Migrate schema annotations to schema_p

FAIRmat-NFDI · Jul 5, 2024 · 8b0d4f3 · 8b0d4f3
1 parent 76b3358
commit 8b0d4f3
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Showing 2 changed files with 166 additions and 151 deletions.
diff --git a/src/nomad_parser_vasp/parsers/xml_parser.py b/src/nomad_parser_vasp/parsers/xml_parser.py
@@ -8,165 +8,15 @@
 from nomad.config import config
 from nomad.parsing import MatchingParser
 from nomad.parsing.file_parser.mapping_parser import (
-    MappingAnnotationModel,
     MetainfoParser,
     XMLParser,
 )
-from nomad_simulations.schema_packages.general import Simulation, Program
-from nomad_simulations.schema_packages.model_system import (
-    ModelSystem,
-    AtomicCell,
-)
-from nomad_simulations.schema_packages.model_method import (
-    DFT,
-    XCFunctional,
-)
-from nomad_simulations.schema_packages.numerical_settings import KMesh
+from nomad_simulations.schema_packages.general import Simulation
 
 configuration = config.get_plugin_entry_point(
     'nomad_parser_vasp.parsers:xml_entry_point'
 )
 
-# TODO move to schema parser and prepare all relevant annotations for every file format
-
-
-# ! vasprun.xml has many meta fields, explaining field semantics
-Simulation.m_def.m_annotations['xml'] = MappingAnnotationModel(path='modeling')
-
-Simulation.program.m_annotations['xml'] = MappingAnnotationModel(path='.generator')
-
-Simulation.model_method.m_annotations['xml'] = MappingAnnotationModel(
-    path='.parameters'
-)
-
-Simulation.model_system.m_annotations['xml'] = MappingAnnotationModel(
-    path='.calculation'
-)
-
-Simulation.model_system.cell.m_annotations['xml'] = MappingAnnotationModel(
-    path='.structure'
-)
-
-Simulation.outputs.m_annotations['xml'] = MappingAnnotationModel(path='.calculation')
-
-Program.name.m_annotations['xml'] = MappingAnnotationModel(
-    path='.i[?"@name"="program"]'
-)
-
-Program.version.m_annotations['xml'] = MappingAnnotationModel(
-    path='.i[?"@name"="version"]'
-)
-
-# ? compilation mode
-Program.compilation_host.m_annotations['xml'] = MappingAnnotationModel(
-    path='.i[?"@name"="platform"]'
-)
-
-DFT.numerical_settings.m_annotations['xml'] = MappingAnnotationModel(
-    path='modeling.kpoints'
-)
-
-dft_path = '.separator[?"@name"="electronic exchange-correlation"]'
-DFT.xc_functionals.m_annotations['xml'] = MappingAnnotationModel(
-    path=dft_path
-)  # start from Simulation.model_method path
-
-DFT.exact_exchange_mixing_factor.m_annotations = dict(
-    xml=MappingAnnotationModel(
-        operator=(
-            lambda mix, cond: mix if cond else 0,
-            [dft_path + '.i[?"@name"="HFALPHA"]', dft_path + '.i[?"@name"="LHFCALC"]'],
-        )
-    )  # TODO convert vasp bool
-)
-
-XCFunctional.libxc_name.m_annotations = dict(
-    xml=MappingAnnotationModel(
-        path=dft_path + '.i[?"@name"="GGA"]'  # TODO add LDA & mGGA, convert_xc
-    )
-)
-
-KMesh.grid.m_annotations['xml'] = MappingAnnotationModel(
-    path='.generation.v[?"@name"="divisions"]'
-)  # start from DFT.numerical_settings
-
-KMesh.offset.m_annotations['xml'] = MappingAnnotationModel(
-    path='.generation.v[?"@name"="shift"]'
-)  # start from DFT.numerical_settings
-
-KMesh.offset.m_annotations['xml'] = MappingAnnotationModel(
-    path='.generation.v[?"@name"="shift"]'
-)  # start from DFT.numerical_settings
-
-KMesh.points.m_annotations['xml'] = MappingAnnotationModel(
-    path='.varray[?"@name"="kpointlist"].v'
-)  # start from DFT.numerical_settings
-
-KMesh.weights.m_annotations['xml'] = MappingAnnotationModel(
-    path='.varray[?"@name"="weights"].v'
-)  # start from DFT.numerical_settings
-
-
-# ? target <structure name="initialpos" > and <structure name="finalpos" >
-
-
-AtomicCell.positions.m_annotations = dict(
-    xml=MappingAnnotationModel(path='.varray[?"@name"="positions"]')
-)  # start from Simulation.model_system.cell path
-
-"""
-...forces.m_annotations['xml'] = MappingAnnotationModel(
-    path='.varray[?"@name"="forces"]'
-)  # start from Simulation.model_system.cell path
-
-...stress.m_annotations['xml'] = MappingAnnotationModel(
-    path='.varray[?"@name"="stress"]'
-)  # start from Simulation.model_system.cell path
-"""
-
-AtomicCell.lattice_vectors.m_annotations['xml'] = MappingAnnotationModel(
-    path='.crystal.varray[?"@name"="basis"]'
-)  # start from Simulation.model_system.cell path
-
-"""
-cell_volume.m_annotations['xml'] = MappingAnnotationModel(
-    path='.crystal.i[?"@name"="volume"]'
-)  # start from Simulation.model_system.cell path
-
-reciprocal_lattice_vectors.m_annotations['xml'] = MappingAnnotationModel(
-    path='.crystal.varray[?"@name"="rec_basis"]'
-)  # start from Simulation.model_system.cell path
-
-total_free_energy.m_annotations['xml'] = MappingAnnotationModel(
-    path='calculation.energy.i[?"@name"="e_fr_energy"]'
-)
-
-total_internal_energy.m_annotations['xml'] = MappingAnnotationModel(
-    path='calculation.energy.i[?"@name"="e_0_energy"]'
-)
-
-...eigenvalues.m_annotations['xml'] = MappingAnnotationModel(
-    path='.eigenvalues.array'
-)
-
-ElectronicEigenvalues.spin_channel.m_annotations['xml'] = MappingAnnotationModel(
-    path='.eigenvalues.set.set[?"@comment"="spin 1"]'
-)  # start from Simulation.outputs path
-
-ElectronicEigenvalues.reciprocal_cell.m_annotations['xml'] = MappingAnnotationModel(
-    path=ElectronicEigenvalues.spin_channel.m_annotations.xml
-    + '.set[?"@comment"="kpoint 1"]'
-)  # TODO not going to work: add conversion to reference
-
-ElectronicEigenvalues.occupation.m_annotations['xml'] = MappingAnnotationModel(
-    path=ElectronicEigenvalues.reciprocal_cell.m_annotations.xml + '.r[0]'
-)
-
-ElectronicEigenvalues.value.m_annotations['xml'] = MappingAnnotationModel(
-    path=ElectronicEigenvalues.reciprocal_cell.m_annotations.xml + '.r[1]'
-)
-"""
-
 
 class VasprunXMLParser(MatchingParser):
     def parse(

diff --git a/src/nomad_parser_vasp/schema_packages/vasp_package.py b/src/nomad_parser_vasp/schema_packages/vasp_package.py
@@ -0,0 +1,165 @@
+from typing import (
+    TYPE_CHECKING,
+)
+
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import (
+        EntryArchive,
+    )
+    from structlog.stdlib import (
+        BoundLogger,
+    )
+
+from nomad.metainfo import SchemaPackage
+from nomad.parsing.file_parser.mapping_parser import MappingAnnotationModel
+from nomad_simulations.schema_packages.general import Simulation, Program
+from nomad_simulations.schema_packages.model_system import (
+    ModelSystem,
+    AtomicCell,
+)
+from nomad_simulations.schema_packages.model_method import (
+    DFT,
+    XCFunctional,
+)
+from nomad_simulations.schema_packages.numerical_settings import KMesh
+
+m_package = SchemaPackage()
+
+# note: vasprun.xml has many meta fields, explaining field semantics
+Simulation.m_def.m_annotations['xml'] = MappingAnnotationModel(path='modeling')
+
+Simulation.program.m_annotations['xml'] = MappingAnnotationModel(path='.generator')
+
+Simulation.model_method.m_annotations['xml'] = MappingAnnotationModel(
+    path='.parameters'
+)
+
+Simulation.model_system.m_annotations['xml'] = MappingAnnotationModel(
+    path='.calculation'
+)
+
+Simulation.model_system.cell.m_annotations['xml'] = MappingAnnotationModel(
+    path='.structure'
+)
+
+Simulation.outputs.m_annotations['xml'] = MappingAnnotationModel(path='.calculation')
+
+Program.name.m_annotations['xml'] = MappingAnnotationModel(
+    path='.i[?"@name"="program"]'
+)
+
+Program.version.m_annotations['xml'] = MappingAnnotationModel(
+    path='.i[?"@name"="version"]'
+)
+
+# ? compilation mode
+Program.compilation_host.m_annotations['xml'] = MappingAnnotationModel(
+    path='.i[?"@name"="platform"]'
+)
+
+DFT.numerical_settings.m_annotations['xml'] = MappingAnnotationModel(
+    path='modeling.kpoints'
+)
+
+dft_path = '.separator[?"@name"="electronic exchange-correlation"]'
+DFT.xc_functionals.m_annotations['xml'] = MappingAnnotationModel(
+    path=dft_path
+)  # start from Simulation.model_method path
+
+DFT.exact_exchange_mixing_factor.m_annotations = dict(
+    xml=MappingAnnotationModel(
+        operator=(
+            lambda mix, cond: mix if cond else 0,
+            [dft_path + '.i[?"@name"="HFALPHA"]', dft_path + '.i[?"@name"="LHFCALC"]'],
+        )
+    )  # TODO convert vasp bool
+)
+
+XCFunctional.libxc_name.m_annotations = dict(
+    xml=MappingAnnotationModel(
+        path=dft_path + '.i[?"@name"="GGA"]'  # TODO add LDA & mGGA, convert_xc
+    )
+)
+
+KMesh.grid.m_annotations['xml'] = MappingAnnotationModel(
+    path='.generation.v[?"@name"="divisions"]'
+)  # start from DFT.numerical_settings
+
+KMesh.offset.m_annotations['xml'] = MappingAnnotationModel(
+    path='.generation.v[?"@name"="shift"]'
+)  # start from DFT.numerical_settings
+
+KMesh.offset.m_annotations['xml'] = MappingAnnotationModel(
+    path='.generation.v[?"@name"="shift"]'
+)  # start from DFT.numerical_settings
+
+KMesh.points.m_annotations['xml'] = MappingAnnotationModel(
+    path='.varray[?"@name"="kpointlist"].v'
+)  # start from DFT.numerical_settings
+
+KMesh.weights.m_annotations['xml'] = MappingAnnotationModel(
+    path='.varray[?"@name"="weights"].v'
+)  # start from DFT.numerical_settings
+
+
+# ? target <structure name="initialpos" > and <structure name="finalpos" >
+
+
+AtomicCell.positions.m_annotations = dict(
+    xml=MappingAnnotationModel(path='.varray[?"@name"="positions"]')
+)  # start from Simulation.model_system.cell path
+
+"""
+...forces.m_annotations['xml'] = MappingAnnotationModel(
+    path='.varray[?"@name"="forces"]'
+)  # start from Simulation.model_system.cell path
+
+...stress.m_annotations['xml'] = MappingAnnotationModel(
+    path='.varray[?"@name"="stress"]'
+)  # start from Simulation.model_system.cell path
+"""
+
+AtomicCell.lattice_vectors.m_annotations['xml'] = MappingAnnotationModel(
+    path='.crystal.varray[?"@name"="basis"]'
+)  # start from Simulation.model_system.cell path
+
+"""
+cell_volume.m_annotations['xml'] = MappingAnnotationModel(
+    path='.crystal.i[?"@name"="volume"]'
+)  # start from Simulation.model_system.cell path
+
+reciprocal_lattice_vectors.m_annotations['xml'] = MappingAnnotationModel(
+    path='.crystal.varray[?"@name"="rec_basis"]'
+)  # start from Simulation.model_system.cell path
+
+total_free_energy.m_annotations['xml'] = MappingAnnotationModel(
+    path='calculation.energy.i[?"@name"="e_fr_energy"]'
+)
+
+total_internal_energy.m_annotations['xml'] = MappingAnnotationModel(
+    path='calculation.energy.i[?"@name"="e_0_energy"]'
+)
+
+...eigenvalues.m_annotations['xml'] = MappingAnnotationModel(
+    path='.eigenvalues.array'
+)
+
+ElectronicEigenvalues.spin_channel.m_annotations['xml'] = MappingAnnotationModel(
+    path='.eigenvalues.set.set[?"@comment"="spin 1"]'
+)  # start from Simulation.outputs path
+
+ElectronicEigenvalues.reciprocal_cell.m_annotations['xml'] = MappingAnnotationModel(
+    path=ElectronicEigenvalues.spin_channel.m_annotations.xml
+    + '.set[?"@comment"="kpoint 1"]'
+)  # TODO not going to work: add conversion to reference
+
+ElectronicEigenvalues.occupation.m_annotations['xml'] = MappingAnnotationModel(
+    path=ElectronicEigenvalues.reciprocal_cell.m_annotations.xml + '.r[0]'
+)
+
+ElectronicEigenvalues.value.m_annotations['xml'] = MappingAnnotationModel(
+    path=ElectronicEigenvalues.reciprocal_cell.m_annotations.xml + '.r[1]'
+)
+"""
+
+m_package.__init_metainfo__()