diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index 0147802d27f47a5d840c5d9fe18ddc0146c457a5..48246a07130d6cb29e3c6352281fa5545be2ba13 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -46,7 +46,6 @@ def _get_transformer(nomad_properties, without_prefix):
if 'search' in q.m_annotations}
quantities['elements'].length_quantity = quantities['nelements']
- quantities['dimension_types'].length_quantity = quantities['dimension_types']
quantities['elements'].has_only_quantity = Quantity(name='only_atoms')
quantities['elements'].nested_quantity = quantities['elements_ratios']
quantities['elements_ratios'].nested_quantity = quantities['elements_ratios']
diff --git a/nomad/app/optimade/infolinks.py b/nomad/app/optimade/infolinks.py
index 0c0d52a6f2f45f957330f47ecfbd5918fa1db77c..dfd82af6562d6aff898b0133d54a3bc70f7285f9 100644
--- a/nomad/app/optimade/infolinks.py
+++ b/nomad/app/optimade/infolinks.py
@@ -48,7 +48,7 @@ class Info(Resource):
}],
'formats': ['json'],
'entry_types_by_format': {
- 'json': ['structures', 'calculations', 'info']
+ 'json': ['structures', 'calculations']
},
'available_endpoints': ['structures', 'calculations', 'info'],
'is_index': False
@@ -73,11 +73,12 @@ class Links(Resource):
result = [
{
- "type": "parent",
+ "type": "links",
"id": "index",
"attributes": {
"name": config.meta.name,
"description": config.meta.description,
+ "link_type": "root",
"base_url": {
"href": url(version=None, prefix='index'),
},
diff --git a/nomad/app/optimade/models.py b/nomad/app/optimade/models.py
index b34a034b497937044a01796095c736b6d3591955..6516b185112c393c222fa6075538fd8a9bea2edc 100644
--- a/nomad/app/optimade/models.py
+++ b/nomad/app/optimade/models.py
@@ -25,9 +25,12 @@ from flask_restplus import fields
import datetime
import math
from cachetools import cached
+import numpy as np
from nomad import config, datamodel, files
from nomad.app.common import RFC3339DateTime
+from nomad.normalizing.optimade import optimade_chemical_formula_reduced
+from nomad.metainfo import Datetime, MEnum
from nomad.datamodel import EntryMetadata
from nomad.datamodel.dft import DFTMetadata
from nomad.datamodel.optimade import OptimadeEntry
@@ -248,7 +251,28 @@ def get_entry_properties(include_optimade: bool = True):
def add_nmd_properties(prefix, section_cls):
for quantity in section_cls.m_def.all_quantities.values():
name = prefix + quantity.name
- properties[name] = dict(description=quantity.description)
+ if quantity.is_scalar:
+ if quantity.type == int:
+ prop_type = 'integer'
+ elif quantity.type == float:
+ prop_type = 'float'
+ elif quantity.type == str:
+ prop_type = 'string'
+ elif quantity.type == bool:
+ prop_type = 'boolean'
+ elif quantity.type == Datetime:
+ prop_type = 'timestamp'
+ elif isinstance(quantity.type, MEnum):
+ prop_type = 'string'
+ elif isinstance(quantity.type, np.dtype):
+ prop_type = 'float'
+ else:
+ prop_type = 'unknown'
+ else:
+ prop_type = 'list'
+ properties[name] = dict(
+ description=quantity.description if quantity.description else quantity.name,
+ type=prop_type)
add_nmd_properties('_nmd_', EntryMetadata)
add_nmd_properties('_nmd_dft_', DFTMetadata)
@@ -276,6 +300,21 @@ class EntryDataObject:
if response_fields is not None:
for request_field in response_fields:
+ if request_field == 'chemical_formula_reduced':
+ # TODO remove when this is fixed in the index
+ # ensure correct order of elements in formula
+ attrs[request_field] = optimade_chemical_formula_reduced(attrs[request_field])
+
+ if request_field == 'dimension_types':
+ # TODO remove when this is fixed in the index
+ # ensure correct order of elements in formula
+ dts = attrs[request_field]
+ if isinstance(dts, int):
+ attrs[request_field] = [1] * dts + [0] * (3 - dts)
+ attrs['nperiodic_dimensions'] = dts
+ elif isinstance(dts, list):
+ attrs['nperiodic_dimensions'] = sum(dts)
+
if not request_field.startswith('_nmd_'):
continue
diff --git a/nomad/datamodel/optimade.py b/nomad/datamodel/optimade.py
index d29e6762dd0a78073b53cd7b8032d21f3b984b0f..df596b9ecc6c4ee22cc91f9ebb18bb29671701ca 100644
--- a/nomad/datamodel/optimade.py
+++ b/nomad/datamodel/optimade.py
@@ -193,8 +193,7 @@ class OptimadeEntry(MSection):
dimension_types = Quantity(
type=int, shape=[3], default=[0, 0, 0],
links=optimade_links('h.6.2.8'),
- a_search=Search(value=lambda a: sum(a.dimension_types), mapping=Integer()),
- a_optimade=Optimade(query=True, entry=True, sortable=False, type='list'),
+ a_optimade=Optimade(query=False, entry=True, sortable=False, type='list'),
description='''
List of three integers. For each of the three directions indicated by the three lattice
vectors (see property lattice_vectors). This list indicates if the direction is
@@ -203,6 +202,16 @@ class OptimadeEntry(MSection):
the Cartesian x, y, z directions.
''')
+ nperiodic_dimensions = Quantity(
+ type=int, derived=lambda a: sum(a.dimension_types),
+ links=optimade_links('h.6.2.8'),
+ a_search=Search(mapping=Integer()),
+ a_optimade=Optimade(query=True, entry=True, sortable=True, type='integer'),
+ description='''
+ An integer specifying the number of periodic dimensions in the structure, equivalent
+ to the number of non-zero entries in dimension_types.
+ ''')
+
lattice_vectors = Quantity(
type=np.dtype('f8'), shape=[3, 3], unit=ureg.angstrom,
links=optimade_links('h.6.2.9'),
@@ -240,7 +249,7 @@ class OptimadeEntry(MSection):
# TODO assemblies
structure_features = Quantity(
- type=MEnum(['disorder', 'unknown_positions', 'assemblies']), shape=['1..*'],
+ type=MEnum(['disorder', 'unknown_positions', 'assemblies']), shape=['1..*'], default=[],
links=optimade_links('h.6.2.15'),
a_search=Search(),
a_optimade=Optimade(query=True, entry=True, sortable=False, type='list'), description='''
diff --git a/nomad/normalizing/optimade.py b/nomad/normalizing/optimade.py
index a3fea0e3f207ea333f978a7509ddd888365cb4ad..201dcc1dbd9fcb106062cec5b5c6defd7c8d0282 100644
--- a/nomad/normalizing/optimade.py
+++ b/nomad/normalizing/optimade.py
@@ -20,6 +20,7 @@ from typing import Any, Dict
import numpy as np
import re
import ase.data
+import ase.formula
from string import ascii_uppercase
import pint.quantity
@@ -31,6 +32,24 @@ from nomad.datamodel.metainfo.public import section_system
species_re = re.compile(r'^([A-Z][a-z]?)(\d*)$')
+def optimade_chemical_formula_reduced(formula: str):
+ if formula is None:
+ return formula
+
+ try:
+ ase_formula = ase.formula.Formula(formula).count()
+ result_formula = ''
+ for element in sorted(ase_formula.keys()):
+ result_formula += element
+ element_count = ase_formula[element]
+ if element_count > 1:
+ result_formula += str(element_count)
+
+ return result_formula
+ except Exception:
+ return formula
+
+
class OptimadeNormalizer(SystemBasedNormalizer):
'''
@@ -92,7 +111,8 @@ class OptimadeNormalizer(SystemBasedNormalizer):
for element in optimade.elements]
# formulas
- optimade.chemical_formula_reduced = get_value(section_system.chemical_composition_reduced)
+ optimade.chemical_formula_reduced = optimade_chemical_formula_reduced(
+ get_value(section_system.chemical_composition_reduced))
optimade.chemical_formula_hill = get_value(section_system.chemical_composition_bulk_reduced)
optimade.chemical_formula_descriptive = optimade.chemical_formula_hill
optimade.chemical_formula_anonymous = ''
diff --git a/tests/app/test_optimade.py b/tests/app/test_optimade.py
index 09d9c417dc9684e6a0813273e83719070cfe1341..e0f186a55fc148fbc9c1589217fe69c5a864ee56 100644
--- a/tests/app/test_optimade.py
+++ b/tests/app/test_optimade.py
@@ -122,10 +122,10 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
('chemical_formula_reduced CONTAINS "H2"', 3),
('chemical_formula_reduced CONTAINS "H"', 4),
('chemical_formula_reduced CONTAINS "C"', 1),
- ('chemical_formula_reduced STARTS "H2"', 3),
- ('chemical_formula_reduced STARTS WITH "H2"', 3),
- ('chemical_formula_reduced ENDS WITH "C"', 1),
- ('chemical_formula_reduced ENDS "C"', 1),
+ ('chemical_formula_reduced STARTS "H2"', 2),
+ ('chemical_formula_reduced STARTS WITH "H2"', 2),
+ ('chemical_formula_reduced ENDS WITH "O"', 4),
+ ('chemical_formula_reduced ENDS "C"', 0),
('chemical_formula_hill CONTAINS "1"', 0),
('chemical_formula_hill STARTS WITH "H" AND chemical_formula_hill ENDS WITH "O"', 3),
('NOT chemical_formula_descriptive ENDS WITH "1"', 4),
@@ -136,14 +136,14 @@ def example_structures(elastic_infra, mongo_infra, raw_files_infra):
('elements LENGTH = 2', 3),
('elements LENGTH 2', 3),
('elements LENGTH = 3', 1),
- ('dimension_types LENGTH = 0', 3),
- ('dimension_types LENGTH = 1', 1),
- ('nelements = 2 AND dimension_types LENGTH = 1', 1),
- ('nelements = 3 AND dimension_types LENGTH = 1', 0),
- ('nelements = 3 OR dimension_types LENGTH = 1', 2),
- ('nelements > 1 OR dimension_types LENGTH = 1 AND nelements = 2', 4),
- ('(nelements > 1 OR dimension_types LENGTH = 1) AND nelements = 2', 3),
- ('NOT dimension_types LENGTH 1', 3),
+ ('nperiodic_dimensions = 0', 3),
+ ('nperiodic_dimensions = 1', 1),
+ ('nelements = 2 AND nperiodic_dimensions = 1', 1),
+ ('nelements = 3 AND nperiodic_dimensions = 1', 0),
+ ('nelements = 3 OR nperiodic_dimensions = 1', 2),
+ ('nelements > 1 OR nperiodic_dimensions = 1 AND nelements = 2', 4),
+ ('(nelements > 1 OR nperiodic_dimensions = 1) AND nelements = 2', 3),
+ ('NOT nperiodic_dimensions = 1', 3),
('nelements LENGTH = 1', -1),
('LENGTH nelements = 1', -1),
('chemical_formula_anonymous starts with "A"', -1),