diff --git a/docs/dev/parser_tutorial.md b/docs/dev/parser_tutorial.md
index 48ff903db5872836346625ffa617ef7afa011a8c..bf00356eb9b956bcbc335f3a95f92425dc20d1ff 100644
--- a/docs/dev/parser_tutorial.md
+++ b/docs/dev/parser_tutorial.md
@@ -358,12 +358,8 @@ Consequently, the parser class implementation is modified as in the following ex
```python
import json
-from .metainfo import m_env
from nomad.parsing.parser import MatchingParser
-from nomad.datamodel.metainfo.common_experimental import section_experiment as msection_experiment
-from nomad.datamodel.metainfo.common_experimental import section_data as msection_data
-from nomad.datamodel.metainfo.general_experimental_method import section_method as msection_method
-from nomad.datamodel.metainfo.general_experimental_sample import section_sample as msection_sample
+from nomad.datamodel.metainfo.common_experimental import Experiment, Data, Method, Sample
class ExampleParser(MatchingParser):
@@ -374,34 +370,32 @@ class ExampleParser(MatchingParser):
)
def run(self, filepath, logger=None):
- self._metainfo_env = m_env
-
with open(filepath, 'rt') as f:
data = json.load(f)
- section_experiment = msection_experiment()
+ experiment = Experiment()
# Read general tool environment details
- section_experiment.experiment_location = data.get('experiment_location')
- section_experiment.experiment_facility_institution = data.get('experiment_facility_institution')
+ experiment.experiment_location = data.get('experiment_location')
+ experiment.experiment_facility_institution = data.get('experiment_facility_institution')
# Read data parameters
- section_data = section_experiment.m_create(msection_data)
+ section_data = experiment.m_create(Data)
section_data.data_repository_name = data.get('data_repository_name')
section_data.data_preview_url = data.get('data_repository_url')
# Read parameters related to method
- section_method = section_experiment.m_create(msection_method)
+ section_method = experiment.m_create(Method)
section_method.experiment_method_name = data.get('experiment_method')
section_method.probing_method = 'electric pulsing'
# Read parameters related to sample
- section_sample = section_experiment.m_create(msection_sample)
+ section_sample = experiment.m_create(Sample)
section_sample.sample_description = data.get('specimen_description')
section_sample.sample_microstructure = data.get('specimen_microstructure')
section_sample.sample_constituents = data.get('specimen_constitution')
- return section_experiment
+ return experiment
```
The parser extends the ``MatchingParser`` class which already implements the determination
of the necessary file for parsing. The main difference to the old framework is the absense
diff --git a/gui/src/components/archive/MetainfoBrowser.js b/gui/src/components/archive/MetainfoBrowser.js
index 411c4701a150f42b79f3b2962b931c2bf792f57c..b18bae3facfe3eb749be4e181d3773a0872f7545 100644
--- a/gui/src/components/archive/MetainfoBrowser.js
+++ b/gui/src/components/archive/MetainfoBrowser.js
@@ -67,6 +67,10 @@ If you bookmark this page, you can save the definition represented by the highli
To learn more about the meta-info, visit the [meta-info documentation](${appBase}/docs/metainfo.html).
`
+function defCompare(a, b) {
+ return a.name.localeCompare(b.name)
+}
+
export const metainfoConfigState = atom({
key: 'metainfoConfig',
default: {
@@ -206,7 +210,7 @@ export class PackagePrefixAdaptor extends MetainfoAdaptor {
return <Content>
<Compartment title="Sections">
- {sectionDefs.filter(def => !def.extends_base_section).map(def => {
+ {sectionDefs.filter(def => !def.extends_base_section).sort(defCompare).map(def => {
const key = `section_definitions@${def._qualifiedName}`
return <Item key={key} itemKey={key}>
<Typography>{def.name}</Typography>
@@ -214,7 +218,7 @@ export class PackagePrefixAdaptor extends MetainfoAdaptor {
})}
</Compartment>
<Compartment title="Section Extensions">
- {sectionDefs.filter(def => def.extends_base_section).map(def => {
+ {sectionDefs.filter(def => def.extends_base_section).sort(defCompare).map(def => {
const key = `section_definitions@${def._qualifiedName}`
return <Item key={key} itemKey={key}>
<Typography>{def.name}</Typography>
@@ -222,7 +226,7 @@ export class PackagePrefixAdaptor extends MetainfoAdaptor {
})}
</Compartment>
<Compartment title="Categories">
- {categoryDefs.map(def => {
+ {categoryDefs.sort(defCompare).map(def => {
const key = `category_definitions@${def._qualifiedName}`
return <Item key={key} itemKey={key}>
<Typography>{def.name}</Typography>
@@ -323,8 +327,10 @@ function SectionDef({def}) {
{def.sub_sections.filter(filter)
.map(subSectionDef => {
const key = subSectionDef.name
+ const categories = subSectionDef.categories?.map(c => resolveRef(c))
+ const unused = categories?.find(c => c.name === 'Unused')
return <Item key={key} itemKey={key}>
- <Typography component="span">
+ <Typography component="span" color={unused && 'error'}>
<Box fontWeight="bold" component="span">
{subSectionDef.name}
</Box>{subSectionDef.repeats && <span> (repeats)</span>}
@@ -337,9 +343,11 @@ function SectionDef({def}) {
{def.quantities.filter(filter)
.map(quantityDef => {
const key = quantityDef.name
+ const categories = quantityDef.categories?.map(c => resolveRef(c))
+ const unused = categories?.find(c => c.name === 'Unused')
return <Item key={key} itemKey={key}>
<Box component="span" whiteSpace="nowrap">
- <Typography component="span">
+ <Typography component="span" color={unused && 'error'}>
<Box fontWeight="bold" component="span">
{quantityDef.name}
</Box>
diff --git a/nomad/archive.py b/nomad/archive.py
index 953b51000c2eec4c61392d73b84c8df9db47f50c..31193d754c85bddfd291adfd1fd562798c01713a 100644
--- a/nomad/archive.py
+++ b/nomad/archive.py
@@ -29,7 +29,7 @@ import re
from nomad import utils, config, infrastructure
from nomad.metainfo import Quantity, Reference, Definition, MSection, Section, SubSection
from nomad.datamodel import EntryArchive
-from nomad.datamodel.metainfo.public import fast_access
+from nomad.datamodel.metainfo.common_dft import FastAccess
'''
The archive storage is made from two tiers. First the whole archive is stored in
@@ -681,7 +681,7 @@ def filter_archive(
def create_partial_archive(archive: EntryArchive) -> Dict:
'''
Creates a partial archive JSON serializable dict that can be stored directly.
- The given archive is filtered based on the metainfo category ``fast_access``.
+ The given archive is filtered based on the metainfo category ``FastAccess``.
Selected sections and other data that they reference (recursively) comprise the
resulting partial archive.
@@ -708,10 +708,10 @@ def create_partial_archive(archive: EntryArchive) -> Dict:
if section.m_def == EntryArchive.m_def:
if definition.m_def == Quantity:
return True
- return fast_access.m_def in definition.categories
+ return FastAccess.m_def in definition.categories
if isinstance(definition, Quantity) and isinstance(definition.type, Reference) \
- and fast_access.m_def in definition.categories:
+ and FastAccess.m_def in definition.categories:
# Reference list in partial archives are not supported
if definition.is_scalar:
referenced = getattr(section, definition.name)
@@ -719,7 +719,7 @@ def create_partial_archive(archive: EntryArchive) -> Dict:
referenceds.append(referenced)
if isinstance(definition, SubSection):
- return fast_access.m_def in definition.categories
+ return FastAccess.m_def in definition.categories
return True
@@ -897,13 +897,13 @@ def compute_required_with_referenced(required):
prop = key.split('[')[0]
prop_definition = parent.all_properties[prop]
if isinstance(prop_definition, SubSection):
- if fast_access.m_def not in prop_definition.categories:
+ if FastAccess.m_def not in prop_definition.categories:
raise _Incomplete()
traverse(value, prop_definition.sub_section)
if isinstance(prop_definition, Quantity) and isinstance(prop_definition.type, Reference):
current[prop] = '*'
- if fast_access.m_def not in prop_definition.categories:
+ if FastAccess.m_def not in prop_definition.categories:
continue
target_section_def = prop_definition.type.target_section_def.m_resolved()
diff --git a/nomad/cli/dev.py b/nomad/cli/dev.py
index a290b3704f021c2d06188f561dfd5a73b5d7a1fc..1c1f12bc92aa7ac5795c4bd64294cb07414493e5 100644
--- a/nomad/cli/dev.py
+++ b/nomad/cli/dev.py
@@ -73,6 +73,7 @@ def metainfo_undecorated():
import nomad.datamodel.ems
import nomad.datamodel.optimade
import nomad.datamodel.encyclopedia
+ from nomad.parsing import LegacyParser
nomad.metainfo.metainfo.m_package.__init_metainfo__()
nomad.datamodel.datamodel.m_package.__init_metainfo__()
nomad.datamodel.dft.m_package.__init_metainfo__() # pylint: disable=no-member
@@ -83,7 +84,8 @@ def metainfo_undecorated():
# Ensure all parser metainfo is loaded
from nomad.parsing.parsers import parsers
for parser in parsers:
- _ = parser.metainfo_env
+ if isinstance(parser, LegacyParser):
+ _ = parser.metainfo_env
export = Environment()
for package in Package.registry.values():
@@ -121,57 +123,6 @@ def search_quantities():
print(json.dumps(export, indent=2))
-@dev.command(help='Generates source-code for the new metainfo from .json files of the old.')
-@click.argument('path', nargs=-1)
-def legacy_metainfo(path):
- from nomad.metainfo.legacy import convert, generate_metainfo_code
-
- if len(path) == 0:
- path = [
- 'abinit.nomadmetainfo.json',
- 'aptfim.nomadmetainfo.json',
- 'atk.nomadmetainfo.json',
- 'band.nomadmetainfo.json',
- 'bigdft.nomadmetainfo.json',
- 'castep.nomadmetainfo.json',
- 'cp2k.nomadmetainfo.json',
- 'cpmd.nomadmetainfo.json',
- 'crystal.nomadmetainfo.json',
- 'dl_poly.nomadmetainfo.json',
- 'dmol3.nomadmetainfo.json',
- 'eels.nomadmetainfo.json',
- 'elastic.nomadmetainfo.json',
- 'elk.nomadmetainfo.json',
- 'exciting.nomadmetainfo.json',
- 'fhi_aims.nomadmetainfo.json',
- 'fleur.nomadmetainfo.json',
- 'gamess.nomadmetainfo.json',
- 'gaussian.nomadmetainfo.json',
- 'gpaw.nomadmetainfo.json',
- 'gulp.nomadmetainfo.json',
- 'lib_atoms.nomadmetainfo.json',
- 'molcas.nomadmetainfo.json',
- 'mpes.nomadmetainfo.json',
- 'nwchem.nomadmetainfo.json',
- 'octopus.nomadmetainfo.json',
- 'onetep.nomadmetainfo.json',
- 'orca.nomadmetainfo.json',
- 'phonopy.nomadmetainfo.json',
- 'photoemission.nomadmetainfo.json',
- 'qbox.nomadmetainfo.json',
- 'quantum_espresso.nomadmetainfo.json',
- 'siesta.nomadmetainfo.json',
- 'turbomole.nomadmetainfo.json',
- 'vasp.nomadmetainfo.json',
- 'wien2k.nomadmetainfo.json',
- 'dft.nomadmetainfo.json',
- 'ems.nomadmetainfo.json']
-
- for element in path:
- env = convert(element)
- generate_metainfo_code(env)
-
-
@dev.command(help='Generates a JSON file that compiles all the parser metadata from each parser project.')
def parser_metadata():
import inspect
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index 9269d98f4be395d9c24f089a1f5b0b94867a655f..71eb6ce3774d48d27354d38fb7e0587c3ba9c962 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -27,7 +27,7 @@ from nomad import metainfo, config
from nomad.metainfo.search_extension import Search
from nomad.metainfo.elastic_extension import ElasticDocument
from nomad.metainfo.mongoengine_extension import Mongo, MongoDocument
-from nomad.datamodel.metainfo.public import fast_access
+from nomad.datamodel.metainfo.common_dft import FastAccess
from .dft import DFTMetadata
from .ems import EMSMetadata
@@ -38,9 +38,9 @@ from .qcms import QCMSMetadata
m_package = metainfo.Package()
from .encyclopedia import EncyclopediaMetadata # noqa
-from .metainfo.public import section_run, Workflow # noqa
+from .metainfo.common_dft import Run, Workflow # noqa
from .metainfo.common_experimental import Experiment # noqa
-from .metainfo.general_qcms import QuantumCMS # noqa
+from .metainfo.common_qcms import QuantumCMS # noqa
def _only_atoms(atoms):
@@ -538,9 +538,9 @@ class EntryMetadata(metainfo.MSection):
a_search=Search())
ems = metainfo.SubSection(sub_section=EMSMetadata, a_search='ems')
- dft = metainfo.SubSection(sub_section=DFTMetadata, a_search='dft', categories=[fast_access])
+ dft = metainfo.SubSection(sub_section=DFTMetadata, a_search='dft', categories=[FastAccess])
qcms = metainfo.SubSection(sub_section=QCMSMetadata, a_search='qcms')
- encyclopedia = metainfo.SubSection(sub_section=EncyclopediaMetadata, categories=[fast_access], a_search='encyclopedia')
+ encyclopedia = metainfo.SubSection(sub_section=EncyclopediaMetadata, categories=[FastAccess], a_search='encyclopedia')
def apply_user_metadata(self, metadata: dict):
''' Applies a user provided metadata dict to this calc. '''
@@ -563,11 +563,11 @@ class EntryMetadata(metainfo.MSection):
class EntryArchive(metainfo.MSection):
- section_run = metainfo.SubSection(sub_section=section_run, repeats=True)
+ section_run = metainfo.SubSection(sub_section=Run, repeats=True)
section_experiment = metainfo.SubSection(sub_section=Experiment)
section_quantum_cms = metainfo.SubSection(sub_section=QuantumCMS)
- section_workflow = metainfo.SubSection(sub_section=Workflow, categories=[fast_access])
- section_metadata = metainfo.SubSection(sub_section=EntryMetadata, categories=[fast_access])
+ section_workflow = metainfo.SubSection(sub_section=Workflow, categories=[FastAccess])
+ section_metadata = metainfo.SubSection(sub_section=EntryMetadata, categories=[FastAccess])
processing_logs = metainfo.Quantity(
type=Any, shape=['0..*'],
diff --git a/nomad/datamodel/dft.py b/nomad/datamodel/dft.py
index 59e1d9a7b2ea8052f38ada427aef46618d16eeed..8f94c09c95cca140f1254e46ebaca44755f7e2d7 100644
--- a/nomad/datamodel/dft.py
+++ b/nomad/datamodel/dft.py
@@ -27,8 +27,8 @@ from nomad.metainfo import MSection, Section, Quantity, MEnum, SubSection
from nomad.metainfo.search_extension import Search
from .optimade import OptimadeEntry
-from .metainfo.public import Workflow, fast_access
-from .metainfo.public import section_XC_functionals
+from .metainfo.common_dft import Workflow, FastAccess
+from .metainfo.common_dft import section_XC_functionals
xc_treatments = {
@@ -238,7 +238,7 @@ class DFTMetadata(MSection):
a_search=Search(many_or='append', group='groups_grouped', metric_name='groups', metric='cardinality'))
labels = SubSection(
- sub_section=Label, repeats=True, categories=[fast_access],
+ sub_section=Label, repeats=True, categories=[FastAccess],
description='The labels taken from AFLOW prototypes and springer.',
a_search='labels')
diff --git a/nomad/datamodel/encyclopedia.py b/nomad/datamodel/encyclopedia.py
index 5b5f455f04ea673c4253c82f51e41f60e7d73d1a..5fd2f07af5159b3fd70a3f4ef5a0673e5d5307aa 100644
--- a/nomad/datamodel/encyclopedia.py
+++ b/nomad/datamodel/encyclopedia.py
@@ -26,7 +26,7 @@ from nomad.metainfo.search_extension import Search
# due to the next imports requireing the m_package already, this would be too late.
m_package = Package()
-from .metainfo.public import section_k_band, section_dos, section_thermodynamical_properties, fast_access # noqa
+from .metainfo.common_dft import section_k_band, section_dos, section_thermodynamical_properties, FastAccess # noqa
class WyckoffVariables(MSection):
@@ -82,7 +82,7 @@ class WyckoffSet(MSection):
Chemical element at this Wyckoff position.
"""
)
- variables = SubSection(sub_section=WyckoffVariables.m_def, repeats=False, categories=[fast_access])
+ variables = SubSection(sub_section=WyckoffVariables.m_def, repeats=False, categories=[FastAccess])
class LatticeParameters(MSection):
@@ -208,8 +208,8 @@ class IdealizedStructure(MSection):
""",
a_search=Search()
)
- wyckoff_sets = SubSection(sub_section=WyckoffSet.m_def, repeats=True, categories=[fast_access])
- lattice_parameters = SubSection(sub_section=LatticeParameters.m_def, categories=[fast_access])
+ wyckoff_sets = SubSection(sub_section=WyckoffSet.m_def, repeats=True, categories=[FastAccess])
+ lattice_parameters = SubSection(sub_section=LatticeParameters.m_def, categories=[FastAccess])
class Bulk(MSection):
@@ -388,10 +388,10 @@ class Material(MSection):
)
# Bulk-specific properties
- bulk = SubSection(sub_section=Bulk.m_def, repeats=False, categories=[fast_access])
+ bulk = SubSection(sub_section=Bulk.m_def, repeats=False, categories=[FastAccess])
# The idealized structure for this material
- idealized_structure = SubSection(sub_section=IdealizedStructure.m_def, repeats=False, categories=[fast_access])
+ idealized_structure = SubSection(sub_section=IdealizedStructure.m_def, repeats=False, categories=[FastAccess])
class Method(MSection):
@@ -593,7 +593,7 @@ class Properties(MSection):
""",
a_search=Search()
)
- energies = SubSection(sub_section=Energies.m_def, repeats=False, categories=[fast_access], a_search='energies')
+ energies = SubSection(sub_section=Energies.m_def, repeats=False, categories=[FastAccess], a_search='energies')
electronic_band_structure = Quantity(
type=Reference(section_k_band.m_def),
shape=[],
@@ -644,10 +644,10 @@ class EncyclopediaMetadata(MSection):
Section which stores information for the NOMAD Encyclopedia.
"""
)
- material = SubSection(sub_section=Material.m_def, repeats=False, categories=[fast_access], a_search='material')
- method = SubSection(sub_section=Method.m_def, repeats=False, categories=[fast_access], a_search='method')
- properties = SubSection(sub_section=Properties.m_def, repeats=False, categories=[fast_access], a_search='properties')
- calculation = SubSection(sub_section=Calculation.m_def, repeats=False, categories=[fast_access], a_search='calculation')
+ material = SubSection(sub_section=Material.m_def, repeats=False, categories=[FastAccess], a_search='material')
+ method = SubSection(sub_section=Method.m_def, repeats=False, categories=[FastAccess], a_search='method')
+ properties = SubSection(sub_section=Properties.m_def, repeats=False, categories=[FastAccess], a_search='properties')
+ calculation = SubSection(sub_section=Calculation.m_def, repeats=False, categories=[FastAccess], a_search='calculation')
status = Quantity(
type=MEnum("success", "unsupported_material_type", "unsupported_method_type", "unsupported_calculation_type", "invalid_metainfo", "failure"),
description="""
diff --git a/nomad/datamodel/metainfo/__init__.py b/nomad/datamodel/metainfo/__init__.py
index 8a3af683d9fd46a972a11d2128cfecf85ecc1709..f72c52263c68850bb9e83a6bce9b677f9382923f 100644
--- a/nomad/datamodel/metainfo/__init__.py
+++ b/nomad/datamodel/metainfo/__init__.py
@@ -19,11 +19,7 @@
import sys
from nomad.metainfo import Environment
from nomad.metainfo.legacy import LegacyMetainfoEnvironment
-import nomad.datamodel.metainfo.common
-import nomad.datamodel.metainfo.public
-import nomad.datamodel.metainfo.general
+import nomad.datamodel.metainfo.common_dft
m_env = LegacyMetainfoEnvironment()
-m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package) # type: ignore
-m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package) # type: ignore
-m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common_dft'].m_package) # type: ignore
diff --git a/nomad/datamodel/metainfo/common.py b/nomad/datamodel/metainfo/common.py
index 5c08eb1dde24cc680b646a071b215b0ca83556fa..4e13e59402e7dd159206d8eb67a3b141be510fd8 100644
--- a/nomad/datamodel/metainfo/common.py
+++ b/nomad/datamodel/metainfo/common.py
@@ -16,1339 +16,10 @@
# limitations under the License.
#
-import numpy as np # pylint: disable=unused-import
-import typing # pylint: disable=unused-import
-from nomad.metainfo import ( # pylint: disable=unused-import
- MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
- Reference
-)
-from nomad.metainfo.legacy import LegacyDefinition
+# This is just for backward compatibility of old imports. All definitions are now in common_dft
-from nomad.datamodel.metainfo import public
+from nomad.metainfo import Package
-m_package = Package(
- name='common_nomadmetainfo_json',
- description='None',
- a_legacy=LegacyDefinition(name='common.nomadmetainfo.json'))
+from .common_dft import *
-
-class settings_atom_in_molecule(MCategory):
- '''
- Parameters of an atom within a molecule.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_atom_in_molecule'))
-
-
-class settings_constraint(MCategory):
- '''
- Some parameters that describe a constraint
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_constraint'))
-
-
-class settings_interaction(MCategory):
- '''
- Some parameters that describe a bonded interaction.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_interaction'))
-
-
-class soap_parameter(MCategory):
- '''
- A soap parameter
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='soap_parameter'))
-
-
-class response_context(MSection):
- '''
- The top level context containing the reponse to an api query, when using jsonAPI they
- are tipically in the meta part
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='response_context'))
-
- shortened_meta_info = Quantity(
- type=str,
- shape=[],
- description='''
- A meta info whose corresponding data has been shortened
- ''',
- a_legacy=LegacyDefinition(name='shortened_meta_info'))
-
- section_response_message = SubSection(
- sub_section=SectionProxy('section_response_message'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_response_message'))
-
-
-class section_atom_type(MSection):
- '''
- Section describing a type of atom in the system.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atom_type'))
-
- atom_type_charge = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='coulomb',
- description='''
- Charge of the atom type.
- ''',
- a_legacy=LegacyDefinition(name='atom_type_charge'))
-
- atom_type_mass = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='kilogram',
- description='''
- Mass of the atom type.
- ''',
- a_legacy=LegacyDefinition(name='atom_type_mass'))
-
- atom_type_name = Quantity(
- type=str,
- shape=[],
- description='''
- Name (label) of the atom type.
- ''',
- a_legacy=LegacyDefinition(name='atom_type_name'))
-
-
-class section_constraint(MSection):
- '''
- Section describing a constraint between arbitrary atoms.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_constraint'))
-
- constraint_atoms = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_constraints', 'number_of_atoms_per_constraint'],
- description='''
- List of the indexes involved in this constraint. The fist atom has index 1, the
- last number_of_topology_atoms.
- ''',
- a_legacy=LegacyDefinition(name='constraint_atoms'))
-
- constraint_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Short and unique name for this constraint type. Valid names are described in the
- [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/constraint-kind).
- ''',
- a_legacy=LegacyDefinition(name='constraint_kind'))
-
- constraint_parameters = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- Explicit constraint parameters for this kind of constraint (depending on the
- constraint type, some might be given implicitly through other means).
- ''',
- a_legacy=LegacyDefinition(name='constraint_parameters'))
-
- number_of_atoms_per_constraint = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms involved in this constraint.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_per_constraint'))
-
- number_of_constraints = Quantity(
- type=int,
- shape=[],
- description='''
- Number of constraints of this type.
- ''',
- a_legacy=LegacyDefinition(name='number_of_constraints'))
-
-
-class section_dft_plus_u_orbital(MSection):
- '''
- Section for DFT+U-settings of a single orbital
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
-
- dft_plus_u_orbital_atom = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- DFT+U-orbital setting: atom index (references index of atom_labels/atom_positions)
- ''',
- a_legacy=LegacyDefinition(name='dft_plus_u_orbital_atom'))
-
- dft_plus_u_orbital_J = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- DFT+U-orbital setting: value J (exchange interaction)
- ''',
- categories=[public.energy_value],
- a_legacy=LegacyDefinition(name='dft_plus_u_orbital_J'))
-
- dft_plus_u_orbital_label = Quantity(
- type=str,
- shape=[],
- description='''
- DFT+U-orbital setting: orbital label (normally (n,l)), notation: '3d', '4f', ...
- ''',
- a_legacy=LegacyDefinition(name='dft_plus_u_orbital_label'))
-
- dft_plus_u_orbital_U_effective = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- DFT+U-orbital setting: value U_{effective} (U-J), if implementation uses it
- ''',
- categories=[public.energy_value],
- a_legacy=LegacyDefinition(name='dft_plus_u_orbital_U_effective'))
-
- dft_plus_u_orbital_U = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- DFT+U-orbital setting: value U (on-site Coulomb interaction)
- ''',
- categories=[public.energy_value],
- a_legacy=LegacyDefinition(name='dft_plus_u_orbital_U'))
-
-
-class section_excited_states(MSection):
- '''
- Excited states properties.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_excited_states'))
-
- excitation_energies = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_excited_states'],
- description='''
- Excitation energies.
- ''',
- categories=[public.energy_value],
- a_legacy=LegacyDefinition(name='excitation_energies'))
-
- number_of_excited_states = Quantity(
- type=int,
- shape=[],
- description='''
- Number of excited states.
- ''',
- a_legacy=LegacyDefinition(name='number_of_excited_states'))
-
- oscillator_strengths = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_excited_states'],
- description='''
- Excited states oscillator strengths.
- ''',
- a_legacy=LegacyDefinition(name='oscillator_strengths'))
-
- transition_dipole_moments = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_excited_states', 3],
- description='''
- Transition dipole moments.
- ''',
- a_legacy=LegacyDefinition(name='transition_dipole_moments'))
-
-
-class section_interaction(MSection):
- '''
- Section containing the description of a bonded interaction between arbitrary atoms.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_interaction'))
-
- interaction_atoms = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_interactions', 'number_of_atoms_per_interaction'],
- description='''
- List of the indexes involved in this interaction. The fist atom has index 1, the
- last atom index number_of_topology_atoms.
- ''',
- a_legacy=LegacyDefinition(name='interaction_atoms'))
-
- interaction_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Short and unique name for this interaction type. Valid names are described in the
- [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/interaction-kind).
- ''',
- a_legacy=LegacyDefinition(name='interaction_kind'))
-
- interaction_parameters = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- Explicit interaction parameters for this kind of interaction (depending on the
- interaction_kind some might be given implicitly through other means).
- ''',
- a_legacy=LegacyDefinition(name='interaction_parameters'))
-
- number_of_atoms_per_interaction = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms involved in this interaction.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_per_interaction'))
-
- number_of_interactions = Quantity(
- type=int,
- shape=[],
- description='''
- Number of interactions of this type.
- ''',
- a_legacy=LegacyDefinition(name='number_of_interactions'))
-
-
-class section_method_basis_set(MSection):
- '''
- This section contains the definition of the basis sets that are defined independently
- of the atomic configuration.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method_basis_set'))
-
- mapping_section_method_basis_set_atom_centered = Quantity(
- type=np.dtype(np.int64),
- shape=['number_of_basis_sets_atom_centered', 2],
- description='''
- Reference to an atom-centered basis set defined in section_basis_set_atom_centered
- and to the atom kind as defined in section_method_atom_kind.
- ''',
- a_legacy=LegacyDefinition(name='mapping_section_method_basis_set_atom_centered'))
-
- mapping_section_method_basis_set_cell_associated = Quantity(
- type=public.section_basis_set_cell_dependent,
- shape=[],
- description='''
- Reference to a cell-associated basis set.
- ''',
- a_legacy=LegacyDefinition(name='mapping_section_method_basis_set_cell_associated'))
-
- method_basis_set_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String describing the use of the basis set, i.e, if it used for expanding a
- wavefunction or an electron density. Allowed values are listed in the
- [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/basis-set-kind).
- ''',
- a_legacy=LegacyDefinition(name='method_basis_set_kind'))
-
- number_of_basis_sets_atom_centered = Quantity(
- type=int,
- shape=[],
- description='''
- String describing the use of the basis set, i.e, if it used for expanding a
- wavefunction or an electron density. Allowed values are listed in the
- [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/basis-set-kind).
- ''',
- a_legacy=LegacyDefinition(name='number_of_basis_sets_atom_centered'))
-
-
-class section_molecule_constraint(MSection):
- '''
- Section describing a constraint between atoms within a molecule.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_molecule_constraint'))
-
- molecule_constraint_atoms = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_molecule_constraints', 'number_of_atoms_per_molecule_constraint'],
- description='''
- List of the indexes involved in this constraint. The fist atom has index 1, the
- last index is number_of_atoms_in_molecule.
- ''',
- a_legacy=LegacyDefinition(name='molecule_constraint_atoms'))
-
- molecule_constraint_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Short and unique name for this constraint type. Valid names are described in the
- [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/constraint-kind).
- ''',
- a_legacy=LegacyDefinition(name='molecule_constraint_kind'))
-
- molecule_constraint_parameters = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- Explicit constraint parameters for this kind of constraint (depending on the
- constraint type some might be given implicitly through other means).
- ''',
- a_legacy=LegacyDefinition(name='molecule_constraint_parameters'))
-
- number_of_atoms_per_molecule_constraint = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms, in this molecule, involved in this constraint.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_per_molecule_constraint'))
-
- number_of_molecule_constraints = Quantity(
- type=int,
- shape=[],
- description='''
- Number of constraints of this type.
- ''',
- a_legacy=LegacyDefinition(name='number_of_molecule_constraints'))
-
-
-class section_molecule_interaction(MSection):
- '''
- Section describing a bonded interaction between atoms within a molecule.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_molecule_interaction'))
-
- molecule_interaction_atoms = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_molecule_interactions', 'number_of_atoms_per_molecule_interaction'],
- description='''
- List of the indexes involved in this bonded interaction within a molecule. The
- first atom has index 1, the last index is number_of_atoms_in_.
- ''',
- a_legacy=LegacyDefinition(name='molecule_interaction_atoms'))
-
- molecule_interaction_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Short and unique name for this interaction type, used for bonded interactions for
- atoms in a molecule. Valid names are described in the [interaction\\_kind wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/interaction-kind).
- ''',
- a_legacy=LegacyDefinition(name='molecule_interaction_kind'))
-
- molecule_interaction_parameters = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- Explicit interaction parameters for this kind of interaction (depending on the
- interaction type some might be given implicitly through other means), used for
- bonded interactions for atoms in a molecule.
- ''',
- a_legacy=LegacyDefinition(name='molecule_interaction_parameters'))
-
- number_of_atoms_per_molecule_interaction = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms, in this molecule, involved in this interaction.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_per_molecule_interaction'))
-
- number_of_molecule_interactions = Quantity(
- type=int,
- shape=[],
- description='''
- Number of bonded interactions of this type.
- ''',
- a_legacy=LegacyDefinition(name='number_of_molecule_interactions'))
-
-
-class section_molecule_type(MSection):
- '''
- Section describing a type of molecule in the system.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_molecule_type'))
-
- atom_in_molecule_charge = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms_in_molecule'],
- unit='coulomb',
- description='''
- Charge of each atom in the molecule.
- ''',
- categories=[settings_atom_in_molecule],
- a_legacy=LegacyDefinition(name='atom_in_molecule_charge'))
-
- atom_in_molecule_name = Quantity(
- type=str,
- shape=['number_of_atoms_in_molecule'],
- description='''
- Name (label) of each atom in the molecule.
- ''',
- categories=[settings_atom_in_molecule],
- a_legacy=LegacyDefinition(name='atom_in_molecule_name'))
-
- atom_in_molecule_to_atom_type_ref = Quantity(
- type=Reference(SectionProxy('section_atom_type')),
- shape=['number_of_atoms_in_molecule'],
- description='''
- Reference to the atom type of each atom in the molecule.
- ''',
- categories=[settings_atom_in_molecule],
- a_legacy=LegacyDefinition(name='atom_in_molecule_to_atom_type_ref'))
-
- molecule_type_name = Quantity(
- type=str,
- shape=[],
- description='''
- Name of the molecule.
- ''',
- a_legacy=LegacyDefinition(name='molecule_type_name'))
-
- number_of_atoms_in_molecule = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms in this molecule.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_in_molecule'))
-
- section_molecule_constraint = SubSection(
- sub_section=SectionProxy('section_molecule_constraint'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_molecule_constraint'))
-
- section_molecule_interaction = SubSection(
- sub_section=SectionProxy('section_molecule_interaction'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_molecule_interaction'))
-
-
-class section_response_message(MSection):
- '''
- Messages outputted by the program formatting the data in the current response
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_response_message'))
-
- response_message_count = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- How many times this message was repeated
- ''',
- a_legacy=LegacyDefinition(name='response_message_count'))
-
- response_message_level = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- level of the message: 0 fatal, 1 error, 2 warning, 3 debug
- ''',
- a_legacy=LegacyDefinition(name='response_message_level'))
-
- response_message = Quantity(
- type=str,
- shape=[],
- description='''
- Message outputted by the program formatting the data in the current format
- ''',
- a_legacy=LegacyDefinition(name='response_message'))
-
-
-class section_soap_coefficients(MSection):
- '''
- Stores the soap coefficients for the pair of atoms given in
- soap_coefficients_atom_pair.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_soap_coefficients'))
-
- number_of_soap_coefficients = Quantity(
- type=int,
- shape=[],
- description='''
- number of soap coefficients
- ''',
- a_legacy=LegacyDefinition(name='number_of_soap_coefficients'))
-
- soap_coefficients_atom_pair = Quantity(
- type=str,
- shape=[],
- description='''
- Pair of atoms described in the current section
- ''',
- a_legacy=LegacyDefinition(name='soap_coefficients_atom_pair'))
-
- soap_coefficients = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_soap_coefficients'],
- description='''
- Compressed coefficient of the soap descriptor for the atom pair
- soap_coefficients_atom_pair
- ''',
- a_legacy=LegacyDefinition(name='soap_coefficients'))
-
-
-class section_soap(MSection):
- '''
- Stores a soap descriptor for this configuration.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_soap'))
-
- soap_angular_basis_L = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- angular basis L
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_angular_basis_L'))
-
- soap_angular_basis_type = Quantity(
- type=str,
- shape=[],
- description='''
- angular basis type
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_angular_basis_type'))
-
- soap_kernel_adaptor = Quantity(
- type=str,
- shape=[],
- description='''
- kernel adaptor
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_kernel_adaptor'))
-
- soap_parameters_gid = Quantity(
- type=str,
- shape=[],
- description='''
- Unique checksum of all the soap parameters (all those with abstract type
- soap_parameter) with prefix psoap
- ''',
- a_legacy=LegacyDefinition(name='soap_parameters_gid'))
-
- soap_radial_basis_integration_steps = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- radial basis integration steps
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_basis_integration_steps'))
-
- soap_radial_basis_mode = Quantity(
- type=str,
- shape=[],
- description='''
- radial basis mode
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_basis_mode'))
-
- soap_radial_basis_n = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- radial basis N
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_basis_n'))
-
- soap_radial_basis_sigma = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- radial basis sigma
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_basis_sigma'))
-
- soap_radial_basis_type = Quantity(
- type=str,
- shape=[],
- description='''
- radial basis type
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_basis_type'))
-
- soap_radial_cutoff_center_weight = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- radial cutoff center weight
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_cutoff_center_weight'))
-
- soap_radial_cutoff_rc_width = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- radial cutoff width
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_cutoff_rc_width'))
-
- soap_radial_cutoff_rc = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- radial cutoff
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_cutoff_rc'))
-
- soap_radial_cutoff_type = Quantity(
- type=str,
- shape=[],
- description='''
- radial cutoff type
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_radial_cutoff_type'))
-
- soap_spectrum_2l1_norm = Quantity(
- type=bool,
- shape=[],
- description='''
- 2l1 norm spectrum
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_spectrum_2l1_norm'))
-
- soap_spectrum_global = Quantity(
- type=bool,
- shape=[],
- description='''
- global spectrum
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_spectrum_global'))
-
- soap_spectrum_gradients = Quantity(
- type=bool,
- shape=[],
- description='''
- gradients in specturm
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_spectrum_gradients'))
-
- soap_type_list = Quantity(
- type=str,
- shape=[],
- description='''
- Type list
- ''',
- categories=[soap_parameter],
- a_legacy=LegacyDefinition(name='soap_type_list'))
-
- section_soap_coefficients = SubSection(
- sub_section=SectionProxy('section_soap_coefficients'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_soap_coefficients'))
-
-
-class section_topology(MSection):
- '''
- Section containing the definition of topology (connectivity among atoms in force
- fileds), force field, and constraints of a system.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_topology'))
-
- atom_to_molecule = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_topology_atoms', 2],
- description='''
- Table mapping atom to molecules: the first column is the index of the molecule and
- the second column the index of the atom, signifying that the atom in the second
- column belongs to the molecule in the first column in the same row.
- ''',
- a_legacy=LegacyDefinition(name='atom_to_molecule'))
-
- molecule_to_molecule_type_map = Quantity(
- type=Reference(SectionProxy('section_molecule_type')),
- shape=['number_of_topology_molecules'],
- description='''
- Mapping from molecules to molecule types.
- ''',
- a_legacy=LegacyDefinition(name='molecule_to_molecule_type_map'))
-
- number_of_topology_atoms = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms in the system described by this topology.
- ''',
- a_legacy=LegacyDefinition(name='number_of_topology_atoms'))
-
- number_of_topology_molecules = Quantity(
- type=int,
- shape=[],
- description='''
- Number of molecules in the system, as described by this topology.
- ''',
- a_legacy=LegacyDefinition(name='number_of_topology_molecules'))
-
- topology_force_field_name = Quantity(
- type=str,
- shape=[],
- description='''
- A unique string idenfiying the force field defined in this section. Strategies to
- define it are discussed in the
- [topology\\_force\\_field\\_name](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/topology-force-field-name).
- ''',
- a_legacy=LegacyDefinition(name='topology_force_field_name'))
-
- section_atom_type = SubSection(
- sub_section=SectionProxy('section_atom_type'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_atom_type'))
-
- section_constraint = SubSection(
- sub_section=SectionProxy('section_constraint'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_constraint'))
-
- section_interaction = SubSection(
- sub_section=SectionProxy('section_interaction'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_interaction'))
-
- section_molecule_type = SubSection(
- sub_section=SectionProxy('section_molecule_type'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_molecule_type'))
-
-
-class section_method(public.section_method):
-
- m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
-
- dft_plus_u_functional = Quantity(
- type=str,
- shape=[],
- description='''
- Type of DFT+U functional (such as DFT/DFT+U double-counting compensation). Valid
- names are described in the [dft\\_plus\\_u\\_functional wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/dft-
- plus-u-functional).
- ''',
- a_legacy=LegacyDefinition(name='dft_plus_u_functional'))
-
- dft_plus_u_projection_type = Quantity(
- type=str,
- shape=[],
- description='''
- DFT+U: Type of orbitals used for projection in order to calculate occupation
- numbers. Valid names are described in the [dft\\_plus\\_u\\_projection\\_type wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/dft-
- plus-u-projection-type).
- ''',
- a_legacy=LegacyDefinition(name='dft_plus_u_projection_type'))
-
- gw_bare_coulomb_cutofftype = Quantity(
- type=str,
- shape=[],
- description='''
- Cutoff type for the calculation of the bare Coulomb potential: none, 0d, 1d, 2d.
- See Rozzi et al., PRB 73, 205119 (2006)
- ''',
- a_legacy=LegacyDefinition(name='gw_bare_coulomb_cutofftype'))
-
- gw_bare_coulomb_gmax = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='1 / meter',
- description='''
- Maximum G for the pw basis for the Coulomb potential.
- ''',
- a_legacy=LegacyDefinition(name='gw_bare_coulomb_gmax'))
-
- gw_basis_set = Quantity(
- type=str,
- shape=[],
- description='''
- Auxillary basis set used for non-local operators: mixed - mixed basis set, Kotani
- and Schilfgaarde, Solid State Comm. 121, 461 (2002).
- ''',
- a_legacy=LegacyDefinition(name='gw_basis_set'))
-
- gw_core_treatment = Quantity(
- type=str,
- shape=[],
- description='''
- It specifies whether the core states are treated in the GW calculation: all - All
- electron calculation; val - Valence electron only calculation; vab - Core
- electrons are excluded from the mixed product basis; xal - All electron treatment
- of the exchange self-energy only
- ''',
- a_legacy=LegacyDefinition(name='gw_core_treatment'))
-
- gw_frequency_grid_type = Quantity(
- type=str,
- shape=[],
- description='''
- Frequency integration grid type for the correlational self energy: 'eqdis' -
- equidistant frequencies from 0 to freqmax; 'gaulag' - Gauss-Laguerre quadrature
- from 0 to infinity; 'gauleg' - Gauss-Legendre quadrature from 0 to freqmax;
- 'gaule2' (default) - double Gauss-Legendre quadrature from 0 to freqmax and from
- freqmax to infinity.
- ''',
- a_legacy=LegacyDefinition(name='gw_frequency_grid_type'))
-
- gw_max_frequency = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Maximum frequency for the calculation of the self energy.
- ''',
- a_legacy=LegacyDefinition(name='gw_max_frequency'))
-
- gw_mixed_basis_gmax = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='1 / meter',
- description='''
- Cut-off parameter for the truncation of the expansion of the plane waves in the
- interstitial region.
- ''',
- a_legacy=LegacyDefinition(name='gw_mixed_basis_gmax'))
-
- gw_mixed_basis_lmax = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Maximum l value used for the radial functions within the muffin-tin.
- ''',
- a_legacy=LegacyDefinition(name='gw_mixed_basis_lmax'))
-
- gw_mixed_basis_tolerance = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Eigenvalue threshold below which the egenvectors are discarded in the construction
- of the radial basis set.
- ''',
- a_legacy=LegacyDefinition(name='gw_mixed_basis_tolerance'))
-
- gw_ngridq = Quantity(
- type=np.dtype(np.int32),
- shape=[3],
- description='''
- k/q-point grid size used in the GW calculation.
- ''',
- a_legacy=LegacyDefinition(name='gw_ngridq'))
-
- gw_frequency_number = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Number referring to the frequency used in the calculation of the self energy.
- ''',
- a_legacy=LegacyDefinition(name='gw_frequency_number'))
-
- gw_frequency_values = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Values of the frequency used in the calculation of the self energy.
- ''',
- a_legacy=LegacyDefinition(name='gw_frequency_values'))
-
- gw_frequency_weights = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Weights of the frequency used in the calculation of the self energy.
- ''',
- a_legacy=LegacyDefinition(name='gw_frequency_weights'))
-
- gw_number_of_frequencies = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Number of frequency points used in the calculation of the self energy.
- ''',
- a_legacy=LegacyDefinition(name='gw_number_of_frequencies'))
-
- gw_polarizability_number_of_empty_states = Quantity(
- type=int,
- shape=[],
- description='''
- Number of empty states used to compute the polarizability P
- ''',
- a_legacy=LegacyDefinition(name='gw_polarizability_number_of_empty_states'))
-
- gw_qp_equation_treatment = Quantity(
- type=str,
- shape=[],
- description='''
- Methods to solve the quasi-particle equation: 'linearization', 'self-consistent'
- ''',
- a_legacy=LegacyDefinition(name='gw_qp_equation_treatment'))
-
- gw_screened_coulomb_volume_average = Quantity(
- type=str,
- shape=[],
- description='''
- Type of volume averaging for the dynamically screened Coulomb potential: isotropic
- - Simple averaging along a specified direction using only diagonal components of
- the dielectric tensor; anisotropic - Anisotropic screening by C. Freysoldt et al.,
- CPC 176, 1-13 (2007)
- ''',
- a_legacy=LegacyDefinition(name='gw_screened_coulomb_volume_average'))
-
- gw_screened_Coulomb = Quantity(
- type=str,
- shape=[],
- description='''
- Model used to calculate the dinamically-screened Coulomb potential: 'rpa' - Full-
- frequency random-phase approximation; 'ppm' - Godby-Needs plasmon-pole model Godby
- and Needs, Phys. Rev. Lett. 62, 1169 (1989); 'ppm_hl' - Hybertsen and Louie, Phys.
- Rev. B 34, 5390 (1986); 'ppm_lh' - von der Linden and P. Horsh, Phys. Rev. B 37,
- 8351 (1988); 'ppm_fe' - Farid and Engel, Phys. Rev. B 47,15931 (1993); 'cdm' -
- Contour deformation method, Phys. Rev. B 67, 155208 (2003).)
- ''',
- a_legacy=LegacyDefinition(name='gw_screened_Coulomb'))
-
- gw_self_energy_c_analytical_continuation = Quantity(
- type=str,
- shape=[],
- description='''
- Models for the correlation self-energy analytical continuation: 'pade' - Pade's
- approximant (by H. J. Vidberg and J. W. Serence, J. Low Temp. Phys. 29, 179
- (1977)); 'mpf' - Multi-Pole Fitting (by H. N Rojas, R. W. Godby and R. J. Needs,
- Phys. Rev. Lett. 74, 1827 (1995)); 'cd' - contour deformation; 'ra' - real axis
- ''',
- a_legacy=LegacyDefinition(name='gw_self_energy_c_analytical_continuation'))
-
- gw_self_energy_c_number_of_empty_states = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Number of empty states to be used to calculate the correlation self energy.
- ''',
- a_legacy=LegacyDefinition(name='gw_self_energy_c_number_of_empty_states'))
-
- gw_self_energy_c_number_of_poles = Quantity(
- type=int,
- shape=[],
- description='''
- Number of poles used in the analytical continuation.
- ''',
- a_legacy=LegacyDefinition(name='gw_self_energy_c_number_of_poles'))
-
- gw_self_energy_singularity_treatment = Quantity(
- type=str,
- shape=[],
- description='''
- Treatment of the integrable singular terms in the calculation of the self energy.
- Values: 'mpb' - Auxiliary function method by S. Massidda, M. Posternak, and A.
- Baldereschi, PRB 48, 5058 (1993); 'crg' - Auxiliary function method by P. Carrier,
- S. Rohra, and A. Goerling, PRB 75, 205126 (2007).
- ''',
- a_legacy=LegacyDefinition(name='gw_self_energy_singularity_treatment'))
-
- gw_starting_point = Quantity(
- type=str,
- shape=[],
- description='''
- Exchange-correlation functional of the ground-state calculation. See XC_functional
- list at https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
- functional
- ''',
- a_legacy=LegacyDefinition(name='gw_starting_point'))
-
- gw_type_test = Quantity(
- type=str,
- shape=[],
- description='''
- GW methodology: exciting test variable
- ''',
- a_legacy=LegacyDefinition(name='gw_type_test'))
-
- gw_type = Quantity(
- type=str,
- shape=[],
- description='''
- GW methodology: G0W0; ev-scGW: (eigenvalues self-consistent GW) – Phys.Rev.B 34,
- 5390 (1986); qp-scGW: (quasi-particle self-consistent GW) – Phys. Rev. Lett. 96,
- 226402 (2006) scGW0: (self-consistent G with fixed W0) – Phys.Rev.B 54, 8411
- (1996); scG0W: (self-consistent W with fixed G0); scGW: (self-consistent GW) –
- Phys. Rev. B 88, 075105 (2013)
- ''',
- a_legacy=LegacyDefinition(name='gw_type'))
-
- method_to_topology_ref = Quantity(
- type=Reference(SectionProxy('section_topology')),
- shape=[],
- description='''
- Reference to the topology and force fields to be used.
- ''',
- a_legacy=LegacyDefinition(name='method_to_topology_ref'))
-
- section_dft_plus_u_orbital = SubSection(
- sub_section=SectionProxy('section_dft_plus_u_orbital'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
-
- section_method_basis_set = SubSection(
- sub_section=SectionProxy('section_method_basis_set'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_method_basis_set'))
-
-
-class section_single_configuration_calculation(public.section_single_configuration_calculation):
-
- m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
-
- energy_C_mGGA = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Component of the correlation (C) energy at the GGA (or MetaGGA) level using the
- self-consistent density of the target XC functional (full unscaled value, i.e.,
- not scaled due to exact-exchange mixing).
- ''',
- categories=[public.energy_component, public.energy_value, public.energy_type_C],
- a_legacy=LegacyDefinition(name='energy_C_mGGA'))
-
- energy_reference_fermi = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- unit='joule',
- description='''
- Fermi energy (separates occupied from unoccupied single-particle states in metals)
- ''',
- categories=[public.energy_type_reference, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_reference_fermi'))
-
- energy_reference_highest_occupied = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- unit='joule',
- description='''
- Highest occupied single-particle state energy (in insulators or HOMO energy in
- finite systems)
- ''',
- categories=[public.energy_type_reference, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_reference_highest_occupied'))
-
- energy_reference_lowest_unoccupied = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- unit='joule',
- description='''
- Lowest unoccupied single-particle state energy (in insulators or LUMO energy in
- finite systems)
- ''',
- categories=[public.energy_type_reference, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_reference_lowest_unoccupied'))
-
- energy_X_mGGA_scaled = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Component of the exchange (X) energy at the GGA (or MetaGGA) level, using the self
- consistent density of the target functional, scaled accordingly to the mixing
- parameter.
- ''',
- categories=[public.energy_component, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_X_mGGA_scaled'))
-
- energy_X_mGGA = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Component of the exchange (X) energy at the GGA (or MetaGGA) level using the self
- consistent density of the target functional (full unscaled value, i.e., not scaled
- due to exact-exchange mixing).
- ''',
- categories=[public.energy_type_X, public.energy_component, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_X_mGGA'))
-
- gw_fermi_energy = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- GW Fermi energy
- ''',
- a_legacy=LegacyDefinition(name='gw_fermi_energy'))
-
- gw_fundamental_gap = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- GW fundamental band gap
- ''',
- a_legacy=LegacyDefinition(name='gw_fundamental_gap'))
-
- gw_optical_gap = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- GW optical band gap
- ''',
- a_legacy=LegacyDefinition(name='gw_optical_gap'))
-
- gw_self_energy_c = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
- unit='joule',
- description='''
- Diagonal matrix elements of the correlation self-energy
- ''',
- a_legacy=LegacyDefinition(name='gw_self_energy_c'))
-
- gw_self_energy_x = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
- unit='joule',
- description='''
- Diagonal matrix elements of the exchange self-energy
- ''',
- a_legacy=LegacyDefinition(name='gw_self_energy_x'))
-
- gw_xc_potential = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
- unit='joule',
- description='''
- Diagonal matrix elements of the exchange-correlation potential
- ''',
- a_legacy=LegacyDefinition(name='gw_xc_potential'))
-
- section_excited_states = SubSection(
- sub_section=SectionProxy('section_excited_states'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_excited_states'))
-
-
-class section_scf_iteration(public.section_scf_iteration):
-
- m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_scf_iteration'))
-
- energy_reference_fermi_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- unit='joule',
- description='''
- Fermi energy (separates occupied from unoccupied single-particle states in metals)
- during the self-consistent field (SCF) iterations.
- ''',
- categories=[public.energy_type_reference, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_reference_fermi_iteration'))
-
- energy_reference_highest_occupied_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- unit='joule',
- description='''
- Highest occupied single-particle state energy (in insulators or HOMO energy in
- finite systems) during the self-consistent field (SCF) iterations.
- ''',
- categories=[public.energy_type_reference, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_reference_highest_occupied_iteration'))
-
- energy_reference_lowest_unoccupied_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- unit='joule',
- description='''
- Lowest unoccupied single-particle state energy (in insulators or LUMO energy in
- finite systems) during the self-consistent field (SCF) iterations.
- ''',
- categories=[public.energy_type_reference, public.energy_value],
- a_legacy=LegacyDefinition(name='energy_reference_lowest_unoccupied_iteration'))
-
-
-class section_eigenvalues(public.section_eigenvalues):
-
- m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_eigenvalues'))
-
- gw_qp_linearization_prefactor = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
- description='''
- Linearization prefactor
- ''',
- a_legacy=LegacyDefinition(name='gw_qp_linearization_prefactor'))
-
-
-class section_system(public.section_system):
-
- m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
-
- number_of_electrons = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels'],
- description='''
- Number of electrons in system
- ''',
- categories=[public.configuration_core],
- a_legacy=LegacyDefinition(name='number_of_electrons'))
-
- topology_ref = Quantity(
- type=Reference(SectionProxy('section_topology')),
- shape=[],
- description='''
- Reference to the topology used for this system; if not given, the trivial topology
- should be assumed.
- ''',
- a_legacy=LegacyDefinition(name='topology_ref'))
-
- is_representative = Quantity(
- type=bool,
- shape=[],
- description='''
- Most systems in a run are only minor variations of each other. Systems marked
- representative where chosen to be representative for all systems in the run.
- ''',
- a_legacy=LegacyDefinition(name='is_representative'))
-
- section_soap = SubSection(
- sub_section=SectionProxy('section_soap'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_soap'))
-
-
-class section_run(public.section_run):
-
- m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
-
- section_topology = SubSection(
- sub_section=SectionProxy('section_topology'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_topology'))
-
-
-m_package.__init_metainfo__()
+m_package = Package(name='common_nomadmetainfo_json')
diff --git a/nomad/datamodel/metainfo/common_dft.py b/nomad/datamodel/metainfo/common_dft.py
new file mode 100644
index 0000000000000000000000000000000000000000..a2876d989b4a3b74fa9cc2382c7d9ed7194f241e
--- /dev/null
+++ b/nomad/datamodel/metainfo/common_dft.py
@@ -0,0 +1,7743 @@
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference, MEnum, derived)
+from nomad.metainfo.legacy import LegacyDefinition
+from nomad.metainfo.search_extension import Search
+
+
+m_package = Package(
+ name='nomad.datamodel.metainfo.public_old',
+ description='None',
+ a_legacy=LegacyDefinition(name='public.nomadmetainfo.json'))
+
+
+class FastAccess(MCategory):
+ '''
+ Used to mark archive objects that need to be stored in a fast 2nd-tier storage medium,
+ because they are frequently accessed via archive API.
+
+ If applied to a sub_section, the section will be added to the fast storage. Currently
+ this only works for *root* sections that are sub_sections of `EntryArchive`.
+
+ If applied to a reference types quantity, the referenced section will also be added to
+ the fast storage, regardless if the referenced section has the category or not.
+ '''
+
+ m_def = Category(
+ aliases=['fast_access'],)
+
+
+class AccessoryInfo(MCategory):
+ '''
+ Information that *in theory* should not affect the results of the calculations (e.g.,
+ timing).
+ '''
+
+ m_def = Category(
+ aliases=['accessory_info'],
+ a_legacy=LegacyDefinition(name='accessory_info'))
+
+
+class AtomForcesType(MCategory):
+ '''
+ The types of forces acting on the atoms (i.e., minus derivatives of the specific type
+ of energy with respect to the atom position).
+ '''
+
+ m_def = Category(
+ aliases=['atom_forces_type'],
+ a_legacy=LegacyDefinition(name='atom_forces_type'))
+
+
+class BasisSetDescription(MCategory):
+ '''
+ One of the parts building the basis set of the system (e.g., some atom-centered basis
+ set, plane-waves or both).
+ '''
+
+ m_def = Category(
+ aliases=['basis_set_description'],
+ a_legacy=LegacyDefinition(name='basis_set_description'))
+
+
+class ConfigurationCore(MCategory):
+ '''
+ Properties defining the current configuration.
+ '''
+
+ m_def = Category(
+ aliases=['configuration_core'],
+ a_legacy=LegacyDefinition(name='configuration_core'))
+
+
+class ConservedQuantity(MCategory):
+ '''
+ A quantity that is preserved during the time propagation (for example,
+ kinetic+potential energy during NVE).
+ '''
+
+ m_def = Category(
+ aliases=['conserved_quantity'],
+ a_legacy=LegacyDefinition(name='conserved_quantity'))
+
+
+class EnergyValue(MCategory):
+ '''
+ This metadata stores an energy value.
+ '''
+
+ m_def = Category(
+ aliases=['energy_value'],
+ a_legacy=LegacyDefinition(name='energy_value'))
+
+
+class ErrorEstimateContribution(MCategory):
+ '''
+ An estimate of a partial quantity contributing to the error for a given quantity.
+ '''
+
+ m_def = Category(
+ aliases=['error_estimate_contribution'],
+ a_legacy=LegacyDefinition(name='error_estimate_contribution'))
+
+
+class MessageDebug(MCategory):
+ '''
+ A debugging message of the computational program.
+ '''
+
+ m_def = Category(
+ aliases=['message_debug'],
+ a_legacy=LegacyDefinition(name='message_debug'))
+
+
+class ParsingMessageDebug(MCategory):
+ '''
+ This field is used for debugging messages of the parsing program.
+ '''
+
+ m_def = Category(
+ aliases=['parsing_message_debug'],
+ a_legacy=LegacyDefinition(name='parsing_message_debug'))
+
+
+class ScfInfo(MCategory):
+ '''
+ Contains information on the self-consistent field (SCF) procedure, i.e. the number of
+ SCF iterations (number_of_scf_iterations) or a section_scf_iteration section with
+ detailed information on the SCF procedure of specified quantities.
+ '''
+
+ m_def = Category(
+ aliases=['scf_info'],
+ a_legacy=LegacyDefinition(name='scf_info'))
+
+
+class SettingsNumericalParameter(MCategory):
+ '''
+ A parameter that can influence the convergence, but not the physics (unlike
+ settings_physical_parameter)
+ '''
+
+ m_def = Category(
+ aliases=['settings_numerical_parameter'],
+ a_legacy=LegacyDefinition(name='settings_numerical_parameter'))
+
+
+class SettingsPhysicalParameter(MCategory):
+ '''
+ A parameter that defines the physical model used. Use settings_numerical_parameter for
+ parameters that that influence only the convergence/accuracy.
+ '''
+
+ m_def = Category(
+ aliases=['settings_physical_parameter'],
+ a_legacy=LegacyDefinition(name='settings_physical_parameter'))
+
+
+class SettingsPotentialEnergySurface(MCategory):
+ '''
+ Contains parameters that control the potential energy surface.
+ '''
+
+ m_def = Category(
+ aliases=['settings_potential_energy_surface'],
+ a_legacy=LegacyDefinition(name='settings_potential_energy_surface'))
+
+
+class SettingsRun(MCategory):
+ '''
+ Contains parameters that control the whole run (but not the *single configuration
+ calculation*, see section_single_configuration_calculation).
+ '''
+
+ m_def = Category(
+ aliases=['settings_run'],
+ a_legacy=LegacyDefinition(name='settings_run'))
+
+
+class SettingsSampling(MCategory):
+ '''
+ Contains parameters controlling the sampling.
+ '''
+
+ m_def = Category(
+ aliases=['settings_sampling'],
+ a_legacy=LegacyDefinition(name='settings_sampling'))
+
+
+class SettingsScf(MCategory):
+ '''
+ Contains parameters connected with the convergence of the self-consistent field (SCF)
+ iterations.
+ '''
+
+ m_def = Category(
+ aliases=['settings_scf'],
+ a_legacy=LegacyDefinition(name='settings_scf'))
+
+
+class SettingsSmearing(MCategory):
+ '''
+ Contain parameters that control the smearing of the orbital occupation at finite
+ electronic temperatures.
+ '''
+
+ m_def = Category(
+ aliases=['settings_smearing'],
+ a_legacy=LegacyDefinition(name='settings_smearing'))
+
+
+class SettingsStressTensor(MCategory):
+ '''
+ Settings to calculate the stress tensor (stress_tensor) consistent with the total
+ energy of the system given in energy_total.
+ '''
+
+ m_def = Category(
+ aliases=['settings_stress_tensor'],
+ a_legacy=LegacyDefinition(name='settings_stress_tensor'))
+
+
+class StressTensorType(MCategory):
+ '''
+ Contains the final value of the default stress tensor (stress_tensor) and/or the value
+ of the stress tensor (stress_tensor_value) of the kind defined in stress_tensor_kind.
+ '''
+
+ m_def = Category(
+ aliases=['stress_tensor_type'],
+ a_legacy=LegacyDefinition(name='stress_tensor_type'))
+
+
+class SettingsAtomInMolecule(MCategory):
+ '''
+ Parameters of an atom within a molecule.
+ '''
+
+ m_def = Category(
+ aliases=['settings_atom_in_molecule'],
+ a_legacy=LegacyDefinition(name='settings_atom_in_molecule'))
+
+
+class SettingsConstraint(MCategory):
+ '''
+ Some parameters that describe a constraint
+ '''
+
+ m_def = Category(
+ aliases=['settings_constraint'],
+ a_legacy=LegacyDefinition(name='settings_constraint'))
+
+
+class SettingsInteraction(MCategory):
+ '''
+ Some parameters that describe a bonded interaction.
+ '''
+
+ m_def = Category(
+ aliases=['settings_interaction'],
+ a_legacy=LegacyDefinition(name='settings_interaction'))
+
+
+class SoapParameter(MCategory):
+ '''
+ A soap parameter
+ '''
+
+ m_def = Category(
+ aliases=['soap_parameter'],
+ a_legacy=LegacyDefinition(name='soap_parameter'))
+
+
+class Unused(MCategory):
+ '''
+ This metainfo definition is not used by NOMAD data.
+ '''
+
+ m_def = Category()
+
+
+class EnergyComponentPerAtom(MCategory):
+ '''
+ A value of an energy component per atom, concurring in defining the total energy per
+ atom.
+ '''
+
+ m_def = Category(
+ aliases=['energy_component_per_atom'],
+ categories=[EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_component_per_atom'))
+
+
+class EnergyComponent(MCategory):
+ '''
+ A value of an energy component, expected to be an extensive property.
+ '''
+
+ m_def = Category(
+ aliases=['energy_component'],
+ categories=[EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_component'))
+
+
+class EnergyTypeReference(MCategory):
+ '''
+ This metadata stores an energy used as reference point.
+ '''
+
+ m_def = Category(
+ aliases=['energy_type_reference'],
+ categories=[EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_type_reference'))
+
+
+class ErrorEstimate(MCategory):
+ '''
+ An estimate of the error on the converged (final) value.
+ '''
+
+ m_def = Category(
+ aliases=['error_estimate'],
+ categories=[ErrorEstimateContribution],
+ a_legacy=LegacyDefinition(name='error_estimate'))
+
+
+class MessageInfo(MCategory):
+ '''
+ An information message of the computational program.
+ '''
+
+ m_def = Category(
+ aliases=['message_info'],
+ categories=[MessageDebug],
+ a_legacy=LegacyDefinition(name='message_info'))
+
+
+class ParallelizationInfo(MCategory):
+ '''
+ Contains information on the parallelization of the program, i.e. which parallel
+ programming language was used and its version, how many cores had been working on the
+ calculation and the flags and parameters needed to run the parallelization of the
+ code.
+ '''
+
+ m_def = Category(
+ aliases=['parallelization_info'],
+ categories=[AccessoryInfo],
+ a_legacy=LegacyDefinition(name='parallelization_info'))
+
+
+class ParsingMessageInfo(MCategory):
+ '''
+ This field is used for info messages of the parsing program.
+ '''
+
+ m_def = Category(
+ aliases=['parsing_message_info'],
+ categories=[ParsingMessageDebug],
+ a_legacy=LegacyDefinition(name='parsing_message_info'))
+
+
+class ProgramInfo(MCategory):
+ '''
+ Contains information on the program that generated the data, i.e. the program_name,
+ program_version, program_compilation_host and program_compilation_datetime as direct
+ children of this field.
+ '''
+
+ m_def = Category(
+ aliases=['program_info'],
+ categories=[AccessoryInfo],
+ a_legacy=LegacyDefinition(name='program_info'))
+
+
+class SettingsGeometryOptimization(MCategory):
+ '''
+ Contains parameters controlling the geometry optimization.
+ '''
+
+ m_def = Category(
+ aliases=['settings_geometry_optimization'],
+ categories=[SettingsSampling],
+ a_legacy=LegacyDefinition(name='settings_geometry_optimization'))
+
+
+class SettingsKPoints(MCategory):
+ '''
+ Contains parameters that control the $k$-point mesh.
+ '''
+
+ m_def = Category(
+ aliases=['settings_k_points'],
+ categories=[SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_k_points'))
+
+
+class SettingsMetadynamics(MCategory):
+ '''
+ Contains parameters that control the metadynamics sampling.
+ '''
+
+ m_def = Category(
+ aliases=['settings_metadynamics'],
+ categories=[SettingsSampling],
+ a_legacy=LegacyDefinition(name='settings_metadynamics'))
+
+
+class SettingsMolecularDynamics(MCategory):
+ '''
+ Contains parameters that control the molecular dynamics sampling.
+ '''
+
+ m_def = Category(
+ aliases=['settings_molecular_dynamics'],
+ categories=[SettingsSampling],
+ a_legacy=LegacyDefinition(name='settings_molecular_dynamics'))
+
+
+class SettingsMonteCarlo(MCategory):
+ '''
+ Contains parameters that control the Monte-Carlo sampling.
+ '''
+
+ m_def = Category(
+ aliases=['settings_Monte_Carlo'],
+ categories=[SettingsSampling],
+ a_legacy=LegacyDefinition(name='settings_Monte_Carlo'))
+
+
+class SettingsXC(MCategory):
+ '''
+ Contains parameters connected with the definition of the exchange-correlation (XC)
+ *method*. Here, the term *method* is a more general concept than just *functionals*
+ and include, e.g., post Hartree-Fock methods, too.
+ '''
+
+ m_def = Category(
+ aliases=['settings_XC'],
+ categories=[SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_XC'))
+
+
+class TimeInfo(MCategory):
+ '''
+ Stores information on the date and timings of the calculation. They are useful for,
+ e.g., debugging or visualization purposes.
+ '''
+
+ m_def = Category(
+ aliases=['time_info'],
+ categories=[AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_info'))
+
+
+class EnergyTotalPotentialPerAtom(MCategory):
+ '''
+ A value of the total potential energy per atom. Note that a direct comparison may not
+ be possible because of a difference in the methods for computing total energies and
+ numerical implementations of various codes might leads to different energy zeros (see
+ section_energy_code_independent for a code-independent definition of the energy).
+ '''
+
+ m_def = Category(
+ aliases=['energy_total_potential_per_atom'],
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_total_potential_per_atom'))
+
+
+class EnergyTotalPotential(MCategory):
+ '''
+ A value of the total potential energy. Note that a direct comparison may not be
+ possible because of a difference in the methods for computing total energies and
+ numerical implementations of various codes might leads to different energy zeros (see
+ section_energy_code_independent for a code-independent definition of the energy).
+ '''
+
+ m_def = Category(
+ aliases=['energy_total_potential'],
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_total_potential'))
+
+
+class EnergyTypeC(MCategory):
+ '''
+ This metadata stores the correlation (C) energy.
+ '''
+
+ m_def = Category(
+ aliases=['energy_type_C'],
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_type_C'))
+
+
+class EnergyTypeVanDerWaals(MCategory):
+ '''
+ This metadata stores the converged van der Waals energy.
+ '''
+
+ m_def = Category(
+ aliases=['energy_type_van_der_Waals'],
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_type_van_der_Waals'))
+
+
+class EnergyTypeXC(MCategory):
+ '''
+ This metadata stores the exchange-correlation (XC) energy.
+ '''
+
+ m_def = Category(
+ aliases=['energy_type_XC'],
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_type_XC'))
+
+
+class EnergyTypeX(MCategory):
+ '''
+ This metadata stores the exchange (X) energy.
+ '''
+
+ m_def = Category(
+ aliases=['energy_type_X'],
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_type_X'))
+
+
+class MessageWarning(MCategory):
+ '''
+ A warning message of the computational program.
+ '''
+
+ m_def = Category(
+ aliases=['message_warning'],
+ categories=[MessageInfo, MessageDebug],
+ a_legacy=LegacyDefinition(name='message_warning'))
+
+
+class ParsingMessageWarning(MCategory):
+ '''
+ This field is used for warning messages of the parsing program.
+ '''
+
+ m_def = Category(
+ aliases=['parsing_message_warning'],
+ categories=[ParsingMessageInfo, ParsingMessageDebug],
+ a_legacy=LegacyDefinition(name='parsing_message_warning'))
+
+
+class SettingsBarostat(MCategory):
+ '''
+ Contains parameters controlling the barostat in a molecular dynamics calculation.
+ '''
+
+ m_def = Category(
+ aliases=['settings_barostat'],
+ categories=[SettingsSampling, SettingsMolecularDynamics],
+ a_legacy=LegacyDefinition(name='settings_barostat'))
+
+
+class SettingsIntegrator(MCategory):
+ '''
+ Contains parameters that control the molecular dynamics (MD) integrator.
+ '''
+
+ m_def = Category(
+ aliases=['settings_integrator'],
+ categories=[SettingsSampling, SettingsMolecularDynamics],
+ a_legacy=LegacyDefinition(name='settings_integrator'))
+
+
+class SettingsPostHartreeFock(MCategory):
+ '''
+ Contains parameters for the post Hartree-Fock method.
+ '''
+
+ m_def = Category(
+ aliases=['settings_post_hartree_fock'],
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_post_hartree_fock'))
+
+
+class SettingsRelativity(MCategory):
+ '''
+ Contains parameters and information connected with the relativistic treatment used in
+ the calculation.
+ '''
+
+ m_def = Category(
+ aliases=['settings_relativity'],
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_relativity'))
+
+
+class SettingsSelfInteractionCorrection(MCategory):
+ '''
+ Contains parameters and information connected with the self-interaction correction
+ (SIC) method being used in self_interaction_correction_method.
+ '''
+
+ m_def = Category(
+ aliases=['settings_self_interaction_correction'],
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_self_interaction_correction'))
+
+
+class SettingsThermostat(MCategory):
+ '''
+ Contains parameters that control the thermostat in the molecular dynamics (MD)
+ calculations.
+ '''
+
+ m_def = Category(
+ aliases=['settings_thermostat'],
+ categories=[SettingsSampling, SettingsMolecularDynamics],
+ a_legacy=LegacyDefinition(name='settings_thermostat'))
+
+
+class SettingsVanDerWaals(MCategory):
+ '''
+ Contain parameters and information connected with the Van der Waals treatment used in
+ the calculation to compute the Van der Waals energy (energy_van_der_Waals).
+ '''
+
+ m_def = Category(
+ aliases=['settings_van_der_Waals'],
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_van_der_Waals'))
+
+
+class SettingsXCFunctional(MCategory):
+ '''
+ Contain parameters connected with the definition of the exchange-correlation (XC)
+ functional (see section_XC_functionals and XC_functional).
+ '''
+
+ m_def = Category(
+ aliases=['settings_XC_functional'],
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_XC_functional'))
+
+
+class MessageError(MCategory):
+ '''
+ An error message of the computational program.
+ '''
+
+ m_def = Category(
+ aliases=['message_error'],
+ categories=[MessageInfo, MessageDebug, MessageWarning],
+ a_legacy=LegacyDefinition(name='message_error'))
+
+
+class ParsingMessageError(MCategory):
+ '''
+ This field is used for error messages of the parsing program.
+ '''
+
+ m_def = Category(
+ aliases=['parsing_message_error'],
+ categories=[ParsingMessageInfo, ParsingMessageWarning, ParsingMessageDebug],
+ a_legacy=LegacyDefinition(name='parsing_message_error'))
+
+
+class SettingsCoupledCluster(MCategory):
+ '''
+ Contains parameters for the coupled-cluster method (CC) in the post Hartree-Fock step.
+ '''
+
+ m_def = Category(
+ aliases=['settings_coupled_cluster'],
+ categories=[SettingsPostHartreeFock, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_coupled_cluster'))
+
+
+class SettingsGW(MCategory):
+ '''
+ Contains parameters for the GW-method in the post Hartree-Fock step, that expands the
+ self-energy in terms of the single particle Green's function $G$ and the screened
+ Coulomb interaction $W$.
+ '''
+
+ m_def = Category(
+ aliases=['settings_GW'],
+ categories=[SettingsPostHartreeFock, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_GW'))
+
+
+class SettingsMCSCF(MCategory):
+ '''
+ Contains parameters for the multi-configurational self-consistent-field (MCSCF)
+ method.
+ '''
+
+ m_def = Category(
+ aliases=['settings_MCSCF'],
+ categories=[SettingsPostHartreeFock, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_MCSCF'))
+
+
+class SettingsMollerPlessetPerturbationTheory(MCategory):
+ '''
+ Contains parameters for Møller–Plesset perturbation theory.
+ '''
+
+ m_def = Category(
+ aliases=['settings_moller_plesset_perturbation_theory'],
+ categories=[SettingsPostHartreeFock, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_moller_plesset_perturbation_theory'))
+
+
+class SettingsMultiReference(MCategory):
+ '''
+ Contains parameters for the multi-reference single and double configuration
+ interaction method.
+ '''
+
+ m_def = Category(
+ aliases=['settings_multi_reference'],
+ categories=[SettingsPostHartreeFock, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='settings_multi_reference'))
+
+
+class ArchiveContext(MSection):
+ '''
+ Contains information relating to an archive.
+ '''
+
+ m_def = Section(
+ aliases=['archive_context'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='archive_context'))
+
+ archive_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ unique identifier of an archive.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='archive_gid'))
+
+
+class CalculationContext(MSection):
+ '''
+ Contains information relating to a calculation.
+ '''
+
+ m_def = Section(
+ aliases=['calculation_context'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='calculation_context'))
+
+ calculation_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ unique identifier of a calculation.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='calculation_gid'))
+
+
+class AtomProjectedDos(MSection):
+ '''
+ Section collecting the information on an atom projected density of states (DOS)
+ evaluation.
+ '''
+
+ m_def = Section(
+ aliases=['section_atom_projected_dos'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_atom_projected_dos'))
+
+ atom_projected_dos_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atom_projected_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the set of discrete energy values for the atom-projected density
+ (electronic-energy) of states (DOS).
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_energies'))
+
+ atom_projected_dos_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_lm_atom_projected_dos', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which atom_projected_dos_values_lm are given. For
+ the quantum number $l$ the conventional meaning of azimuthal quantum number is
+ always adopted. For the integer number $m$, besides the conventional use as
+ magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
+ different conventions is accepted (see the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ The adopted convention is specified by atom_projected_dos_m_kind.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atom_projected_dos_lm'))
+
+ atom_projected_dos_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing what the integer numbers of $m$ in atom_projected_dos_lm mean.
+ The allowed values are listed in the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_m_kind'))
+
+ atom_projected_dos_values_lm = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_lm_atom_projected_dos', 'number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
+ description='''
+ Values correspond to the number of states for a given energy (the set of discrete
+ energy values is given in atom_projected_dos_energies) divided into contributions
+ from each $l,m$ channel for the atom-projected density (electronic-energy) of
+ states. Here, there are as many atom-projected DOS as the number_of_atoms, the
+ list of labels of the atoms and their meanings are in atom_labels.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_values_lm'))
+
+ atom_projected_dos_values_total = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
+ description='''
+ Values correspond to the number of states for a given energy (the set of discrete
+ energy values is given in atom_projected_dos_energies) divided into contributions
+ summed up over all $l$ channels for the atom-projected density (electronic-energy)
+ of states (DOS). Here, there are as many atom-projected DOS as the
+ number_of_atoms, the list of labels of the atoms and their meanings are in
+ atom_labels.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atom_projected_dos_values_total'))
+
+ number_of_atom_projected_dos_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of energy values for the atom-projected density of states (DOS)
+ based on atom_projected_dos_values_lm and atom_projected_dos_values_total.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atom_projected_dos_values'))
+
+ number_of_lm_atom_projected_dos = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for the atom projected density of states
+ (DOS) defined in section_atom_projected_dos.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_lm_atom_projected_dos'))
+
+
+class AtomicMultipoles(MSection):
+ '''
+ Section describing multipoles (charges/monopoles, dipoles, quadrupoles, ...) for each
+ atom.
+ '''
+
+ m_def = Section(
+ aliases=['section_atomic_multipoles'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_atomic_multipoles'))
+
+ atomic_multipole_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the method used to obtain the electrostatic multipoles
+ (including the electric charge, dipole, etc.) for each atom. Such multipoles
+ require a charge-density partitioning scheme, specified by the value of this
+ metadata. Allowed values are listed in the [atomic_multipole_kind wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/atomic-
+ multipole-kind).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atomic_multipole_kind'))
+
+ atomic_multipole_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_lm_atomic_multipoles', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which the atomic multipoles (including the
+ electric charge, dipole, etc.) are given. The method used to obtain the multipoles
+ is specified by atomic_multipole_kind. The meaning of the integer number $l$ is
+ monopole/charge for $l=0$, dipole for $l=1$, quadrupole for $l=2$, etc. The
+ meaning of the integer numbers $m$ is specified by atomic_multipole_m_kind.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atomic_multipole_lm'))
+
+ atomic_multipole_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the definition for each integer number $m$ in
+ atomic_multipole_lm. Allowed values are listed in the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atomic_multipole_m_kind'))
+
+ atomic_multipole_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_lm_atomic_multipoles', 'number_of_atoms'],
+ description='''
+ Value of the multipoles (including the monopole/charge for $l$ = 0, the dipole for
+ $l$ = 1, etc.) for each atom, calculated as described in atomic_multipole_kind.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atomic_multipole_values'))
+
+ number_of_lm_atomic_multipoles = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for atomic multipoles
+ atomic_multipole_lm.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_lm_atomic_multipoles'))
+
+
+class BasisFunctionsAtomCentered(MSection):
+ '''
+ This section contains the description of the basis functions (at least one function)
+ of the (atom-centered) basis set defined in section_basis_set_atom_centered.
+ '''
+
+ m_def = Section(
+ aliases=['section_basis_functions_atom_centered'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))
+
+
+class BasisSetAtomCentered(MSection):
+ '''
+ This section describes the atom-centered basis set. The main contained information is
+ a short, non unique but human-interpretable, name for identifying the basis set
+ (basis_set_atom_centered_short_name), a longer, unique name
+ (basis_set_atom_centered_unique_name), the atomic number of the atomic species the
+ basis set is meant for (basis_set_atom_number), and a list of actual basis functions
+ in the section_basis_functions_atom_centered section.
+ '''
+
+ m_def = Section(
+ aliases=['section_basis_set_atom_centered'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
+
+ basis_set_atom_centered_ls = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_kinds_in_basis_set_atom_centered'],
+ description='''
+ Azimuthal quantum number ($l$) values (of the angular part given by the spherical
+ harmonic $Y_{lm}$) of the atom-centered basis function defined in the current
+ section_basis_set_atom_centered.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_ls'))
+
+ basis_set_atom_centered_radial_functions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_kinds_in_basis_set_atom_centered', 401, 5],
+ description='''
+ Values of the radial function of the different basis function kinds. The values
+ are numerically tabulated on a default 0.01-nm equally spaced grid from 0 to 4 nm.
+ The 5 tabulated values are $r$, $f(r)$, $f'(r)$, $f(r) \\cdot r$,
+ $\\frac{d}{dr}(f(r) \\cdot r)$.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_radial_functions'))
+
+ basis_set_atom_centered_short_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Code-specific, but explicative, base name for the basis set (not unique). Details
+ are explained in the [basis_set_atom_centered_short_name wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
+ set-atom-centered-short-name), this name should not contain the *atom kind* (to
+ simplify the use of a single name for multiple elements).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_short_name'))
+
+ basis_set_atom_centered_unique_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Code-specific, but explicative, base name for the basis set (not unique). This
+ string starts with basis_set_atom_centered_short_name. If the basis set defined in
+ this section_basis_set_atom_centered is not identical to the default definition
+ (stored in a database) of the basis set with the same name stored in a database,
+ then the string is extended by 10 identifiable characters as explained in the
+ [basis_set_atom_centered_name wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/basis-set-atom-centered-unique-name). The
+ reason for this procedure is that often atom-centered basis sets are obtained by
+ fine tuning basis sets provided by the code developers or other sources. Each
+ basis sets, which has normally a standard name, often reported in publications,
+ has also several parameters that can be tuned. This metadata tries to keep track
+ of the original basis set and its modifications. This string here defined should
+ not contain the *atom kind* for which this basis set is intended for, in order to
+ simplify the use of a single name for multiple *atom kinds* (see atom_labels for
+ the actual meaning of *atom kind*).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_unique_name'))
+
+ basis_set_atom_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Atomic number (i.e., number of protons) of the atom for which this basis set is
+ constructed (0 means unspecified or a pseudo atom).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_number'))
+
+ number_of_basis_functions_in_basis_set_atom_centered = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different basis functions in a section_basis_set_atom_centered
+ section. This equals the number of actual coefficients that are specified when
+ using this basis set.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_basis_functions_in_basis_set_atom_centered'))
+
+ number_of_kinds_in_basis_set_atom_centered = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different *kinds* of radial basis functions in the
+ section_basis_set_atom_centered section. Specifically, basis functions with the
+ same $n$ and $l$ quantum numbers are grouped in sets. Each set counts as one
+ *kind*.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_kinds_in_basis_set_atom_centered'))
+
+ section_basis_functions_atom_centered = SubSection(
+ sub_section=SectionProxy('BasisFunctionsAtomCentered'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))
+
+ section_gaussian_basis_group = SubSection(
+ sub_section=SectionProxy('GaussianBasisGroup'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))
+
+
+class BasisSetCellDependent(MSection):
+ '''
+ Section describing a cell-dependent (atom-independent) basis set, e.g. plane waves.
+ The contained information is the type of basis set (in basis_set_cell_dependent_kind),
+ its parameters (e.g., for plane waves in basis_set_planewave_cutoff), and a name that
+ identifies the actually used basis set (a string combining the type and the
+ parameter(s), stored in basis_set_cell_dependent_name).
+ '''
+
+ m_def = Section(
+ aliases=['section_basis_set_cell_dependent'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))
+
+ basis_set_cell_dependent_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A string defining the type of the cell-dependent basis set (i.e., non atom
+ centered such as plane-waves). Allowed values are listed in the
+ [basis_set_cell_dependent_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/basis-set-cell-dependent-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_cell_dependent_kind'))
+
+ basis_set_cell_dependent_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A label identifying the cell-dependent basis set (i.e., non atom centered such as
+ plane-waves). Allowed values are listed in the [basis_set_cell_dependent_name wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
+ set-cell-dependent-name).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_cell_dependent_name'))
+
+ basis_set_planewave_cutoff = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Spherical cutoff in reciprocal space for a plane-wave basis set. It is the energy
+ of the highest plan-ewave ($\\frac{\\hbar^2|k+G|^2}{2m_e}$) included in the basis
+ set. Note that normally this basis set is used for the wavefunctions, and the
+ density would have 4 times the cutoff, but this actually depends on the use of the
+ basis set by the method.
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_planewave_cutoff'))
+
+
+class BasisSet(MSection):
+ '''
+ This section contains references to *all* basis sets used in this
+ section_single_configuration_calculation. More than one basis set instance per *single
+ configuration calculation* (see section_single_configuration_calculation) may be
+ needed. This is true for example, for codes that implement adaptive basis sets along
+ the self-consistent field (SCF) convergence (e.g., exciting). In such cases, there is
+ a section_basis_set instance per SCF iteration, if necessary. Another example is
+ having a basis set for wavefunctions, a different one for the density, an auxiliary
+ basis set for resolution of identity (RI), etc.
+
+ Supported are the two broad classes of basis sets: *atom-centered* (e.g., Gaussian-
+ type, numerical atomic orbitals) and *cell-dependent* (like plane waves or real-space
+ grids, so named because they are typically used for periodic-system calculations and
+ dependent to the simulated cell as a whole).
+
+ Basis sets used in this section_single_configuration_calculation, belonging to either
+ class, are defined in the dedicated section: [section_basis_set_cell_dependent
+ ](section_basis_set_cell_dependent) or section_basis_set_atom_centered. The
+ correspondence between the basis sets listed in this section and the definition given
+ in the dedicated sessions is given by the two concrete metadata:
+ mapping_section_basis_set_cell_dependent and mapping_section_basis_set_atom_centered.
+ The latter metadata is a list that connects each atom in the system with its basis
+ set, where the same basis set can be assigned to more than one atom.
+ '''
+
+ m_def = Section(
+ aliases=['section_basis_set'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_basis_set'))
+
+ basis_set_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the use of the basis set, i.e, if it used for expanding a wave-
+ function or an electron density. Allowed values are listed in the [basis_set_kind
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/basis-set-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_kind'))
+
+ basis_set_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String identifying the basis set in an unique way. The rules for building this
+ string are specified in the [basis_set_name wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
+ set-name).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_name'))
+
+ mapping_section_basis_set_atom_centered = Quantity(
+ type=Reference(SectionProxy('BasisSetAtomCentered')),
+ shape=['number_of_atoms'],
+ description='''
+ An array of the dimension of number_of_atoms where each atom (identified by the
+ index in the array) is assigned to an atom-centered basis set, for this
+ section_single_configuration_calculation. The actual definition of the atom-
+ centered basis set is in the section_basis_set_atom_centered that is referred to
+ by this metadata.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_basis_set_atom_centered'))
+
+ mapping_section_basis_set_cell_dependent = Quantity(
+ type=Reference(SectionProxy('BasisSetCellDependent')),
+ shape=[],
+ description='''
+ Assignment of the cell-dependent (i.e., non atom centered, e.g., plane-waves)
+ parts of the basis set, which is defined (type, parameters) in
+ section_basis_set_cell_dependent that is referred to by this metadata.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_basis_set_cell_dependent'))
+
+ number_of_basis_functions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Stores the total number of basis functions in a section_basis_set section.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_basis_functions'))
+
+
+class RestrictedUri(MSection):
+ '''
+ Restricted URIs on this calculation (Coverage: any info or files that are related with
+ this calculation can be subject to restriction)
+ '''
+
+ m_def = Section(
+ aliases=['section_restricted_uri'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_restricted_uri'))
+
+ number_of_restricted_uri = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ The number of restricted uris in restricted_uri list.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_restricted_uri'))
+
+ restricted_uri = Quantity(
+ type=str,
+ shape=['number_of_restricted_uri'],
+ description='''
+ The list of nomad uri(s) identifying the restricted info/file corresponding to
+ this calculation
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='restricted_uri'))
+
+ restricted_uri_reason = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The reason of restriction for the uri or file. The reason can be 'propriety
+ license', 'open-source redistribution restricted license', 'other license', or
+ 'author restricted'.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='restricted_uri_reason'))
+
+ restricted_uri_issue_authority = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The issue authority is the restriction owner for the uri or file. This can be
+ license owner such as 'VASP' or 'AMBER', 'NOMAD', or the author of the uri. For
+ example the repository user name of the author.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='restricted_uri_issue_authority'))
+
+ restricted_uri_end_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The deadline date of the restriction for the uri or file. The end date can be in
+ date format string for those restrictions set by authors or NOMAD otherwise it is
+ set to 'unlimited' for the restriction related to license.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='restricted_uri_end_date'))
+
+ restricted_uri_restriction = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of restriction for the uri or file. The type can be 'any access' or
+ 'license permitted'.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='restricted_uri_restriction'))
+
+ restricted_uri_license = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The info of the license that is the reason of restriction.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='restricted_uri_license'))
+
+ number_of_restricted_uri_files = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ The number of restricted files in restricted_uri_files list.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_restricted_uri_files'))
+
+
+class CalculationToCalculationRefs(MSection):
+ '''
+ Section that describes the relationship between different
+ section_single_configuration_calculation sections.
+
+ For instance, one calculation is a perturbation performed using a self-consistent
+ field (SCF) calculation as starting point, or a simulated system is partitioned in
+ regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated
+ via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
+
+ The kind of relationship between the calculation defined in this section and the
+ referenced one is described by calculation_to_calculation_kind. The referenced
+ section_single_configuration_calculation is identified via
+ calculation_to_calculation_ref (typically used for a
+ section_single_configuration_calculation in the same section_run) or
+ calculation_to_calculation_external_url.
+ '''
+
+ m_def = Section(
+ aliases=['section_calculation_to_calculation_refs'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))
+
+ calculation_to_calculation_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ URL used to reference an externally stored calculation. The kind of relationship
+ between the present and the referenced section_single_configuration_calculation is
+ specified by calculation_to_calculation_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_calculation_external_url'))
+
+ calculation_to_calculation_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the relationship between the referenced
+ section_single_configuration_calculation and the present
+ section_single_configuration_calculation. Valid values are described in the
+ [calculation_to_calculation_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/calculation-to-calculation-kind). Often
+ calculations are connected, for instance, one calculation is a perturbation
+ performed using a self-consistent field (SCF) calculation as starting point, or a
+ simulated system is partitioned in regions with different but connected
+ Hamiltonians (e.g., QM/MM, or a region treated via Kohn-Sham DFT embedded into a
+ region treated via orbital-free DFT). Hence, the need of keeping track of these
+ connected calculations. The referenced calculation is identified via
+ calculation_to_calculation_ref (typically used for a calculation in the same
+ section_run) or calculation_to_calculation_external_url.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_calculation_kind'))
+
+ calculation_to_calculation_ref = Quantity(
+ type=Reference(SectionProxy('SingleConfigurationCalculation')),
+ shape=[],
+ description='''
+ Reference to another calculation. If both this and
+ calculation_to_calculation_external_url are given, then
+ calculation_to_calculation_ref is a local copy of the URL given in
+ calculation_to_calculation_external_url. The kind of relationship between the
+ present and the referenced section_single_configuration_calculation is specified
+ by calculation_to_calculation_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_calculation_ref'))
+
+
+class CalculationToFolderRefs(MSection):
+ '''
+ Section that describes the relationship between
+ section_single_configuration_calculationa and the folder containing the original
+ calulations
+ '''
+
+ m_def = Section(
+ aliases=['section_calculation_to_folder_refs'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))
+
+ calculation_to_folder_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ URL used to reference a folder containing external calculations. The kind of
+ relationship between the present and the referenced
+ section_single_configuration_calculation is specified by
+ calculation_to_folder_kind.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='calculation_to_folder_external_url'))
+
+ calculation_to_folder_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the relationship between the referenced
+ section_single_configuration_calculation and a folder containing calculations.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='calculation_to_folder_kind'))
+
+
+class DosFingerprint(MSection):
+ '''
+ Section for the fingerprint of the electronic density-of-states (DOS). DOS
+ fingerprints are a modification of the D-Fingerprints reported in Chem. Mater. 2015,
+ 27, 3, 735–743 (doi:10.1021/cm503507h). The fingerprint consists of a binary
+ representation of the DOS, that is used to evaluate the similarity of materials based
+ on their electronic structure.
+ '''
+
+ m_def = Section(
+ aliases=['section_dos_fingerprint'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_dos_fingerprint'))
+
+ bins = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Byte representation of the DOS fingerprint.
+ ''',
+ a_legacy=LegacyDefinition(name='bins'))
+
+ indices = Quantity(
+ type=np.dtype(np.int16),
+ shape=[2],
+ description='''
+ Indices used to compare DOS fingerprints of different energy ranges.
+ ''',
+ a_legacy=LegacyDefinition(name='indices'))
+
+ stepsize = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Stepsize of interpolation in the first step of the generation of DOS fingerprints.
+ ''',
+ a_legacy=LegacyDefinition(name='stepsize'))
+
+ filling_factor = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Proportion of 1 bins in the DOS fingerprint.
+ ''',
+ a_legacy=LegacyDefinition(name='filling_factor'))
+
+ grid_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifier of the DOS grid that was used for the creation of the fingerprint.
+ Similarity can only be calculated if the same grid was used for both fingerprints.
+ ''',
+ a_legacy=LegacyDefinition(name='grid_id'))
+
+
+class Dos(MSection):
+ '''
+ Section collecting information of a (electronic-energy or vibrational-energy) density
+ of states (DOS) evaluation.
+ '''
+
+ m_def = Section(
+ aliases=['section_dos'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_dos'))
+
+ dos_energies_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the set of discrete energy values with respect to the highest
+ occupied energy level. This is the total DOS, see atom_projected_dos_energies and
+ species_projected_dos_energies for partial density of states.
+
+ If not available through energy_reference_highest_occupied, the highest occupied
+ energy level is detected by searching for a non-zero DOS value below (or nearby)
+ the reported energy_reference_fermi. In case the highest occupied energy level
+ cannot be detected accurately, the normalized values are not reported. For
+ calculations with multiple spin-channels, the normalization is determined by the
+ first channel.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_energies_normalized'))
+
+ dos_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the set of discrete energy values for the density (electronic-
+ energy or vibrational energy) of states (DOS). This is the total DOS, see
+ atom_projected_dos_energies and species_projected_dos_energies for partial density
+ of states.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_energies'))
+
+ dos_integrated_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_dos_values'],
+ description='''
+ Integrated density of states (starting at $-\\infty$), pseudo potential
+ calculations should start with the number of core electrons if they cover only the
+ active electrons
+ ''',
+ a_legacy=LegacyDefinition(name='dos_integrated_values'))
+
+ dos_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String to specify the kind of density of states (either electronic or
+ vibrational).
+ ''',
+ a_legacy=LegacyDefinition(name='dos_kind'))
+
+ dos_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_dos_lms', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which dos_values_lm are given. For the quantum
+ number $l$ the conventional meaning of azimuthal quantum number is always adopted.
+ For the integer number $m$, besides the conventional use as magnetic quantum
+ number ($l+1$ integer values from $-l$ to $l$), a set of different conventions is
+ accepted (see the [m_kind wiki page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/m-kind). The actual adopted convention is specified by
+ dos_m_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_lm'))
+
+ dos_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing what the integer numbers of $m$ in dos_lm mean. The allowed
+ values are listed in the [m_kind wiki page](https://gitlab.rzg.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='dos_m_kind'))
+
+ dos_values_lm = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_dos_lms', 'number_of_spin_channels', 'number_of_atoms', 'number_of_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the density (electronic-energy) of states values projected on the
+ various spherical harmonics (integrated on all atoms), see
+ atom_projected_dos_values_lm for atom values.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_values_lm'))
+
+ dos_values_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_dos_values'],
+ description='''
+ Density of states (DOS) values divided by the unit cell volume and by the number
+ of atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_values_normalized'))
+
+ dos_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_dos_values'],
+ description='''
+ Values (number of states for a given energy, the set of discrete energy values is
+ given in dos_energies) of density (electronic-energy or vibrational-energy) of
+ states. This refers to the simulation cell, i.e. integrating over all energies
+ will give the number of electrons in the simulation cell.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_values'))
+
+ number_of_dos_lms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for the given projected density of
+ states (DOS) in dos_values and dos_values_lm.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_dos_lms'))
+
+ number_of_dos_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of energy values for the density of states (DOS), see
+ dos_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_dos_values'))
+
+ section_dos_fingerprint = SubSection(
+ sub_section=SectionProxy('DosFingerprint'),
+ repeats=False,
+ a_legacy=LegacyDefinition(name='section_dos_fingerprint'))
+
+
+class Eigenvalues(MSection):
+ '''
+ Section containing (electronic-energy) eigenvalues for one spin channel. If, for
+ example, the eigenvalues of the Kohn-Sham operator are to be stored, a string
+ identifying this kind of eigenvalues is put in eigenvalues_kind, the coordinates of
+ the $k$-points at which the eigenvalues are evaluated is stored in
+ eigenvalues_kpoints, and the energy values of the eigenstates and their occupation is
+ stored in eigenvalues_values and eigenvalues_occupation, respectively.
+ '''
+
+ m_def = Section(
+ aliases=['section_eigenvalues'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_eigenvalues'))
+
+ eigenvalues_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A short string describing the kind of eigenvalues, as defined in the
+ [eigenvalues_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/eigenvalues-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_kind'))
+
+ eigenvalues_kpoints_multiplicity = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_eigenvalues_kpoints'],
+ description='''
+ Multiplicity of the $k$ point (i.e., how many distinct points per cell this
+ expands to after applying all symmetries). This defaults to 1. If expansion is
+ preformed then each point will have weight
+ eigenvalues_kpoints_weights/eigenvalues_kpoints_multiplicity.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='eigenvalues_kpoints_multiplicity'))
+
+ eigenvalues_kpoints_weights = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_eigenvalues_kpoints'],
+ description='''
+ Weights of the $k$ points (in the basis of the reciprocal lattice vectors) used
+ for the evaluation of the eigenvalues tabulated in eigenvalues_values, should
+ account for symmetry too.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='eigenvalues_kpoints_weights'))
+
+ eigenvalues_kpoints = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_eigenvalues_kpoints', 3],
+ description='''
+ Coordinates of the $k$ points (in the basis of the reciprocal lattice vectors)
+ used for the evaluation of the eigenvalues tabulated in eigenvalues_values.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_kpoints'))
+
+ eigenvalues_occupation = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ description='''
+ Occupation of the eigenstates. The corresponding eigenvalues (energy) are given in
+ eigenvalues_values. The coordinates in the reciprocal space are defined in
+ eigenvalues_kpoints.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_occupation'))
+
+ eigenvalues_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Values of the (electronic-energy) eigenvalues. The coordinates of the
+ corresponding eigenstates in the reciprocal space are defined in
+ eigenvalues_kpoints and their occupations are given in eigenvalues_occupation.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_values'))
+
+ number_of_band_segment_eigenvalues = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of eigenvalues in a band segment, see band_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_band_segment_eigenvalues'))
+
+ number_of_eigenvalues_kpoints = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $k$ points, see eigenvalues_kpoints. $k$ points are calculated
+ within a run and are irreducible if a symmetry is used.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_eigenvalues_kpoints'))
+
+ number_of_eigenvalues = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of eigenvalues, see eigenvalues_values.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_eigenvalues'))
+
+ number_of_normalized_band_segment_eigenvalues = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of normalized eigenvalues in a band segment, see
+
+ band_energies_normalized.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_normalized_band_segment_eigenvalues'))
+
+ gw_qp_linearization_prefactor = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ description='''
+ Linearization prefactor
+ ''',
+ a_legacy=LegacyDefinition(name='gw_qp_linearization_prefactor'))
+
+
+class EnergyCodeIndependent(MSection):
+ '''
+ Section describing a code-independent total energy obtained by subtracting some
+ reference energy calculated with the same code. It contains the type in
+ energy_code_independent_kind and the computed code-independent total energy in
+ energy_code_independent_value. The computed energy allows for comparisons among
+ different codes and numerical settings.
+ '''
+
+ m_def = Section(
+ aliases=['section_energy_code_independent'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_energy_code_independent'))
+
+ energy_code_independent_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of the code-independent total energy (obtained by subtracting a reference
+ energy calculated with the same code), created to be comparable among different
+ codes and numerical settings. Details can be found on the [energy_code_independent
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/energy-code-independent).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='energy_code_independent_kind'))
+
+ energy_code_independent_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the code-independent total energy (obtained by subtracting a reference
+ energy calculated with the same code). This value is created to be comparable
+ among different codes and numerical settings. Details can be found on the
+ [energy_code_independent wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/energy-code-independent).
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential, Unused],
+ a_legacy=LegacyDefinition(name='energy_code_independent_value'))
+
+
+class EnergyVanDerWaals(MSection):
+ '''
+ Section containing the Van der Waals energy value (energy_van_der_Waals_value) of type
+ van_der_Waals_kind. This is used when more than one Van der Waals methods are applied
+ in the same *single configuration calculation*, see
+ section_single_configuration_calculation. The main Van der Waals method (the one
+ concurring to energy_current, and used, e.g., for evaluating the forces for a
+ relaxation or dynamics) is given in energy_van_der_Waals and is defined in
+ settings_van_der_Waals.
+ '''
+
+ m_def = Section(
+ aliases=['section_energy_van_der_Waals'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
+
+ energy_van_der_Waals_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to compute van der Waals energy stored in energy_van_der_Waals_value.
+ This metadata is used when more than one van der Waals method is applied in the
+ same *single configuration calculation* (see
+ section_single_configuration_calculation). The method used for van der Waals (the
+ one consistent with energy_current and, e.g., for evaluating the forces for a
+ relaxation or dynamics) is defined in settings_van_der_Waals.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='energy_van_der_Waals_kind'))
+
+ energy_van_der_Waals_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of van der Waals energy, calculated with the method defined in
+ energy_van_der_Waals_kind. This metadata is used when more than one van der Waals
+ method is applied in the same *single configuration calculation* (see
+ section_single_configuration_calculation). The value of the van der Waals energy
+ consistent with energy_current and used, e.g., for evaluating the forces for a
+ relaxation or dynamics, is given in energy_van_der_Waals and defined in
+ settings_van_der_Waals.
+ ''',
+ categories=[EnergyTypeVanDerWaals, EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_van_der_Waals_value'))
+
+ energy_van_der_Waals = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value for the converged van der Waals energy calculated using the method described
+ in van_der_Waals_method, and used in energy_current. This is the van der Waals
+ method consistent with, e.g., forces used for relaxation or dynamics. Alternative
+ methods are listed in section_energy_van_der_Waals.
+ ''',
+ categories=[EnergyTypeVanDerWaals, EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_van_der_Waals'))
+
+
+class EnergyContribution(MSection):
+ '''
+ Section describing the contributions to the total energy.
+ '''
+
+ m_def = Section(
+ aliases=['section_energy_contribution'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_energy_contribution'))
+
+ energy_contibution_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The kind of the energy contribution. Can be one of bond, pair, coulomb, etc.
+ ''',
+ a_legacy=LegacyDefinition(name='energy_contibution_kind'))
+
+ energy_contribution_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy contribution.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_contribution_value'))
+
+
+class FrameSequenceUserQuantity(MSection):
+ '''
+ Section collecting some user-defined quantities evaluated along a sequence of frame.
+ '''
+
+ m_def = Section(
+ aliases=['section_frame_sequence_user_quantity'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_frame_sequence_user_quantity'))
+
+ frame_sequence_user_quantity_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_user_quantity_evaluations_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_user_quantity. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_frames'))
+
+ frame_sequence_user_quantity_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Descriptive name of a user-defined quantity, sampled along this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ Dedicated metadata are created for the conserved energy-like quantity
+ (frame_sequence_conserved_quantity), the kinetic and potential energies
+ (frame_sequence_kinetic_energy and frame_sequence_potential_energy), the
+ instantaneous temperature (frame_sequence_temperature) and pressure
+ (frame_sequence_pressure). This metadata should be used for other quantities that
+ are monitored along a sequence of frames.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_name'))
+
+ frame_sequence_user_quantity_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2, 'number_of_frame_sequence_user_quantity_components'],
+ description='''
+ Average of frame_sequence_user_quantity and its standard deviation in this
+ sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_stats'))
+
+ frame_sequence_user_quantity = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_user_quantity_evaluations_in_sequence', 'number_of_frame_sequence_user_quantity_components'],
+ description='''
+ Array containing the values of the user-defined quantity defined in
+ frame_sequence_user_quantity_name, evaluated along this sequence of frames (i.e.,
+ trajectory, a frame is one section_single_configuration_calculation). If not all
+ frames have a value the indices of the frames that have a value are stored in
+ frame_sequence_kinetic_energy_frames. If not all frames have a value the indices
+ of the frames that have a value are stored in
+ frame_sequence_kinetic_energy_frames.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity'))
+
+ number_of_frame_sequence_user_quantity_components = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of user-defined quantity defined by
+ frame_sequence_user_quantity_name and monitored in a sequence of frames. A
+ sequence is a trajectory, which can have number_of_frames_in_sequence each
+ representing one section_single_configuration_calculation section.
+
+ Dedicated metadata monitored along a sequence of frames are created for the
+ conserved energy-like quantity (frame_sequence_conserved_quantity), the kinetic
+ and potential energies ([frame_sequence_kinetic_energy and
+ frame_sequence_potential_energy](frame_sequence_kinetic_energy and
+ frame_sequence_potential_energy)), the instantaneous temperature
+ (frame_sequence_temperature) and the pressure (frame_sequence_pressure).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_frame_sequence_user_quantity_components'))
+
+ number_of_user_quantity_evaluations_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of user defined quantity evaluations along a sequence of
+ frame_sequence_user_quantity frames. A sequence is a trajectory, which can have
+ number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_user_quantity_evaluations_in_sequence'))
+
+
+class FrameSequence(MSection):
+ '''
+ Section containing a sequence of frames, i.e. a trajectory which can have
+ number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section evaluated with a sampling method
+ (e.g, molecular dynamics, Monte Carlo, geometry optimization). The sampling method
+ might be a subset of the whole trajectory.
+
+ Information on the method used for the sampling can be found in the
+ section_sampling_method section and information of each frame of the sequence are
+ found in the section_single_configuration_calculation section.
+ '''
+
+ m_def = Section(
+ aliases=['section_frame_sequence'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_frame_sequence'))
+
+ frame_sequence_conserved_quantity_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_conserved_quantity_evaluations_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices of the frames the
+ frame_sequence_conserved_quantity values refers to. If not given it defaults to
+ the trivial mapping 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity_frames'))
+
+ frame_sequence_conserved_quantity_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='joule',
+ description='''
+ Average value of energy-like frame_sequence_conserved_quantity, and its standard
+ deviation, over this sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity_stats'))
+
+ frame_sequence_conserved_quantity = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_conserved_quantity_evaluations_in_sequence'],
+ unit='joule',
+ description='''
+ Array containing the values of a quantity that should be conserved, along a
+ sequence of frames (i.e., a trajectory). A frame is one
+ section_single_configuration_calculation), for example the total energy in the NVE
+ ensemble. If not all frames have a value the indices of the frames that have a
+ value are stored in frame_sequence_conserved_quantity_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity'))
+
+ frame_sequence_continuation_kind = Quantity(
+ type=Reference(SectionProxy('FrameSequence')),
+ shape=[],
+ description='''
+ Type of continuation that has been performed from the previous sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation),
+ upon restart.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_continuation_kind'))
+
+ frame_sequence_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ If the energy, forces, and other quantities for the frames (a frame is one
+ section_single_configuration_calculation) in section_frame_sequence are obtained
+ by calling a different code than the code that drives the sequence (e.g., a
+ wrapper that drives a molecular dynamics, Monte Carlo, geometry optimization and
+ calls an electronic-structure code for energy and forces for each configuration),
+ this metadata holds the reference to where the
+ section_single_configuration_calculation for each frame are located. The format
+ for this reference is described in the [frame_sequence_external_url wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/frame-
+ sequence-external-url).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_external_url'))
+
+ frame_sequence_kinetic_energy_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_kinetic_energies_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_kinetic_energy. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy_frames'))
+
+ frame_sequence_kinetic_energy_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='joule',
+ description='''
+ Average kinetic energy and its standard deviation over this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy_stats'))
+
+ frame_sequence_kinetic_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_kinetic_energies_in_sequence'],
+ unit='joule',
+ description='''
+ Array containing the values of the kinetic energy along this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation). If
+ not all frames have a value the indices of the frames that have a value are stored
+ in frame_sequence_kinetic_energy_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy'))
+
+ frame_sequence_local_frames_ref = Quantity(
+ type=Reference(SectionProxy('SingleConfigurationCalculation')),
+ shape=['number_of_frames_in_sequence'],
+ description='''
+ Reference from each frame (a frame is one
+ section_single_configuration_calculation) in this section_frame_sequence to the
+ corresponding section_single_configuration_calculation. Each
+ section_frame_sequence binds a collection of
+ section_single_configuration_calculation, because they all belong to, e.g., a
+ molecular dynamics trajectory, or geometry optimization. The full information for
+ each frame is stored in section_single_configuration_calculation and this metadata
+ establishes the link for each frame.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_local_frames_ref'))
+
+ frame_sequence_potential_energy_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_potential_energies_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_potential_energy. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_potential_energy_frames'))
+
+ frame_sequence_potential_energy_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='joule',
+ description='''
+ Average potential energy and its standard deviation over this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_potential_energy_stats'))
+
+ frame_sequence_potential_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_potential_energies_in_sequence'],
+ unit='joule',
+ description='''
+ Array containing the value of the potential energy along this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ This is equal to energy_total of the corresponding
+ section_single_configuration_calculation and repeated here in a summary array for
+ easier access. If not all frames have a value the indices of the frames that have
+ a value are stored in frame_sequence_potential_energy_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_potential_energy'))
+
+ frame_sequence_pressure_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_pressure_evaluations_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_pressure. If not given it defaults to the trivial mapping 0,1,...
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_pressure_frames'))
+
+ frame_sequence_pressure_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='pascal',
+ description='''
+ Average pressure (one third of the trace of the stress tensor) and standard
+ deviation over this sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_pressure_stats'))
+
+ frame_sequence_pressure = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_pressure_evaluations_in_sequence'],
+ unit='pascal',
+ description='''
+ Array containing the values of the pressure (one third of the trace of the stress
+ tensor) along this sequence of frames (a frame is one
+ section_single_configuration_calculation). If not all frames have a value the
+ indices of the frames that have a value are stored in
+ frame_sequence_pressure_frames.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='frame_sequence_pressure'))
+
+ frame_sequence_temperature_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_temperatures_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_temperature. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_temperature_frames'))
+
+ frame_sequence_temperature_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='kelvin',
+ description='''
+ Average temperature and its standard deviation over this sequence of frames (i.e.,
+ a trajectory, a frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_temperature_stats'))
+
+ frame_sequence_temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_temperatures_in_sequence'],
+ unit='kelvin',
+ description='''
+ Array containing the values of the instantaneous temperature (a quantity,
+ proportional to frame_sequence_kinetic_energy, whose ensemble average equals the
+ thermodynamic temperature) along this sequence of frames (i.e., a trajectory, a
+ frame is one section_single_configuration_calculation). If not all frames have a
+ value the indices of the frames that have a value are stored in
+ frame_sequence_temperature_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_temperature'))
+
+ frame_sequence_time = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_frames_in_sequence'],
+ unit='second',
+ description='''
+ Time along this sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation). Time start is arbitrary, but when a
+ sequence is a continuation of another time should be continued too.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_time'))
+
+ frame_sequence_to_sampling_ref = Quantity(
+ type=Reference(SectionProxy('SamplingMethod')),
+ shape=[],
+ description='''
+ Reference from the present section_frame_sequence to the section_sampling_method,
+ that defines the parameters used in this sequence of frames (i.e., a trajectory, a
+ frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_to_sampling_ref'))
+
+ geometry_optimization_converged = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Arrays specify whether a geometry optimization is converged.
+ ''',
+ a_legacy=LegacyDefinition(name='geometry_optimization_converged'))
+
+ number_of_conserved_quantity_evaluations_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of conserved quantity evaluations in this sequence. A sequence is
+ a trajectory, which can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_conserved_quantity_evaluations_in_sequence'))
+
+ number_of_frames_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of frames in a sequence. A sequence is a trajectory, which can
+ have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_frames_in_sequence'))
+
+ number_of_kinetic_energies_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of kinetic energy evaluations in this sequence of frames, see
+ frame_sequence_kinetic_energy.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_kinetic_energies_in_sequence'))
+
+ number_of_potential_energies_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of potential energies evaluation in this sequence. A sequence is
+ a trajectory, which can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_potential_energies_in_sequence'))
+
+ number_of_pressure_evaluations_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of pressure evaluations in this sequence. A sequence is a
+ trajectory, which can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_pressure_evaluations_in_sequence'))
+
+ number_of_temperatures_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of temperature frames (frame_sequence_temperature) used in the
+ section_frame_sequence. A sequence is a trajectory, which can have
+ number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_temperatures_in_sequence'))
+
+ previous_sequence_ref = Quantity(
+ type=Reference(SectionProxy('FrameSequence')),
+ shape=[],
+ description='''
+ Contains a reference to the previous sequence. A sequence is a trajectory, which
+ can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section. If not given, a start from an
+ initial configuration is assumed.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='previous_sequence_ref'))
+
+ section_frame_sequence_user_quantity = SubSection(
+ sub_section=SectionProxy('FrameSequenceUserQuantity'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_frame_sequence_user_quantity'))
+
+ section_thermodynamical_properties = SubSection(
+ sub_section=SectionProxy('ThermodynamicalProperties'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_thermodynamical_properties'))
+
+
+class GaussianBasisGroup(MSection):
+ '''
+ Section that describes a group of Gaussian contractions. Groups allow one to calculate
+ the primitive Gaussian integrals once for several different linear combinations of
+ them. This defines basis functions with radial part $f_i(r) = r^{l_i} \\sum_{j} c_{i j}
+ A(l_i, \\alpha_j) exp(-\\alpha_j r^2)$ where $A(l_i, \\alpha_j)$ is a the normalization
+ coefficient for primitive Gaussian basis functions. Here, $\\alpha_j$ is defined in
+ gaussian_basis_group_exponents, $l_i$ is given in gaussian_basis_group_ls, and $c_{i
+ j}$ is given in gaussian_basis_group_contractions, whereas the radial part is given by
+ the spherical harmonics $Y_{l m}$.
+
+ This section is defined only if the original basis function uses Gaussian basis
+ functions, and the sequence of radial functions $f_i$ across all
+ section_gaussian_basis_group in section_basis_set_atom_centered should match the one
+ of basis_set_atom_centered_radial_functions.
+ '''
+
+ m_def = Section(
+ aliases=['section_gaussian_basis_group'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))
+
+ gaussian_basis_group_contractions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_gaussian_basis_group_contractions', 'number_of_gaussian_basis_group_exponents'],
+ description='''
+ contraction coefficients $c_{i j}$ defining the contracted basis functions with
+ respect to *normalized* primitive Gaussian functions. They define the Gaussian
+ basis functions as described in section_gaussian_basis_group.
+ ''',
+ a_legacy=LegacyDefinition(name='gaussian_basis_group_contractions'))
+
+ gaussian_basis_group_exponents = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_gaussian_basis_group_exponents'],
+ unit='1 / meter ** 2',
+ description='''
+ Exponents $\\alpha_j$ of the Gaussian functions defining this basis set
+ $exp(-\\alpha_j r^2)$. One should be careful about the units of the coefficients.
+ ''',
+ a_legacy=LegacyDefinition(name='gaussian_basis_group_exponents'))
+
+ gaussian_basis_group_ls = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_gaussian_basis_group_contractions'],
+ description='''
+ Azimuthal quantum number ($l$) values (of the angular part given by the spherical
+ harmonic $Y_{l m}$ of the various contracted basis functions).
+ ''',
+ a_legacy=LegacyDefinition(name='gaussian_basis_group_ls'))
+
+ number_of_gaussian_basis_group_contractions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different contractions, i.e. resulting basis functions in a
+ section_gaussian_basis_group section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_gaussian_basis_group_contractions'))
+
+ number_of_gaussian_basis_group_exponents = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different Gaussian exponents in a section_gaussian_basis_group
+ section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_gaussian_basis_group_exponents'))
+
+
+class KBandNormalized(MSection):
+ '''
+ This section stores information on a normalized $k$-band (electronic band structure)
+ evaluation along one-dimensional pathways in the $k$ (reciprocal) space given in
+ section_k_band_segment. Eigenvalues calculated at the actual $k$-mesh used for
+ energy_total evaluations, can be found in the section_eigenvalues section.
+ '''
+
+ m_def = Section(
+ aliases=['section_k_band_normalized'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_k_band_normalized'))
+
+ k_band_path_normalized_is_standard = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ If the normalized path is along the default path defined in W. Setyawan and S.
+ Curtarolo, [Comput. Mater. Sci. **49**, 299-312
+ (2010)](http://dx.doi.org/10.1016/j.commatsci.2010.05.010).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='k_band_path_normalized_is_standard'))
+
+ section_k_band_segment_normalized = SubSection(
+ sub_section=SectionProxy('KBandSegmentNormalized'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band_segment_normalized'))
+
+
+class KBandSegmentNormalized(MSection):
+ '''
+ Section collecting the information on a normalized $k$-band segment. This section
+ stores band structures along a one-dimensional pathway in the $k$ (reciprocal) space.
+
+ Eigenvalues calculated at the actual $k$-mesh used for energy_total evaluations are
+ defined in section_eigenvalues and the band structures are represented as third-order
+ tensors: one dimension for the spin channels, one for the sequence of $k$ points for
+ the segment (given in number_of_k_points_per_segment), and one for the sequence of
+ eigenvalues at a given $k$ point. The values of the $k$ points in each segment are
+ stored in band_k_points. The energies and occupation for each eigenstate, at each $k$
+ point, segment, and spin channel are stored in band_energies and band_occupations,
+ respectively. The labels for the segment are specified in band_segm_labels.
+ '''
+
+ m_def = Section(
+ aliases=['section_k_band_segment_normalized'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_k_band_segment_normalized'))
+
+ band_energies_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_normalized_k_points_per_segment', 'number_of_normalized_band_segment_eigenvalues'],
+ unit='joule',
+ description='''
+ $k$-dependent energies of the electronic band segment (electronic band structure)
+ with respect to the top of the valence band. This is a third-order tensor, with
+ one dimension used for the spin channels, one for the $k$ points for each segment,
+ and one for the eigenvalue sequence.
+ ''',
+ a_legacy=LegacyDefinition(name='band_energies_normalized'))
+
+ band_k_points_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_normalized_k_points_per_segment', 3],
+ description='''
+ Fractional coordinates of the $k$ points (in the basis of the reciprocal-lattice
+ vectors) for which the normalized electronic energies are given.
+ ''',
+ a_legacy=LegacyDefinition(name='band_k_points_normalized'))
+
+ band_occupations_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_normalized_k_points_per_segment', 'number_of_normalized_band_segment_eigenvalues'],
+ description='''
+ Occupation of the $k$-points along the normalized electronic band. The size of the
+ dimensions of this third-order tensor are the same as for the tensor in
+ band_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='band_occupations_normalized'))
+
+ band_segm_labels_normalized = Quantity(
+ type=str,
+ shape=[2],
+ description='''
+ Start and end labels of the points in the segment (one-dimensional pathways)
+ sampled in the $k$-space, using the conventional symbols, e.g., Gamma, K, L. The
+ coordinates (fractional, in the reciprocal space) of the start and end points for
+ each segment are given in band_segm_start_end_normalized
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='band_segm_labels_normalized'))
+
+ band_segm_start_end_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2, 3],
+ description='''
+ Fractional coordinates of the start and end point (in the basis of the reciprocal
+ lattice vectors) of the segment sampled in the $k$ space. The conventional symbols
+ (e.g., Gamma, K, L) of the same points are given in band_segm_labels
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_start_end_normalized'))
+
+ number_of_normalized_k_points_per_segment = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $k$ points in the segment of the normalized band structure
+ (see section_k_band_segment_normalized).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_normalized_k_points_per_segment'))
+
+
+class KBandSegment(MSection):
+ '''
+ Section collecting the information on a $k$-band or $q$-band segment. This section
+ stores band structures along a one-dimensional pathway in the $k$ or $q$ (reciprocal)
+ space.
+
+ Eigenvalues calculated at the actual $k$-mesh used for energy_total evaluations are
+ defined in section_eigenvalues and the band structures are represented as third-order
+ tensors: one dimension for the spin channels, one for the sequence of $k$ or $q$
+ points for the segment (given in number_of_k_points_per_segment), and one for the
+ sequence of eigenvalues at a given $k$ or $q$ point. The values of the $k$ or $q$
+ points in each segment are stored in band_k_points. The energies and occupation for
+ each eigenstate, at each $k$ or $q$ point, segment, and spin channel are stored in
+ band_energies and band_occupations, respectively. The labels for the segment are
+ specified in band_segm_labels.
+ '''
+
+ m_def = Section(
+ aliases=['section_k_band_segment'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_k_band_segment'))
+
+ band_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_k_points_per_segment', 'number_of_band_segment_eigenvalues'],
+ unit='joule',
+ description='''
+ $k$-dependent or $q$-dependent energies of the electronic or vibrational band
+ segment (electronic/vibrational band structure). This is a third-order tensor,
+ with one dimension used for the spin channels (1 in case of a vibrational band
+ structure), one for the $k$ or $q$ points for each segment, and one for the
+ eigenvalue sequence.
+ ''',
+ a_legacy=LegacyDefinition(name='band_energies'))
+
+ band_k_points = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_k_points_per_segment', 3],
+ description='''
+ Fractional coordinates of the $k$ or $q$ points (in the basis of the reciprocal-
+ lattice vectors) for which the electronic energy are given.
+ ''',
+ a_legacy=LegacyDefinition(name='band_k_points'))
+
+ band_occupations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_k_points_per_segment', 'number_of_band_segment_eigenvalues'],
+ description='''
+ Occupation of the $k$-points along the electronic band. The size of the dimensions
+ of this third-order tensor are the same as for the tensor in band_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='band_occupations'))
+
+ band_segm_labels = Quantity(
+ type=str,
+ shape=[2],
+ description='''
+ Start and end labels of the points in the segment (one-dimensional pathways)
+ sampled in the $k$-space or $q$-space, using the conventional symbols, e.g.,
+ Gamma, K, L. The coordinates (fractional, in the reciprocal space) of the start
+ and end points for each segment are given in band_segm_start_end
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_labels'))
+
+ band_segm_start_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2, 3],
+ description='''
+ Fractional coordinates of the start and end point (in the basis of the reciprocal
+ lattice vectors) of the segment sampled in the $k$ space. The conventional symbols
+ (e.g., Gamma, K, L) of the same points are given in band_segm_labels
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_start_end'))
+
+ number_of_k_points_per_segment = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $k$ points in the segment of the band structure, see
+ section_k_band_segment.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_k_points_per_segment'))
+
+
+class BandGap(MSection):
+ '''
+ This section stores information for a band gap within a band structure.
+ '''
+
+ m_def = Section(
+ aliases=['section_band_gap'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_band_gap'))
+
+ value = Quantity(
+ type=float,
+ shape=[],
+ unit='joule',
+ description='''
+ Band gap energy. Value of zero corresponds to a band structure without a band gap.
+ ''',
+ a_legacy=LegacyDefinition(name='value'))
+
+ type = Quantity(
+ type=MEnum('direct', 'indirect'),
+ shape=[],
+ description='''
+ Type of band gap.
+ ''',
+ a_legacy=LegacyDefinition(name='type'))
+
+ conduction_band_min_energy = Quantity(
+ type=float,
+ shape=[],
+ unit='joule',
+ description='''
+ Conduction band minimum energy.
+ ''',
+ a_legacy=LegacyDefinition(name='conduction_band_min_energy'))
+
+ valence_band_max_energy = Quantity(
+ type=float,
+ shape=[],
+ unit='joule',
+ description='''
+ Valence band maximum energy.
+ ''',
+ a_legacy=LegacyDefinition(name='valence_band_max_energy'))
+
+ conduction_band_min_k_point = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ unit='1 / meter',
+ description='''
+ Coordinate of the conduction band minimum in k-space.
+ ''',
+ a_legacy=LegacyDefinition(name='conduction_band_min_k_point'))
+
+ valence_band_max_k_point = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ unit='1 / meter',
+ description='''
+ Coordinate of the valence band minimum in k-space.
+ ''',
+ a_legacy=LegacyDefinition(name='valence_band_max_k_point'))
+
+
+class BrillouinZone(MSection):
+ '''
+ Defines a polyhedra for the Brillouin zone in reciprocal space.
+ '''
+
+ m_def = Section(
+ aliases=['section_brillouin_zone'],
+ 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 KBand(MSection):
+ '''
+ This section stores information on a $k$-band (electronic or vibrational band
+ structure) evaluation along one-dimensional pathways in the $k$ or $q$ (reciprocal)
+ space given in section_k_band_segment. Eigenvalues calculated at the actual $k$-mesh
+ used for energy_total evaluations, can be found in the section_eigenvalues section.
+ '''
+
+ m_def = Section(
+ aliases=['section_k_band'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_k_band'))
+
+ band_structure_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String to specify the kind of band structure (either electronic or vibrational).
+ ''',
+ a_legacy=LegacyDefinition(name='band_structure_kind'))
+
+ reciprocal_cell = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='1 / meter',
+ description='''
+ The reciprocal cell within which the band structure is calculated.
+ ''',
+ a_legacy=LegacyDefinition(name='reciprocal_cell'))
+
+ is_standard_path = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Boolean indicating whether the path follows the standard path for this bravais
+ lattice. The AFLOW standard by Setyawan and Curtarolo is used
+ (https://doi.org/10.1016/j.commatsci.2010.05.010).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='is_standard_path'))
+
+ brillouin_zone = SubSection(
+ sub_section=SectionProxy('BrillouinZone'),
+ repeats=False,
+ a_legacy=LegacyDefinition(name='brillouin_zone'))
+
+ section_band_gap = SubSection(
+ sub_section=SectionProxy('BandGap'),
+ repeats=True,
+ description='''
+ , Contains information for band gaps detected in the band structure. Contains a
+ section for each spin channel in the same order as reported for the band energies.
+ For channels without a band gap, a band gap value of zero is reported.
+ ''',
+ a_legacy=LegacyDefinition(name='section_band_gap'))
+
+ section_k_band_segment = SubSection(
+ sub_section=SectionProxy('KBandSegment'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band_segment'))
+
+
+class MethodAtomKind(MSection):
+ '''
+ Every section_method_atom_kind section contains method-related information about a
+ kind of atom, and is identified by one or more strings stored in
+ method_atom_kind_label.
+
+ This categorization into atom kinds is more flexible than just atomic species, because
+ to different atoms of the same species different atom-centered basis sets or pseudo-
+ potentials may be assigned. For instance, if two different oxygen atoms are assigned
+ to different basis sets or pseudo-potentials, they have to distinguished into two
+ different *kinds* of O atoms, by creating two distinct section_method_atom_kind
+ sections.
+ '''
+
+ m_def = Section(
+ aliases=['section_method_atom_kind'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_method_atom_kind'))
+
+ method_atom_kind_atom_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Atomic number (number of protons) of this atom kind, use 0 if not an atom.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_atom_number'))
+
+ method_atom_kind_explicit_electrons = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Number of explicit electrons (often called valence).
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_explicit_electrons'))
+
+ method_atom_kind_label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String used to identify the atoms of this kind. This should correspond to the
+ atom_labels of the configuration. It is possible for one atom kind to have
+ multiple labels (in order to allow two atoms of the same kind to have two
+ differently defined sets of atom-centered basis functions or two different pseudo-
+ potentials). Atom kind is typically the symbol of the atomic species but it can be
+ also a ghost or pseudo-atom.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_label'))
+
+ method_atom_kind_mass = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='unified_atomic_mass_unit',
+ description='''
+ Mass of the kind of this kind of atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_mass'))
+
+ method_atom_kind_pseudopotential_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name identifying the pseudopotential used.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_pseudopotential_name'))
+
+
+class MethodToMethodRefs(MSection):
+ '''
+ Section that describes the relationship between different section_method sections. For
+ instance, one calculation is a perturbation performed using a self-consistent field
+ (SCF) calculation as starting point, or a simulated system is partitioned in regions
+ with different but connected Hamiltonians (e.g., QM/MM, or a region treated via Kohn-
+ Sham DFT embedded into a region treated via orbital-free DFT).
+
+ The kind of relationship between the method defined in this section and the referenced
+ one is described by method_to_method_kind. The referenced section section_method is
+ identified via method_to_method_ref (typically used for a section_method section in
+ the same section_run) or method_to_method_external_url.
+ '''
+
+ m_def = Section(
+ aliases=['section_method_to_method_refs'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_method_to_method_refs'))
+
+ method_to_method_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ URL used to reference an externally stored section_method. The kind of
+ relationship between the present and the referenced section_method is specified by
+ method_to_method_kind.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='method_to_method_external_url'))
+
+ method_to_method_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the kind of relationship that the referenced section_method has
+ with the present section_method. Valid values are described in the
+ [method_to_method_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/method-to-method-kind). Often calculations are connected,
+ for instance, one calculation is a perturbation performed using a self-consistent
+ field (SCF) calculation as starting point, or a simulated system is partitioned in
+ regions with different but connected Hamiltonians (e.g., QM/MM, or a region
+ treated via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
+ Hence, the need of keeping track of these connected calculations. The referenced
+ section_method is identified via method_to_method_ref (typically used for a
+ section_method in the same section_run) or method_to_method_external_url.
+ ''',
+ a_legacy=LegacyDefinition(name='method_to_method_kind'))
+
+ method_to_method_ref = Quantity(
+ type=Reference(SectionProxy('Method')),
+ shape=[],
+ description='''
+ Reference to a local section_method. If both method_to_method_ref and
+ method_to_method_external_url are given, then method_to_method_ref is a local copy
+ of the value contained in method_to_method_external_url. The kind of relationship
+ between the method defined in the present section_method and the referenced one is
+ described by method_to_method_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='method_to_method_ref'))
+
+
+class Method(MSection):
+ '''
+ Section containing the various parameters that define the theory and the
+ approximations (convergence, thresholds,...) to perform a *single configuration
+ calculation*, see section_single_configuration_calculation.
+
+ *NOTE*: This section does not contain settings for molecular dynamics, geometry
+ optimization etc. See section frame_sequence for these other settings instead.
+ '''
+
+ m_def = Section(
+ aliases=['section_method'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_method'))
+
+ basis_set = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Unique string identifying the basis set used for the final wavefunctions
+ calculated with XC_method. It might identify a class of basis sets, often matches
+ one of the strings given in any of basis_set_name.
+ ''',
+ categories=[SettingsNumericalParameter, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='basis_set'))
+
+ calculation_method_current = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String that represents the method used to calculate the energy_current. If the
+ method is perturbative, this string does not describe the starting point method,
+ the latter being referenced to by section_method_to_method_refs. For self-
+ consistent field (SCF) ab initio calculations, for example, this is composed by
+ concatenating XC_method_current and basis_set. See [calculation_method_current
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/calculation-method-current) for the details.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='calculation_method_current'))
+
+ calculation_method_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Kind of method in calculation_method_current.
+
+ Accepted values are:
+
+ - absolute
+
+ - perturbative.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_method_kind'))
+
+ calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String that uniquely represents the method used to calculate energy_total, If the
+ present calculation_method_current is a perturbative method Y that uses method X
+ as starting point, this string is automatically created as X@Y, where X is taken
+ from calculation_method_current and Y from method_to_method_ref. In order to
+ activate this, method_to_method_kind must have the value starting_point (see the
+ [method_to_method_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/method-to-method-kind)).
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_method'))
+
+ electronic_structure_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Non-unique string identifying the used electronic structure method. It is not
+ unique in the sense that two calculations with the same
+ electronic_structure_method string may have not been performed with exactly the
+ same method. The allowed strings are given in the [electronic structure method
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/electronic-structure-method).
+ ''',
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='electronic_structure_method'))
+
+ k_mesh_points = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_k_mesh_points', 3],
+ description='''
+ List of all the k points in the $k$-point mesh. These are the k point used to
+ evaluate energy_total, and are in fractional coordinates (in the basis of the
+ reciprocal-lattice vectors).
+ ''',
+ categories=[SettingsKPoints, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='k_mesh_points'))
+
+ k_mesh_weights = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_k_mesh_points'],
+ description='''
+ Weights of all the k points in the $k$-point mesh. These are the weights for
+ k_mesh_points (i.e. the k point used to evaluate energy_total).
+ ''',
+ categories=[SettingsKPoints, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='k_mesh_weights'))
+
+ number_of_k_mesh_points = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of k points in the mesh (i.e. the k points used to evaluate energy_total).
+ ''',
+ categories=[SettingsKPoints, SettingsPotentialEnergySurface, Unused],
+ a_legacy=LegacyDefinition(name='number_of_k_mesh_points'))
+
+ number_of_spin_channels = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of spin channels, see section_method.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_spin_channels'))
+
+ relativity_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the relativistic treatment used for the calculation of the final energy
+ and related quantities. If skipped or empty, no relativistic treatment is applied.
+ ''',
+ categories=[SettingsRelativity, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='relativity_method'))
+
+ scf_max_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Specifies the maximum number of allowed self-consistent field (SCF) iterations in
+ a calculation run, see section_run.
+ ''',
+ categories=[SettingsScf],
+ a_legacy=LegacyDefinition(name='scf_max_iteration'))
+
+ scf_threshold_energy_change = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Specifies the threshold for the energy_total_scf_iteration change between two
+ subsequent self-consistent field (SCF) iterations. The SCF is considered converged
+ when the total-energy change between two SCF cycles is below the threshold
+ (possibly in combination with other criteria).
+ ''',
+ categories=[SettingsScf],
+ a_legacy=LegacyDefinition(name='scf_threshold_energy_change'))
+
+ self_interaction_correction_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Contains the name for the self-interaction correction (SIC) treatment used to
+ calculate the final energy and related quantities. If skipped or empty, no special
+ correction is applied.
+
+ The following SIC methods are available:
+
+ | SIC method | Description |
+
+ | ------------------------- | -------------------------------- |
+
+ | `""` | No correction |
+
+ | `"SIC_AD"` | The average density correction |
+
+ | `"SIC_SOSEX"` | Second order screened exchange |
+
+ | `"SIC_EXPLICIT_ORBITALS"` | (scaled) Perdew-Zunger correction explicitly on a
+ set of orbitals |
+
+ | `"SIC_MAURI_SPZ"` | (scaled) Perdew-Zunger expression on the spin
+ density / doublet unpaired orbital |
+
+ | `"SIC_MAURI_US"` | A (scaled) correction proposed by Mauri and co-
+ workers on the spin density / doublet unpaired orbital |
+ ''',
+ categories=[SettingsSelfInteractionCorrection, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='self_interaction_correction_method'))
+
+ smearing_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the kind of smearing on the electron occupation used to calculate the
+ free energy (see energy_free)
+
+ Valid values are:
+
+ | Smearing kind | Description |
+
+ | ------------------------- | --------------------------------- |
+
+ | `"empty"` | No smearing is applied |
+
+ | `"gaussian"` | Gaussian smearing |
+
+ | `"fermi"` | Fermi smearing |
+
+ | `"marzari-vanderbilt"` | Marzari-Vanderbilt smearing |
+
+ | `"methfessel-paxton"` | Methfessel-Paxton smearing |
+
+ | `"tetrahedra"` | Interpolation of state energies and occupations
+ (ignores smearing_width) |
+ ''',
+ categories=[SettingsSmearing],
+ a_legacy=LegacyDefinition(name='smearing_kind'))
+
+ smearing_width = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Specifies the width of the smearing in energy for the electron occupation used to
+ calculate the free energy (see energy_free).
+
+ *NOTE:* Not all methods specified in smearing_kind uses this value.
+ ''',
+ categories=[SettingsSmearing],
+ a_legacy=LegacyDefinition(name='smearing_width'))
+
+ spin_target_multiplicity = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Stores the target (user-imposed) value of the spin multiplicity $M=2S+1$, where
+ $S$ is the total spin. It is an integer number. This value is not necessarily the
+ value obtained at the end of the calculation. See spin_S2 for the converged value
+ of the spin moment.
+ ''',
+ a_legacy=LegacyDefinition(name='spin_target_multiplicity'))
+
+ stress_tensor_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the method used to calculate stress_tensor for, e.g., molecular dynamics
+ and geometry optimization.
+
+ The allowed values are:
+
+ * numeric
+
+ * analytic
+ ''',
+ categories=[SettingsStressTensor],
+ a_legacy=LegacyDefinition(name='stress_tensor_method'))
+
+ total_charge = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ unit='coulomb',
+ description='''
+ Provides the total amount of charge of the system in a run.
+ ''',
+ a_legacy=LegacyDefinition(name='total_charge'))
+
+ van_der_Waals_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the Van der Waals method. If skipped or an empty string is used, it
+ means no Van der Waals correction is applied.
+
+ Allowed values are:
+
+ | Van der Waals method | Description |
+
+ | --------------------- | ----------------------------------------- |
+
+ | `""` | No Van der Waals correction |
+
+ | `"TS"` | A. Tkatchenko and M. Scheffler, [Phys. Rev. Lett.
+ **102**, 073005 (2009)](http://dx.doi.org/10.1103/PhysRevLett.102.073005) |
+
+ | `"OBS"` | F. Ortmann, F. Bechstedt, and W. G. Schmidt, [Phys. Rev.
+ B **73**, 205101 (2006)](http://dx.doi.org/10.1103/PhysRevB.73.205101) |
+
+ | `"G06"` | S. Grimme, [J. Comput. Chem. **27**, 1787
+ (2006)](http://dx.doi.org/10.1002/jcc.20495) |
+
+ | `"JCHS"` | P. JureÄka, J. ÄŒerný, P. Hobza, and D. R. Salahub,
+ [Journal of Computational Chemistry **28**, 555
+ (2007)](http://dx.doi.org/10.1002/jcc.20570) |
+
+ | `"MDB"` | Many-body dispersion. A. Tkatchenko, R. A. Di Stasio Jr,
+ R. Car, and M. Scheffler, [Physical Review Letters **108**, 236402
+ (2012)](http://dx.doi.org/10.1103/PhysRevLett.108.236402) and A. Ambrosetti, A. M.
+ Reilly, R. A. Di Stasio Jr, and A. Tkatchenko, [The Journal of Chemical Physics
+ **140**, 18A508 (2014)](http://dx.doi.org/10.1063/1.4865104) |
+
+ | `"XC"` | The method to calculate the Van der Waals energy uses a
+ non-local functional which is described in section_XC_functionals. |
+ ''',
+ categories=[SettingsVanDerWaals, SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='van_der_Waals_method'))
+
+ XC_functional = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This value describes a DFT exchange-correlation (XC) functional used for
+ evaluating the energy value stored in energy_XC_functional and related quantities
+ (e.g., forces).
+
+ It is a unique short name obtained by combining the data stored in
+ section_XC_functionals, more specifically by combining different
+ XC_functional_name as described in the [XC_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional).
+ ''',
+ categories=[SettingsPotentialEnergySurface, SettingsPhysicalParameter, SettingsXCFunctional, SettingsXC],
+ a_legacy=LegacyDefinition(name='XC_functional'))
+
+ XC_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the exchange correlation (XC) method used for evaluating the XC energy
+ (energy_XC). Differently from XC_functional, perturbative treatments are also
+ accounted for, where the string contains the reference to both the perturbative
+ (e.g., MP2) and the starting point (e.g, Hartree-Fock) XC method defined in the
+ section section_method.
+
+ The value consists of XC_method_current concatenated with the `@` character and
+ the XC method (XC_method) defined in section_method that is referred to by
+ method_to_method_ref where method_to_method_kind = "starting_point_method".
+ ''',
+ categories=[SettingsXC, SettingsPotentialEnergySurface, Unused],
+ a_legacy=LegacyDefinition(name='XC_method'))
+
+ XC_method_current = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifies the exchange correlation (XC) method used for energy_XC and related
+ quantities in a standardized short form as a string.
+
+ It is built by joining the values in the following order using the underscore `_`
+ character: electronic_structure_method, XC_functional,
+ self_interaction_correction_method, van_der_Waals_method and relativity_method.
+
+ If any of the methods listed in the string contain non-standard settings, then the
+ first 10 characters of the Base64 URL encoding of SHA 512 checksum of a normalized
+ JSON with all non-redundant non-derived settings_XC are appended to the the string
+ preceded by an underscore.
+
+ With empty strings, the underscore `_` character is skipped.
+
+ If the method defined in the section_method section is perturbative, the
+ XC_method_current contains only the perturbative method, not the starting point
+ (e.g. the DFT XC functional used as a starting point for a RPA perturbative
+ calculation). In this case, the string that contains both the perturbative and
+ starting point method is stored in XC_method.
+ ''',
+ categories=[SettingsXC, SettingsPotentialEnergySurface],
+ a_legacy=LegacyDefinition(name='XC_method_current'))
+
+ dft_plus_u_functional = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of DFT+U functional (such as DFT/DFT+U double-counting compensation). Valid
+ names are described in the [dft\\_plus\\_u\\_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/dft-
+ plus-u-functional).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_functional'))
+
+ dft_plus_u_projection_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ DFT+U: Type of orbitals used for projection in order to calculate occupation
+ numbers. Valid names are described in the [dft\\_plus\\_u\\_projection\\_type wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/dft-
+ plus-u-projection-type).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_projection_type'))
+
+ gw_bare_coulomb_cutofftype = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Cutoff type for the calculation of the bare Coulomb potential: none, 0d, 1d, 2d.
+ See Rozzi et al., PRB 73, 205119 (2006)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_bare_coulomb_cutofftype'))
+
+ gw_bare_coulomb_gmax = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='1 / meter',
+ description='''
+ Maximum G for the pw basis for the Coulomb potential.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_bare_coulomb_gmax'))
+
+ gw_basis_set = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Auxillary basis set used for non-local operators: mixed - mixed basis set, Kotani
+ and Schilfgaarde, Solid State Comm. 121, 461 (2002).
+ ''',
+ a_legacy=LegacyDefinition(name='gw_basis_set'))
+
+ gw_core_treatment = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ It specifies whether the core states are treated in the GW calculation: all - All
+ electron calculation; val - Valence electron only calculation; vab - Core
+ electrons are excluded from the mixed product basis; xal - All electron treatment
+ of the exchange self-energy only
+ ''',
+ a_legacy=LegacyDefinition(name='gw_core_treatment'))
+
+ gw_frequency_grid_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Frequency integration grid type for the correlational self energy: 'eqdis' -
+ equidistant frequencies from 0 to freqmax; 'gaulag' - Gauss-Laguerre quadrature
+ from 0 to infinity; 'gauleg' - Gauss-Legendre quadrature from 0 to freqmax;
+ 'gaule2' (default) - double Gauss-Legendre quadrature from 0 to freqmax and from
+ freqmax to infinity.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_grid_type'))
+
+ gw_max_frequency = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum frequency for the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_max_frequency'))
+
+ gw_mixed_basis_gmax = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='1 / meter',
+ description='''
+ Cut-off parameter for the truncation of the expansion of the plane waves in the
+ interstitial region.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_mixed_basis_gmax'))
+
+ gw_mixed_basis_lmax = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Maximum l value used for the radial functions within the muffin-tin.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_mixed_basis_lmax'))
+
+ gw_mixed_basis_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Eigenvalue threshold below which the egenvectors are discarded in the construction
+ of the radial basis set.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_mixed_basis_tolerance'))
+
+ gw_ngridq = Quantity(
+ type=np.dtype(np.int32),
+ shape=[3],
+ description='''
+ k/q-point grid size used in the GW calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_ngridq'))
+
+ gw_frequency_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number referring to the frequency used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_number'))
+
+ gw_frequency_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Values of the frequency used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_values'))
+
+ gw_frequency_weights = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Weights of the frequency used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_weights'))
+
+ gw_number_of_frequencies = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of frequency points used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_number_of_frequencies'))
+
+ gw_polarizability_number_of_empty_states = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of empty states used to compute the polarizability P
+ ''',
+ a_legacy=LegacyDefinition(name='gw_polarizability_number_of_empty_states'))
+
+ gw_qp_equation_treatment = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Methods to solve the quasi-particle equation: 'linearization', 'self-consistent'
+ ''',
+ a_legacy=LegacyDefinition(name='gw_qp_equation_treatment'))
+
+ gw_screened_coulomb_volume_average = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of volume averaging for the dynamically screened Coulomb potential: isotropic
+ - Simple averaging along a specified direction using only diagonal components of
+ the dielectric tensor; anisotropic - Anisotropic screening by C. Freysoldt et al.,
+ CPC 176, 1-13 (2007)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_screened_coulomb_volume_average'))
+
+ gw_screened_Coulomb = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Model used to calculate the dinamically-screened Coulomb potential: 'rpa' - Full-
+ frequency random-phase approximation; 'ppm' - Godby-Needs plasmon-pole model Godby
+ and Needs, Phys. Rev. Lett. 62, 1169 (1989); 'ppm_hl' - Hybertsen and Louie, Phys.
+ Rev. B 34, 5390 (1986); 'ppm_lh' - von der Linden and P. Horsh, Phys. Rev. B 37,
+ 8351 (1988); 'ppm_fe' - Farid and Engel, Phys. Rev. B 47,15931 (1993); 'cdm' -
+ Contour deformation method, Phys. Rev. B 67, 155208 (2003).)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_screened_Coulomb'))
+
+ gw_self_energy_c_analytical_continuation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Models for the correlation self-energy analytical continuation: 'pade' - Pade's
+ approximant (by H. J. Vidberg and J. W. Serence, J. Low Temp. Phys. 29, 179
+ (1977)); 'mpf' - Multi-Pole Fitting (by H. N Rojas, R. W. Godby and R. J. Needs,
+ Phys. Rev. Lett. 74, 1827 (1995)); 'cd' - contour deformation; 'ra' - real axis
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c_analytical_continuation'))
+
+ gw_self_energy_c_number_of_empty_states = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of empty states to be used to calculate the correlation self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c_number_of_empty_states'))
+
+ gw_self_energy_c_number_of_poles = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of poles used in the analytical continuation.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c_number_of_poles'))
+
+ gw_self_energy_singularity_treatment = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Treatment of the integrable singular terms in the calculation of the self energy.
+ Values: 'mpb' - Auxiliary function method by S. Massidda, M. Posternak, and A.
+ Baldereschi, PRB 48, 5058 (1993); 'crg' - Auxiliary function method by P. Carrier,
+ S. Rohra, and A. Goerling, PRB 75, 205126 (2007).
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_singularity_treatment'))
+
+ gw_starting_point = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Exchange-correlation functional of the ground-state calculation. See XC_functional
+ list at https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional
+ ''',
+ a_legacy=LegacyDefinition(name='gw_starting_point'))
+
+ gw_type_test = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ GW methodology: exciting test variable
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='gw_type_test'))
+
+ gw_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ GW methodology: G0W0; ev-scGW: (eigenvalues self-consistent GW) – Phys.Rev.B 34,
+ 5390 (1986); qp-scGW: (quasi-particle self-consistent GW) – Phys. Rev. Lett. 96,
+ 226402 (2006) scGW0: (self-consistent G with fixed W0) – Phys.Rev.B 54, 8411
+ (1996); scG0W: (self-consistent W with fixed G0); scGW: (self-consistent GW) –
+ Phys. Rev. B 88, 075105 (2013)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_type'))
+
+ method_to_topology_ref = Quantity(
+ type=Reference(SectionProxy('Topology')),
+ shape=[],
+ description='''
+ Reference to the topology and force fields to be used.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='method_to_topology_ref'))
+
+ section_method_atom_kind = SubSection(
+ sub_section=SectionProxy('MethodAtomKind'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method_atom_kind'))
+
+ section_method_to_method_refs = SubSection(
+ sub_section=SectionProxy('MethodToMethodRefs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method_to_method_refs'))
+
+ section_XC_functionals = SubSection(
+ sub_section=SectionProxy('XCFunctionals'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_XC_functionals'))
+
+ section_dft_plus_u_orbital = SubSection(
+ sub_section=SectionProxy('DftPlusUOrbital'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
+
+ section_method_basis_set = SubSection(
+ sub_section=SectionProxy('MethodBasisSet'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method_basis_set'))
+
+
+class OriginalSystem(MSection):
+ '''
+ Section containing symmetry information that is specific to the original system.
+ '''
+
+ m_def = Section(
+ aliases=['section_original_system'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_original_system'))
+
+ equivalent_atoms_original = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms'],
+ description='''
+ Gives a mapping table of atoms to symmetrically independent atoms in the original
+ cell. This is used to find symmetrically equivalent atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='equivalent_atoms_original'))
+
+ wyckoff_letters_original = Quantity(
+ type=str,
+ shape=['number_of_atoms'],
+ description='''
+ Wyckoff letters for atoms in the original cell.
+ ''',
+ a_legacy=LegacyDefinition(name='wyckoff_letters_original'))
+
+
+class PrimitiveSystem(MSection):
+ '''
+ Section containing symmetry information that is specific to the primitive system. The
+ primitive system is derived from the standardized system with a transformation that is
+ specific to the centring. The transformation matrices can be found e.g. from here:
+ https://atztogo.github.io/spglib/definition.html#transformation-to-the-primitive-cell
+ '''
+
+ m_def = Section(
+ aliases=['section_primitive_system'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_primitive_system'))
+
+ atom_positions_primitive = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms_primitive', 3],
+ description='''
+ Atom positions in the primitive cell in reduced units.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_positions_primitive'))
+
+ atomic_numbers_primitive = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_primitive'],
+ description='''
+ Atomic numbers in the primitive cell.
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_numbers_primitive'))
+
+ equivalent_atoms_primitive = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_primitive'],
+ description='''
+ Gives a mapping table of atoms to symmetrically independent atoms in the primitive
+ cell. This is used to find symmetrically equivalent atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='equivalent_atoms_primitive'))
+
+ lattice_vectors_primitive = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ Primitive lattice vectors. The vectors are the rows of this matrix.
+ ''',
+ a_legacy=LegacyDefinition(name='lattice_vectors_primitive'))
+
+ number_of_atoms_primitive = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in primitive system.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_atoms_primitive'))
+
+ wyckoff_letters_primitive = Quantity(
+ type=str,
+ shape=['number_of_atoms_primitive'],
+ description='''
+ Wyckoff letters for atoms in the primitive cell.
+ ''',
+ a_legacy=LegacyDefinition(name='wyckoff_letters_primitive'))
+
+
+class ProcessorInfo(MSection):
+ '''
+ Section with information about a processor that generated or added information to the
+ current calculation.
+ '''
+
+ m_def = Section(
+ aliases=['section_processor_info'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_processor_info'))
+
+ processor_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Id (name+version) of the processor that generated or added information to the
+ current calculation.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_id'))
+
+ processor_number_of_evaluated_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts evaluated with this processor in the current current
+ calculation.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_number_of_evaluated_contexts'))
+
+ processor_number_of_failed_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts in the current current calculation that had failure for this
+ processor.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_number_of_failed_contexts'))
+
+ processor_number_of_skipped_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts skipped by this processor in the current current calculation.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_number_of_skipped_contexts'))
+
+ processor_number_of_successful_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts in the current calculation that where successfully handled by
+ this processor.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_number_of_successful_contexts'))
+
+ processor_version_details = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ detailed version information on the processor that generated or added information
+ to the current calculation.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_version_details'))
+
+
+class ProcessorLogEvent(MSection):
+ '''
+ A log event
+ '''
+
+ m_def = Section(
+ aliases=['section_processor_log_event'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_processor_log_event'))
+
+ processor_log_event_level = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Level of the logging, a lower number has more priority. The levels are the same as
+ log4j: FATAL -> 100, ERROR -> 200, WARN -> 300, INFO -> 400, DEBUG -> 500, TRACE
+ -> 600
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_log_event_level'))
+
+ processor_log_event_message = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The log message
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_log_event_message'))
+
+
+class ProcessorLog(MSection):
+ '''
+ log of a processor
+ '''
+
+ m_def = Section(
+ aliases=['section_processor_log'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_processor_log'))
+
+ processor_log_processor_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The processor id of the processor creating this log
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_log_processor_id'))
+
+ processor_log_start = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Start of the log (in ansi notation YYYY-MM-TT...)
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='processor_log_start'))
+
+ section_processor_log_event = SubSection(
+ sub_section=SectionProxy('ProcessorLogEvent'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_processor_log_event'))
+
+
+class Prototype(MSection):
+ '''
+ Information on the prototype corresponding to the current section.
+ '''
+
+ m_def = Section(
+ aliases=['section_prototype'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_prototype'))
+
+ prototype_aflow_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ AFLOW id of the prototype (see
+ http://aflowlib.org/CrystalDatabase/prototype_index.html) identified on the basis
+ of the space_group and normalized_wyckoff.
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_aflow_id'))
+
+ prototype_aflow_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Url to the AFLOW definition of the prototype (see
+ http://aflowlib.org/CrystalDatabase/prototype_index.html) identified on the basis
+ of the space_group and normalized_wyckoff.
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_aflow_url'))
+
+ prototype_assignment_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to identify the prototype.
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_assignment_method'))
+
+ prototype_label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Label of the prototype identified on the basis of the space_group and
+ normalized_wyckoff. The label is in the same format as in the read_prototypes
+ function: <space_group_number>-<prototype_name>-<Pearson's symbol>).
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_label'))
+
+
+class Run(MSection):
+ '''
+ Every section_run represents a single call of a program. What exactly is contained in
+ a run depends on the run type (see for example section_method and
+ section_single_configuration_calculation) and the program (see [program_info
+ ](program_info)).
+ '''
+
+ m_def = Section(
+ aliases=['section_run'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_run'))
+
+ calculation_file_uri = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Contains the nomad uri of a raw the data file connected to the current run. There
+ should be an value for the main_file_uri and all ancillary files.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_file_uri'))
+
+ message_debug_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A debugging message of the computational program, associated with a run.
+ ''',
+ categories=[MessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='message_debug_run'))
+
+ message_error_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An error message of the computational program, associated with a run.
+ ''',
+ categories=[MessageInfo, MessageDebug, MessageError, MessageWarning, Unused],
+ a_legacy=LegacyDefinition(name='message_error_run'))
+
+ message_info_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An information message of the computational program, associated with a run.
+ ''',
+ categories=[MessageInfo, MessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='message_info_run'))
+
+ message_warning_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A warning message of the computational program, associated with a run.
+ ''',
+ categories=[MessageInfo, MessageDebug, MessageWarning, Unused],
+ a_legacy=LegacyDefinition(name='message_warning_run'))
+
+ parsing_message_debug_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for debugging messages of the parsing program associated with a
+ single configuration calculation, see section_single_configuration_calculation.
+ ''',
+ categories=[ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_debug_run'))
+
+ parsing_message_error_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for error messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[ParsingMessageInfo, ParsingMessageError, ParsingMessageWarning, ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_error_run'))
+
+ parsing_message_info_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for info messages of the parsing program associated with a run,
+ see section_run.
+ ''',
+ categories=[ParsingMessageInfo, ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_info_run'))
+
+ parsing_message_warning_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for warning messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[ParsingMessageInfo, ParsingMessageWarning, ParsingMessageDebug],
+ a_legacy=LegacyDefinition(name='parsing_message_warning_run'))
+
+ program_basis_set_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of basis set used by the program to represent wave functions. Valid
+ values are: [`Numeric AOs`, `Gaussians`, `(L)APW+lo`, `plane waves`, `psinc
+ functions`, `real-space grid`].
+ ''',
+ a_legacy=LegacyDefinition(name='program_basis_set_type'))
+
+ program_compilation_datetime = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Contains the program compilation date and time from *Unix epoch* (00:00:00 UTC on
+ 1 January 1970) in seconds. For date and times without a timezone, the default
+ timezone GMT is used.
+ ''',
+ categories=[AccessoryInfo, ProgramInfo],
+ a_legacy=LegacyDefinition(name='program_compilation_datetime'))
+
+ program_compilation_host = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the host on which the program was compiled.
+ ''',
+ categories=[AccessoryInfo, ProgramInfo],
+ a_legacy=LegacyDefinition(name='program_compilation_host'))
+
+ program_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the name of the program that generated the data.
+ ''',
+ categories=[AccessoryInfo, ProgramInfo],
+ a_legacy=LegacyDefinition(name='program_name'))
+
+ program_version = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the version of the program that was used. This should be the version
+ number of an official release, the version tag or a commit id as well as the
+ location of the repository.
+ ''',
+ categories=[AccessoryInfo, ProgramInfo],
+ a_legacy=LegacyDefinition(name='program_version'))
+
+ run_clean_end = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates whether this run terminated properly (true), or if it was killed or
+ exited with an error code unequal to zero (false).
+ ''',
+ a_legacy=LegacyDefinition(name='run_clean_end'))
+
+ run_hosts = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ An associative list of host(s) that performed this simulation. This is an
+ associative list that contains program-dependent information (*key*) on how the
+ host was used (*value*). Useful for debugging purposes.
+ ''',
+ categories=[ParallelizationInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='run_hosts'))
+
+ raw_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An optional calculation id, if one is found in the code input/output files.
+ ''',
+ a_legacy=LegacyDefinition(name='raw_id'))
+
+ time_run_cpu1_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end time of the run on CPU 1.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_run_cpu1_end'))
+
+ time_run_cpu1_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start time of the run on CPU 1.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_run_cpu1_start'))
+
+ time_run_date_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end date of the run as time since the *Unix epoch* (00:00:00 UTC on 1
+ January 1970) in seconds. For date and times without a timezone, the default
+ timezone GMT is used.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_run_date_end'))
+
+ time_run_date_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start date of the run as time since the *Unix epoch* (00:00:00 UTC on 1
+ January 1970) in seconds. For date and times without a timezone, the default
+ timezone GMT is used.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_run_date_start'))
+
+ time_run_wall_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time at the end of the run.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_run_wall_end'))
+
+ time_run_wall_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time from the start of the run.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_run_wall_start'))
+
+ section_basis_set_atom_centered = SubSection(
+ sub_section=SectionProxy('BasisSetAtomCentered'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
+
+ section_basis_set_cell_dependent = SubSection(
+ sub_section=SectionProxy('BasisSetCellDependent'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))
+
+ section_frame_sequence = SubSection(
+ sub_section=SectionProxy('FrameSequence'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_frame_sequence'))
+
+ section_method = SubSection(
+ sub_section=SectionProxy('Method'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method'))
+
+ section_sampling_method = SubSection(
+ sub_section=SectionProxy('SamplingMethod'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_sampling_method'))
+
+ section_single_configuration_calculation = SubSection(
+ sub_section=SectionProxy('SingleConfigurationCalculation'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ section_system = SubSection(
+ sub_section=SectionProxy('System'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_system'))
+
+ section_topology = SubSection(
+ sub_section=SectionProxy('Topology'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_topology'))
+
+
+class SamplingMethod(MSection):
+ '''
+ Section containing the settings describing a (potential-energy surface) sampling
+ method.
+
+ Results and monitored quantities of such sampling are collected in a sequence of
+ frames, section_frame_sequence.
+ '''
+
+ m_def = Section(
+ aliases=['section_sampling_method'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_sampling_method'))
+
+ ensemble_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Kind of sampled ensemble stored in section_frame_sequence; valid values are
+ defined in [ensemble_type wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/ensemble-type).
+ ''',
+ a_legacy=LegacyDefinition(name='ensemble_type'))
+
+ geometry_optimization_energy_change = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of threshold for the energy_total change between two geometry optimization
+ steps, as convergence criterion of the geometry_optimization_method. A geometry
+ optimization is considered converged when the energy_total change between two
+ geometry optimization steps is below the threshold (possibly in combination with
+ other criteria)
+ ''',
+ categories=[SettingsGeometryOptimization, SettingsSampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_energy_change'))
+
+ geometry_optimization_geometry_change = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='meter',
+ description='''
+ Value of threshold for the displacement of the nuclei between two geometry
+ optimization steps as convergence criterion of the geometry_optimization_method. A
+ geometry optimization is considered converged when the maximum among the
+ displacements of the nuclei between two geometry optimization steps is below the
+ threshold (possibly in combination with other criteria)
+ ''',
+ categories=[SettingsGeometryOptimization, SettingsSampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_geometry_change'))
+
+ geometry_optimization_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Algorithm for the geometry optimization. Allowed values are listed in the
+ [geometry_optimization_method wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/geometry-optimization-method).
+ ''',
+ categories=[SettingsGeometryOptimization, SettingsSampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_method'))
+
+ geometry_optimization_threshold_force = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ Value of threshold for the force modulus as convergence criterion of the
+ geometry_optimization_method. A geometry optimization is considered converged when
+ the maximum of the moduli of the force on each of the atoms is below this
+ threshold (possibly in combination with other criteria)
+ ''',
+ categories=[SettingsGeometryOptimization, SettingsSampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_threshold_force'))
+
+ sampling_method_expansion_order = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Order up to which the potential energy surface was expanded in a Taylor series
+ (see sampling_method).
+ ''',
+ a_legacy=LegacyDefinition(name='sampling_method_expansion_order'))
+
+ sampling_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of method used to do the sampling.
+
+ Allowed values are:
+
+ | Sampling method | Description |
+
+ | ------------------------------ | -------------------------------- |
+
+ | `"geometry_optimization"` | Geometry optimization |
+
+ | `"molecular_dynamics"` | Molecular dynamics |
+
+ | `"montecarlo"` | (Metropolis) Monte Carlo |
+
+ | `"steered_molecular_dynamics"` | Steered molecular dynamics (with time dependent
+ external forces) |
+
+ | `"meta_dynamics"` | Biased molecular dynamics with history-
+ dependent Hamiltonian |
+
+ | `"wang_landau_montecarlo"` | Monte Carlo according to the Wang-Landau
+ formulation. |
+
+ | `"blue_moon"` | Blue Moon sampling |
+
+ | `"langevin_dynamics"` | Langevin dynamics |
+
+ | `"taylor_expansion"` | Taylor expansion of the potential energy
+ surface |
+ ''',
+ a_legacy=LegacyDefinition(name='sampling_method'))
+
+
+class ScfIteration(MSection):
+ '''
+ Every section_scf_iteration represents a self-consistent field (SCF) iteration, see
+ scf_info, and gives detailed information on the SCF procedure of the specified
+ quantities.
+ '''
+
+ m_def = Section(
+ aliases=['section_scf_iteration'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+ electronic_kinetic_energy_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Electronic kinetic energy as defined in XC_method during the self-consistent field
+ (SCF) iterations.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='electronic_kinetic_energy_scf_iteration'))
+
+ energy_change_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Stores the change of total energy with respect to the previous self-consistent
+ field (SCF) iteration.
+ ''',
+ categories=[ErrorEstimateContribution, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_change_scf_iteration'))
+
+ energy_correction_entropy_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Entropy correction to the potential energy to compensate for the change in
+ occupation so that forces at finite T do not need to keep the change of occupation
+ in account. The array lists the values of the entropy correction for each self-
+ consistent field (SCF) iteration. Defined consistently with XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_correction_entropy_scf_iteration'))
+
+ energy_correction_hartree_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Correction to the density-density electrostatic energy in the sum of eigenvalues
+ (that uses the mixed density on one side), and the fully consistent density-
+ density electrostatic energy during the self-consistent field (SCF) iterations.
+ Defined consistently with XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_correction_hartree_scf_iteration'))
+
+ energy_electrostatic_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total electrostatic energy (nuclei + electrons) during each self-consistent field
+ (SCF) iteration.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_electrostatic_scf_iteration'))
+
+ energy_free_per_atom_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy per atom (whose minimum gives the smeared occupation density
+ calculated with smearing_kind) calculated with XC_method during the self-
+ consistent field (SCF) iterations.
+ ''',
+ categories=[EnergyComponentPerAtom, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_free_per_atom_scf_iteration'))
+
+ energy_free_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy (whose minimum gives the smeared occupation density calculated with
+ smearing_kind) calculated with the method described in XC_method during the self-
+ consistent field (SCF) iterations.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_free_scf_iteration'))
+
+ energy_hartree_error_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Error in the Hartree (electrostatic) potential energy during each self-consistent
+ field (SCF) iteration. Defined consistently with XC_method.
+ ''',
+ categories=[ErrorEstimateContribution, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_hartree_error_scf_iteration'))
+
+ energy_sum_eigenvalues_per_atom_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy per atom, where the energy is defined as the sum of the
+ eigenvalues of the Hamiltonian matrix given by XC_method, during each self-
+ consistent field (SCF) iteration.
+ ''',
+ categories=[EnergyComponentPerAtom, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_per_atom_scf_iteration'))
+
+ energy_sum_eigenvalues_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Sum of the eigenvalues of the Hamiltonian matrix defined by XC_method, during each
+ self-consistent field (SCF) iteration.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_scf_iteration'))
+
+ energy_total_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total electronic energy calculated with the method described in
+ XC_method during each self-consistent field (SCF) iteration.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_total_scf_iteration'))
+
+ energy_total_T0_per_atom_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy, calculated with the method described in XC_method per
+ atom extrapolated to $T=0$, based on a free-electron gas argument, during each
+ self-consistent field (SCF) iteration.
+ ''',
+ categories=[EnergyTotalPotentialPerAtom, EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_total_T0_per_atom_scf_iteration'))
+
+ energy_total_T0_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy (or equivalently free energy), calculated with the
+ method described in XC_method and extrapolated to $T=0$, based on a free-electron
+ gas argument, during each self-consistent field (SCF) iteration.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_total_T0_scf_iteration'))
+
+ energy_XC_potential_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value for exchange-correlation (XC) potential energy: the integral of the first
+ order derivative of the functional stored in XC_functional (integral of
+ v_xc*electron_density), i.e., the component of XC that is in the sum of the
+ eigenvalues. Values are given for each self-consistent field (SCF) iteration
+ (i.e., not the converged value, the latter being stored in energy_XC_potential).
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_XC_potential_scf_iteration'))
+
+ energy_XC_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value for exchange-correlation (XC) energy obtained during each self-consistent
+ field (SCF) iteration, using the method described in XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_XC_scf_iteration'))
+
+ spin_S2_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Stores the value of the total spin moment operator $S^2$ during the self-
+ consistent field (SCF) iterations of the XC_method. It can be used to calculate
+ the spin contamination in spin-unrestricted calculations.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='spin_S2_scf_iteration'))
+
+ time_scf_iteration_cpu1_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end time of a self-consistent field (SCF) iteration on CPU 1.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_cpu1_end'))
+
+ time_scf_iteration_cpu1_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start time of a self-consistent field (SCF) iteration on CPU 1.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_cpu1_start'))
+
+ time_scf_iteration_date_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end date of a self-consistent field (SCF) iteration as time since the
+ *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds. For date and times
+ without a timezone, the default timezone GMT is used.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_date_end'))
+
+ time_scf_iteration_date_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start date of a self-consistent field (SCF) iteration as time since the
+ *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds. For date and times
+ without a timezone, the default timezone GMT is used.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_date_start'))
+
+ time_scf_iteration_wall_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time at the end of a self-consistent field (SCF)
+ iteration.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_wall_end'))
+
+ time_scf_iteration_wall_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time from the start of a self-consistent field
+ (SCF) iteration.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_wall_start'))
+
+ energy_reference_fermi_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Fermi energy (separates occupied from unoccupied single-particle states in metals)
+ during the self-consistent field (SCF) iterations.
+ ''',
+ categories=[EnergyTypeReference, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_reference_fermi_iteration'))
+
+ energy_reference_highest_occupied_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Highest occupied single-particle state energy (in insulators or HOMO energy in
+ finite systems) during the self-consistent field (SCF) iterations.
+ ''',
+ categories=[EnergyTypeReference, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_reference_highest_occupied_iteration'))
+
+ energy_reference_lowest_unoccupied_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Lowest unoccupied single-particle state energy (in insulators or LUMO energy in
+ finite systems) during the self-consistent field (SCF) iterations.
+ ''',
+ categories=[EnergyTypeReference, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_reference_lowest_unoccupied_iteration'))
+
+
+class SingleConfigurationCalculation(MSection):
+ '''
+ Every section_single_configuration_calculation section contains the values computed
+ during a *single configuration calculation*, i.e. a calculation performed on a given
+ configuration of the system (as defined in section_system) and a given computational
+ method (e.g., exchange-correlation method, basis sets, as defined in section_method).
+
+ The link between the current section_single_configuration_calculation and the related
+ section_system and section_method sections is established by the values stored in
+ single_configuration_calculation_to_system_ref and
+ single_configuration_to_calculation_method_ref, respectively.
+
+ The reason why information on the system configuration and computational method is
+ stored separately is that several *single configuration calculations* can be performed
+ on the same system configuration, viz. several system configurations can be evaluated
+ with the same computational method. This storage strategy avoids redundancies.
+ '''
+
+ m_def = Section(
+ aliases=['section_single_configuration_calculation'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ atom_forces_free_raw = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_free,
+ **without** constraints. The derivatives with respect to displacements of nuclei
+ are evaluated in Cartesian coordinates. The (electronic) energy_free contains the
+ change in (fractional) occupation of the electronic eigenstates, which are
+ accounted for in the derivatives, yielding a truly energy-conserved quantity.
+ These forces may contain unitary transformations (center-of-mass translations and
+ rigid rotations for non-periodic systems) that are normally filtered separately
+ (see atom_forces_free for the filtered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are also considered
+ separately (see atom_forces_free for the filtered counterpart).
+ ''',
+ categories=[AtomForcesType],
+ a_legacy=LegacyDefinition(name='atom_forces_free_raw'))
+
+ atom_forces_free = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_free,
+ **including** constraints, if present. The derivatives with respect to
+ displacements of the nuclei are evaluated in Cartesian coordinates. The
+ (electronic) energy_free contains the information on the change in (fractional)
+ occupation of the electronic eigenstates, which are accounted for in the
+ derivatives, yielding a truly energy-conserved quantity. In addition, these forces
+ are obtained by filtering out the unitary transformations (center-of-mass
+ translations and rigid rotations for non-periodic systems, see
+ atom_forces_free_raw for the unfiltered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are included (see
+ atom_forces_free_raw for the unfiltered counterpart).
+ ''',
+ categories=[AtomForcesType],
+ a_legacy=LegacyDefinition(name='atom_forces_free'))
+
+ atom_forces_raw = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total,
+ **without** constraints. The derivatives with respect to displacements of the
+ nuclei are evaluated in Cartesian coordinates. These forces may contain unitary
+ transformations (center-of-mass translations and rigid rotations for non-periodic
+ systems) that are normally filtered separately (see atom_forces for the filtered
+ counterpart). Forces due to constraints such as fixed atoms, distances, angles,
+ dihedrals, etc. are also considered separately (see atom_forces for the filtered
+ counterpart).
+ ''',
+ categories=[AtomForcesType],
+ a_legacy=LegacyDefinition(name='atom_forces_raw'))
+
+ atom_forces_T0_raw = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total_T0,
+ **without** constraints. The derivatives with respect to displacements of the
+ nuclei are evaluated in Cartesian coordinates. These forces may contain unitary
+ transformations (center-of-mass translations and rigid rotations for non-periodic
+ systems) that are normally filtered separately (see atom_forces_T0 for the
+ filtered counterpart). Forces due to constraints such as fixed atoms, distances,
+ angles, dihedrals, etc. are also considered separately (see atom_forces_T0 for the
+ filtered counterpart).
+ ''',
+ categories=[AtomForcesType, Unused],
+ a_legacy=LegacyDefinition(name='atom_forces_T0_raw'))
+
+ atom_forces_T0 = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total_T0,
+ **including** constraints, if present. The derivatives with respect to
+ displacements of the nuclei are evaluated in Cartesian coordinates. In addition,
+ these forces are obtained by filtering out the unitary transformations (center-of-
+ mass translations and rigid rotations for non-periodic systems, see
+ atom_forces_free_T0_raw for the unfiltered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are also included (see
+ atom_forces_free_T0_raw for the unfiltered counterpart).
+ ''',
+ categories=[AtomForcesType, Unused],
+ a_legacy=LegacyDefinition(name='atom_forces_T0'))
+
+ atom_forces = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total,
+ **including** constraints, if present. The derivatives with respect to
+ displacements of nuclei are evaluated in Cartesian coordinates. In addition, these
+ forces are obtained by filtering out the unitary transformations (center-of-mass
+ translations and rigid rotations for non-periodic systems, see
+ atom_forces_free_raw for the unfiltered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are included (see
+ atom_forces_raw for the unfiltered counterpart).
+ ''',
+ categories=[AtomForcesType],
+ a_legacy=LegacyDefinition(name='atom_forces'))
+
+ electronic_kinetic_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Self-consistent electronic kinetic energy as defined in XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='electronic_kinetic_energy'))
+
+ energy_C = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Correlation (C) energy calculated with the method described in XC_functional.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTypeC],
+ a_legacy=LegacyDefinition(name='energy_C'))
+
+ energy_correction_entropy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Entropy correction to the potential energy to compensate for the change in
+ occupation so that forces at finite T do not need to keep the change of occupation
+ in account. Defined consistently with XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_correction_entropy'))
+
+ energy_correction_hartree = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Correction to the density-density electrostatic energy in the sum of eigenvalues
+ (that uses the mixed density on one side), and the fully consistent density-
+ density electrostatic energy. Defined consistently with XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_correction_hartree'))
+
+ energy_current = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy calculated with calculation_method_current. energy_current is
+ equal to energy_total for non-perturbative methods. For perturbative methods,
+ energy_current is equal to the correction: energy_total minus energy_total of the
+ calculation_to_calculation_ref with calculation_to_calculation_kind =
+ starting_point (see the [method_to_method_kind wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/method-
+ to-method-kind)). See also [energy_current wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/energy-
+ current).
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_current'))
+
+ energy_electrostatic = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total electrostatic energy (nuclei + electrons), defined consistently with
+ calculation_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_electrostatic'))
+
+ energy_free_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy per atom (whose minimum gives the smeared occupation density
+ calculated with smearing_kind) calculated with XC_method.
+ ''',
+ categories=[EnergyComponentPerAtom, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_free_per_atom'))
+
+ energy_free = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy (nuclei + electrons) (whose minimum gives the smeared occupation
+ density calculated with smearing_kind) calculated with the method described in
+ XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_free'))
+
+ energy_hartree_error = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Error in the Hartree (electrostatic) potential energy. Defined consistently with
+ XC_method.
+ ''',
+ categories=[ErrorEstimateContribution, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_hartree_error'))
+
+ energy_hartree_fock_X_scaled = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Scaled exact-exchange energy that depends on the mixing parameter of the
+ functional. For example in hybrid functionals, the exchange energy is given as a
+ linear combination of exact-energy and exchange energy of an approximate DFT
+ functional; the exact exchange energy multiplied by the mixing coefficient of the
+ hybrid functional would be stored in this metadata. Defined consistently with
+ XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_hartree_fock_X_scaled'))
+
+ energy_hartree_fock_X = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Converged exact-exchange (Hartree-Fock) energy. Defined consistently with
+ XC_method.
+ ''',
+ categories=[EnergyTypeX, EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_hartree_fock_X'))
+
+ energy_method_current = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy calculated with the method calculation_method_current.
+ Depending on calculation_method_kind it might be a total energy or only a
+ correction.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_method_current'))
+
+ energy_sum_eigenvalues_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy per atom, where the energy is defined as the sum of the
+ eigenvalues of the Hamiltonian matrix given by XC_method.
+ ''',
+ categories=[EnergyComponentPerAtom, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_per_atom'))
+
+ energy_sum_eigenvalues = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Sum of the eigenvalues of the Hamiltonian matrix defined by XC_method.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues'))
+
+ energy_T0_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy per atom, calculated with the method described in
+ XC_method and extrapolated to $T=0$, based on a free-electron gas argument.
+ ''',
+ categories=[EnergyTotalPotentialPerAtom, EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_T0_per_atom'))
+
+ energy_total_T0_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy, calculated with the method described in XC_method per
+ atom extrapolated to $T=0$, based on a free-electron gas argument.
+ ''',
+ categories=[EnergyTotalPotentialPerAtom, EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_total_T0_per_atom'))
+
+ energy_total_T0 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy (or equivalently free energy), calculated with the
+ method described in XC_method and extrapolated to $T=0$, based on a free-electron
+ gas argument.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_total_T0'))
+
+ energy_total = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy, calculated with the method described in XC_method and
+ extrapolated to $T=0$, based on a free-electron gas argument.
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTotalPotential],
+ a_legacy=LegacyDefinition(name='energy_total'))
+
+ energy_XC_functional = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the exchange-correlation (XC) energy calculated with the functional
+ stored in XC_functional.
+ ''',
+ categories=[EnergyTypeXC, EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_XC_functional'))
+
+ energy_XC_potential = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the exchange-correlation (XC) potential energy: the integral of the first
+ order derivative of the functional stored in XC_functional (integral of
+ v_xc*electron_density), i.e., the component of XC that is in the sum of the
+ eigenvalues. Value associated with the configuration, should be the most converged
+ value.
+ ''',
+ categories=[EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_XC_potential'))
+
+ energy_XC = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the exchange-correlation (XC) energy calculated with the method described
+ in XC_method.
+ ''',
+ categories=[EnergyTypeXC, EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_XC'))
+
+ energy_X = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value fo the exchange (X) energy calculated with the method described in
+ XC_method.
+ ''',
+ categories=[EnergyTypeX, EnergyComponent, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_X'))
+
+ energy_zero_point = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value for the converged zero-point vibrations energy calculated using the method
+ described in zero_point_method , and used in energy_current .
+ ''',
+ a_legacy=LegacyDefinition(name='energy_zero_point'))
+
+ hessian_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 'number_of_atoms', 3, 3],
+ description='''
+ The matrix with the second derivative with respect to atom displacements.
+ ''',
+ a_legacy=LegacyDefinition(name='hessian_matrix'))
+
+ message_debug_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A debugging message of the computational program, associated with a *single
+ configuration calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[MessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='message_debug_evaluation'))
+
+ message_error_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An error message of the computational program, associated with a *single
+ configuration calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[MessageInfo, MessageDebug, MessageError, MessageWarning, Unused],
+ a_legacy=LegacyDefinition(name='message_error_evaluation'))
+
+ message_info_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An information message of the computational program, associated with a *single
+ configuration calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[MessageInfo, MessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='message_info_evaluation'))
+
+ message_warning_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A warning message of the computational program.
+ ''',
+ categories=[MessageInfo, MessageDebug, MessageWarning, Unused],
+ a_legacy=LegacyDefinition(name='message_warning_evaluation'))
+
+ number_of_scf_iterations = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of performed self-consistent field (SCF) iterations at a specfied
+ level of theory.
+ ''',
+ categories=[ScfInfo],
+ a_legacy=LegacyDefinition(name='number_of_scf_iterations'))
+
+ parsing_message_debug_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for debugging messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_debug_evaluation'))
+
+ parsing_message_error_single_configuration = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for error messages of the parsing program associated with a
+ single configuration calculation, see section_single_configuration_calculation.
+ ''',
+ categories=[ParsingMessageInfo, ParsingMessageError, ParsingMessageWarning, ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_error_single_configuration'))
+
+ parsing_message_info_single_configuration = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for info messages of the parsing program associated with a
+ single configuration calculation, see section_single_configuration_calculation.
+ ''',
+ categories=[ParsingMessageInfo, ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_info_single_configuration'))
+
+ parsing_message_warning_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for warning messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[ParsingMessageInfo, ParsingMessageWarning, ParsingMessageDebug, Unused],
+ a_legacy=LegacyDefinition(name='parsing_message_warning_evaluation'))
+
+ single_configuration_calculation_converged = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Determines whether a *single configuration calculation* in
+ section_single_configuration_calculation is converged.
+ ''',
+ a_legacy=LegacyDefinition(name='single_configuration_calculation_converged'))
+
+ single_configuration_calculation_to_system_ref = Quantity(
+ type=Reference(SectionProxy('System')),
+ shape=[],
+ description='''
+ Reference to the system (atomic configuration, cell, ...) that is calculated in
+ section_single_configuration_calculation.
+ ''',
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='single_configuration_calculation_to_system_ref'))
+
+ single_configuration_to_calculation_method_ref = Quantity(
+ type=Reference(SectionProxy('Method')),
+ shape=[],
+ description='''
+ Reference to the method used for the calculation in
+ section_single_configuration_calculation.
+ ''',
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='single_configuration_to_calculation_method_ref'))
+
+ spin_S2 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Stores the value of the total spin moment operator $S^2$ for the converged
+ wavefunctions calculated with the XC_method. It can be used to calculate the spin
+ contamination in spin-unrestricted calculations.
+ ''',
+ a_legacy=LegacyDefinition(name='spin_S2'))
+
+ stress_tensor = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='pascal',
+ description='''
+ Stores the final value of the default stress tensor consistent with energy_total
+ and calculated with the method specified in stress_tensor_method.
+
+ This value is used (if needed) for, e.g., molecular dynamics and geometry
+ optimization. Alternative definitions of the stress tensor can be assigned with
+ stress_tensor_kind
+ ''',
+ categories=[StressTensorType],
+ a_legacy=LegacyDefinition(name='stress_tensor'))
+
+ time_calculation = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the wall-clock time needed for a calculation using
+ calculation_method_current. Basically, it tracks the real time that has been
+ elapsed from start to end.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_calculation'))
+
+ time_single_configuration_calculation_cpu1_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end time of the *single configuration calculation* (see
+ section_single_configuration_calculation) on CPU 1.
+ ''',
+ categories=[TimeInfo, AccessoryInfo],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_cpu1_end'))
+
+ time_single_configuration_calculation_cpu1_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start time of the *single configuration calculation* (see
+ section_single_configuration_calculation) on CPU 1.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_cpu1_start'))
+
+ time_single_configuration_calculation_date_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end date of the *single configuration calculation* (see
+ section_single_configuration_calculation) as time since the *Unix epoch* (00:00:00
+ UTC on 1 January 1970) in seconds. For date and times without a timezone, the
+ default timezone GMT is used.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_date_end'))
+
+ time_single_configuration_calculation_date_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start date of the *single configuration calculation* (see
+ section_single_configuration_calculation) as time since the *Unix epoch* (00:00:00
+ UTC on 1 January 1970) in seconds. For date and times without a timezone, the
+ default timezone GMT is used.
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_date_start'))
+
+ time_single_configuration_calculation_wall_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time at the end of the *single configuration
+ calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_wall_end'))
+
+ time_single_configuration_calculation_wall_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time from the start of the *single configuration
+ calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[TimeInfo, AccessoryInfo, Unused],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_wall_start'))
+
+ zero_point_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the zero-point vibrations method. If skipped or an empty string is used,
+ it means no zero-point vibrations correction is applied.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='zero_point_method'))
+
+ enthalpy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the calculated enthalpy i.e. energy_total + pressure * volume.
+ ''',
+ categories=[EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_enthalpy'))
+
+ pressure = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Value of the pressure of the system.
+ ''',
+ a_legacy=LegacyDefinition(name='pressure'))
+
+ temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='kelvin',
+ description='''
+ Value of the temperature of the system.
+ ''',
+ a_legacy=LegacyDefinition(name='temperature'))
+
+ time_step = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ The number of time steps with respect to the start of the calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='time_step'))
+
+ energy_C_mGGA = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Component of the correlation (C) energy at the GGA (or MetaGGA) level using the
+ self-consistent density of the target XC functional (full unscaled value, i.e.,
+ not scaled due to exact-exchange mixing).
+ ''',
+ categories=[EnergyComponent, EnergyValue, EnergyTypeC, Unused],
+ a_legacy=LegacyDefinition(name='energy_C_mGGA'))
+
+ energy_reference_fermi = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Fermi energy (separates occupied from unoccupied single-particle states in metals)
+ ''',
+ categories=[EnergyTypeReference, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_reference_fermi'))
+
+ energy_reference_highest_occupied = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Highest occupied single-particle state energy (in insulators or HOMO energy in
+ finite systems)
+ ''',
+ categories=[EnergyTypeReference, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_reference_highest_occupied'))
+
+ energy_reference_lowest_unoccupied = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Lowest unoccupied single-particle state energy (in insulators or LUMO energy in
+ finite systems)
+ ''',
+ categories=[EnergyTypeReference, EnergyValue],
+ a_legacy=LegacyDefinition(name='energy_reference_lowest_unoccupied'))
+
+ energy_X_mGGA_scaled = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Component of the exchange (X) energy at the GGA (or MetaGGA) level, using the self
+ consistent density of the target functional, scaled accordingly to the mixing
+ parameter.
+ ''',
+ categories=[EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_X_mGGA_scaled'))
+
+ energy_X_mGGA = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Component of the exchange (X) energy at the GGA (or MetaGGA) level using the self
+ consistent density of the target functional (full unscaled value, i.e., not scaled
+ due to exact-exchange mixing).
+ ''',
+ categories=[EnergyTypeX, EnergyComponent, EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='energy_X_mGGA'))
+
+ gw_fermi_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ GW Fermi energy
+ ''',
+ a_legacy=LegacyDefinition(name='gw_fermi_energy'))
+
+ gw_fundamental_gap = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ GW fundamental band gap
+ ''',
+ a_legacy=LegacyDefinition(name='gw_fundamental_gap'))
+
+ gw_optical_gap = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ GW optical band gap
+ ''',
+ a_legacy=LegacyDefinition(name='gw_optical_gap'))
+
+ gw_self_energy_c = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Diagonal matrix elements of the correlation self-energy
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c'))
+
+ gw_self_energy_x = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Diagonal matrix elements of the exchange self-energy
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_x'))
+
+ gw_xc_potential = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Diagonal matrix elements of the exchange-correlation potential
+ ''',
+ a_legacy=LegacyDefinition(name='gw_xc_potential'))
+
+ section_atom_projected_dos = SubSection(
+ sub_section=SectionProxy('AtomProjectedDos'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_atom_projected_dos'))
+
+ section_atomic_multipoles = SubSection(
+ sub_section=SectionProxy('AtomicMultipoles'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_atomic_multipoles'))
+
+ section_basis_set = SubSection(
+ sub_section=SectionProxy('BasisSet'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_set'))
+
+ section_calculation_to_calculation_refs = SubSection(
+ sub_section=SectionProxy('CalculationToCalculationRefs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))
+
+ section_calculation_to_folder_refs = SubSection(
+ sub_section=SectionProxy('CalculationToFolderRefs'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))
+
+ section_dos = SubSection(
+ sub_section=SectionProxy('Dos'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_dos'))
+
+ section_eigenvalues = SubSection(
+ sub_section=SectionProxy('Eigenvalues'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_eigenvalues'))
+
+ section_energy_code_independent = SubSection(
+ sub_section=SectionProxy('EnergyCodeIndependent'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_energy_code_independent'))
+
+ section_energy_van_der_Waals = SubSection(
+ sub_section=SectionProxy('EnergyVanDerWaals'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
+
+ section_energy_contribution = SubSection(
+ sub_section=SectionProxy('EnergyContribution'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_energy_contribution'))
+
+ section_k_band_normalized = SubSection(
+ sub_section=SectionProxy('KBandNormalized'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band_normalized'))
+
+ section_k_band = SubSection(
+ sub_section=SectionProxy('KBand'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band'))
+
+ section_scf_iteration = SubSection(
+ sub_section=SectionProxy('ScfIteration'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+ section_species_projected_dos = SubSection(
+ sub_section=SectionProxy('SpeciesProjectedDos'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_species_projected_dos'))
+
+ section_stress_tensor = SubSection(
+ sub_section=SectionProxy('StressTensor'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_stress_tensor'))
+
+ section_volumetric_data = SubSection(
+ sub_section=SectionProxy('VolumetricData'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_volumetric_data'))
+
+ section_excited_states = SubSection(
+ sub_section=SectionProxy('ExcitedStates'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_excited_states'))
+
+
+class SpeciesProjectedDos(MSection):
+ '''
+ Section collecting the information on a species-projected density of states (DOS)
+ evaluation.
+ '''
+
+ m_def = Section(
+ aliases=['section_species_projected_dos'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_species_projected_dos'))
+
+ number_of_lm_species_projected_dos = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for the species-projected density of
+ states (DOS) defined in section_species_projected_dos.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_lm_species_projected_dos'))
+
+ number_of_species_projected_dos_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of energy values for the species-projected density of states
+ (DOS) defined in section_species_projected_dos.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_species_projected_dos_values'))
+
+ number_of_species = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of species for the species-projected density of states (DOS)
+ defined in section_species_projected_dos.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_species'))
+
+ species_projected_dos_energies_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_species_projected_dos_values'],
+ unit='joule',
+ description='''
+ Contains the set of discrete energy values with respect to the top of the valence
+ band for the species-projected density of states (DOS). It is derived from the
+ species_projected_dos_energies species field.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_energies_normalized'))
+
+ species_projected_dos_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_species_projected_dos_values'],
+ unit='joule',
+ description='''
+ Contains the set of discrete energy values for the species-projected density of
+ states (DOS).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_energies'))
+
+ species_projected_dos_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_lm_species_projected_dos', 2],
+ description='''
+ Consists of tuples of $l$ and $m$ values for all given values in the
+ species_projected_dos_values_lm species field.
+
+ The quantum number $l$ represents the azimuthal quantum number, whereas for the
+ quantum number $m$, besides the conventional use as magnetic quantum number ($l+1$
+ integer values from $-l$ to $l$), a set of different conventions is accepted. The
+ adopted convention is specified by atom_projected_dos_m_kind.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_lm'))
+
+ species_projected_dos_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the kind of the integer numbers $m$ used in species_projected_dos_lm.
+
+ Allowed values are listed in the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind)
+ and can be (quantum) numbers of
+
+ * spherical
+
+ * polynomial
+
+ * real_orbital
+
+ * integrated
+
+ functions or values.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_m_kind'))
+
+ species_projected_dos_species_label = Quantity(
+ type=str,
+ shape=['number_of_species'],
+ description='''
+ Contains labels of the atomic species for the species-projected density of states
+ (DOS).
+
+ Differently from atom_labels, which allow more than one label for the same atomic
+ species (by adding a number or a string to the label), this list is expected to
+ refer to actual atomic species, i.e. belonging to the periodic table of elements.
+ Thus, the species-projected DOS are expected to be as many as the different atomic
+ species in the system.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_species_label'))
+
+ species_projected_dos_values_lm = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_lm_species_projected_dos', 'number_of_spin_channels', 'number_of_species', 'number_of_species_projected_dos_values'],
+ description='''
+ Holds species-projected density of states (DOS) values, divided into contributions
+ from each $l,m$ channel.
+
+ Here, there are as many species-projected DOS as the number of species,
+ number_of_species. The list of labels of the species is given in
+ species_projected_dos_species_label.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_values_lm'))
+
+ species_projected_dos_values_total = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_species', 'number_of_species_projected_dos_values'],
+ description='''
+ Holds species-projected density of states (DOS) values, summed up over all
+ azimuthal quantum numbers $l$.
+
+ Here, there are as many species-projected DOS as the number of species,
+ number_of_species. The list of labels of the species is given in
+ species_projected_dos_species_label.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='species_projected_dos_values_total'))
+
+
+class SpringerMaterial(MSection):
+ '''
+ Every section_springer_material contains results of classification of materials with
+ the same formula according to Springer Materials - it contains
+ section_springer_classsification, section_springer_compound, section_springer_id,
+ section_springer_references
+ '''
+
+ m_def = Section(
+ aliases=['section_springer_material'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_springer_material'))
+
+ springer_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Id of the classified material according to Springer Materials
+ ''',
+ a_legacy=LegacyDefinition(name='springer_id'))
+
+ springer_alphabetical_formula = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The alphabetical formula of the material according to Springer Materials Database
+ ''',
+ a_legacy=LegacyDefinition(name='springer_alphabetical_formula'))
+
+ springer_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Url to the source page in Springer Materials describing the current entry
+ ''',
+ a_legacy=LegacyDefinition(name='springer_url'))
+
+ springer_compound_class = Quantity(
+ type=str,
+ shape=['N'],
+ description='''
+ Name of a class of the current compound, as defined in by Springer Materials. This
+ is a property of the chemical formula of the compound
+ ''',
+ a_legacy=LegacyDefinition(name='springer_compound_class'))
+
+ springer_classification = Quantity(
+ type=str,
+ shape=['N'],
+ description='''
+ Contains the classification name of the current material according to Springer
+ Materials
+ ''',
+ a_legacy=LegacyDefinition(name='springer_classification'))
+
+ section_springer_id = SubSection(
+ sub_section=SectionProxy('SpringerId'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_springer_id'))
+
+
+class SpringerId(MSection):
+ '''
+ Identifiers used by Springer Materials
+ '''
+
+ m_def = Section(
+ aliases=['section_springer_id'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_springer_id'))
+
+
+class StdSystem(MSection):
+ '''
+ Section containing symmetry information that is specific to the standardized system.
+ The standardized system is defined as given by spglib and the details can be found
+ from https://arxiv.org/abs/1506.01455
+ '''
+
+ m_def = Section(
+ aliases=['section_std_system'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_std_system'))
+
+ atom_positions_std = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms_std', 3],
+ description='''
+ Standardized atom positions in reduced units.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_positions_std'))
+
+ atomic_numbers_std = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_std'],
+ description='''
+ Atomic numbers of the atoms in the standardized cell.
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_numbers_std'))
+
+ equivalent_atoms_std = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_std'],
+ description='''
+ Gives a mapping table of atoms to symmetrically independent atoms in the
+ standardized cell. This is used to find symmetrically equivalent atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='equivalent_atoms_std'))
+
+ lattice_vectors_std = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ Standardized lattice vectors of the conventional cell. The vectors are the rows of
+ this matrix.
+ ''',
+ a_legacy=LegacyDefinition(name='lattice_vectors_std'))
+
+ number_of_atoms_std = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in standardized system.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_atoms_std'))
+
+ wyckoff_letters_std = Quantity(
+ type=str,
+ shape=['number_of_atoms_std'],
+ description='''
+ Wyckoff letters for atoms in the standardized cell.
+ ''',
+ a_legacy=LegacyDefinition(name='wyckoff_letters_std'))
+
+
+class StressTensor(MSection):
+ '''
+ Section collecting alternative values to stress_tensor that have been calculated. This
+ section allows the storage of multiple definitions and evaluated values of the stress
+ tensor, while only one definition is used for, e.g., molecular dynamics or geometry
+ optimization (if needed).
+ '''
+
+ m_def = Section(
+ aliases=['section_stress_tensor'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_stress_tensor'))
+
+ stress_tensor_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the method used to compute the stress tensor stored in
+ stress_tensor_value. This is an *alternative* to the stress tensor defined in
+ stress_tensor_method, which is stored in stress_tensor.
+
+ This field allows for multiple definitions and evaluated values of the stress
+ tensor, while only one definition is used for, e.g., molecular dynamics and
+ geometry optimization.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='stress_tensor_kind'))
+
+ stress_tensor_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='pascal',
+ description='''
+ Contains the value of the stress tensor of the kind defined in stress_tensor_kind.
+ This is an *alternative* to the stress tensor defined in stress_tensor_method.
+
+ This field allows for multiple definitions and evaluated values of the stress
+ tensor, while only one definition is used for, e.g., molecular dynamics and
+ geometry optimization.
+ ''',
+ categories=[StressTensorType, Unused],
+ a_legacy=LegacyDefinition(name='stress_tensor_value'))
+
+
+class Symmetry(MSection):
+ '''
+ Section containing information about the symmetry properties of the system.
+ '''
+
+ m_def = Section(
+ aliases=['section_symmetry'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_symmetry'))
+
+ bravais_lattice = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifier for the Bravais lattice in Pearson notation. The first lowercase letter
+ identifies the crystal family and can be one of the following: a (triclinic), b
+ (monoclinic), o (orthorhombic), t (tetragonal), h (hexagonal) or c (cubic). The
+ second uppercase letter identifies the centring and can be one of the following: P
+ (primitive), S (face centred), I (body centred), R (rhombohedral centring) or F
+ (all faces centred).
+ ''',
+ a_legacy=LegacyDefinition(name='bravais_lattice'))
+
+ choice = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String that specifies the centering, origin and basis vector settings of the 3D
+ space group that defines the symmetry group of the simulated physical system (see
+ section_system). Values are as defined by spglib.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='choice'))
+
+ crystal_system = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of the crystal system. Can be one of the following: triclinic, monoclinic,
+ orthorhombic, tetragonal, trigonal, hexagonal or cubic.
+ ''',
+ a_legacy=LegacyDefinition(name='crystal_system'))
+
+ hall_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ The Hall number for this system.
+ ''',
+ a_legacy=LegacyDefinition(name='hall_number'))
+
+ hall_symbol = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The Hall symbol for this system.
+ ''',
+ a_legacy=LegacyDefinition(name='hall_symbol'))
+
+ international_short_symbol = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the International Union of Crystallography (IUC) short symbol of the 3D
+ space group of this system
+ ''',
+ a_legacy=LegacyDefinition(name='international_short_symbol'))
+
+ origin_shift = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ description='''
+ Vector $\\mathbf{p}$ from the origin of the standardized system to the origin of
+ the original system. Together with the matrix $\\mathbf{P}$, found in
+ space_group_3D_transformation_matrix, the transformation between the standardized
+ coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by
+ $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.
+ ''',
+ a_legacy=LegacyDefinition(name='origin_shift'))
+
+ point_group = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Symbol of the crystallographic point group in the Hermann-Mauguin notation.
+ ''',
+ a_legacy=LegacyDefinition(name='point_group'))
+
+ space_group_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Specifies the International Union of Crystallography (IUC) number of the 3D space
+ group of this system.
+ ''',
+ a_legacy=LegacyDefinition(name='space_group_number'))
+
+ symmetry_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifies the source of the symmetry information contained within this section.
+ If equal to 'spg_normalized' the information comes from a normalization step.
+ ''',
+ a_legacy=LegacyDefinition(name='symmetry_method'))
+
+ transformation_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ description='''
+ Matrix $\\mathbf{P}$ that is used to transform the standardized coordinates to the
+ original coordinates. Together with the vector $\\mathbf{p}$, found in
+ space_group_3D_origin_shift, the transformation between the standardized
+ coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by
+ $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.
+ ''',
+ a_legacy=LegacyDefinition(name='transformation_matrix'))
+
+ section_original_system = SubSection(
+ sub_section=SectionProxy('OriginalSystem'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_original_system'))
+
+ section_primitive_system = SubSection(
+ sub_section=SectionProxy('PrimitiveSystem'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_primitive_system'))
+
+ section_std_system = SubSection(
+ sub_section=SectionProxy('StdSystem'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_std_system'))
+
+
+class SystemToSystemRefs(MSection):
+ '''
+ Section that describes the relationship between different section_system sections. For
+ instance, if a phonon calculation using a finite difference approach is performed the
+ force evaluation is typically done in a larger supercell but the properties such as
+ the phonon band structure are still calculated for the primitive cell.
+
+ The kind of relationship between the system defined in this section and the referenced
+ one is described by system_to_system_kind. The referenced section_system is identified
+ via system_to_system_ref.
+ '''
+
+ m_def = Section(
+ aliases=['section_system_to_system_refs'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_system_to_system_refs'))
+
+ system_to_system_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the relationship between the referenced section_system and the
+ present section_system. Often systems are connected for example if a phonon
+ calculation using finite differences is performed the force ealuation is done in a
+ larger supercell but properties such as the phonon band structure are still
+ calculated for the primitive cell. Hence, the need of keeping track of these
+ connected systems. The referenced system is identified via system_to_system_ref.
+ ''',
+ a_legacy=LegacyDefinition(name='system_to_system_kind'))
+
+ system_to_system_ref = Quantity(
+ type=Reference(SectionProxy('System')),
+ shape=[],
+ description='''
+ Reference to another system. The kind of relationship between the present and the
+ referenced section_system is specified by system_to_system_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='system_to_system_ref'))
+
+
+class System(MSection):
+ '''
+ Every section_system contains all needed properties required to describe the simulated
+ physical system, e.g. the given atomic configuration, the definition of periodic cell
+ (if present), the external potentials and other parameters.
+ '''
+
+ m_def = Section(
+ aliases=['section_system'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_system'))
+
+ atom_atom_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_sites'],
+ description='''
+ Atomic number Z of the atom.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_atom_number'))
+
+ atom_concentrations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms'],
+ description='''
+ concentration of the atom species in a variable composition, by default it should
+ be considered an array of ones. Summing these should give the number_of_sites
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='atom_concentrations'))
+
+ atom_labels = Quantity(
+ type=str,
+ shape=['number_of_atoms'],
+ description='''
+ Labels of the atoms. These strings identify the atom kind and conventionally start
+ with the symbol of the atomic species, possibly followed by the atomic number. The
+ same atomic species can be labeled with more than one atom_labels in order to
+ distinguish, e.g., atoms of the same species assigned to different atom-centered
+ basis sets or pseudo-potentials, or simply atoms in different locations in the
+ structure (e.g., bulk and surface). These labels can also be used for *particles*
+ that do not correspond to physical atoms (e.g., ghost atoms in some codes using
+ atom-centered basis sets). This metadata defines a configuration and is therefore
+ required.
+ ''',
+ categories=[ConfigurationCore],
+ a_legacy=LegacyDefinition(name='atom_labels'))
+
+ atom_positions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='meter',
+ description='''
+ Positions of all the atoms, in Cartesian coordinates. This metadata defines a
+ configuration and is therefore required. For alloys where concentrations of
+ species are given for each site in the unit cell, it stores the position of the
+ sites.
+ ''',
+ categories=[ConfigurationCore],
+ a_legacy=LegacyDefinition(name='atom_positions'))
+
+ atom_species = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms'],
+ description='''
+ Species of the atom (normally the atomic number Z, 0 or negative for unidentifed
+ species or particles that are not atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_species'))
+
+ atom_velocities = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='meter / second',
+ description='''
+ Velocities of the nuclei, defined as the change in Cartesian coordinates of the
+ nuclei with respect to time.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_velocities'))
+
+ configuration_periodic_dimensions = Quantity(
+ type=bool,
+ shape=[3],
+ description='''
+ Array labeling which of the lattice vectors use periodic boundary conditions. Note
+ for the parser developers: This value is not expected to be given for each
+ section_single_configuration_calculation. It is assumed to be valid from the
+ section_single_configuration_calculation where it is defined for all subsequent
+ section_single_configuration_calculation in section_run, until redefined.
+ ''',
+ categories=[ConfigurationCore],
+ a_legacy=LegacyDefinition(name='configuration_periodic_dimensions'))
+
+ configuration_raw_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ checksum of the configuration_core, i.e. the geometry of the system. The values
+ are not normalized in any way so equivalent configurations might have different
+ values
+ ''',
+ a_legacy=LegacyDefinition(name='configuration_raw_gid'))
+
+ embedded_system = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Is the system embedded into a host geometry?.
+ ''',
+ categories=[ConfigurationCore, Unused],
+ a_legacy=LegacyDefinition(name='embedded_system'))
+
+ lattice_vectors = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ Holds the lattice vectors (in Cartesian coordinates) of the simulation cell. The
+ last (fastest) index runs over the $x,y,z$ Cartesian coordinates, and the first
+ index runs over the 3 lattice vectors.
+ ''',
+ categories=[ConfigurationCore],
+ a_legacy=LegacyDefinition(name='lattice_vectors'))
+
+ local_rotations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3, 3],
+ description='''
+ A rotation matrix defining the orientation of each atom. If the rotation matrix
+ only needs to be specified for some atoms, the remaining atoms should set it to
+ the zero matrix (not the identity!)
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='local_rotations'))
+
+ number_of_atoms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Stores the total number of atoms used in the calculation. For alloys where
+ concentrations of species are given for each site in the unit cell, it stores the
+ number of sites.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms'))
+
+ number_of_sites = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of sites in a variable composition representation. By default (no variable
+ composition) it is the same as number_of_atoms.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_sites'))
+
+ SC_matrix = Quantity(
+ type=np.dtype(np.int32),
+ shape=[3, 3],
+ description='''
+ Specifies the matrix that transforms the unit-cell into the super-cell in which
+ the actual calculation is performed.
+ ''',
+ a_legacy=LegacyDefinition(name='SC_matrix'))
+
+ simulation_cell = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ DEPRECATED, use lattice_vectors instead. Holds the lattice vectors (in Cartesian
+ coordinates) of the simulation cell. The last (fastest) index runs over the
+ $x,y,z$ Cartesian coordinates, and the first index runs over the 3 lattice
+ vectors.
+ ''',
+ categories=[ConfigurationCore],
+ a_legacy=LegacyDefinition(name='simulation_cell'))
+
+ symmorphic = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Is the space group symmorphic? Set to True if all translations are zero.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='symmorphic'))
+
+ system_composition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Composition, i.e. cumulative chemical formula with atoms ordered by decreasing
+ atomic number Z.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='system_composition'))
+
+ system_configuration_consistent = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Flag set is the configuration is consistent
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='system_configuration_consistent'))
+
+ system_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the name of the system. This information is provided by the user in some
+ codes and is stored here for debugging or visualization purposes.
+ ''',
+ a_legacy=LegacyDefinition(name='system_name'))
+
+ system_reweighted_composition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Composition, i.e. cumulative chemical with atoms ordered by decreasing atomic
+ number Z reweighted so that the sum is close to 100, and values are rounded up,
+ and are stable (i.e. it is a fixed point).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='system_reweighted_composition'))
+
+ system_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of the system
+ ''',
+ a_legacy=LegacyDefinition(name='system_type'))
+
+ time_reversal_symmetry = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Is time-reversal symmetry present?
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='time_reversal_symmetry'))
+
+ chemical_composition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The chemical composition as full formula of the system, based on atom species.
+ ''',
+ a_legacy=LegacyDefinition(name='chemical_composition'))
+
+ chemical_composition_reduced = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The chemical composition as reduced formula of the system, based on atom species.
+ ''',
+ a_legacy=LegacyDefinition(name='chemical_composition_reduced'))
+
+ chemical_composition_bulk_reduced = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The chemical composition as reduced bulk formula of the system, based on atom
+ species.
+ ''',
+ a_legacy=LegacyDefinition(name='chemical_composition_bulk_reduced'))
+
+ number_of_electrons = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ description='''
+ Number of electrons in system
+ ''',
+ categories=[ConfigurationCore],
+ a_legacy=LegacyDefinition(name='number_of_electrons'))
+
+ topology_ref = Quantity(
+ type=Reference(SectionProxy('Topology')),
+ shape=[],
+ description='''
+ Reference to the topology used for this system; if not given, the trivial topology
+ should be assumed.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='topology_ref'))
+
+ is_representative = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Most systems in a run are only minor variations of each other. Systems marked
+ representative where chosen to be representative for all systems in the run.
+ ''',
+ a_legacy=LegacyDefinition(name='is_representative'))
+
+ section_prototype = SubSection(
+ sub_section=SectionProxy('Prototype'),
+ repeats=True,
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='section_prototype'))
+
+ section_springer_material = SubSection(
+ sub_section=SectionProxy('SpringerMaterial'),
+ repeats=True,
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='section_springer_material'))
+
+ section_symmetry = SubSection(
+ sub_section=SectionProxy('Symmetry'),
+ repeats=True,
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='section_symmetry'))
+
+ section_system_to_system_refs = SubSection(
+ sub_section=SectionProxy('SystemToSystemRefs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_system_to_system_refs'))
+
+ section_soap = SubSection(
+ sub_section=SectionProxy('Soap'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_soap'))
+
+
+class ThermodynamicalProperties(MSection):
+ '''
+ Section that defines thermodynamical properties about the system in a
+ section_frame_sequence.
+ '''
+
+ m_def = Section(
+ aliases=['section_thermodynamical_properties'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_thermodynamical_properties'))
+
+ helmholz_free_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule',
+ description='''
+ Stores the Helmholtz free energy per unit cell at constant volume of a
+ thermodynamic calculation.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='helmholz_free_energy'))
+
+ number_of_thermodynamical_property_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of thermal properties values available in
+ section_thermodynamical_properties.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_thermodynamical_property_values'))
+
+ thermodynamical_properties_calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to calculate the thermodynamic quantities.
+
+ Valid values:
+
+ * harmonic
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='thermodynamical_properties_calculation_method'))
+
+ thermodynamical_property_heat_capacity_C_v = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kelvin',
+ description='''
+ Stores the heat capacity per cell unit at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='thermodynamical_property_heat_capacity_C_v'))
+
+ @derived(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kelvin * kilogram',
+ description='''
+ Stores the specific heat capacity at constant volume.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='specific_heat_capacity'),
+ cached=True
+ )
+ def specific_heat_capacity(self) -> np.array:
+ """Returns the specific heat capacity by dividing the heat capacity per
+ cell with the mass of the atoms in the cell.
+ """
+ import nomad.atomutils
+ s_frame_sequence = self.m_parent
+ first_frame = s_frame_sequence.frame_sequence_local_frames_ref[0]
+ system = first_frame.single_configuration_calculation_to_system_ref
+ atomic_numbers = system.atom_species
+ mass_per_unit_cell = nomad.atomutils.get_summed_atomic_mass(atomic_numbers)
+ heat_capacity = self.thermodynamical_property_heat_capacity_C_v
+ specific_heat_capacity = heat_capacity / mass_per_unit_cell
+
+ return specific_heat_capacity
+
+ thermodynamical_property_temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='kelvin',
+ description='''
+ Specifies the temperatures at which properties such as the Helmholtz free energy
+ are calculated.
+ ''',
+ a_legacy=LegacyDefinition(name='thermodynamical_property_temperature'))
+
+ vibrational_free_energy_at_constant_volume = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule',
+ description='''
+ Holds the vibrational free energy per atom at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='vibrational_free_energy_at_constant_volume'))
+
+ specific_vibrational_free_energy_at_constant_volume = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kilogram',
+ description='''
+ Stores the specific vibrational free energy at constant volume.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='specific_vibrational_free_energy_at_constant_volume'))
+
+
+class VolumetricData(MSection):
+ '''
+ Section defining a set of volumetric data on a uniform real-space grid.
+
+ To store an array (e.g. a density or a potential), define:
+
+ * three grid point displacement vectors ("displacements")
+
+ * number of grid points along each axis ("nx", "ny" and "nz")
+
+ * the origin of the coordinate system, i.e. coordinates of the first grid
+
+ point ("origin")
+
+ * how many spatial functions are represented, e.g., two for a
+
+ normal spin-polarized density ("multiplicity")
+
+ * the values for each grid point ("values")
+
+ * the unit that applies to each value ("units")
+
+ * the kind of array represented by the volumetric data ("kind").
+
+ Allowed kinds are (please add new kinds as necessary): "density",
+
+ "potential_hartree" and "potential_effective". Densities and
+
+ potentials that are spin-polarized should have multiplicity two.
+
+ Rules for more complex spins are to be decided when necessary.
+ '''
+
+ m_def = Section(
+ aliases=['section_volumetric_data'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_volumetric_data'))
+
+ volumetric_data_displacements = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ displacement vectors between grid points along each axis; same indexing rules as
+ lattice_vectors. In many cases, displacements and number of points are related to
+ lattice_vectors through: [displacement] * [number of points + N] =
+ [lattice_vector],where N is 1 for periodic directions and 0 for non-periodic ones
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_displacements'))
+
+ volumetric_data_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The kind of function, e.g. density, potential_hartree, potential_effective. The
+ unit of measurement for "volumetric_data_values" depends on the kind: Densities
+ are 1/m^3 and potentials are J/m^3. See [full specification on the
+ wiki](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/volumetric-data).
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_kind'))
+
+ volumetric_data_multiplicity = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of functions stored
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='volumetric_data_multiplicity'))
+
+ volumetric_data_nx = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of points along x axis
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='volumetric_data_nx'))
+
+ volumetric_data_ny = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of points along y axis
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='volumetric_data_ny'))
+
+ volumetric_data_nz = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of points along z axis
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='volumetric_data_nz'))
+
+ volumetric_data_origin = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ description='''
+ location of the first grid point; same coordinate system as atom_positions when
+ applicable.
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_origin'))
+
+ volumetric_data_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['volumetric_data_multiplicity', 'volumetric_data_nx', 'volumetric_data_ny', 'volumetric_data_nz'],
+ description='''
+ Array of shape (multiplicity, nx, ny, nz) containing the values. The units of
+ these values depend on which kind of data the values represent; see
+ "volumetric_data_kind".
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_values'))
+
+
+class XCFunctionals(MSection):
+ '''
+ Section containing one of the exchange-correlation (XC) functionals for the present
+ section_method that are combined to form the XC_functional.
+ '''
+
+ m_def = Section(
+ aliases=['section_XC_functionals'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_XC_functionals'))
+
+ XC_functional_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Provides the name of one of the exchange and/or correlation (XC) functionals
+ combined in XC_functional.
+
+ The valid unique names that can be used are listed in the [XC_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional).
+
+ *NOTE*: This value should refer to a correlation, an exchange or an exchange-
+ correlation functional only.
+ ''',
+ categories=[SettingsPhysicalParameter],
+ a_legacy=LegacyDefinition(name='XC_functional_name'))
+
+ XC_functional_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Contains an associative list of non-default values of the parameters for the
+ functional declared in XC_functional_name of the section_XC_functionals section.
+
+ For example, if a calculations using a hybrid XC functional (e.g., HSE06)
+ specifies a user-given value of the mixing parameter between exact and GGA
+ exchange, then this non-default value is stored in this metadata.
+
+ The labels and units of these values are defined in the paragraph dedicated to the
+ specified functional declared in XC_functional_name of the [XC_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional).
+
+ If this metadata is not given, the default parameter values for the
+ XC_functional_name are assumed.
+ ''',
+ categories=[SettingsPhysicalParameter],
+ a_legacy=LegacyDefinition(name='XC_functional_parameters'))
+
+ XC_functional_weight = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Provides the value of the weight for the exchange, correlation, or exchange-
+ correlation functional declared in XC_functional_name (see
+ section_XC_functionals).
+
+ This weight is used in the linear combination of the different XC functional names
+ (XC_functional_name) in different section_XC_functionals sections to form the
+ XC_functional used for evaluating energy_XC_functional and related quantities.
+
+ If not specified then the default is set to 1.
+ ''',
+ categories=[SettingsPhysicalParameter],
+ a_legacy=LegacyDefinition(name='XC_functional_weight'))
+
+
+class GeometryOptimization(MSection):
+ '''
+ Section containing the results of a geometry_optimization workflow.
+ '''
+
+ m_def = Section(
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_geometry_optimization'))
+
+ geometry_optimization_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of geometry optimization can either be ionic, cell_shape, cell_volume.
+ ''',
+ a_legacy=LegacyDefinition(name='geometry_optimization_type'))
+
+ input_energy_difference_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ The input energy difference tolerance criterion.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='input_energy_difference_tolerance'))
+
+ input_force_maximum_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ The input maximum net force tolerance criterion.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='input_force_maximum_tolerance'))
+
+ final_energy_difference = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ The difference in the energy between the last two steps during optimization.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='final_energy_difference'))
+
+ final_force_maximum = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ The maximum net force in the last optimization step.
+ ''',
+ a_legacy=LegacyDefinition(name='final_force_maximum'))
+
+ optimization_steps = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of optimization steps.
+ ''',
+ a_legacy=LegacyDefinition(name='optimization_steps'))
+
+
+class Phonon(MSection):
+ '''
+ Section containing the results of a phonon workflow.
+ '''
+
+ m_def = Section(
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_phonon'))
+
+ force_calculator = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of the program used to calculate the forces.
+ ''',
+ a_legacy=LegacyDefinition(name='force_calculator'))
+
+ mesh_density = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='1 / meter ** 3',
+ description='''
+ Density of the k-mesh for sampling.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='mesh_density'))
+
+ n_imaginary_frequencies = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of modes with imaginary frequencies.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='n_imaginary_frequencies'))
+
+ random_displacements = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Identifies if displacements are made randomly.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='random_displacements'))
+
+ with_non_analytic_correction = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Identifies if non-analytical term corrections are applied to dynamical matrix.
+ ''',
+ categories=[Unused],
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='with_non_analytic_correction'))
+
+ with_grueneisen_parameters = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Identifies if Grueneisen parameters are calculated.
+ ''',
+ categories=[Unused],
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='with_grueneisen_parameters'))
+
+
+class Elastic(MSection):
+ '''
+ Section containing the results of an elastic workflow.
+ '''
+
+ m_def = Section(
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_elastic'))
+
+ energy_stress_calculator = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of program used to calculate energy or stress.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='energy_stress_calculator'))
+
+ elastic_calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to calculate elastic constants, can either be energy or stress.
+ ''',
+ a_legacy=LegacyDefinition(name='elastic_calculation_method'))
+
+ elastic_constants_order = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Order of the calculated elastic constants.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='elastic_constants_order'))
+
+ is_mechanically_stable = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if structure is mechanically stable from the calculated values of the
+ elastic constants.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='is_mechanically_stable'))
+
+ fitting_error_maximum = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum error in polynomial fit.
+ ''',
+ a_legacy=LegacyDefinition(name='fitting_error_maximum'))
+
+ strain_maximum = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum strain applied to crystal.
+ ''',
+ a_legacy=LegacyDefinition(name='strain_maximum'))
+
+
+class MolecularDynamics(MSection):
+ '''
+ Section containing results of molecular dynamics workflow.
+ '''
+
+ m_def = Section(
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
+
+ finished_normally = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if calculation terminated normally.
+ ''',
+ a_legacy=LegacyDefinition(name='finished_normally'))
+
+ with_trajectory = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if calculation includes trajectory data.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='with_trajectory'))
+
+ with_thermodynamics = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if calculation contains thermodynamic data.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='with_thermodynamics'))
+
+
+class Workflow(MSection):
+ '''
+ Section containing the results of a workflow.
+ '''
+
+ m_def = Section(
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_workflow'))
+
+ workflow_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of calculation workflow. Can be one of geometry_optimization, elastic,
+ phonon, molecular_dynamics.
+ ''',
+ a_search=Search(),
+ a_legacy=LegacyDefinition(name='workflow_type'))
+
+ calculation_result_ref = Quantity(
+ type=Reference(SectionProxy('SingleConfigurationCalculation')),
+ shape=[],
+ description='''
+ Reference to calculation result. In the case of geometry_optimization and
+ molecular dynamics, this corresponds to the final step in the simulation. For the
+ rest of the workflow types, it refers to the original system.
+ ''',
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='calculation_result_ref'))
+
+ calculations_ref = Quantity(
+ type=Reference(SectionProxy('SingleConfigurationCalculation')),
+ shape=['optimization_steps'],
+ description='''
+ List of references to each section_single_configuration_calculation in the
+ simulation.
+ ''',
+ a_legacy=LegacyDefinition(name='calculations_ref'))
+
+ section_geometry_optimization = SubSection(
+ sub_section=SectionProxy('GeometryOptimization'),
+ repeats=False,
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='section_geometry_optimization'))
+
+ section_phonon = SubSection(
+ sub_section=SectionProxy('Phonon'),
+ repeats=False,
+ categories=[FastAccess],
+ a_legacy=LegacyDefinition(name='section_phonon'))
+
+ section_elastic = SubSection(
+ sub_section=SectionProxy('Elastic'),
+ repeats=False,
+ a_legacy=LegacyDefinition(name='section_elastic'))
+
+ section_molecular_dynamics = SubSection(
+ sub_section=SectionProxy('MolecularDynamics'),
+ repeats=False,
+ a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
+
+
+class ResponseContext(MSection):
+ '''
+ The top level context containing the reponse to an api query, when using jsonAPI they
+ are tipically in the meta part
+ '''
+
+ m_def = Section(
+ aliases=['response_context'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='response_context'))
+
+ shortened_meta_info = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A meta info whose corresponding data has been shortened
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='shortened_meta_info'))
+
+ section_response_message = SubSection(
+ sub_section=SectionProxy('ResponseMessage'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_response_message'))
+
+
+class AtomType(MSection):
+ '''
+ Section describing a type of atom in the system.
+ '''
+
+ m_def = Section(
+ aliases=['section_atom_type'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_atom_type'))
+
+ atom_type_charge = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='coulomb',
+ description='''
+ Charge of the atom type.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_type_charge'))
+
+ atom_type_mass = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='kilogram',
+ description='''
+ Mass of the atom type.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_type_mass'))
+
+ atom_type_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name (label) of the atom type.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_type_name'))
+
+
+class Constraint(MSection):
+ '''
+ Section describing a constraint between arbitrary atoms.
+ '''
+
+ m_def = Section(
+ aliases=['section_constraint'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_constraint'))
+
+ constraint_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_constraints', 'number_of_atoms_per_constraint'],
+ description='''
+ List of the indexes involved in this constraint. The fist atom has index 1, the
+ last number_of_topology_atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='constraint_atoms'))
+
+ constraint_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this constraint type. Valid names are described in the
+ [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/constraint-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='constraint_kind'))
+
+ constraint_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit constraint parameters for this kind of constraint (depending on the
+ constraint type, some might be given implicitly through other means).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='constraint_parameters'))
+
+ number_of_atoms_per_constraint = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms involved in this constraint.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_constraint'))
+
+ number_of_constraints = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of constraints of this type.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_constraints'))
+
+
+class DftPlusUOrbital(MSection):
+ '''
+ Section for DFT+U-settings of a single orbital
+ '''
+
+ m_def = Section(
+ aliases=['section_dft_plus_u_orbital'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
+
+ dft_plus_u_orbital_atom = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: atom index (references index of atom_labels/atom_positions)
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_atom'))
+
+ dft_plus_u_orbital_J = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: value J (exchange interaction)
+ ''',
+ categories=[EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_J'))
+
+ dft_plus_u_orbital_label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ DFT+U-orbital setting: orbital label (normally (n,l)), notation: '3d', '4f', ...
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_label'))
+
+ dft_plus_u_orbital_U_effective = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: value U_{effective} (U-J), if implementation uses it
+ ''',
+ categories=[EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_U_effective'))
+
+ dft_plus_u_orbital_U = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: value U (on-site Coulomb interaction)
+ ''',
+ categories=[EnergyValue, Unused],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_U'))
+
+
+class ExcitedStates(MSection):
+ '''
+ Excited states properties.
+ '''
+
+ m_def = Section(
+ aliases=['section_excited_states'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_excited_states'))
+
+ excitation_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_excited_states'],
+ description='''
+ Excitation energies.
+ ''',
+ categories=[EnergyValue],
+ a_legacy=LegacyDefinition(name='excitation_energies'))
+
+ number_of_excited_states = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of excited states.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_excited_states'))
+
+ oscillator_strengths = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_excited_states'],
+ description='''
+ Excited states oscillator strengths.
+ ''',
+ a_legacy=LegacyDefinition(name='oscillator_strengths'))
+
+ transition_dipole_moments = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_excited_states', 3],
+ description='''
+ Transition dipole moments.
+ ''',
+ a_legacy=LegacyDefinition(name='transition_dipole_moments'))
+
+
+class Interaction(MSection):
+ '''
+ Section containing the description of a bonded interaction between arbitrary atoms.
+ '''
+
+ m_def = Section(
+ aliases=['section_interaction'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_interaction'))
+
+ interaction_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_interactions', 'number_of_atoms_per_interaction'],
+ description='''
+ List of the indexes involved in this interaction. The fist atom has index 1, the
+ last atom index number_of_topology_atoms.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='interaction_atoms'))
+
+ interaction_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this interaction type. Valid names are described in the
+ [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/interaction-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='interaction_kind'))
+
+ interaction_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit interaction parameters for this kind of interaction (depending on the
+ interaction_kind some might be given implicitly through other means).
+ ''',
+ a_legacy=LegacyDefinition(name='interaction_parameters'))
+
+ number_of_atoms_per_interaction = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms involved in this interaction.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_interaction'))
+
+ number_of_interactions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of interactions of this type.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_interactions'))
+
+
+class MethodBasisSet(MSection):
+ '''
+ This section contains the definition of the basis sets that are defined independently
+ of the atomic configuration.
+ '''
+
+ m_def = Section(
+ aliases=['section_method_basis_set'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_method_basis_set'))
+
+ mapping_section_method_basis_set_atom_centered = Quantity(
+ type=np.dtype(np.int64),
+ shape=['number_of_basis_sets_atom_centered', 2],
+ description='''
+ Reference to an atom-centered basis set defined in section_basis_set_atom_centered
+ and to the atom kind as defined in section_method_atom_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_method_basis_set_atom_centered'))
+
+ mapping_section_method_basis_set_cell_associated = Quantity(
+ type=Reference(SectionProxy('BasisSetCellDependent')),
+ shape=[],
+ description='''
+ Reference to a cell-associated basis set.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_method_basis_set_cell_associated'))
+
+ method_basis_set_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the use of the basis set, i.e, if it used for expanding a
+ wavefunction or an electron density. Allowed values are listed in the
+ [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/basis-set-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='method_basis_set_kind'))
+
+ number_of_basis_sets_atom_centered = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ String describing the use of the basis set, i.e, if it used for expanding a
+ wavefunction or an electron density. Allowed values are listed in the
+ [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/basis-set-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_basis_sets_atom_centered'))
+
+
+class MoleculeConstraint(MSection):
+ '''
+ Section describing a constraint between atoms within a molecule.
+ '''
+
+ m_def = Section(
+ aliases=['section_molecule_constraint'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_molecule_constraint'))
+
+ molecule_constraint_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_molecule_constraints', 'number_of_atoms_per_molecule_constraint'],
+ description='''
+ List of the indexes involved in this constraint. The fist atom has index 1, the
+ last index is number_of_atoms_in_molecule.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='molecule_constraint_atoms'))
+
+ molecule_constraint_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this constraint type. Valid names are described in the
+ [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/constraint-kind).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='molecule_constraint_kind'))
+
+ molecule_constraint_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit constraint parameters for this kind of constraint (depending on the
+ constraint type some might be given implicitly through other means).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='molecule_constraint_parameters'))
+
+ number_of_atoms_per_molecule_constraint = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms, in this molecule, involved in this constraint.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_molecule_constraint'))
+
+ number_of_molecule_constraints = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of constraints of this type.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_molecule_constraints'))
+
+
+class MoleculeInteraction(MSection):
+ '''
+ Section describing a bonded interaction between atoms within a molecule.
+ '''
+
+ m_def = Section(
+ aliases=['section_molecule_interaction'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_molecule_interaction'))
+
+ molecule_interaction_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_molecule_interactions', 'number_of_atoms_per_molecule_interaction'],
+ description='''
+ List of the indexes involved in this bonded interaction within a molecule. The
+ first atom has index 1, the last index is number_of_atoms_in_.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='molecule_interaction_atoms'))
+
+ molecule_interaction_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this interaction type, used for bonded interactions for
+ atoms in a molecule. Valid names are described in the [interaction\\_kind wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/interaction-kind).
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='molecule_interaction_kind'))
+
+ molecule_interaction_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit interaction parameters for this kind of interaction (depending on the
+ interaction type some might be given implicitly through other means), used for
+ bonded interactions for atoms in a molecule.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='molecule_interaction_parameters'))
+
+ number_of_atoms_per_molecule_interaction = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms, in this molecule, involved in this interaction.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_molecule_interaction'))
+
+ number_of_molecule_interactions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of bonded interactions of this type.
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_molecule_interactions'))
+
+
+class MoleculeType(MSection):
+ '''
+ Section describing a type of molecule in the system.
+ '''
+
+ m_def = Section(
+ aliases=['section_molecule_type'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_molecule_type'))
+
+ atom_in_molecule_charge = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms_in_molecule'],
+ unit='coulomb',
+ description='''
+ Charge of each atom in the molecule.
+ ''',
+ categories=[SettingsAtomInMolecule],
+ a_legacy=LegacyDefinition(name='atom_in_molecule_charge'))
+
+ atom_in_molecule_name = Quantity(
+ type=str,
+ shape=['number_of_atoms_in_molecule'],
+ description='''
+ Name (label) of each atom in the molecule.
+ ''',
+ categories=[SettingsAtomInMolecule],
+ a_legacy=LegacyDefinition(name='atom_in_molecule_name'))
+
+ atom_in_molecule_to_atom_type_ref = Quantity(
+ type=Reference(SectionProxy('AtomType')),
+ shape=['number_of_atoms_in_molecule'],
+ description='''
+ Reference to the atom type of each atom in the molecule.
+ ''',
+ categories=[SettingsAtomInMolecule],
+ a_legacy=LegacyDefinition(name='atom_in_molecule_to_atom_type_ref'))
+
+ molecule_type_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of the molecule.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_type_name'))
+
+ number_of_atoms_in_molecule = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in this molecule.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_in_molecule'))
+
+ section_molecule_constraint = SubSection(
+ sub_section=SectionProxy('MoleculeConstraint'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_molecule_constraint'))
+
+ section_molecule_interaction = SubSection(
+ sub_section=SectionProxy('MoleculeInteraction'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_molecule_interaction'))
+
+
+class ResponseMessage(MSection):
+ '''
+ Messages outputted by the program formatting the data in the current response
+ '''
+
+ m_def = Section(
+ aliases=['section_response_message'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_response_message'))
+
+ response_message_count = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ How many times this message was repeated
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='response_message_count'))
+
+ response_message_level = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ level of the message: 0 fatal, 1 error, 2 warning, 3 debug
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='response_message_level'))
+
+ response_message = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Message outputted by the program formatting the data in the current format
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='response_message'))
+
+
+class SoapCoefficients(MSection):
+ '''
+ Stores the soap coefficients for the pair of atoms given in
+ soap_coefficients_atom_pair.
+ '''
+
+ m_def = Section(
+ aliases=['section_soap_coefficients'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_soap_coefficients'))
+
+ number_of_soap_coefficients = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of soap coefficients
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='number_of_soap_coefficients'))
+
+ soap_coefficients_atom_pair = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Pair of atoms described in the current section
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='soap_coefficients_atom_pair'))
+
+ soap_coefficients = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_soap_coefficients'],
+ description='''
+ Compressed coefficient of the soap descriptor for the atom pair
+ soap_coefficients_atom_pair
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='soap_coefficients'))
+
+
+class Soap(MSection):
+ '''
+ Stores a soap descriptor for this configuration.
+ '''
+
+ m_def = Section(
+ aliases=['section_soap'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_soap'))
+
+ soap_angular_basis_L = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ angular basis L
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_angular_basis_L'))
+
+ soap_angular_basis_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ angular basis type
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_angular_basis_type'))
+
+ soap_kernel_adaptor = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ kernel adaptor
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_kernel_adaptor'))
+
+ soap_parameters_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Unique checksum of all the soap parameters (all those with abstract type
+ soap_parameter) with prefix psoap
+ ''',
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='soap_parameters_gid'))
+
+ soap_radial_basis_integration_steps = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ radial basis integration steps
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_integration_steps'))
+
+ soap_radial_basis_mode = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ radial basis mode
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_mode'))
+
+ soap_radial_basis_n = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ radial basis N
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_n'))
+
+ soap_radial_basis_sigma = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ radial basis sigma
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_sigma'))
+
+ soap_radial_basis_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ radial basis type
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_type'))
+
+ soap_radial_cutoff_center_weight = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ radial cutoff center weight
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_center_weight'))
+
+ soap_radial_cutoff_rc_width = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ radial cutoff width
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_rc_width'))
+
+ soap_radial_cutoff_rc = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ radial cutoff
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_rc'))
+
+ soap_radial_cutoff_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ radial cutoff type
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_type'))
+
+ soap_spectrum_2l1_norm = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ 2l1 norm spectrum
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_spectrum_2l1_norm'))
+
+ soap_spectrum_global = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ global spectrum
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_spectrum_global'))
+
+ soap_spectrum_gradients = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ gradients in specturm
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_spectrum_gradients'))
+
+ soap_type_list = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type list
+ ''',
+ categories=[SoapParameter, Unused],
+ a_legacy=LegacyDefinition(name='soap_type_list'))
+
+ section_soap_coefficients = SubSection(
+ sub_section=SectionProxy('SoapCoefficients'),
+ repeats=True,
+ categories=[Unused],
+ a_legacy=LegacyDefinition(name='section_soap_coefficients'))
+
+
+class Topology(MSection):
+ '''
+ Section containing the definition of topology (connectivity among atoms in force
+ fileds), force field, and constraints of a system.
+ '''
+
+ m_def = Section(
+ aliases=['section_topology'],
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_topology'))
+
+ atom_to_molecule = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_topology_atoms', 2],
+ description='''
+ Table mapping atom to molecules: the first column is the index of the molecule and
+ the second column the index of the atom, signifying that the atom in the second
+ column belongs to the molecule in the first column in the same row.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_to_molecule'))
+
+ molecule_to_molecule_type_map = Quantity(
+ type=Reference(SectionProxy('MoleculeType')),
+ shape=['number_of_topology_molecules'],
+ description='''
+ Mapping from molecules to molecule types.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_to_molecule_type_map'))
+
+ number_of_topology_atoms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in the system described by this topology.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_topology_atoms'))
+
+ number_of_topology_molecules = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of molecules in the system, as described by this topology.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_topology_molecules'))
+
+ topology_force_field_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A unique string idenfiying the force field defined in this section. Strategies to
+ define it are discussed in the
+ [topology\\_force\\_field\\_name](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/topology-force-field-name).
+ ''',
+ a_legacy=LegacyDefinition(name='topology_force_field_name'))
+
+ section_atom_type = SubSection(
+ sub_section=SectionProxy('AtomType'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_atom_type'))
+
+ section_constraint = SubSection(
+ sub_section=SectionProxy('Constraint'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_constraint'))
+
+ section_interaction = SubSection(
+ sub_section=SectionProxy('Interaction'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_interaction'))
+
+ section_molecule_type = SubSection(
+ sub_section=SectionProxy('MoleculeType'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_molecule_type'))
+
+
+m_package.__init_metainfo__()
+
+
+fast_access = FastAccess
+accessory_info = AccessoryInfo
+atom_forces_type = AtomForcesType
+basis_set_description = BasisSetDescription
+configuration_core = ConfigurationCore
+conserved_quantity = ConservedQuantity
+energy_value = EnergyValue
+error_estimate_contribution = ErrorEstimateContribution
+message_debug = MessageDebug
+parsing_message_debug = ParsingMessageDebug
+scf_info = ScfInfo
+settings_numerical_parameter = SettingsNumericalParameter
+settings_physical_parameter = SettingsPhysicalParameter
+settings_potential_energy_surface = SettingsPotentialEnergySurface
+settings_run = SettingsRun
+settings_sampling = SettingsSampling
+settings_scf = SettingsScf
+settings_smearing = SettingsSmearing
+settings_stress_tensor = SettingsStressTensor
+stress_tensor_type = StressTensorType
+energy_component_per_atom = EnergyComponentPerAtom
+energy_component = EnergyComponent
+energy_type_reference = EnergyTypeReference
+error_estimate = ErrorEstimate
+message_info = MessageInfo
+parallelization_info = ParallelizationInfo
+parsing_message_info = ParsingMessageInfo
+program_info = ProgramInfo
+settings_geometry_optimization = SettingsGeometryOptimization
+settings_k_points = SettingsKPoints
+settings_metadynamics = SettingsMetadynamics
+settings_molecular_dynamics = SettingsMolecularDynamics
+settings_Monte_Carlo = SettingsMonteCarlo
+settings_XC = SettingsXC
+time_info = TimeInfo
+energy_total_potential_per_atom = EnergyTotalPotentialPerAtom
+energy_total_potential = EnergyTotalPotential
+energy_type_C = EnergyTypeC
+energy_type_van_der_Waals = EnergyTypeVanDerWaals
+energy_type_XC = EnergyTypeXC
+energy_type_X = EnergyTypeX
+message_warning = MessageWarning
+parsing_message_warning = ParsingMessageWarning
+settings_barostat = SettingsBarostat
+settings_integrator = SettingsIntegrator
+settings_post_hartree_fock = SettingsPostHartreeFock
+settings_relativity = SettingsRelativity
+settings_self_interaction_correction = SettingsSelfInteractionCorrection
+settings_thermostat = SettingsThermostat
+settings_van_der_Waals = SettingsVanDerWaals
+settings_XC_functional = SettingsXCFunctional
+message_error = MessageError
+parsing_message_error = ParsingMessageError
+settings_coupled_cluster = SettingsCoupledCluster
+settings_GW = SettingsGW
+settings_MCSCF = SettingsMCSCF
+settings_moller_plesset_perturbation_theory = SettingsMollerPlessetPerturbationTheory
+settings_multi_reference = SettingsMultiReference
+settings_atom_in_molecule = SettingsAtomInMolecule
+settings_constraint = SettingsConstraint
+settings_interaction = SettingsInteraction
+soap_parameter = SoapParameter
+archive_context = ArchiveContext
+calculation_context = CalculationContext
+section_atom_projected_dos = AtomProjectedDos
+section_atomic_multipoles = AtomicMultipoles
+section_basis_functions_atom_centered = BasisFunctionsAtomCentered
+section_basis_set_atom_centered = BasisSetAtomCentered
+section_basis_set_cell_dependent = BasisSetCellDependent
+section_basis_set = BasisSet
+section_restricted_uri = RestrictedUri
+section_calculation_to_calculation_refs = CalculationToCalculationRefs
+section_calculation_to_folder_refs = CalculationToFolderRefs
+section_dos_fingerprint = DosFingerprint
+section_dos = Dos
+section_eigenvalues = Eigenvalues
+section_energy_code_independent = EnergyCodeIndependent
+section_energy_van_der_Waals = EnergyVanDerWaals
+section_energy_contribution = EnergyContribution
+section_frame_sequence_user_quantity = FrameSequenceUserQuantity
+section_frame_sequence = FrameSequence
+section_gaussian_basis_group = GaussianBasisGroup
+section_k_band_normalized = KBandNormalized
+section_k_band_segment_normalized = KBandSegmentNormalized
+section_k_band_segment = KBandSegment
+section_band_gap = BandGap
+section_brillouin_zone = BrillouinZone
+section_k_band = KBand
+section_method_atom_kind = MethodAtomKind
+section_method_to_method_refs = MethodToMethodRefs
+section_method = Method
+section_original_system = OriginalSystem
+section_primitive_system = PrimitiveSystem
+section_processor_info = ProcessorInfo
+section_processor_log_event = ProcessorLogEvent
+section_processor_log = ProcessorLog
+section_prototype = Prototype
+section_run = Run
+section_sampling_method = SamplingMethod
+section_scf_iteration = ScfIteration
+section_single_configuration_calculation = SingleConfigurationCalculation
+section_species_projected_dos = SpeciesProjectedDos
+section_springer_material = SpringerMaterial
+section_springer_id = SpringerId
+section_std_system = StdSystem
+section_stress_tensor = StressTensor
+section_symmetry = Symmetry
+section_system_to_system_refs = SystemToSystemRefs
+section_system = System
+section_thermodynamical_properties = ThermodynamicalProperties
+section_volumetric_data = VolumetricData
+section_XC_functionals = XCFunctionals
+response_context = ResponseContext
+section_atom_type = AtomType
+section_constraint = Constraint
+section_dft_plus_u_orbital = DftPlusUOrbital
+section_excited_states = ExcitedStates
+section_interaction = Interaction
+section_method_basis_set = MethodBasisSet
+section_molecule_constraint = MoleculeConstraint
+section_molecule_interaction = MoleculeInteraction
+section_molecule_type = MoleculeType
+section_response_message = ResponseMessage
+section_soap_coefficients = SoapCoefficients
+section_soap = Soap
+section_topology = Topology
diff --git a/nomad/datamodel/metainfo/common_experimental.py b/nomad/datamodel/metainfo/common_experimental.py
index 09864cd595e496e638ebdd3573a8ad125db23efb..1ce81fa34299993b24f50c78a4d0803a657e0822 100644
--- a/nomad/datamodel/metainfo/common_experimental.py
+++ b/nomad/datamodel/metainfo/common_experimental.py
@@ -23,7 +23,7 @@ from nomad.metainfo import (
Datetime, JSON)
-m_package = Package(name='common_experimental')
+m_package = Package(name='experimental_common')
class Experiment(MSection):
diff --git a/nomad/datamodel/metainfo/common_old.py b/nomad/datamodel/metainfo/common_old.py
new file mode 100644
index 0000000000000000000000000000000000000000..cf74b07931bd9533db1d80be7f66d8a9c2063c93
--- /dev/null
+++ b/nomad/datamodel/metainfo/common_old.py
@@ -0,0 +1,1354 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public_old as public
+
+m_package = Package(
+ name='common_nomadmetainfo_json',
+ description='None',
+ a_legacy=LegacyDefinition(name='common.nomadmetainfo.json'))
+
+
+class settings_atom_in_molecule(MCategory):
+ '''
+ Parameters of an atom within a molecule.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_atom_in_molecule'))
+
+
+class settings_constraint(MCategory):
+ '''
+ Some parameters that describe a constraint
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_constraint'))
+
+
+class settings_interaction(MCategory):
+ '''
+ Some parameters that describe a bonded interaction.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_interaction'))
+
+
+class soap_parameter(MCategory):
+ '''
+ A soap parameter
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='soap_parameter'))
+
+
+class response_context(MSection):
+ '''
+ The top level context containing the reponse to an api query, when using jsonAPI they
+ are tipically in the meta part
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='response_context'))
+
+ shortened_meta_info = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A meta info whose corresponding data has been shortened
+ ''',
+ a_legacy=LegacyDefinition(name='shortened_meta_info'))
+
+ section_response_message = SubSection(
+ sub_section=SectionProxy('section_response_message'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_response_message'))
+
+
+class section_atom_type(MSection):
+ '''
+ Section describing a type of atom in the system.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atom_type'))
+
+ atom_type_charge = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='coulomb',
+ description='''
+ Charge of the atom type.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_type_charge'))
+
+ atom_type_mass = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='kilogram',
+ description='''
+ Mass of the atom type.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_type_mass'))
+
+ atom_type_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name (label) of the atom type.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_type_name'))
+
+
+class section_constraint(MSection):
+ '''
+ Section describing a constraint between arbitrary atoms.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_constraint'))
+
+ constraint_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_constraints', 'number_of_atoms_per_constraint'],
+ description='''
+ List of the indexes involved in this constraint. The fist atom has index 1, the
+ last number_of_topology_atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='constraint_atoms'))
+
+ constraint_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this constraint type. Valid names are described in the
+ [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/constraint-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='constraint_kind'))
+
+ constraint_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit constraint parameters for this kind of constraint (depending on the
+ constraint type, some might be given implicitly through other means).
+ ''',
+ a_legacy=LegacyDefinition(name='constraint_parameters'))
+
+ number_of_atoms_per_constraint = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms involved in this constraint.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_constraint'))
+
+ number_of_constraints = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of constraints of this type.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_constraints'))
+
+
+class section_dft_plus_u_orbital(MSection):
+ '''
+ Section for DFT+U-settings of a single orbital
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
+
+ dft_plus_u_orbital_atom = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: atom index (references index of atom_labels/atom_positions)
+ ''',
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_atom'))
+
+ dft_plus_u_orbital_J = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: value J (exchange interaction)
+ ''',
+ categories=[public.energy_value],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_J'))
+
+ dft_plus_u_orbital_label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ DFT+U-orbital setting: orbital label (normally (n,l)), notation: '3d', '4f', ...
+ ''',
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_label'))
+
+ dft_plus_u_orbital_U_effective = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: value U_{effective} (U-J), if implementation uses it
+ ''',
+ categories=[public.energy_value],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_U_effective'))
+
+ dft_plus_u_orbital_U = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ DFT+U-orbital setting: value U (on-site Coulomb interaction)
+ ''',
+ categories=[public.energy_value],
+ a_legacy=LegacyDefinition(name='dft_plus_u_orbital_U'))
+
+
+class section_excited_states(MSection):
+ '''
+ Excited states properties.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_excited_states'))
+
+ excitation_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_excited_states'],
+ description='''
+ Excitation energies.
+ ''',
+ categories=[public.energy_value],
+ a_legacy=LegacyDefinition(name='excitation_energies'))
+
+ number_of_excited_states = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of excited states.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_excited_states'))
+
+ oscillator_strengths = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_excited_states'],
+ description='''
+ Excited states oscillator strengths.
+ ''',
+ a_legacy=LegacyDefinition(name='oscillator_strengths'))
+
+ transition_dipole_moments = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_excited_states', 3],
+ description='''
+ Transition dipole moments.
+ ''',
+ a_legacy=LegacyDefinition(name='transition_dipole_moments'))
+
+
+class section_interaction(MSection):
+ '''
+ Section containing the description of a bonded interaction between arbitrary atoms.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_interaction'))
+
+ interaction_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_interactions', 'number_of_atoms_per_interaction'],
+ description='''
+ List of the indexes involved in this interaction. The fist atom has index 1, the
+ last atom index number_of_topology_atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='interaction_atoms'))
+
+ interaction_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this interaction type. Valid names are described in the
+ [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/interaction-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='interaction_kind'))
+
+ interaction_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit interaction parameters for this kind of interaction (depending on the
+ interaction_kind some might be given implicitly through other means).
+ ''',
+ a_legacy=LegacyDefinition(name='interaction_parameters'))
+
+ number_of_atoms_per_interaction = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms involved in this interaction.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_interaction'))
+
+ number_of_interactions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of interactions of this type.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_interactions'))
+
+
+class section_method_basis_set(MSection):
+ '''
+ This section contains the definition of the basis sets that are defined independently
+ of the atomic configuration.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method_basis_set'))
+
+ mapping_section_method_basis_set_atom_centered = Quantity(
+ type=np.dtype(np.int64),
+ shape=['number_of_basis_sets_atom_centered', 2],
+ description='''
+ Reference to an atom-centered basis set defined in section_basis_set_atom_centered
+ and to the atom kind as defined in section_method_atom_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_method_basis_set_atom_centered'))
+
+ mapping_section_method_basis_set_cell_associated = Quantity(
+ type=public.section_basis_set_cell_dependent,
+ shape=[],
+ description='''
+ Reference to a cell-associated basis set.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_method_basis_set_cell_associated'))
+
+ method_basis_set_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the use of the basis set, i.e, if it used for expanding a
+ wavefunction or an electron density. Allowed values are listed in the
+ [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/basis-set-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='method_basis_set_kind'))
+
+ number_of_basis_sets_atom_centered = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ String describing the use of the basis set, i.e, if it used for expanding a
+ wavefunction or an electron density. Allowed values are listed in the
+ [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/basis-set-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_basis_sets_atom_centered'))
+
+
+class section_molecule_constraint(MSection):
+ '''
+ Section describing a constraint between atoms within a molecule.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_molecule_constraint'))
+
+ molecule_constraint_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_molecule_constraints', 'number_of_atoms_per_molecule_constraint'],
+ description='''
+ List of the indexes involved in this constraint. The fist atom has index 1, the
+ last index is number_of_atoms_in_molecule.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_constraint_atoms'))
+
+ molecule_constraint_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this constraint type. Valid names are described in the
+ [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/constraint-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_constraint_kind'))
+
+ molecule_constraint_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit constraint parameters for this kind of constraint (depending on the
+ constraint type some might be given implicitly through other means).
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_constraint_parameters'))
+
+ number_of_atoms_per_molecule_constraint = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms, in this molecule, involved in this constraint.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_molecule_constraint'))
+
+ number_of_molecule_constraints = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of constraints of this type.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_molecule_constraints'))
+
+
+class section_molecule_interaction(MSection):
+ '''
+ Section describing a bonded interaction between atoms within a molecule.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_molecule_interaction'))
+
+ molecule_interaction_atoms = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_molecule_interactions', 'number_of_atoms_per_molecule_interaction'],
+ description='''
+ List of the indexes involved in this bonded interaction within a molecule. The
+ first atom has index 1, the last index is number_of_atoms_in_.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_interaction_atoms'))
+
+ molecule_interaction_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Short and unique name for this interaction type, used for bonded interactions for
+ atoms in a molecule. Valid names are described in the [interaction\\_kind wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/interaction-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_interaction_kind'))
+
+ molecule_interaction_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Explicit interaction parameters for this kind of interaction (depending on the
+ interaction type some might be given implicitly through other means), used for
+ bonded interactions for atoms in a molecule.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_interaction_parameters'))
+
+ number_of_atoms_per_molecule_interaction = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms, in this molecule, involved in this interaction.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_per_molecule_interaction'))
+
+ number_of_molecule_interactions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of bonded interactions of this type.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_molecule_interactions'))
+
+
+class section_molecule_type(MSection):
+ '''
+ Section describing a type of molecule in the system.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_molecule_type'))
+
+ atom_in_molecule_charge = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms_in_molecule'],
+ unit='coulomb',
+ description='''
+ Charge of each atom in the molecule.
+ ''',
+ categories=[settings_atom_in_molecule],
+ a_legacy=LegacyDefinition(name='atom_in_molecule_charge'))
+
+ atom_in_molecule_name = Quantity(
+ type=str,
+ shape=['number_of_atoms_in_molecule'],
+ description='''
+ Name (label) of each atom in the molecule.
+ ''',
+ categories=[settings_atom_in_molecule],
+ a_legacy=LegacyDefinition(name='atom_in_molecule_name'))
+
+ atom_in_molecule_to_atom_type_ref = Quantity(
+ type=Reference(SectionProxy('section_atom_type')),
+ shape=['number_of_atoms_in_molecule'],
+ description='''
+ Reference to the atom type of each atom in the molecule.
+ ''',
+ categories=[settings_atom_in_molecule],
+ a_legacy=LegacyDefinition(name='atom_in_molecule_to_atom_type_ref'))
+
+ molecule_type_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of the molecule.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_type_name'))
+
+ number_of_atoms_in_molecule = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in this molecule.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_in_molecule'))
+
+ section_molecule_constraint = SubSection(
+ sub_section=SectionProxy('section_molecule_constraint'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_molecule_constraint'))
+
+ section_molecule_interaction = SubSection(
+ sub_section=SectionProxy('section_molecule_interaction'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_molecule_interaction'))
+
+
+class section_response_message(MSection):
+ '''
+ Messages outputted by the program formatting the data in the current response
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_response_message'))
+
+ response_message_count = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ How many times this message was repeated
+ ''',
+ a_legacy=LegacyDefinition(name='response_message_count'))
+
+ response_message_level = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ level of the message: 0 fatal, 1 error, 2 warning, 3 debug
+ ''',
+ a_legacy=LegacyDefinition(name='response_message_level'))
+
+ response_message = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Message outputted by the program formatting the data in the current format
+ ''',
+ a_legacy=LegacyDefinition(name='response_message'))
+
+
+class section_soap_coefficients(MSection):
+ '''
+ Stores the soap coefficients for the pair of atoms given in
+ soap_coefficients_atom_pair.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_soap_coefficients'))
+
+ number_of_soap_coefficients = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of soap coefficients
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_soap_coefficients'))
+
+ soap_coefficients_atom_pair = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Pair of atoms described in the current section
+ ''',
+ a_legacy=LegacyDefinition(name='soap_coefficients_atom_pair'))
+
+ soap_coefficients = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_soap_coefficients'],
+ description='''
+ Compressed coefficient of the soap descriptor for the atom pair
+ soap_coefficients_atom_pair
+ ''',
+ a_legacy=LegacyDefinition(name='soap_coefficients'))
+
+
+class section_soap(MSection):
+ '''
+ Stores a soap descriptor for this configuration.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_soap'))
+
+ soap_angular_basis_L = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ angular basis L
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_angular_basis_L'))
+
+ soap_angular_basis_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ angular basis type
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_angular_basis_type'))
+
+ soap_kernel_adaptor = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ kernel adaptor
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_kernel_adaptor'))
+
+ soap_parameters_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Unique checksum of all the soap parameters (all those with abstract type
+ soap_parameter) with prefix psoap
+ ''',
+ a_legacy=LegacyDefinition(name='soap_parameters_gid'))
+
+ soap_radial_basis_integration_steps = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ radial basis integration steps
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_integration_steps'))
+
+ soap_radial_basis_mode = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ radial basis mode
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_mode'))
+
+ soap_radial_basis_n = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ radial basis N
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_n'))
+
+ soap_radial_basis_sigma = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ radial basis sigma
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_sigma'))
+
+ soap_radial_basis_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ radial basis type
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_basis_type'))
+
+ soap_radial_cutoff_center_weight = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ radial cutoff center weight
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_center_weight'))
+
+ soap_radial_cutoff_rc_width = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ radial cutoff width
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_rc_width'))
+
+ soap_radial_cutoff_rc = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ radial cutoff
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_rc'))
+
+ soap_radial_cutoff_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ radial cutoff type
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_radial_cutoff_type'))
+
+ soap_spectrum_2l1_norm = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ 2l1 norm spectrum
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_spectrum_2l1_norm'))
+
+ soap_spectrum_global = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ global spectrum
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_spectrum_global'))
+
+ soap_spectrum_gradients = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ gradients in specturm
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_spectrum_gradients'))
+
+ soap_type_list = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type list
+ ''',
+ categories=[soap_parameter],
+ a_legacy=LegacyDefinition(name='soap_type_list'))
+
+ section_soap_coefficients = SubSection(
+ sub_section=SectionProxy('section_soap_coefficients'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_soap_coefficients'))
+
+
+class section_topology(MSection):
+ '''
+ Section containing the definition of topology (connectivity among atoms in force
+ fileds), force field, and constraints of a system.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_topology'))
+
+ atom_to_molecule = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_topology_atoms', 2],
+ description='''
+ Table mapping atom to molecules: the first column is the index of the molecule and
+ the second column the index of the atom, signifying that the atom in the second
+ column belongs to the molecule in the first column in the same row.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_to_molecule'))
+
+ molecule_to_molecule_type_map = Quantity(
+ type=Reference(SectionProxy('section_molecule_type')),
+ shape=['number_of_topology_molecules'],
+ description='''
+ Mapping from molecules to molecule types.
+ ''',
+ a_legacy=LegacyDefinition(name='molecule_to_molecule_type_map'))
+
+ number_of_topology_atoms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in the system described by this topology.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_topology_atoms'))
+
+ number_of_topology_molecules = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of molecules in the system, as described by this topology.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_topology_molecules'))
+
+ topology_force_field_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A unique string idenfiying the force field defined in this section. Strategies to
+ define it are discussed in the
+ [topology\\_force\\_field\\_name](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/topology-force-field-name).
+ ''',
+ a_legacy=LegacyDefinition(name='topology_force_field_name'))
+
+ section_atom_type = SubSection(
+ sub_section=SectionProxy('section_atom_type'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_atom_type'))
+
+ section_constraint = SubSection(
+ sub_section=SectionProxy('section_constraint'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_constraint'))
+
+ section_interaction = SubSection(
+ sub_section=SectionProxy('section_interaction'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_interaction'))
+
+ section_molecule_type = SubSection(
+ sub_section=SectionProxy('section_molecule_type'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_molecule_type'))
+
+
+class section_method(public.section_method):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+ dft_plus_u_functional = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of DFT+U functional (such as DFT/DFT+U double-counting compensation). Valid
+ names are described in the [dft\\_plus\\_u\\_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/dft-
+ plus-u-functional).
+ ''',
+ a_legacy=LegacyDefinition(name='dft_plus_u_functional'))
+
+ dft_plus_u_projection_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ DFT+U: Type of orbitals used for projection in order to calculate occupation
+ numbers. Valid names are described in the [dft\\_plus\\_u\\_projection\\_type wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/dft-
+ plus-u-projection-type).
+ ''',
+ a_legacy=LegacyDefinition(name='dft_plus_u_projection_type'))
+
+ gw_bare_coulomb_cutofftype = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Cutoff type for the calculation of the bare Coulomb potential: none, 0d, 1d, 2d.
+ See Rozzi et al., PRB 73, 205119 (2006)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_bare_coulomb_cutofftype'))
+
+ gw_bare_coulomb_gmax = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='1 / meter',
+ description='''
+ Maximum G for the pw basis for the Coulomb potential.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_bare_coulomb_gmax'))
+
+ gw_basis_set = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Auxillary basis set used for non-local operators: mixed - mixed basis set, Kotani
+ and Schilfgaarde, Solid State Comm. 121, 461 (2002).
+ ''',
+ a_legacy=LegacyDefinition(name='gw_basis_set'))
+
+ gw_core_treatment = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ It specifies whether the core states are treated in the GW calculation: all - All
+ electron calculation; val - Valence electron only calculation; vab - Core
+ electrons are excluded from the mixed product basis; xal - All electron treatment
+ of the exchange self-energy only
+ ''',
+ a_legacy=LegacyDefinition(name='gw_core_treatment'))
+
+ gw_frequency_grid_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Frequency integration grid type for the correlational self energy: 'eqdis' -
+ equidistant frequencies from 0 to freqmax; 'gaulag' - Gauss-Laguerre quadrature
+ from 0 to infinity; 'gauleg' - Gauss-Legendre quadrature from 0 to freqmax;
+ 'gaule2' (default) - double Gauss-Legendre quadrature from 0 to freqmax and from
+ freqmax to infinity.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_grid_type'))
+
+ gw_max_frequency = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum frequency for the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_max_frequency'))
+
+ gw_mixed_basis_gmax = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='1 / meter',
+ description='''
+ Cut-off parameter for the truncation of the expansion of the plane waves in the
+ interstitial region.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_mixed_basis_gmax'))
+
+ gw_mixed_basis_lmax = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Maximum l value used for the radial functions within the muffin-tin.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_mixed_basis_lmax'))
+
+ gw_mixed_basis_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Eigenvalue threshold below which the egenvectors are discarded in the construction
+ of the radial basis set.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_mixed_basis_tolerance'))
+
+ gw_ngridq = Quantity(
+ type=np.dtype(np.int32),
+ shape=[3],
+ description='''
+ k/q-point grid size used in the GW calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_ngridq'))
+
+ gw_frequency_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number referring to the frequency used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_number'))
+
+ gw_frequency_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Values of the frequency used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_values'))
+
+ gw_frequency_weights = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Weights of the frequency used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_frequency_weights'))
+
+ gw_number_of_frequencies = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of frequency points used in the calculation of the self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_number_of_frequencies'))
+
+ gw_polarizability_number_of_empty_states = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of empty states used to compute the polarizability P
+ ''',
+ a_legacy=LegacyDefinition(name='gw_polarizability_number_of_empty_states'))
+
+ gw_qp_equation_treatment = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Methods to solve the quasi-particle equation: 'linearization', 'self-consistent'
+ ''',
+ a_legacy=LegacyDefinition(name='gw_qp_equation_treatment'))
+
+ gw_screened_coulomb_volume_average = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of volume averaging for the dynamically screened Coulomb potential: isotropic
+ - Simple averaging along a specified direction using only diagonal components of
+ the dielectric tensor; anisotropic - Anisotropic screening by C. Freysoldt et al.,
+ CPC 176, 1-13 (2007)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_screened_coulomb_volume_average'))
+
+ gw_screened_Coulomb = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Model used to calculate the dinamically-screened Coulomb potential: 'rpa' - Full-
+ frequency random-phase approximation; 'ppm' - Godby-Needs plasmon-pole model Godby
+ and Needs, Phys. Rev. Lett. 62, 1169 (1989); 'ppm_hl' - Hybertsen and Louie, Phys.
+ Rev. B 34, 5390 (1986); 'ppm_lh' - von der Linden and P. Horsh, Phys. Rev. B 37,
+ 8351 (1988); 'ppm_fe' - Farid and Engel, Phys. Rev. B 47,15931 (1993); 'cdm' -
+ Contour deformation method, Phys. Rev. B 67, 155208 (2003).)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_screened_Coulomb'))
+
+ gw_self_energy_c_analytical_continuation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Models for the correlation self-energy analytical continuation: 'pade' - Pade's
+ approximant (by H. J. Vidberg and J. W. Serence, J. Low Temp. Phys. 29, 179
+ (1977)); 'mpf' - Multi-Pole Fitting (by H. N Rojas, R. W. Godby and R. J. Needs,
+ Phys. Rev. Lett. 74, 1827 (1995)); 'cd' - contour deformation; 'ra' - real axis
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c_analytical_continuation'))
+
+ gw_self_energy_c_number_of_empty_states = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of empty states to be used to calculate the correlation self energy.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c_number_of_empty_states'))
+
+ gw_self_energy_c_number_of_poles = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of poles used in the analytical continuation.
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c_number_of_poles'))
+
+ gw_self_energy_singularity_treatment = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Treatment of the integrable singular terms in the calculation of the self energy.
+ Values: 'mpb' - Auxiliary function method by S. Massidda, M. Posternak, and A.
+ Baldereschi, PRB 48, 5058 (1993); 'crg' - Auxiliary function method by P. Carrier,
+ S. Rohra, and A. Goerling, PRB 75, 205126 (2007).
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_singularity_treatment'))
+
+ gw_starting_point = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Exchange-correlation functional of the ground-state calculation. See XC_functional
+ list at https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional
+ ''',
+ a_legacy=LegacyDefinition(name='gw_starting_point'))
+
+ gw_type_test = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ GW methodology: exciting test variable
+ ''',
+ a_legacy=LegacyDefinition(name='gw_type_test'))
+
+ gw_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ GW methodology: G0W0; ev-scGW: (eigenvalues self-consistent GW) – Phys.Rev.B 34,
+ 5390 (1986); qp-scGW: (quasi-particle self-consistent GW) – Phys. Rev. Lett. 96,
+ 226402 (2006) scGW0: (self-consistent G with fixed W0) – Phys.Rev.B 54, 8411
+ (1996); scG0W: (self-consistent W with fixed G0); scGW: (self-consistent GW) –
+ Phys. Rev. B 88, 075105 (2013)
+ ''',
+ a_legacy=LegacyDefinition(name='gw_type'))
+
+ method_to_topology_ref = Quantity(
+ type=Reference(SectionProxy('section_topology')),
+ shape=[],
+ description='''
+ Reference to the topology and force fields to be used.
+ ''',
+ a_legacy=LegacyDefinition(name='method_to_topology_ref'))
+
+ section_dft_plus_u_orbital = SubSection(
+ sub_section=SectionProxy('section_dft_plus_u_orbital'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_dft_plus_u_orbital'))
+
+ section_method_basis_set = SubSection(
+ sub_section=SectionProxy('section_method_basis_set'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method_basis_set'))
+
+
+class section_single_configuration_calculation(public.section_single_configuration_calculation):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ energy_C_mGGA = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Component of the correlation (C) energy at the GGA (or MetaGGA) level using the
+ self-consistent density of the target XC functional (full unscaled value, i.e.,
+ not scaled due to exact-exchange mixing).
+ ''',
+ categories=[public.energy_component, public.energy_value, public.energy_type_C],
+ a_legacy=LegacyDefinition(name='energy_C_mGGA'))
+
+ energy_reference_fermi = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Fermi energy (separates occupied from unoccupied single-particle states in metals)
+ ''',
+ categories=[public.energy_type_reference, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_reference_fermi'))
+
+ energy_reference_highest_occupied = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Highest occupied single-particle state energy (in insulators or HOMO energy in
+ finite systems)
+ ''',
+ categories=[public.energy_type_reference, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_reference_highest_occupied'))
+
+ energy_reference_lowest_unoccupied = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Lowest unoccupied single-particle state energy (in insulators or LUMO energy in
+ finite systems)
+ ''',
+ categories=[public.energy_type_reference, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_reference_lowest_unoccupied'))
+
+ energy_X_mGGA_scaled = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Component of the exchange (X) energy at the GGA (or MetaGGA) level, using the self
+ consistent density of the target functional, scaled accordingly to the mixing
+ parameter.
+ ''',
+ categories=[public.energy_component, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_X_mGGA_scaled'))
+
+ energy_X_mGGA = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Component of the exchange (X) energy at the GGA (or MetaGGA) level using the self
+ consistent density of the target functional (full unscaled value, i.e., not scaled
+ due to exact-exchange mixing).
+ ''',
+ categories=[public.energy_type_X, public.energy_component, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_X_mGGA'))
+
+ gw_fermi_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ GW Fermi energy
+ ''',
+ a_legacy=LegacyDefinition(name='gw_fermi_energy'))
+
+ gw_fundamental_gap = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ GW fundamental band gap
+ ''',
+ a_legacy=LegacyDefinition(name='gw_fundamental_gap'))
+
+ gw_optical_gap = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ GW optical band gap
+ ''',
+ a_legacy=LegacyDefinition(name='gw_optical_gap'))
+
+ gw_self_energy_c = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Diagonal matrix elements of the correlation self-energy
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_c'))
+
+ gw_self_energy_x = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Diagonal matrix elements of the exchange self-energy
+ ''',
+ a_legacy=LegacyDefinition(name='gw_self_energy_x'))
+
+ gw_xc_potential = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Diagonal matrix elements of the exchange-correlation potential
+ ''',
+ a_legacy=LegacyDefinition(name='gw_xc_potential'))
+
+ section_excited_states = SubSection(
+ sub_section=SectionProxy('section_excited_states'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_excited_states'))
+
+
+class section_scf_iteration(public.section_scf_iteration):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+ energy_reference_fermi_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Fermi energy (separates occupied from unoccupied single-particle states in metals)
+ during the self-consistent field (SCF) iterations.
+ ''',
+ categories=[public.energy_type_reference, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_reference_fermi_iteration'))
+
+ energy_reference_highest_occupied_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Highest occupied single-particle state energy (in insulators or HOMO energy in
+ finite systems) during the self-consistent field (SCF) iterations.
+ ''',
+ categories=[public.energy_type_reference, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_reference_highest_occupied_iteration'))
+
+ energy_reference_lowest_unoccupied_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ unit='joule',
+ description='''
+ Lowest unoccupied single-particle state energy (in insulators or LUMO energy in
+ finite systems) during the self-consistent field (SCF) iterations.
+ ''',
+ categories=[public.energy_type_reference, public.energy_value],
+ a_legacy=LegacyDefinition(name='energy_reference_lowest_unoccupied_iteration'))
+
+
+class section_eigenvalues(public.section_eigenvalues):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_eigenvalues'))
+
+ gw_qp_linearization_prefactor = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ description='''
+ Linearization prefactor
+ ''',
+ a_legacy=LegacyDefinition(name='gw_qp_linearization_prefactor'))
+
+
+class section_system(public.section_system):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
+
+ number_of_electrons = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels'],
+ description='''
+ Number of electrons in system
+ ''',
+ categories=[public.configuration_core],
+ a_legacy=LegacyDefinition(name='number_of_electrons'))
+
+ topology_ref = Quantity(
+ type=Reference(SectionProxy('section_topology')),
+ shape=[],
+ description='''
+ Reference to the topology used for this system; if not given, the trivial topology
+ should be assumed.
+ ''',
+ a_legacy=LegacyDefinition(name='topology_ref'))
+
+ is_representative = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Most systems in a run are only minor variations of each other. Systems marked
+ representative where chosen to be representative for all systems in the run.
+ ''',
+ a_legacy=LegacyDefinition(name='is_representative'))
+
+ section_soap = SubSection(
+ sub_section=SectionProxy('section_soap'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_soap'))
+
+
+class section_run(public.section_run):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
+
+ section_topology = SubSection(
+ sub_section=SectionProxy('section_topology'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_topology'))
+
+
+m_package.__init_metainfo__()
diff --git a/nomad/datamodel/metainfo/general_qcms.py b/nomad/datamodel/metainfo/common_qcms.py
similarity index 100%
rename from nomad/datamodel/metainfo/general_qcms.py
rename to nomad/datamodel/metainfo/common_qcms.py
diff --git a/nomad/datamodel/metainfo/general.py b/nomad/datamodel/metainfo/general.py
index 0606de2a91d0b262a2477d9ef161cee4cb28d7d7..3bee89a6a3cdb1d45c6bfdac7906fa458b8266ef 100644
--- a/nomad/datamodel/metainfo/general.py
+++ b/nomad/datamodel/metainfo/general.py
@@ -16,164 +16,10 @@
# limitations under the License.
#
-import numpy as np # pylint: disable=unused-import
-import typing # pylint: disable=unused-import
-from nomad.metainfo import ( # pylint: disable=unused-import
- MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
- Reference
-)
-from nomad.metainfo.legacy import LegacyDefinition
+# This is just for backward compatibility of old imports. All definitions are now in common_dft
+from nomad.metainfo import Package
-m_package = Package(
- name='general_nomadmetainfo_json',
- description='None',
- a_legacy=LegacyDefinition(name='general.nomadmetainfo.json'))
+from .common_dft import *
-
-class section_entry_info(MSection):
- '''
- General information about this entry that is independent from its domain, field, or
- used parser
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_entry_info'))
-
- entry_upload_time = Quantity(
- type=np.dtype(np.int64),
- shape=[],
- description='''
- Upload datetime, given as total number of seconds is the elapsed since the unix
- epoch (1 January 1970)
- ''',
- a_legacy=LegacyDefinition(name='entry_upload_time'))
-
- entry_uploader_name = Quantity(
- type=str,
- shape=[],
- description='''
- Name of the uploader, given as lastname, firstname.
- ''',
- a_legacy=LegacyDefinition(name='entry_uploader_name'))
-
- entry_uploader_id = Quantity(
- type=str,
- shape=[],
- description='''
- The id of the uploader.
- ''',
- a_legacy=LegacyDefinition(name='entry_uploader_id'))
-
- upload_id = Quantity(
- type=str,
- shape=[],
- description='''
- Nomad upload id
- ''',
- a_legacy=LegacyDefinition(name='upload_id'))
-
- calc_id = Quantity(
- type=str,
- shape=[],
- description='''
- Nomad calc id.
- ''',
- a_legacy=LegacyDefinition(name='calc_id'))
-
- calc_hash = Quantity(
- type=str,
- shape=[],
- description='''
- Calculation hash based on raw file contents.
- ''',
- a_legacy=LegacyDefinition(name='calc_hash'))
-
- mainfile = Quantity(
- type=str,
- shape=[],
- description='''
- Path to the main file within the upload.
- ''',
- a_legacy=LegacyDefinition(name='mainfile'))
-
- parser_name = Quantity(
- type=str,
- shape=[],
- description='''
- Name of the parser used to extract this information.
- ''',
- a_legacy=LegacyDefinition(name='parser_name'))
-
- filepaths = Quantity(
- type=str,
- shape=['number_of_files'],
- description='''
- Filepaths of files that belong to this entry, i.e. files in the same directory.
- Filepaths are relative to the upload.
- ''',
- a_legacy=LegacyDefinition(name='filepaths'))
-
- number_of_files = Quantity(
- type=int,
- shape=[],
- description='''
- Number of files that belong to this entry.
- ''',
- a_legacy=LegacyDefinition(name='number_of_files'))
-
- section_archive_processing_info = SubSection(
- sub_section=SectionProxy('section_archive_processing_info'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_archive_processing_info'))
-
-
-class section_archive_processing_info(MSection):
- '''
- Information about the used archive processing steps and their execution.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_archive_processing_info'))
-
- archive_processor_name = Quantity(
- type=str,
- shape=[],
- description='''
- Name of the applied archive processing program.
- ''',
- a_legacy=LegacyDefinition(name='archive_processor_name'))
-
- archive_processor_error = Quantity(
- type=str,
- shape=[],
- description='''
- The main error during execution of the archive processing program that failed the
- program.
- ''',
- a_legacy=LegacyDefinition(name='archive_processor_error'))
-
- number_of_archive_processor_warnings = Quantity(
- type=int,
- shape=[],
- description='''
- Number of warnings during execution of the archive processing program.
- ''',
- a_legacy=LegacyDefinition(name='number_of_archive_processor_warnings'))
-
- archive_processor_warnings = Quantity(
- type=str,
- shape=['number_of_archive_processor_warnings'],
- description='''
- Warnings during execution of the archive processing program.
- ''',
- a_legacy=LegacyDefinition(name='archive_processor_warnings'))
-
- archive_processor_status = Quantity(
- type=str,
- shape=[],
- description='''
- Status returned by archive processing program.
- ''',
- a_legacy=LegacyDefinition(name='archive_processor_status'))
-
-
-m_package.__init_metainfo__()
+m_package = Package(name='general_nomadmetainfo_json')
diff --git a/nomad/datamodel/metainfo/public.py b/nomad/datamodel/metainfo/public.py
index fc30912cc763d2a4b3a88db438fe36e2f2bc05ca..cdf532b9e7ca18bf09312662628bb6ce62a87bcb 100644
--- a/nomad/datamodel/metainfo/public.py
+++ b/nomad/datamodel/metainfo/public.py
@@ -16,5926 +16,6 @@
# limitations under the License.
#
-import numpy as np # pylint: disable=unused-import
-import typing # pylint: disable=unused-import
-from nomad.metainfo import ( # pylint: disable=unused-import
- MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
- Reference, MEnum, derived
-)
-from nomad.metainfo.search_extension import Search
-from nomad.metainfo.legacy import LegacyDefinition
+# This is just for backward compatibility of old imports. All definitions are now in common_dft
-
-m_package = Package(
- name='public_nomadmetainfo_json',
- description='None',
- a_legacy=LegacyDefinition(name='public.nomadmetainfo.json'))
-
-
-class fast_access(MCategory):
- '''
- Used to mark archive objects that need to be stored in a fast 2nd-tier storage
- medium, because they are frequently accessed via archive API.
-
- If applied to a sub_section, the section will be added to the fast storage. Currently
- this only works for *root* sections that are sub_sections of `EntryArchive`.
-
- If applied to a reference types quantity, the referenced section will also be added
- to the fast storage, regardless if the referenced section has the category or not.
- '''
-
- m_def = Category()
-
-
-class accessory_info(MCategory):
- '''
- Information that *in theory* should not affect the results of the calculations (e.g.,
- timing).
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='accessory_info'))
-
-
-class atom_forces_type(MCategory):
- '''
- The types of forces acting on the atoms (i.e., minus derivatives of the specific type
- of energy with respect to the atom position).
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='atom_forces_type'))
-
-
-class basis_set_description(MCategory):
- '''
- One of the parts building the basis set of the system (e.g., some atom-centered basis
- set, plane-waves or both).
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='basis_set_description'))
-
-
-class configuration_core(MCategory):
- '''
- Properties defining the current configuration.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='configuration_core'))
-
-
-class conserved_quantity(MCategory):
- '''
- A quantity that is preserved during the time propagation (for example,
- kinetic+potential energy during NVE).
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='conserved_quantity'))
-
-
-class energy_value(MCategory):
- '''
- This metadata stores an energy value.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='energy_value'))
-
-
-class error_estimate_contribution(MCategory):
- '''
- An estimate of a partial quantity contributing to the error for a given quantity.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='error_estimate_contribution'))
-
-
-class message_debug(MCategory):
- '''
- A debugging message of the computational program.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='message_debug'))
-
-
-class parsing_message_debug(MCategory):
- '''
- This field is used for debugging messages of the parsing program.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='parsing_message_debug'))
-
-
-class scf_info(MCategory):
- '''
- Contains information on the self-consistent field (SCF) procedure, i.e. the number of
- SCF iterations (number_of_scf_iterations) or a section_scf_iteration section with
- detailed information on the SCF procedure of specified quantities.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='scf_info'))
-
-
-class settings_numerical_parameter(MCategory):
- '''
- A parameter that can influence the convergence, but not the physics (unlike
- settings_physical_parameter)
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_numerical_parameter'))
-
-
-class settings_physical_parameter(MCategory):
- '''
- A parameter that defines the physical model used. Use settings_numerical_parameter for
- parameters that that influence only the convergence/accuracy.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_physical_parameter'))
-
-
-class settings_potential_energy_surface(MCategory):
- '''
- Contains parameters that control the potential energy surface.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_potential_energy_surface'))
-
-
-class settings_run(MCategory):
- '''
- Contains parameters that control the whole run (but not the *single configuration
- calculation*, see section_single_configuration_calculation).
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_run'))
-
-
-class settings_sampling(MCategory):
- '''
- Contains parameters controlling the sampling.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_sampling'))
-
-
-class settings_scf(MCategory):
- '''
- Contains parameters connected with the convergence of the self-consistent field (SCF)
- iterations.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_scf'))
-
-
-class settings_smearing(MCategory):
- '''
- Contain parameters that control the smearing of the orbital occupation at finite
- electronic temperatures.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_smearing'))
-
-
-class settings_stress_tensor(MCategory):
- '''
- Settings to calculate the stress tensor (stress_tensor) consistent with the total
- energy of the system given in energy_total.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='settings_stress_tensor'))
-
-
-class stress_tensor_type(MCategory):
- '''
- Contains the final value of the default stress tensor (stress_tensor) and/or the value
- of the stress tensor (stress_tensor_value) of the kind defined in stress_tensor_kind.
- '''
-
- m_def = Category(
- a_legacy=LegacyDefinition(name='stress_tensor_type'))
-
-
-class energy_component_per_atom(MCategory):
- '''
- A value of an energy component per atom, concurring in defining the total energy per
- atom.
- '''
-
- m_def = Category(
- categories=[energy_value],
- a_legacy=LegacyDefinition(name='energy_component_per_atom'))
-
-
-class energy_component(MCategory):
- '''
- A value of an energy component, expected to be an extensive property.
- '''
-
- m_def = Category(
- categories=[energy_value],
- a_legacy=LegacyDefinition(name='energy_component'))
-
-
-class energy_type_reference(MCategory):
- '''
- This metadata stores an energy used as reference point.
- '''
-
- m_def = Category(
- categories=[energy_value],
- a_legacy=LegacyDefinition(name='energy_type_reference'))
-
-
-class error_estimate(MCategory):
- '''
- An estimate of the error on the converged (final) value.
- '''
-
- m_def = Category(
- categories=[error_estimate_contribution],
- a_legacy=LegacyDefinition(name='error_estimate'))
-
-
-class message_info(MCategory):
- '''
- An information message of the computational program.
- '''
-
- m_def = Category(
- categories=[message_debug],
- a_legacy=LegacyDefinition(name='message_info'))
-
-
-class parallelization_info(MCategory):
- '''
- Contains information on the parallelization of the program, i.e. which parallel
- programming language was used and its version, how many cores had been working on the
- calculation and the flags and parameters needed to run the parallelization of the
- code.
- '''
-
- m_def = Category(
- categories=[accessory_info],
- a_legacy=LegacyDefinition(name='parallelization_info'))
-
-
-class parsing_message_info(MCategory):
- '''
- This field is used for info messages of the parsing program.
- '''
-
- m_def = Category(
- categories=[parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_info'))
-
-
-class program_info(MCategory):
- '''
- Contains information on the program that generated the data, i.e. the program_name,
- program_version, program_compilation_host and program_compilation_datetime as direct
- children of this field.
- '''
-
- m_def = Category(
- categories=[accessory_info],
- a_legacy=LegacyDefinition(name='program_info'))
-
-
-class settings_geometry_optimization(MCategory):
- '''
- Contains parameters controlling the geometry optimization.
- '''
-
- m_def = Category(
- categories=[settings_sampling],
- a_legacy=LegacyDefinition(name='settings_geometry_optimization'))
-
-
-class settings_k_points(MCategory):
- '''
- Contains parameters that control the $k$-point mesh.
- '''
-
- m_def = Category(
- categories=[settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_k_points'))
-
-
-class settings_metadynamics(MCategory):
- '''
- Contains parameters that control the metadynamics sampling.
- '''
-
- m_def = Category(
- categories=[settings_sampling],
- a_legacy=LegacyDefinition(name='settings_metadynamics'))
-
-
-class settings_molecular_dynamics(MCategory):
- '''
- Contains parameters that control the molecular dynamics sampling.
- '''
-
- m_def = Category(
- categories=[settings_sampling],
- a_legacy=LegacyDefinition(name='settings_molecular_dynamics'))
-
-
-class settings_Monte_Carlo(MCategory):
- '''
- Contains parameters that control the Monte-Carlo sampling.
- '''
-
- m_def = Category(
- categories=[settings_sampling],
- a_legacy=LegacyDefinition(name='settings_Monte_Carlo'))
-
-
-class settings_XC(MCategory):
- '''
- Contains parameters connected with the definition of the exchange-correlation (XC)
- *method*. Here, the term *method* is a more general concept than just *functionals*
- and include, e.g., post Hartree-Fock methods, too.
- '''
-
- m_def = Category(
- categories=[settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_XC'))
-
-
-class time_info(MCategory):
- '''
- Stores information on the date and timings of the calculation. They are useful for,
- e.g., debugging or visualization purposes.
- '''
-
- m_def = Category(
- categories=[accessory_info],
- a_legacy=LegacyDefinition(name='time_info'))
-
-
-class energy_total_potential_per_atom(MCategory):
- '''
- A value of the total potential energy per atom. Note that a direct comparison may not
- be possible because of a difference in the methods for computing total energies and
- numerical implementations of various codes might leads to different energy zeros (see
- section_energy_code_independent for a code-independent definition of the energy).
- '''
-
- m_def = Category(
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_total_potential_per_atom'))
-
-
-class energy_total_potential(MCategory):
- '''
- A value of the total potential energy. Note that a direct comparison may not be
- possible because of a difference in the methods for computing total energies and
- numerical implementations of various codes might leads to different energy zeros (see
- section_energy_code_independent for a code-independent definition of the energy).
- '''
-
- m_def = Category(
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_total_potential'))
-
-
-class energy_type_C(MCategory):
- '''
- This metadata stores the correlation (C) energy.
- '''
-
- m_def = Category(
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_type_C'))
-
-
-class energy_type_van_der_Waals(MCategory):
- '''
- This metadata stores the converged van der Waals energy.
- '''
-
- m_def = Category(
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_type_van_der_Waals'))
-
-
-class energy_type_XC(MCategory):
- '''
- This metadata stores the exchange-correlation (XC) energy.
- '''
-
- m_def = Category(
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_type_XC'))
-
-
-class energy_type_X(MCategory):
- '''
- This metadata stores the exchange (X) energy.
- '''
-
- m_def = Category(
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_type_X'))
-
-
-class message_warning(MCategory):
- '''
- A warning message of the computational program.
- '''
-
- m_def = Category(
- categories=[message_info, message_debug],
- a_legacy=LegacyDefinition(name='message_warning'))
-
-
-class parsing_message_warning(MCategory):
- '''
- This field is used for warning messages of the parsing program.
- '''
-
- m_def = Category(
- categories=[parsing_message_info, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_warning'))
-
-
-class settings_barostat(MCategory):
- '''
- Contains parameters controlling the barostat in a molecular dynamics calculation.
- '''
-
- m_def = Category(
- categories=[settings_sampling, settings_molecular_dynamics],
- a_legacy=LegacyDefinition(name='settings_barostat'))
-
-
-class settings_integrator(MCategory):
- '''
- Contains parameters that control the molecular dynamics (MD) integrator.
- '''
-
- m_def = Category(
- categories=[settings_sampling, settings_molecular_dynamics],
- a_legacy=LegacyDefinition(name='settings_integrator'))
-
-
-class settings_post_hartree_fock(MCategory):
- '''
- Contains parameters for the post Hartree-Fock method.
- '''
-
- m_def = Category(
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_post_hartree_fock'))
-
-
-class settings_relativity(MCategory):
- '''
- Contains parameters and information connected with the relativistic treatment used in
- the calculation.
- '''
-
- m_def = Category(
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_relativity'))
-
-
-class settings_self_interaction_correction(MCategory):
- '''
- Contains parameters and information connected with the self-interaction correction
- (SIC) method being used in self_interaction_correction_method.
- '''
-
- m_def = Category(
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_self_interaction_correction'))
-
-
-class settings_thermostat(MCategory):
- '''
- Contains parameters that control the thermostat in the molecular dynamics (MD)
- calculations.
- '''
-
- m_def = Category(
- categories=[settings_sampling, settings_molecular_dynamics],
- a_legacy=LegacyDefinition(name='settings_thermostat'))
-
-
-class settings_van_der_Waals(MCategory):
- '''
- Contain parameters and information connected with the Van der Waals treatment used in
- the calculation to compute the Van der Waals energy (energy_van_der_Waals).
- '''
-
- m_def = Category(
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_van_der_Waals'))
-
-
-class settings_XC_functional(MCategory):
- '''
- Contain parameters connected with the definition of the exchange-correlation (XC)
- functional (see section_XC_functionals and XC_functional).
- '''
-
- m_def = Category(
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_XC_functional'))
-
-
-class message_error(MCategory):
- '''
- An error message of the computational program.
- '''
-
- m_def = Category(
- categories=[message_info, message_debug, message_warning],
- a_legacy=LegacyDefinition(name='message_error'))
-
-
-class parsing_message_error(MCategory):
- '''
- This field is used for error messages of the parsing program.
- '''
-
- m_def = Category(
- categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_error'))
-
-
-class settings_coupled_cluster(MCategory):
- '''
- Contains parameters for the coupled-cluster method (CC) in the post Hartree-Fock step.
- '''
-
- m_def = Category(
- categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_coupled_cluster'))
-
-
-class settings_GW(MCategory):
- '''
- Contains parameters for the GW-method in the post Hartree-Fock step, that expands the
- self-energy in terms of the single particle Green's function $G$ and the screened
- Coulomb interaction $W$.
- '''
-
- m_def = Category(
- categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_GW'))
-
-
-class settings_MCSCF(MCategory):
- '''
- Contains parameters for the multi-configurational self-consistent-field (MCSCF)
- method.
- '''
-
- m_def = Category(
- categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_MCSCF'))
-
-
-class settings_moller_plesset_perturbation_theory(MCategory):
- '''
- Contains parameters for Møller–Plesset perturbation theory.
- '''
-
- m_def = Category(
- categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_moller_plesset_perturbation_theory'))
-
-
-class settings_multi_reference(MCategory):
- '''
- Contains parameters for the multi-reference single and double configuration
- interaction method.
- '''
-
- m_def = Category(
- categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='settings_multi_reference'))
-
-
-class archive_context(MSection):
- '''
- Contains information relating to an archive.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='archive_context'))
-
- archive_gid = Quantity(
- type=str,
- shape=[],
- description='''
- unique identifier of an archive.
- ''',
- a_legacy=LegacyDefinition(name='archive_gid'))
-
-
-class calculation_context(MSection):
- '''
- Contains information relating to a calculation.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='calculation_context'))
-
- calculation_gid = Quantity(
- type=str,
- shape=[],
- description='''
- unique identifier of a calculation.
- ''',
- a_legacy=LegacyDefinition(name='calculation_gid'))
-
-
-class section_atom_projected_dos(MSection):
- '''
- Section collecting the information on an atom projected density of states (DOS)
- evaluation.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atom_projected_dos'))
-
- atom_projected_dos_energies = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atom_projected_dos_values'],
- unit='joule',
- description='''
- Array containing the set of discrete energy values for the atom-projected density
- (electronic-energy) of states (DOS).
- ''',
- a_legacy=LegacyDefinition(name='atom_projected_dos_energies'))
-
- atom_projected_dos_lm = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_lm_atom_projected_dos', 2],
- description='''
- Tuples of $l$ and $m$ values for which atom_projected_dos_values_lm are given. For
- the quantum number $l$ the conventional meaning of azimuthal quantum number is
- always adopted. For the integer number $m$, besides the conventional use as
- magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
- different conventions is accepted (see the [m_kind wiki
- page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
- The adopted convention is specified by atom_projected_dos_m_kind.
- ''',
- a_legacy=LegacyDefinition(name='atom_projected_dos_lm'))
-
- atom_projected_dos_m_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String describing what the integer numbers of $m$ in atom_projected_dos_lm mean.
- The allowed values are listed in the [m_kind wiki
- page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
- ''',
- a_legacy=LegacyDefinition(name='atom_projected_dos_m_kind'))
-
- atom_projected_dos_values_lm = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_lm_atom_projected_dos', 'number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
- description='''
- Values correspond to the number of states for a given energy (the set of discrete
- energy values is given in atom_projected_dos_energies) divided into contributions
- from each $l,m$ channel for the atom-projected density (electronic-energy) of
- states. Here, there are as many atom-projected DOS as the number_of_atoms, the
- list of labels of the atoms and their meanings are in atom_labels.
- ''',
- a_legacy=LegacyDefinition(name='atom_projected_dos_values_lm'))
-
- atom_projected_dos_values_total = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
- description='''
- Values correspond to the number of states for a given energy (the set of discrete
- energy values is given in atom_projected_dos_energies) divided into contributions
- summed up over all $l$ channels for the atom-projected density (electronic-energy)
- of states (DOS). Here, there are as many atom-projected DOS as the
- number_of_atoms, the list of labels of the atoms and their meanings are in
- atom_labels.
- ''',
- a_legacy=LegacyDefinition(name='atom_projected_dos_values_total'))
-
- number_of_atom_projected_dos_values = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of energy values for the atom-projected density of states (DOS)
- based on atom_projected_dos_values_lm and atom_projected_dos_values_total.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atom_projected_dos_values'))
-
- number_of_lm_atom_projected_dos = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $l$, $m$ combinations for the atom projected density of states
- (DOS) defined in section_atom_projected_dos.
- ''',
- a_legacy=LegacyDefinition(name='number_of_lm_atom_projected_dos'))
-
-
-class section_atomic_multipoles(MSection):
- '''
- Section describing multipoles (charges/monopoles, dipoles, quadrupoles, ...) for each
- atom.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atomic_multipoles'))
-
- atomic_multipole_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String describing the method used to obtain the electrostatic multipoles
- (including the electric charge, dipole, etc.) for each atom. Such multipoles
- require a charge-density partitioning scheme, specified by the value of this
- metadata. Allowed values are listed in the [atomic_multipole_kind wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/atomic-
- multipole-kind).
- ''',
- a_legacy=LegacyDefinition(name='atomic_multipole_kind'))
-
- atomic_multipole_lm = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_lm_atomic_multipoles', 2],
- description='''
- Tuples of $l$ and $m$ values for which the atomic multipoles (including the
- electric charge, dipole, etc.) are given. The method used to obtain the multipoles
- is specified by atomic_multipole_kind. The meaning of the integer number $l$ is
- monopole/charge for $l=0$, dipole for $l=1$, quadrupole for $l=2$, etc. The
- meaning of the integer numbers $m$ is specified by atomic_multipole_m_kind.
- ''',
- a_legacy=LegacyDefinition(name='atomic_multipole_lm'))
-
- atomic_multipole_m_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String describing the definition for each integer number $m$ in
- atomic_multipole_lm. Allowed values are listed in the [m_kind wiki
- page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
- ''',
- a_legacy=LegacyDefinition(name='atomic_multipole_m_kind'))
-
- atomic_multipole_values = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_lm_atomic_multipoles', 'number_of_atoms'],
- description='''
- Value of the multipoles (including the monopole/charge for $l$ = 0, the dipole for
- $l$ = 1, etc.) for each atom, calculated as described in atomic_multipole_kind.
- ''',
- a_legacy=LegacyDefinition(name='atomic_multipole_values'))
-
- number_of_lm_atomic_multipoles = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $l$, $m$ combinations for atomic multipoles
- atomic_multipole_lm.
- ''',
- a_legacy=LegacyDefinition(name='number_of_lm_atomic_multipoles'))
-
-
-class section_basis_functions_atom_centered(MSection):
- '''
- This section contains the description of the basis functions (at least one function)
- of the (atom-centered) basis set defined in section_basis_set_atom_centered.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))
-
-
-class section_basis_set_atom_centered(MSection):
- '''
- This section describes the atom-centered basis set. The main contained information is
- a short, non unique but human-interpretable, name for identifying the basis set
- (basis_set_atom_centered_short_name), a longer, unique name
- (basis_set_atom_centered_unique_name), the atomic number of the atomic species the
- basis set is meant for (basis_set_atom_number), and a list of actual basis functions
- in the section_basis_functions_atom_centered section.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
-
- basis_set_atom_centered_ls = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_kinds_in_basis_set_atom_centered'],
- description='''
- Azimuthal quantum number ($l$) values (of the angular part given by the spherical
- harmonic $Y_{lm}$) of the atom-centered basis function defined in the current
- section_basis_set_atom_centered.
- ''',
- a_legacy=LegacyDefinition(name='basis_set_atom_centered_ls'))
-
- basis_set_atom_centered_radial_functions = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_kinds_in_basis_set_atom_centered', 401, 5],
- description='''
- Values of the radial function of the different basis function kinds. The values
- are numerically tabulated on a default 0.01-nm equally spaced grid from 0 to 4 nm.
- The 5 tabulated values are $r$, $f(r)$, $f'(r)$, $f(r) \\cdot r$,
- $\\frac{d}{dr}(f(r) \\cdot r)$.
- ''',
- a_legacy=LegacyDefinition(name='basis_set_atom_centered_radial_functions'))
-
- basis_set_atom_centered_short_name = Quantity(
- type=str,
- shape=[],
- description='''
- Code-specific, but explicative, base name for the basis set (not unique). Details
- are explained in the [basis_set_atom_centered_short_name wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
- set-atom-centered-short-name), this name should not contain the *atom kind* (to
- simplify the use of a single name for multiple elements).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_atom_centered_short_name'))
-
- basis_set_atom_centered_unique_name = Quantity(
- type=str,
- shape=[],
- description='''
- Code-specific, but explicative, base name for the basis set (not unique). This
- string starts with basis_set_atom_centered_short_name. If the basis set defined in
- this section_basis_set_atom_centered is not identical to the default definition
- (stored in a database) of the basis set with the same name stored in a database,
- then the string is extended by 10 identifiable characters as explained in the
- [basis_set_atom_centered_name wiki page](https://gitlab.mpcdf.mpg.de/nomad-
- lab/nomad-meta-info/wikis/metainfo/basis-set-atom-centered-unique-name). The
- reason for this procedure is that often atom-centered basis sets are obtained by
- fine tuning basis sets provided by the code developers or other sources. Each
- basis sets, which has normally a standard name, often reported in publications,
- has also several parameters that can be tuned. This metadata tries to keep track
- of the original basis set and its modifications. This string here defined should
- not contain the *atom kind* for which this basis set is intended for, in order to
- simplify the use of a single name for multiple *atom kinds* (see atom_labels for
- the actual meaning of *atom kind*).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_atom_centered_unique_name'))
-
- basis_set_atom_number = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Atomic number (i.e., number of protons) of the atom for which this basis set is
- constructed (0 means unspecified or a pseudo atom).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_atom_number'))
-
- number_of_basis_functions_in_basis_set_atom_centered = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of different basis functions in a section_basis_set_atom_centered
- section. This equals the number of actual coefficients that are specified when
- using this basis set.
- ''',
- a_legacy=LegacyDefinition(name='number_of_basis_functions_in_basis_set_atom_centered'))
-
- number_of_kinds_in_basis_set_atom_centered = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of different *kinds* of radial basis functions in the
- section_basis_set_atom_centered section. Specifically, basis functions with the
- same $n$ and $l$ quantum numbers are grouped in sets. Each set counts as one
- *kind*.
- ''',
- a_legacy=LegacyDefinition(name='number_of_kinds_in_basis_set_atom_centered'))
-
- section_basis_functions_atom_centered = SubSection(
- sub_section=SectionProxy('section_basis_functions_atom_centered'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))
-
- section_gaussian_basis_group = SubSection(
- sub_section=SectionProxy('section_gaussian_basis_group'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))
-
-
-class section_basis_set_cell_dependent(MSection):
- '''
- Section describing a cell-dependent (atom-independent) basis set, e.g. plane waves.
- The contained information is the type of basis set (in basis_set_cell_dependent_kind),
- its parameters (e.g., for plane waves in basis_set_planewave_cutoff), and a name that
- identifies the actually used basis set (a string combining the type and the
- parameter(s), stored in basis_set_cell_dependent_name).
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))
-
- basis_set_cell_dependent_kind = Quantity(
- type=str,
- shape=[],
- description='''
- A string defining the type of the cell-dependent basis set (i.e., non atom
- centered such as plane-waves). Allowed values are listed in the
- [basis_set_cell_dependent_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
- lab/nomad-meta-info/wikis/metainfo/basis-set-cell-dependent-kind).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_cell_dependent_kind'))
-
- basis_set_cell_dependent_name = Quantity(
- type=str,
- shape=[],
- description='''
- A label identifying the cell-dependent basis set (i.e., non atom centered such as
- plane-waves). Allowed values are listed in the [basis_set_cell_dependent_name wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
- set-cell-dependent-name).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_cell_dependent_name'))
-
- basis_set_planewave_cutoff = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Spherical cutoff in reciprocal space for a plane-wave basis set. It is the energy
- of the highest plan-ewave ($\\frac{\\hbar^2|k+G|^2}{2m_e}$) included in the basis
- set. Note that normally this basis set is used for the wavefunctions, and the
- density would have 4 times the cutoff, but this actually depends on the use of the
- basis set by the method.
- ''',
- a_legacy=LegacyDefinition(name='basis_set_planewave_cutoff'))
-
-
-class section_basis_set(MSection):
- '''
- This section contains references to *all* basis sets used in this
- section_single_configuration_calculation. More than one basis set instance per *single
- configuration calculation* (see section_single_configuration_calculation) may be
- needed. This is true for example, for codes that implement adaptive basis sets along
- the self-consistent field (SCF) convergence (e.g., exciting). In such cases, there is
- a section_basis_set instance per SCF iteration, if necessary. Another example is
- having a basis set for wavefunctions, a different one for the density, an auxiliary
- basis set for resolution of identity (RI), etc.
-
- Supported are the two broad classes of basis sets: *atom-centered* (e.g., Gaussian-
- type, numerical atomic orbitals) and *cell-dependent* (like plane waves or real-space
- grids, so named because they are typically used for periodic-system calculations and
- dependent to the simulated cell as a whole).
-
- Basis sets used in this section_single_configuration_calculation, belonging to either
- class, are defined in the dedicated section: [section_basis_set_cell_dependent
- ](section_basis_set_cell_dependent) or section_basis_set_atom_centered. The
- correspondence between the basis sets listed in this section and the definition given
- in the dedicated sessions is given by the two concrete metadata:
- mapping_section_basis_set_cell_dependent and mapping_section_basis_set_atom_centered.
- The latter metadata is a list that connects each atom in the system with its basis
- set, where the same basis set can be assigned to more than one atom.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set'))
-
- basis_set_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String describing the use of the basis set, i.e, if it used for expanding a wave-
- function or an electron density. Allowed values are listed in the [basis_set_kind
- wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/basis-set-kind).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_kind'))
-
- basis_set_name = Quantity(
- type=str,
- shape=[],
- description='''
- String identifying the basis set in an unique way. The rules for building this
- string are specified in the [basis_set_name wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
- set-name).
- ''',
- a_legacy=LegacyDefinition(name='basis_set_name'))
-
- mapping_section_basis_set_atom_centered = Quantity(
- type=Reference(SectionProxy('section_basis_set_atom_centered')),
- shape=['number_of_atoms'],
- description='''
- An array of the dimension of number_of_atoms where each atom (identified by the
- index in the array) is assigned to an atom-centered basis set, for this
- section_single_configuration_calculation. The actual definition of the atom-
- centered basis set is in the section_basis_set_atom_centered that is referred to
- by this metadata.
- ''',
- a_legacy=LegacyDefinition(name='mapping_section_basis_set_atom_centered'))
-
- mapping_section_basis_set_cell_dependent = Quantity(
- type=Reference(SectionProxy('section_basis_set_cell_dependent')),
- shape=[],
- description='''
- Assignment of the cell-dependent (i.e., non atom centered, e.g., plane-waves)
- parts of the basis set, which is defined (type, parameters) in
- section_basis_set_cell_dependent that is referred to by this metadata.
- ''',
- a_legacy=LegacyDefinition(name='mapping_section_basis_set_cell_dependent'))
-
- number_of_basis_functions = Quantity(
- type=int,
- shape=[],
- description='''
- Stores the total number of basis functions in a section_basis_set section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_basis_functions'))
-
-
-class section_restricted_uri(MSection):
- '''
- Restricted URIs on this calculation (Coverage: any info or files that are related with
- this calculation can be subject to restriction)
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_restricted_uri'))
-
- number_of_restricted_uri = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- The number of restricted uris in restricted_uri list.
- ''',
- a_legacy=LegacyDefinition(name='number_of_restricted_uri'))
-
- restricted_uri = Quantity(
- type=str,
- shape=['number_of_restricted_uri'],
- description='''
- The list of nomad uri(s) identifying the restricted info/file corresponding to
- this calculation
- ''',
- a_legacy=LegacyDefinition(name='restricted_uri'))
-
- restricted_uri_reason = Quantity(
- type=str,
- shape=[],
- description='''
- The reason of restriction for the uri or file. The reason can be 'propriety
- license', 'open-source redistribution restricted license', 'other license', or
- 'author restricted'.
- ''',
- a_legacy=LegacyDefinition(name='restricted_uri_reason'))
-
- restricted_uri_issue_authority = Quantity(
- type=str,
- shape=[],
- description='''
- The issue authority is the restriction owner for the uri or file. This can be
- license owner such as 'VASP' or 'AMBER', 'NOMAD', or the author of the uri. For
- example the repository user name of the author.
- ''',
- a_legacy=LegacyDefinition(name='restricted_uri_issue_authority'))
-
- restricted_uri_end_date = Quantity(
- type=str,
- shape=[],
- description='''
- The deadline date of the restriction for the uri or file. The end date can be in
- date format string for those restrictions set by authors or NOMAD otherwise it is
- set to 'unlimited' for the restriction related to license.
- ''',
- a_legacy=LegacyDefinition(name='restricted_uri_end_date'))
-
- restricted_uri_restriction = Quantity(
- type=str,
- shape=[],
- description='''
- The type of restriction for the uri or file. The type can be 'any access' or
- 'license permitted'.
- ''',
- a_legacy=LegacyDefinition(name='restricted_uri_restriction'))
-
- restricted_uri_license = Quantity(
- type=str,
- shape=[],
- description='''
- The info of the license that is the reason of restriction.
- ''',
- a_legacy=LegacyDefinition(name='restricted_uri_license'))
-
- number_of_restricted_uri_files = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- The number of restricted files in restricted_uri_files list.
- ''',
- a_legacy=LegacyDefinition(name='number_of_restricted_uri_files'))
-
-
-class section_calculation_to_calculation_refs(MSection):
- '''
- Section that describes the relationship between different
- section_single_configuration_calculation sections.
-
- For instance, one calculation is a perturbation performed using a self-consistent
- field (SCF) calculation as starting point, or a simulated system is partitioned in
- regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated
- via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
-
- The kind of relationship between the calculation defined in this section and the
- referenced one is described by calculation_to_calculation_kind. The referenced
- section_single_configuration_calculation is identified via
- calculation_to_calculation_ref (typically used for a
- section_single_configuration_calculation in the same section_run) or
- calculation_to_calculation_external_url.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))
-
- calculation_to_calculation_external_url = Quantity(
- type=str,
- shape=[],
- description='''
- URL used to reference an externally stored calculation. The kind of relationship
- between the present and the referenced section_single_configuration_calculation is
- specified by calculation_to_calculation_kind.
- ''',
- a_legacy=LegacyDefinition(name='calculation_to_calculation_external_url'))
-
- calculation_to_calculation_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String defining the relationship between the referenced
- section_single_configuration_calculation and the present
- section_single_configuration_calculation. Valid values are described in the
- [calculation_to_calculation_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
- lab/nomad-meta-info/wikis/metainfo/calculation-to-calculation-kind). Often
- calculations are connected, for instance, one calculation is a perturbation
- performed using a self-consistent field (SCF) calculation as starting point, or a
- simulated system is partitioned in regions with different but connected
- Hamiltonians (e.g., QM/MM, or a region treated via Kohn-Sham DFT embedded into a
- region treated via orbital-free DFT). Hence, the need of keeping track of these
- connected calculations. The referenced calculation is identified via
- calculation_to_calculation_ref (typically used for a calculation in the same
- section_run) or calculation_to_calculation_external_url.
- ''',
- a_legacy=LegacyDefinition(name='calculation_to_calculation_kind'))
-
- calculation_to_calculation_ref = Quantity(
- type=Reference(SectionProxy('section_single_configuration_calculation')),
- shape=[],
- description='''
- Reference to another calculation. If both this and
- calculation_to_calculation_external_url are given, then
- calculation_to_calculation_ref is a local copy of the URL given in
- calculation_to_calculation_external_url. The kind of relationship between the
- present and the referenced section_single_configuration_calculation is specified
- by calculation_to_calculation_kind.
- ''',
- a_legacy=LegacyDefinition(name='calculation_to_calculation_ref'))
-
-
-class section_calculation_to_folder_refs(MSection):
- '''
- Section that describes the relationship between
- section_single_configuration_calculationa and the folder containing the original
- calulations
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))
-
- calculation_to_folder_external_url = Quantity(
- type=str,
- shape=[],
- description='''
- URL used to reference a folder containing external calculations. The kind of
- relationship between the present and the referenced
- section_single_configuration_calculation is specified by
- calculation_to_folder_kind.
- ''',
- a_legacy=LegacyDefinition(name='calculation_to_folder_external_url'))
-
- calculation_to_folder_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String defining the relationship between the referenced
- section_single_configuration_calculation and a folder containing calculations.
- ''',
- a_legacy=LegacyDefinition(name='calculation_to_folder_kind'))
-
-
-class section_dos_fingerprint(MSection):
- '''
- Section for the fingerprint of the electronic density-of-states (DOS).
- DOS fingerprints are a modification of the D-Fingerprints reported in Chem. Mater. 2015, 27, 3, 735–743
- (doi:10.1021/cm503507h). The fingerprint consists of a binary representation of the DOS,
- that is used to evaluate the similarity of materials based on their electronic structure.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dos_fingerprint'))
-
- bins = Quantity(
- type=str,
- description='''
- Byte representation of the DOS fingerprint.
- ''',
- a_legacy=LegacyDefinition(name='bins'))
-
- indices = Quantity(
- type=np.dtype(np.int16),
- shape=[2],
- description='''
- Indices used to compare DOS fingerprints of different energy ranges.
- ''',
- a_legacy=LegacyDefinition(name='indices'))
-
- stepsize = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Stepsize of interpolation in the first step of the generation of DOS fingerprints.
- ''',
- a_legacy=LegacyDefinition(name='stepsize'))
-
- filling_factor = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Proportion of 1 bins in the DOS fingerprint.
- ''',
- a_legacy=LegacyDefinition(name='filling_factor'))
-
- grid_id = Quantity(
- type=str,
- description='''
- Identifier of the DOS grid that was used for the creation of the fingerprint.
- Similarity can only be calculated if the same grid was used for both fingerprints.
- ''',
- a_legacy=LegacyDefinition(name='grid_id'))
-
-
-class section_dos(MSection):
- '''
- Section collecting information of a (electronic-energy or vibrational-energy) density
- of states (DOS) evaluation.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dos'))
-
- dos_energies_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_dos_values'],
- unit='joule',
- description='''
- Array containing the set of discrete energy values with respect to the
- highest occupied energy level. This is the total DOS, see
- atom_projected_dos_energies and species_projected_dos_energies for
- partial density of states.
-
- If not available through energy_reference_highest_occupied, the highest
- occupied energy level is detected by searching for a non-zero DOS value
- below (or nearby) the reported energy_reference_fermi. In case the
- highest occupied energy level cannot be detected accurately, the
- normalized values are not reported. For calculations with multiple
- spin-channels, the normalization is determined by the first channel.
- ''',
- a_legacy=LegacyDefinition(name='dos_energies_normalized'))
-
- dos_energies = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_dos_values'],
- unit='joule',
- description='''
- Array containing the set of discrete energy values for the density (electronic-
- energy or vibrational energy) of states (DOS). This is the total DOS, see
- atom_projected_dos_energies and species_projected_dos_energies for partial density
- of states.
- ''',
- a_legacy=LegacyDefinition(name='dos_energies'))
-
- dos_integrated_values = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_dos_values'],
- description='''
- Integrated density of states (starting at $-\\infty$), pseudo potential
- calculations should start with the number of core electrons if they cover only the
- active electrons
- ''',
- a_legacy=LegacyDefinition(name='dos_integrated_values'))
-
- dos_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String to specify the kind of density of states (either electronic or
- vibrational).
- ''',
- a_legacy=LegacyDefinition(name='dos_kind'))
-
- dos_lm = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_dos_lms', 2],
- description='''
- Tuples of $l$ and $m$ values for which dos_values_lm are given. For the quantum
- number $l$ the conventional meaning of azimuthal quantum number is always adopted.
- For the integer number $m$, besides the conventional use as magnetic quantum
- number ($l+1$ integer values from $-l$ to $l$), a set of different conventions is
- accepted (see the [m_kind wiki page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-
- meta-info/wikis/metainfo/m-kind). The actual adopted convention is specified by
- dos_m_kind.
- ''',
- a_legacy=LegacyDefinition(name='dos_lm'))
-
- dos_m_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String describing what the integer numbers of $m$ in dos_lm mean. The allowed
- values are listed in the [m_kind wiki page](https://gitlab.rzg.mpg.de/nomad-
- lab/nomad-meta-info/wikis/metainfo/m-kind).
- ''',
- a_legacy=LegacyDefinition(name='dos_m_kind'))
-
- dos_values_lm = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_dos_lms', 'number_of_spin_channels', 'number_of_atoms', 'number_of_dos_values'],
- unit='joule',
- description='''
- Array containing the density (electronic-energy) of states values projected on the
- various spherical harmonics (integrated on all atoms), see
- atom_projected_dos_values_lm for atom values.
- ''',
- a_legacy=LegacyDefinition(name='dos_values_lm'))
-
- dos_values_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_dos_values'],
- description='''
- Density of states (DOS) values divided by the unit cell volume and by the number
- of atoms.
- ''',
- a_legacy=LegacyDefinition(name='dos_values_normalized'))
-
- dos_values = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_dos_values'],
- description='''
- Values (number of states for a given energy, the set of discrete energy values is
- given in dos_energies) of density (electronic-energy or vibrational-energy) of
- states. This refers to the simulation cell, i.e. integrating over all energies
- will give the number of electrons in the simulation cell.
- ''',
- a_legacy=LegacyDefinition(name='dos_values'))
-
- number_of_dos_lms = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $l$, $m$ combinations for the given projected density of
- states (DOS) in dos_values and dos_values_lm.
- ''',
- a_legacy=LegacyDefinition(name='number_of_dos_lms'))
-
- number_of_dos_values = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of energy values for the density of states (DOS), see
- dos_energies.
- ''',
- a_legacy=LegacyDefinition(name='number_of_dos_values'))
-
- section_dos_fingerprint = SubSection(
- sub_section=SectionProxy('section_dos_fingerprint'),
- repeats=False,
- a_legacy=LegacyDefinition(name='section_dos_fingerprint'))
-
-
-class section_eigenvalues(MSection):
- '''
- Section containing (electronic-energy) eigenvalues for one spin channel. If, for
- example, the eigenvalues of the Kohn-Sham operator are to be stored, a string
- identifying this kind of eigenvalues is put in eigenvalues_kind, the coordinates of
- the $k$-points at which the eigenvalues are evaluated is stored in
- eigenvalues_kpoints, and the energy values of the eigenstates and their occupation is
- stored in eigenvalues_values and eigenvalues_occupation, respectively.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_eigenvalues'))
-
- eigenvalues_kind = Quantity(
- type=str,
- shape=[],
- description='''
- A short string describing the kind of eigenvalues, as defined in the
- [eigenvalues_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/eigenvalues-kind).
- ''',
- a_legacy=LegacyDefinition(name='eigenvalues_kind'))
-
- eigenvalues_kpoints_multiplicity = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_eigenvalues_kpoints'],
- description='''
- Multiplicity of the $k$ point (i.e., how many distinct points per cell this
- expands to after applying all symmetries). This defaults to 1. If expansion is
- preformed then each point will have weight
- eigenvalues_kpoints_weights/eigenvalues_kpoints_multiplicity.
- ''',
- a_legacy=LegacyDefinition(name='eigenvalues_kpoints_multiplicity'))
-
- eigenvalues_kpoints_weights = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_eigenvalues_kpoints'],
- description='''
- Weights of the $k$ points (in the basis of the reciprocal lattice vectors) used
- for the evaluation of the eigenvalues tabulated in eigenvalues_values, should
- account for symmetry too.
- ''',
- a_legacy=LegacyDefinition(name='eigenvalues_kpoints_weights'))
-
- eigenvalues_kpoints = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_eigenvalues_kpoints', 3],
- description='''
- Coordinates of the $k$ points (in the basis of the reciprocal lattice vectors)
- used for the evaluation of the eigenvalues tabulated in eigenvalues_values.
- ''',
- a_legacy=LegacyDefinition(name='eigenvalues_kpoints'))
-
- eigenvalues_occupation = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
- description='''
- Occupation of the eigenstates. The corresponding eigenvalues (energy) are given in
- eigenvalues_values. The coordinates in the reciprocal space are defined in
- eigenvalues_kpoints.
- ''',
- a_legacy=LegacyDefinition(name='eigenvalues_occupation'))
-
- eigenvalues_values = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
- unit='joule',
- description='''
- Values of the (electronic-energy) eigenvalues. The coordinates of the
- corresponding eigenstates in the reciprocal space are defined in
- eigenvalues_kpoints and their occupations are given in eigenvalues_occupation.
- ''',
- a_legacy=LegacyDefinition(name='eigenvalues_values'))
-
- number_of_band_segment_eigenvalues = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of eigenvalues in a band segment, see band_energies.
- ''',
- a_legacy=LegacyDefinition(name='number_of_band_segment_eigenvalues'))
-
- number_of_eigenvalues_kpoints = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $k$ points, see eigenvalues_kpoints. $k$ points are calculated
- within a run and are irreducible if a symmetry is used.
- ''',
- a_legacy=LegacyDefinition(name='number_of_eigenvalues_kpoints'))
-
- number_of_eigenvalues = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of eigenvalues, see eigenvalues_values.
- ''',
- a_legacy=LegacyDefinition(name='number_of_eigenvalues'))
-
- number_of_normalized_band_segment_eigenvalues = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of normalized eigenvalues in a band segment, see
-
- band_energies_normalized.
- ''',
- a_legacy=LegacyDefinition(name='number_of_normalized_band_segment_eigenvalues'))
-
-
-class section_energy_code_independent(MSection):
- '''
- Section describing a code-independent total energy obtained by subtracting some
- reference energy calculated with the same code. It contains the type in
- energy_code_independent_kind and the computed code-independent total energy in
- energy_code_independent_value. The computed energy allows for comparisons among
- different codes and numerical settings.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_code_independent'))
-
- energy_code_independent_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Type of the code-independent total energy (obtained by subtracting a reference
- energy calculated with the same code), created to be comparable among different
- codes and numerical settings. Details can be found on the [energy_code_independent
- wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/energy-code-independent).
- ''',
- a_legacy=LegacyDefinition(name='energy_code_independent_kind'))
-
- energy_code_independent_value = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the code-independent total energy (obtained by subtracting a reference
- energy calculated with the same code). This value is created to be comparable
- among different codes and numerical settings. Details can be found on the
- [energy_code_independent wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
- meta-info/wikis/metainfo/energy-code-independent).
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_code_independent_value'))
-
-
-class section_energy_van_der_Waals(MSection):
- '''
- Section containing the Van der Waals energy value (energy_van_der_Waals_value) of type
- van_der_Waals_kind. This is used when more than one Van der Waals methods are applied
- in the same *single configuration calculation*, see
- section_single_configuration_calculation. The main Van der Waals method (the one
- concurring to energy_current, and used, e.g., for evaluating the forces for a
- relaxation or dynamics) is given in energy_van_der_Waals and is defined in
- settings_van_der_Waals.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
-
- energy_van_der_Waals_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Method used to compute van der Waals energy stored in energy_van_der_Waals_value.
- This metadata is used when more than one van der Waals method is applied in the
- same *single configuration calculation* (see
- section_single_configuration_calculation). The method used for van der Waals (the
- one consistent with energy_current and, e.g., for evaluating the forces for a
- relaxation or dynamics) is defined in settings_van_der_Waals.
- ''',
- a_legacy=LegacyDefinition(name='energy_van_der_Waals_kind'))
-
- energy_van_der_Waals_value = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of van der Waals energy, calculated with the method defined in
- energy_van_der_Waals_kind. This metadata is used when more than one van der Waals
- method is applied in the same *single configuration calculation* (see
- section_single_configuration_calculation). The value of the van der Waals energy
- consistent with energy_current and used, e.g., for evaluating the forces for a
- relaxation or dynamics, is given in energy_van_der_Waals and defined in
- settings_van_der_Waals.
- ''',
- categories=[energy_type_van_der_Waals, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_van_der_Waals_value'))
-
- energy_van_der_Waals = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value for the converged van der Waals energy calculated using the method described
- in van_der_Waals_method, and used in energy_current. This is the van der Waals
- method consistent with, e.g., forces used for relaxation or dynamics. Alternative
- methods are listed in section_energy_van_der_Waals.
- ''',
- categories=[energy_type_van_der_Waals, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_van_der_Waals'))
-
-
-class section_energy_contribution(MSection):
- '''
- Section describing the contributions to the total energy.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_contribution'))
-
- energy_contibution_kind = Quantity(
- type=str,
- shape=[],
- description='''
- The kind of the energy contribution. Can be one of bond, pair, coulomb, etc.
- ''',
- a_legacy=LegacyDefinition(name='energy_contibution_kind'))
-
- energy_contribution_value = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the energy contribution.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_contribution_value'))
-
-
-class section_frame_sequence_user_quantity(MSection):
- '''
- Section collecting some user-defined quantities evaluated along a sequence of frame.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_frame_sequence_user_quantity'))
-
- frame_sequence_user_quantity_frames = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_user_quantity_evaluations_in_sequence'],
- description='''
- Array containing the strictly increasing indices referring to the frames of
- frame_sequence_user_quantity. If not given it defaults to the trivial mapping
- 0,1,...
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_frames'))
-
- frame_sequence_user_quantity_name = Quantity(
- type=str,
- shape=[],
- description='''
- Descriptive name of a user-defined quantity, sampled along this sequence of frames
- (i.e., a trajectory, a frame is one section_single_configuration_calculation).
- Dedicated metadata are created for the conserved energy-like quantity
- (frame_sequence_conserved_quantity), the kinetic and potential energies
- (frame_sequence_kinetic_energy and frame_sequence_potential_energy), the
- instantaneous temperature (frame_sequence_temperature) and pressure
- (frame_sequence_pressure). This metadata should be used for other quantities that
- are monitored along a sequence of frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_name'))
-
- frame_sequence_user_quantity_stats = Quantity(
- type=np.dtype(np.float64),
- shape=[2, 'number_of_frame_sequence_user_quantity_components'],
- description='''
- Average of frame_sequence_user_quantity and its standard deviation in this
- sequence of frames (i.e., a trajectory, a frame is one
- section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_stats'))
-
- frame_sequence_user_quantity = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_user_quantity_evaluations_in_sequence', 'number_of_frame_sequence_user_quantity_components'],
- description='''
- Array containing the values of the user-defined quantity defined in
- frame_sequence_user_quantity_name, evaluated along this sequence of frames (i.e.,
- trajectory, a frame is one section_single_configuration_calculation). If not all
- frames have a value the indices of the frames that have a value are stored in
- frame_sequence_kinetic_energy_frames. If not all frames have a value the indices
- of the frames that have a value are stored in
- frame_sequence_kinetic_energy_frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_user_quantity'))
-
- number_of_frame_sequence_user_quantity_components = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of user-defined quantity defined by
- frame_sequence_user_quantity_name and monitored in a sequence of frames. A
- sequence is a trajectory, which can have number_of_frames_in_sequence each
- representing one section_single_configuration_calculation section.
-
- Dedicated metadata monitored along a sequence of frames are created for the
- conserved energy-like quantity (frame_sequence_conserved_quantity), the kinetic
- and potential energies ([frame_sequence_kinetic_energy and
- frame_sequence_potential_energy](frame_sequence_kinetic_energy and
- frame_sequence_potential_energy)), the instantaneous temperature
- (frame_sequence_temperature) and the pressure (frame_sequence_pressure).
- ''',
- a_legacy=LegacyDefinition(name='number_of_frame_sequence_user_quantity_components'))
-
- number_of_user_quantity_evaluations_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of user defined quantity evaluations along a sequence of
- frame_sequence_user_quantity frames. A sequence is a trajectory, which can have
- number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_user_quantity_evaluations_in_sequence'))
-
-
-class section_frame_sequence(MSection):
- '''
- Section containing a sequence of frames, i.e. a trajectory which can have
- number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section evaluated with a sampling method
- (e.g, molecular dynamics, Monte Carlo, geometry optimization). The sampling method
- might be a subset of the whole trajectory.
-
- Information on the method used for the sampling can be found in the
- section_sampling_method section and information of each frame of the sequence are
- found in the section_single_configuration_calculation section.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_frame_sequence'))
-
- frame_sequence_conserved_quantity_frames = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_conserved_quantity_evaluations_in_sequence'],
- description='''
- Array containing the strictly increasing indices of the frames the
- frame_sequence_conserved_quantity values refers to. If not given it defaults to
- the trivial mapping 0,1,...
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity_frames'))
-
- frame_sequence_conserved_quantity_stats = Quantity(
- type=np.dtype(np.float64),
- shape=[2],
- unit='joule',
- description='''
- Average value of energy-like frame_sequence_conserved_quantity, and its standard
- deviation, over this sequence of frames (i.e., a trajectory, a frame is one
- section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity_stats'))
-
- frame_sequence_conserved_quantity = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_conserved_quantity_evaluations_in_sequence'],
- unit='joule',
- description='''
- Array containing the values of a quantity that should be conserved, along a
- sequence of frames (i.e., a trajectory). A frame is one
- section_single_configuration_calculation), for example the total energy in the NVE
- ensemble. If not all frames have a value the indices of the frames that have a
- value are stored in frame_sequence_conserved_quantity_frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity'))
-
- frame_sequence_continuation_kind = Quantity(
- type=Reference(SectionProxy('section_frame_sequence')),
- shape=[],
- description='''
- Type of continuation that has been performed from the previous sequence of frames
- (i.e., a trajectory, a frame is one section_single_configuration_calculation),
- upon restart.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_continuation_kind'))
-
- frame_sequence_external_url = Quantity(
- type=str,
- shape=[],
- description='''
- If the energy, forces, and other quantities for the frames (a frame is one
- section_single_configuration_calculation) in section_frame_sequence are obtained
- by calling a different code than the code that drives the sequence (e.g., a
- wrapper that drives a molecular dynamics, Monte Carlo, geometry optimization and
- calls an electronic-structure code for energy and forces for each configuration),
- this metadata holds the reference to where the
- section_single_configuration_calculation for each frame are located. The format
- for this reference is described in the [frame_sequence_external_url wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/frame-
- sequence-external-url).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_external_url'))
-
- frame_sequence_kinetic_energy_frames = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_kinetic_energies_in_sequence'],
- description='''
- Array containing the strictly increasing indices referring to the frames of
- frame_sequence_kinetic_energy. If not given it defaults to the trivial mapping
- 0,1,...
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy_frames'))
-
- frame_sequence_kinetic_energy_stats = Quantity(
- type=np.dtype(np.float64),
- shape=[2],
- unit='joule',
- description='''
- Average kinetic energy and its standard deviation over this sequence of frames
- (i.e., a trajectory, a frame is one section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy_stats'))
-
- frame_sequence_kinetic_energy = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_kinetic_energies_in_sequence'],
- unit='joule',
- description='''
- Array containing the values of the kinetic energy along this sequence of frames
- (i.e., a trajectory, a frame is one section_single_configuration_calculation). If
- not all frames have a value the indices of the frames that have a value are stored
- in frame_sequence_kinetic_energy_frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy'))
-
- frame_sequence_local_frames_ref = Quantity(
- type=Reference(SectionProxy('section_single_configuration_calculation')),
- shape=['number_of_frames_in_sequence'],
- description='''
- Reference from each frame (a frame is one
- section_single_configuration_calculation) in this section_frame_sequence to the
- corresponding section_single_configuration_calculation. Each
- section_frame_sequence binds a collection of
- section_single_configuration_calculation, because they all belong to, e.g., a
- molecular dynamics trajectory, or geometry optimization. The full information for
- each frame is stored in section_single_configuration_calculation and this metadata
- establishes the link for each frame.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_local_frames_ref'))
-
- frame_sequence_potential_energy_frames = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_potential_energies_in_sequence'],
- description='''
- Array containing the strictly increasing indices referring to the frames of
- frame_sequence_potential_energy. If not given it defaults to the trivial mapping
- 0,1,...
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_potential_energy_frames'))
-
- frame_sequence_potential_energy_stats = Quantity(
- type=np.dtype(np.float64),
- shape=[2],
- unit='joule',
- description='''
- Average potential energy and its standard deviation over this sequence of frames
- (i.e., a trajectory, a frame is one section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_potential_energy_stats'))
-
- frame_sequence_potential_energy = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_potential_energies_in_sequence'],
- unit='joule',
- description='''
- Array containing the value of the potential energy along this sequence of frames
- (i.e., a trajectory, a frame is one section_single_configuration_calculation).
- This is equal to energy_total of the corresponding
- section_single_configuration_calculation and repeated here in a summary array for
- easier access. If not all frames have a value the indices of the frames that have
- a value are stored in frame_sequence_potential_energy_frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_potential_energy'))
-
- frame_sequence_pressure_frames = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_pressure_evaluations_in_sequence'],
- description='''
- Array containing the strictly increasing indices referring to the frames of
- frame_sequence_pressure. If not given it defaults to the trivial mapping 0,1,...
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_pressure_frames'))
-
- frame_sequence_pressure_stats = Quantity(
- type=np.dtype(np.float64),
- shape=[2],
- unit='pascal',
- description='''
- Average pressure (one third of the trace of the stress tensor) and standard
- deviation over this sequence of frames (i.e., a trajectory, a frame is one
- section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_pressure_stats'))
-
- frame_sequence_pressure = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_pressure_evaluations_in_sequence'],
- unit='pascal',
- description='''
- Array containing the values of the pressure (one third of the trace of the stress
- tensor) along this sequence of frames (a frame is one
- section_single_configuration_calculation). If not all frames have a value the
- indices of the frames that have a value are stored in
- frame_sequence_pressure_frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_pressure'))
-
- frame_sequence_temperature_frames = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_temperatures_in_sequence'],
- description='''
- Array containing the strictly increasing indices referring to the frames of
- frame_sequence_temperature. If not given it defaults to the trivial mapping
- 0,1,...
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_temperature_frames'))
-
- frame_sequence_temperature_stats = Quantity(
- type=np.dtype(np.float64),
- shape=[2],
- unit='kelvin',
- description='''
- Average temperature and its standard deviation over this sequence of frames (i.e.,
- a trajectory, a frame is one section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_temperature_stats'))
-
- frame_sequence_temperature = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_temperatures_in_sequence'],
- unit='kelvin',
- description='''
- Array containing the values of the instantaneous temperature (a quantity,
- proportional to frame_sequence_kinetic_energy, whose ensemble average equals the
- thermodynamic temperature) along this sequence of frames (i.e., a trajectory, a
- frame is one section_single_configuration_calculation). If not all frames have a
- value the indices of the frames that have a value are stored in
- frame_sequence_temperature_frames.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_temperature'))
-
- frame_sequence_time = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_frames_in_sequence'],
- unit='second',
- description='''
- Time along this sequence of frames (i.e., a trajectory, a frame is one
- section_single_configuration_calculation). Time start is arbitrary, but when a
- sequence is a continuation of another time should be continued too.
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_time'))
-
- frame_sequence_to_sampling_ref = Quantity(
- type=Reference(SectionProxy('section_sampling_method')),
- shape=[],
- description='''
- Reference from the present section_frame_sequence to the section_sampling_method,
- that defines the parameters used in this sequence of frames (i.e., a trajectory, a
- frame is one section_single_configuration_calculation).
- ''',
- a_legacy=LegacyDefinition(name='frame_sequence_to_sampling_ref'))
-
- geometry_optimization_converged = Quantity(
- type=bool,
- shape=[],
- description='''
- Arrays specify whether a geometry optimization is converged.
- ''',
- a_legacy=LegacyDefinition(name='geometry_optimization_converged'))
-
- number_of_conserved_quantity_evaluations_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of conserved quantity evaluations in this sequence. A sequence is
- a trajectory, which can have number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_conserved_quantity_evaluations_in_sequence'))
-
- number_of_frames_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of frames in a sequence. A sequence is a trajectory, which can
- have number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_frames_in_sequence'))
-
- number_of_kinetic_energies_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of kinetic energy evaluations in this sequence of frames, see
- frame_sequence_kinetic_energy.
- ''',
- a_legacy=LegacyDefinition(name='number_of_kinetic_energies_in_sequence'))
-
- number_of_potential_energies_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of potential energies evaluation in this sequence. A sequence is
- a trajectory, which can have number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_potential_energies_in_sequence'))
-
- number_of_pressure_evaluations_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of pressure evaluations in this sequence. A sequence is a
- trajectory, which can have number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_pressure_evaluations_in_sequence'))
-
- number_of_temperatures_in_sequence = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of temperature frames (frame_sequence_temperature) used in the
- section_frame_sequence. A sequence is a trajectory, which can have
- number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_temperatures_in_sequence'))
-
- previous_sequence_ref = Quantity(
- type=Reference(SectionProxy('section_frame_sequence')),
- shape=[],
- description='''
- Contains a reference to the previous sequence. A sequence is a trajectory, which
- can have number_of_frames_in_sequence each representing one
- section_single_configuration_calculation section. If not given, a start from an
- initial configuration is assumed.
- ''',
- a_legacy=LegacyDefinition(name='previous_sequence_ref'))
-
- section_frame_sequence_user_quantity = SubSection(
- sub_section=SectionProxy('section_frame_sequence_user_quantity'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_frame_sequence_user_quantity'))
-
- section_thermodynamical_properties = SubSection(
- sub_section=SectionProxy('section_thermodynamical_properties'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_thermodynamical_properties'))
-
-
-class section_gaussian_basis_group(MSection):
- '''
- Section that describes a group of Gaussian contractions. Groups allow one to calculate
- the primitive Gaussian integrals once for several different linear combinations of
- them. This defines basis functions with radial part $f_i(r) = r^{l_i} \\sum_{j} c_{i
- j} A(l_i, \\alpha_j) exp(-\\alpha_j r^2)$ where $A(l_i, \\alpha_j)$ is a the
- normalization coefficient for primitive Gaussian basis functions. Here, $\\alpha_j$ is
- defined in gaussian_basis_group_exponents, $l_i$ is given in gaussian_basis_group_ls,
- and $c_{i j}$ is given in gaussian_basis_group_contractions, whereas the radial part
- is given by the spherical harmonics $Y_{l m}$.
-
- This section is defined only if the original basis function uses Gaussian basis
- functions, and the sequence of radial functions $f_i$ across all
- section_gaussian_basis_group in section_basis_set_atom_centered should match the one
- of basis_set_atom_centered_radial_functions.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))
-
- gaussian_basis_group_contractions = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_gaussian_basis_group_contractions', 'number_of_gaussian_basis_group_exponents'],
- description='''
- contraction coefficients $c_{i j}$ defining the contracted basis functions with
- respect to *normalized* primitive Gaussian functions. They define the Gaussian
- basis functions as described in section_gaussian_basis_group.
- ''',
- a_legacy=LegacyDefinition(name='gaussian_basis_group_contractions'))
-
- gaussian_basis_group_exponents = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_gaussian_basis_group_exponents'],
- unit='1 / meter ** 2',
- description='''
- Exponents $\\alpha_j$ of the Gaussian functions defining this basis set
- $exp(-\\alpha_j r^2)$. One should be careful about the units of the coefficients.
- ''',
- a_legacy=LegacyDefinition(name='gaussian_basis_group_exponents'))
-
- gaussian_basis_group_ls = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_gaussian_basis_group_contractions'],
- description='''
- Azimuthal quantum number ($l$) values (of the angular part given by the spherical
- harmonic $Y_{l m}$ of the various contracted basis functions).
- ''',
- a_legacy=LegacyDefinition(name='gaussian_basis_group_ls'))
-
- number_of_gaussian_basis_group_contractions = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of different contractions, i.e. resulting basis functions in a
- section_gaussian_basis_group section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_gaussian_basis_group_contractions'))
-
- number_of_gaussian_basis_group_exponents = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of different Gaussian exponents in a section_gaussian_basis_group
- section.
- ''',
- a_legacy=LegacyDefinition(name='number_of_gaussian_basis_group_exponents'))
-
-
-class section_k_band_normalized(MSection):
- '''
- This section stores information on a normalized $k$-band (electronic band structure)
- evaluation along one-dimensional pathways in the $k$ (reciprocal) space given in
- section_k_band_segment. Eigenvalues calculated at the actual $k$-mesh used for
- energy_total evaluations, can be found in the section_eigenvalues section.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band_normalized'))
-
- k_band_path_normalized_is_standard = Quantity(
- type=bool,
- shape=[],
- description='''
- If the normalized path is along the default path defined in W. Setyawan and S.
- Curtarolo, [Comput. Mater. Sci. **49**, 299-312
- (2010)](http://dx.doi.org/10.1016/j.commatsci.2010.05.010).
- ''',
- a_legacy=LegacyDefinition(name='k_band_path_normalized_is_standard'))
-
- section_k_band_segment_normalized = SubSection(
- sub_section=SectionProxy('section_k_band_segment_normalized'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_k_band_segment_normalized'))
-
-
-class section_k_band_segment_normalized(MSection):
- '''
- Section collecting the information on a normalized $k$-band segment. This section
- stores band structures along a one-dimensional pathway in the $k$ (reciprocal) space.
-
- Eigenvalues calculated at the actual $k$-mesh used for energy_total evaluations are
- defined in section_eigenvalues and the band structures are represented as third-order
- tensors: one dimension for the spin channels, one for the sequence of $k$ points for
- the segment (given in number_of_k_points_per_segment), and one for the sequence of
- eigenvalues at a given $k$ point. The values of the $k$ points in each segment are
- stored in band_k_points. The energies and occupation for each eigenstate, at each $k$
- point, segment, and spin channel are stored in band_energies and band_occupations,
- respectively. The labels for the segment are specified in band_segm_labels.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band_segment_normalized'))
-
- band_energies_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_normalized_k_points_per_segment', 'number_of_normalized_band_segment_eigenvalues'],
- unit='joule',
- description='''
- $k$-dependent energies of the electronic band segment (electronic band structure)
- with respect to the top of the valence band. This is a third-order tensor, with
- one dimension used for the spin channels, one for the $k$ points for each segment,
- and one for the eigenvalue sequence.
- ''',
- a_legacy=LegacyDefinition(name='band_energies_normalized'))
-
- band_k_points_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_normalized_k_points_per_segment', 3],
- description='''
- Fractional coordinates of the $k$ points (in the basis of the reciprocal-lattice
- vectors) for which the normalized electronic energies are given.
- ''',
- a_legacy=LegacyDefinition(name='band_k_points_normalized'))
-
- band_occupations_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_normalized_k_points_per_segment', 'number_of_normalized_band_segment_eigenvalues'],
- description='''
- Occupation of the $k$-points along the normalized electronic band. The size of the
- dimensions of this third-order tensor are the same as for the tensor in
- band_energies.
- ''',
- a_legacy=LegacyDefinition(name='band_occupations_normalized'))
-
- band_segm_labels_normalized = Quantity(
- type=str,
- shape=[2],
- description='''
- Start and end labels of the points in the segment (one-dimensional pathways)
- sampled in the $k$-space, using the conventional symbols, e.g., Gamma, K, L. The
- coordinates (fractional, in the reciprocal space) of the start and end points for
- each segment are given in band_segm_start_end_normalized
- ''',
- a_legacy=LegacyDefinition(name='band_segm_labels_normalized'))
-
- band_segm_start_end_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=[2, 3],
- description='''
- Fractional coordinates of the start and end point (in the basis of the reciprocal
- lattice vectors) of the segment sampled in the $k$ space. The conventional symbols
- (e.g., Gamma, K, L) of the same points are given in band_segm_labels
- ''',
- a_legacy=LegacyDefinition(name='band_segm_start_end_normalized'))
-
- number_of_normalized_k_points_per_segment = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $k$ points in the segment of the normalized band structure
- (see section_k_band_segment_normalized).
- ''',
- a_legacy=LegacyDefinition(name='number_of_normalized_k_points_per_segment'))
-
-
-class section_k_band_segment(MSection):
- '''
- Section collecting the information on a $k$-band or $q$-band segment. This section
- stores band structures along a one-dimensional pathway in the $k$ or $q$ (reciprocal)
- space.
-
- Eigenvalues calculated at the actual $k$-mesh used for energy_total evaluations are
- defined in section_eigenvalues and the band structures are represented as third-order
- tensors: one dimension for the spin channels, one for the sequence of $k$ or $q$
- points for the segment (given in number_of_k_points_per_segment), and one for the
- sequence of eigenvalues at a given $k$ or $q$ point. The values of the $k$ or $q$
- points in each segment are stored in band_k_points. The energies and occupation for
- each eigenstate, at each $k$ or $q$ point, segment, and spin channel are stored in
- band_energies and band_occupations, respectively. The labels for the segment are
- specified in band_segm_labels.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band_segment'))
-
- band_energies = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_k_points_per_segment', 'number_of_band_segment_eigenvalues'],
- unit='joule',
- description='''
- $k$-dependent or $q$-dependent energies of the electronic or vibrational band
- segment (electronic/vibrational band structure). This is a third-order tensor,
- with one dimension used for the spin channels (1 in case of a vibrational band
- structure), one for the $k$ or $q$ points for each segment, and one for the
- eigenvalue sequence.
- ''',
- a_legacy=LegacyDefinition(name='band_energies'))
-
- band_k_points = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_k_points_per_segment', 3],
- description='''
- Fractional coordinates of the $k$ or $q$ points (in the basis of the reciprocal-
- lattice vectors) for which the electronic energy are given.
- ''',
- a_legacy=LegacyDefinition(name='band_k_points'))
-
- band_occupations = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_k_points_per_segment', 'number_of_band_segment_eigenvalues'],
- description='''
- Occupation of the $k$-points along the electronic band. The size of the dimensions
- of this third-order tensor are the same as for the tensor in band_energies.
- ''',
- a_legacy=LegacyDefinition(name='band_occupations'))
-
- band_segm_labels = Quantity(
- type=str,
- shape=[2],
- description='''
- Start and end labels of the points in the segment (one-dimensional pathways)
- sampled in the $k$-space or $q$-space, using the conventional symbols, e.g.,
- Gamma, K, L. The coordinates (fractional, in the reciprocal space) of the start
- and end points for each segment are given in band_segm_start_end
- ''',
- a_legacy=LegacyDefinition(name='band_segm_labels'))
-
- band_segm_start_end = Quantity(
- type=np.dtype(np.float64),
- shape=[2, 3],
- description='''
- Fractional coordinates of the start and end point (in the basis of the reciprocal
- lattice vectors) of the segment sampled in the $k$ space. The conventional symbols
- (e.g., Gamma, K, L) of the same points are given in band_segm_labels
- ''',
- a_legacy=LegacyDefinition(name='band_segm_start_end'))
-
- number_of_k_points_per_segment = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $k$ points in the segment of the band structure, see
- section_k_band_segment.
- ''',
- a_legacy=LegacyDefinition(name='number_of_k_points_per_segment'))
-
-
-class section_band_gap(MSection):
- '''
- This section stores information for a band gap within a band structure.
- '''
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_band_gap'))
-
- value = Quantity(
- type=float,
- unit="joule",
- description="""
- Band gap energy. Value of zero corresponds to a band structure without
- a band gap.
- """,
- a_legacy=LegacyDefinition(name='value')
- )
- type = Quantity(
- type=MEnum("direct", "indirect"),
- description="""
- Type of band gap.
- """,
- a_legacy=LegacyDefinition(name='type')
- )
- conduction_band_min_energy = Quantity(
- type=float,
- unit="joule",
- description="""
- Conduction band minimum energy.
- """,
- a_legacy=LegacyDefinition(name='conduction_band_min_energy')
- )
- valence_band_max_energy = Quantity(
- type=float,
- unit="joule",
- description="""
- Valence band maximum energy.
- """,
- a_legacy=LegacyDefinition(name='valence_band_max_energy')
- )
- conduction_band_min_k_point = Quantity(
- type=np.dtype(np.float64),
- shape=[3],
- unit="1 / meter",
- description="""
- Coordinate of the conduction band minimum in k-space.
- """,
- a_legacy=LegacyDefinition(name='conduction_band_min_k_point')
- )
- valence_band_max_k_point = Quantity(
- type=np.dtype(np.float64),
- shape=[3],
- unit="1 / meter",
- description="""
- Coordinate of the valence band minimum in k-space.
- """,
- a_legacy=LegacyDefinition(name='valence_band_max_k_point')
- )
-
-
-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
- structure) evaluation along one-dimensional pathways in the $k$ or $q$ (reciprocal)
- space given in section_k_band_segment. Eigenvalues calculated at the actual $k$-mesh
- used for energy_total evaluations, can be found in the section_eigenvalues section.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band'))
-
- band_structure_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String to specify the kind of band structure (either electronic or vibrational).
- ''',
- a_legacy=LegacyDefinition(name='band_structure_kind'))
-
- reciprocal_cell = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit="1 / meter",
- description="""
- The reciprocal cell within which the band structure is calculated.
- """,
- a_legacy=LegacyDefinition(name='reciprocal_cell')
- )
-
- brillouin_zone = SubSection(
- sub_section=SectionProxy('section_brillouin_zone'),
- repeats=False,
- a_legacy=LegacyDefinition(name='brillouin_zone'))
-
- section_band_gap = SubSection(
- sub_section=section_band_gap.m_def,
- repeats=True,
- description=""",
- Contains information for band gaps detected in the band structure.
- Contains a section for each spin channel in the same order as reported
- for the band energies. For channels without a band gap, a band gap
- value of zero is reported.
- """,
- a_legacy=LegacyDefinition(name='section_band_gap')
- )
-
- is_standard_path = Quantity(
- type=bool,
- description="""
- Boolean indicating whether the path follows the standard path for this
- bravais lattice. The AFLOW standard by Setyawan and Curtarolo is used
- (https://doi.org/10.1016/j.commatsci.2010.05.010).
- """,
- a_legacy=LegacyDefinition(name='is_standard_path')
- )
-
- section_k_band_segment = SubSection(
- sub_section=SectionProxy('section_k_band_segment'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_k_band_segment'))
-
-
-class section_method_atom_kind(MSection):
- '''
- Every section_method_atom_kind section contains method-related information about a
- kind of atom, and is identified by one or more strings stored in
- method_atom_kind_label.
-
- This categorization into atom kinds is more flexible than just atomic species, because
- to different atoms of the same species different atom-centered basis sets or pseudo-
- potentials may be assigned. For instance, if two different oxygen atoms are assigned
- to different basis sets or pseudo-potentials, they have to distinguished into two
- different *kinds* of O atoms, by creating two distinct section_method_atom_kind
- sections.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method_atom_kind'))
-
- method_atom_kind_atom_number = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Atomic number (number of protons) of this atom kind, use 0 if not an atom.
- ''',
- a_legacy=LegacyDefinition(name='method_atom_kind_atom_number'))
-
- method_atom_kind_explicit_electrons = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Number of explicit electrons (often called valence).
- ''',
- a_legacy=LegacyDefinition(name='method_atom_kind_explicit_electrons'))
-
- method_atom_kind_label = Quantity(
- type=str,
- shape=[],
- description='''
- String used to identify the atoms of this kind. This should correspond to the
- atom_labels of the configuration. It is possible for one atom kind to have
- multiple labels (in order to allow two atoms of the same kind to have two
- differently defined sets of atom-centered basis functions or two different pseudo-
- potentials). Atom kind is typically the symbol of the atomic species but it can be
- also a ghost or pseudo-atom.
- ''',
- a_legacy=LegacyDefinition(name='method_atom_kind_label'))
-
- method_atom_kind_mass = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='unified_atomic_mass_unit',
- description='''
- Mass of the kind of this kind of atoms.
- ''',
- a_legacy=LegacyDefinition(name='method_atom_kind_mass'))
-
- method_atom_kind_pseudopotential_name = Quantity(
- type=str,
- shape=[],
- description='''
- Name identifying the pseudopotential used.
- ''',
- a_legacy=LegacyDefinition(name='method_atom_kind_pseudopotential_name'))
-
-
-class section_method_to_method_refs(MSection):
- '''
- Section that describes the relationship between different section_method sections.
-
- For instance, one calculation is a perturbation performed using a self-consistent
- field (SCF) calculation as starting point, or a simulated system is partitioned in
- regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated
- via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
-
- The kind of relationship between the method defined in this section and the referenced
- one is described by method_to_method_kind. The referenced section section_method is
- identified via method_to_method_ref (typically used for a section_method section in
- the same section_run) or method_to_method_external_url.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method_to_method_refs'))
-
- method_to_method_external_url = Quantity(
- type=str,
- shape=[],
- description='''
- URL used to reference an externally stored section_method. The kind of
- relationship between the present and the referenced section_method is specified by
- method_to_method_kind.
- ''',
- a_legacy=LegacyDefinition(name='method_to_method_external_url'))
-
- method_to_method_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String defining the kind of relationship that the referenced section_method has
- with the present section_method. Valid values are described in the
- [method_to_method_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
- meta-info/wikis/metainfo/method-to-method-kind). Often calculations are connected,
- for instance, one calculation is a perturbation performed using a self-consistent
- field (SCF) calculation as starting point, or a simulated system is partitioned in
- regions with different but connected Hamiltonians (e.g., QM/MM, or a region
- treated via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
- Hence, the need of keeping track of these connected calculations. The referenced
- section_method is identified via method_to_method_ref (typically used for a
- section_method in the same section_run) or method_to_method_external_url.
- ''',
- a_legacy=LegacyDefinition(name='method_to_method_kind'))
-
- method_to_method_ref = Quantity(
- type=Reference(SectionProxy('section_method')),
- shape=[],
- description='''
- Reference to a local section_method. If both method_to_method_ref and
- method_to_method_external_url are given, then method_to_method_ref is a local copy
- of the value contained in method_to_method_external_url. The kind of relationship
- between the method defined in the present section_method and the referenced one is
- described by method_to_method_kind.
- ''',
- a_legacy=LegacyDefinition(name='method_to_method_ref'))
-
-
-class section_method(MSection):
- '''
- Section containing the various parameters that define the theory and the
- approximations (convergence, thresholds,...) to perform a *single configuration
- calculation*, see section_single_configuration_calculation.
-
- *NOTE*: This section does not contain settings for molecular dynamics, geometry
- optimization etc. See section frame_sequence for these other settings instead.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method'))
-
- basis_set = Quantity(
- type=str,
- shape=[],
- description='''
- Unique string identifying the basis set used for the final wavefunctions
- calculated with XC_method. It might identify a class of basis sets, often matches
- one of the strings given in any of basis_set_name.
- ''',
- categories=[settings_numerical_parameter, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='basis_set'))
-
- calculation_method_current = Quantity(
- type=str,
- shape=[],
- description='''
- String that represents the method used to calculate the energy_current. If the
- method is perturbative, this string does not describe the starting point method,
- the latter being referenced to by section_method_to_method_refs. For self-
- consistent field (SCF) ab initio calculations, for example, this is composed by
- concatenating XC_method_current and basis_set. See [calculation_method_current
- wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/calculation-method-current) for the details.
- ''',
- a_legacy=LegacyDefinition(name='calculation_method_current'))
-
- calculation_method_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Kind of method in calculation_method_current.
-
- Accepted values are:
-
- - absolute
-
- - perturbative.
- ''',
- a_legacy=LegacyDefinition(name='calculation_method_kind'))
-
- calculation_method = Quantity(
- type=str,
- shape=[],
- description='''
- String that uniquely represents the method used to calculate energy_total, If the
- present calculation_method_current is a perturbative method Y that uses method X
- as starting point, this string is automatically created as X@Y, where X is taken
- from calculation_method_current and Y from method_to_method_ref. In order to
- activate this, method_to_method_kind must have the value starting_point (see the
- [method_to_method_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
- meta-info/wikis/metainfo/method-to-method-kind)).
- ''',
- a_legacy=LegacyDefinition(name='calculation_method'))
-
- electronic_structure_method = Quantity(
- type=str,
- shape=[],
- description='''
- Non-unique string identifying the used electronic structure method. It is not
- unique in the sense that two calculations with the same
- electronic_structure_method string may have not been performed with exactly the
- same method. The allowed strings are given in the [electronic structure method
- wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/electronic-structure-method).
- ''',
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='electronic_structure_method'))
-
- k_mesh_points = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_k_mesh_points', 3],
- description='''
- List of all the k points in the $k$-point mesh. These are the k point used to
- evaluate energy_total, and are in fractional coordinates (in the basis of the
- reciprocal-lattice vectors).
- ''',
- categories=[settings_k_points, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='k_mesh_points'))
-
- k_mesh_weights = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_k_mesh_points'],
- description='''
- Weights of all the k points in the $k$-point mesh. These are the weights for
- k_mesh_points (i.e. the k point used to evaluate energy_total).
- ''',
- categories=[settings_k_points, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='k_mesh_weights'))
-
- number_of_k_mesh_points = Quantity(
- type=int,
- shape=[],
- description='''
- number of k points in the mesh (i.e. the k points used to evaluate energy_total).
- ''',
- categories=[settings_k_points, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='number_of_k_mesh_points'))
-
- number_of_spin_channels = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of spin channels, see section_method.
- ''',
- a_legacy=LegacyDefinition(name='number_of_spin_channels'))
-
- relativity_method = Quantity(
- type=str,
- shape=[],
- description='''
- Describes the relativistic treatment used for the calculation of the final energy
- and related quantities. If skipped or empty, no relativistic treatment is applied.
- ''',
- categories=[settings_relativity, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='relativity_method'))
-
- scf_max_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Specifies the maximum number of allowed self-consistent field (SCF) iterations in
- a calculation run, see section_run.
- ''',
- categories=[settings_scf],
- a_legacy=LegacyDefinition(name='scf_max_iteration'))
-
- scf_threshold_energy_change = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Specifies the threshold for the energy_total_scf_iteration change between two
- subsequent self-consistent field (SCF) iterations. The SCF is considered converged
- when the total-energy change between two SCF cycles is below the threshold
- (possibly in combination with other criteria).
- ''',
- categories=[settings_scf],
- a_legacy=LegacyDefinition(name='scf_threshold_energy_change'))
-
- self_interaction_correction_method = Quantity(
- type=str,
- shape=[],
- description='''
- Contains the name for the self-interaction correction (SIC) treatment used to
- calculate the final energy and related quantities. If skipped or empty, no special
- correction is applied.
-
- The following SIC methods are available:
-
- | SIC method | Description |
-
- | ------------------------- | -------------------------------- |
-
- | `""` | No correction |
-
- | `"SIC_AD"` | The average density correction |
-
- | `"SIC_SOSEX"` | Second order screened exchange |
-
- | `"SIC_EXPLICIT_ORBITALS"` | (scaled) Perdew-Zunger correction explicitly on a
- set of orbitals |
-
- | `"SIC_MAURI_SPZ"` | (scaled) Perdew-Zunger expression on the spin
- density / doublet unpaired orbital |
-
- | `"SIC_MAURI_US"` | A (scaled) correction proposed by Mauri and co-
- workers on the spin density / doublet unpaired orbital |
- ''',
- categories=[settings_self_interaction_correction, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='self_interaction_correction_method'))
-
- smearing_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the kind of smearing on the electron occupation used to calculate the
- free energy (see energy_free)
-
- Valid values are:
-
- | Smearing kind | Description |
-
- | ------------------------- | --------------------------------- |
-
- | `"empty"` | No smearing is applied |
-
- | `"gaussian"` | Gaussian smearing |
-
- | `"fermi"` | Fermi smearing |
-
- | `"marzari-vanderbilt"` | Marzari-Vanderbilt smearing |
-
- | `"methfessel-paxton"` | Methfessel-Paxton smearing |
-
- | `"tetrahedra"` | Interpolation of state energies and occupations
- (ignores smearing_width) |
- ''',
- categories=[settings_smearing],
- a_legacy=LegacyDefinition(name='smearing_kind'))
-
- smearing_width = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Specifies the width of the smearing in energy for the electron occupation used to
- calculate the free energy (see energy_free).
-
- *NOTE:* Not all methods specified in smearing_kind uses this value.
- ''',
- categories=[settings_smearing],
- a_legacy=LegacyDefinition(name='smearing_width'))
-
- spin_target_multiplicity = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Stores the target (user-imposed) value of the spin multiplicity $M=2S+1$, where
- $S$ is the total spin. It is an integer number. This value is not necessarily the
- value obtained at the end of the calculation. See spin_S2 for the converged value
- of the spin moment.
- ''',
- a_legacy=LegacyDefinition(name='spin_target_multiplicity'))
-
- stress_tensor_method = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the method used to calculate stress_tensor for, e.g., molecular dynamics
- and geometry optimization.
-
- The allowed values are:
-
- * numeric
-
- * analytic
- ''',
- categories=[settings_stress_tensor],
- a_legacy=LegacyDefinition(name='stress_tensor_method'))
-
- total_charge = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- unit='coulomb',
- description='''
- Provides the total amount of charge of the system in a run.
- ''',
- a_legacy=LegacyDefinition(name='total_charge'))
-
- van_der_Waals_method = Quantity(
- type=str,
- shape=[],
- description='''
- Describes the Van der Waals method. If skipped or an empty string is used, it
- means no Van der Waals correction is applied.
-
- Allowed values are:
-
- | Van der Waals method | Description |
-
- | --------------------- | ----------------------------------------- |
-
- | `""` | No Van der Waals correction |
-
- | `"TS"` | A. Tkatchenko and M. Scheffler, [Phys. Rev. Lett.
- **102**, 073005 (2009)](http://dx.doi.org/10.1103/PhysRevLett.102.073005) |
-
- | `"OBS"` | F. Ortmann, F. Bechstedt, and W. G. Schmidt, [Phys. Rev.
- B **73**, 205101 (2006)](http://dx.doi.org/10.1103/PhysRevB.73.205101) |
-
- | `"G06"` | S. Grimme, [J. Comput. Chem. **27**, 1787
- (2006)](http://dx.doi.org/10.1002/jcc.20495) |
-
- | `"JCHS"` | P. JureÄka, J. ÄŒerný, P. Hobza, and D. R. Salahub,
- [Journal of Computational Chemistry **28**, 555
- (2007)](http://dx.doi.org/10.1002/jcc.20570) |
-
- | `"MDB"` | Many-body dispersion. A. Tkatchenko, R. A. Di Stasio Jr,
- R. Car, and M. Scheffler, [Physical Review Letters **108**, 236402
- (2012)](http://dx.doi.org/10.1103/PhysRevLett.108.236402) and A. Ambrosetti, A. M.
- Reilly, R. A. Di Stasio Jr, and A. Tkatchenko, [The Journal of Chemical Physics
- **140**, 18A508 (2014)](http://dx.doi.org/10.1063/1.4865104) |
-
- | `"XC"` | The method to calculate the Van der Waals energy uses a
- non-local functional which is described in section_XC_functionals. |
- ''',
- categories=[settings_van_der_Waals, settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='van_der_Waals_method'))
-
- XC_functional = Quantity(
- type=str,
- shape=[],
- description='''
- This value describes a DFT exchange-correlation (XC) functional used for
- evaluating the energy value stored in energy_XC_functional and related quantities
- (e.g., forces).
-
- It is a unique short name obtained by combining the data stored in
- section_XC_functionals, more specifically by combining different
- XC_functional_name as described in the [XC_functional wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
- functional).
- ''',
- categories=[settings_potential_energy_surface, settings_physical_parameter, settings_XC_functional, settings_XC],
- a_legacy=LegacyDefinition(name='XC_functional'))
-
- XC_method = Quantity(
- type=str,
- shape=[],
- description='''
- Describes the exchange correlation (XC) method used for evaluating the XC energy
- (energy_XC). Differently from XC_functional, perturbative treatments are also
- accounted for, where the string contains the reference to both the perturbative
- (e.g., MP2) and the starting point (e.g, Hartree-Fock) XC method defined in the
- section section_method.
-
- The value consists of XC_method_current concatenated with the `@` character and
- the XC method (XC_method) defined in section_method that is referred to by
- method_to_method_ref where method_to_method_kind = "starting_point_method".
- ''',
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='XC_method'))
-
- XC_method_current = Quantity(
- type=str,
- shape=[],
- description='''
- Identifies the exchange correlation (XC) method used for energy_XC and related
- quantities in a standardized short form as a string.
-
- It is built by joining the values in the following order using the underscore `_`
- character: electronic_structure_method, XC_functional,
- self_interaction_correction_method, van_der_Waals_method and relativity_method.
-
- If any of the methods listed in the string contain non-standard settings, then the
- first 10 characters of the Base64 URL encoding of SHA 512 checksum of a normalized
- JSON with all non-redundant non-derived settings_XC are appended to the the string
- preceded by an underscore.
-
- With empty strings, the underscore `_` character is skipped.
-
- If the method defined in the section_method section is perturbative, the
- XC_method_current contains only the perturbative method, not the starting point
- (e.g. the DFT XC functional used as a starting point for a RPA perturbative
- calculation). In this case, the string that contains both the perturbative and
- starting point method is stored in XC_method.
- ''',
- categories=[settings_XC, settings_potential_energy_surface],
- a_legacy=LegacyDefinition(name='XC_method_current'))
-
- section_method_atom_kind = SubSection(
- sub_section=SectionProxy('section_method_atom_kind'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_method_atom_kind'))
-
- section_method_to_method_refs = SubSection(
- sub_section=SectionProxy('section_method_to_method_refs'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_method_to_method_refs'))
-
- section_XC_functionals = SubSection(
- sub_section=SectionProxy('section_XC_functionals'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_XC_functionals'))
-
-
-class section_original_system(MSection):
- '''
- Section containing symmetry information that is specific to the original system.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_original_system'))
-
- equivalent_atoms_original = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_atoms'],
- description='''
- Gives a mapping table of atoms to symmetrically independent atoms in the original
- cell. This is used to find symmetrically equivalent atoms.
- ''',
- a_legacy=LegacyDefinition(name='equivalent_atoms_original'))
-
- wyckoff_letters_original = Quantity(
- type=str,
- shape=['number_of_atoms'],
- description='''
- Wyckoff letters for atoms in the original cell.
- ''',
- a_legacy=LegacyDefinition(name='wyckoff_letters_original'))
-
-
-class section_primitive_system(MSection):
- '''
- Section containing symmetry information that is specific to the primitive system. The
- primitive system is derived from the standardized system with a transformation that is
- specific to the centring. The transformation matrices can be found e.g. from here:
- https://atztogo.github.io/spglib/definition.html#transformation-to-the-primitive-cell
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_primitive_system'))
-
- atom_positions_primitive = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms_primitive', 3],
- description='''
- Atom positions in the primitive cell in reduced units.
- ''',
- a_legacy=LegacyDefinition(name='atom_positions_primitive'))
-
- atomic_numbers_primitive = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_atoms_primitive'],
- description='''
- Atomic numbers in the primitive cell.
- ''',
- a_legacy=LegacyDefinition(name='atomic_numbers_primitive'))
-
- equivalent_atoms_primitive = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_atoms_primitive'],
- description='''
- Gives a mapping table of atoms to symmetrically independent atoms in the primitive
- cell. This is used to find symmetrically equivalent atoms.
- ''',
- a_legacy=LegacyDefinition(name='equivalent_atoms_primitive'))
-
- lattice_vectors_primitive = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='meter',
- description='''
- Primitive lattice vectors. The vectors are the rows of this matrix.
- ''',
- a_legacy=LegacyDefinition(name='lattice_vectors_primitive'))
-
- number_of_atoms_primitive = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms in primitive system.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_primitive'))
-
- wyckoff_letters_primitive = Quantity(
- type=str,
- shape=['number_of_atoms_primitive'],
- description='''
- Wyckoff letters for atoms in the primitive cell.
- ''',
- a_legacy=LegacyDefinition(name='wyckoff_letters_primitive'))
-
-
-class section_processor_info(MSection):
- '''
- Section with information about a processor that generated or added information to the
- current calculation.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_processor_info'))
-
- processor_id = Quantity(
- type=str,
- shape=[],
- description='''
- Id (name+version) of the processor that generated or added information to the
- current calculation.
- ''',
- a_legacy=LegacyDefinition(name='processor_id'))
-
- processor_number_of_evaluated_contexts = Quantity(
- type=np.dtype(np.int64),
- shape=[],
- description='''
- number of contexts evaluated with this processor in the current current
- calculation.
- ''',
- a_legacy=LegacyDefinition(name='processor_number_of_evaluated_contexts'))
-
- processor_number_of_failed_contexts = Quantity(
- type=np.dtype(np.int64),
- shape=[],
- description='''
- number of contexts in the current current calculation that had failure for this
- processor.
- ''',
- a_legacy=LegacyDefinition(name='processor_number_of_failed_contexts'))
-
- processor_number_of_skipped_contexts = Quantity(
- type=np.dtype(np.int64),
- shape=[],
- description='''
- number of contexts skipped by this processor in the current current calculation.
- ''',
- a_legacy=LegacyDefinition(name='processor_number_of_skipped_contexts'))
-
- processor_number_of_successful_contexts = Quantity(
- type=np.dtype(np.int64),
- shape=[],
- description='''
- number of contexts in the current calculation that where successfully handled by
- this processor.
- ''',
- a_legacy=LegacyDefinition(name='processor_number_of_successful_contexts'))
-
- processor_version_details = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- detailed version information on the processor that generated or added information
- to the current calculation.
- ''',
- a_legacy=LegacyDefinition(name='processor_version_details'))
-
-
-class section_processor_log_event(MSection):
- '''
- A log event
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_processor_log_event'))
-
- processor_log_event_level = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Level of the logging, a lower number has more priority. The levels are the same as
- log4j: FATAL -> 100, ERROR -> 200, WARN -> 300, INFO -> 400, DEBUG -> 500, TRACE
- -> 600
- ''',
- a_legacy=LegacyDefinition(name='processor_log_event_level'))
-
- processor_log_event_message = Quantity(
- type=str,
- shape=[],
- description='''
- The log message
- ''',
- a_legacy=LegacyDefinition(name='processor_log_event_message'))
-
-
-class section_processor_log(MSection):
- '''
- log of a processor
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_processor_log'))
-
- processor_log_processor_id = Quantity(
- type=str,
- shape=[],
- description='''
- The processor id of the processor creating this log
- ''',
- a_legacy=LegacyDefinition(name='processor_log_processor_id'))
-
- processor_log_start = Quantity(
- type=str,
- shape=[],
- description='''
- Start of the log (in ansi notation YYYY-MM-TT...)
- ''',
- a_legacy=LegacyDefinition(name='processor_log_start'))
-
- section_processor_log_event = SubSection(
- sub_section=SectionProxy('section_processor_log_event'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_processor_log_event'))
-
-
-class section_prototype(MSection):
- '''
- Information on the prototype corresponding to the current section.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_prototype'))
-
- prototype_aflow_id = Quantity(
- type=str,
- shape=[],
- description='''
- AFLOW id of the prototype (see
- http://aflowlib.org/CrystalDatabase/prototype_index.html) identified on the basis
- of the space_group and normalized_wyckoff.
- ''',
- a_legacy=LegacyDefinition(name='prototype_aflow_id'))
-
- prototype_aflow_url = Quantity(
- type=str,
- shape=[],
- description='''
- Url to the AFLOW definition of the prototype (see
- http://aflowlib.org/CrystalDatabase/prototype_index.html) identified on the basis
- of the space_group and normalized_wyckoff.
- ''',
- a_legacy=LegacyDefinition(name='prototype_aflow_url'))
-
- prototype_assignment_method = Quantity(
- type=str,
- shape=[],
- description='''
- Method used to identify the prototype.
- ''',
- a_legacy=LegacyDefinition(name='prototype_assignment_method'))
-
- prototype_label = Quantity(
- type=str,
- shape=[],
- description='''
- Label of the prototype identified on the basis of the space_group and
- normalized_wyckoff. The label is in the same format as in the read_prototypes
- function: <space_group_number>-<prototype_name>-<Pearson's symbol>).
- ''',
- a_legacy=LegacyDefinition(name='prototype_label'))
-
-
-class section_run(MSection):
- '''
- Every section_run represents a single call of a program. What exactly is contained in
- a run depends on the run type (see for example section_method and
- section_single_configuration_calculation) and the program (see [program_info
- ](program_info)).
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_run'))
-
- calculation_file_uri = Quantity(
- type=str,
- shape=[],
- description='''
- Contains the nomad uri of a raw the data file connected to the current run. There
- should be an value for the main_file_uri and all ancillary files.
- ''',
- a_legacy=LegacyDefinition(name='calculation_file_uri'))
-
- message_debug_run = Quantity(
- type=str,
- shape=[],
- description='''
- A debugging message of the computational program, associated with a run.
- ''',
- categories=[message_debug],
- a_legacy=LegacyDefinition(name='message_debug_run'))
-
- message_error_run = Quantity(
- type=str,
- shape=[],
- description='''
- An error message of the computational program, associated with a run.
- ''',
- categories=[message_info, message_debug, message_error, message_warning],
- a_legacy=LegacyDefinition(name='message_error_run'))
-
- message_info_run = Quantity(
- type=str,
- shape=[],
- description='''
- An information message of the computational program, associated with a run.
- ''',
- categories=[message_info, message_debug],
- a_legacy=LegacyDefinition(name='message_info_run'))
-
- message_warning_run = Quantity(
- type=str,
- shape=[],
- description='''
- A warning message of the computational program, associated with a run.
- ''',
- categories=[message_info, message_debug, message_warning],
- a_legacy=LegacyDefinition(name='message_warning_run'))
-
- parsing_message_debug_run = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for debugging messages of the parsing program associated with a
- single configuration calculation, see section_single_configuration_calculation.
- ''',
- categories=[parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_debug_run'))
-
- parsing_message_error_run = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for error messages of the parsing program associated with a
- run, see section_run.
- ''',
- categories=[parsing_message_info, parsing_message_error, parsing_message_warning, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_error_run'))
-
- parsing_message_info_run = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for info messages of the parsing program associated with a run,
- see section_run.
- ''',
- categories=[parsing_message_info, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_info_run'))
-
- parsing_message_warning_run = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for warning messages of the parsing program associated with a
- run, see section_run.
- ''',
- categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_warning_run'))
-
- program_basis_set_type = Quantity(
- type=str,
- shape=[],
- description='''
- The type of basis set used by the program to represent wave functions. Valid values
- are: [`Numeric AOs`, `Gaussians`, `(L)APW+lo`, `plane waves`, `psinc functions`,
- `real-space grid`].
- ''',
- a_legacy=LegacyDefinition(name='program_basis_set_type'))
-
- program_compilation_datetime = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Contains the program compilation date and time from *Unix epoch* (00:00:00 UTC on
- 1 January 1970) in seconds. For date and times without a timezone, the default
- timezone GMT is used.
- ''',
- categories=[accessory_info, program_info],
- a_legacy=LegacyDefinition(name='program_compilation_datetime'))
-
- program_compilation_host = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the host on which the program was compiled.
- ''',
- categories=[accessory_info, program_info],
- a_legacy=LegacyDefinition(name='program_compilation_host'))
-
- program_name = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the name of the program that generated the data.
- ''',
- categories=[accessory_info, program_info],
- a_legacy=LegacyDefinition(name='program_name'))
-
- program_version = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the version of the program that was used. This should be the version
- number of an official release, the version tag or a commit id as well as the
- location of the repository.
- ''',
- categories=[accessory_info, program_info],
- a_legacy=LegacyDefinition(name='program_version'))
-
- run_clean_end = Quantity(
- type=bool,
- shape=[],
- description='''
- Indicates whether this run terminated properly (true), or if it was killed or
- exited with an error code unequal to zero (false).
- ''',
- a_legacy=LegacyDefinition(name='run_clean_end'))
-
- run_hosts = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- An associative list of host(s) that performed this simulation. This is an
- associative list that contains program-dependent information (*key*) on how the
- host was used (*value*). Useful for debugging purposes.
- ''',
- categories=[parallelization_info, accessory_info],
- a_legacy=LegacyDefinition(name='run_hosts'))
-
- raw_id = Quantity(
- type=str,
- shape=[],
- description='''
- An optional calculation id, if one is found in the code input/output files.
- ''',
- a_legacy=LegacyDefinition(name='raw_id'))
-
- time_run_cpu1_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the end time of the run on CPU 1.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_run_cpu1_end'))
-
- time_run_cpu1_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the start time of the run on CPU 1.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_run_cpu1_start'))
-
- time_run_date_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the end date of the run as time since the *Unix epoch* (00:00:00 UTC on 1
- January 1970) in seconds. For date and times without a timezone, the default
- timezone GMT is used.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_run_date_end'))
-
- time_run_date_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the start date of the run as time since the *Unix epoch* (00:00:00 UTC on 1
- January 1970) in seconds. For date and times without a timezone, the default
- timezone GMT is used.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_run_date_start'))
-
- time_run_wall_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the internal wall-clock time at the end of the run.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_run_wall_end'))
-
- time_run_wall_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the internal wall-clock time from the start of the run.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_run_wall_start'))
-
- section_basis_set_atom_centered = SubSection(
- sub_section=SectionProxy('section_basis_set_atom_centered'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
-
- section_basis_set_cell_dependent = SubSection(
- sub_section=SectionProxy('section_basis_set_cell_dependent'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))
-
- section_frame_sequence = SubSection(
- sub_section=SectionProxy('section_frame_sequence'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_frame_sequence'))
-
- section_method = SubSection(
- sub_section=SectionProxy('section_method'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_method'))
-
- section_sampling_method = SubSection(
- sub_section=SectionProxy('section_sampling_method'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_sampling_method'))
-
- section_single_configuration_calculation = SubSection(
- sub_section=SectionProxy('section_single_configuration_calculation'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
-
- section_system = SubSection(
- sub_section=SectionProxy('section_system'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_system'))
-
-
-class section_sampling_method(MSection):
- '''
- Section containing the settings describing a (potential-energy surface) sampling
- method.
-
- Results and monitored quantities of such sampling are collected in a sequence of
- frames, section_frame_sequence.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_sampling_method'))
-
- ensemble_type = Quantity(
- type=str,
- shape=[],
- description='''
- Kind of sampled ensemble stored in section_frame_sequence; valid values are
- defined in [ensemble_type wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
- meta-info/wikis/metainfo/ensemble-type).
- ''',
- a_legacy=LegacyDefinition(name='ensemble_type'))
-
- geometry_optimization_energy_change = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of threshold for the energy_total change between two geometry optimization
- steps, as convergence criterion of the geometry_optimization_method. A geometry
- optimization is considered converged when the energy_total change between two
- geometry optimization steps is below the threshold (possibly in combination with
- other criteria)
- ''',
- categories=[settings_geometry_optimization, settings_sampling],
- a_legacy=LegacyDefinition(name='geometry_optimization_energy_change'))
-
- geometry_optimization_geometry_change = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='meter',
- description='''
- Value of threshold for the displacement of the nuclei between two geometry
- optimization steps as convergence criterion of the geometry_optimization_method. A
- geometry optimization is considered converged when the maximum among the
- displacements of the nuclei between two geometry optimization steps is below the
- threshold (possibly in combination with other criteria)
- ''',
- categories=[settings_geometry_optimization, settings_sampling],
- a_legacy=LegacyDefinition(name='geometry_optimization_geometry_change'))
-
- geometry_optimization_method = Quantity(
- type=str,
- shape=[],
- description='''
- Algorithm for the geometry optimization. Allowed values are listed in the
- [geometry_optimization_method wiki page](https://gitlab.mpcdf.mpg.de/nomad-
- lab/nomad-meta-info/wikis/metainfo/geometry-optimization-method).
- ''',
- categories=[settings_geometry_optimization, settings_sampling],
- a_legacy=LegacyDefinition(name='geometry_optimization_method'))
-
- geometry_optimization_threshold_force = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='newton',
- description='''
- Value of threshold for the force modulus as convergence criterion of the
- geometry_optimization_method. A geometry optimization is considered converged when
- the maximum of the moduli of the force on each of the atoms is below this
- threshold (possibly in combination with other criteria)
- ''',
- categories=[settings_geometry_optimization, settings_sampling],
- a_legacy=LegacyDefinition(name='geometry_optimization_threshold_force'))
-
- sampling_method_expansion_order = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Order up to which the potential energy surface was expanded in a Taylor series
- (see sampling_method).
- ''',
- a_legacy=LegacyDefinition(name='sampling_method_expansion_order'))
-
- sampling_method = Quantity(
- type=str,
- shape=[],
- description='''
- Type of method used to do the sampling.
-
- Allowed values are:
-
- | Sampling method | Description |
-
- | ------------------------------ | -------------------------------- |
-
- | `"geometry_optimization"` | Geometry optimization |
-
- | `"molecular_dynamics"` | Molecular dynamics |
-
- | `"montecarlo"` | (Metropolis) Monte Carlo |
-
- | `"steered_molecular_dynamics"` | Steered molecular dynamics (with time dependent
- external forces) |
-
- | `"meta_dynamics"` | Biased molecular dynamics with history-
- dependent Hamiltonian |
-
- | `"wang_landau_montecarlo"` | Monte Carlo according to the Wang-Landau
- formulation. |
-
- | `"blue_moon"` | Blue Moon sampling |
-
- | `"langevin_dynamics"` | Langevin dynamics |
-
- | `"taylor_expansion"` | Taylor expansion of the potential energy
- surface |
- ''',
- a_legacy=LegacyDefinition(name='sampling_method'))
-
-
-class section_scf_iteration(MSection):
- '''
- Every section_scf_iteration represents a self-consistent field (SCF) iteration, see
- scf_info, and gives detailed information on the SCF procedure of the specified
- quantities.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_scf_iteration'))
-
- electronic_kinetic_energy_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Electronic kinetic energy as defined in XC_method during the self-consistent field
- (SCF) iterations.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='electronic_kinetic_energy_scf_iteration'))
-
- energy_change_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Stores the change of total energy with respect to the previous self-consistent
- field (SCF) iteration.
- ''',
- categories=[error_estimate_contribution, energy_value],
- a_legacy=LegacyDefinition(name='energy_change_scf_iteration'))
-
- energy_correction_entropy_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Entropy correction to the potential energy to compensate for the change in
- occupation so that forces at finite T do not need to keep the change of occupation
- in account. The array lists the values of the entropy correction for each self-
- consistent field (SCF) iteration. Defined consistently with XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_correction_entropy_scf_iteration'))
-
- energy_correction_hartree_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Correction to the density-density electrostatic energy in the sum of eigenvalues
- (that uses the mixed density on one side), and the fully consistent density-
- density electrostatic energy during the self-consistent field (SCF) iterations.
- Defined consistently with XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_correction_hartree_scf_iteration'))
-
- energy_electrostatic_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Total electrostatic energy (nuclei + electrons) during each self-consistent field
- (SCF) iteration.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_electrostatic_scf_iteration'))
-
- energy_free_per_atom_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Free energy per atom (whose minimum gives the smeared occupation density
- calculated with smearing_kind) calculated with XC_method during the self-
- consistent field (SCF) iterations.
- ''',
- categories=[energy_component_per_atom, energy_value],
- a_legacy=LegacyDefinition(name='energy_free_per_atom_scf_iteration'))
-
- energy_free_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Free energy (whose minimum gives the smeared occupation density calculated with
- smearing_kind) calculated with the method described in XC_method during the self-
- consistent field (SCF) iterations.
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_free_scf_iteration'))
-
- energy_hartree_error_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Error in the Hartree (electrostatic) potential energy during each self-consistent
- field (SCF) iteration. Defined consistently with XC_method.
- ''',
- categories=[error_estimate_contribution, energy_value],
- a_legacy=LegacyDefinition(name='energy_hartree_error_scf_iteration'))
-
- energy_sum_eigenvalues_per_atom_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the energy per atom, where the energy is defined as the sum of the
- eigenvalues of the Hamiltonian matrix given by XC_method, during each self-
- consistent field (SCF) iteration.
- ''',
- categories=[energy_component_per_atom, energy_value],
- a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_per_atom_scf_iteration'))
-
- energy_sum_eigenvalues_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Sum of the eigenvalues of the Hamiltonian matrix defined by XC_method, during each
- self-consistent field (SCF) iteration.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_scf_iteration'))
-
- energy_total_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total electronic energy calculated with the method described in
- XC_method during each self-consistent field (SCF) iteration.
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_total_scf_iteration'))
-
- energy_total_T0_per_atom_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total energy, calculated with the method described in XC_method per
- atom extrapolated to $T=0$, based on a free-electron gas argument, during each
- self-consistent field (SCF) iteration.
- ''',
- categories=[energy_total_potential_per_atom, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_total_T0_per_atom_scf_iteration'))
-
- energy_total_T0_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total energy (or equivalently free energy), calculated with the
- method described in XC_method and extrapolated to $T=0$, based on a free-electron
- gas argument, during each self-consistent field (SCF) iteration.
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_total_T0_scf_iteration'))
-
- energy_XC_potential_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value for exchange-correlation (XC) potential energy: the integral of the first
- order derivative of the functional stored in XC_functional (integral of
- v_xc*electron_density), i.e., the component of XC that is in the sum of the
- eigenvalues. Values are given for each self-consistent field (SCF) iteration
- (i.e., not the converged value, the latter being stored in energy_XC_potential).
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_XC_potential_scf_iteration'))
-
- energy_XC_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value for exchange-correlation (XC) energy obtained during each self-consistent
- field (SCF) iteration, using the method described in XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_XC_scf_iteration'))
-
- spin_S2_scf_iteration = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Stores the value of the total spin moment operator $S^2$ during the self-
- consistent field (SCF) iterations of the XC_method. It can be used to calculate
- the spin contamination in spin-unrestricted calculations.
- ''',
- a_legacy=LegacyDefinition(name='spin_S2_scf_iteration'))
-
- time_scf_iteration_cpu1_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the end time of a self-consistent field (SCF) iteration on CPU 1.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_scf_iteration_cpu1_end'))
-
- time_scf_iteration_cpu1_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the start time of a self-consistent field (SCF) iteration on CPU 1.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_scf_iteration_cpu1_start'))
-
- time_scf_iteration_date_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the end date of a self-consistent field (SCF) iteration as time since the
- *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds. For date and times
- without a timezone, the default timezone GMT is used.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_scf_iteration_date_end'))
-
- time_scf_iteration_date_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the start date of a self-consistent field (SCF) iteration as time since the
- *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds. For date and times
- without a timezone, the default timezone GMT is used.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_scf_iteration_date_start'))
-
- time_scf_iteration_wall_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the internal wall-clock time at the end of a self-consistent field (SCF)
- iteration.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_scf_iteration_wall_end'))
-
- time_scf_iteration_wall_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the internal wall-clock time from the start of a self-consistent field
- (SCF) iteration.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_scf_iteration_wall_start'))
-
-
-class section_single_configuration_calculation(MSection):
- '''
- Every section_single_configuration_calculation section contains the values computed
- during a *single configuration calculation*, i.e. a calculation performed on a given
- configuration of the system (as defined in section_system) and a given computational
- method (e.g., exchange-correlation method, basis sets, as defined in section_method).
-
- The link between the current section_single_configuration_calculation and the related
- section_system and section_method sections is established by the values stored in
- single_configuration_calculation_to_system_ref and
- single_configuration_to_calculation_method_ref, respectively.
-
- The reason why information on the system configuration and computational method is
- stored separately is that several *single configuration calculations* can be performed
- on the same system configuration, viz. several system configurations can be evaluated
- with the same computational method. This storage strategy avoids redundancies.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
-
- atom_forces_free_raw = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='newton',
- description='''
- Forces acting on the atoms, calculated as minus gradient of energy_free,
- **without** constraints. The derivatives with respect to displacements of nuclei
- are evaluated in Cartesian coordinates. The (electronic) energy_free contains the
- change in (fractional) occupation of the electronic eigenstates, which are
- accounted for in the derivatives, yielding a truly energy-conserved quantity.
- These forces may contain unitary transformations (center-of-mass translations and
- rigid rotations for non-periodic systems) that are normally filtered separately
- (see atom_forces_free for the filtered counterpart). Forces due to constraints
- such as fixed atoms, distances, angles, dihedrals, etc. are also considered
- separately (see atom_forces_free for the filtered counterpart).
- ''',
- categories=[atom_forces_type],
- a_legacy=LegacyDefinition(name='atom_forces_free_raw'))
-
- atom_forces_free = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='newton',
- description='''
- Forces acting on the atoms, calculated as minus gradient of energy_free,
- **including** constraints, if present. The derivatives with respect to
- displacements of the nuclei are evaluated in Cartesian coordinates. The
- (electronic) energy_free contains the information on the change in (fractional)
- occupation of the electronic eigenstates, which are accounted for in the
- derivatives, yielding a truly energy-conserved quantity. In addition, these forces
- are obtained by filtering out the unitary transformations (center-of-mass
- translations and rigid rotations for non-periodic systems, see
- atom_forces_free_raw for the unfiltered counterpart). Forces due to constraints
- such as fixed atoms, distances, angles, dihedrals, etc. are included (see
- atom_forces_free_raw for the unfiltered counterpart).
- ''',
- categories=[atom_forces_type],
- a_legacy=LegacyDefinition(name='atom_forces_free'))
-
- atom_forces_raw = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='newton',
- description='''
- Forces acting on the atoms, calculated as minus gradient of energy_total,
- **without** constraints. The derivatives with respect to displacements of the
- nuclei are evaluated in Cartesian coordinates. These forces may contain unitary
- transformations (center-of-mass translations and rigid rotations for non-periodic
- systems) that are normally filtered separately (see atom_forces for the filtered
- counterpart). Forces due to constraints such as fixed atoms, distances, angles,
- dihedrals, etc. are also considered separately (see atom_forces for the filtered
- counterpart).
- ''',
- categories=[atom_forces_type],
- a_legacy=LegacyDefinition(name='atom_forces_raw'))
-
- atom_forces_T0_raw = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='newton',
- description='''
- Forces acting on the atoms, calculated as minus gradient of energy_total_T0,
- **without** constraints. The derivatives with respect to displacements of the
- nuclei are evaluated in Cartesian coordinates. These forces may contain unitary
- transformations (center-of-mass translations and rigid rotations for non-periodic
- systems) that are normally filtered separately (see atom_forces_T0 for the
- filtered counterpart). Forces due to constraints such as fixed atoms, distances,
- angles, dihedrals, etc. are also considered separately (see atom_forces_T0 for the
- filtered counterpart).
- ''',
- categories=[atom_forces_type],
- a_legacy=LegacyDefinition(name='atom_forces_T0_raw'))
-
- atom_forces_T0 = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='newton',
- description='''
- Forces acting on the atoms, calculated as minus gradient of energy_total_T0,
- **including** constraints, if present. The derivatives with respect to
- displacements of the nuclei are evaluated in Cartesian coordinates. In addition,
- these forces are obtained by filtering out the unitary transformations (center-of-
- mass translations and rigid rotations for non-periodic systems, see
- atom_forces_free_T0_raw for the unfiltered counterpart). Forces due to constraints
- such as fixed atoms, distances, angles, dihedrals, etc. are also included (see
- atom_forces_free_T0_raw for the unfiltered counterpart).
- ''',
- categories=[atom_forces_type],
- a_legacy=LegacyDefinition(name='atom_forces_T0'))
-
- atom_forces = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='newton',
- description='''
- Forces acting on the atoms, calculated as minus gradient of energy_total,
- **including** constraints, if present. The derivatives with respect to
- displacements of nuclei are evaluated in Cartesian coordinates. In addition, these
- forces are obtained by filtering out the unitary transformations (center-of-mass
- translations and rigid rotations for non-periodic systems, see
- atom_forces_free_raw for the unfiltered counterpart). Forces due to constraints
- such as fixed atoms, distances, angles, dihedrals, etc. are included (see
- atom_forces_raw for the unfiltered counterpart).
- ''',
- categories=[atom_forces_type],
- a_legacy=LegacyDefinition(name='atom_forces'))
-
- electronic_kinetic_energy = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Self-consistent electronic kinetic energy as defined in XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='electronic_kinetic_energy'))
-
- energy_C = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Correlation (C) energy calculated with the method described in XC_functional.
- ''',
- categories=[energy_component, energy_value, energy_type_C],
- a_legacy=LegacyDefinition(name='energy_C'))
-
- energy_correction_entropy = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Entropy correction to the potential energy to compensate for the change in
- occupation so that forces at finite T do not need to keep the change of occupation
- in account. Defined consistently with XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_correction_entropy'))
-
- energy_correction_hartree = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Correction to the density-density electrostatic energy in the sum of eigenvalues
- (that uses the mixed density on one side), and the fully consistent density-
- density electrostatic energy. Defined consistently with XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_correction_hartree'))
-
- energy_current = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the energy calculated with calculation_method_current. energy_current is
- equal to energy_total for non-perturbative methods. For perturbative methods,
- energy_current is equal to the correction: energy_total minus energy_total of the
- calculation_to_calculation_ref with calculation_to_calculation_kind =
- starting_point (see the [method_to_method_kind wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/method-
- to-method-kind)). See also [energy_current wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/energy-
- current).
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_current'))
-
- energy_electrostatic = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Total electrostatic energy (nuclei + electrons), defined consistently with
- calculation_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_electrostatic'))
-
- energy_free_per_atom = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Free energy per atom (whose minimum gives the smeared occupation density
- calculated with smearing_kind) calculated with XC_method.
- ''',
- categories=[energy_component_per_atom, energy_value],
- a_legacy=LegacyDefinition(name='energy_free_per_atom'))
-
- energy_free = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Free energy (nuclei + electrons) (whose minimum gives the smeared occupation
- density calculated with smearing_kind) calculated with the method described in
- XC_method.
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_free'))
-
- energy_hartree_error = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Error in the Hartree (electrostatic) potential energy. Defined consistently with
- XC_method.
- ''',
- categories=[error_estimate_contribution, energy_value],
- a_legacy=LegacyDefinition(name='energy_hartree_error'))
-
- energy_hartree_fock_X_scaled = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Scaled exact-exchange energy that depends on the mixing parameter of the
- functional. For example in hybrid functionals, the exchange energy is given as a
- linear combination of exact-energy and exchange energy of an approximate DFT
- functional; the exact exchange energy multiplied by the mixing coefficient of the
- hybrid functional would be stored in this metadata. Defined consistently with
- XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_hartree_fock_X_scaled'))
-
- energy_hartree_fock_X = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Converged exact-exchange (Hartree-Fock) energy. Defined consistently with
- XC_method.
- ''',
- categories=[energy_type_X, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_hartree_fock_X'))
-
- energy_method_current = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the energy calculated with the method calculation_method_current.
- Depending on calculation_method_kind it might be a total energy or only a
- correction.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_method_current'))
-
- energy_sum_eigenvalues_per_atom = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the energy per atom, where the energy is defined as the sum of the
- eigenvalues of the Hamiltonian matrix given by XC_method.
- ''',
- categories=[energy_component_per_atom, energy_value],
- a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_per_atom'))
-
- energy_sum_eigenvalues = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Sum of the eigenvalues of the Hamiltonian matrix defined by XC_method.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_sum_eigenvalues'))
-
- energy_T0_per_atom = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total energy per atom, calculated with the method described in
- XC_method and extrapolated to $T=0$, based on a free-electron gas argument.
- ''',
- categories=[energy_total_potential_per_atom, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_T0_per_atom'))
-
- energy_total_T0_per_atom = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total energy, calculated with the method described in XC_method per
- atom extrapolated to $T=0$, based on a free-electron gas argument.
- ''',
- categories=[energy_total_potential_per_atom, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_total_T0_per_atom'))
-
- energy_total_T0 = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total energy (or equivalently free energy), calculated with the
- method described in XC_method and extrapolated to $T=0$, based on a free-electron
- gas argument.
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_total_T0'))
-
- energy_total = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the total energy, calculated with the method described in XC_method and
- extrapolated to $T=0$, based on a free-electron gas argument.
- ''',
- categories=[energy_component, energy_value, energy_total_potential],
- a_legacy=LegacyDefinition(name='energy_total'))
-
- energy_XC_functional = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the exchange-correlation (XC) energy calculated with the functional
- stored in XC_functional.
- ''',
- categories=[energy_type_XC, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_XC_functional'))
-
- energy_XC_potential = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the exchange-correlation (XC) potential energy: the integral of the first
- order derivative of the functional stored in XC_functional (integral of
- v_xc*electron_density), i.e., the component of XC that is in the sum of the
- eigenvalues. Value associated with the configuration, should be the most converged
- value.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_XC_potential'))
-
- energy_XC = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the exchange-correlation (XC) energy calculated with the method described
- in XC_method.
- ''',
- categories=[energy_type_XC, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_XC'))
-
- energy_X = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value fo the exchange (X) energy calculated with the method described in
- XC_method.
- ''',
- categories=[energy_type_X, energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_X'))
-
- energy_zero_point = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Value for the converged zero-point vibrations energy calculated using the method
- described in zero_point_method , and used in energy_current .
- ''',
- a_legacy=LegacyDefinition(name='energy_zero_point'))
-
- hessian_matrix = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 'number_of_atoms', 3, 3],
- description='''
- The matrix with the second derivative with respect to atom displacements.
- ''',
- a_legacy=LegacyDefinition(name='hessian_matrix'))
-
- message_debug_evaluation = Quantity(
- type=str,
- shape=[],
- description='''
- A debugging message of the computational program, associated with a *single
- configuration calculation* (see section_single_configuration_calculation).
- ''',
- categories=[message_debug],
- a_legacy=LegacyDefinition(name='message_debug_evaluation'))
-
- message_error_evaluation = Quantity(
- type=str,
- shape=[],
- description='''
- An error message of the computational program, associated with a *single
- configuration calculation* (see section_single_configuration_calculation).
- ''',
- categories=[message_info, message_debug, message_error, message_warning],
- a_legacy=LegacyDefinition(name='message_error_evaluation'))
-
- message_info_evaluation = Quantity(
- type=str,
- shape=[],
- description='''
- An information message of the computational program, associated with a *single
- configuration calculation* (see section_single_configuration_calculation).
- ''',
- categories=[message_info, message_debug],
- a_legacy=LegacyDefinition(name='message_info_evaluation'))
-
- message_warning_evaluation = Quantity(
- type=str,
- shape=[],
- description='''
- A warning message of the computational program.
- ''',
- categories=[message_info, message_debug, message_warning],
- a_legacy=LegacyDefinition(name='message_warning_evaluation'))
-
- number_of_scf_iterations = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of performed self-consistent field (SCF) iterations at a specfied
- level of theory.
- ''',
- categories=[scf_info],
- a_legacy=LegacyDefinition(name='number_of_scf_iterations'))
-
- parsing_message_debug_evaluation = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for debugging messages of the parsing program associated with a
- run, see section_run.
- ''',
- categories=[parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_debug_evaluation'))
-
- parsing_message_error_single_configuration = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for error messages of the parsing program associated with a
- single configuration calculation, see section_single_configuration_calculation.
- ''',
- categories=[parsing_message_info, parsing_message_error, parsing_message_warning, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_error_single_configuration'))
-
- parsing_message_info_single_configuration = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for info messages of the parsing program associated with a
- single configuration calculation, see section_single_configuration_calculation.
- ''',
- categories=[parsing_message_info, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_info_single_configuration'))
-
- parsing_message_warning_evaluation = Quantity(
- type=str,
- shape=[],
- description='''
- This field is used for warning messages of the parsing program associated with a
- run, see section_run.
- ''',
- categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
- a_legacy=LegacyDefinition(name='parsing_message_warning_evaluation'))
-
- single_configuration_calculation_converged = Quantity(
- type=bool,
- shape=[],
- description='''
- Determines whether a *single configuration calculation* in
- section_single_configuration_calculation is converged.
- ''',
- a_legacy=LegacyDefinition(name='single_configuration_calculation_converged'))
-
- single_configuration_calculation_to_system_ref = Quantity(
- type=Reference(SectionProxy('section_system')),
- shape=[],
- description='''
- Reference to the system (atomic configuration, cell, ...) that is calculated in
- section_single_configuration_calculation.
- ''',
- categories=[fast_access],
- a_legacy=LegacyDefinition(name='single_configuration_calculation_to_system_ref'))
-
- single_configuration_to_calculation_method_ref = Quantity(
- type=Reference(SectionProxy('section_method')),
- shape=[],
- categories=[fast_access],
- description='''
- Reference to the method used for the calculation in
- section_single_configuration_calculation.
- ''',
- a_legacy=LegacyDefinition(name='single_configuration_to_calculation_method_ref'))
-
- spin_S2 = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Stores the value of the total spin moment operator $S^2$ for the converged
- wavefunctions calculated with the XC_method. It can be used to calculate the spin
- contamination in spin-unrestricted calculations.
- ''',
- a_legacy=LegacyDefinition(name='spin_S2'))
-
- stress_tensor = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='pascal',
- description='''
- Stores the final value of the default stress tensor consistent with energy_total
- and calculated with the method specified in stress_tensor_method.
-
- This value is used (if needed) for, e.g., molecular dynamics and geometry
- optimization. Alternative definitions of the stress tensor can be assigned with
- stress_tensor_kind
- ''',
- categories=[stress_tensor_type],
- a_legacy=LegacyDefinition(name='stress_tensor'))
-
- time_calculation = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the wall-clock time needed for a calculation using
- calculation_method_current. Basically, it tracks the real time that has been
- elapsed from start to end.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_calculation'))
-
- time_single_configuration_calculation_cpu1_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the end time of the *single configuration calculation* (see
- section_single_configuration_calculation) on CPU 1.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_single_configuration_calculation_cpu1_end'))
-
- time_single_configuration_calculation_cpu1_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the start time of the *single configuration calculation* (see
- section_single_configuration_calculation) on CPU 1.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_single_configuration_calculation_cpu1_start'))
-
- time_single_configuration_calculation_date_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the end date of the *single configuration calculation* (see
- section_single_configuration_calculation) as time since the *Unix epoch* (00:00:00
- UTC on 1 January 1970) in seconds. For date and times without a timezone, the
- default timezone GMT is used.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_single_configuration_calculation_date_end'))
-
- time_single_configuration_calculation_date_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the start date of the *single configuration calculation* (see
- section_single_configuration_calculation) as time since the *Unix epoch* (00:00:00
- UTC on 1 January 1970) in seconds. For date and times without a timezone, the
- default timezone GMT is used.
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_single_configuration_calculation_date_start'))
-
- time_single_configuration_calculation_wall_end = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the internal wall-clock time at the end of the *single configuration
- calculation* (see section_single_configuration_calculation).
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_single_configuration_calculation_wall_end'))
-
- time_single_configuration_calculation_wall_start = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='second',
- description='''
- Stores the internal wall-clock time from the start of the *single configuration
- calculation* (see section_single_configuration_calculation).
- ''',
- categories=[time_info, accessory_info],
- a_legacy=LegacyDefinition(name='time_single_configuration_calculation_wall_start'))
-
- zero_point_method = Quantity(
- type=str,
- shape=[],
- description='''
- Describes the zero-point vibrations method. If skipped or an empty string is used,
- it means no zero-point vibrations correction is applied.
- ''',
- a_legacy=LegacyDefinition(name='zero_point_method'))
-
- enthalpy = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the calculated enthalpy i.e. energy_total + pressure * volume.
- ''',
- categories=[energy_component, energy_value],
- a_legacy=LegacyDefinition(name='energy_enthalpy'))
-
- pressure = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='pascal',
- description='''
- Value of the pressure of the system.
- ''',
- a_legacy=LegacyDefinition(name='pressure'))
-
- temperature = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='kelvin',
- description='''
- Value of the temperature of the system.
- ''',
- a_legacy=LegacyDefinition(name='temperature'))
-
- time_step = Quantity(
- type=int,
- shape=[],
- description='''
- The number of time steps with respect to the start of the calculation.
- ''',
- a_legacy=LegacyDefinition(name='time_step'))
-
- section_atom_projected_dos = SubSection(
- sub_section=SectionProxy('section_atom_projected_dos'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_atom_projected_dos'))
-
- section_atomic_multipoles = SubSection(
- sub_section=SectionProxy('section_atomic_multipoles'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_atomic_multipoles'))
-
- section_basis_set = SubSection(
- sub_section=SectionProxy('section_basis_set'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_basis_set'))
-
- section_calculation_to_calculation_refs = SubSection(
- sub_section=SectionProxy('section_calculation_to_calculation_refs'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))
-
- section_calculation_to_folder_refs = SubSection(
- sub_section=SectionProxy('section_calculation_to_folder_refs'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))
-
- section_dos = SubSection(
- sub_section=SectionProxy('section_dos'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_dos'))
-
- section_eigenvalues = SubSection(
- sub_section=SectionProxy('section_eigenvalues'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_eigenvalues'))
-
- section_energy_code_independent = SubSection(
- sub_section=SectionProxy('section_energy_code_independent'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_energy_code_independent'))
-
- section_energy_van_der_Waals = SubSection(
- sub_section=SectionProxy('section_energy_van_der_Waals'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
-
- section_energy_contribution = SubSection(
- sub_section=SectionProxy('section_energy_contribution'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_energy_contribution'))
-
- section_k_band_normalized = SubSection(
- sub_section=SectionProxy('section_k_band_normalized'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_k_band_normalized'))
-
- section_k_band = SubSection(
- sub_section=SectionProxy('section_k_band'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_k_band'))
-
- section_scf_iteration = SubSection(
- sub_section=SectionProxy('section_scf_iteration'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_scf_iteration'))
-
- section_species_projected_dos = SubSection(
- sub_section=SectionProxy('section_species_projected_dos'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_species_projected_dos'))
-
- section_stress_tensor = SubSection(
- sub_section=SectionProxy('section_stress_tensor'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_stress_tensor'))
-
- section_volumetric_data = SubSection(
- sub_section=SectionProxy('section_volumetric_data'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_volumetric_data'))
-
-
-class section_species_projected_dos(MSection):
- '''
- Section collecting the information on a species-projected density of states (DOS)
- evaluation.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_species_projected_dos'))
-
- number_of_lm_species_projected_dos = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of $l$, $m$ combinations for the species-projected density of
- states (DOS) defined in section_species_projected_dos.
- ''',
- a_legacy=LegacyDefinition(name='number_of_lm_species_projected_dos'))
-
- number_of_species_projected_dos_values = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of energy values for the species-projected density of states
- (DOS) defined in section_species_projected_dos.
- ''',
- a_legacy=LegacyDefinition(name='number_of_species_projected_dos_values'))
-
- number_of_species = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of species for the species-projected density of states (DOS)
- defined in section_species_projected_dos.
- ''',
- a_legacy=LegacyDefinition(name='number_of_species'))
-
- species_projected_dos_energies_normalized = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_species_projected_dos_values'],
- unit='joule',
- description='''
- Contains the set of discrete energy values with respect to the top of the valence
- band for the species-projected density of states (DOS). It is derived from the
- species_projected_dos_energies species field.
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_energies_normalized'))
-
- species_projected_dos_energies = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_species_projected_dos_values'],
- unit='joule',
- description='''
- Contains the set of discrete energy values for the species-projected density of
- states (DOS).
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_energies'))
-
- species_projected_dos_lm = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_lm_species_projected_dos', 2],
- description='''
- Consists of tuples of $l$ and $m$ values for all given values in the
- species_projected_dos_values_lm species field.
-
- The quantum number $l$ represents the azimuthal quantum number, whereas for the
- quantum number $m$, besides the conventional use as magnetic quantum number ($l+1$
- integer values from $-l$ to $l$), a set of different conventions is accepted. The
- adopted convention is specified by atom_projected_dos_m_kind.
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_lm'))
-
- species_projected_dos_m_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the kind of the integer numbers $m$ used in species_projected_dos_lm.
-
- Allowed values are listed in the [m_kind wiki
- page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind)
- and can be (quantum) numbers of
-
- * spherical
-
- * polynomial
-
- * real_orbital
-
- * integrated
-
- functions or values.
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_m_kind'))
-
- species_projected_dos_species_label = Quantity(
- type=str,
- shape=['number_of_species'],
- description='''
- Contains labels of the atomic species for the species-projected density of states
- (DOS).
-
- Differently from atom_labels, which allow more than one label for the same atomic
- species (by adding a number or a string to the label), this list is expected to
- refer to actual atomic species, i.e. belonging to the periodic table of elements.
- Thus, the species-projected DOS are expected to be as many as the different atomic
- species in the system.
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_species_label'))
-
- species_projected_dos_values_lm = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_lm_species_projected_dos', 'number_of_spin_channels', 'number_of_species', 'number_of_species_projected_dos_values'],
- description='''
- Holds species-projected density of states (DOS) values, divided into contributions
- from each $l,m$ channel.
-
- Here, there are as many species-projected DOS as the number of species,
- number_of_species. The list of labels of the species is given in
- species_projected_dos_species_label.
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_values_lm'))
-
- species_projected_dos_values_total = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_spin_channels', 'number_of_species', 'number_of_species_projected_dos_values'],
- description='''
- Holds species-projected density of states (DOS) values, summed up over all
- azimuthal quantum numbers $l$.
-
- Here, there are as many species-projected DOS as the number of species,
- number_of_species. The list of labels of the species is given in
- species_projected_dos_species_label.
- ''',
- a_legacy=LegacyDefinition(name='species_projected_dos_values_total'))
-
-
-class section_springer_material(MSection):
- '''
- Every section_springer_material contains results of classification of materials with
- the same formula according to Springer Materials - it contains
- section_springer_classsification, section_springer_compound, section_springer_id,
- section_springer_references
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_springer_material'))
-
- springer_id = Quantity(
- type=str,
- shape=[],
- description='''
- Id of the classified material according to Springer Materials
- ''',
- a_legacy=LegacyDefinition(name='springer_id'))
-
- springer_alphabetical_formula = Quantity(
- type=str,
- shape=[],
- description='''
- The alphabetical formula of the material according to Springer Materials Database
- ''',
- a_legacy=LegacyDefinition(name='springer_alphabetical_formula'))
-
- springer_url = Quantity(
- type=str,
- shape=[],
- description='''
- Url to the source page in Springer Materials describing the current entry
- ''',
- a_legacy=LegacyDefinition(name='springer_url'))
-
- springer_compound_class = Quantity(
- type=str,
- shape=['N'],
- description='''
- Name of a class of the current compound, as defined in by Springer Materials. This
- is a property of the chemical formula of the compound
- ''',
- a_legacy=LegacyDefinition(name='springer_compound_class'))
-
- springer_classification = Quantity(
- type=str,
- shape=['N'],
- description='''
- Contains the classification name of the current material according to Springer
- Materials
- ''',
- a_legacy=LegacyDefinition(name='springer_classification'))
-
- section_springer_id = SubSection(
- sub_section=SectionProxy('section_springer_id'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_springer_id'))
-
-
-class section_springer_id(MSection):
- '''
- Identifiers used by Springer Materials
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_springer_id'))
-
-
-class section_std_system(MSection):
- '''
- Section containing symmetry information that is specific to the standardized system.
- The standardized system is defined as given by spglib and the details can be found
- from https://arxiv.org/abs/1506.01455
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_std_system'))
-
- atom_positions_std = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms_std', 3],
- description='''
- Standardized atom positions in reduced units.
- ''',
- a_legacy=LegacyDefinition(name='atom_positions_std'))
-
- atomic_numbers_std = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_atoms_std'],
- description='''
- Atomic numbers of the atoms in the standardized cell.
- ''',
- a_legacy=LegacyDefinition(name='atomic_numbers_std'))
-
- equivalent_atoms_std = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_atoms_std'],
- description='''
- Gives a mapping table of atoms to symmetrically independent atoms in the
- standardized cell. This is used to find symmetrically equivalent atoms.
- ''',
- a_legacy=LegacyDefinition(name='equivalent_atoms_std'))
-
- lattice_vectors_std = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='meter',
- description='''
- Standardized lattice vectors of the conventional cell. The vectors are the rows of
- this matrix.
- ''',
- a_legacy=LegacyDefinition(name='lattice_vectors_std'))
-
- number_of_atoms_std = Quantity(
- type=int,
- shape=[],
- description='''
- Number of atoms in standardized system.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms_std'))
-
- wyckoff_letters_std = Quantity(
- type=str,
- shape=['number_of_atoms_std'],
- description='''
- Wyckoff letters for atoms in the standardized cell.
- ''',
- a_legacy=LegacyDefinition(name='wyckoff_letters_std'))
-
-
-class section_stress_tensor(MSection):
- '''
- Section collecting alternative values to stress_tensor that have been calculated.
-
- This section allows the storage of multiple definitions and evaluated values of the
- stress tensor, while only one definition is used for, e.g., molecular dynamics or
- geometry optimization (if needed).
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_stress_tensor'))
-
- stress_tensor_kind = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the method used to compute the stress tensor stored in
- stress_tensor_value. This is an *alternative* to the stress tensor defined in
- stress_tensor_method, which is stored in stress_tensor.
-
- This field allows for multiple definitions and evaluated values of the stress
- tensor, while only one definition is used for, e.g., molecular dynamics and
- geometry optimization.
- ''',
- a_legacy=LegacyDefinition(name='stress_tensor_kind'))
-
- stress_tensor_value = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='pascal',
- description='''
- Contains the value of the stress tensor of the kind defined in stress_tensor_kind.
- This is an *alternative* to the stress tensor defined in stress_tensor_method.
-
- This field allows for multiple definitions and evaluated values of the stress
- tensor, while only one definition is used for, e.g., molecular dynamics and
- geometry optimization.
- ''',
- categories=[stress_tensor_type],
- a_legacy=LegacyDefinition(name='stress_tensor_value'))
-
-
-class section_symmetry(MSection):
- '''
- Section containing information about the symmetry properties of the system.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_symmetry'))
-
- bravais_lattice = Quantity(
- type=str,
- shape=[],
- description='''
- Identifier for the Bravais lattice in Pearson notation. The first lowercase letter
- identifies the crystal family and can be one of the following: a (triclinic), b
- (monoclinic), o (orthorhombic), t (tetragonal), h (hexagonal) or c (cubic). The
- second uppercase letter identifies the centring and can be one of the following: P
- (primitive), S (face centred), I (body centred), R (rhombohedral centring) or F
- (all faces centred).
- ''',
- a_legacy=LegacyDefinition(name='bravais_lattice'))
-
- choice = Quantity(
- type=str,
- shape=[],
- description='''
- String that specifies the centering, origin and basis vector settings of the 3D
- space group that defines the symmetry group of the simulated physical system (see
- section_system). Values are as defined by spglib.
- ''',
- a_legacy=LegacyDefinition(name='choice'))
-
- crystal_system = Quantity(
- type=str,
- shape=[],
- description='''
- Name of the crystal system. Can be one of the following: triclinic, monoclinic,
- orthorhombic, tetragonal, trigonal, hexagonal or cubic.
- ''',
- a_legacy=LegacyDefinition(name='crystal_system'))
-
- hall_number = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- The Hall number for this system.
- ''',
- a_legacy=LegacyDefinition(name='hall_number'))
-
- hall_symbol = Quantity(
- type=str,
- shape=[],
- description='''
- The Hall symbol for this system.
- ''',
- a_legacy=LegacyDefinition(name='hall_symbol'))
-
- international_short_symbol = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the International Union of Crystallography (IUC) short symbol of the 3D
- space group of this system
- ''',
- a_legacy=LegacyDefinition(name='international_short_symbol'))
-
- origin_shift = Quantity(
- type=np.dtype(np.float64),
- shape=[3],
- description='''
- Vector $\\mathbf{p}$ from the origin of the standardized system to the origin of
- the original system. Together with the matrix $\\mathbf{P}$, found in
- space_group_3D_transformation_matrix, the transformation between the standardized
- coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by
- $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.
- ''',
- a_legacy=LegacyDefinition(name='origin_shift'))
-
- point_group = Quantity(
- type=str,
- shape=[],
- description='''
- Symbol of the crystallographic point group in the Hermann-Mauguin notation.
- ''',
- a_legacy=LegacyDefinition(name='point_group'))
-
- space_group_number = Quantity(
- type=np.dtype(np.int32),
- shape=[],
- description='''
- Specifies the International Union of Crystallography (IUC) number of the 3D space
- group of this system.
- ''',
- a_legacy=LegacyDefinition(name='space_group_number'))
-
- symmetry_method = Quantity(
- type=str,
- shape=[],
- description='''
- Identifies the source of the symmetry information contained within this section.
- If equal to 'spg_normalized' the information comes from a normalization step.
- ''',
- a_legacy=LegacyDefinition(name='symmetry_method'))
-
- transformation_matrix = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- description='''
- Matrix $\\mathbf{P}$ that is used to transform the standardized coordinates to the
- original coordinates. Together with the vector $\\mathbf{p}$, found in
- space_group_3D_origin_shift, the transformation between the standardized
- coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by
- $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.
- ''',
- a_legacy=LegacyDefinition(name='transformation_matrix'))
-
- section_original_system = SubSection(
- sub_section=SectionProxy('section_original_system'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_original_system'))
-
- section_primitive_system = SubSection(
- sub_section=SectionProxy('section_primitive_system'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_primitive_system'))
-
- section_std_system = SubSection(
- sub_section=SectionProxy('section_std_system'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_std_system'))
-
-
-class section_system_to_system_refs(MSection):
- '''
- Section that describes the relationship between different section_system sections.
-
- For instance, if a phonon calculation using a finite difference approach is performed
- the force evaluation is typically done in a larger supercell but the properties such
- as the phonon band structure are still calculated for the primitive cell.
-
- The kind of relationship between the system defined in this section and the referenced
- one is described by system_to_system_kind. The referenced section_system is identified
- via system_to_system_ref.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_system_to_system_refs'))
-
- system_to_system_kind = Quantity(
- type=str,
- shape=[],
- description='''
- String defining the relationship between the referenced section_system and the
- present section_system. Often systems are connected for example if a phonon
- calculation using finite differences is performed the force ealuation is done in a
- larger supercell but properties such as the phonon band structure are still
- calculated for the primitive cell. Hence, the need of keeping track of these
- connected systems. The referenced system is identified via system_to_system_ref.
- ''',
- a_legacy=LegacyDefinition(name='system_to_system_kind'))
-
- system_to_system_ref = Quantity(
- type=Reference(SectionProxy('section_system')),
- shape=[],
- description='''
- Reference to another system. The kind of relationship between the present and the
- referenced section_system is specified by system_to_system_kind.
- ''',
- a_legacy=LegacyDefinition(name='system_to_system_ref'))
-
-
-class section_system(MSection):
- '''
- Every section_system contains all needed properties required to describe the simulated
- physical system, e.g. the given atomic configuration, the definition of periodic cell
- (if present), the external potentials and other parameters.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_system'))
-
- atom_atom_number = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_sites'],
- description='''
- Atomic number Z of the atom.
- ''',
- a_legacy=LegacyDefinition(name='atom_atom_number'))
-
- atom_concentrations = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms'],
- description='''
- concentration of the atom species in a variable composition, by default it should
- be considered an array of ones. Summing these should give the number_of_sites
- ''',
- a_legacy=LegacyDefinition(name='atom_concentrations'))
-
- atom_labels = Quantity(
- type=str,
- shape=['number_of_atoms'],
- aliases=['elements'],
- description='''
- Labels of the atoms. These strings identify the atom kind and conventionally start
- with the symbol of the atomic species, possibly followed by the atomic number. The
- same atomic species can be labeled with more than one atom_labels in order to
- distinguish, e.g., atoms of the same species assigned to different atom-centered
- basis sets or pseudo-potentials, or simply atoms in different locations in the
- structure (e.g., bulk and surface). These labels can also be used for *particles*
- that do not correspond to physical atoms (e.g., ghost atoms in some codes using
- atom-centered basis sets). This metadata defines a configuration and is therefore
- required.
- ''',
- categories=[configuration_core],
- a_legacy=LegacyDefinition(name='atom_labels'))
-
- atom_positions = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='meter',
- description='''
- Positions of all the atoms, in Cartesian coordinates. This metadata defines a
- configuration and is therefore required. For alloys where concentrations of
- species are given for each site in the unit cell, it stores the position of the
- sites.
- ''',
- categories=[configuration_core],
- a_legacy=LegacyDefinition(name='atom_positions'))
-
- atom_species = Quantity(
- type=np.dtype(np.int32),
- shape=['number_of_atoms'],
- description='''
- Species of the atom (normally the atomic number Z, 0 or negative for unidentifed
- species or particles that are not atoms.
- ''',
- a_legacy=LegacyDefinition(name='atom_species'))
-
- atom_velocities = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3],
- unit='meter / second',
- description='''
- Velocities of the nuclei, defined as the change in Cartesian coordinates of the
- nuclei with respect to time.
- ''',
- a_legacy=LegacyDefinition(name='atom_velocities'))
-
- configuration_periodic_dimensions = Quantity(
- type=bool,
- shape=[3],
- description='''
- Array labeling which of the lattice vectors use periodic boundary conditions. Note
- for the parser developers: This value is not expected to be given for each
- section_single_configuration_calculation. It is assumed to be valid from the
- section_single_configuration_calculation where it is defined for all subsequent
- section_single_configuration_calculation in section_run, until redefined.
- ''',
- categories=[configuration_core],
- a_legacy=LegacyDefinition(name='configuration_periodic_dimensions'))
-
- configuration_raw_gid = Quantity(
- type=str,
- shape=[],
- description='''
- checksum of the configuration_core, i.e. the geometry of the system. The values
- are not normalized in any way so equivalent configurations might have different
- values
- ''',
- a_legacy=LegacyDefinition(name='configuration_raw_gid'))
-
- embedded_system = Quantity(
- type=bool,
- shape=[],
- description='''
- Is the system embedded into a host geometry?.
- ''',
- categories=[configuration_core],
- a_legacy=LegacyDefinition(name='embedded_system'))
-
- lattice_vectors = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='meter',
- description='''
- Holds the lattice vectors (in Cartesian coordinates) of the simulation cell. The
- last (fastest) index runs over the $x,y,z$ Cartesian coordinates, and the first
- index runs over the 3 lattice vectors.
- ''',
- categories=[configuration_core],
- a_legacy=LegacyDefinition(name='lattice_vectors'))
-
- local_rotations = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_atoms', 3, 3],
- description='''
- A rotation matrix defining the orientation of each atom. If the rotation matrix
- only needs to be specified for some atoms, the remaining atoms should set it to
- the zero matrix (not the identity!)
- ''',
- a_legacy=LegacyDefinition(name='local_rotations'))
-
- number_of_atoms = Quantity(
- type=int,
- shape=[],
- description='''
- Stores the total number of atoms used in the calculation. For alloys where
- concentrations of species are given for each site in the unit cell, it stores the
- number of sites.
- ''',
- a_legacy=LegacyDefinition(name='number_of_atoms'))
-
- number_of_sites = Quantity(
- type=int,
- shape=[],
- description='''
- number of sites in a variable composition representation. By default (no variable
- composition) it is the same as number_of_atoms.
- ''',
- a_legacy=LegacyDefinition(name='number_of_sites'))
-
- SC_matrix = Quantity(
- type=np.dtype(np.int32),
- shape=[3, 3],
- description='''
- Specifies the matrix that transforms the unit-cell into the super-cell in which
- the actual calculation is performed.
- ''',
- a_legacy=LegacyDefinition(name='SC_matrix'))
-
- simulation_cell = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='meter',
- description='''
- DEPRECATED, use lattice_vectors instead. Holds the lattice vectors (in Cartesian
- coordinates) of the simulation cell. The last (fastest) index runs over the
- $x,y,z$ Cartesian coordinates, and the first index runs over the 3 lattice
- vectors.
- ''',
- categories=[configuration_core],
- a_legacy=LegacyDefinition(name='simulation_cell'))
-
- symmorphic = Quantity(
- type=bool,
- shape=[],
- description='''
- Is the space group symmorphic? Set to True if all translations are zero.
- ''',
- a_legacy=LegacyDefinition(name='symmorphic'))
-
- system_composition = Quantity(
- type=str,
- shape=[],
- description='''
- Composition, i.e. cumulative chemical formula with atoms ordered by decreasing
- atomic number Z.
- ''',
- a_legacy=LegacyDefinition(name='system_composition'))
-
- system_configuration_consistent = Quantity(
- type=bool,
- shape=[],
- description='''
- Flag set is the configuration is consistent
- ''',
- a_legacy=LegacyDefinition(name='system_configuration_consistent'))
-
- system_name = Quantity(
- type=str,
- shape=[],
- description='''
- Specifies the name of the system. This information is provided by the user in some
- codes and is stored here for debugging or visualization purposes.
- ''',
- a_legacy=LegacyDefinition(name='system_name'))
-
- system_reweighted_composition = Quantity(
- type=str,
- shape=[],
- description='''
- Composition, i.e. cumulative chemical with atoms ordered by decreasing atomic
- number Z reweighted so that the sum is close to 100, and values are rounded up,
- and are stable (i.e. it is a fixed point).
- ''',
- a_legacy=LegacyDefinition(name='system_reweighted_composition'))
-
- system_type = Quantity(
- type=str,
- shape=[],
- description='''
- Type of the system
- ''',
- a_legacy=LegacyDefinition(name='system_type'))
-
- time_reversal_symmetry = Quantity(
- type=bool,
- shape=[],
- description='''
- Is time-reversal symmetry present?
- ''',
- a_legacy=LegacyDefinition(name='time_reversal_symmetry'))
-
- chemical_composition = Quantity(
- type=str,
- shape=[],
- description='''
- The chemical composition as full formula of the system, based on atom species.
- ''',
- a_legacy=LegacyDefinition(name='chemical_composition'))
-
- chemical_composition_reduced = Quantity(
- type=str,
- shape=[],
- description='''
- The chemical composition as reduced formula of the system, based on atom species.
- ''',
- a_legacy=LegacyDefinition(name='chemical_composition_reduced'))
-
- chemical_composition_bulk_reduced = Quantity(
- type=str,
- shape=[],
- description='''
- The chemical composition as reduced bulk formula of the system, based on atom
- species.
- ''',
- a_legacy=LegacyDefinition(name='chemical_composition_bulk_reduced'))
-
- section_prototype = SubSection(
- sub_section=SectionProxy('section_prototype'),
- repeats=True, categories=[fast_access],
- a_legacy=LegacyDefinition(name='section_prototype'))
-
- section_springer_material = SubSection(
- sub_section=SectionProxy('section_springer_material'),
- repeats=True, categories=[fast_access],
- a_legacy=LegacyDefinition(name='section_springer_material'))
-
- section_symmetry = SubSection(
- sub_section=SectionProxy('section_symmetry'),
- repeats=True, categories=[fast_access],
- a_legacy=LegacyDefinition(name='section_symmetry'))
-
- section_system_to_system_refs = SubSection(
- sub_section=SectionProxy('section_system_to_system_refs'),
- repeats=True,
- a_legacy=LegacyDefinition(name='section_system_to_system_refs'))
-
-
-class section_thermodynamical_properties(MSection):
- '''
- Section that defines thermodynamical properties about the system in a
- section_frame_sequence.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_thermodynamical_properties'))
-
- helmholz_free_energy = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_thermodynamical_property_values'],
- unit='joule',
- description='''
- Stores the Helmholtz free energy per unit cell at constant volume of a
- thermodynamic calculation.
- ''',
- a_legacy=LegacyDefinition(name='helmholz_free_energy'))
-
- number_of_thermodynamical_property_values = Quantity(
- type=int,
- shape=[],
- description='''
- Gives the number of thermal properties values available in
- section_thermodynamical_properties.
- ''',
- a_legacy=LegacyDefinition(name='number_of_thermodynamical_property_values'))
-
- thermodynamical_properties_calculation_method = Quantity(
- type=str,
- shape=[],
- description='''
- Method used to calculate the thermodynamic quantities.
-
- Valid values:
-
- * harmonic
- ''',
- a_legacy=LegacyDefinition(name='thermodynamical_properties_calculation_method'))
-
- thermodynamical_property_heat_capacity_C_v = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_thermodynamical_property_values'],
- unit='joule / kelvin',
- description='''
- Stores the heat capacity per cell unit at constant volume.
- ''',
- a_legacy=LegacyDefinition(name='thermodynamical_property_heat_capacity_C_v'))
-
- @derived(
- type=np.dtype(np.float64),
- shape=['number_of_thermodynamical_property_values'],
- unit='joule / kelvin * kilogram',
- description='''
- Stores the specific heat capacity at constant volume.
- ''',
- a_legacy=LegacyDefinition(name='specific_heat_capacity'),
- cached=True
- )
- def specific_heat_capacity(self) -> np.array:
- """Returns the specific heat capacity by dividing the heat capacity per
- cell with the mass of the atoms in the cell.
- """
- import nomad.atomutils
- s_frame_sequence = self.m_parent
- first_frame = s_frame_sequence.frame_sequence_local_frames_ref[0]
- system = first_frame.single_configuration_calculation_to_system_ref
- atomic_numbers = system.atom_species
- mass_per_unit_cell = nomad.atomutils.get_summed_atomic_mass(atomic_numbers)
- heat_capacity = self.thermodynamical_property_heat_capacity_C_v
- specific_heat_capacity = heat_capacity / mass_per_unit_cell
-
- return specific_heat_capacity
-
- thermodynamical_property_temperature = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_thermodynamical_property_values'],
- unit='kelvin',
- description='''
- Specifies the temperatures at which properties such as the Helmholtz free energy
- are calculated.
- ''',
- a_legacy=LegacyDefinition(name='thermodynamical_property_temperature'))
-
- vibrational_free_energy_at_constant_volume = Quantity(
- type=np.dtype(np.float64),
- shape=['number_of_thermodynamical_property_values'],
- unit='joule',
- description='''
- Holds the vibrational free energy per atom at constant volume.
- ''',
- a_legacy=LegacyDefinition(name='vibrational_free_energy_at_constant_volume'))
-
- @derived(
- type=np.dtype(np.float64),
- shape=['number_of_thermodynamical_property_values'],
- unit='joule / kilogram',
- description='''
- Stores the specific vibrational free energy at constant volume.
- ''',
- a_legacy=LegacyDefinition(name='specific_vibrational_free_energy_at_constant_volume'),
- cached=True
- )
- def specific_vibrational_free_energy_at_constant_volume(self) -> np.array:
- """Returns the specific vibrational free energy by dividing the vibrational free energy per
- cell with the mass of the atoms in the cell.
- """
- import nomad.atomutils
- s_frame_sequence = self.m_parent
- first_frame = s_frame_sequence.frame_sequence_local_frames_ref[0]
- system = first_frame.single_configuration_calculation_to_system_ref
- atomic_numbers = system.atom_species
- n_atoms = len(atomic_numbers)
- mass_per_atom = nomad.atomutils.get_summed_atomic_mass(atomic_numbers) / n_atoms
- free_energy = self.vibrational_free_energy_at_constant_volume
- specific_vibrational_free_energy_at_constant_volume = free_energy / mass_per_atom
-
- return specific_vibrational_free_energy_at_constant_volume
-
-
-class section_volumetric_data(MSection):
- '''
- Section defining a set of volumetric data on a uniform real-space
-
- grid.
-
- To store an array (e.g. a density or a potential), define:
-
- * three grid point displacement vectors ("displacements")
-
- * number of grid points along each axis ("nx", "ny" and "nz")
-
- * the origin of the coordinate system, i.e. coordinates of the first grid
-
- point ("origin")
-
- * how many spatial functions are represented, e.g., two for a
-
- normal spin-polarized density ("multiplicity")
-
- * the values for each grid point ("values")
-
- * the unit that applies to each value ("units")
-
- * the kind of array represented by the volumetric data ("kind").
-
- Allowed kinds are (please add new kinds as necessary): "density",
-
- "potential_hartree" and "potential_effective". Densities and
-
- potentials that are spin-polarized should have multiplicity two.
-
- Rules for more complex spins are to be decided when necessary.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_volumetric_data'))
-
- volumetric_data_displacements = Quantity(
- type=np.dtype(np.float64),
- shape=[3, 3],
- unit='meter',
- description='''
- displacement vectors between grid points along each axis; same indexing rules as
- lattice_vectors. In many cases, displacements and number of points are related to
- lattice_vectors through: [displacement] * [number of points + N] =
- [lattice_vector],where N is 1 for periodic directions and 0 for non-periodic ones
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_displacements'))
-
- volumetric_data_kind = Quantity(
- type=str,
- shape=[],
- description='''
- The kind of function, e.g. density, potential_hartree, potential_effective. The
- unit of measurement for "volumetric_data_values" depends on the kind: Densities
- are 1/m^3 and potentials are J/m^3. See [full specification on the
- wiki](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
- info/wikis/metainfo/volumetric-data).
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_kind'))
-
- volumetric_data_multiplicity = Quantity(
- type=int,
- shape=[],
- description='''
- number of functions stored
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_multiplicity'))
-
- volumetric_data_nx = Quantity(
- type=int,
- shape=[],
- description='''
- number of points along x axis
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_nx'))
-
- volumetric_data_ny = Quantity(
- type=int,
- shape=[],
- description='''
- number of points along y axis
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_ny'))
-
- volumetric_data_nz = Quantity(
- type=int,
- shape=[],
- description='''
- number of points along z axis
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_nz'))
-
- volumetric_data_origin = Quantity(
- type=np.dtype(np.float64),
- shape=[3],
- description='''
- location of the first grid point; same coordinate system as atom_positions when
- applicable.
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_origin'))
-
- volumetric_data_values = Quantity(
- type=np.dtype(np.float64),
- shape=['volumetric_data_multiplicity', 'volumetric_data_nx', 'volumetric_data_ny', 'volumetric_data_nz'],
- description='''
- Array of shape (multiplicity, nx, ny, nz) containing the values. The units of
- these values depend on which kind of data the values represent; see
- "volumetric_data_kind".
- ''',
- a_legacy=LegacyDefinition(name='volumetric_data_values'))
-
-
-class section_XC_functionals(MSection):
- '''
- Section containing one of the exchange-correlation (XC) functionals for the present
- section_method that are combined to form the XC_functional.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_XC_functionals'))
-
- XC_functional_name = Quantity(
- type=str,
- shape=[],
- description='''
- Provides the name of one of the exchange and/or correlation (XC) functionals
- combined in XC_functional.
-
- The valid unique names that can be used are listed in the [XC_functional wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
- functional).
-
- *NOTE*: This value should refer to a correlation, an exchange or an exchange-
- correlation functional only.
- ''',
- categories=[settings_physical_parameter],
- a_legacy=LegacyDefinition(name='XC_functional_name'))
-
- XC_functional_parameters = Quantity(
- type=typing.Any,
- shape=[],
- description='''
- Contains an associative list of non-default values of the parameters for the
- functional declared in XC_functional_name of the section_XC_functionals section.
-
- For example, if a calculations using a hybrid XC functional (e.g., HSE06)
- specifies a user-given value of the mixing parameter between exact and GGA
- exchange, then this non-default value is stored in this metadata.
-
- The labels and units of these values are defined in the paragraph dedicated to the
- specified functional declared in XC_functional_name of the [XC_functional wiki
- page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
- functional).
-
- If this metadata is not given, the default parameter values for the
- XC_functional_name are assumed.
- ''',
- categories=[settings_physical_parameter],
- a_legacy=LegacyDefinition(name='XC_functional_parameters'))
-
- XC_functional_weight = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Provides the value of the weight for the exchange, correlation, or exchange-
- correlation functional declared in XC_functional_name (see
- section_XC_functionals).
-
- This weight is used in the linear combination of the different XC functional names
- (XC_functional_name) in different section_XC_functionals sections to form the
- XC_functional used for evaluating energy_XC_functional and related quantities.
-
- If not specified then the default is set to 1.
- ''',
- categories=[settings_physical_parameter],
- a_legacy=LegacyDefinition(name='XC_functional_weight'))
-
-
-class GeometryOptimization(MSection):
- '''
- Section containing the results of a geometry_optimization workflow.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_geometry_optimization'))
-
- geometry_optimization_type = Quantity(
- type=str,
- shape=[],
- description='''
- The type of geometry optimization can either be ionic, cell_shape, cell_volume.
- ''',
- a_legacy=LegacyDefinition(name='geometry_optimization_type')
- )
-
- input_energy_difference_tolerance = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- The input energy difference tolerance criterion.
- ''',
- a_legacy=LegacyDefinition(name='input_energy_difference_tolerance'))
-
- input_force_maximum_tolerance = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='newton',
- description='''
- The input maximum net force tolerance criterion.
- ''',
- a_legacy=LegacyDefinition(name='input_force_maximum_tolerance'))
-
- final_energy_difference = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- The difference in the energy between the last two steps during optimization.
- ''',
- a_legacy=LegacyDefinition(name='final_energy_difference'),
- a_search=Search())
-
- final_force_maximum = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='newton',
- description='''
- The maximum net force in the last optimization step.
- ''',
- a_legacy=LegacyDefinition(name='final_force_maximum'))
-
- optimization_steps = Quantity(
- type=int,
- shape=[],
- description='''
- Number of optimization steps.
- ''',
- a_legacy=LegacyDefinition(name='optimization_steps'))
-
-
-class Phonon(MSection):
- '''
- Section containing the results of a phonon workflow.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_phonon'))
-
- force_calculator = Quantity(
- type=str,
- shape=[],
- description='''
- Name of the program used to calculate the forces.
- ''',
- a_legacy=LegacyDefinition(name='force_calculator'))
-
- mesh_density = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='1 / m ** 3',
- description='''
- Density of the k-mesh for sampling.
- ''',
- a_legacy=LegacyDefinition(name='mesh_density'),
- a_search=Search())
-
- n_imaginary_frequencies = Quantity(
- type=int,
- shape=[],
- description='''
- Number of modes with imaginary frequencies.
- ''',
- a_legacy=LegacyDefinition(name='n_imaginary_frequencies'),
- a_search=Search())
-
- random_displacements = Quantity(
- type=bool,
- shape=[],
- description='''
- Identifies if displacements are made randomly.
- ''',
- a_legacy=LegacyDefinition(name='random_displacements'))
-
- with_non_analytic_correction = Quantity(
- type=bool,
- shape=[],
- description='''
- Identifies if non-analytical term corrections are applied to dynamical matrix.
- ''',
- a_legacy=LegacyDefinition(name='with_non_analytic_correction'),
- a_search=Search())
-
- with_grueneisen_parameters = Quantity(
- type=bool,
- shape=[],
- description='''
- Identifies if Grueneisen parameters are calculated.
- ''',
- a_legacy=LegacyDefinition(name='with_grueneisen_parameters'),
- a_search=Search())
-
-
-class Elastic(MSection):
- '''
- Section containing the results of an elastic workflow.
- '''
-
- m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_elastic'))
-
- energy_stress_calculator = Quantity(
- type=str,
- shape=[],
- description='''
- Name of program used to calculate energy or stress.
- ''',
- a_legacy=LegacyDefinition(name='energy_stress_calculator'))
-
- elastic_calculation_method = Quantity(
- type=str,
- shape=[],
- description='''
- Method used to calculate elastic constants, can either be energy or stress.
- ''',
- a_legacy=LegacyDefinition(name='elastic_calculation_method'))
-
- elastic_constants_order = Quantity(
- type=int,
- shape=[],
- description='''
- Order of the calculated elastic constants.
- ''',
- a_legacy=LegacyDefinition(name='elastic_constants_order'),
- a_search=Search())
-
- is_mechanically_stable = Quantity(
- type=bool,
- shape=[],
- description='''
- Indicates if structure is mechanically stable from the calculated values
- of the elastic constants.
- ''',
- a_legacy=LegacyDefinition(name='is_mechanically_stable'),
- a_search=Search())
-
- fitting_error_maximum = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Maximum error in polynomial fit.
- ''',
- a_legacy=LegacyDefinition(name='fitting_error_maximum'))
-
- strain_maximum = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- description='''
- Maximum strain applied to crystal.
- ''',
- a_legacy=LegacyDefinition(name='strain_maximum'))
-
-
-class MolecularDynamics(MSection):
- '''
- Section containing results of molecular dynamics workflow.
- '''
-
- m_def = Section(
- validate=False, a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
-
- finished_normally = Quantity(
- type=bool,
- shape=[],
- description='''
- Indicates if calculation terminated normally.
- ''',
- a_legacy=LegacyDefinition(name='finished_normally'))
-
- with_trajectory = Quantity(
- type=bool,
- shape=[],
- description='''
- Indicates if calculation includes trajectory data.
- ''',
- a_legacy=LegacyDefinition(name='with_trajectory'),
- a_search=Search())
-
- with_thermodynamics = Quantity(
- type=bool,
- shape=[],
- description='''
- Indicates if calculation contains thermodynamic data.
- ''',
- a_legacy=LegacyDefinition(name='with_thermodynamics'),
- a_search=Search())
-
-
-class Workflow(MSection):
- '''
- Section containing the results of a workflow.
- '''
-
- m_def = Section(
- validate=False,
- a_legacy=LegacyDefinition(name='section_workflow'))
-
- workflow_type = Quantity(
- type=str,
- shape=[],
- description='''
- The type of calculation workflow. Can be one of geometry_optimization, elastic,
- phonon, molecular_dynamics.
- ''',
- a_legacy=LegacyDefinition(name='workflow_type'),
- a_search=Search(statistic_size=4, statistic_order='_count'))
-
- calculation_result_ref = Quantity(
- type=Reference(SectionProxy('section_single_configuration_calculation')),
- categories=[fast_access],
- shape=[],
- description='''
- Reference to calculation result. In the case of geometry_optimization and
- molecular dynamics, this corresponds to the final step in the simulation. For the
- rest of the workflow types, it refers to the original system.
- ''',
- a_legacy=LegacyDefinition(name='calculation_result_ref'))
-
- calculations_ref = Quantity(
- type=Reference(SectionProxy('section_single_configuration_calculation')),
- shape=['optimization_steps'],
- description='''
- List of references to each section_single_configuration_calculation in the
- simulation.
- ''',
- a_legacy=LegacyDefinition(name='calculations_ref'))
-
- section_geometry_optimization = SubSection(
- sub_section=SectionProxy('GeometryOptimization'), categories=[fast_access],
- a_legacy=LegacyDefinition(name='section_geometry_optimization'))
-
- section_phonon = SubSection(
- sub_section=SectionProxy('Phonon'), categories=[fast_access],
- a_legacy=LegacyDefinition(name='section_phonon'))
-
- section_elastic = SubSection(
- sub_section=SectionProxy('Elastic'),
- a_legacy=LegacyDefinition(name='section_elastic'))
-
- section_molecular_dynamics = SubSection(
- sub_section=SectionProxy('MolecularDynamics'),
- a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
-
-
-m_package.__init_metainfo__()
+from .common_dft import *
diff --git a/nomad/datamodel/metainfo/public_old.py b/nomad/datamodel/metainfo/public_old.py
new file mode 100644
index 0000000000000000000000000000000000000000..ccc6a49c9f0c611f2a6eb06fbb0b2c4efe4beaaf
--- /dev/null
+++ b/nomad/datamodel/metainfo/public_old.py
@@ -0,0 +1,5942 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference, MEnum, derived
+)
+from nomad.metainfo.search_extension import Search
+from nomad.metainfo.legacy import LegacyDefinition
+
+
+m_package = Package(
+ name='public_nomadmetainfo_json',
+ description='None',
+ a_legacy=LegacyDefinition(
+ name='public.nomadmetainfo.json'))
+
+
+class fast_access(MCategory):
+ '''
+ Used to mark archive objects that need to be stored in a fast 2nd-tier storage
+ medium, because they are frequently accessed via archive API.
+
+ If applied to a sub_section, the section will be added to the fast storage. Currently
+ this only works for *root* sections that are sub_sections of `EntryArchive`.
+
+ If applied to a reference types quantity, the referenced section will also be added
+ to the fast storage, regardless if the referenced section has the category or not.
+ '''
+
+ m_def = Category()
+
+
+class accessory_info(MCategory):
+ '''
+ Information that *in theory* should not affect the results of the calculations (e.g.,
+ timing).
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='accessory_info'))
+
+
+class atom_forces_type(MCategory):
+ '''
+ The types of forces acting on the atoms (i.e., minus derivatives of the specific type
+ of energy with respect to the atom position).
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='atom_forces_type'))
+
+
+class basis_set_description(MCategory):
+ '''
+ One of the parts building the basis set of the system (e.g., some atom-centered basis
+ set, plane-waves or both).
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='basis_set_description'))
+
+
+class configuration_core(MCategory):
+ '''
+ Properties defining the current configuration.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='configuration_core'))
+
+
+class conserved_quantity(MCategory):
+ '''
+ A quantity that is preserved during the time propagation (for example,
+ kinetic+potential energy during NVE).
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='conserved_quantity'))
+
+
+class energy_value(MCategory):
+ '''
+ This metadata stores an energy value.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='energy_value'))
+
+
+class error_estimate_contribution(MCategory):
+ '''
+ An estimate of a partial quantity contributing to the error for a given quantity.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='error_estimate_contribution'))
+
+
+class message_debug(MCategory):
+ '''
+ A debugging message of the computational program.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='message_debug'))
+
+
+class parsing_message_debug(MCategory):
+ '''
+ This field is used for debugging messages of the parsing program.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='parsing_message_debug'))
+
+
+class scf_info(MCategory):
+ '''
+ Contains information on the self-consistent field (SCF) procedure, i.e. the number of
+ SCF iterations (number_of_scf_iterations) or a section_scf_iteration section with
+ detailed information on the SCF procedure of specified quantities.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='scf_info'))
+
+
+class settings_numerical_parameter(MCategory):
+ '''
+ A parameter that can influence the convergence, but not the physics (unlike
+ settings_physical_parameter)
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_numerical_parameter'))
+
+
+class settings_physical_parameter(MCategory):
+ '''
+ A parameter that defines the physical model used. Use settings_numerical_parameter for
+ parameters that that influence only the convergence/accuracy.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_physical_parameter'))
+
+
+class settings_potential_energy_surface(MCategory):
+ '''
+ Contains parameters that control the potential energy surface.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_potential_energy_surface'))
+
+
+class settings_run(MCategory):
+ '''
+ Contains parameters that control the whole run (but not the *single configuration
+ calculation*, see section_single_configuration_calculation).
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_run'))
+
+
+class settings_sampling(MCategory):
+ '''
+ Contains parameters controlling the sampling.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_sampling'))
+
+
+class settings_scf(MCategory):
+ '''
+ Contains parameters connected with the convergence of the self-consistent field (SCF)
+ iterations.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_scf'))
+
+
+class settings_smearing(MCategory):
+ '''
+ Contain parameters that control the smearing of the orbital occupation at finite
+ electronic temperatures.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_smearing'))
+
+
+class settings_stress_tensor(MCategory):
+ '''
+ Settings to calculate the stress tensor (stress_tensor) consistent with the total
+ energy of the system given in energy_total.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='settings_stress_tensor'))
+
+
+class stress_tensor_type(MCategory):
+ '''
+ Contains the final value of the default stress tensor (stress_tensor) and/or the value
+ of the stress tensor (stress_tensor_value) of the kind defined in stress_tensor_kind.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='stress_tensor_type'))
+
+
+class energy_component_per_atom(MCategory):
+ '''
+ A value of an energy component per atom, concurring in defining the total energy per
+ atom.
+ '''
+
+ m_def = Category(
+ categories=[energy_value],
+ a_legacy=LegacyDefinition(name='energy_component_per_atom'))
+
+
+class energy_component(MCategory):
+ '''
+ A value of an energy component, expected to be an extensive property.
+ '''
+
+ m_def = Category(
+ categories=[energy_value],
+ a_legacy=LegacyDefinition(name='energy_component'))
+
+
+class energy_type_reference(MCategory):
+ '''
+ This metadata stores an energy used as reference point.
+ '''
+
+ m_def = Category(
+ categories=[energy_value],
+ a_legacy=LegacyDefinition(name='energy_type_reference'))
+
+
+class error_estimate(MCategory):
+ '''
+ An estimate of the error on the converged (final) value.
+ '''
+
+ m_def = Category(
+ categories=[error_estimate_contribution],
+ a_legacy=LegacyDefinition(name='error_estimate'))
+
+
+class message_info(MCategory):
+ '''
+ An information message of the computational program.
+ '''
+
+ m_def = Category(
+ categories=[message_debug],
+ a_legacy=LegacyDefinition(name='message_info'))
+
+
+class parallelization_info(MCategory):
+ '''
+ Contains information on the parallelization of the program, i.e. which parallel
+ programming language was used and its version, how many cores had been working on the
+ calculation and the flags and parameters needed to run the parallelization of the
+ code.
+ '''
+
+ m_def = Category(
+ categories=[accessory_info],
+ a_legacy=LegacyDefinition(name='parallelization_info'))
+
+
+class parsing_message_info(MCategory):
+ '''
+ This field is used for info messages of the parsing program.
+ '''
+
+ m_def = Category(
+ categories=[parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_info'))
+
+
+class program_info(MCategory):
+ '''
+ Contains information on the program that generated the data, i.e. the program_name,
+ program_version, program_compilation_host and program_compilation_datetime as direct
+ children of this field.
+ '''
+
+ m_def = Category(
+ categories=[accessory_info],
+ a_legacy=LegacyDefinition(name='program_info'))
+
+
+class settings_geometry_optimization(MCategory):
+ '''
+ Contains parameters controlling the geometry optimization.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling],
+ a_legacy=LegacyDefinition(name='settings_geometry_optimization'))
+
+
+class settings_k_points(MCategory):
+ '''
+ Contains parameters that control the $k$-point mesh.
+ '''
+
+ m_def = Category(
+ categories=[settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_k_points'))
+
+
+class settings_metadynamics(MCategory):
+ '''
+ Contains parameters that control the metadynamics sampling.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling],
+ a_legacy=LegacyDefinition(name='settings_metadynamics'))
+
+
+class settings_molecular_dynamics(MCategory):
+ '''
+ Contains parameters that control the molecular dynamics sampling.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling],
+ a_legacy=LegacyDefinition(name='settings_molecular_dynamics'))
+
+
+class settings_Monte_Carlo(MCategory):
+ '''
+ Contains parameters that control the Monte-Carlo sampling.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling],
+ a_legacy=LegacyDefinition(name='settings_Monte_Carlo'))
+
+
+class settings_XC(MCategory):
+ '''
+ Contains parameters connected with the definition of the exchange-correlation (XC)
+ *method*. Here, the term *method* is a more general concept than just *functionals*
+ and include, e.g., post Hartree-Fock methods, too.
+ '''
+
+ m_def = Category(
+ categories=[settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_XC'))
+
+
+class time_info(MCategory):
+ '''
+ Stores information on the date and timings of the calculation. They are useful for,
+ e.g., debugging or visualization purposes.
+ '''
+
+ m_def = Category(
+ categories=[accessory_info],
+ a_legacy=LegacyDefinition(name='time_info'))
+
+
+class energy_total_potential_per_atom(MCategory):
+ '''
+ A value of the total potential energy per atom. Note that a direct comparison may not
+ be possible because of a difference in the methods for computing total energies and
+ numerical implementations of various codes might leads to different energy zeros (see
+ section_energy_code_independent for a code-independent definition of the energy).
+ '''
+
+ m_def = Category(
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_total_potential_per_atom'))
+
+
+class energy_total_potential(MCategory):
+ '''
+ A value of the total potential energy. Note that a direct comparison may not be
+ possible because of a difference in the methods for computing total energies and
+ numerical implementations of various codes might leads to different energy zeros (see
+ section_energy_code_independent for a code-independent definition of the energy).
+ '''
+
+ m_def = Category(
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_total_potential'))
+
+
+class energy_type_C(MCategory):
+ '''
+ This metadata stores the correlation (C) energy.
+ '''
+
+ m_def = Category(
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_type_C'))
+
+
+class energy_type_van_der_Waals(MCategory):
+ '''
+ This metadata stores the converged van der Waals energy.
+ '''
+
+ m_def = Category(
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_type_van_der_Waals'))
+
+
+class energy_type_XC(MCategory):
+ '''
+ This metadata stores the exchange-correlation (XC) energy.
+ '''
+
+ m_def = Category(
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_type_XC'))
+
+
+class energy_type_X(MCategory):
+ '''
+ This metadata stores the exchange (X) energy.
+ '''
+
+ m_def = Category(
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_type_X'))
+
+
+class message_warning(MCategory):
+ '''
+ A warning message of the computational program.
+ '''
+
+ m_def = Category(
+ categories=[message_info, message_debug],
+ a_legacy=LegacyDefinition(name='message_warning'))
+
+
+class parsing_message_warning(MCategory):
+ '''
+ This field is used for warning messages of the parsing program.
+ '''
+
+ m_def = Category(
+ categories=[parsing_message_info, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_warning'))
+
+
+class settings_barostat(MCategory):
+ '''
+ Contains parameters controlling the barostat in a molecular dynamics calculation.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling, settings_molecular_dynamics],
+ a_legacy=LegacyDefinition(name='settings_barostat'))
+
+
+class settings_integrator(MCategory):
+ '''
+ Contains parameters that control the molecular dynamics (MD) integrator.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling, settings_molecular_dynamics],
+ a_legacy=LegacyDefinition(name='settings_integrator'))
+
+
+class settings_post_hartree_fock(MCategory):
+ '''
+ Contains parameters for the post Hartree-Fock method.
+ '''
+
+ m_def = Category(
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_post_hartree_fock'))
+
+
+class settings_relativity(MCategory):
+ '''
+ Contains parameters and information connected with the relativistic treatment used in
+ the calculation.
+ '''
+
+ m_def = Category(
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_relativity'))
+
+
+class settings_self_interaction_correction(MCategory):
+ '''
+ Contains parameters and information connected with the self-interaction correction
+ (SIC) method being used in self_interaction_correction_method.
+ '''
+
+ m_def = Category(
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_self_interaction_correction'))
+
+
+class settings_thermostat(MCategory):
+ '''
+ Contains parameters that control the thermostat in the molecular dynamics (MD)
+ calculations.
+ '''
+
+ m_def = Category(
+ categories=[settings_sampling, settings_molecular_dynamics],
+ a_legacy=LegacyDefinition(name='settings_thermostat'))
+
+
+class settings_van_der_Waals(MCategory):
+ '''
+ Contain parameters and information connected with the Van der Waals treatment used in
+ the calculation to compute the Van der Waals energy (energy_van_der_Waals).
+ '''
+
+ m_def = Category(
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_van_der_Waals'))
+
+
+class settings_XC_functional(MCategory):
+ '''
+ Contain parameters connected with the definition of the exchange-correlation (XC)
+ functional (see section_XC_functionals and XC_functional).
+ '''
+
+ m_def = Category(
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_XC_functional'))
+
+
+class message_error(MCategory):
+ '''
+ An error message of the computational program.
+ '''
+
+ m_def = Category(
+ categories=[message_info, message_debug, message_warning],
+ a_legacy=LegacyDefinition(name='message_error'))
+
+
+class parsing_message_error(MCategory):
+ '''
+ This field is used for error messages of the parsing program.
+ '''
+
+ m_def = Category(
+ categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_error'))
+
+
+class settings_coupled_cluster(MCategory):
+ '''
+ Contains parameters for the coupled-cluster method (CC) in the post Hartree-Fock step.
+ '''
+
+ m_def = Category(
+ categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_coupled_cluster'))
+
+
+class settings_GW(MCategory):
+ '''
+ Contains parameters for the GW-method in the post Hartree-Fock step, that expands the
+ self-energy in terms of the single particle Green's function $G$ and the screened
+ Coulomb interaction $W$.
+ '''
+
+ m_def = Category(
+ categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_GW'))
+
+
+class settings_MCSCF(MCategory):
+ '''
+ Contains parameters for the multi-configurational self-consistent-field (MCSCF)
+ method.
+ '''
+
+ m_def = Category(
+ categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_MCSCF'))
+
+
+class settings_moller_plesset_perturbation_theory(MCategory):
+ '''
+ Contains parameters for Møller–Plesset perturbation theory.
+ '''
+
+ m_def = Category(
+ categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_moller_plesset_perturbation_theory'))
+
+
+class settings_multi_reference(MCategory):
+ '''
+ Contains parameters for the multi-reference single and double configuration
+ interaction method.
+ '''
+
+ m_def = Category(
+ categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='settings_multi_reference'))
+
+
+class archive_context(MSection):
+ '''
+ Contains information relating to an archive.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='archive_context'))
+
+ archive_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ unique identifier of an archive.
+ ''',
+ a_legacy=LegacyDefinition(name='archive_gid'))
+
+
+class calculation_context(MSection):
+ '''
+ Contains information relating to a calculation.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='calculation_context'))
+
+ calculation_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ unique identifier of a calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_gid'))
+
+
+class section_atom_projected_dos(MSection):
+ '''
+ Section collecting the information on an atom projected density of states (DOS)
+ evaluation.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atom_projected_dos'))
+
+ atom_projected_dos_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atom_projected_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the set of discrete energy values for the atom-projected density
+ (electronic-energy) of states (DOS).
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_energies'))
+
+ atom_projected_dos_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_lm_atom_projected_dos', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which atom_projected_dos_values_lm are given. For
+ the quantum number $l$ the conventional meaning of azimuthal quantum number is
+ always adopted. For the integer number $m$, besides the conventional use as
+ magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
+ different conventions is accepted (see the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ The adopted convention is specified by atom_projected_dos_m_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_lm'))
+
+ atom_projected_dos_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing what the integer numbers of $m$ in atom_projected_dos_lm mean.
+ The allowed values are listed in the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_m_kind'))
+
+ atom_projected_dos_values_lm = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_lm_atom_projected_dos', 'number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
+ description='''
+ Values correspond to the number of states for a given energy (the set of discrete
+ energy values is given in atom_projected_dos_energies) divided into contributions
+ from each $l,m$ channel for the atom-projected density (electronic-energy) of
+ states. Here, there are as many atom-projected DOS as the number_of_atoms, the
+ list of labels of the atoms and their meanings are in atom_labels.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_values_lm'))
+
+ atom_projected_dos_values_total = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
+ description='''
+ Values correspond to the number of states for a given energy (the set of discrete
+ energy values is given in atom_projected_dos_energies) divided into contributions
+ summed up over all $l$ channels for the atom-projected density (electronic-energy)
+ of states (DOS). Here, there are as many atom-projected DOS as the
+ number_of_atoms, the list of labels of the atoms and their meanings are in
+ atom_labels.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_projected_dos_values_total'))
+
+ number_of_atom_projected_dos_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of energy values for the atom-projected density of states (DOS)
+ based on atom_projected_dos_values_lm and atom_projected_dos_values_total.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atom_projected_dos_values'))
+
+ number_of_lm_atom_projected_dos = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for the atom projected density of states
+ (DOS) defined in section_atom_projected_dos.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_lm_atom_projected_dos'))
+
+
+class section_atomic_multipoles(MSection):
+ '''
+ Section describing multipoles (charges/monopoles, dipoles, quadrupoles, ...) for each
+ atom.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atomic_multipoles'))
+
+ atomic_multipole_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the method used to obtain the electrostatic multipoles
+ (including the electric charge, dipole, etc.) for each atom. Such multipoles
+ require a charge-density partitioning scheme, specified by the value of this
+ metadata. Allowed values are listed in the [atomic_multipole_kind wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/atomic-
+ multipole-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_multipole_kind'))
+
+ atomic_multipole_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_lm_atomic_multipoles', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which the atomic multipoles (including the
+ electric charge, dipole, etc.) are given. The method used to obtain the multipoles
+ is specified by atomic_multipole_kind. The meaning of the integer number $l$ is
+ monopole/charge for $l=0$, dipole for $l=1$, quadrupole for $l=2$, etc. The
+ meaning of the integer numbers $m$ is specified by atomic_multipole_m_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_multipole_lm'))
+
+ atomic_multipole_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the definition for each integer number $m$ in
+ atomic_multipole_lm. Allowed values are listed in the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_multipole_m_kind'))
+
+ atomic_multipole_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_lm_atomic_multipoles', 'number_of_atoms'],
+ description='''
+ Value of the multipoles (including the monopole/charge for $l$ = 0, the dipole for
+ $l$ = 1, etc.) for each atom, calculated as described in atomic_multipole_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_multipole_values'))
+
+ number_of_lm_atomic_multipoles = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for atomic multipoles
+ atomic_multipole_lm.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_lm_atomic_multipoles'))
+
+
+class section_basis_functions_atom_centered(MSection):
+ '''
+ This section contains the description of the basis functions (at least one function)
+ of the (atom-centered) basis set defined in section_basis_set_atom_centered.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))
+
+
+class section_basis_set_atom_centered(MSection):
+ '''
+ This section describes the atom-centered basis set. The main contained information is
+ a short, non unique but human-interpretable, name for identifying the basis set
+ (basis_set_atom_centered_short_name), a longer, unique name
+ (basis_set_atom_centered_unique_name), the atomic number of the atomic species the
+ basis set is meant for (basis_set_atom_number), and a list of actual basis functions
+ in the section_basis_functions_atom_centered section.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
+
+ basis_set_atom_centered_ls = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_kinds_in_basis_set_atom_centered'],
+ description='''
+ Azimuthal quantum number ($l$) values (of the angular part given by the spherical
+ harmonic $Y_{lm}$) of the atom-centered basis function defined in the current
+ section_basis_set_atom_centered.
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_ls'))
+
+ basis_set_atom_centered_radial_functions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_kinds_in_basis_set_atom_centered', 401, 5],
+ description='''
+ Values of the radial function of the different basis function kinds. The values
+ are numerically tabulated on a default 0.01-nm equally spaced grid from 0 to 4 nm.
+ The 5 tabulated values are $r$, $f(r)$, $f'(r)$, $f(r) \\cdot r$,
+ $\\frac{d}{dr}(f(r) \\cdot r)$.
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_radial_functions'))
+
+ basis_set_atom_centered_short_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Code-specific, but explicative, base name for the basis set (not unique). Details
+ are explained in the [basis_set_atom_centered_short_name wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
+ set-atom-centered-short-name), this name should not contain the *atom kind* (to
+ simplify the use of a single name for multiple elements).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_short_name'))
+
+ basis_set_atom_centered_unique_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Code-specific, but explicative, base name for the basis set (not unique). This
+ string starts with basis_set_atom_centered_short_name. If the basis set defined in
+ this section_basis_set_atom_centered is not identical to the default definition
+ (stored in a database) of the basis set with the same name stored in a database,
+ then the string is extended by 10 identifiable characters as explained in the
+ [basis_set_atom_centered_name wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/basis-set-atom-centered-unique-name). The
+ reason for this procedure is that often atom-centered basis sets are obtained by
+ fine tuning basis sets provided by the code developers or other sources. Each
+ basis sets, which has normally a standard name, often reported in publications,
+ has also several parameters that can be tuned. This metadata tries to keep track
+ of the original basis set and its modifications. This string here defined should
+ not contain the *atom kind* for which this basis set is intended for, in order to
+ simplify the use of a single name for multiple *atom kinds* (see atom_labels for
+ the actual meaning of *atom kind*).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_centered_unique_name'))
+
+ basis_set_atom_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Atomic number (i.e., number of protons) of the atom for which this basis set is
+ constructed (0 means unspecified or a pseudo atom).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_atom_number'))
+
+ number_of_basis_functions_in_basis_set_atom_centered = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different basis functions in a section_basis_set_atom_centered
+ section. This equals the number of actual coefficients that are specified when
+ using this basis set.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_basis_functions_in_basis_set_atom_centered'))
+
+ number_of_kinds_in_basis_set_atom_centered = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different *kinds* of radial basis functions in the
+ section_basis_set_atom_centered section. Specifically, basis functions with the
+ same $n$ and $l$ quantum numbers are grouped in sets. Each set counts as one
+ *kind*.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_kinds_in_basis_set_atom_centered'))
+
+ section_basis_functions_atom_centered = SubSection(
+ sub_section=SectionProxy('section_basis_functions_atom_centered'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))
+
+ section_gaussian_basis_group = SubSection(
+ sub_section=SectionProxy('section_gaussian_basis_group'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))
+
+
+class section_basis_set_cell_dependent(MSection):
+ '''
+ Section describing a cell-dependent (atom-independent) basis set, e.g. plane waves.
+ The contained information is the type of basis set (in basis_set_cell_dependent_kind),
+ its parameters (e.g., for plane waves in basis_set_planewave_cutoff), and a name that
+ identifies the actually used basis set (a string combining the type and the
+ parameter(s), stored in basis_set_cell_dependent_name).
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))
+
+ basis_set_cell_dependent_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A string defining the type of the cell-dependent basis set (i.e., non atom
+ centered such as plane-waves). Allowed values are listed in the
+ [basis_set_cell_dependent_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/basis-set-cell-dependent-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_cell_dependent_kind'))
+
+ basis_set_cell_dependent_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A label identifying the cell-dependent basis set (i.e., non atom centered such as
+ plane-waves). Allowed values are listed in the [basis_set_cell_dependent_name wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
+ set-cell-dependent-name).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_cell_dependent_name'))
+
+ basis_set_planewave_cutoff = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Spherical cutoff in reciprocal space for a plane-wave basis set. It is the energy
+ of the highest plan-ewave ($\\frac{\\hbar^2|k+G|^2}{2m_e}$) included in the basis
+ set. Note that normally this basis set is used for the wavefunctions, and the
+ density would have 4 times the cutoff, but this actually depends on the use of the
+ basis set by the method.
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_planewave_cutoff'))
+
+
+class section_basis_set(MSection):
+ '''
+ This section contains references to *all* basis sets used in this
+ section_single_configuration_calculation. More than one basis set instance per *single
+ configuration calculation* (see section_single_configuration_calculation) may be
+ needed. This is true for example, for codes that implement adaptive basis sets along
+ the self-consistent field (SCF) convergence (e.g., exciting). In such cases, there is
+ a section_basis_set instance per SCF iteration, if necessary. Another example is
+ having a basis set for wavefunctions, a different one for the density, an auxiliary
+ basis set for resolution of identity (RI), etc.
+
+ Supported are the two broad classes of basis sets: *atom-centered* (e.g., Gaussian-
+ type, numerical atomic orbitals) and *cell-dependent* (like plane waves or real-space
+ grids, so named because they are typically used for periodic-system calculations and
+ dependent to the simulated cell as a whole).
+
+ Basis sets used in this section_single_configuration_calculation, belonging to either
+ class, are defined in the dedicated section: [section_basis_set_cell_dependent
+ ](section_basis_set_cell_dependent) or section_basis_set_atom_centered. The
+ correspondence between the basis sets listed in this section and the definition given
+ in the dedicated sessions is given by the two concrete metadata:
+ mapping_section_basis_set_cell_dependent and mapping_section_basis_set_atom_centered.
+ The latter metadata is a list that connects each atom in the system with its basis
+ set, where the same basis set can be assigned to more than one atom.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set'))
+
+ basis_set_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing the use of the basis set, i.e, if it used for expanding a wave-
+ function or an electron density. Allowed values are listed in the [basis_set_kind
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/basis-set-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_kind'))
+
+ basis_set_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String identifying the basis set in an unique way. The rules for building this
+ string are specified in the [basis_set_name wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
+ set-name).
+ ''',
+ a_legacy=LegacyDefinition(name='basis_set_name'))
+
+ mapping_section_basis_set_atom_centered = Quantity(
+ type=Reference(SectionProxy('section_basis_set_atom_centered')),
+ shape=['number_of_atoms'],
+ description='''
+ An array of the dimension of number_of_atoms where each atom (identified by the
+ index in the array) is assigned to an atom-centered basis set, for this
+ section_single_configuration_calculation. The actual definition of the atom-
+ centered basis set is in the section_basis_set_atom_centered that is referred to
+ by this metadata.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_basis_set_atom_centered'))
+
+ mapping_section_basis_set_cell_dependent = Quantity(
+ type=Reference(SectionProxy('section_basis_set_cell_dependent')),
+ shape=[],
+ description='''
+ Assignment of the cell-dependent (i.e., non atom centered, e.g., plane-waves)
+ parts of the basis set, which is defined (type, parameters) in
+ section_basis_set_cell_dependent that is referred to by this metadata.
+ ''',
+ a_legacy=LegacyDefinition(name='mapping_section_basis_set_cell_dependent'))
+
+ number_of_basis_functions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Stores the total number of basis functions in a section_basis_set section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_basis_functions'))
+
+
+class section_restricted_uri(MSection):
+ '''
+ Restricted URIs on this calculation (Coverage: any info or files that are related with
+ this calculation can be subject to restriction)
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_restricted_uri'))
+
+ number_of_restricted_uri = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ The number of restricted uris in restricted_uri list.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_restricted_uri'))
+
+ restricted_uri = Quantity(
+ type=str,
+ shape=['number_of_restricted_uri'],
+ description='''
+ The list of nomad uri(s) identifying the restricted info/file corresponding to
+ this calculation
+ ''',
+ a_legacy=LegacyDefinition(name='restricted_uri'))
+
+ restricted_uri_reason = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The reason of restriction for the uri or file. The reason can be 'propriety
+ license', 'open-source redistribution restricted license', 'other license', or
+ 'author restricted'.
+ ''',
+ a_legacy=LegacyDefinition(name='restricted_uri_reason'))
+
+ restricted_uri_issue_authority = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The issue authority is the restriction owner for the uri or file. This can be
+ license owner such as 'VASP' or 'AMBER', 'NOMAD', or the author of the uri. For
+ example the repository user name of the author.
+ ''',
+ a_legacy=LegacyDefinition(name='restricted_uri_issue_authority'))
+
+ restricted_uri_end_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The deadline date of the restriction for the uri or file. The end date can be in
+ date format string for those restrictions set by authors or NOMAD otherwise it is
+ set to 'unlimited' for the restriction related to license.
+ ''',
+ a_legacy=LegacyDefinition(name='restricted_uri_end_date'))
+
+ restricted_uri_restriction = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of restriction for the uri or file. The type can be 'any access' or
+ 'license permitted'.
+ ''',
+ a_legacy=LegacyDefinition(name='restricted_uri_restriction'))
+
+ restricted_uri_license = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The info of the license that is the reason of restriction.
+ ''',
+ a_legacy=LegacyDefinition(name='restricted_uri_license'))
+
+ number_of_restricted_uri_files = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ The number of restricted files in restricted_uri_files list.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_restricted_uri_files'))
+
+
+class section_calculation_to_calculation_refs(MSection):
+ '''
+ Section that describes the relationship between different
+ section_single_configuration_calculation sections.
+
+ For instance, one calculation is a perturbation performed using a self-consistent
+ field (SCF) calculation as starting point, or a simulated system is partitioned in
+ regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated
+ via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
+
+ The kind of relationship between the calculation defined in this section and the
+ referenced one is described by calculation_to_calculation_kind. The referenced
+ section_single_configuration_calculation is identified via
+ calculation_to_calculation_ref (typically used for a
+ section_single_configuration_calculation in the same section_run) or
+ calculation_to_calculation_external_url.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))
+
+ calculation_to_calculation_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ URL used to reference an externally stored calculation. The kind of relationship
+ between the present and the referenced section_single_configuration_calculation is
+ specified by calculation_to_calculation_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_calculation_external_url'))
+
+ calculation_to_calculation_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the relationship between the referenced
+ section_single_configuration_calculation and the present
+ section_single_configuration_calculation. Valid values are described in the
+ [calculation_to_calculation_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/calculation-to-calculation-kind). Often
+ calculations are connected, for instance, one calculation is a perturbation
+ performed using a self-consistent field (SCF) calculation as starting point, or a
+ simulated system is partitioned in regions with different but connected
+ Hamiltonians (e.g., QM/MM, or a region treated via Kohn-Sham DFT embedded into a
+ region treated via orbital-free DFT). Hence, the need of keeping track of these
+ connected calculations. The referenced calculation is identified via
+ calculation_to_calculation_ref (typically used for a calculation in the same
+ section_run) or calculation_to_calculation_external_url.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_calculation_kind'))
+
+ calculation_to_calculation_ref = Quantity(
+ type=Reference(SectionProxy('section_single_configuration_calculation')),
+ shape=[],
+ description='''
+ Reference to another calculation. If both this and
+ calculation_to_calculation_external_url are given, then
+ calculation_to_calculation_ref is a local copy of the URL given in
+ calculation_to_calculation_external_url. The kind of relationship between the
+ present and the referenced section_single_configuration_calculation is specified
+ by calculation_to_calculation_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_calculation_ref'))
+
+
+class section_calculation_to_folder_refs(MSection):
+ '''
+ Section that describes the relationship between
+ section_single_configuration_calculationa and the folder containing the original
+ calulations
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))
+
+ calculation_to_folder_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ URL used to reference a folder containing external calculations. The kind of
+ relationship between the present and the referenced
+ section_single_configuration_calculation is specified by
+ calculation_to_folder_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_folder_external_url'))
+
+ calculation_to_folder_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the relationship between the referenced
+ section_single_configuration_calculation and a folder containing calculations.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_to_folder_kind'))
+
+
+class section_dos_fingerprint(MSection):
+ '''
+ Section for the fingerprint of the electronic density-of-states (DOS).
+ DOS fingerprints are a modification of the D-Fingerprints reported in Chem. Mater. 2015, 27, 3, 735–743
+ (doi:10.1021/cm503507h). The fingerprint consists of a binary representation of the DOS,
+ that is used to evaluate the similarity of materials based on their electronic structure.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dos_fingerprint'))
+
+ bins = Quantity(
+ type=str,
+ description='''
+ Byte representation of the DOS fingerprint.
+ ''',
+ a_legacy=LegacyDefinition(name='bins'))
+
+ indices = Quantity(
+ type=np.dtype(np.int16),
+ shape=[2],
+ description='''
+ Indices used to compare DOS fingerprints of different energy ranges.
+ ''',
+ a_legacy=LegacyDefinition(name='indices'))
+
+ stepsize = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Stepsize of interpolation in the first step of the generation of DOS fingerprints.
+ ''',
+ a_legacy=LegacyDefinition(name='stepsize'))
+
+ filling_factor = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Proportion of 1 bins in the DOS fingerprint.
+ ''',
+ a_legacy=LegacyDefinition(name='filling_factor'))
+
+ grid_id = Quantity(
+ type=str,
+ description='''
+ Identifier of the DOS grid that was used for the creation of the fingerprint.
+ Similarity can only be calculated if the same grid was used for both fingerprints.
+ ''',
+ a_legacy=LegacyDefinition(name='grid_id'))
+
+
+class section_dos(MSection):
+ '''
+ Section collecting information of a (electronic-energy or vibrational-energy) density
+ of states (DOS) evaluation.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dos'))
+
+ dos_energies_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the set of discrete energy values with respect to the
+ highest occupied energy level. This is the total DOS, see
+ atom_projected_dos_energies and species_projected_dos_energies for
+ partial density of states.
+
+ If not available through energy_reference_highest_occupied, the highest
+ occupied energy level is detected by searching for a non-zero DOS value
+ below (or nearby) the reported energy_reference_fermi. In case the
+ highest occupied energy level cannot be detected accurately, the
+ normalized values are not reported. For calculations with multiple
+ spin-channels, the normalization is determined by the first channel.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_energies_normalized'))
+
+ dos_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the set of discrete energy values for the density (electronic-
+ energy or vibrational energy) of states (DOS). This is the total DOS, see
+ atom_projected_dos_energies and species_projected_dos_energies for partial density
+ of states.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_energies'))
+
+ dos_integrated_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_dos_values'],
+ description='''
+ Integrated density of states (starting at $-\\infty$), pseudo potential
+ calculations should start with the number of core electrons if they cover only the
+ active electrons
+ ''',
+ a_legacy=LegacyDefinition(name='dos_integrated_values'))
+
+ dos_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String to specify the kind of density of states (either electronic or
+ vibrational).
+ ''',
+ a_legacy=LegacyDefinition(name='dos_kind'))
+
+ dos_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_dos_lms', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which dos_values_lm are given. For the quantum
+ number $l$ the conventional meaning of azimuthal quantum number is always adopted.
+ For the integer number $m$, besides the conventional use as magnetic quantum
+ number ($l+1$ integer values from $-l$ to $l$), a set of different conventions is
+ accepted (see the [m_kind wiki page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/m-kind). The actual adopted convention is specified by
+ dos_m_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_lm'))
+
+ dos_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing what the integer numbers of $m$ in dos_lm mean. The allowed
+ values are listed in the [m_kind wiki page](https://gitlab.rzg.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='dos_m_kind'))
+
+ dos_values_lm = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_dos_lms', 'number_of_spin_channels', 'number_of_atoms', 'number_of_dos_values'],
+ unit='joule',
+ description='''
+ Array containing the density (electronic-energy) of states values projected on the
+ various spherical harmonics (integrated on all atoms), see
+ atom_projected_dos_values_lm for atom values.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_values_lm'))
+
+ dos_values_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_dos_values'],
+ description='''
+ Density of states (DOS) values divided by the unit cell volume and by the number
+ of atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_values_normalized'))
+
+ dos_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_dos_values'],
+ description='''
+ Values (number of states for a given energy, the set of discrete energy values is
+ given in dos_energies) of density (electronic-energy or vibrational-energy) of
+ states. This refers to the simulation cell, i.e. integrating over all energies
+ will give the number of electrons in the simulation cell.
+ ''',
+ a_legacy=LegacyDefinition(name='dos_values'))
+
+ number_of_dos_lms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for the given projected density of
+ states (DOS) in dos_values and dos_values_lm.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_dos_lms'))
+
+ number_of_dos_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of energy values for the density of states (DOS), see
+ dos_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_dos_values'))
+
+ section_dos_fingerprint = SubSection(
+ sub_section=SectionProxy('section_dos_fingerprint'),
+ repeats=False,
+ a_legacy=LegacyDefinition(name='section_dos_fingerprint'))
+
+
+class section_eigenvalues(MSection):
+ '''
+ Section containing (electronic-energy) eigenvalues for one spin channel. If, for
+ example, the eigenvalues of the Kohn-Sham operator are to be stored, a string
+ identifying this kind of eigenvalues is put in eigenvalues_kind, the coordinates of
+ the $k$-points at which the eigenvalues are evaluated is stored in
+ eigenvalues_kpoints, and the energy values of the eigenstates and their occupation is
+ stored in eigenvalues_values and eigenvalues_occupation, respectively.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_eigenvalues'))
+
+ eigenvalues_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A short string describing the kind of eigenvalues, as defined in the
+ [eigenvalues_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/eigenvalues-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_kind'))
+
+ eigenvalues_kpoints_multiplicity = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_eigenvalues_kpoints'],
+ description='''
+ Multiplicity of the $k$ point (i.e., how many distinct points per cell this
+ expands to after applying all symmetries). This defaults to 1. If expansion is
+ preformed then each point will have weight
+ eigenvalues_kpoints_weights/eigenvalues_kpoints_multiplicity.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_kpoints_multiplicity'))
+
+ eigenvalues_kpoints_weights = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_eigenvalues_kpoints'],
+ description='''
+ Weights of the $k$ points (in the basis of the reciprocal lattice vectors) used
+ for the evaluation of the eigenvalues tabulated in eigenvalues_values, should
+ account for symmetry too.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_kpoints_weights'))
+
+ eigenvalues_kpoints = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_eigenvalues_kpoints', 3],
+ description='''
+ Coordinates of the $k$ points (in the basis of the reciprocal lattice vectors)
+ used for the evaluation of the eigenvalues tabulated in eigenvalues_values.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_kpoints'))
+
+ eigenvalues_occupation = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ description='''
+ Occupation of the eigenstates. The corresponding eigenvalues (energy) are given in
+ eigenvalues_values. The coordinates in the reciprocal space are defined in
+ eigenvalues_kpoints.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_occupation'))
+
+ eigenvalues_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Values of the (electronic-energy) eigenvalues. The coordinates of the
+ corresponding eigenstates in the reciprocal space are defined in
+ eigenvalues_kpoints and their occupations are given in eigenvalues_occupation.
+ ''',
+ a_legacy=LegacyDefinition(name='eigenvalues_values'))
+
+ number_of_band_segment_eigenvalues = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of eigenvalues in a band segment, see band_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_band_segment_eigenvalues'))
+
+ number_of_eigenvalues_kpoints = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $k$ points, see eigenvalues_kpoints. $k$ points are calculated
+ within a run and are irreducible if a symmetry is used.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_eigenvalues_kpoints'))
+
+ number_of_eigenvalues = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of eigenvalues, see eigenvalues_values.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_eigenvalues'))
+
+ number_of_normalized_band_segment_eigenvalues = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of normalized eigenvalues in a band segment, see
+
+ band_energies_normalized.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_normalized_band_segment_eigenvalues'))
+
+
+class section_energy_code_independent(MSection):
+ '''
+ Section describing a code-independent total energy obtained by subtracting some
+ reference energy calculated with the same code. It contains the type in
+ energy_code_independent_kind and the computed code-independent total energy in
+ energy_code_independent_value. The computed energy allows for comparisons among
+ different codes and numerical settings.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_code_independent'))
+
+ energy_code_independent_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of the code-independent total energy (obtained by subtracting a reference
+ energy calculated with the same code), created to be comparable among different
+ codes and numerical settings. Details can be found on the [energy_code_independent
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/energy-code-independent).
+ ''',
+ a_legacy=LegacyDefinition(name='energy_code_independent_kind'))
+
+ energy_code_independent_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the code-independent total energy (obtained by subtracting a reference
+ energy calculated with the same code). This value is created to be comparable
+ among different codes and numerical settings. Details can be found on the
+ [energy_code_independent wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/energy-code-independent).
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_code_independent_value'))
+
+
+class section_energy_van_der_Waals(MSection):
+ '''
+ Section containing the Van der Waals energy value (energy_van_der_Waals_value) of type
+ van_der_Waals_kind. This is used when more than one Van der Waals methods are applied
+ in the same *single configuration calculation*, see
+ section_single_configuration_calculation. The main Van der Waals method (the one
+ concurring to energy_current, and used, e.g., for evaluating the forces for a
+ relaxation or dynamics) is given in energy_van_der_Waals and is defined in
+ settings_van_der_Waals.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
+
+ energy_van_der_Waals_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to compute van der Waals energy stored in energy_van_der_Waals_value.
+ This metadata is used when more than one van der Waals method is applied in the
+ same *single configuration calculation* (see
+ section_single_configuration_calculation). The method used for van der Waals (the
+ one consistent with energy_current and, e.g., for evaluating the forces for a
+ relaxation or dynamics) is defined in settings_van_der_Waals.
+ ''',
+ a_legacy=LegacyDefinition(name='energy_van_der_Waals_kind'))
+
+ energy_van_der_Waals_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of van der Waals energy, calculated with the method defined in
+ energy_van_der_Waals_kind. This metadata is used when more than one van der Waals
+ method is applied in the same *single configuration calculation* (see
+ section_single_configuration_calculation). The value of the van der Waals energy
+ consistent with energy_current and used, e.g., for evaluating the forces for a
+ relaxation or dynamics, is given in energy_van_der_Waals and defined in
+ settings_van_der_Waals.
+ ''',
+ categories=[energy_type_van_der_Waals, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_van_der_Waals_value'))
+
+ energy_van_der_Waals = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value for the converged van der Waals energy calculated using the method described
+ in van_der_Waals_method, and used in energy_current. This is the van der Waals
+ method consistent with, e.g., forces used for relaxation or dynamics. Alternative
+ methods are listed in section_energy_van_der_Waals.
+ ''',
+ categories=[energy_type_van_der_Waals, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_van_der_Waals'))
+
+
+class section_energy_contribution(MSection):
+ '''
+ Section describing the contributions to the total energy.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_contribution'))
+
+ energy_contibution_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The kind of the energy contribution. Can be one of bond, pair, coulomb, etc.
+ ''',
+ a_legacy=LegacyDefinition(name='energy_contibution_kind'))
+
+ energy_contribution_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy contribution.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_contribution_value'))
+
+
+class section_frame_sequence_user_quantity(MSection):
+ '''
+ Section collecting some user-defined quantities evaluated along a sequence of frame.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_frame_sequence_user_quantity'))
+
+ frame_sequence_user_quantity_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_user_quantity_evaluations_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_user_quantity. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_frames'))
+
+ frame_sequence_user_quantity_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Descriptive name of a user-defined quantity, sampled along this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ Dedicated metadata are created for the conserved energy-like quantity
+ (frame_sequence_conserved_quantity), the kinetic and potential energies
+ (frame_sequence_kinetic_energy and frame_sequence_potential_energy), the
+ instantaneous temperature (frame_sequence_temperature) and pressure
+ (frame_sequence_pressure). This metadata should be used for other quantities that
+ are monitored along a sequence of frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_name'))
+
+ frame_sequence_user_quantity_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2, 'number_of_frame_sequence_user_quantity_components'],
+ description='''
+ Average of frame_sequence_user_quantity and its standard deviation in this
+ sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity_stats'))
+
+ frame_sequence_user_quantity = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_user_quantity_evaluations_in_sequence', 'number_of_frame_sequence_user_quantity_components'],
+ description='''
+ Array containing the values of the user-defined quantity defined in
+ frame_sequence_user_quantity_name, evaluated along this sequence of frames (i.e.,
+ trajectory, a frame is one section_single_configuration_calculation). If not all
+ frames have a value the indices of the frames that have a value are stored in
+ frame_sequence_kinetic_energy_frames. If not all frames have a value the indices
+ of the frames that have a value are stored in
+ frame_sequence_kinetic_energy_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_user_quantity'))
+
+ number_of_frame_sequence_user_quantity_components = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of user-defined quantity defined by
+ frame_sequence_user_quantity_name and monitored in a sequence of frames. A
+ sequence is a trajectory, which can have number_of_frames_in_sequence each
+ representing one section_single_configuration_calculation section.
+
+ Dedicated metadata monitored along a sequence of frames are created for the
+ conserved energy-like quantity (frame_sequence_conserved_quantity), the kinetic
+ and potential energies ([frame_sequence_kinetic_energy and
+ frame_sequence_potential_energy](frame_sequence_kinetic_energy and
+ frame_sequence_potential_energy)), the instantaneous temperature
+ (frame_sequence_temperature) and the pressure (frame_sequence_pressure).
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_frame_sequence_user_quantity_components'))
+
+ number_of_user_quantity_evaluations_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of user defined quantity evaluations along a sequence of
+ frame_sequence_user_quantity frames. A sequence is a trajectory, which can have
+ number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_user_quantity_evaluations_in_sequence'))
+
+
+class section_frame_sequence(MSection):
+ '''
+ Section containing a sequence of frames, i.e. a trajectory which can have
+ number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section evaluated with a sampling method
+ (e.g, molecular dynamics, Monte Carlo, geometry optimization). The sampling method
+ might be a subset of the whole trajectory.
+
+ Information on the method used for the sampling can be found in the
+ section_sampling_method section and information of each frame of the sequence are
+ found in the section_single_configuration_calculation section.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_frame_sequence'))
+
+ frame_sequence_conserved_quantity_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_conserved_quantity_evaluations_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices of the frames the
+ frame_sequence_conserved_quantity values refers to. If not given it defaults to
+ the trivial mapping 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity_frames'))
+
+ frame_sequence_conserved_quantity_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='joule',
+ description='''
+ Average value of energy-like frame_sequence_conserved_quantity, and its standard
+ deviation, over this sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity_stats'))
+
+ frame_sequence_conserved_quantity = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_conserved_quantity_evaluations_in_sequence'],
+ unit='joule',
+ description='''
+ Array containing the values of a quantity that should be conserved, along a
+ sequence of frames (i.e., a trajectory). A frame is one
+ section_single_configuration_calculation), for example the total energy in the NVE
+ ensemble. If not all frames have a value the indices of the frames that have a
+ value are stored in frame_sequence_conserved_quantity_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_conserved_quantity'))
+
+ frame_sequence_continuation_kind = Quantity(
+ type=Reference(SectionProxy('section_frame_sequence')),
+ shape=[],
+ description='''
+ Type of continuation that has been performed from the previous sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation),
+ upon restart.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_continuation_kind'))
+
+ frame_sequence_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ If the energy, forces, and other quantities for the frames (a frame is one
+ section_single_configuration_calculation) in section_frame_sequence are obtained
+ by calling a different code than the code that drives the sequence (e.g., a
+ wrapper that drives a molecular dynamics, Monte Carlo, geometry optimization and
+ calls an electronic-structure code for energy and forces for each configuration),
+ this metadata holds the reference to where the
+ section_single_configuration_calculation for each frame are located. The format
+ for this reference is described in the [frame_sequence_external_url wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/frame-
+ sequence-external-url).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_external_url'))
+
+ frame_sequence_kinetic_energy_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_kinetic_energies_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_kinetic_energy. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy_frames'))
+
+ frame_sequence_kinetic_energy_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='joule',
+ description='''
+ Average kinetic energy and its standard deviation over this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy_stats'))
+
+ frame_sequence_kinetic_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_kinetic_energies_in_sequence'],
+ unit='joule',
+ description='''
+ Array containing the values of the kinetic energy along this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation). If
+ not all frames have a value the indices of the frames that have a value are stored
+ in frame_sequence_kinetic_energy_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_kinetic_energy'))
+
+ frame_sequence_local_frames_ref = Quantity(
+ type=Reference(SectionProxy('section_single_configuration_calculation')),
+ shape=['number_of_frames_in_sequence'],
+ description='''
+ Reference from each frame (a frame is one
+ section_single_configuration_calculation) in this section_frame_sequence to the
+ corresponding section_single_configuration_calculation. Each
+ section_frame_sequence binds a collection of
+ section_single_configuration_calculation, because they all belong to, e.g., a
+ molecular dynamics trajectory, or geometry optimization. The full information for
+ each frame is stored in section_single_configuration_calculation and this metadata
+ establishes the link for each frame.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_local_frames_ref'))
+
+ frame_sequence_potential_energy_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_potential_energies_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_potential_energy. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_potential_energy_frames'))
+
+ frame_sequence_potential_energy_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='joule',
+ description='''
+ Average potential energy and its standard deviation over this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_potential_energy_stats'))
+
+ frame_sequence_potential_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_potential_energies_in_sequence'],
+ unit='joule',
+ description='''
+ Array containing the value of the potential energy along this sequence of frames
+ (i.e., a trajectory, a frame is one section_single_configuration_calculation).
+ This is equal to energy_total of the corresponding
+ section_single_configuration_calculation and repeated here in a summary array for
+ easier access. If not all frames have a value the indices of the frames that have
+ a value are stored in frame_sequence_potential_energy_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_potential_energy'))
+
+ frame_sequence_pressure_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_pressure_evaluations_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_pressure. If not given it defaults to the trivial mapping 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_pressure_frames'))
+
+ frame_sequence_pressure_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='pascal',
+ description='''
+ Average pressure (one third of the trace of the stress tensor) and standard
+ deviation over this sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_pressure_stats'))
+
+ frame_sequence_pressure = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_pressure_evaluations_in_sequence'],
+ unit='pascal',
+ description='''
+ Array containing the values of the pressure (one third of the trace of the stress
+ tensor) along this sequence of frames (a frame is one
+ section_single_configuration_calculation). If not all frames have a value the
+ indices of the frames that have a value are stored in
+ frame_sequence_pressure_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_pressure'))
+
+ frame_sequence_temperature_frames = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_temperatures_in_sequence'],
+ description='''
+ Array containing the strictly increasing indices referring to the frames of
+ frame_sequence_temperature. If not given it defaults to the trivial mapping
+ 0,1,...
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_temperature_frames'))
+
+ frame_sequence_temperature_stats = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2],
+ unit='kelvin',
+ description='''
+ Average temperature and its standard deviation over this sequence of frames (i.e.,
+ a trajectory, a frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_temperature_stats'))
+
+ frame_sequence_temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_temperatures_in_sequence'],
+ unit='kelvin',
+ description='''
+ Array containing the values of the instantaneous temperature (a quantity,
+ proportional to frame_sequence_kinetic_energy, whose ensemble average equals the
+ thermodynamic temperature) along this sequence of frames (i.e., a trajectory, a
+ frame is one section_single_configuration_calculation). If not all frames have a
+ value the indices of the frames that have a value are stored in
+ frame_sequence_temperature_frames.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_temperature'))
+
+ frame_sequence_time = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_frames_in_sequence'],
+ unit='second',
+ description='''
+ Time along this sequence of frames (i.e., a trajectory, a frame is one
+ section_single_configuration_calculation). Time start is arbitrary, but when a
+ sequence is a continuation of another time should be continued too.
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_time'))
+
+ frame_sequence_to_sampling_ref = Quantity(
+ type=Reference(SectionProxy('section_sampling_method')),
+ shape=[],
+ description='''
+ Reference from the present section_frame_sequence to the section_sampling_method,
+ that defines the parameters used in this sequence of frames (i.e., a trajectory, a
+ frame is one section_single_configuration_calculation).
+ ''',
+ a_legacy=LegacyDefinition(name='frame_sequence_to_sampling_ref'))
+
+ geometry_optimization_converged = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Arrays specify whether a geometry optimization is converged.
+ ''',
+ a_legacy=LegacyDefinition(name='geometry_optimization_converged'))
+
+ number_of_conserved_quantity_evaluations_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of conserved quantity evaluations in this sequence. A sequence is
+ a trajectory, which can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_conserved_quantity_evaluations_in_sequence'))
+
+ number_of_frames_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of frames in a sequence. A sequence is a trajectory, which can
+ have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_frames_in_sequence'))
+
+ number_of_kinetic_energies_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of kinetic energy evaluations in this sequence of frames, see
+ frame_sequence_kinetic_energy.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_kinetic_energies_in_sequence'))
+
+ number_of_potential_energies_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of potential energies evaluation in this sequence. A sequence is
+ a trajectory, which can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_potential_energies_in_sequence'))
+
+ number_of_pressure_evaluations_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of pressure evaluations in this sequence. A sequence is a
+ trajectory, which can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_pressure_evaluations_in_sequence'))
+
+ number_of_temperatures_in_sequence = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of temperature frames (frame_sequence_temperature) used in the
+ section_frame_sequence. A sequence is a trajectory, which can have
+ number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_temperatures_in_sequence'))
+
+ previous_sequence_ref = Quantity(
+ type=Reference(SectionProxy('section_frame_sequence')),
+ shape=[],
+ description='''
+ Contains a reference to the previous sequence. A sequence is a trajectory, which
+ can have number_of_frames_in_sequence each representing one
+ section_single_configuration_calculation section. If not given, a start from an
+ initial configuration is assumed.
+ ''',
+ a_legacy=LegacyDefinition(name='previous_sequence_ref'))
+
+ section_frame_sequence_user_quantity = SubSection(
+ sub_section=SectionProxy('section_frame_sequence_user_quantity'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_frame_sequence_user_quantity'))
+
+ section_thermodynamical_properties = SubSection(
+ sub_section=SectionProxy('section_thermodynamical_properties'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_thermodynamical_properties'))
+
+
+class section_gaussian_basis_group(MSection):
+ '''
+ Section that describes a group of Gaussian contractions. Groups allow one to calculate
+ the primitive Gaussian integrals once for several different linear combinations of
+ them. This defines basis functions with radial part $f_i(r) = r^{l_i} \\sum_{j} c_{i
+ j} A(l_i, \\alpha_j) exp(-\\alpha_j r^2)$ where $A(l_i, \\alpha_j)$ is a the
+ normalization coefficient for primitive Gaussian basis functions. Here, $\\alpha_j$ is
+ defined in gaussian_basis_group_exponents, $l_i$ is given in gaussian_basis_group_ls,
+ and $c_{i j}$ is given in gaussian_basis_group_contractions, whereas the radial part
+ is given by the spherical harmonics $Y_{l m}$.
+
+ This section is defined only if the original basis function uses Gaussian basis
+ functions, and the sequence of radial functions $f_i$ across all
+ section_gaussian_basis_group in section_basis_set_atom_centered should match the one
+ of basis_set_atom_centered_radial_functions.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))
+
+ gaussian_basis_group_contractions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_gaussian_basis_group_contractions', 'number_of_gaussian_basis_group_exponents'],
+ description='''
+ contraction coefficients $c_{i j}$ defining the contracted basis functions with
+ respect to *normalized* primitive Gaussian functions. They define the Gaussian
+ basis functions as described in section_gaussian_basis_group.
+ ''',
+ a_legacy=LegacyDefinition(name='gaussian_basis_group_contractions'))
+
+ gaussian_basis_group_exponents = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_gaussian_basis_group_exponents'],
+ unit='1 / meter ** 2',
+ description='''
+ Exponents $\\alpha_j$ of the Gaussian functions defining this basis set
+ $exp(-\\alpha_j r^2)$. One should be careful about the units of the coefficients.
+ ''',
+ a_legacy=LegacyDefinition(name='gaussian_basis_group_exponents'))
+
+ gaussian_basis_group_ls = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_gaussian_basis_group_contractions'],
+ description='''
+ Azimuthal quantum number ($l$) values (of the angular part given by the spherical
+ harmonic $Y_{l m}$ of the various contracted basis functions).
+ ''',
+ a_legacy=LegacyDefinition(name='gaussian_basis_group_ls'))
+
+ number_of_gaussian_basis_group_contractions = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different contractions, i.e. resulting basis functions in a
+ section_gaussian_basis_group section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_gaussian_basis_group_contractions'))
+
+ number_of_gaussian_basis_group_exponents = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of different Gaussian exponents in a section_gaussian_basis_group
+ section.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_gaussian_basis_group_exponents'))
+
+
+class section_k_band_normalized(MSection):
+ '''
+ This section stores information on a normalized $k$-band (electronic band structure)
+ evaluation along one-dimensional pathways in the $k$ (reciprocal) space given in
+ section_k_band_segment. Eigenvalues calculated at the actual $k$-mesh used for
+ energy_total evaluations, can be found in the section_eigenvalues section.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band_normalized'))
+
+ k_band_path_normalized_is_standard = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ If the normalized path is along the default path defined in W. Setyawan and S.
+ Curtarolo, [Comput. Mater. Sci. **49**, 299-312
+ (2010)](http://dx.doi.org/10.1016/j.commatsci.2010.05.010).
+ ''',
+ a_legacy=LegacyDefinition(name='k_band_path_normalized_is_standard'))
+
+ section_k_band_segment_normalized = SubSection(
+ sub_section=SectionProxy('section_k_band_segment_normalized'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band_segment_normalized'))
+
+
+class section_k_band_segment_normalized(MSection):
+ '''
+ Section collecting the information on a normalized $k$-band segment. This section
+ stores band structures along a one-dimensional pathway in the $k$ (reciprocal) space.
+
+ Eigenvalues calculated at the actual $k$-mesh used for energy_total evaluations are
+ defined in section_eigenvalues and the band structures are represented as third-order
+ tensors: one dimension for the spin channels, one for the sequence of $k$ points for
+ the segment (given in number_of_k_points_per_segment), and one for the sequence of
+ eigenvalues at a given $k$ point. The values of the $k$ points in each segment are
+ stored in band_k_points. The energies and occupation for each eigenstate, at each $k$
+ point, segment, and spin channel are stored in band_energies and band_occupations,
+ respectively. The labels for the segment are specified in band_segm_labels.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band_segment_normalized'))
+
+ band_energies_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_normalized_k_points_per_segment', 'number_of_normalized_band_segment_eigenvalues'],
+ unit='joule',
+ description='''
+ $k$-dependent energies of the electronic band segment (electronic band structure)
+ with respect to the top of the valence band. This is a third-order tensor, with
+ one dimension used for the spin channels, one for the $k$ points for each segment,
+ and one for the eigenvalue sequence.
+ ''',
+ a_legacy=LegacyDefinition(name='band_energies_normalized'))
+
+ band_k_points_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_normalized_k_points_per_segment', 3],
+ description='''
+ Fractional coordinates of the $k$ points (in the basis of the reciprocal-lattice
+ vectors) for which the normalized electronic energies are given.
+ ''',
+ a_legacy=LegacyDefinition(name='band_k_points_normalized'))
+
+ band_occupations_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_normalized_k_points_per_segment', 'number_of_normalized_band_segment_eigenvalues'],
+ description='''
+ Occupation of the $k$-points along the normalized electronic band. The size of the
+ dimensions of this third-order tensor are the same as for the tensor in
+ band_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='band_occupations_normalized'))
+
+ band_segm_labels_normalized = Quantity(
+ type=str,
+ shape=[2],
+ description='''
+ Start and end labels of the points in the segment (one-dimensional pathways)
+ sampled in the $k$-space, using the conventional symbols, e.g., Gamma, K, L. The
+ coordinates (fractional, in the reciprocal space) of the start and end points for
+ each segment are given in band_segm_start_end_normalized
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_labels_normalized'))
+
+ band_segm_start_end_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2, 3],
+ description='''
+ Fractional coordinates of the start and end point (in the basis of the reciprocal
+ lattice vectors) of the segment sampled in the $k$ space. The conventional symbols
+ (e.g., Gamma, K, L) of the same points are given in band_segm_labels
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_start_end_normalized'))
+
+ number_of_normalized_k_points_per_segment = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $k$ points in the segment of the normalized band structure
+ (see section_k_band_segment_normalized).
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_normalized_k_points_per_segment'))
+
+
+class section_k_band_segment(MSection):
+ '''
+ Section collecting the information on a $k$-band or $q$-band segment. This section
+ stores band structures along a one-dimensional pathway in the $k$ or $q$ (reciprocal)
+ space.
+
+ Eigenvalues calculated at the actual $k$-mesh used for energy_total evaluations are
+ defined in section_eigenvalues and the band structures are represented as third-order
+ tensors: one dimension for the spin channels, one for the sequence of $k$ or $q$
+ points for the segment (given in number_of_k_points_per_segment), and one for the
+ sequence of eigenvalues at a given $k$ or $q$ point. The values of the $k$ or $q$
+ points in each segment are stored in band_k_points. The energies and occupation for
+ each eigenstate, at each $k$ or $q$ point, segment, and spin channel are stored in
+ band_energies and band_occupations, respectively. The labels for the segment are
+ specified in band_segm_labels.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band_segment'))
+
+ band_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_k_points_per_segment', 'number_of_band_segment_eigenvalues'],
+ unit='joule',
+ description='''
+ $k$-dependent or $q$-dependent energies of the electronic or vibrational band
+ segment (electronic/vibrational band structure). This is a third-order tensor,
+ with one dimension used for the spin channels (1 in case of a vibrational band
+ structure), one for the $k$ or $q$ points for each segment, and one for the
+ eigenvalue sequence.
+ ''',
+ a_legacy=LegacyDefinition(name='band_energies'))
+
+ band_k_points = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_k_points_per_segment', 3],
+ description='''
+ Fractional coordinates of the $k$ or $q$ points (in the basis of the reciprocal-
+ lattice vectors) for which the electronic energy are given.
+ ''',
+ a_legacy=LegacyDefinition(name='band_k_points'))
+
+ band_occupations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_k_points_per_segment', 'number_of_band_segment_eigenvalues'],
+ description='''
+ Occupation of the $k$-points along the electronic band. The size of the dimensions
+ of this third-order tensor are the same as for the tensor in band_energies.
+ ''',
+ a_legacy=LegacyDefinition(name='band_occupations'))
+
+ band_segm_labels = Quantity(
+ type=str,
+ shape=[2],
+ description='''
+ Start and end labels of the points in the segment (one-dimensional pathways)
+ sampled in the $k$-space or $q$-space, using the conventional symbols, e.g.,
+ Gamma, K, L. The coordinates (fractional, in the reciprocal space) of the start
+ and end points for each segment are given in band_segm_start_end
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_labels'))
+
+ band_segm_start_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[2, 3],
+ description='''
+ Fractional coordinates of the start and end point (in the basis of the reciprocal
+ lattice vectors) of the segment sampled in the $k$ space. The conventional symbols
+ (e.g., Gamma, K, L) of the same points are given in band_segm_labels
+ ''',
+ a_legacy=LegacyDefinition(name='band_segm_start_end'))
+
+ number_of_k_points_per_segment = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $k$ points in the segment of the band structure, see
+ section_k_band_segment.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_k_points_per_segment'))
+
+
+class section_band_gap(MSection):
+ '''
+ This section stores information for a band gap within a band structure.
+ '''
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_band_gap'))
+
+ value = Quantity(
+ type=float,
+ unit="joule",
+ description="""
+ Band gap energy. Value of zero corresponds to a band structure without
+ a band gap.
+ """,
+ a_legacy=LegacyDefinition(name='value')
+ )
+ type = Quantity(
+ type=MEnum("direct", "indirect"),
+ description="""
+ Type of band gap.
+ """,
+ a_legacy=LegacyDefinition(name='type')
+ )
+ conduction_band_min_energy = Quantity(
+ type=float,
+ unit="joule",
+ description="""
+ Conduction band minimum energy.
+ """,
+ a_legacy=LegacyDefinition(name='conduction_band_min_energy')
+ )
+ valence_band_max_energy = Quantity(
+ type=float,
+ unit="joule",
+ description="""
+ Valence band maximum energy.
+ """,
+ a_legacy=LegacyDefinition(name='valence_band_max_energy')
+ )
+ conduction_band_min_k_point = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ unit="1 / meter",
+ description="""
+ Coordinate of the conduction band minimum in k-space.
+ """,
+ a_legacy=LegacyDefinition(name='conduction_band_min_k_point')
+ )
+ valence_band_max_k_point = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ unit="1 / meter",
+ description="""
+ Coordinate of the valence band minimum in k-space.
+ """,
+ a_legacy=LegacyDefinition(name='valence_band_max_k_point')
+ )
+
+
+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
+ structure) evaluation along one-dimensional pathways in the $k$ or $q$ (reciprocal)
+ space given in section_k_band_segment. Eigenvalues calculated at the actual $k$-mesh
+ used for energy_total evaluations, can be found in the section_eigenvalues section.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_k_band'))
+
+ band_structure_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String to specify the kind of band structure (either electronic or vibrational).
+ ''',
+ a_legacy=LegacyDefinition(name='band_structure_kind'))
+
+ reciprocal_cell = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit="1 / meter",
+ description="""
+ The reciprocal cell within which the band structure is calculated.
+ """,
+ a_legacy=LegacyDefinition(name='reciprocal_cell')
+ )
+
+ brillouin_zone = SubSection(
+ sub_section=SectionProxy('section_brillouin_zone'),
+ repeats=False,
+ a_legacy=LegacyDefinition(name='brillouin_zone'))
+
+ section_band_gap = SubSection(
+ sub_section=section_band_gap.m_def,
+ repeats=True,
+ description=""",
+ Contains information for band gaps detected in the band structure.
+ Contains a section for each spin channel in the same order as reported
+ for the band energies. For channels without a band gap, a band gap
+ value of zero is reported.
+ """,
+ a_legacy=LegacyDefinition(name='section_band_gap')
+ )
+
+ is_standard_path = Quantity(
+ type=bool,
+ description="""
+ Boolean indicating whether the path follows the standard path for this
+ bravais lattice. The AFLOW standard by Setyawan and Curtarolo is used
+ (https://doi.org/10.1016/j.commatsci.2010.05.010).
+ """,
+ a_legacy=LegacyDefinition(name='is_standard_path')
+ )
+
+ section_k_band_segment = SubSection(
+ sub_section=SectionProxy('section_k_band_segment'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band_segment'))
+
+
+class section_method_atom_kind(MSection):
+ '''
+ Every section_method_atom_kind section contains method-related information about a
+ kind of atom, and is identified by one or more strings stored in
+ method_atom_kind_label.
+
+ This categorization into atom kinds is more flexible than just atomic species, because
+ to different atoms of the same species different atom-centered basis sets or pseudo-
+ potentials may be assigned. For instance, if two different oxygen atoms are assigned
+ to different basis sets or pseudo-potentials, they have to distinguished into two
+ different *kinds* of O atoms, by creating two distinct section_method_atom_kind
+ sections.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method_atom_kind'))
+
+ method_atom_kind_atom_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Atomic number (number of protons) of this atom kind, use 0 if not an atom.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_atom_number'))
+
+ method_atom_kind_explicit_electrons = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Number of explicit electrons (often called valence).
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_explicit_electrons'))
+
+ method_atom_kind_label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String used to identify the atoms of this kind. This should correspond to the
+ atom_labels of the configuration. It is possible for one atom kind to have
+ multiple labels (in order to allow two atoms of the same kind to have two
+ differently defined sets of atom-centered basis functions or two different pseudo-
+ potentials). Atom kind is typically the symbol of the atomic species but it can be
+ also a ghost or pseudo-atom.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_label'))
+
+ method_atom_kind_mass = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='unified_atomic_mass_unit',
+ description='''
+ Mass of the kind of this kind of atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_mass'))
+
+ method_atom_kind_pseudopotential_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name identifying the pseudopotential used.
+ ''',
+ a_legacy=LegacyDefinition(name='method_atom_kind_pseudopotential_name'))
+
+
+class section_method_to_method_refs(MSection):
+ '''
+ Section that describes the relationship between different section_method sections.
+
+ For instance, one calculation is a perturbation performed using a self-consistent
+ field (SCF) calculation as starting point, or a simulated system is partitioned in
+ regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated
+ via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
+
+ The kind of relationship between the method defined in this section and the referenced
+ one is described by method_to_method_kind. The referenced section section_method is
+ identified via method_to_method_ref (typically used for a section_method section in
+ the same section_run) or method_to_method_external_url.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method_to_method_refs'))
+
+ method_to_method_external_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ URL used to reference an externally stored section_method. The kind of
+ relationship between the present and the referenced section_method is specified by
+ method_to_method_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='method_to_method_external_url'))
+
+ method_to_method_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the kind of relationship that the referenced section_method has
+ with the present section_method. Valid values are described in the
+ [method_to_method_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/method-to-method-kind). Often calculations are connected,
+ for instance, one calculation is a perturbation performed using a self-consistent
+ field (SCF) calculation as starting point, or a simulated system is partitioned in
+ regions with different but connected Hamiltonians (e.g., QM/MM, or a region
+ treated via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).
+ Hence, the need of keeping track of these connected calculations. The referenced
+ section_method is identified via method_to_method_ref (typically used for a
+ section_method in the same section_run) or method_to_method_external_url.
+ ''',
+ a_legacy=LegacyDefinition(name='method_to_method_kind'))
+
+ method_to_method_ref = Quantity(
+ type=Reference(SectionProxy('section_method')),
+ shape=[],
+ description='''
+ Reference to a local section_method. If both method_to_method_ref and
+ method_to_method_external_url are given, then method_to_method_ref is a local copy
+ of the value contained in method_to_method_external_url. The kind of relationship
+ between the method defined in the present section_method and the referenced one is
+ described by method_to_method_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='method_to_method_ref'))
+
+
+class section_method(MSection):
+ '''
+ Section containing the various parameters that define the theory and the
+ approximations (convergence, thresholds,...) to perform a *single configuration
+ calculation*, see section_single_configuration_calculation.
+
+ *NOTE*: This section does not contain settings for molecular dynamics, geometry
+ optimization etc. See section frame_sequence for these other settings instead.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_method'))
+
+ basis_set = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Unique string identifying the basis set used for the final wavefunctions
+ calculated with XC_method. It might identify a class of basis sets, often matches
+ one of the strings given in any of basis_set_name.
+ ''',
+ categories=[settings_numerical_parameter, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='basis_set'))
+
+ calculation_method_current = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String that represents the method used to calculate the energy_current. If the
+ method is perturbative, this string does not describe the starting point method,
+ the latter being referenced to by section_method_to_method_refs. For self-
+ consistent field (SCF) ab initio calculations, for example, this is composed by
+ concatenating XC_method_current and basis_set. See [calculation_method_current
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/calculation-method-current) for the details.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_method_current'))
+
+ calculation_method_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Kind of method in calculation_method_current.
+
+ Accepted values are:
+
+ - absolute
+
+ - perturbative.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_method_kind'))
+
+ calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String that uniquely represents the method used to calculate energy_total, If the
+ present calculation_method_current is a perturbative method Y that uses method X
+ as starting point, this string is automatically created as X@Y, where X is taken
+ from calculation_method_current and Y from method_to_method_ref. In order to
+ activate this, method_to_method_kind must have the value starting_point (see the
+ [method_to_method_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/method-to-method-kind)).
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_method'))
+
+ electronic_structure_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Non-unique string identifying the used electronic structure method. It is not
+ unique in the sense that two calculations with the same
+ electronic_structure_method string may have not been performed with exactly the
+ same method. The allowed strings are given in the [electronic structure method
+ wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/electronic-structure-method).
+ ''',
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='electronic_structure_method'))
+
+ k_mesh_points = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_k_mesh_points', 3],
+ description='''
+ List of all the k points in the $k$-point mesh. These are the k point used to
+ evaluate energy_total, and are in fractional coordinates (in the basis of the
+ reciprocal-lattice vectors).
+ ''',
+ categories=[settings_k_points, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='k_mesh_points'))
+
+ k_mesh_weights = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_k_mesh_points'],
+ description='''
+ Weights of all the k points in the $k$-point mesh. These are the weights for
+ k_mesh_points (i.e. the k point used to evaluate energy_total).
+ ''',
+ categories=[settings_k_points, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='k_mesh_weights'))
+
+ number_of_k_mesh_points = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of k points in the mesh (i.e. the k points used to evaluate energy_total).
+ ''',
+ categories=[settings_k_points, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='number_of_k_mesh_points'))
+
+ number_of_spin_channels = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of spin channels, see section_method.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_spin_channels'))
+
+ relativity_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the relativistic treatment used for the calculation of the final energy
+ and related quantities. If skipped or empty, no relativistic treatment is applied.
+ ''',
+ categories=[settings_relativity, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='relativity_method'))
+
+ scf_max_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Specifies the maximum number of allowed self-consistent field (SCF) iterations in
+ a calculation run, see section_run.
+ ''',
+ categories=[settings_scf],
+ a_legacy=LegacyDefinition(name='scf_max_iteration'))
+
+ scf_threshold_energy_change = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Specifies the threshold for the energy_total_scf_iteration change between two
+ subsequent self-consistent field (SCF) iterations. The SCF is considered converged
+ when the total-energy change between two SCF cycles is below the threshold
+ (possibly in combination with other criteria).
+ ''',
+ categories=[settings_scf],
+ a_legacy=LegacyDefinition(name='scf_threshold_energy_change'))
+
+ self_interaction_correction_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Contains the name for the self-interaction correction (SIC) treatment used to
+ calculate the final energy and related quantities. If skipped or empty, no special
+ correction is applied.
+
+ The following SIC methods are available:
+
+ | SIC method | Description |
+
+ | ------------------------- | -------------------------------- |
+
+ | `""` | No correction |
+
+ | `"SIC_AD"` | The average density correction |
+
+ | `"SIC_SOSEX"` | Second order screened exchange |
+
+ | `"SIC_EXPLICIT_ORBITALS"` | (scaled) Perdew-Zunger correction explicitly on a
+ set of orbitals |
+
+ | `"SIC_MAURI_SPZ"` | (scaled) Perdew-Zunger expression on the spin
+ density / doublet unpaired orbital |
+
+ | `"SIC_MAURI_US"` | A (scaled) correction proposed by Mauri and co-
+ workers on the spin density / doublet unpaired orbital |
+ ''',
+ categories=[settings_self_interaction_correction, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='self_interaction_correction_method'))
+
+ smearing_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the kind of smearing on the electron occupation used to calculate the
+ free energy (see energy_free)
+
+ Valid values are:
+
+ | Smearing kind | Description |
+
+ | ------------------------- | --------------------------------- |
+
+ | `"empty"` | No smearing is applied |
+
+ | `"gaussian"` | Gaussian smearing |
+
+ | `"fermi"` | Fermi smearing |
+
+ | `"marzari-vanderbilt"` | Marzari-Vanderbilt smearing |
+
+ | `"methfessel-paxton"` | Methfessel-Paxton smearing |
+
+ | `"tetrahedra"` | Interpolation of state energies and occupations
+ (ignores smearing_width) |
+ ''',
+ categories=[settings_smearing],
+ a_legacy=LegacyDefinition(name='smearing_kind'))
+
+ smearing_width = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Specifies the width of the smearing in energy for the electron occupation used to
+ calculate the free energy (see energy_free).
+
+ *NOTE:* Not all methods specified in smearing_kind uses this value.
+ ''',
+ categories=[settings_smearing],
+ a_legacy=LegacyDefinition(name='smearing_width'))
+
+ spin_target_multiplicity = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Stores the target (user-imposed) value of the spin multiplicity $M=2S+1$, where
+ $S$ is the total spin. It is an integer number. This value is not necessarily the
+ value obtained at the end of the calculation. See spin_S2 for the converged value
+ of the spin moment.
+ ''',
+ a_legacy=LegacyDefinition(name='spin_target_multiplicity'))
+
+ stress_tensor_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the method used to calculate stress_tensor for, e.g., molecular dynamics
+ and geometry optimization.
+
+ The allowed values are:
+
+ * numeric
+
+ * analytic
+ ''',
+ categories=[settings_stress_tensor],
+ a_legacy=LegacyDefinition(name='stress_tensor_method'))
+
+ total_charge = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ unit='coulomb',
+ description='''
+ Provides the total amount of charge of the system in a run.
+ ''',
+ a_legacy=LegacyDefinition(name='total_charge'))
+
+ van_der_Waals_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the Van der Waals method. If skipped or an empty string is used, it
+ means no Van der Waals correction is applied.
+
+ Allowed values are:
+
+ | Van der Waals method | Description |
+
+ | --------------------- | ----------------------------------------- |
+
+ | `""` | No Van der Waals correction |
+
+ | `"TS"` | A. Tkatchenko and M. Scheffler, [Phys. Rev. Lett.
+ **102**, 073005 (2009)](http://dx.doi.org/10.1103/PhysRevLett.102.073005) |
+
+ | `"OBS"` | F. Ortmann, F. Bechstedt, and W. G. Schmidt, [Phys. Rev.
+ B **73**, 205101 (2006)](http://dx.doi.org/10.1103/PhysRevB.73.205101) |
+
+ | `"G06"` | S. Grimme, [J. Comput. Chem. **27**, 1787
+ (2006)](http://dx.doi.org/10.1002/jcc.20495) |
+
+ | `"JCHS"` | P. JureÄka, J. ÄŒerný, P. Hobza, and D. R. Salahub,
+ [Journal of Computational Chemistry **28**, 555
+ (2007)](http://dx.doi.org/10.1002/jcc.20570) |
+
+ | `"MDB"` | Many-body dispersion. A. Tkatchenko, R. A. Di Stasio Jr,
+ R. Car, and M. Scheffler, [Physical Review Letters **108**, 236402
+ (2012)](http://dx.doi.org/10.1103/PhysRevLett.108.236402) and A. Ambrosetti, A. M.
+ Reilly, R. A. Di Stasio Jr, and A. Tkatchenko, [The Journal of Chemical Physics
+ **140**, 18A508 (2014)](http://dx.doi.org/10.1063/1.4865104) |
+
+ | `"XC"` | The method to calculate the Van der Waals energy uses a
+ non-local functional which is described in section_XC_functionals. |
+ ''',
+ categories=[settings_van_der_Waals, settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='van_der_Waals_method'))
+
+ XC_functional = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This value describes a DFT exchange-correlation (XC) functional used for
+ evaluating the energy value stored in energy_XC_functional and related quantities
+ (e.g., forces).
+
+ It is a unique short name obtained by combining the data stored in
+ section_XC_functionals, more specifically by combining different
+ XC_functional_name as described in the [XC_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional).
+ ''',
+ categories=[settings_potential_energy_surface, settings_physical_parameter, settings_XC_functional, settings_XC],
+ a_legacy=LegacyDefinition(name='XC_functional'))
+
+ XC_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the exchange correlation (XC) method used for evaluating the XC energy
+ (energy_XC). Differently from XC_functional, perturbative treatments are also
+ accounted for, where the string contains the reference to both the perturbative
+ (e.g., MP2) and the starting point (e.g, Hartree-Fock) XC method defined in the
+ section section_method.
+
+ The value consists of XC_method_current concatenated with the `@` character and
+ the XC method (XC_method) defined in section_method that is referred to by
+ method_to_method_ref where method_to_method_kind = "starting_point_method".
+ ''',
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='XC_method'))
+
+ XC_method_current = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifies the exchange correlation (XC) method used for energy_XC and related
+ quantities in a standardized short form as a string.
+
+ It is built by joining the values in the following order using the underscore `_`
+ character: electronic_structure_method, XC_functional,
+ self_interaction_correction_method, van_der_Waals_method and relativity_method.
+
+ If any of the methods listed in the string contain non-standard settings, then the
+ first 10 characters of the Base64 URL encoding of SHA 512 checksum of a normalized
+ JSON with all non-redundant non-derived settings_XC are appended to the the string
+ preceded by an underscore.
+
+ With empty strings, the underscore `_` character is skipped.
+
+ If the method defined in the section_method section is perturbative, the
+ XC_method_current contains only the perturbative method, not the starting point
+ (e.g. the DFT XC functional used as a starting point for a RPA perturbative
+ calculation). In this case, the string that contains both the perturbative and
+ starting point method is stored in XC_method.
+ ''',
+ categories=[settings_XC, settings_potential_energy_surface],
+ a_legacy=LegacyDefinition(name='XC_method_current'))
+
+ section_method_atom_kind = SubSection(
+ sub_section=SectionProxy('section_method_atom_kind'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method_atom_kind'))
+
+ section_method_to_method_refs = SubSection(
+ sub_section=SectionProxy('section_method_to_method_refs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method_to_method_refs'))
+
+ section_XC_functionals = SubSection(
+ sub_section=SectionProxy('section_XC_functionals'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_XC_functionals'))
+
+
+class section_original_system(MSection):
+ '''
+ Section containing symmetry information that is specific to the original system.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_original_system'))
+
+ equivalent_atoms_original = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms'],
+ description='''
+ Gives a mapping table of atoms to symmetrically independent atoms in the original
+ cell. This is used to find symmetrically equivalent atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='equivalent_atoms_original'))
+
+ wyckoff_letters_original = Quantity(
+ type=str,
+ shape=['number_of_atoms'],
+ description='''
+ Wyckoff letters for atoms in the original cell.
+ ''',
+ a_legacy=LegacyDefinition(name='wyckoff_letters_original'))
+
+
+class section_primitive_system(MSection):
+ '''
+ Section containing symmetry information that is specific to the primitive system. The
+ primitive system is derived from the standardized system with a transformation that is
+ specific to the centring. The transformation matrices can be found e.g. from here:
+ https://atztogo.github.io/spglib/definition.html#transformation-to-the-primitive-cell
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_primitive_system'))
+
+ atom_positions_primitive = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms_primitive', 3],
+ description='''
+ Atom positions in the primitive cell in reduced units.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_positions_primitive'))
+
+ atomic_numbers_primitive = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_primitive'],
+ description='''
+ Atomic numbers in the primitive cell.
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_numbers_primitive'))
+
+ equivalent_atoms_primitive = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_primitive'],
+ description='''
+ Gives a mapping table of atoms to symmetrically independent atoms in the primitive
+ cell. This is used to find symmetrically equivalent atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='equivalent_atoms_primitive'))
+
+ lattice_vectors_primitive = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ Primitive lattice vectors. The vectors are the rows of this matrix.
+ ''',
+ a_legacy=LegacyDefinition(name='lattice_vectors_primitive'))
+
+ number_of_atoms_primitive = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in primitive system.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_primitive'))
+
+ wyckoff_letters_primitive = Quantity(
+ type=str,
+ shape=['number_of_atoms_primitive'],
+ description='''
+ Wyckoff letters for atoms in the primitive cell.
+ ''',
+ a_legacy=LegacyDefinition(name='wyckoff_letters_primitive'))
+
+
+class section_processor_info(MSection):
+ '''
+ Section with information about a processor that generated or added information to the
+ current calculation.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_processor_info'))
+
+ processor_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Id (name+version) of the processor that generated or added information to the
+ current calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='processor_id'))
+
+ processor_number_of_evaluated_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts evaluated with this processor in the current current
+ calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='processor_number_of_evaluated_contexts'))
+
+ processor_number_of_failed_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts in the current current calculation that had failure for this
+ processor.
+ ''',
+ a_legacy=LegacyDefinition(name='processor_number_of_failed_contexts'))
+
+ processor_number_of_skipped_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts skipped by this processor in the current current calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='processor_number_of_skipped_contexts'))
+
+ processor_number_of_successful_contexts = Quantity(
+ type=np.dtype(np.int64),
+ shape=[],
+ description='''
+ number of contexts in the current calculation that where successfully handled by
+ this processor.
+ ''',
+ a_legacy=LegacyDefinition(name='processor_number_of_successful_contexts'))
+
+ processor_version_details = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ detailed version information on the processor that generated or added information
+ to the current calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='processor_version_details'))
+
+
+class section_processor_log_event(MSection):
+ '''
+ A log event
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_processor_log_event'))
+
+ processor_log_event_level = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Level of the logging, a lower number has more priority. The levels are the same as
+ log4j: FATAL -> 100, ERROR -> 200, WARN -> 300, INFO -> 400, DEBUG -> 500, TRACE
+ -> 600
+ ''',
+ a_legacy=LegacyDefinition(name='processor_log_event_level'))
+
+ processor_log_event_message = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The log message
+ ''',
+ a_legacy=LegacyDefinition(name='processor_log_event_message'))
+
+
+class section_processor_log(MSection):
+ '''
+ log of a processor
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_processor_log'))
+
+ processor_log_processor_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The processor id of the processor creating this log
+ ''',
+ a_legacy=LegacyDefinition(name='processor_log_processor_id'))
+
+ processor_log_start = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Start of the log (in ansi notation YYYY-MM-TT...)
+ ''',
+ a_legacy=LegacyDefinition(name='processor_log_start'))
+
+ section_processor_log_event = SubSection(
+ sub_section=SectionProxy('section_processor_log_event'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_processor_log_event'))
+
+
+class section_prototype(MSection):
+ '''
+ Information on the prototype corresponding to the current section.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_prototype'))
+
+ prototype_aflow_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ AFLOW id of the prototype (see
+ http://aflowlib.org/CrystalDatabase/prototype_index.html) identified on the basis
+ of the space_group and normalized_wyckoff.
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_aflow_id'))
+
+ prototype_aflow_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Url to the AFLOW definition of the prototype (see
+ http://aflowlib.org/CrystalDatabase/prototype_index.html) identified on the basis
+ of the space_group and normalized_wyckoff.
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_aflow_url'))
+
+ prototype_assignment_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to identify the prototype.
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_assignment_method'))
+
+ prototype_label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Label of the prototype identified on the basis of the space_group and
+ normalized_wyckoff. The label is in the same format as in the read_prototypes
+ function: <space_group_number>-<prototype_name>-<Pearson's symbol>).
+ ''',
+ a_legacy=LegacyDefinition(name='prototype_label'))
+
+
+class section_run(MSection):
+ '''
+ Every section_run represents a single call of a program. What exactly is contained in
+ a run depends on the run type (see for example section_method and
+ section_single_configuration_calculation) and the program (see [program_info
+ ](program_info)).
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_run'))
+
+ calculation_file_uri = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Contains the nomad uri of a raw the data file connected to the current run. There
+ should be an value for the main_file_uri and all ancillary files.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_file_uri'))
+
+ message_debug_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A debugging message of the computational program, associated with a run.
+ ''',
+ categories=[message_debug],
+ a_legacy=LegacyDefinition(name='message_debug_run'))
+
+ message_error_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An error message of the computational program, associated with a run.
+ ''',
+ categories=[message_info, message_debug, message_error, message_warning],
+ a_legacy=LegacyDefinition(name='message_error_run'))
+
+ message_info_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An information message of the computational program, associated with a run.
+ ''',
+ categories=[message_info, message_debug],
+ a_legacy=LegacyDefinition(name='message_info_run'))
+
+ message_warning_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A warning message of the computational program, associated with a run.
+ ''',
+ categories=[message_info, message_debug, message_warning],
+ a_legacy=LegacyDefinition(name='message_warning_run'))
+
+ parsing_message_debug_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for debugging messages of the parsing program associated with a
+ single configuration calculation, see section_single_configuration_calculation.
+ ''',
+ categories=[parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_debug_run'))
+
+ parsing_message_error_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for error messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[parsing_message_info, parsing_message_error, parsing_message_warning, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_error_run'))
+
+ parsing_message_info_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for info messages of the parsing program associated with a run,
+ see section_run.
+ ''',
+ categories=[parsing_message_info, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_info_run'))
+
+ parsing_message_warning_run = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for warning messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_warning_run'))
+
+ program_basis_set_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of basis set used by the program to represent wave functions. Valid values
+ are: [`Numeric AOs`, `Gaussians`, `(L)APW+lo`, `plane waves`, `psinc functions`,
+ `real-space grid`].
+ ''',
+ a_legacy=LegacyDefinition(name='program_basis_set_type'))
+
+ program_compilation_datetime = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Contains the program compilation date and time from *Unix epoch* (00:00:00 UTC on
+ 1 January 1970) in seconds. For date and times without a timezone, the default
+ timezone GMT is used.
+ ''',
+ categories=[accessory_info, program_info],
+ a_legacy=LegacyDefinition(name='program_compilation_datetime'))
+
+ program_compilation_host = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the host on which the program was compiled.
+ ''',
+ categories=[accessory_info, program_info],
+ a_legacy=LegacyDefinition(name='program_compilation_host'))
+
+ program_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the name of the program that generated the data.
+ ''',
+ categories=[accessory_info, program_info],
+ a_legacy=LegacyDefinition(name='program_name'))
+
+ program_version = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the version of the program that was used. This should be the version
+ number of an official release, the version tag or a commit id as well as the
+ location of the repository.
+ ''',
+ categories=[accessory_info, program_info],
+ a_legacy=LegacyDefinition(name='program_version'))
+
+ run_clean_end = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates whether this run terminated properly (true), or if it was killed or
+ exited with an error code unequal to zero (false).
+ ''',
+ a_legacy=LegacyDefinition(name='run_clean_end'))
+
+ run_hosts = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ An associative list of host(s) that performed this simulation. This is an
+ associative list that contains program-dependent information (*key*) on how the
+ host was used (*value*). Useful for debugging purposes.
+ ''',
+ categories=[parallelization_info, accessory_info],
+ a_legacy=LegacyDefinition(name='run_hosts'))
+
+ raw_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An optional calculation id, if one is found in the code input/output files.
+ ''',
+ a_legacy=LegacyDefinition(name='raw_id'))
+
+ time_run_cpu1_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end time of the run on CPU 1.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_run_cpu1_end'))
+
+ time_run_cpu1_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start time of the run on CPU 1.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_run_cpu1_start'))
+
+ time_run_date_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end date of the run as time since the *Unix epoch* (00:00:00 UTC on 1
+ January 1970) in seconds. For date and times without a timezone, the default
+ timezone GMT is used.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_run_date_end'))
+
+ time_run_date_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start date of the run as time since the *Unix epoch* (00:00:00 UTC on 1
+ January 1970) in seconds. For date and times without a timezone, the default
+ timezone GMT is used.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_run_date_start'))
+
+ time_run_wall_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time at the end of the run.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_run_wall_end'))
+
+ time_run_wall_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time from the start of the run.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_run_wall_start'))
+
+ section_basis_set_atom_centered = SubSection(
+ sub_section=SectionProxy('section_basis_set_atom_centered'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
+
+ section_basis_set_cell_dependent = SubSection(
+ sub_section=SectionProxy('section_basis_set_cell_dependent'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))
+
+ section_frame_sequence = SubSection(
+ sub_section=SectionProxy('section_frame_sequence'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_frame_sequence'))
+
+ section_method = SubSection(
+ sub_section=SectionProxy('section_method'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_method'))
+
+ section_sampling_method = SubSection(
+ sub_section=SectionProxy('section_sampling_method'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_sampling_method'))
+
+ section_single_configuration_calculation = SubSection(
+ sub_section=SectionProxy('section_single_configuration_calculation'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ section_system = SubSection(
+ sub_section=SectionProxy('section_system'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_system'))
+
+
+class section_sampling_method(MSection):
+ '''
+ Section containing the settings describing a (potential-energy surface) sampling
+ method.
+
+ Results and monitored quantities of such sampling are collected in a sequence of
+ frames, section_frame_sequence.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_sampling_method'))
+
+ ensemble_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Kind of sampled ensemble stored in section_frame_sequence; valid values are
+ defined in [ensemble_type wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-
+ meta-info/wikis/metainfo/ensemble-type).
+ ''',
+ a_legacy=LegacyDefinition(name='ensemble_type'))
+
+ geometry_optimization_energy_change = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of threshold for the energy_total change between two geometry optimization
+ steps, as convergence criterion of the geometry_optimization_method. A geometry
+ optimization is considered converged when the energy_total change between two
+ geometry optimization steps is below the threshold (possibly in combination with
+ other criteria)
+ ''',
+ categories=[settings_geometry_optimization, settings_sampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_energy_change'))
+
+ geometry_optimization_geometry_change = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='meter',
+ description='''
+ Value of threshold for the displacement of the nuclei between two geometry
+ optimization steps as convergence criterion of the geometry_optimization_method. A
+ geometry optimization is considered converged when the maximum among the
+ displacements of the nuclei between two geometry optimization steps is below the
+ threshold (possibly in combination with other criteria)
+ ''',
+ categories=[settings_geometry_optimization, settings_sampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_geometry_change'))
+
+ geometry_optimization_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Algorithm for the geometry optimization. Allowed values are listed in the
+ [geometry_optimization_method wiki page](https://gitlab.mpcdf.mpg.de/nomad-
+ lab/nomad-meta-info/wikis/metainfo/geometry-optimization-method).
+ ''',
+ categories=[settings_geometry_optimization, settings_sampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_method'))
+
+ geometry_optimization_threshold_force = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ Value of threshold for the force modulus as convergence criterion of the
+ geometry_optimization_method. A geometry optimization is considered converged when
+ the maximum of the moduli of the force on each of the atoms is below this
+ threshold (possibly in combination with other criteria)
+ ''',
+ categories=[settings_geometry_optimization, settings_sampling],
+ a_legacy=LegacyDefinition(name='geometry_optimization_threshold_force'))
+
+ sampling_method_expansion_order = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Order up to which the potential energy surface was expanded in a Taylor series
+ (see sampling_method).
+ ''',
+ a_legacy=LegacyDefinition(name='sampling_method_expansion_order'))
+
+ sampling_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of method used to do the sampling.
+
+ Allowed values are:
+
+ | Sampling method | Description |
+
+ | ------------------------------ | -------------------------------- |
+
+ | `"geometry_optimization"` | Geometry optimization |
+
+ | `"molecular_dynamics"` | Molecular dynamics |
+
+ | `"montecarlo"` | (Metropolis) Monte Carlo |
+
+ | `"steered_molecular_dynamics"` | Steered molecular dynamics (with time dependent
+ external forces) |
+
+ | `"meta_dynamics"` | Biased molecular dynamics with history-
+ dependent Hamiltonian |
+
+ | `"wang_landau_montecarlo"` | Monte Carlo according to the Wang-Landau
+ formulation. |
+
+ | `"blue_moon"` | Blue Moon sampling |
+
+ | `"langevin_dynamics"` | Langevin dynamics |
+
+ | `"taylor_expansion"` | Taylor expansion of the potential energy
+ surface |
+ ''',
+ a_legacy=LegacyDefinition(name='sampling_method'))
+
+
+class section_scf_iteration(MSection):
+ '''
+ Every section_scf_iteration represents a self-consistent field (SCF) iteration, see
+ scf_info, and gives detailed information on the SCF procedure of the specified
+ quantities.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+ electronic_kinetic_energy_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Electronic kinetic energy as defined in XC_method during the self-consistent field
+ (SCF) iterations.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='electronic_kinetic_energy_scf_iteration'))
+
+ energy_change_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Stores the change of total energy with respect to the previous self-consistent
+ field (SCF) iteration.
+ ''',
+ categories=[error_estimate_contribution, energy_value],
+ a_legacy=LegacyDefinition(name='energy_change_scf_iteration'))
+
+ energy_correction_entropy_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Entropy correction to the potential energy to compensate for the change in
+ occupation so that forces at finite T do not need to keep the change of occupation
+ in account. The array lists the values of the entropy correction for each self-
+ consistent field (SCF) iteration. Defined consistently with XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_correction_entropy_scf_iteration'))
+
+ energy_correction_hartree_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Correction to the density-density electrostatic energy in the sum of eigenvalues
+ (that uses the mixed density on one side), and the fully consistent density-
+ density electrostatic energy during the self-consistent field (SCF) iterations.
+ Defined consistently with XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_correction_hartree_scf_iteration'))
+
+ energy_electrostatic_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total electrostatic energy (nuclei + electrons) during each self-consistent field
+ (SCF) iteration.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_electrostatic_scf_iteration'))
+
+ energy_free_per_atom_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy per atom (whose minimum gives the smeared occupation density
+ calculated with smearing_kind) calculated with XC_method during the self-
+ consistent field (SCF) iterations.
+ ''',
+ categories=[energy_component_per_atom, energy_value],
+ a_legacy=LegacyDefinition(name='energy_free_per_atom_scf_iteration'))
+
+ energy_free_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy (whose minimum gives the smeared occupation density calculated with
+ smearing_kind) calculated with the method described in XC_method during the self-
+ consistent field (SCF) iterations.
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_free_scf_iteration'))
+
+ energy_hartree_error_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Error in the Hartree (electrostatic) potential energy during each self-consistent
+ field (SCF) iteration. Defined consistently with XC_method.
+ ''',
+ categories=[error_estimate_contribution, energy_value],
+ a_legacy=LegacyDefinition(name='energy_hartree_error_scf_iteration'))
+
+ energy_sum_eigenvalues_per_atom_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy per atom, where the energy is defined as the sum of the
+ eigenvalues of the Hamiltonian matrix given by XC_method, during each self-
+ consistent field (SCF) iteration.
+ ''',
+ categories=[energy_component_per_atom, energy_value],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_per_atom_scf_iteration'))
+
+ energy_sum_eigenvalues_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Sum of the eigenvalues of the Hamiltonian matrix defined by XC_method, during each
+ self-consistent field (SCF) iteration.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_scf_iteration'))
+
+ energy_total_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total electronic energy calculated with the method described in
+ XC_method during each self-consistent field (SCF) iteration.
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_total_scf_iteration'))
+
+ energy_total_T0_per_atom_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy, calculated with the method described in XC_method per
+ atom extrapolated to $T=0$, based on a free-electron gas argument, during each
+ self-consistent field (SCF) iteration.
+ ''',
+ categories=[energy_total_potential_per_atom, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_total_T0_per_atom_scf_iteration'))
+
+ energy_total_T0_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy (or equivalently free energy), calculated with the
+ method described in XC_method and extrapolated to $T=0$, based on a free-electron
+ gas argument, during each self-consistent field (SCF) iteration.
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_total_T0_scf_iteration'))
+
+ energy_XC_potential_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value for exchange-correlation (XC) potential energy: the integral of the first
+ order derivative of the functional stored in XC_functional (integral of
+ v_xc*electron_density), i.e., the component of XC that is in the sum of the
+ eigenvalues. Values are given for each self-consistent field (SCF) iteration
+ (i.e., not the converged value, the latter being stored in energy_XC_potential).
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_XC_potential_scf_iteration'))
+
+ energy_XC_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value for exchange-correlation (XC) energy obtained during each self-consistent
+ field (SCF) iteration, using the method described in XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_XC_scf_iteration'))
+
+ spin_S2_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Stores the value of the total spin moment operator $S^2$ during the self-
+ consistent field (SCF) iterations of the XC_method. It can be used to calculate
+ the spin contamination in spin-unrestricted calculations.
+ ''',
+ a_legacy=LegacyDefinition(name='spin_S2_scf_iteration'))
+
+ time_scf_iteration_cpu1_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end time of a self-consistent field (SCF) iteration on CPU 1.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_cpu1_end'))
+
+ time_scf_iteration_cpu1_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start time of a self-consistent field (SCF) iteration on CPU 1.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_cpu1_start'))
+
+ time_scf_iteration_date_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end date of a self-consistent field (SCF) iteration as time since the
+ *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds. For date and times
+ without a timezone, the default timezone GMT is used.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_date_end'))
+
+ time_scf_iteration_date_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start date of a self-consistent field (SCF) iteration as time since the
+ *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds. For date and times
+ without a timezone, the default timezone GMT is used.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_date_start'))
+
+ time_scf_iteration_wall_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time at the end of a self-consistent field (SCF)
+ iteration.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_wall_end'))
+
+ time_scf_iteration_wall_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time from the start of a self-consistent field
+ (SCF) iteration.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_scf_iteration_wall_start'))
+
+
+class section_single_configuration_calculation(MSection):
+ '''
+ Every section_single_configuration_calculation section contains the values computed
+ during a *single configuration calculation*, i.e. a calculation performed on a given
+ configuration of the system (as defined in section_system) and a given computational
+ method (e.g., exchange-correlation method, basis sets, as defined in section_method).
+
+ The link between the current section_single_configuration_calculation and the related
+ section_system and section_method sections is established by the values stored in
+ single_configuration_calculation_to_system_ref and
+ single_configuration_to_calculation_method_ref, respectively.
+
+ The reason why information on the system configuration and computational method is
+ stored separately is that several *single configuration calculations* can be performed
+ on the same system configuration, viz. several system configurations can be evaluated
+ with the same computational method. This storage strategy avoids redundancies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ atom_forces_free_raw = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_free,
+ **without** constraints. The derivatives with respect to displacements of nuclei
+ are evaluated in Cartesian coordinates. The (electronic) energy_free contains the
+ change in (fractional) occupation of the electronic eigenstates, which are
+ accounted for in the derivatives, yielding a truly energy-conserved quantity.
+ These forces may contain unitary transformations (center-of-mass translations and
+ rigid rotations for non-periodic systems) that are normally filtered separately
+ (see atom_forces_free for the filtered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are also considered
+ separately (see atom_forces_free for the filtered counterpart).
+ ''',
+ categories=[atom_forces_type],
+ a_legacy=LegacyDefinition(name='atom_forces_free_raw'))
+
+ atom_forces_free = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_free,
+ **including** constraints, if present. The derivatives with respect to
+ displacements of the nuclei are evaluated in Cartesian coordinates. The
+ (electronic) energy_free contains the information on the change in (fractional)
+ occupation of the electronic eigenstates, which are accounted for in the
+ derivatives, yielding a truly energy-conserved quantity. In addition, these forces
+ are obtained by filtering out the unitary transformations (center-of-mass
+ translations and rigid rotations for non-periodic systems, see
+ atom_forces_free_raw for the unfiltered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are included (see
+ atom_forces_free_raw for the unfiltered counterpart).
+ ''',
+ categories=[atom_forces_type],
+ a_legacy=LegacyDefinition(name='atom_forces_free'))
+
+ atom_forces_raw = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total,
+ **without** constraints. The derivatives with respect to displacements of the
+ nuclei are evaluated in Cartesian coordinates. These forces may contain unitary
+ transformations (center-of-mass translations and rigid rotations for non-periodic
+ systems) that are normally filtered separately (see atom_forces for the filtered
+ counterpart). Forces due to constraints such as fixed atoms, distances, angles,
+ dihedrals, etc. are also considered separately (see atom_forces for the filtered
+ counterpart).
+ ''',
+ categories=[atom_forces_type],
+ a_legacy=LegacyDefinition(name='atom_forces_raw'))
+
+ atom_forces_T0_raw = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total_T0,
+ **without** constraints. The derivatives with respect to displacements of the
+ nuclei are evaluated in Cartesian coordinates. These forces may contain unitary
+ transformations (center-of-mass translations and rigid rotations for non-periodic
+ systems) that are normally filtered separately (see atom_forces_T0 for the
+ filtered counterpart). Forces due to constraints such as fixed atoms, distances,
+ angles, dihedrals, etc. are also considered separately (see atom_forces_T0 for the
+ filtered counterpart).
+ ''',
+ categories=[atom_forces_type],
+ a_legacy=LegacyDefinition(name='atom_forces_T0_raw'))
+
+ atom_forces_T0 = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total_T0,
+ **including** constraints, if present. The derivatives with respect to
+ displacements of the nuclei are evaluated in Cartesian coordinates. In addition,
+ these forces are obtained by filtering out the unitary transformations (center-of-
+ mass translations and rigid rotations for non-periodic systems, see
+ atom_forces_free_T0_raw for the unfiltered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are also included (see
+ atom_forces_free_T0_raw for the unfiltered counterpart).
+ ''',
+ categories=[atom_forces_type],
+ a_legacy=LegacyDefinition(name='atom_forces_T0'))
+
+ atom_forces = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total,
+ **including** constraints, if present. The derivatives with respect to
+ displacements of nuclei are evaluated in Cartesian coordinates. In addition, these
+ forces are obtained by filtering out the unitary transformations (center-of-mass
+ translations and rigid rotations for non-periodic systems, see
+ atom_forces_free_raw for the unfiltered counterpart). Forces due to constraints
+ such as fixed atoms, distances, angles, dihedrals, etc. are included (see
+ atom_forces_raw for the unfiltered counterpart).
+ ''',
+ categories=[atom_forces_type],
+ a_legacy=LegacyDefinition(name='atom_forces'))
+
+ electronic_kinetic_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Self-consistent electronic kinetic energy as defined in XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='electronic_kinetic_energy'))
+
+ energy_C = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Correlation (C) energy calculated with the method described in XC_functional.
+ ''',
+ categories=[energy_component, energy_value, energy_type_C],
+ a_legacy=LegacyDefinition(name='energy_C'))
+
+ energy_correction_entropy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Entropy correction to the potential energy to compensate for the change in
+ occupation so that forces at finite T do not need to keep the change of occupation
+ in account. Defined consistently with XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_correction_entropy'))
+
+ energy_correction_hartree = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Correction to the density-density electrostatic energy in the sum of eigenvalues
+ (that uses the mixed density on one side), and the fully consistent density-
+ density electrostatic energy. Defined consistently with XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_correction_hartree'))
+
+ energy_current = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy calculated with calculation_method_current. energy_current is
+ equal to energy_total for non-perturbative methods. For perturbative methods,
+ energy_current is equal to the correction: energy_total minus energy_total of the
+ calculation_to_calculation_ref with calculation_to_calculation_kind =
+ starting_point (see the [method_to_method_kind wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/method-
+ to-method-kind)). See also [energy_current wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/energy-
+ current).
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_current'))
+
+ energy_electrostatic = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total electrostatic energy (nuclei + electrons), defined consistently with
+ calculation_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_electrostatic'))
+
+ energy_free_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy per atom (whose minimum gives the smeared occupation density
+ calculated with smearing_kind) calculated with XC_method.
+ ''',
+ categories=[energy_component_per_atom, energy_value],
+ a_legacy=LegacyDefinition(name='energy_free_per_atom'))
+
+ energy_free = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Free energy (nuclei + electrons) (whose minimum gives the smeared occupation
+ density calculated with smearing_kind) calculated with the method described in
+ XC_method.
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_free'))
+
+ energy_hartree_error = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Error in the Hartree (electrostatic) potential energy. Defined consistently with
+ XC_method.
+ ''',
+ categories=[error_estimate_contribution, energy_value],
+ a_legacy=LegacyDefinition(name='energy_hartree_error'))
+
+ energy_hartree_fock_X_scaled = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Scaled exact-exchange energy that depends on the mixing parameter of the
+ functional. For example in hybrid functionals, the exchange energy is given as a
+ linear combination of exact-energy and exchange energy of an approximate DFT
+ functional; the exact exchange energy multiplied by the mixing coefficient of the
+ hybrid functional would be stored in this metadata. Defined consistently with
+ XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_hartree_fock_X_scaled'))
+
+ energy_hartree_fock_X = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Converged exact-exchange (Hartree-Fock) energy. Defined consistently with
+ XC_method.
+ ''',
+ categories=[energy_type_X, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_hartree_fock_X'))
+
+ energy_method_current = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy calculated with the method calculation_method_current.
+ Depending on calculation_method_kind it might be a total energy or only a
+ correction.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_method_current'))
+
+ energy_sum_eigenvalues_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the energy per atom, where the energy is defined as the sum of the
+ eigenvalues of the Hamiltonian matrix given by XC_method.
+ ''',
+ categories=[energy_component_per_atom, energy_value],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues_per_atom'))
+
+ energy_sum_eigenvalues = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Sum of the eigenvalues of the Hamiltonian matrix defined by XC_method.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_sum_eigenvalues'))
+
+ energy_T0_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy per atom, calculated with the method described in
+ XC_method and extrapolated to $T=0$, based on a free-electron gas argument.
+ ''',
+ categories=[energy_total_potential_per_atom, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_T0_per_atom'))
+
+ energy_total_T0_per_atom = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy, calculated with the method described in XC_method per
+ atom extrapolated to $T=0$, based on a free-electron gas argument.
+ ''',
+ categories=[energy_total_potential_per_atom, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_total_T0_per_atom'))
+
+ energy_total_T0 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy (or equivalently free energy), calculated with the
+ method described in XC_method and extrapolated to $T=0$, based on a free-electron
+ gas argument.
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_total_T0'))
+
+ energy_total = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the total energy, calculated with the method described in XC_method and
+ extrapolated to $T=0$, based on a free-electron gas argument.
+ ''',
+ categories=[energy_component, energy_value, energy_total_potential],
+ a_legacy=LegacyDefinition(name='energy_total'))
+
+ energy_XC_functional = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the exchange-correlation (XC) energy calculated with the functional
+ stored in XC_functional.
+ ''',
+ categories=[energy_type_XC, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_XC_functional'))
+
+ energy_XC_potential = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the exchange-correlation (XC) potential energy: the integral of the first
+ order derivative of the functional stored in XC_functional (integral of
+ v_xc*electron_density), i.e., the component of XC that is in the sum of the
+ eigenvalues. Value associated with the configuration, should be the most converged
+ value.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_XC_potential'))
+
+ energy_XC = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the exchange-correlation (XC) energy calculated with the method described
+ in XC_method.
+ ''',
+ categories=[energy_type_XC, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_XC'))
+
+ energy_X = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value fo the exchange (X) energy calculated with the method described in
+ XC_method.
+ ''',
+ categories=[energy_type_X, energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_X'))
+
+ energy_zero_point = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value for the converged zero-point vibrations energy calculated using the method
+ described in zero_point_method , and used in energy_current .
+ ''',
+ a_legacy=LegacyDefinition(name='energy_zero_point'))
+
+ hessian_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 'number_of_atoms', 3, 3],
+ description='''
+ The matrix with the second derivative with respect to atom displacements.
+ ''',
+ a_legacy=LegacyDefinition(name='hessian_matrix'))
+
+ message_debug_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A debugging message of the computational program, associated with a *single
+ configuration calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[message_debug],
+ a_legacy=LegacyDefinition(name='message_debug_evaluation'))
+
+ message_error_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An error message of the computational program, associated with a *single
+ configuration calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[message_info, message_debug, message_error, message_warning],
+ a_legacy=LegacyDefinition(name='message_error_evaluation'))
+
+ message_info_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ An information message of the computational program, associated with a *single
+ configuration calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[message_info, message_debug],
+ a_legacy=LegacyDefinition(name='message_info_evaluation'))
+
+ message_warning_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ A warning message of the computational program.
+ ''',
+ categories=[message_info, message_debug, message_warning],
+ a_legacy=LegacyDefinition(name='message_warning_evaluation'))
+
+ number_of_scf_iterations = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of performed self-consistent field (SCF) iterations at a specfied
+ level of theory.
+ ''',
+ categories=[scf_info],
+ a_legacy=LegacyDefinition(name='number_of_scf_iterations'))
+
+ parsing_message_debug_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for debugging messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_debug_evaluation'))
+
+ parsing_message_error_single_configuration = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for error messages of the parsing program associated with a
+ single configuration calculation, see section_single_configuration_calculation.
+ ''',
+ categories=[parsing_message_info, parsing_message_error, parsing_message_warning, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_error_single_configuration'))
+
+ parsing_message_info_single_configuration = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for info messages of the parsing program associated with a
+ single configuration calculation, see section_single_configuration_calculation.
+ ''',
+ categories=[parsing_message_info, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_info_single_configuration'))
+
+ parsing_message_warning_evaluation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ This field is used for warning messages of the parsing program associated with a
+ run, see section_run.
+ ''',
+ categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
+ a_legacy=LegacyDefinition(name='parsing_message_warning_evaluation'))
+
+ single_configuration_calculation_converged = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Determines whether a *single configuration calculation* in
+ section_single_configuration_calculation is converged.
+ ''',
+ a_legacy=LegacyDefinition(name='single_configuration_calculation_converged'))
+
+ single_configuration_calculation_to_system_ref = Quantity(
+ type=Reference(SectionProxy('section_system')),
+ shape=[],
+ description='''
+ Reference to the system (atomic configuration, cell, ...) that is calculated in
+ section_single_configuration_calculation.
+ ''',
+ categories=[fast_access],
+ a_legacy=LegacyDefinition(name='single_configuration_calculation_to_system_ref'))
+
+ single_configuration_to_calculation_method_ref = Quantity(
+ type=Reference(SectionProxy('section_method')),
+ shape=[],
+ categories=[fast_access],
+ description='''
+ Reference to the method used for the calculation in
+ section_single_configuration_calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='single_configuration_to_calculation_method_ref'))
+
+ spin_S2 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Stores the value of the total spin moment operator $S^2$ for the converged
+ wavefunctions calculated with the XC_method. It can be used to calculate the spin
+ contamination in spin-unrestricted calculations.
+ ''',
+ a_legacy=LegacyDefinition(name='spin_S2'))
+
+ stress_tensor = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='pascal',
+ description='''
+ Stores the final value of the default stress tensor consistent with energy_total
+ and calculated with the method specified in stress_tensor_method.
+
+ This value is used (if needed) for, e.g., molecular dynamics and geometry
+ optimization. Alternative definitions of the stress tensor can be assigned with
+ stress_tensor_kind
+ ''',
+ categories=[stress_tensor_type],
+ a_legacy=LegacyDefinition(name='stress_tensor'))
+
+ time_calculation = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the wall-clock time needed for a calculation using
+ calculation_method_current. Basically, it tracks the real time that has been
+ elapsed from start to end.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_calculation'))
+
+ time_single_configuration_calculation_cpu1_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end time of the *single configuration calculation* (see
+ section_single_configuration_calculation) on CPU 1.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_cpu1_end'))
+
+ time_single_configuration_calculation_cpu1_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start time of the *single configuration calculation* (see
+ section_single_configuration_calculation) on CPU 1.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_cpu1_start'))
+
+ time_single_configuration_calculation_date_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the end date of the *single configuration calculation* (see
+ section_single_configuration_calculation) as time since the *Unix epoch* (00:00:00
+ UTC on 1 January 1970) in seconds. For date and times without a timezone, the
+ default timezone GMT is used.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_date_end'))
+
+ time_single_configuration_calculation_date_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the start date of the *single configuration calculation* (see
+ section_single_configuration_calculation) as time since the *Unix epoch* (00:00:00
+ UTC on 1 January 1970) in seconds. For date and times without a timezone, the
+ default timezone GMT is used.
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_date_start'))
+
+ time_single_configuration_calculation_wall_end = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time at the end of the *single configuration
+ calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_wall_end'))
+
+ time_single_configuration_calculation_wall_start = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='second',
+ description='''
+ Stores the internal wall-clock time from the start of the *single configuration
+ calculation* (see section_single_configuration_calculation).
+ ''',
+ categories=[time_info, accessory_info],
+ a_legacy=LegacyDefinition(name='time_single_configuration_calculation_wall_start'))
+
+ zero_point_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the zero-point vibrations method. If skipped or an empty string is used,
+ it means no zero-point vibrations correction is applied.
+ ''',
+ a_legacy=LegacyDefinition(name='zero_point_method'))
+
+ enthalpy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the calculated enthalpy i.e. energy_total + pressure * volume.
+ ''',
+ categories=[energy_component, energy_value],
+ a_legacy=LegacyDefinition(name='energy_enthalpy'))
+
+ pressure = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Value of the pressure of the system.
+ ''',
+ a_legacy=LegacyDefinition(name='pressure'))
+
+ temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='kelvin',
+ description='''
+ Value of the temperature of the system.
+ ''',
+ a_legacy=LegacyDefinition(name='temperature'))
+
+ time_step = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ The number of time steps with respect to the start of the calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='time_step'))
+
+ section_atom_projected_dos = SubSection(
+ sub_section=SectionProxy('section_atom_projected_dos'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_atom_projected_dos'))
+
+ section_atomic_multipoles = SubSection(
+ sub_section=SectionProxy('section_atomic_multipoles'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_atomic_multipoles'))
+
+ section_basis_set = SubSection(
+ sub_section=SectionProxy('section_basis_set'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_basis_set'))
+
+ section_calculation_to_calculation_refs = SubSection(
+ sub_section=SectionProxy('section_calculation_to_calculation_refs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))
+
+ section_calculation_to_folder_refs = SubSection(
+ sub_section=SectionProxy('section_calculation_to_folder_refs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))
+
+ section_dos = SubSection(
+ sub_section=SectionProxy('section_dos'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_dos'))
+
+ section_eigenvalues = SubSection(
+ sub_section=SectionProxy('section_eigenvalues'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_eigenvalues'))
+
+ section_energy_code_independent = SubSection(
+ sub_section=SectionProxy('section_energy_code_independent'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_energy_code_independent'))
+
+ section_energy_van_der_Waals = SubSection(
+ sub_section=SectionProxy('section_energy_van_der_Waals'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
+
+ section_energy_contribution = SubSection(
+ sub_section=SectionProxy('section_energy_contribution'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_energy_contribution'))
+
+ section_k_band_normalized = SubSection(
+ sub_section=SectionProxy('section_k_band_normalized'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band_normalized'))
+
+ section_k_band = SubSection(
+ sub_section=SectionProxy('section_k_band'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_k_band'))
+
+ section_scf_iteration = SubSection(
+ sub_section=SectionProxy('section_scf_iteration'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+ section_species_projected_dos = SubSection(
+ sub_section=SectionProxy('section_species_projected_dos'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_species_projected_dos'))
+
+ section_stress_tensor = SubSection(
+ sub_section=SectionProxy('section_stress_tensor'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_stress_tensor'))
+
+ section_volumetric_data = SubSection(
+ sub_section=SectionProxy('section_volumetric_data'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_volumetric_data'))
+
+
+class section_species_projected_dos(MSection):
+ '''
+ Section collecting the information on a species-projected density of states (DOS)
+ evaluation.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_species_projected_dos'))
+
+ number_of_lm_species_projected_dos = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of $l$, $m$ combinations for the species-projected density of
+ states (DOS) defined in section_species_projected_dos.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_lm_species_projected_dos'))
+
+ number_of_species_projected_dos_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of energy values for the species-projected density of states
+ (DOS) defined in section_species_projected_dos.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_species_projected_dos_values'))
+
+ number_of_species = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of species for the species-projected density of states (DOS)
+ defined in section_species_projected_dos.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_species'))
+
+ species_projected_dos_energies_normalized = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_species_projected_dos_values'],
+ unit='joule',
+ description='''
+ Contains the set of discrete energy values with respect to the top of the valence
+ band for the species-projected density of states (DOS). It is derived from the
+ species_projected_dos_energies species field.
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_energies_normalized'))
+
+ species_projected_dos_energies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_species_projected_dos_values'],
+ unit='joule',
+ description='''
+ Contains the set of discrete energy values for the species-projected density of
+ states (DOS).
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_energies'))
+
+ species_projected_dos_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_lm_species_projected_dos', 2],
+ description='''
+ Consists of tuples of $l$ and $m$ values for all given values in the
+ species_projected_dos_values_lm species field.
+
+ The quantum number $l$ represents the azimuthal quantum number, whereas for the
+ quantum number $m$, besides the conventional use as magnetic quantum number ($l+1$
+ integer values from $-l$ to $l$), a set of different conventions is accepted. The
+ adopted convention is specified by atom_projected_dos_m_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_lm'))
+
+ species_projected_dos_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the kind of the integer numbers $m$ used in species_projected_dos_lm.
+
+ Allowed values are listed in the [m_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind)
+ and can be (quantum) numbers of
+
+ * spherical
+
+ * polynomial
+
+ * real_orbital
+
+ * integrated
+
+ functions or values.
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_m_kind'))
+
+ species_projected_dos_species_label = Quantity(
+ type=str,
+ shape=['number_of_species'],
+ description='''
+ Contains labels of the atomic species for the species-projected density of states
+ (DOS).
+
+ Differently from atom_labels, which allow more than one label for the same atomic
+ species (by adding a number or a string to the label), this list is expected to
+ refer to actual atomic species, i.e. belonging to the periodic table of elements.
+ Thus, the species-projected DOS are expected to be as many as the different atomic
+ species in the system.
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_species_label'))
+
+ species_projected_dos_values_lm = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_lm_species_projected_dos', 'number_of_spin_channels', 'number_of_species', 'number_of_species_projected_dos_values'],
+ description='''
+ Holds species-projected density of states (DOS) values, divided into contributions
+ from each $l,m$ channel.
+
+ Here, there are as many species-projected DOS as the number of species,
+ number_of_species. The list of labels of the species is given in
+ species_projected_dos_species_label.
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_values_lm'))
+
+ species_projected_dos_values_total = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_species', 'number_of_species_projected_dos_values'],
+ description='''
+ Holds species-projected density of states (DOS) values, summed up over all
+ azimuthal quantum numbers $l$.
+
+ Here, there are as many species-projected DOS as the number of species,
+ number_of_species. The list of labels of the species is given in
+ species_projected_dos_species_label.
+ ''',
+ a_legacy=LegacyDefinition(name='species_projected_dos_values_total'))
+
+
+class section_springer_material(MSection):
+ '''
+ Every section_springer_material contains results of classification of materials with
+ the same formula according to Springer Materials - it contains
+ section_springer_classsification, section_springer_compound, section_springer_id,
+ section_springer_references
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_springer_material'))
+
+ springer_id = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Id of the classified material according to Springer Materials
+ ''',
+ a_legacy=LegacyDefinition(name='springer_id'))
+
+ springer_alphabetical_formula = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The alphabetical formula of the material according to Springer Materials Database
+ ''',
+ a_legacy=LegacyDefinition(name='springer_alphabetical_formula'))
+
+ springer_url = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Url to the source page in Springer Materials describing the current entry
+ ''',
+ a_legacy=LegacyDefinition(name='springer_url'))
+
+ springer_compound_class = Quantity(
+ type=str,
+ shape=['N'],
+ description='''
+ Name of a class of the current compound, as defined in by Springer Materials. This
+ is a property of the chemical formula of the compound
+ ''',
+ a_legacy=LegacyDefinition(name='springer_compound_class'))
+
+ springer_classification = Quantity(
+ type=str,
+ shape=['N'],
+ description='''
+ Contains the classification name of the current material according to Springer
+ Materials
+ ''',
+ a_legacy=LegacyDefinition(name='springer_classification'))
+
+ section_springer_id = SubSection(
+ sub_section=SectionProxy('section_springer_id'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_springer_id'))
+
+
+class section_springer_id(MSection):
+ '''
+ Identifiers used by Springer Materials
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_springer_id'))
+
+
+class section_std_system(MSection):
+ '''
+ Section containing symmetry information that is specific to the standardized system.
+ The standardized system is defined as given by spglib and the details can be found
+ from https://arxiv.org/abs/1506.01455
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_std_system'))
+
+ atom_positions_std = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms_std', 3],
+ description='''
+ Standardized atom positions in reduced units.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_positions_std'))
+
+ atomic_numbers_std = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_std'],
+ description='''
+ Atomic numbers of the atoms in the standardized cell.
+ ''',
+ a_legacy=LegacyDefinition(name='atomic_numbers_std'))
+
+ equivalent_atoms_std = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms_std'],
+ description='''
+ Gives a mapping table of atoms to symmetrically independent atoms in the
+ standardized cell. This is used to find symmetrically equivalent atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='equivalent_atoms_std'))
+
+ lattice_vectors_std = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ Standardized lattice vectors of the conventional cell. The vectors are the rows of
+ this matrix.
+ ''',
+ a_legacy=LegacyDefinition(name='lattice_vectors_std'))
+
+ number_of_atoms_std = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of atoms in standardized system.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms_std'))
+
+ wyckoff_letters_std = Quantity(
+ type=str,
+ shape=['number_of_atoms_std'],
+ description='''
+ Wyckoff letters for atoms in the standardized cell.
+ ''',
+ a_legacy=LegacyDefinition(name='wyckoff_letters_std'))
+
+
+class section_stress_tensor(MSection):
+ '''
+ Section collecting alternative values to stress_tensor that have been calculated.
+
+ This section allows the storage of multiple definitions and evaluated values of the
+ stress tensor, while only one definition is used for, e.g., molecular dynamics or
+ geometry optimization (if needed).
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_stress_tensor'))
+
+ stress_tensor_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the method used to compute the stress tensor stored in
+ stress_tensor_value. This is an *alternative* to the stress tensor defined in
+ stress_tensor_method, which is stored in stress_tensor.
+
+ This field allows for multiple definitions and evaluated values of the stress
+ tensor, while only one definition is used for, e.g., molecular dynamics and
+ geometry optimization.
+ ''',
+ a_legacy=LegacyDefinition(name='stress_tensor_kind'))
+
+ stress_tensor_value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='pascal',
+ description='''
+ Contains the value of the stress tensor of the kind defined in stress_tensor_kind.
+ This is an *alternative* to the stress tensor defined in stress_tensor_method.
+
+ This field allows for multiple definitions and evaluated values of the stress
+ tensor, while only one definition is used for, e.g., molecular dynamics and
+ geometry optimization.
+ ''',
+ categories=[stress_tensor_type],
+ a_legacy=LegacyDefinition(name='stress_tensor_value'))
+
+
+class section_symmetry(MSection):
+ '''
+ Section containing information about the symmetry properties of the system.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_symmetry'))
+
+ bravais_lattice = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifier for the Bravais lattice in Pearson notation. The first lowercase letter
+ identifies the crystal family and can be one of the following: a (triclinic), b
+ (monoclinic), o (orthorhombic), t (tetragonal), h (hexagonal) or c (cubic). The
+ second uppercase letter identifies the centring and can be one of the following: P
+ (primitive), S (face centred), I (body centred), R (rhombohedral centring) or F
+ (all faces centred).
+ ''',
+ a_legacy=LegacyDefinition(name='bravais_lattice'))
+
+ choice = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String that specifies the centering, origin and basis vector settings of the 3D
+ space group that defines the symmetry group of the simulated physical system (see
+ section_system). Values are as defined by spglib.
+ ''',
+ a_legacy=LegacyDefinition(name='choice'))
+
+ crystal_system = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of the crystal system. Can be one of the following: triclinic, monoclinic,
+ orthorhombic, tetragonal, trigonal, hexagonal or cubic.
+ ''',
+ a_legacy=LegacyDefinition(name='crystal_system'))
+
+ hall_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ The Hall number for this system.
+ ''',
+ a_legacy=LegacyDefinition(name='hall_number'))
+
+ hall_symbol = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The Hall symbol for this system.
+ ''',
+ a_legacy=LegacyDefinition(name='hall_symbol'))
+
+ international_short_symbol = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the International Union of Crystallography (IUC) short symbol of the 3D
+ space group of this system
+ ''',
+ a_legacy=LegacyDefinition(name='international_short_symbol'))
+
+ origin_shift = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ description='''
+ Vector $\\mathbf{p}$ from the origin of the standardized system to the origin of
+ the original system. Together with the matrix $\\mathbf{P}$, found in
+ space_group_3D_transformation_matrix, the transformation between the standardized
+ coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by
+ $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.
+ ''',
+ a_legacy=LegacyDefinition(name='origin_shift'))
+
+ point_group = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Symbol of the crystallographic point group in the Hermann-Mauguin notation.
+ ''',
+ a_legacy=LegacyDefinition(name='point_group'))
+
+ space_group_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Specifies the International Union of Crystallography (IUC) number of the 3D space
+ group of this system.
+ ''',
+ a_legacy=LegacyDefinition(name='space_group_number'))
+
+ symmetry_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Identifies the source of the symmetry information contained within this section.
+ If equal to 'spg_normalized' the information comes from a normalization step.
+ ''',
+ a_legacy=LegacyDefinition(name='symmetry_method'))
+
+ transformation_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ description='''
+ Matrix $\\mathbf{P}$ that is used to transform the standardized coordinates to the
+ original coordinates. Together with the vector $\\mathbf{p}$, found in
+ space_group_3D_origin_shift, the transformation between the standardized
+ coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by
+ $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.
+ ''',
+ a_legacy=LegacyDefinition(name='transformation_matrix'))
+
+ section_original_system = SubSection(
+ sub_section=SectionProxy('section_original_system'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_original_system'))
+
+ section_primitive_system = SubSection(
+ sub_section=SectionProxy('section_primitive_system'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_primitive_system'))
+
+ section_std_system = SubSection(
+ sub_section=SectionProxy('section_std_system'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_std_system'))
+
+
+class section_system_to_system_refs(MSection):
+ '''
+ Section that describes the relationship between different section_system sections.
+
+ For instance, if a phonon calculation using a finite difference approach is performed
+ the force evaluation is typically done in a larger supercell but the properties such
+ as the phonon band structure are still calculated for the primitive cell.
+
+ The kind of relationship between the system defined in this section and the referenced
+ one is described by system_to_system_kind. The referenced section_system is identified
+ via system_to_system_ref.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_system_to_system_refs'))
+
+ system_to_system_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String defining the relationship between the referenced section_system and the
+ present section_system. Often systems are connected for example if a phonon
+ calculation using finite differences is performed the force ealuation is done in a
+ larger supercell but properties such as the phonon band structure are still
+ calculated for the primitive cell. Hence, the need of keeping track of these
+ connected systems. The referenced system is identified via system_to_system_ref.
+ ''',
+ a_legacy=LegacyDefinition(name='system_to_system_kind'))
+
+ system_to_system_ref = Quantity(
+ type=Reference(SectionProxy('section_system')),
+ shape=[],
+ description='''
+ Reference to another system. The kind of relationship between the present and the
+ referenced section_system is specified by system_to_system_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='system_to_system_ref'))
+
+
+class section_system(MSection):
+ '''
+ Every section_system contains all needed properties required to describe the simulated
+ physical system, e.g. the given atomic configuration, the definition of periodic cell
+ (if present), the external potentials and other parameters.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_system'))
+
+ atom_atom_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_sites'],
+ description='''
+ Atomic number Z of the atom.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_atom_number'))
+
+ atom_concentrations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms'],
+ description='''
+ concentration of the atom species in a variable composition, by default it should
+ be considered an array of ones. Summing these should give the number_of_sites
+ ''',
+ a_legacy=LegacyDefinition(name='atom_concentrations'))
+
+ atom_labels = Quantity(
+ type=str,
+ shape=['number_of_atoms'],
+ aliases=['elements'],
+ description='''
+ Labels of the atoms. These strings identify the atom kind and conventionally start
+ with the symbol of the atomic species, possibly followed by the atomic number. The
+ same atomic species can be labeled with more than one atom_labels in order to
+ distinguish, e.g., atoms of the same species assigned to different atom-centered
+ basis sets or pseudo-potentials, or simply atoms in different locations in the
+ structure (e.g., bulk and surface). These labels can also be used for *particles*
+ that do not correspond to physical atoms (e.g., ghost atoms in some codes using
+ atom-centered basis sets). This metadata defines a configuration and is therefore
+ required.
+ ''',
+ categories=[configuration_core],
+ a_legacy=LegacyDefinition(name='atom_labels'))
+
+ atom_positions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='meter',
+ description='''
+ Positions of all the atoms, in Cartesian coordinates. This metadata defines a
+ configuration and is therefore required. For alloys where concentrations of
+ species are given for each site in the unit cell, it stores the position of the
+ sites.
+ ''',
+ categories=[configuration_core],
+ a_legacy=LegacyDefinition(name='atom_positions'))
+
+ atom_species = Quantity(
+ type=np.dtype(np.int32),
+ shape=['number_of_atoms'],
+ description='''
+ Species of the atom (normally the atomic number Z, 0 or negative for unidentifed
+ species or particles that are not atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_species'))
+
+ atom_velocities = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='meter / second',
+ description='''
+ Velocities of the nuclei, defined as the change in Cartesian coordinates of the
+ nuclei with respect to time.
+ ''',
+ a_legacy=LegacyDefinition(name='atom_velocities'))
+
+ configuration_periodic_dimensions = Quantity(
+ type=bool,
+ shape=[3],
+ description='''
+ Array labeling which of the lattice vectors use periodic boundary conditions. Note
+ for the parser developers: This value is not expected to be given for each
+ section_single_configuration_calculation. It is assumed to be valid from the
+ section_single_configuration_calculation where it is defined for all subsequent
+ section_single_configuration_calculation in section_run, until redefined.
+ ''',
+ categories=[configuration_core],
+ a_legacy=LegacyDefinition(name='configuration_periodic_dimensions'))
+
+ configuration_raw_gid = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ checksum of the configuration_core, i.e. the geometry of the system. The values
+ are not normalized in any way so equivalent configurations might have different
+ values
+ ''',
+ a_legacy=LegacyDefinition(name='configuration_raw_gid'))
+
+ embedded_system = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Is the system embedded into a host geometry?.
+ ''',
+ categories=[configuration_core],
+ a_legacy=LegacyDefinition(name='embedded_system'))
+
+ lattice_vectors = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ Holds the lattice vectors (in Cartesian coordinates) of the simulation cell. The
+ last (fastest) index runs over the $x,y,z$ Cartesian coordinates, and the first
+ index runs over the 3 lattice vectors.
+ ''',
+ categories=[configuration_core],
+ a_legacy=LegacyDefinition(name='lattice_vectors'))
+
+ local_rotations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3, 3],
+ description='''
+ A rotation matrix defining the orientation of each atom. If the rotation matrix
+ only needs to be specified for some atoms, the remaining atoms should set it to
+ the zero matrix (not the identity!)
+ ''',
+ a_legacy=LegacyDefinition(name='local_rotations'))
+
+ number_of_atoms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Stores the total number of atoms used in the calculation. For alloys where
+ concentrations of species are given for each site in the unit cell, it stores the
+ number of sites.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_atoms'))
+
+ number_of_sites = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of sites in a variable composition representation. By default (no variable
+ composition) it is the same as number_of_atoms.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_sites'))
+
+ SC_matrix = Quantity(
+ type=np.dtype(np.int32),
+ shape=[3, 3],
+ description='''
+ Specifies the matrix that transforms the unit-cell into the super-cell in which
+ the actual calculation is performed.
+ ''',
+ a_legacy=LegacyDefinition(name='SC_matrix'))
+
+ simulation_cell = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ DEPRECATED, use lattice_vectors instead. Holds the lattice vectors (in Cartesian
+ coordinates) of the simulation cell. The last (fastest) index runs over the
+ $x,y,z$ Cartesian coordinates, and the first index runs over the 3 lattice
+ vectors.
+ ''',
+ categories=[configuration_core],
+ a_legacy=LegacyDefinition(name='simulation_cell'))
+
+ symmorphic = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Is the space group symmorphic? Set to True if all translations are zero.
+ ''',
+ a_legacy=LegacyDefinition(name='symmorphic'))
+
+ system_composition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Composition, i.e. cumulative chemical formula with atoms ordered by decreasing
+ atomic number Z.
+ ''',
+ a_legacy=LegacyDefinition(name='system_composition'))
+
+ system_configuration_consistent = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Flag set is the configuration is consistent
+ ''',
+ a_legacy=LegacyDefinition(name='system_configuration_consistent'))
+
+ system_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies the name of the system. This information is provided by the user in some
+ codes and is stored here for debugging or visualization purposes.
+ ''',
+ a_legacy=LegacyDefinition(name='system_name'))
+
+ system_reweighted_composition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Composition, i.e. cumulative chemical with atoms ordered by decreasing atomic
+ number Z reweighted so that the sum is close to 100, and values are rounded up,
+ and are stable (i.e. it is a fixed point).
+ ''',
+ a_legacy=LegacyDefinition(name='system_reweighted_composition'))
+
+ system_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of the system
+ ''',
+ a_legacy=LegacyDefinition(name='system_type'))
+
+ time_reversal_symmetry = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Is time-reversal symmetry present?
+ ''',
+ a_legacy=LegacyDefinition(name='time_reversal_symmetry'))
+
+ chemical_composition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The chemical composition as full formula of the system, based on atom species.
+ ''',
+ a_legacy=LegacyDefinition(name='chemical_composition'))
+
+ chemical_composition_reduced = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The chemical composition as reduced formula of the system, based on atom species.
+ ''',
+ a_legacy=LegacyDefinition(name='chemical_composition_reduced'))
+
+ chemical_composition_bulk_reduced = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The chemical composition as reduced bulk formula of the system, based on atom
+ species.
+ ''',
+ a_legacy=LegacyDefinition(name='chemical_composition_bulk_reduced'))
+
+ section_prototype = SubSection(
+ sub_section=SectionProxy('section_prototype'),
+ repeats=True, categories=[fast_access],
+ a_legacy=LegacyDefinition(name='section_prototype'))
+
+ section_springer_material = SubSection(
+ sub_section=SectionProxy('section_springer_material'),
+ repeats=True, categories=[fast_access],
+ a_legacy=LegacyDefinition(name='section_springer_material'))
+
+ section_symmetry = SubSection(
+ sub_section=SectionProxy('section_symmetry'),
+ repeats=True, categories=[fast_access],
+ a_legacy=LegacyDefinition(name='section_symmetry'))
+
+ section_system_to_system_refs = SubSection(
+ sub_section=SectionProxy('section_system_to_system_refs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='section_system_to_system_refs'))
+
+
+class section_thermodynamical_properties(MSection):
+ '''
+ Section that defines thermodynamical properties about the system in a
+ section_frame_sequence.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_thermodynamical_properties'))
+
+ helmholz_free_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule',
+ description='''
+ Stores the Helmholtz free energy per unit cell at constant volume of a
+ thermodynamic calculation.
+ ''',
+ a_legacy=LegacyDefinition(name='helmholz_free_energy'))
+
+ number_of_thermodynamical_property_values = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Gives the number of thermal properties values available in
+ section_thermodynamical_properties.
+ ''',
+ a_legacy=LegacyDefinition(name='number_of_thermodynamical_property_values'))
+
+ thermodynamical_properties_calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to calculate the thermodynamic quantities.
+
+ Valid values:
+
+ * harmonic
+ ''',
+ a_legacy=LegacyDefinition(name='thermodynamical_properties_calculation_method'))
+
+ thermodynamical_property_heat_capacity_C_v = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kelvin',
+ description='''
+ Stores the heat capacity per cell unit at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='thermodynamical_property_heat_capacity_C_v'))
+
+ @derived(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kelvin * kilogram',
+ description='''
+ Stores the specific heat capacity at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='specific_heat_capacity'),
+ cached=True
+ )
+ def specific_heat_capacity(self) -> np.array:
+ """Returns the specific heat capacity by dividing the heat capacity per
+ cell with the mass of the atoms in the cell.
+ """
+ import nomad.atomutils
+ s_frame_sequence = self.m_parent
+ first_frame = s_frame_sequence.frame_sequence_local_frames_ref[0]
+ system = first_frame.single_configuration_calculation_to_system_ref
+ atomic_numbers = system.atom_species
+ mass_per_unit_cell = nomad.atomutils.get_summed_atomic_mass(atomic_numbers)
+ heat_capacity = self.thermodynamical_property_heat_capacity_C_v
+ specific_heat_capacity = heat_capacity / mass_per_unit_cell
+
+ return specific_heat_capacity
+
+ thermodynamical_property_temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='kelvin',
+ description='''
+ Specifies the temperatures at which properties such as the Helmholtz free energy
+ are calculated.
+ ''',
+ a_legacy=LegacyDefinition(name='thermodynamical_property_temperature'))
+
+ vibrational_free_energy_at_constant_volume = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule',
+ description='''
+ Holds the vibrational free energy per atom at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='vibrational_free_energy_at_constant_volume'))
+
+ @derived(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kilogram',
+ description='''
+ Stores the specific vibrational free energy at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='specific_vibrational_free_energy_at_constant_volume'),
+ cached=True
+ )
+ def specific_vibrational_free_energy_at_constant_volume(self) -> np.array:
+ """Returns the specific vibrational free energy by dividing the vibrational free energy per
+ cell with the mass of the atoms in the cell.
+ """
+ import nomad.atomutils
+ s_frame_sequence = self.m_parent
+ first_frame = s_frame_sequence.frame_sequence_local_frames_ref[0]
+ system = first_frame.single_configuration_calculation_to_system_ref
+ atomic_numbers = system.atom_species
+ n_atoms = len(atomic_numbers)
+ mass_per_atom = nomad.atomutils.get_summed_atomic_mass(atomic_numbers) / n_atoms
+ free_energy = self.vibrational_free_energy_at_constant_volume
+ specific_vibrational_free_energy_at_constant_volume = free_energy / mass_per_atom
+
+ return specific_vibrational_free_energy_at_constant_volume
+
+
+class section_volumetric_data(MSection):
+ '''
+ Section defining a set of volumetric data on a uniform real-space
+
+ grid.
+
+ To store an array (e.g. a density or a potential), define:
+
+ * three grid point displacement vectors ("displacements")
+
+ * number of grid points along each axis ("nx", "ny" and "nz")
+
+ * the origin of the coordinate system, i.e. coordinates of the first grid
+
+ point ("origin")
+
+ * how many spatial functions are represented, e.g., two for a
+
+ normal spin-polarized density ("multiplicity")
+
+ * the values for each grid point ("values")
+
+ * the unit that applies to each value ("units")
+
+ * the kind of array represented by the volumetric data ("kind").
+
+ Allowed kinds are (please add new kinds as necessary): "density",
+
+ "potential_hartree" and "potential_effective". Densities and
+
+ potentials that are spin-polarized should have multiplicity two.
+
+ Rules for more complex spins are to be decided when necessary.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_volumetric_data'))
+
+ volumetric_data_displacements = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3, 3],
+ unit='meter',
+ description='''
+ displacement vectors between grid points along each axis; same indexing rules as
+ lattice_vectors. In many cases, displacements and number of points are related to
+ lattice_vectors through: [displacement] * [number of points + N] =
+ [lattice_vector],where N is 1 for periodic directions and 0 for non-periodic ones
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_displacements'))
+
+ volumetric_data_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The kind of function, e.g. density, potential_hartree, potential_effective. The
+ unit of measurement for "volumetric_data_values" depends on the kind: Densities
+ are 1/m^3 and potentials are J/m^3. See [full specification on the
+ wiki](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
+ info/wikis/metainfo/volumetric-data).
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_kind'))
+
+ volumetric_data_multiplicity = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of functions stored
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_multiplicity'))
+
+ volumetric_data_nx = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of points along x axis
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_nx'))
+
+ volumetric_data_ny = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of points along y axis
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_ny'))
+
+ volumetric_data_nz = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ number of points along z axis
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_nz'))
+
+ volumetric_data_origin = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ description='''
+ location of the first grid point; same coordinate system as atom_positions when
+ applicable.
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_origin'))
+
+ volumetric_data_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['volumetric_data_multiplicity', 'volumetric_data_nx', 'volumetric_data_ny', 'volumetric_data_nz'],
+ description='''
+ Array of shape (multiplicity, nx, ny, nz) containing the values. The units of
+ these values depend on which kind of data the values represent; see
+ "volumetric_data_kind".
+ ''',
+ a_legacy=LegacyDefinition(name='volumetric_data_values'))
+
+
+class section_XC_functionals(MSection):
+ '''
+ Section containing one of the exchange-correlation (XC) functionals for the present
+ section_method that are combined to form the XC_functional.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_XC_functionals'))
+
+ XC_functional_name = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Provides the name of one of the exchange and/or correlation (XC) functionals
+ combined in XC_functional.
+
+ The valid unique names that can be used are listed in the [XC_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional).
+
+ *NOTE*: This value should refer to a correlation, an exchange or an exchange-
+ correlation functional only.
+ ''',
+ categories=[settings_physical_parameter],
+ a_legacy=LegacyDefinition(name='XC_functional_name'))
+
+ XC_functional_parameters = Quantity(
+ type=typing.Any,
+ shape=[],
+ description='''
+ Contains an associative list of non-default values of the parameters for the
+ functional declared in XC_functional_name of the section_XC_functionals section.
+
+ For example, if a calculations using a hybrid XC functional (e.g., HSE06)
+ specifies a user-given value of the mixing parameter between exact and GGA
+ exchange, then this non-default value is stored in this metadata.
+
+ The labels and units of these values are defined in the paragraph dedicated to the
+ specified functional declared in XC_functional_name of the [XC_functional wiki
+ page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-
+ functional).
+
+ If this metadata is not given, the default parameter values for the
+ XC_functional_name are assumed.
+ ''',
+ categories=[settings_physical_parameter],
+ a_legacy=LegacyDefinition(name='XC_functional_parameters'))
+
+ XC_functional_weight = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Provides the value of the weight for the exchange, correlation, or exchange-
+ correlation functional declared in XC_functional_name (see
+ section_XC_functionals).
+
+ This weight is used in the linear combination of the different XC functional names
+ (XC_functional_name) in different section_XC_functionals sections to form the
+ XC_functional used for evaluating energy_XC_functional and related quantities.
+
+ If not specified then the default is set to 1.
+ ''',
+ categories=[settings_physical_parameter],
+ a_legacy=LegacyDefinition(name='XC_functional_weight'))
+
+
+class GeometryOptimization(MSection):
+ '''
+ Section containing the results of a geometry_optimization workflow.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_geometry_optimization'))
+
+ geometry_optimization_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of geometry optimization can either be ionic, cell_shape, cell_volume.
+ ''',
+ a_legacy=LegacyDefinition(name='geometry_optimization_type')
+ )
+
+ input_energy_difference_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ The input energy difference tolerance criterion.
+ ''',
+ a_legacy=LegacyDefinition(name='input_energy_difference_tolerance'))
+
+ input_force_maximum_tolerance = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ The input maximum net force tolerance criterion.
+ ''',
+ a_legacy=LegacyDefinition(name='input_force_maximum_tolerance'))
+
+ final_energy_difference = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ The difference in the energy between the last two steps during optimization.
+ ''',
+ a_legacy=LegacyDefinition(name='final_energy_difference'),
+ a_search=Search())
+
+ final_force_maximum = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ The maximum net force in the last optimization step.
+ ''',
+ a_legacy=LegacyDefinition(name='final_force_maximum'))
+
+ optimization_steps = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of optimization steps.
+ ''',
+ a_legacy=LegacyDefinition(name='optimization_steps'))
+
+
+class Phonon(MSection):
+ '''
+ Section containing the results of a phonon workflow.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_phonon'))
+
+ force_calculator = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of the program used to calculate the forces.
+ ''',
+ a_legacy=LegacyDefinition(name='force_calculator'))
+
+ mesh_density = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='1 / m ** 3',
+ description='''
+ Density of the k-mesh for sampling.
+ ''',
+ a_legacy=LegacyDefinition(name='mesh_density'),
+ a_search=Search())
+
+ n_imaginary_frequencies = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of modes with imaginary frequencies.
+ ''',
+ a_legacy=LegacyDefinition(name='n_imaginary_frequencies'),
+ a_search=Search())
+
+ random_displacements = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Identifies if displacements are made randomly.
+ ''',
+ a_legacy=LegacyDefinition(name='random_displacements'))
+
+ with_non_analytic_correction = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Identifies if non-analytical term corrections are applied to dynamical matrix.
+ ''',
+ a_legacy=LegacyDefinition(name='with_non_analytic_correction'),
+ a_search=Search())
+
+ with_grueneisen_parameters = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Identifies if Grueneisen parameters are calculated.
+ ''',
+ a_legacy=LegacyDefinition(name='with_grueneisen_parameters'),
+ a_search=Search())
+
+
+class Elastic(MSection):
+ '''
+ Section containing the results of an elastic workflow.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_elastic'))
+
+ energy_stress_calculator = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of program used to calculate energy or stress.
+ ''',
+ a_legacy=LegacyDefinition(name='energy_stress_calculator'))
+
+ elastic_calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method used to calculate elastic constants, can either be energy or stress.
+ ''',
+ a_legacy=LegacyDefinition(name='elastic_calculation_method'))
+
+ elastic_constants_order = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Order of the calculated elastic constants.
+ ''',
+ a_legacy=LegacyDefinition(name='elastic_constants_order'),
+ a_search=Search())
+
+ is_mechanically_stable = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if structure is mechanically stable from the calculated values
+ of the elastic constants.
+ ''',
+ a_legacy=LegacyDefinition(name='is_mechanically_stable'),
+ a_search=Search())
+
+ fitting_error_maximum = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum error in polynomial fit.
+ ''',
+ a_legacy=LegacyDefinition(name='fitting_error_maximum'))
+
+ strain_maximum = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum strain applied to crystal.
+ ''',
+ a_legacy=LegacyDefinition(name='strain_maximum'))
+
+
+class MolecularDynamics(MSection):
+ '''
+ Section containing results of molecular dynamics workflow.
+ '''
+
+ m_def = Section(
+ validate=False, a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
+
+ finished_normally = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if calculation terminated normally.
+ ''',
+ a_legacy=LegacyDefinition(name='finished_normally'))
+
+ with_trajectory = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if calculation includes trajectory data.
+ ''',
+ a_legacy=LegacyDefinition(name='with_trajectory'),
+ a_search=Search())
+
+ with_thermodynamics = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Indicates if calculation contains thermodynamic data.
+ ''',
+ a_legacy=LegacyDefinition(name='with_thermodynamics'),
+ a_search=Search())
+
+
+class Workflow(MSection):
+ '''
+ Section containing the results of a workflow.
+ '''
+
+ m_def = Section(
+ validate=False,
+ a_legacy=LegacyDefinition(name='section_workflow'))
+
+ workflow_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The type of calculation workflow. Can be one of geometry_optimization, elastic,
+ phonon, molecular_dynamics.
+ ''',
+ a_legacy=LegacyDefinition(name='workflow_type'),
+ a_search=Search(statistic_size=4, statistic_order='_count'))
+
+ calculation_result_ref = Quantity(
+ type=Reference(SectionProxy('section_single_configuration_calculation')),
+ categories=[fast_access],
+ shape=[],
+ description='''
+ Reference to calculation result. In the case of geometry_optimization and
+ molecular dynamics, this corresponds to the final step in the simulation. For the
+ rest of the workflow types, it refers to the original system.
+ ''',
+ a_legacy=LegacyDefinition(name='calculation_result_ref'))
+
+ calculations_ref = Quantity(
+ type=Reference(SectionProxy('section_single_configuration_calculation')),
+ shape=['optimization_steps'],
+ description='''
+ List of references to each section_single_configuration_calculation in the
+ simulation.
+ ''',
+ a_legacy=LegacyDefinition(name='calculations_ref'))
+
+ section_geometry_optimization = SubSection(
+ sub_section=SectionProxy('GeometryOptimization'), categories=[fast_access],
+ a_legacy=LegacyDefinition(name='section_geometry_optimization'))
+
+ section_phonon = SubSection(
+ sub_section=SectionProxy('Phonon'), categories=[fast_access],
+ a_legacy=LegacyDefinition(name='section_phonon'))
+
+ section_elastic = SubSection(
+ sub_section=SectionProxy('Elastic'),
+ a_legacy=LegacyDefinition(name='section_elastic'))
+
+ section_molecular_dynamics = SubSection(
+ sub_section=SectionProxy('MolecularDynamics'),
+ a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
+
+
+m_package.__init_metainfo__()
diff --git a/nomad/metainfo/generate.py b/nomad/metainfo/generate.py
new file mode 100644
index 0000000000000000000000000000000000000000..7a4485c1a502bece25f305ddd4579348c1743888
--- /dev/null
+++ b/nomad/metainfo/generate.py
@@ -0,0 +1,178 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+'''
+This module contains functionality to generate metainfo source-code from metainfo
+definitions.
+'''
+
+import numpy as np
+
+from nomad import utils
+from nomad.metainfo import Definition, SubSection, Package, Quantity, Section, Reference, MEnum
+
+logger = utils.get_logger(__name__)
+
+
+def generate_metainfo_code(metainfo_pkg: Package, python_package_path: str):
+ '''
+ Generates python code with metainfo definitions from the given :class:`Package`.
+
+ Arguments:
+ metainfo_pkg: The metainfo package.
+ python_package_path:
+ The file path for the python module file that should be generated.
+ '''
+ from jinja2 import Environment as JinjaEnvironment, PackageLoader, select_autoescape
+ import textwrap
+
+ def format_description(description, indent=0, width=90):
+ paragraphs = [paragraph.strip() for paragraph in description.split('\n\n')]
+
+ def format_paragraph(paragraph, first):
+ lines = textwrap.wrap(text=paragraph, width=width - indent * 4)
+ lines = [line.replace('\\', '\\\\') for line in lines]
+ return textwrap.indent(
+ '\n'.join(lines), ' ' * 4 * indent, lambda x: not (first and x.startswith(lines[0])))
+
+ return '\n\n'.join([
+ format_paragraph(p, i == 0)
+ for i, p in enumerate(paragraphs) if p != ''])
+
+ def format_type(pkg, mi_type):
+ if type(mi_type) == np.dtype:
+ if mi_type == np.dtype('U'):
+ return 'np.dtype(\'U\')'
+
+ return 'np.dtype(np.%s)' % mi_type
+
+ if mi_type in [int, float, str, bool]:
+ return mi_type.__name__
+
+ if isinstance(mi_type, Reference):
+ if pkg == mi_type.target_section_def.m_parent:
+ return "Reference(SectionProxy('%s'))" % mi_type.target_section_def.name
+
+ else:
+ python_module = mi_type.target_section_def.m_parent.a_legacy.python_module
+ return '%s.%s' % (python_module.split('.')[-1], mi_type.target_section_def.name)
+
+ if isinstance(mi_type, MEnum):
+ return 'MEnum(%s)' % ', '.join(["'%s'" % item for item in mi_type])
+
+ return str(mi_type)
+
+ def format_unit(unit):
+ return "'%s'" % unit
+
+ def format_definition_refs(pkg, definitions):
+ def format_definition_ref(definition: Definition):
+ if pkg == definition.m_parent:
+ return definition.name
+ else:
+ python_module = definition.m_parent.a_legacy.python_module
+ return '%s.%s' % (python_module.split('.')[-1], definition.name)
+
+ return ', '.join([format_definition_ref(definition) for definition in definitions])
+
+ def fromat_package_import(pkg):
+ python_module = pkg.a_legacy.python_module
+ modules = python_module.split('.')
+ return 'from %s import %s' % ('.'.join(modules[:-1]), modules[-1])
+
+ def format_aliases(pkg):
+ result = ''
+ for definition in pkg.category_definitions + pkg.section_definitions:
+ for alias in definition.aliases:
+ result += '%s = %s\n' % (alias, definition.name)
+
+ if result != '':
+ return '\n\n\n%s' % result
+
+ def order_categories(categories):
+ return sorted(categories, key=lambda c: len(c.categories))
+
+ env = JinjaEnvironment(
+ loader=PackageLoader('nomad.metainfo', 'templates'),
+ autoescape=select_autoescape(['python']))
+ env.globals.update(
+ order_categories=order_categories,
+ format_description=format_description,
+ format_type=format_type,
+ format_unit=format_unit,
+ format_definition_refs=format_definition_refs,
+ fromat_package_import=fromat_package_import,
+ format_aliases=format_aliases)
+
+ with open(python_package_path, 'wt') as f:
+ code = env.get_template('package_new.j2').render(pkg=metainfo_pkg)
+ code = '\n'.join([
+ line.rstrip() if line.strip() != '' else ''
+ for line in code.split('\n')])
+ f.write(code)
+
+
+if __name__ == '__main__':
+ # Simple use case that merges old common/public defs
+ import json
+
+ from nomad.metainfo import Category
+ from nomad.datamodel.metainfo.public_old import m_package
+ from nomad.datamodel.metainfo.common_old import m_package as common_pkg
+
+ for section in common_pkg.section_definitions: # pylint: disable=not-an-iterable
+ if section.extends_base_section:
+ base_section = section.base_sections[0]
+ for name, attr in section.section_cls.__dict__.items():
+ if isinstance(attr, Quantity):
+ base_section.m_add_sub_section(Section.quantities, attr.m_copy(deep=True))
+ elif isinstance(attr, SubSection):
+ base_section.m_add_sub_section(Section.sub_sections, attr.m_copy(deep=True))
+ else:
+ m_package.m_add_sub_section(Package.section_definitions, section)
+
+ for category in common_pkg.category_definitions: # pylint: disable=not-an-iterable
+ m_package.m_add_sub_section(Package.category_definitions, category)
+
+ for definition in m_package.section_definitions + m_package.category_definitions:
+ old_name = definition.name
+ new_name = ''.join([item[0].title() + item[1:] for item in old_name.split('_')])
+ if new_name.startswith('Section'):
+ new_name = new_name[7:]
+ if new_name != old_name:
+ definition.aliases = [old_name]
+ definition.name = new_name
+
+ unused_category = m_package.m_create(Category)
+ unused_category.name = 'Unused'
+ unused_category.description = 'This metainfo definition is not used by NOMAD data.'
+
+ with open('local/metainfostats.json', 'rt') as f:
+ stats = json.load(f)
+
+ unused = []
+ for (definition, _, _) in m_package.m_traverse():
+ if isinstance(definition, (SubSection, Quantity)):
+ if definition.name not in stats:
+ unused.append(definition)
+
+ for definition in unused:
+ if unused_category not in definition.categories:
+ definition.categories += [unused_category]
+
+ generate_metainfo_code(m_package, 'nomad/datamodel/metainfo/common_dft.py')
diff --git a/nomad/metainfo/legacy.py b/nomad/metainfo/legacy.py
index 25c1b30dfee0c809af32845e77ba9185f1fae1f5..50afebffe26a379a5399da68f37fc886a7e7a2f6 100644
--- a/nomad/metainfo/legacy.py
+++ b/nomad/metainfo/legacy.py
@@ -22,17 +22,15 @@ new nomad@fairdi infrastructure. This covers aspects like the new metainfo, a un
wrapper for parsers, parser logging, and a parser backend.
'''
-from typing import cast, Dict, List, Union, Any, Set, Iterable, Tuple, Type
+from typing import cast, Dict, List, Any, Tuple, Type
import numpy as np
-from pint.errors import UndefinedUnitError
import os.path
import importlib
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl, InfoKindEnv
+from nomadcore.local_meta_info import InfoKindEl, InfoKindEnv
from nomad import utils
-from nomad.units import ureg
from nomad.metainfo import (
Definition, SubSection, Package, Quantity, Category, Section, Reference,
Environment, MEnum, MSection, DefinitionAnnotation, MetainfoError, MSectionBound)
@@ -51,14 +49,6 @@ class LegacyDefinition(DefinitionAnnotation):
self.name = name
-class LegacyPackage(LegacyDefinition):
- def __init__(self, name, python_module, python_path):
- super().__init__(name)
-
- self.python_module = python_module
- self.python_path = python_path
-
-
def def_name(definition):
try:
return definition.a_legacy.name
@@ -285,376 +275,3 @@ class LegacyMetainfoEnvironment(Environment):
for dependency in dependencies],
'metaInfos': definitions
}
-
-
-class EnvironmentConversion:
- def __init__(self, legacy_env_or_path: Union[InfoKindEnv, str]):
- if isinstance(legacy_env_or_path, str):
- self.legacy_env, _ = loadJsonFile(filePath=legacy_env_or_path)
-
- else:
- self.legacy_env = cast(InfoKindEnv, legacy_env_or_path)
-
- self.__fix_legacy_super_names()
-
- self.package_conversions: Dict[str, PackageConversion] = {}
-
- for legacy_def in self.legacy_env.infoKindEls():
- if legacy_def.package in _ignored_packages:
- continue
- # legacy_def.package = normalized_package_name(legacy_def.package)
- package_conversion = self.package_conversions.get(legacy_def.package)
- if package_conversion is None:
- package_conversion = PackageConversion(self, legacy_def.package)
- self.package_conversions[legacy_def.package] = package_conversion
-
- package_conversion.legacy_defs.append(legacy_def)
-
- for package_conversion in self.package_conversions.values():
- package_conversion.create_definitions()
-
- for package_conversion in self.package_conversions.values():
- package_conversion.set_super_names()
-
- for package_conversion in self.package_conversions.values():
- package_conversion.init_definitions()
-
- def create_env(self) -> LegacyMetainfoEnvironment:
- env = LegacyMetainfoEnvironment()
- env.legacy_package_name = normalized_package_name(self.legacy_env.name)
- for package_conv in self.package_conversions.values():
- package = package_conv.package
- errors, warnings = package.m_all_validate()
- if len(errors) > 0:
- logger.error(
- '%s. There are %d more errors in converted legacy package %s' %
- (errors[0], len(errors) - 1, package))
- if len(warnings) > 0:
- logger.warn(
- '%s. There are %d more warnings in converted legacy package %s' %
- (warnings[0], len(warnings) - 1, package))
- env.m_add_sub_section(Environment.packages, package)
- package.init_metainfo()
- return env
-
- def __fix_legacy_super_names(self):
-
- def get_super_names(legacy_def: InfoKindEl, super_categories: Set[str] = None):
- super_section: str = None
- if super_categories is None:
- super_categories = set()
-
- for super_name in legacy_def.superNames:
- super_def = self.legacy_env.infoKindEl(super_name)
-
- if super_def.kindStr == 'type_section':
- super_section = super_def.name
-
- elif super_def.kindStr == 'type_abstract_document_content':
- super_categories.add(super_def.name)
- super_super_section, _ = get_super_names(super_def, super_categories=super_categories)
-
- if super_super_section is None:
- pass
-
- elif super_section is None:
- super_section = super_super_section
-
- elif super_section == super_super_section:
- pass
-
- else:
- logger.error('conflicting parent sections %s, %s for %s' % (
- super_section, super_def.name, legacy_def.name))
-
- return super_section, super_categories
-
- for legacy_def in self.legacy_env.infoKindEls():
- super_section, super_categories = get_super_names(legacy_def)
-
- if super_section is None:
- legacy_def.superNames = list(super_categories)
-
- else:
- legacy_def.superNames = [super_section] + list(super_categories)
-
- def resolve(self, name: str) -> Iterable[Definition]:
- for package_conversion in self.package_conversions.values():
- definition = package_conversion.package.all_definitions.get(name)
- if definition is not None:
- yield definition
-
-
-class PackageConversion:
-
- def __init__(self, env_conversion: EnvironmentConversion, name: str):
- self.env_conversion = env_conversion
- self.legacy_defs: List[InfoKindEl] = []
-
- python_module, python_path = python_package_mapping(name)
-
- self.package = Package(
- name=normalize_name(name),
- a_legacy=LegacyPackage(name, python_module, python_path))
-
- self.quantities: Dict[str, Quantity] = {}
-
- self.logger = logger.bind(package=name)
-
- def create_definitions(self):
- for legacy_def in self.legacy_defs:
- name = normalize_name(legacy_def.name)
-
- if legacy_def.kindStr == 'type_abstract_document_content':
- self.package.m_create(
- Category, name=name, a_legacy=LegacyDefinition(name=legacy_def.name))
-
- elif legacy_def.kindStr == 'type_section':
- self.package.m_create(
- Section, name=name,
- a_legacy=LegacyDefinition(name=legacy_def.name))
-
- elif legacy_def.kindStr in ['type_dimension', 'type_document_content']:
- definition = Quantity(
- name=name,
- a_legacy=LegacyDefinition(name=legacy_def.name))
- self.quantities[name] = (definition)
-
- else:
- logger.error('unknown kindStr %s for %s' % (legacy_def.kindStr, name))
-
- def __resolve(self, name: str, create_extends: bool = False):
- definition: Definition = self.package.all_definitions.get(name)
- if definition is None:
- definition = self.quantities.get(name)
-
- if definition is not None:
- if not (isinstance(definition, Section) and definition.extends_base_section) or create_extends:
- return definition
-
- for definition in self.env_conversion.resolve(name):
- if isinstance(definition, Section) and definition.extends_base_section:
- continue
-
- if create_extends and isinstance(definition, Section):
- extending_def = self.package.m_create(
- Section, name=definition.name,
- a_legacy=LegacyDefinition(name=definition.a_legacy.name))
- extending_def.base_sections = [definition]
- extending_def.extends_base_section = True
- return extending_def
-
- return definition
-
- assert False, 'definition %s must be created now' % name
-
- def set_super_names(self):
- for legacy_def in self.legacy_defs:
- name = normalize_name(legacy_def.name)
- definition = self.__resolve(name)
- assert definition is not None, 'definition %s must exist' % name
-
- if isinstance(definition, Section):
- parent_section: Section = None
- for super_name in legacy_def.superNames:
- super_def = self.__resolve(normalize_name(super_name), create_extends=True)
- if isinstance(super_def, Section):
- parent_section = cast(Section, super_def)
-
- if parent_section is not None:
- sub_section = parent_section.m_create(
- SubSection, name=definition.name,
- a_legacy=LegacyDefinition(name=legacy_def.name))
- sub_section.sub_section = definition
- sub_section.repeats = legacy_def.repeats is None or legacy_def.repeats
-
- if isinstance(definition, Quantity):
- parent_section: Section = None
- for super_name in legacy_def.superNames:
- super_def = self.__resolve(normalize_name(super_name), create_extends=True)
- if isinstance(super_def, Section):
- parent_section = cast(Section, super_def)
-
- parent_section.m_add_sub_section(Section.quantities, definition)
-
- def init_definitions(self):
- for legacy_def in self.legacy_defs:
- name = normalize_name(legacy_def.name)
- definition = self.__resolve(name)
- assert definition is not None, 'definition %s must exist' % name
- logger = self.logger.bind(definition=definition.name)
-
- # common properties
- if legacy_def.description is not None and legacy_def.description.strip() != '':
- definition.description = legacy_def.description
-
- if isinstance(definition, Definition):
- # deal with categories
- categories: List[Category] = []
- for super_name in legacy_def.superNames:
- super_def = self.__resolve(normalize_name(super_name))
- if isinstance(super_def, Category):
- categories.append(super_def)
-
- definition.categories = categories
-
- if isinstance(definition, Quantity):
- # type
- referenced_sections = legacy_def.extra_args.get('referencedSections', [])
- if len(referenced_sections) == 1:
- referenced_section = self.__resolve(referenced_sections[0])
- if referenced_section is None:
- logger.error('could not find referencedSection %s of %s' % (
- referenced_sections[0], definition.name))
- definition.type = int
- else:
- definition.type = Reference(referenced_section)
-
- elif len(referenced_sections) > 1:
- logger.error(
- 'higher dimensional references not yet supported: %s' % name)
- definition.type = np.dtype(int)
-
- elif legacy_def.kindStr == 'type_dimension':
- definition.type = int
- elif legacy_def.dtypeStr == 'D':
- definition.type = Any
- elif legacy_def.dtypeStr == 'C':
- definition.type = str
- elif legacy_def.dtypeStr == 'r':
- logger.error('r typed quantity %s doesn\'t have referencedSections' % name)
- definition.type = int
- elif legacy_def.dtypeStr == 'b':
- definition.type = bool
- elif legacy_def.dtypeStr == 'i64':
- definition.type = np.dtype(np.int64)
- elif legacy_def.dtypeStr == 'f':
- definition.type = np.dtype(np.float64)
- else:
- definition.type = np.dtype(legacy_def.dtypeStr)
-
- # shapes
- legacy_shape = legacy_def.shape
- if legacy_shape is None:
- legacy_shape = []
-
- definition.shape = legacy_shape
- if len(definition.shape) > 1 and definition.type == str:
- # Usually only np types have higher shapes in old metainfo;
- # str is one exception.
- definition.type = np.dtype('U')
-
- # units
- if legacy_def.units is not None:
- try:
- definition.unit = ureg.parse_units(legacy_def.units)
- except UndefinedUnitError:
- logger.error('unknown unit %s' % legacy_def.units)
- except ValueError as e:
- logger.error('cannot parse unit %s' % legacy_def.units, exc_info=e)
-
-
-def convert(metainfo_path: str) -> LegacyMetainfoEnvironment:
- return EnvironmentConversion(metainfo_path).create_env()
-
-
-def generate_metainfo_code(metainfo_env: LegacyMetainfoEnvironment):
- '''
- Generates python code with metainfo definitions for all packages in the given
- environement
-
- Arguments:
- env: The metainfo environment.
- python_package_path: An optional directory path. The directory must exist. Default
- is the working directory. The path will be used to form the module prefix
- for generated Python modules.
- '''
- from jinja2 import Environment as JinjaEnvironment, PackageLoader, select_autoescape
- import textwrap
-
- def format_description(description, indent=0, width=90):
- paragraphs = [paragraph.strip() for paragraph in description.split('\n')]
-
- def format_paragraph(paragraph, first):
- lines = textwrap.wrap(text=paragraph, width=width - indent * 4)
- lines = [line.replace('\\', '\\\\') for line in lines]
- return textwrap.indent(
- '\n'.join(lines), ' ' * 4 * indent, lambda x: not (first and x.startswith(lines[0])))
-
- return '\n\n'.join([
- format_paragraph(p, i == 0)
- for i, p in enumerate(paragraphs) if p != ''])
-
- def format_type(pkg, mi_type):
- if type(mi_type) == np.dtype:
- if mi_type == np.dtype('U'):
- return 'np.dtype(\'U\')'
-
- return 'np.dtype(np.%s)' % mi_type
-
- if mi_type in [int, float, str, bool]:
- return mi_type.__name__
-
- if isinstance(mi_type, Reference):
- if pkg == mi_type.target_section_def.m_parent:
- return "Reference(SectionProxy('%s'))" % mi_type.target_section_def.name
-
- else:
- python_module = mi_type.target_section_def.m_parent.a_legacy.python_module
- return '%s.%s' % (python_module.split('.')[-1], mi_type.target_section_def.name)
-
- else:
- return str(mi_type)
-
- def format_unit(unit):
- return "'%s'" % unit
-
- def format_definition_refs(pkg, definitions):
- def format_definition_ref(definition: Definition):
- if pkg == definition.m_parent:
- return definition.name
- else:
- python_module = definition.m_parent.a_legacy.python_module
- return '%s.%s' % (python_module.split('.')[-1], definition.name)
-
- return ', '.join([format_definition_ref(definition) for definition in definitions])
-
- def fromat_package_import(pkg):
- python_module = pkg.a_legacy.python_module
- modules = python_module.split('.')
- return 'from %s import %s' % ('.'.join(modules[:-1]), modules[-1])
-
- def order_categories(categories):
- return sorted(categories, key=lambda c: len(c.categories))
-
- env = JinjaEnvironment(
- loader=PackageLoader('nomad.metainfo', 'templates'),
- autoescape=select_autoescape(['python']))
- env.globals.update(
- order_categories=order_categories,
- format_description=format_description,
- format_type=format_type,
- format_unit=format_unit,
- format_definition_refs=format_definition_refs,
- fromat_package_import=fromat_package_import)
-
- for package in metainfo_env.packages:
- path = package.a_legacy.python_path
- if not os.path.exists(os.path.dirname(path)):
- os.makedirs(os.path.dirname(path))
-
- with open(path, 'wt') as f:
- code = env.get_template('package.j2').render(pkg=package)
- code = '\n'.join([
- line.rstrip() if line.strip() != '' else ''
- for line in code.split('\n')])
- f.write(code)
-
- _, path = python_package_mapping(metainfo_env.legacy_package_name)
- with open(os.path.join(os.path.dirname(path), '__init__.py'), 'wt') as f:
-
- code = env.get_template('environment.j2').render(env=metainfo_env)
- code = '\n'.join([
- line.rstrip() if line.strip() != '' else ''
- for line in code.split('\n')])
- f.write(code)
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index a9bbea2b7fa25b72d258d3450b570ef17c91482b..ab1fcbf5120d8730079cc8721286dd9239ae25be 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -2767,6 +2767,8 @@ def all_definitions(self):
for sub_section_def in [Package.section_definitions, Package.category_definitions]:
for definition in self.m_get_sub_sections(sub_section_def):
all_definitions[definition.name] = definition
+ for alias in definition.aliases:
+ all_definitions[alias] = definition
return all_definitions
@@ -2841,9 +2843,10 @@ class Environment(MSection):
all_definitions_by_name: Dict[str, List[Definition]] = dict()
for definition in self.m_all_contents():
if isinstance(definition, Definition):
- definitions = all_definitions_by_name.setdefault(definition.name, [])
- assert definition not in definitions, '%s must be unique' % definitions
- definitions.append(definition)
+ for name in [definition.name] + definition.aliases:
+ definitions = all_definitions_by_name.setdefault(name, [])
+ assert definition not in definitions, '%s must be unique' % definitions
+ definitions.append(definition)
return all_definitions_by_name
diff --git a/nomad/metainfo/templates/package.j2 b/nomad/metainfo/templates/package.j2
index b6945e4b241cb2bbccdcf892759b7d27e37394dc..e5dee0e450f4864d11ded30b784a0bf2f8487cf7 100644
--- a/nomad/metainfo/templates/package.j2
+++ b/nomad/metainfo/templates/package.j2
@@ -12,7 +12,9 @@ from nomad.metainfo.legacy import LegacyDefinition
m_package = Package(
name='{{ pkg.name }}',
description='{{ pkg.description }}',
- a_legacy=LegacyDefinition(name='{{pkg.a_legacy.name}}'))
+ {% if pkg.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{pkg.a_legacy.name}}')
+ {% endif -%})
{% for category in order_categories(pkg.category_definitions) %}
class {{ category.name }}(MCategory):
@@ -26,7 +28,9 @@ class {{ category.name }}(MCategory):
{% if category.categories | length > 0 -%}
categories=[{{ format_definition_refs(pkg, category.categories) }}],
{% endif -%}
- a_legacy=LegacyDefinition(name='{{category.a_legacy.name}}'))
+ {% if category.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{category.a_legacy.name}}')
+ {% endif -%})
{% endfor -%}
{% for section in pkg.section_definitions %}
@@ -37,7 +41,12 @@ class {{ section.name }}({%- if section.extends_base_section -%}{{ format_defini
{{ format_description(section.description, indent=1) }}
'''
{% endif %}
- m_def = Section(validate=False{%- if section.extends_base_section -%}, extends_base_section=True{%- endif -%}, a_legacy=LegacyDefinition(name='{{section.a_legacy.name}}'))
+ m_def = Section(
+ validate=False{%- if section.extends_base_section -%},
+ extends_base_section=True{%- endif -%},
+ {% if section.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{section.a_legacy.name}}')
+ {% endif -%})
{% for quantity in section.quantities %}
{{ quantity.name }} = Quantity(
type={{ format_type(pkg, quantity.type) }},
@@ -52,7 +61,9 @@ class {{ section.name }}({%- if section.extends_base_section -%}{{ format_defini
{%- if quantity.categories | length > 0 -%},
categories=[{{ format_definition_refs(pkg, quantity.categories) }}]
{%- endif -%},
- a_legacy=LegacyDefinition(name='{{quantity.a_legacy.name}}'))
+ {% if quantity.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{quantity.a_legacy.name}}')
+ {% endif -%})
{% endfor -%}
{%- for sub_section in section.sub_sections %}
@@ -63,7 +74,9 @@ class {{ section.name }}({%- if section.extends_base_section -%}{{ format_defini
description='''
{{ format_description(sub_section.description, indent=2) }}
'''{%- endif -%},
- a_legacy=LegacyDefinition(name='{{sub_section.a_legacy.name}}'))
+ {% if sub_section.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{sub_section.a_legacy.name}}')
+ {% endif -%})
{% endfor -%}
{%- endfor %}
diff --git a/nomad/metainfo/templates/package_new.j2 b/nomad/metainfo/templates/package_new.j2
new file mode 100644
index 0000000000000000000000000000000000000000..9aea88c9e295afe77fec0778e94d5db5057c1a34
--- /dev/null
+++ b/nomad/metainfo/templates/package_new.j2
@@ -0,0 +1,96 @@
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference, MEnum)
+from nomad.metainfo.legacy import LegacyDefinition
+from nomad.metainfo.search_extension import Search
+{% for dependency in pkg.dependencies %}
+{{ fromat_package_import(dependency) }}
+{%- endfor %}
+
+m_package = Package(
+ name='{{ pkg.name }}',
+ description='{{ pkg.description }}'
+ {%- if pkg.a_legacy is defined %},
+ a_legacy=LegacyDefinition(name='{{pkg.a_legacy.name}}')
+ {%- endif %})
+{% for category in order_categories(pkg.category_definitions) %}
+
+class {{ category.name }}(MCategory):
+ {% if category.description is not none -%}
+ '''
+ {{ format_description(category.description, indent=1) }}
+ '''
+ {%- endif %}
+
+ m_def = Category(
+ {%- if category.aliases | length > 0 %}
+ aliases=['{{ category.aliases[0] }}'],
+ {%- endif -%}
+ {%- if category.categories | length > 0 %}
+ categories=[{{ format_definition_refs(pkg, category.categories) }}],
+ {%- endif -%}
+ {%- if category.a_legacy is defined %}
+ a_legacy=LegacyDefinition(name='{{category.a_legacy.name}}')
+ {%- endif %})
+{% endfor -%}
+
+{% for section in pkg.section_definitions %}
+
+class {{ section.name }}({%- if section.extends_base_section -%}{{ format_definition_refs(pkg, section.base_sections)}}{%- else -%}MSection{%- endif -%}):
+ {% if section.description is not none -%}
+ '''
+ {{ format_description(section.description, indent=1) }}
+ '''
+ {% endif %}
+ m_def = Section(
+ {%- if section.aliases | length > 0 %}
+ aliases=['{{ section.aliases[0] }}'],
+ {%- endif %}
+ validate=False{%- if section.extends_base_section -%},
+ extends_base_section=True{%- endif -%},
+ {% if section.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{section.a_legacy.name}}')
+ {%- endif -%})
+ {% for quantity in section.quantities %}
+ {{ quantity.name }} = Quantity(
+ type={{ format_type(pkg, quantity.type) }},
+ shape={{ quantity.shape }}
+ {%- if quantity.unit is not none -%},
+ unit={{ format_unit(quantity.unit) }}
+ {%- endif -%}
+ {%- if quantity.description is not none -%},
+ description='''
+ {{ format_description(quantity.description, indent=2) }}
+ '''{%- endif -%}
+ {%- if quantity.categories | length > 0 -%},
+ categories=[{{ format_definition_refs(pkg, quantity.categories) }}]
+ {%- endif -%},
+ {%- if quantity.a_search is defined %}
+ a_search=Search(),
+ {%- endif -%}
+ {%- if quantity.a_legacy is defined %}
+ a_legacy=LegacyDefinition(name='{{quantity.a_legacy.name}}')
+ {%- endif -%})
+ {% endfor -%}
+
+ {%- for sub_section in section.sub_sections %}
+ {{ sub_section.name }} = SubSection(
+ sub_section=SectionProxy('{{ sub_section.sub_section.name }}'),
+ repeats={{ sub_section.repeats }}
+ {%- if sub_section.description is not none -%},
+ description='''
+ {{ format_description(sub_section.description, indent=2) }}
+ '''{%- endif -%},
+ {%- if sub_section.categories | length > 0 %}
+ categories=[{{ format_definition_refs(pkg, sub_section.categories) }}],
+ {%- endif %}
+ {% if sub_section.a_legacy is defined -%}
+ a_legacy=LegacyDefinition(name='{{sub_section.a_legacy.name}}')
+ {%- endif -%})
+ {% endfor -%}
+{%- endfor %}
+
+m_package.__init_metainfo__()
+{{- format_aliases(pkg) -}}
diff --git a/nomad/parsing/artificial.py b/nomad/parsing/artificial.py
index 21e1ae5e2382320d433d33bb85061d628b2abb6e..ebbf091b394452c18fbd058d62e638c95f71e7cf 100644
--- a/nomad/parsing/artificial.py
+++ b/nomad/parsing/artificial.py
@@ -33,7 +33,7 @@ import signal
from nomad import metainfo
from nomad.datamodel import EntryArchive
-from nomad.datamodel.metainfo.common import section_run as Run
+from nomad.datamodel.metainfo.common_dft import Run
from .legacy import Backend
from .parser import Parser, MatchingParser
@@ -69,8 +69,6 @@ class TemplateParser(ArtificalParser):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- from nomad.datamodel.metainfo import m_env as metainfo_env
- self._metainfo_env = metainfo_env
self.code_name = 'Template'
def is_mainfile(
diff --git a/nomad/parsing/legacy.py b/nomad/parsing/legacy.py
index 60c95c297101272bf100f4b9e15a2bf1bce55418..9e6c1ca262a4b327fd9b2a1b079d65a7c516b1e0 100644
--- a/nomad/parsing/legacy.py
+++ b/nomad/parsing/legacy.py
@@ -371,6 +371,7 @@ class LegacyParser(MatchingParser):
parser_class_name = self.parser_class_name.split('.')[-1]
self.__parser_impl = module_name, parser_class_name
self.__parser_class = None
+ self._metainfo_env = None
@property
def metainfo_env(self):
@@ -379,7 +380,7 @@ class LegacyParser(MatchingParser):
module = importlib.import_module('.'.join(module_name + ['metainfo']))
self._metainfo_env = getattr(module, 'm_env')
- return super().metainfo_env
+ return self._metainfo_env
@property
def parser_class(self):
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index 1cdc9fba2efbffde332591a202559c429ee70b72..32670d8e73cded721f0d6978efdab528235f83d4 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -21,7 +21,6 @@ from abc import ABCMeta, abstractmethod
import re
from nomad import config
-from nomad.metainfo import Environment
from nomad.datamodel import EntryArchive, UserProvidableMetadata, EntryMetadata
@@ -34,11 +33,6 @@ class Parser(metaclass=ABCMeta):
def __init__(self):
self.domain = 'dft'
- self._metainfo_env: Environment = None
-
- @property
- def metainfo_env(self):
- return self._metainfo_env
@abstractmethod
def is_mainfile(
diff --git a/tests/metainfo/test_legacy.py b/tests/metainfo/test_legacy.py
deleted file mode 100644
index 32e71f3319d3813d43b9b88b92c72e926b619409..0000000000000000000000000000000000000000
--- a/tests/metainfo/test_legacy.py
+++ /dev/null
@@ -1,108 +0,0 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-import pytest
-import numpy as np
-
-from nomadcore.local_meta_info import InfoKindEl, InfoKindEnv
-
-from nomad.metainfo.metainfo import Section, Quantity, SubSection
-from nomad.metainfo.legacy import LegacyMetainfoEnvironment, convert, python_package_mapping
-
-
-@pytest.fixture(scope='session')
-def legacy_example():
- return {
- 'type': 'nomad_meta_info_1_0',
- 'metaInfos': [
- dict(name='section_run', kindStr='type_section'),
- dict(
- name='program_name', dtypeStr='C', superNames=['program_info']),
- dict(name='bool_test', dtypeStr='b', superNames=['section_run']),
- dict(name='section_system', kindStr='type_section', superNames=['section_run']),
- dict(
- name='atom_labels', dtypeStr='C', shape=['number_of_atoms'],
- superNames=['section_system']),
- dict(
- name='atom_positions', dtypeStr='f', shape=['number_of_atoms', 3],
- superNames=['section_system']),
- dict(
- name='number_of_atoms', dtypeStr='i', kindStr='type_dimension',
- superNames=['section_system', 'system_info']),
- dict(name='section_method', kindStr='type_section', superNames=['section_run']),
- dict(
- name='method_system_ref', dtypeStr='i',
- referencedSections=['section_system'],
- superNames=['section_method']),
- dict(
- name='program_info', kindStr='type_abstract_document_content',
- superNames=['section_run']),
- dict(name='system_info', kindStr='type_abstract_document_content')
- ]
- }
-
-
-@pytest.fixture(scope='session')
-def legacy_env(legacy_example):
- env = InfoKindEnv()
- env.name = 'test.nomadmetainfo.json'
- for definition in legacy_example.get('metaInfos'):
- env.addInfoKindEl(InfoKindEl(
- description='test_description', package='test_package', **definition))
- return env
-
-
-@pytest.fixture(scope='session')
-def env(legacy_env):
- return convert(legacy_env)
-
-
-@pytest.mark.parametrize('package,path,name', [
- (
- 'vasp',
- 'dependencies/parsers/vasp/vaspparser/metainfo/vasp.py',
- 'vaspparser.metainfo.vasp'),
- (
- 'common',
- 'nomad/datamodel/metainfo/common.py',
- 'nomad.datamodel.metainfo.common'),
- (
- 'fhi_aims',
- 'dependencies/parsers/fhi-aims/fhiaimsparser/metainfo/fhi_aims.py',
- 'fhiaimsparser.metainfo.fhi_aims')
-])
-def test_package_mapping(package, path, name):
- assert python_package_mapping(package) == (name, path)
-
-
-def test_environment(env: LegacyMetainfoEnvironment, no_warn):
- assert env.packages[0].name == 'test_package'
- assert 'section_system' in env.packages[0].all_definitions
- section_run_def = env.resolve_definition('section_run', Section)
- assert section_run_def is not None
- assert section_run_def.section_cls is not None
- assert env.resolve_definition('section_run', Section) is not None
- assert env.resolve_definition('section_system', Section) is not None
- assert env.resolve_definition('section_system', SubSection) is not None
-
- assert env.resolve_definition('method_system_ref', Quantity).type.target_section_def == \
- env.resolve_definition('section_system', Section)
- assert env.resolve_definition('atom_labels', Quantity).type == str
- assert env.resolve_definition('atom_positions', Quantity).type == np.dtype('float64')
- assert env.resolve_definition('bool_test', Quantity).type == bool
- assert env.resolve_definition('program_name', Quantity).m_parent.name == 'section_run'
diff --git a/tests/normalizing/test_workflow.py b/tests/normalizing/test_workflow.py
index 537566689911b843430b3e94e1319229186f8dd9..47afd50dc93286bc37cbe4ea92db8bd65a7b4dab 100644
--- a/tests/normalizing/test_workflow.py
+++ b/tests/normalizing/test_workflow.py
@@ -44,7 +44,7 @@ def test_geometry_optimization_workflow(workflow_archive):
assert sec_workflow.workflow_type == 'geometry_optimization'
assert sec_workflow.calculations_ref is not None
- assert sec_workflow.calculation_result_ref.m_def.name == 'section_single_configuration_calculation'
+ assert sec_workflow.calculation_result_ref.m_def.name == 'SingleConfigurationCalculation'
assert sec_workflow.section_geometry_optimization.geometry_optimization_type == 'cell_shape'
assert sec_workflow.section_geometry_optimization.final_energy_difference > 0.0
assert sec_workflow.section_geometry_optimization.optimization_steps == 3
@@ -58,7 +58,7 @@ def test_elastic_workflow(workflow_archive):
assert sec_workflow.workflow_type == 'elastic'
assert sec_workflow.calculations_ref is not None
- assert sec_workflow.calculation_result_ref.m_def.name == 'section_single_configuration_calculation'
+ assert sec_workflow.calculation_result_ref.m_def.name == 'SingleConfigurationCalculation'
assert sec_workflow.section_elastic.elastic_calculation_method == 'energy'
assert sec_workflow.section_elastic.elastic_constants_order == 2
assert sec_workflow.section_elastic.is_mechanically_stable
@@ -74,7 +74,7 @@ def test_phonon_workflow(workflow_archive):
sec_workflow = phonopy_archive.section_workflow
assert sec_workflow.workflow_type == 'phonon'
assert sec_workflow.calculations_ref is not None
- assert sec_workflow.calculation_result_ref.m_def.name == 'section_single_configuration_calculation'
+ assert sec_workflow.calculation_result_ref.m_def.name == 'SingleConfigurationCalculation'
assert sec_workflow.section_phonon.force_calculator == 'fhi-aims'
assert sec_workflow.section_phonon.mesh_density > 0.0
assert sec_workflow.section_phonon.n_imaginary_frequencies > 0
@@ -90,7 +90,7 @@ def test_molecular_dynamics_workflow(workflow_archive):
sec_workflow = lammmps_archive.section_workflow
assert sec_workflow.workflow_type == 'molecular_dynamics'
assert sec_workflow.calculations_ref is not None
- assert sec_workflow.calculation_result_ref.m_def.name == 'section_single_configuration_calculation'
+ assert sec_workflow.calculation_result_ref.m_def.name == 'SingleConfigurationCalculation'
assert sec_workflow.section_molecular_dynamics.finished_normally
assert sec_workflow.section_molecular_dynamics.with_trajectory
assert sec_workflow.section_molecular_dynamics.with_thermodynamics
diff --git a/tests/test_archive.py b/tests/test_archive.py
index b997f2a5becddf27954b9333024ff09b57ccfe7b..5d4827ca460854acfd2699f2af32cd9df198e7e0 100644
--- a/tests/test_archive.py
+++ b/tests/test_archive.py
@@ -348,8 +348,9 @@ def assert_partial_archive(archive: EntryArchive) -> EntryArchive:
assert archive.section_workflow.calculation_result_ref.energy_total is not None
assert len(archive.section_workflow.calculation_result_ref.section_eigenvalues) == 0
# test refs of refs
- assert archive.section_workflow.calculation_result_ref.single_configuration_calculation_to_system_ref.atom_labels == ['H']
- assert archive.section_workflow.calculation_result_ref.single_configuration_calculation_to_system_ref.section_symmetry[0].space_group_number == 221
+ system = archive.section_workflow.calculation_result_ref.single_configuration_calculation_to_system_ref
+ assert system.atom_labels == ['H']
+ assert system.section_symmetry[0].space_group_number == 221
return archive
diff --git a/tests/test_datamodel.py b/tests/test_datamodel.py
index 30c37dd9befa525fa4d7484b791fc8323dbd4aa6..4020350c2f35540cae9de348b763edbc98714e84 100644
--- a/tests/test_datamodel.py
+++ b/tests/test_datamodel.py
@@ -117,19 +117,19 @@ def generate_calc(pid: int = 0, calc_id: str = None, upload_id: str = None) -> d
def test_common_metainfo():
- from nomad.datamodel.metainfo import public
+ from nomad.datamodel.metainfo import common_dft
- run = public.section_run()
- system = run.m_create(public.section_system)
+ run = common_dft.Run()
+ system = run.m_create(common_dft.System)
system.atom_labels = ['H', 'H', 'O']
assert run.section_system[0].atom_labels == ['H', 'H', 'O']
def test_vasp_metainfo():
- from nomad.datamodel.metainfo import public
+ from nomad.datamodel.metainfo import common_dft
from vaspparser.metainfo import m_env # pylint: disable=unused-import
- run = public.section_run()
+ run = common_dft.Run()
assert 'vasp_src_date' in run.m_def.all_quantities
diff --git a/tests/test_parsing.py b/tests/test_parsing.py
index 87f76ec522068760f9cd151f12470ccf482e6638..17eaed9f7bb713d8a6042cd4e4ed351e611cdc97 100644
--- a/tests/test_parsing.py
+++ b/tests/test_parsing.py
@@ -187,8 +187,8 @@ class TestBackend(object):
backend.openSection('section_method')
backend.closeSection('section_method', -1)
- from nomad.datamodel.metainfo.public import section_run
- runs = backend.resource.all(section_run)
+ from nomad.datamodel.metainfo.common_dft import Run
+ runs = backend.resource.all(Run)
assert len(runs) == 2
assert len(runs[0]['section_method']) == 2
assert len(runs[1]['section_method']) == 1
@@ -201,8 +201,8 @@ class TestBackend(object):
backend.closeSection('section_dos', dos_index)
backend.closeSection('section_run', run_index)
- from nomad.datamodel.metainfo.public import section_run
- runs = backend.resource.all(section_run)
+ from nomad.datamodel.metainfo.common_dft import Run
+ runs = backend.resource.all(Run)
assert len(runs) == 1
run = runs[0]
assert len(run['section_single_configuration_calculation']) == 1
@@ -222,8 +222,8 @@ class TestBackend(object):
backend.closeSection('section_dos', dos_index)
backend.closeSection('section_run', run_index)
- from nomad.datamodel.metainfo.public import section_run
- runs = backend.resource.all(section_run)
+ from nomad.datamodel.metainfo.common_dft import Run
+ runs = backend.resource.all(Run)
assert len(runs) == 1
run = runs[0]
assert len(run['section_single_configuration_calculation']) == 2
diff --git a/tests/test_search.py b/tests/test_search.py
index 411004424231a9fa5c38c074307a870b723fe249..e7b3d34c84d4403b19701e7ea23bc8cb308e834e 100644
--- a/tests/test_search.py
+++ b/tests/test_search.py
@@ -42,7 +42,6 @@ def test_index_normalized_calc(elastic, normalized: datamodel.EntryArchive):
entry_metadata.m_update(
domain='dft', upload_id='test upload id', calc_id='test id')
entry_metadata.apply_domain_metadata(normalized)
-
search_entry = create_entry(entry_metadata)
entry = search.flat(search_entry.to_dict())