From 76b3358832f26e812966e461de043462d46fe9f7 Mon Sep 17 00:00:00 2001
From: nathan <n.daelman@hotmail.com>
Date: Fri, 5 Jul 2024 14:19:30 +0200
Subject: [PATCH] Add back in the annotated output

---
 src/nomad_parser_vasp/parsers/xml_parser.py | 120 +++++++++++++++++++-
 1 file changed, 118 insertions(+), 2 deletions(-)

diff --git a/src/nomad_parser_vasp/parsers/xml_parser.py b/src/nomad_parser_vasp/parsers/xml_parser.py
index ee144c7..9d9e236 100644
--- a/src/nomad_parser_vasp/parsers/xml_parser.py
+++ b/src/nomad_parser_vasp/parsers/xml_parser.py
@@ -21,7 +21,6 @@
     DFT,
     XCFunctional,
 )
-from nomad_simulations.schema_packages.outputs import ElectronicEigenvalues
 from nomad_simulations.schema_packages.numerical_settings import KMesh
 
 configuration = config.get_plugin_entry_point(
@@ -36,12 +35,24 @@
 
 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"]'
 )
@@ -51,6 +62,111 @@
     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(