tutorial_DcEnergies

src/nomad_parser_vasp/schema_packages/vasp_package.py

@@ -3,24 +3,18 @@
 )
 
 if TYPE_CHECKING:
-    from nomad.datamodel.datamodel import (
-        EntryArchive,
-    )
-    from structlog.stdlib import (
-        BoundLogger,
-    )
+    pass
 
 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.general import Program, Simulation
 from nomad_simulations.schema_packages.model_method import (
     DFT,
     XCFunctional,
 )
+from nomad_simulations.schema_packages.model_system import (
+    AtomicCell,
+)
 from nomad_simulations.schema_packages.numerical_settings import KMesh
 
 m_package = SchemaPackage()

src/nomad_parser_vasp/schema_packages/vasp_package_extended.py

@@ -0,0 +1,167 @@
+from typing import (
+    TYPE_CHECKING,
+)
+
+if TYPE_CHECKING:
+    pass
+
+from nomad.metainfo import SchemaPackage
+from nomad.parsing.file_parser.mapping_parser import MappingAnnotationModel
+from nomad_simulations.schema_packages.general import Program, Simulation
+from nomad_simulations.schema_packages.model_method import (
+    DFT,
+    XCFunctional,
+)
+from nomad_simulations.schema_packages.model_system import (
+    AtomicCell,
+)
+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]'
+)
+
+electronic_energy_correction.m_annotations['xml'] = MappingAnnotationModel(
+    path='calculation.energy.i[?"@name"="hartreedc"]'
+)
+
+exchange_correlation_energy_correction.m_annotations['xml'] = MappingAnnotationModel(
+    path='calculation.energy.i[?"@name"="XCdc"]'
+)
+"""
+
+m_package.__init_metainfo__()