diff --git a/gui/src/metainfo.json b/gui/src/metainfo.json
index 4a4aab724272bc529b62de5dbe857e3b7534b0a0..5168d8421a44e770320e559c41d71b243212c9d6 100644
--- a/gui/src/metainfo.json
+++ b/gui/src/metainfo.json
@@ -12874,7 +12874,9 @@
},
"shape": [
"0..*"
- ]
+ ],
+ "default": [],
+ "virtual": true
}
],
"sub_sections": [
diff --git a/nomad/datamodel/metainfo/eln/perovskite_solar_cell_database/__init__.py b/nomad/datamodel/metainfo/eln/perovskite_solar_cell_database/__init__.py
index 8cbc09b3acba85bcfd03b65c550e2f309bbed3f3..24177cf64aad08d4e9d9c040271c67ff6ecf8eea 100644
--- a/nomad/datamodel/metainfo/eln/perovskite_solar_cell_database/__init__.py
+++ b/nomad/datamodel/metainfo/eln/perovskite_solar_cell_database/__init__.py
@@ -37,11 +37,6 @@ def add_band_gap(archive, band_gap):
band_structure = BandStructureElectronic(band_gap=[band_gap])
electronic = ElectronicProperties(band_structure_electronic=[band_structure])
archive.results.properties.electronic = electronic
- props = archive.results.properties.available_properties
- if not props:
- props = []
- props.append('electronic.band_structure_electronic.band_gap')
- archive.results.properties.available_properties = props
def add_solar_cell(archive):
@@ -54,12 +49,6 @@ def add_solar_cell(archive):
archive.results.properties.optoelectronic = OptoelectronicProperties()
if not archive.results.properties.optoelectronic.solar_cell:
archive.results.properties.optoelectronic.solar_cell = SolarCell()
- props = archive.results.properties.available_properties
- if not props:
- props = []
- if 'solar_cell' not in props:
- props.append('solar_cell')
- archive.results.properties.available_properties = props
class Ref(MSection):
diff --git a/nomad/datamodel/results.py b/nomad/datamodel/results.py
index 2fe228ced265f7343d252098fad5bcaeb6c81622..a38792b18e35dcc3d1ead01c0dd1b762fe514b59 100644
--- a/nomad/datamodel/results.py
+++ b/nomad/datamodel/results.py
@@ -16,12 +16,14 @@
# limitations under the License.
#
+from typing import List
import numpy as np
from elasticsearch_dsl import Text
from ase.data import chemical_symbols
from nomad import config
+from nomad.utils import traverse_reversed
from nomad.atomutils import Formula
from nomad.datamodel.metainfo.measurements import Spectrum
from nomad.datamodel.metainfo.simulation.system import Atoms
@@ -190,6 +192,43 @@ def get_formula_iupac(formula: str) -> str:
return None if formula is None else Formula(formula).format('iupac')
+def available_properties(root: MSection) -> List[str]:
+ '''Returns a list of property names that are available in results.properties.
+
+ Args:
+ root: The metainfo section containing the properties
+
+ Returns:
+ List of property names that are present
+ '''
+ available_property_names = {
+ 'electronic.band_structure_electronic.band_gap': 'electronic.band_structure_electronic.band_gap',
+ 'electronic.band_structure_electronic': 'band_structure_electronic',
+ 'electronic.dos_electronic': 'dos_electronic',
+ 'electronic.greens_functions_electronic': 'greens_functions_electronic',
+ 'vibrational.dos_phonon': 'dos_phonon',
+ 'vibrational.band_structure_phonon': 'band_structure_phonon',
+ 'vibrational.energy_free_helmholtz': 'energy_free_helmholtz',
+ 'vibrational.heat_capacity_constant_volume': 'heat_capacity_constant_volume',
+ 'thermodynamic.trajectory': 'trajectory',
+ 'structural.radial_distribution_function': 'radial_distribution_function',
+ 'dynamical.mean_squared_displacement': 'mean_squared_displacement',
+ 'structural.radius_of_gyration': 'radius_of_gyration',
+ 'geometry_optimization': 'geometry_optimization',
+ 'mechanical.bulk_modulus': 'bulk_modulus',
+ 'mechanical.shear_modulus': 'shear_modulus',
+ 'mechanical.energy_volume_curve': 'energy_volume_curve',
+ 'spectroscopy.eels': 'eels',
+ 'optoelectronic.solar_cell': 'solar_cell',
+ }
+ available_properties: List[str] = []
+ for path, shortcut in available_property_names.items():
+ for _ in traverse_reversed(root, path.split('.')):
+ available_properties.append(shortcut)
+ break
+ return sorted(available_properties)
+
+
tokenizer_formula = get_tokenizer(r'[A-Z][a-z]?\d*')
@@ -2512,6 +2551,8 @@ class Properties(MSection):
)
available_properties = Quantity(
type=str,
+ default=[],
+ derived=lambda a: available_properties(a),
shape=['0..*'],
description='Subset of the property names that are present in this entry.',
a_elasticsearch=Elasticsearch(material_entry_type),
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index 22d1a93073c326203b468180c1997e46c7c0c8e2..7c785bac6bbc3d9990183403eac6e5952a2372e8 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -26,6 +26,7 @@ import matid.geometry # pylint: disable=import-error
from nomad import config
from nomad import atomutils
+from nomad.utils import traverse_reversed
from nomad.atomutils import Formula
from nomad.normalizing.normalizer import Normalizer
from nomad.normalizing.method import MethodNormalizer
@@ -114,34 +115,6 @@ class ResultsNormalizer(Normalizer):
for measurement in self.entry_archive.measurement:
self.normalize_measurement(measurement)
- # Add the list of available_properties: it is a selected subset of the
- # stored properties.
- available_property_names = {
- "results.properties.electronic.band_structure_electronic.band_gap": "electronic.band_structure_electronic.band_gap",
- "results.properties.electronic.band_structure_electronic": "band_structure_electronic",
- "results.properties.electronic.dos_electronic": "dos_electronic",
- "results.properties.electronic.greens_functions_electronic": "greens_functions_electronic",
- "results.properties.vibrational.dos_phonon": "dos_phonon",
- "results.properties.vibrational.band_structure_phonon": "band_structure_phonon",
- "results.properties.vibrational.energy_free_helmholtz": "energy_free_helmholtz",
- "results.properties.vibrational.heat_capacity_constant_volume": "heat_capacity_constant_volume",
- "results.properties.thermodynamic.trajectory": "trajectory",
- "results.properties.structural.radial_distribution_function": "radial_distribution_function",
- "results.properties.dynamical.mean_squared_displacement": "mean_squared_displacement",
- "results.properties.structural.radius_of_gyration": "radius_of_gyration",
- "results.properties.geometry_optimization": "geometry_optimization",
- "results.properties.mechanical.bulk_modulus": "bulk_modulus",
- "results.properties.mechanical.shear_modulus": "shear_modulus",
- "results.properties.mechanical.energy_volume_curve": "energy_volume_curve",
- "results.properties.spectroscopy.eels": "eels",
- }
- available_properties: List[str] = []
- for path, shortcut in available_property_names.items():
- for _ in self.traverse_reversed(path.split('.')):
- available_properties.append(shortcut)
- break
- results.properties.available_properties = sorted(available_properties)
-
def normalize_sample(self, sample) -> None:
results = self.entry_archive.results
@@ -260,7 +233,7 @@ class ResultsNormalizer(Normalizer):
- There is a non-empty array of energies.
"""
def resolve_band_structure(path):
- for bs in self.traverse_reversed(path):
+ for bs in traverse_reversed(self.entry_archive, path):
if not bs.segment:
continue
valid = True
@@ -319,7 +292,7 @@ class ResultsNormalizer(Normalizer):
"""
def resolve_dos(path):
- for dos in self.traverse_reversed(path):
+ for dos in traverse_reversed(self.entry_archive, path):
energies = dos.energies
values = np.array([d.value.magnitude for d in dos.total])
if valid_array(energies) and valid_array(values):
@@ -366,7 +339,7 @@ class ResultsNormalizer(Normalizer):
"""
def resolve_greens_functions(path):
- for gfs in self.traverse_reversed(path):
+ for gfs in traverse_reversed(self.entry_archive, path):
tau = gfs.tau
iw = gfs.matsubara_freq
values_gtau = np.array([np.absolute(gtau) for gtau in gfs.greens_function_tau.real])
@@ -403,7 +376,7 @@ class ResultsNormalizer(Normalizer):
- There is a non-empty array of energies.
"""
path = ["run", "calculation", "band_structure_phonon"]
- for bs in self.traverse_reversed(path):
+ for bs in traverse_reversed(self.entry_archive, path):
if not bs.segment:
continue
valid = True
@@ -430,7 +403,7 @@ class ResultsNormalizer(Normalizer):
- There is a non-empty array of energies.
"""
path = ["run", "calculation", "dos_phonon"]
- for dos in self.traverse_reversed(path):
+ for dos in traverse_reversed(self.entry_archive, path):
energies = dos.energies
values = np.array([d.value.magnitude for d in dos.total])
if valid_array(energies) and valid_array(values):
@@ -450,7 +423,7 @@ class ResultsNormalizer(Normalizer):
- There is a non-empty array of energies.
"""
path = ["workflow", "thermodynamics"]
- for thermo_prop in self.traverse_reversed(path):
+ for thermo_prop in traverse_reversed(self.entry_archive, path):
temperatures = thermo_prop.temperature
energies = thermo_prop.vibrational_free_energy_at_constant_volume
if valid_array(temperatures) and valid_array(energies):
@@ -470,7 +443,7 @@ class ResultsNormalizer(Normalizer):
- There is a non-empty array of energies.
"""
path = ["workflow", "thermodynamics"]
- for thermo_prop in self.traverse_reversed(path):
+ for thermo_prop in traverse_reversed(self.entry_archive, path):
temperatures = thermo_prop.temperature
heat_capacities = thermo_prop.heat_capacity_c_v
if valid_array(temperatures) and valid_array(heat_capacities):
@@ -486,7 +459,7 @@ class ResultsNormalizer(Normalizer):
properties based on the first found geometry optimization workflow.
"""
path = ["workflow"]
- for workflow in self.traverse_reversed(path):
+ for workflow in traverse_reversed(self.entry_archive, path):
# Check validity
if workflow.type == "geometry_optimization" and workflow.calculations_ref:
@@ -529,7 +502,7 @@ class ResultsNormalizer(Normalizer):
"""
path = ["workflow"]
trajs = []
- for workflow in self.traverse_reversed(path):
+ for workflow in traverse_reversed(self.entry_archive, path):
# Check validity
if workflow.type == "molecular_dynamics":
traj = Trajectory()
@@ -590,7 +563,7 @@ class ResultsNormalizer(Normalizer):
"""
path = ["workflow", "molecular_dynamics", "results", "radial_distribution_functions"]
rdfs = []
- for rdf_workflow in self.traverse_reversed(path):
+ for rdf_workflow in traverse_reversed(self.entry_archive, path):
rdf_values = rdf_workflow.radial_distribution_function_values
if rdf_values is not None:
for rdf_value in rdf_values or []:
@@ -620,7 +593,7 @@ class ResultsNormalizer(Normalizer):
"""
path_workflow = ["workflow"]
rgs: List[RadiusOfGyration] = []
- for workflow in self.traverse_reversed(path_workflow):
+ for workflow in traverse_reversed(self.entry_archive, path_workflow):
# Check validity
if workflow.type == "molecular_dynamics":
@@ -654,7 +627,7 @@ class ResultsNormalizer(Normalizer):
"""
path = ["workflow", "molecular_dynamics", "results", "mean_squared_displacements"]
msds = []
- for msd_workflow in self.traverse_reversed(path):
+ for msd_workflow in traverse_reversed(self.entry_archive, path):
msd_values = msd_workflow.mean_squared_displacement_values
if msd_values is not None:
for msd_value in msd_values or []:
@@ -1011,28 +984,3 @@ class ResultsNormalizer(Normalizer):
))
return shear_modulus
-
- def traverse_reversed(self, path: List[str]) -> Any:
- """Traverses the given metainfo path in reverse order. Useful in
- finding the latest reported section or value.
- """
- def traverse(root, path, i):
- if not root:
- return
- sections = getattr(root, path[i])
- if isinstance(sections, list):
- for section in reversed(sections):
- if i == len(path) - 1:
- yield section
- else:
- for s in traverse(section, path, i + 1):
- yield s
- else:
- if i == len(path) - 1:
- yield sections
- else:
- for s in traverse(sections, path, i + 1):
- yield s
- for t in traverse(self.entry_archive, path, 0):
- if t is not None:
- yield t
diff --git a/nomad/utils/__init__.py b/nomad/utils/__init__.py
index d23b6bb0ef323aaa9c49f524951caa4c48befdea..0c793cb797ddec14d020a031393ab9bd5aba1018 100644
--- a/nomad/utils/__init__.py
+++ b/nomad/utils/__init__.py
@@ -589,3 +589,37 @@ def query_list_to_dict(path_list: List[Union[str, int]], value: Any) -> Dict[str
current = current[key]
i += 1
return returned
+
+
+def traverse_reversed(archive: Any, path: List[str]) -> Any:
+ '''Traverses the given metainfo path in reverse order. Useful in finding the
+ latest reported section or value.
+
+ Args:
+ archive: The root section to traverse
+ path: List of path names to traverse
+
+ Returns:
+ Returns the last metainfo section or quantity in the given path or None
+ if not found.
+ '''
+ def traverse(root, path, i):
+ if not root:
+ return
+ sections = getattr(root, path[i])
+ if isinstance(sections, list):
+ for section in reversed(sections):
+ if i == len(path) - 1:
+ yield section
+ else:
+ for s in traverse(section, path, i + 1):
+ yield s
+ else:
+ if i == len(path) - 1:
+ yield sections
+ else:
+ for s in traverse(sections, path, i + 1):
+ yield s
+ for t in traverse(archive, path, 0):
+ if t is not None:
+ yield t