ems')
     dft = metainfo.SubSection(sub_section=DFTMetadata, a_search='dft', categories=[fast_access])
     qcms = metainfo.SubSection(sub_section=QCMSMetadata, a_search='qcms')
-    encyclopedia = metainfo.SubSection(sub_section=EncyclopediaMetadata, a_search='encyclopedia')
+    encyclopedia = metainfo.SubSection(sub_section=EncyclopediaMetadata, categories=[fast_access], a_search='encyclopedia')
 
     def apply_user_metadata(self, metadata: dict):
         ''' Applies a user provided metadata dict to this calc. '''

nomad/datamodel/encyclopedia.py

@@ -64,7 +64,7 @@ class WyckoffSet(MSection):
         Chemical element at this Wyckoff position.
         """
     )
-    variables = SubSection(sub_section=WyckoffVariables.m_def, repeats=False)
+    variables = SubSection(sub_section=WyckoffVariables.m_def, repeats=False, categories=[fast_access])
 
 
 class LatticeParameters(MSection):
@@ -190,8 +190,8 @@ class IdealizedStructure(MSection):
         """,
         a_search=Search()
     )
-    wyckoff_sets = SubSection(sub_section=WyckoffSet.m_def, repeats=True)
-    lattice_parameters = SubSection(sub_section=LatticeParameters.m_def)
+    wyckoff_sets = SubSection(sub_section=WyckoffSet.m_def, repeats=True, categories=[fast_access])
+    lattice_parameters = SubSection(sub_section=LatticeParameters.m_def, categories=[fast_access])
 
 
 class Bulk(MSection):
@@ -370,10 +370,10 @@ class Material(MSection):
     )
 
     # Bulk-specific properties
-    bulk = SubSection(sub_section=Bulk.m_def, repeats=False)
+    bulk = SubSection(sub_section=Bulk.m_def, repeats=False, categories=[fast_access])
 
     # The idealized structure for this material
-    idealized_structure = SubSection(sub_section=IdealizedStructure.m_def, repeats=False)
+    idealized_structure = SubSection(sub_section=IdealizedStructure.m_def, repeats=False, categories=[fast_access])
 
 
 class Method(MSection):
@@ -575,11 +575,10 @@ class Properties(MSection):
         """,
         a_search=Search()
     )
-    energies = SubSection(sub_section=Energies.m_def, repeats=False, a_search='energies')
+    energies = SubSection(sub_section=Energies.m_def, repeats=False, categories=[fast_access], a_search='energies')
     electronic_band_structure = Quantity(
         type=Reference(section_k_band.m_def),
         shape=[],
-        categories=[fast_access],
         description="""
         Reference to an electronic band structure.
         """,
@@ -588,7 +587,6 @@ class Properties(MSection):
     electronic_dos = Quantity(
         type=Reference(section_dos.m_def),
         shape=[],
-        categories=[fast_access],
         description="""
         Reference to an electronic density of states.
         """,
@@ -597,7 +595,6 @@ class Properties(MSection):