From 241ad2b31fab23809aaea1a1448a1582806234f2 Mon Sep 17 00:00:00 2001
From: Daria Tomecka <zarvok79@yahoo.com>
Date: Tue, 6 Sep 2016 23:20:33 +0200
Subject: [PATCH] wien2k: cleanup
---
parser/parser-wien2k/wien2k_parser.py | 2 +-
.../wien2k_parser_backups/setup_paths.py | 6 -
.../wien2k.nomadmetainfo.json | 439 ------------------
.../wien2k.nomadmetainfo_old.json | 132 ------
.../wien2k_parser_backups/wien2k_parser.py | 175 -------
.../wien2k_parser_in0.py | 69 ---
.../wien2k_parser_in1.py | 69 ---
.../wien2k_parser_in1c.py | 69 ---
.../wien2k_parser_in2.py | 69 ---
.../wien2k_parser_in2c.py | 57 ---
.../wien2k_parser_old.py | 90 ----
.../wien2k_parser_struct.py | 92 ----
.../wien2k_parser_struct_old.py | 66 ---
13 files changed, 1 insertion(+), 1334 deletions(-)
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/setup_paths.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo.json
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo_old.json
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in0.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1c.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2c.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_old.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct.py
delete mode 100644 parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct_old.py
diff --git a/parser/parser-wien2k/wien2k_parser.py b/parser/parser-wien2k/wien2k_parser.py
index 76e8eb6..5fd941e 100644
--- a/parser/parser-wien2k/wien2k_parser.py
+++ b/parser/parser-wien2k/wien2k_parser.py
@@ -8,7 +8,7 @@ import wien2k_parser_struct, wien2k_parser_in0, wien2k_parser_in1c, wien2k_pars
################################################################
-# This is the parser for the main output file (.scp) of WIEN2k.
+# This is the parser for the main output file (.scf) of WIEN2k.
################################################################
diff --git a/parser/parser-wien2k/wien2k_parser_backups/setup_paths.py b/parser/parser-wien2k/wien2k_parser_backups/setup_paths.py
deleted file mode 100644
index e0a0fb0..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/setup_paths.py
+++ /dev/null
@@ -1,6 +0,0 @@
-import sys, os, os.path
-baseDir = os.path.dirname(os.path.abspath(__file__))
-commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
-
-if not commonDir in sys.path:
- sys.path.insert(0, commonDir)
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo.json b/parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo.json
deleted file mode 100644
index fcc98fa..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo.json
+++ /dev/null
@@ -1,439 +0,0 @@
-{
- "type": "nomad_meta_info_1_0",
- "description": "meta info used by the wien2k parser. All names are expected to start with x_wien2k_",
- "dependencies": [ {
- "relativePath": "common.nomadmetainfo.json"
- }, {
- "relativePath": "meta_types.nomadmetainfo.json"
- }],
- "metaInfos": [ {
- "description": "position of atom x in internal units",
- "dtypeStr": "f",
- "name": "x_wien2k_atom_pos_x",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- }, {
- "description": "position of atom y in internal units",
- "dtypeStr": "f",
- "name": "x_wien2k_atom_pos_y",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- }, {
- "description": "position of atom z in internal units",
- "dtypeStr": "f",
- "name": "x_wien2k_atom_pos_z",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- },{
- "description": "name of atom, labelling non-equvalent atoms",
- "dtypeStr": "C",
- "name": "x_wien2k_atom_name",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- },{
- "description": "number of radial mesh points",
- "dtypeStr": "i",
- "name": "x_wien2k_NPT",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- },{
- "description": "atomic sphere radius (muffin-tin radius)",
- "dtypeStr": "f",
- "name": "x_wien2k_RMT",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- },{
- "description": "first radial mesh point",
- "dtypeStr": "f",
- "name": "x_wien2k_R0",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- },{
- "description": "atomic number Z",
- "dtypeStr": "f",
- "name": "x_wien2k_atomic_number_Z",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- }, {
- "description": "header (labels) of wien2k.",
- "kindStr": "type_section",
- "name": "x_wien2k_header",
- "superNames": [
- "section_run"
- ]
- }, {
- "description": "scf iteration number",
- "dtypeStr": "i",
- "name": "x_wien2k_iteration_number",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "number of inequivalent atoms in the unit cell",
- "dtypeStr": "i",
- "name": "x_wien2k_nonequiv_atoms",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "number of independent atoms in the cell",
- "dtypeStr": "i",
- "name": "x_wien2k_number_of_independent_atoms",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "exchange correlation potential option",
- "dtypeStr": "i",
- "name": "x_wien2k_potential_option",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "Release date of wien2k.",
- "dtypeStr": "C",
- "name": "x_wien2k_release_date",
- "shape": [],
- "superNames": [
- "x_wien2k_header"
- ]
- }, {
- "description": "section containing a class of equivalent atoms",
- "kindStr": "type_section",
- "name": "x_wien2k_section_equiv_atoms",
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "user given name for this system given in the struct file",
- "dtypeStr": "C",
- "name": "x_wien2k_system_nameIn",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "user given name for this system",
- "dtypeStr": "C",
- "name": "x_wien2k_system_name",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "relativistic or nonrelativistic calculation mode",
- "dtypeStr": "C",
- "name": "x_wien2k_calc_mode",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "unit cell parameters - a",
- "dtypeStr": "f",
- "name": "x_wien2k_unit_cell_param_a",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "unit cell parameters - b",
- "dtypeStr": "f",
- "name": "x_wien2k_unit_cell_param_b",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "unit cell parameters - c",
- "dtypeStr": "f",
- "name": "x_wien2k_unit_cell_param_c",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "unit cell parameters - alfa",
- "dtypeStr": "f",
- "name": "x_wien2k_angle_between_unit_axis_alfa",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "unit cell parameters - beta",
- "dtypeStr": "f",
- "name": "x_wien2k_angle_between_unit_axis_beta",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "unit cell parameters - gamma",
- "dtypeStr": "f",
- "name": "x_wien2k_angle_between_unit_axis_gamma",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "total number of atoms in the cell",
- "dtypeStr": "i",
- "name": "x_wien2k_total_atoms",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "lattice parameter a in this calculation",
- "dtypeStr": "f",
- "name": "x_wien2k_lattice_const_a",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "lattice parameter b in this calculation",
- "dtypeStr": "f",
- "name": "x_wien2k_lattice_const_b",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "lattice parameter c in this calculation",
- "dtypeStr": "f",
- "name": "x_wien2k_lattice_const_c",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "unit cell volume",
- "dtypeStr": "f",
- "name": "x_wien2k_unit_cell_volume",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ],
- "units": "bohr^3"
- }, {
- "description": "total energy",
- "dtypeStr": "f",
- "name": "x_wien2k_total_ene",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ],
- "units": "Ry"
- }, {
- "description": "Fermi energy",
- "dtypeStr": "f",
- "name": "x_wien2k_fermi_ene",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ],
- "units": "Ry"
- }, {
- "description": "energy gap in Ry",
- "dtypeStr": "f",
- "name": "x_wien2k_ene_gap_Ry",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ],
- "units": "Ry"
- }, {
- "description": "energy gap in eV",
- "dtypeStr": "f",
- "name": "x_wien2k_ene_gap_eV",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ],
- "units": "eV"
- }, {
- "description": "matrix size",
- "dtypeStr": "i",
- "name": "x_wien2k_matrix_size",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "rkm",
- "dtypeStr": "f",
- "name": "x_wien2k_rkm",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "LOs",
- "dtypeStr": "i",
- "name": "x_wien2k_LOs",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "total magnetic moment in cell",
- "dtypeStr": "f",
- "name": "x_wien2k_mmtot",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "magnetic moment in the interstital region",
- "dtypeStr": "f",
- "name": "x_wien2k_mmint",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "magnetic moment inside the sphere",
- "dtypeStr": "f",
- "name": "x_wien2k_mmi001",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the local (for each atom) cartesian coordinate system): |F|",
- "dtypeStr": "f",
- "name": "x_wien2k_for_abs",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the local (for each atom) cartesian coordinate system): Fx",
- "dtypeStr": "f",
- "name": "x_wien2k_for_x",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the local (for each atom) cartesian coordinate system): Fy",
- "dtypeStr": "f",
- "name": "x_wien2k_for_y",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the local (for each atom) cartesian coordinate system): Fz",
- "dtypeStr": "f",
- "name": "x_wien2k_for_z",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the global coordinate system of the unit cell (in the same way as the atomic positions are specified)): Fx",
- "dtypeStr": "f",
- "name": "x_wien2k_for_x_gl",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the global coordinate system of the unit cell (in the same way as the atomic positions are specified)): Fy",
- "dtypeStr": "f",
- "name": "x_wien2k_for_y_gl",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "force on atom xx in mRy/bohr (in the global coordinate system of the unit cell (in the same way as the atomic positions are specified)): Fz",
- "dtypeStr": "f",
- "name": "x_wien2k_for_z_gl",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "number of atom, labelling atoms",
- "dtypeStr": "C",
- "name": "x_wien2k_atom_nr",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "number of sphere, labelling spheres",
- "dtypeStr": "C",
- "name": "x_wien2k_sphere_nr",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "total difference charge density for atom xx between last 2 iterations",
- "dtypeStr": "f",
- "name": "x_wien2k_tot_diff_charge",
- "repeats": true,
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "total interstitial charge",
- "dtypeStr": "f",
- "name": "x_wien2k_tot_int_charge",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "Version of WIEN2k.",
- "dtypeStr": "C",
- "name": "x_wien2k_version",
- "shape": [],
- "superNames": [
- "x_wien2k_header"
- ]
- }]
-}
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo_old.json b/parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo_old.json
deleted file mode 100644
index 7c4dc3e..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k.nomadmetainfo_old.json
+++ /dev/null
@@ -1,132 +0,0 @@
-{
- "type": "nomad_meta_info_1_0",
- "description": "meta info used by the wien2k parser. All names are expected to start with x_wien2k_",
- "dependencies": [ {
- "relativePath": "common.nomadmetainfo.json"
- }, {
- "relativePath": "meta_types.nomadmetainfo.json"
- }],
- "metaInfos": [ {
- "description": "position of atom x in internal units",
- "dtypeStr": "f",
- "name": "x_wien2k_atom_pos_x",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- }, {
- "description": "position of atom y in internal units",
- "dtypeStr": "f",
- "name": "x_wien2k_atom_pos_y",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- }, {
- "description": "position of atom z in internal units",
- "dtypeStr": "f",
- "name": "x_wien2k_atom_pos_z",
- "repeats": true,
- "shape": [],
- "superNames": [
- "x_wien2k_section_equiv_atoms"
- ]
- }, {
- "description": "header (labels) of wien2k.",
- "kindStr": "type_section",
- "name": "x_wien2k_header",
- "superNames": [
- "section_run"
- ]
- }, {
- "description": "scf iteration number",
- "dtypeStr": "i",
- "name": "x_wien2k_iteration_number",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "number of inequivalent atoms in the unit cell",
- "dtypeStr": "i",
- "name": "x_wien2k_nonequiv_atoms",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "number of independent atoms in the cell",
- "dtypeStr": "i",
- "name": "x_wien2k_number_of_independent_atoms",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "exchange correlation potential option",
- "dtypeStr": "i",
- "name": "x_wien2k_potential_option",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "Release date of wien2k.",
- "dtypeStr": "C",
- "name": "x_wien2k_release_date",
- "shape": [],
- "superNames": [
- "x_wien2k_header"
- ]
- }, {
- "description": "section containing a class of equivalent atoms",
- "kindStr": "type_section",
- "name": "x_wien2k_section_equiv_atoms",
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "user given name for this system given in the struct file",
- "dtypeStr": "C",
- "name": "x_wien2k_system_nameIn",
- "shape": [],
- "superNames": [
- "section_system"
- ]
- }, {
- "description": "user given name for this system",
- "dtypeStr": "C",
- "name": "x_wien2k_system_name",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "total number of atoms in the cell",
- "dtypeStr": "i",
- "name": "x_wien2k_total_atoms",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ]
- }, {
- "description": "unit cell volume",
- "dtypeStr": "f",
- "name": "x_wien2k_unit_cell_volume",
- "shape": [],
- "superNames": [
- "section_scf_iteration"
- ],
- "units": "m^3"
- }, {
- "description": "Version of wien2k.",
- "dtypeStr": "C",
- "name": "x_wien2k_version",
- "shape": [],
- "superNames": [
- "x_wien2k_header"
- ]
- }]
-}
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser.py
deleted file mode 100644
index b56404a..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser.py
+++ /dev/null
@@ -1,175 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-import wien2k_parser_struct, wien2k_parser_in0, wien2k_parser_in1c, wien2k_parser_in2c, wien2k_parser_in1, wien2k_parser_in2
-
-class Wien2kContext(object):
- """context for wien2k parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
- def onClose_x_wien2k_header(self, backend, gIndex, section):
- backend.addValue("program_version",
- section["x_wien2k_version"][0] + " " +
- section["x_wien2k_release_date"][0])
-
- def onOpen_section_system(self, backend, gIndex, section):
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".struct"
- if os.path.exists(fName):
- structSuperContext = wien2k_parser_struct.Wien2kStructContext()
- structParser = AncillaryParser(
- fileDescription = wien2k_parser_struct.buildStructureMatchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_struct.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = structSuperContext)
-
- with open(fName) as fIn:
- structParser.parseFile(fIn)
-
- def onOpen_section_method(self, backend, gIndex, section):
-
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".in0"
- if os.path.exists(fName):
- subSuperContext = wien2k_parser_in0.Wien2kIn0Context()
- subParser = AncillaryParser(
- fileDescription = wien2k_parser_in0.buildIn0Matchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_in0.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = subSuperContext)
- with open(fName) as fIn:
- subParser.parseFile(fIn)
-
-
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".in1c"
- if os.path.exists(fName):
- subSuperContext = wien2k_parser_in1c.Wien2kIn1cContext()
- subParser = AncillaryParser(
- fileDescription = wien2k_parser_in1c.buildIn1cMatchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_in1c.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = subSuperContext)
- with open(fName) as fIn:
- subParser.parseFile(fIn)
-
-
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".in2c"
- if os.path.exists(fName):
- subSuperContext = wien2k_parser_in2c.Wien2kIn2cContext()
- subParser = AncillaryParser(
- fileDescription = wien2k_parser_in2c.buildIn2cMatchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_in2c.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = subSuperContext)
- with open(fName) as fIn:
- subParser.parseFile(fIn)
-
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".in1"
- if os.path.exists(fName):
- subSuperContext = wien2k_parser_in1.Wien2kIn1Context()
- subParser = AncillaryParser(
- fileDescription = wien2k_parser_in1.buildIn1Matchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_in1.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = subSuperContext)
- with open(fName) as fIn:
- subParser.parseFile(fIn)
-
-
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".in2"
- if os.path.exists(fName):
- subSuperContext = wien2k_parser_in2.Wien2kIn2Context()
- subParser = AncillaryParser(
- fileDescription = wien2k_parser_in2.buildIn2Matchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_in2.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = subSuperContext)
- with open(fName) as fIn:
- subParser.parseFile(fIn)
-
-# description of the input
-mainFileDescription = SM(
- name = 'root',
- weak = True,
- startReStr = "",
- subMatchers = [
- SM(name = 'newRun',
- startReStr = r"\s*:LABEL[0-9]+: using WIEN2k_(?:[0-9.]+) \(Release (?:[0-9/.]+)\) in ",
- repeats = True,
- required = True,
- forwardMatch = True,
- sections = ['section_run', 'section_method', 'section_system', 'section_single_configuration_calculation'],
- subMatchers = [
- SM(
- name = 'header',
- startReStr = r"\s*:LABEL[0-9]+: using WIEN2k_(?P<x_wien2k_version>[0-9.]+) \(Release (?P<x_wien2k_release_date>[0-9/.]+)\) in ",
- sections=["x_wien2k_header"],
- fixedStartValues={'program_name': 'WIEN2k', 'program_basis_set_type': '(L)APW+lo' }
- ), SM(
- name = "scf iteration",
- startReStr = r"\s*:ITE(?P<x_wien2k_iteration_number>[0-9]+):\s*[0-9]*. ITERATION",
- sections=["section_scf_iteration"],
- repeats = True,
- subMatchers=[
- SM(r":NATO\s*:\s*(?P<x_wien2k_nr_of_independent_atoms>[0-9]+)\s*INDEPENDENT AND\s*(?P<x_wien2k_total_atoms>[0-9]+)\s*TOTAL ATOMS IN UNITCELL"),
- SM(r"\s*SUBSTANCE: (?P<x_wien2k_system_name>.*)"),
- SM(r":POT\s*:\s*POTENTIAL OPTION\s*(?P<x_wien2k_potential_option>[0-9]+)"),
- SM(r":LAT\s*:\s*LATTICE CONSTANTS=\s*(?P<x_wien2k_lattice_const_a>[0-9.]+)\s*(?P<x_wien2k_lattice_const_b>[0-9.]+)\s*(?P<x_wien2k_lattice_const_c>[0-9.]+)"),
- SM(r":VOL\s*:\s*UNIT CELL VOLUME\s*=\s*(?P<x_wien2k_unit_cell_volume_bohr3>[0-9.]+)"),
- SM(r":RKM : MATRIX SIZE (?P<x_wien2k_matrix_size>[0-9]+)\s*LOs:\s*(?P<x_wien2k_LOs>[0-9.]+)\s*RKM=\s*(?P<x_wien2k_rkm>[0-9.]+)\s*WEIGHT=\s*[0-9.]*\s*\w*:"),
- SM(r":KPT\s*:\s*NUMBER\s*OF\s*K-POINTS:\s*(?P<x_wien2k_nr_kpts>[-+0-9.]+)"),
- SM(r":GMA\s*:\s*POTENTIAL\sAND\sCHARGE\sCUT-OFF\s*(?P<x_wien2k_cutoff>[0-9.]+)\s*Ry\W\W[0-9.]+"),
- SM(r":GAP\s*:\s*(?P<x_wien2k_ene_gap_Ry>[-+0-9.]+)\s*Ry\s*=\s*(?P<x_wien2k_ene_gap_eV>[-+0-9.]+)\s*eV\s*.*"),
- SM(r":NOE\s*:\s*NUMBER\sOF\sELECTRONS\s*=\s*(?P<x_wien2k_noe>[0-9.]+)"),
- SM(r":FER\s*:\s(\w*\s*)*-\s\w*\W\w*\WM\W*=\s*(?P<x_wien2k_fermi_ene>[-+0-9.]+)"),
- SM(r":GMA\s*:\s*POTENTIAL\sAND\sCHARGE\sCUT-OFF\s*[0-9.]+\s*Ry\W\W[0-9.]+"),
- SM(r":MMTOT: TOTAL MAGNETIC MOMENT IN CELL =\s*(?P<x_wien2k_mmtot>[-+0-9.]+)"),
- SM(r":MMINT: MAGNETIC MOMENT IN INTERSTITIAL =\s*(?P<x_wien2k_mmint>[-+0-9.]+)"),
- SM(r":MMI001: MAGNETIC MOMENT IN SPHERE 1 =\s*(?P<x_wien2k_mmi001>[-+0-9.]+)"),
- SM(r":NTO\s*:\s*\sTOTAL\s*INTERSTITIAL\s*CHARGE=\s*(?P<x_wien2k_tot_int_charge_nm>[-+0-9.]+)"),
- SM(r":NTO(?P<x_wien2k_atom_nr>[-+0-9]+)[0-9]*:\s*\sTOTAL\s*CHARGE\s*IN\s*SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_charge_in_sphere_nm>[-+0-9.]+)",repeats = True),
- SM(r":DTO(?P<x_wien2k_atom_nr>[-+0-9]+)[0-9]*:\sTOTAL\s*DIFFERENCE\s*CHARGE\W*\w*\s*IN\s*SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_diff_charge>[-+0-9.]+)", repeats = True),
- SM(r":DIS\s*:\s*CHARGE\sDISTANCE\s*\W*[0-9.]+\sfor\satom\s*[0-9]*\sspin\s[0-9]*\W\s*(?P<x_wien2k_charge_distance>[0-9.]+)"),
- SM(r":CTO\s*:\s*\sTOTAL\s*INTERSTITIAL\s*CHARGE=\s*(?P<x_wien2k_tot_int_charge>[-+0-9.]+)"),
- SM(r":CTO(?P<x_wien2k_atom_nr>[-+0-9]+)[0-9]*:\s*\sTOTAL\s*CHARGE\s*IN\s*SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_charge_in_sphere>[-+0-9.]+)",repeats = True),
- SM(r":ENE\s*:\s*\W*\w*\W*\s*TOTAL\s*ENERGY\s*IN\s*Ry\s*=\s*(?P<energy_total>[-+0-9.]+)"),
- SM(r":FOR[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_abs>[0-9.]+)\s*(?P<x_wien2k_for_x>[-++0-9.]+)\s*(?P<x_wien2k_for_y>[-+0-9.]+)\s*(?P<x_wien2k_for_z>[-+0-9.]+)\s*partial\sforces", repeats = True),
- SM(r":FGL[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_x_gl>[-+0-9.]+)\s*(?P<x_wien2k_for_y_gl>[-+0-9.]+)\s*(?P<x_wien2k_for_z_gl>[-+0-9.]+)\s*partial\sforces", repeats = True)
- ]
- )
- ]
- )
- ])
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
-
-parserInfo = {
- "name": "Wien2k"
-# "version": "1.0"
-}
-
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/wien2k.nomadmetainfo.json"))
-metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
-
-if __name__ == "__main__":
- superContext = Wien2kContext()
- mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in0.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in0.py
deleted file mode 100644
index b602d6a..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in0.py
+++ /dev/null
@@ -1,69 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-
-class Wien2kIn0Context(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
-
-# description of the input
-def buildIn0Matchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_method"],
- subMatchers = [
-# SM(name = 'systemName',
-# startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
- SM(r"(?P<x_wien2k_switch>\w*)\s*(?P<x_wien2k_indxc>[0-9]+)\s*.*"),
- SM(r"\s*(?P<x_wien2k_ifft_x>[0-9]+)\s*(?P<x_wien2k_ifft_y>[0-9]+)\s*(?P<x_wien2k_ifft_z>[0-9]+)\s*(?P<x_wien2k_ifft_factor>[0-9.]+)\s*(?P<x_wien2k_iprint>[0-9]+).*")
-# SM(r"(?P<x_wien2k_calc_mode>.*)"),
-# SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
-# SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True,
-# sections=["x_wien2k_section_equiv_atoms"],
-# subMatchers=[
-# SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True
-# ),
-# SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
-# ]
-# )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_method': CachingLvl
- }
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1.py
deleted file mode 100644
index ab4a58b..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1.py
+++ /dev/null
@@ -1,69 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-
-class Wien2kIn1Context(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
-
-# description of the input
-def buildIn1Matchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_method"],
- subMatchers = [
-# SM(name = 'systemName',
-# startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
- SM(r"\s*(?P<x_wien2k_wf_switch>[\w*]+)\s*EF=[-+.0-9]*\s*\W*WFFIL, WFPRI, ENFIL, SUPWF\W"),
- SM(r"\s*(?P<x_wien2k_rkmax>[0-9.]+)\s*[0-9]+\s*[0-9]+\s*\WR-..\WK-...; MAX \w*.*")
-# SM(r"(?P<x_wien2k_calc_mode>.*)"),
-# SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
-# SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True,
-# sections=["x_wien2k_section_equiv_atoms"],
-# subMatchers=[
-# SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True
-# ),
-# SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
-# ]
-# )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_method': CachingLvl
- }
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1c.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1c.py
deleted file mode 100644
index 218e775..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in1c.py
+++ /dev/null
@@ -1,69 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-
-class Wien2kIn1cContext(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
-
-# description of the input
-def buildIn1cMatchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_method"],
- subMatchers = [
-# SM(name = 'systemName',
-# startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
- SM(r"\s*(?P<x_wien2k_wf_switch>[\w*]+)\s*EF=[-+.0-9]*\s*\W*WFFIL, WFPRI, ENFIL, SUPWF\W"),
- SM(r"\s*(?P<x_wien2k_rkmax>[0-9.]+)\s*[0-9]+\s*[0-9]+\s*\WR-..\WK-...; MAX \w*.*")
-# SM(r"(?P<x_wien2k_calc_mode>.*)"),
-# SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
-# SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True,
-# sections=["x_wien2k_section_equiv_atoms"],
-# subMatchers=[
-# SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True
-# ),
-# SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
-# ]
-# )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_method': CachingLvl
- }
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2.py
deleted file mode 100644
index 947daf5..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2.py
+++ /dev/null
@@ -1,69 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-
-class Wien2kIn2Context(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
-
-# description of the input
-def buildIn2Matchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_method"],
- subMatchers = [
-# SM(name = 'systemName',
-# startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
- SM(r"\s*(?P<x_wien2k_in2c_switch>[A-Z]+)\s*.*")
-# SM(r"\s*(?P<x_wien2k_rkmax>[0-9.]+)\s*[0-9]+\s*[0-9]+\s*\WR-..\WK-...; MAX \w*.*")
-# SM(r"(?P<x_wien2k_calc_mode>.*)"),
-# SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
-# SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True,
-# sections=["x_wien2k_section_equiv_atoms"],
-# subMatchers=[
-# SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
-# repeats=True
-# ),
-# SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
-# ]
-# )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_method': CachingLvl
- }
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2c.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2c.py
deleted file mode 100644
index 4d0d171..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_in2c.py
+++ /dev/null
@@ -1,57 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-
-class Wien2kIn2cContext(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
-
-# description of the input
-def buildIn2cMatchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_method"],
- subMatchers = [
- SM(r"\s*(?P<x_wien2k_in2c_switch>[A-Z]+)\s*.*"),
- SM(r"\s*(?P<x_wien2k_in2c_emin>[-+0-9.]+)\s*(?P<x_wien2k_in2c_ne>[-+0-9.]+)\s*(?P<x_wien2k_in2c_espermin>[-+0-9.]+)\s*(?P<x_wien2k_in2c_esper0>[-+0-9.]+)\s*.*"),
- SM(r"\s*(?P<smearing_kind>[A-Z]+)\s*\s*(?P<smearing_width>[-+0-9.]+)\s*.*"),
- SM(r"\s*(?P<x_wien2k_in2c_gmax>[-+0-9.]+)\s*GMAX")
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_method': CachingLvl
- }
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_old.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_old.py
deleted file mode 100644
index 7554864..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_old.py
+++ /dev/null
@@ -1,90 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-import wien2k_parser_struct
-
-class Wien2kContext(object):
- """context for wien2k parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
- def onClose_x_wien2k_header(self, backend, gIndex, section):
- backend.addValue("program_version",
- section["x_wien2k_version"][0] + " " +
- section["x_wien2k_release_date"][0])
-
- def onOpen_section_system(self, backend, gIndex, section):
-
- structSuperContext = wien2k_parser_struct.Wien2kStructContext()
- structParser = AncillaryParser(
- fileDescription = wien2k_parser_struct.buildStructureMatchers(),
- parser = self.parser,
- cachingLevelForMetaName = wien2k_parser_struct.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = structSuperContext)
-
- mainFile = self.parser.fIn.fIn.name
- fName = mainFile[:-4] + ".struct"
- if os.path.exists(fName):
- with open(fName) as fIn:
- structParser.parseFile(fIn)
-
-# description of the input
-mainFileDescription = SM(
- name = 'root',
- weak = True,
- startReStr = "",
- subMatchers = [
- SM(name = 'newRun',
- startReStr = r"\s*:LABEL[0-9]+: using WIEN2k_(?:[0-9.]+) \(Release (?:[0-9/.]+)\) in ",
- repeats = True,
- required = True,
- forwardMatch = True,
- sections = ['section_run', 'section_method', 'section_system', 'section_single_configuration_calculation'],
- subMatchers = [
- SM(
- name = 'header',
- startReStr = r"\s*:LABEL[0-9]+: using WIEN2k_(?P<x_wien2k_version>[0-9.]+) \(Release (?P<x_wien2k_release_date>[0-9/.]+)\) in ",
- sections=["x_wien2k_header"],
- fixedStartValues={'program_name': 'WIEN2k', 'program_basis_set_type': '(L)APW+lo' }
- ), SM(
- name = "scf iteration",
- startReStr = r"\s*:ITE(?P<x_wien2k_iteration_number>[0-9]+):\s*[0-9]*. ITERATION",
- sections=["section_scf_iteration"],
- repeats = True,
- subMatchers=[
- SM(r":NATO :\s*(?P<x_wien2k_number_of_independent_atoms>[0-9]+)INDEPENDENT AND\s*(?P<x_wien2k_total_atoms>[0-9]+)\s*TOTAL ATOMS IN UNITCELL"),
- SM(r"\s*SUBSTANCE: (?P<x_wien2k_system_name>.*)"),
- SM(r":POT\s*:\s*POTENTIAL OPTION\s*(?P<x_wien2k_potential_option>[0-9]+)"),
- SM(r":VOL\s*:\s*UNIT CELL VOLUME\s*=\s*(?P<x_wien2k_unit_cell_volume__angstrom3>[0-9.]+)")
- ]
- )
- ]
- )
- ])
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
-
-parserInfo = {
- "name": "Wien2k"
-}
-
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/wien2k.nomadmetainfo.json"))
-metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
-
-if __name__ == "__main__":
- superContext = Wien2kContext()
- mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct.py
deleted file mode 100644
index 01d3c49..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct.py
+++ /dev/null
@@ -1,92 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json, logging
-import numpy as np
-
-class Wien2kStructContext(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
- def onClose_section_system(self, backend, gIndex, section):
- equiv_atoms = section["x_wien2k_section_equiv_atoms"]
- #logging.error("section: %s", section)
- labels = []
- pos = []
- for eqAtoms in equiv_atoms:
- label = eqAtoms["x_wien2k_atom_name"][0]
- x = eqAtoms["x_wien2k_atom_pos_x"]
- y = eqAtoms["x_wien2k_atom_pos_y"]
- z = eqAtoms["x_wien2k_atom_pos_z"]
- if len(x) != len(y) or len(x) != len(z):
- raise Exception("incorrect parsing, different number of x,y,z components")
- groupPos = [[x[i],y[i],z[i]] for i in range(len(x))]
- nAt = len(groupPos)
- labels += [label for i in range(nAt)]
- pos += groupPos
- backend.addValue("atom_labels", labels)
- backend.addValue("atom_positions", pos)
-
-
-# description of the input
-def buildStructureMatchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_system"],
- subMatchers = [
- SM(name = 'systemName',
- startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
- SM(r"\w+\s*LATTICE,NONEQUIV\.ATOMS.\s*(?P<x_wien2k_nonequiv_atoms>[0-9]+)"),
- SM(r"(?P<x_wien2k_calc_mode>.*)"),
- # SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9.eEdD]+)\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9.eEdD]+)\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9.eEdD]+)\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+0-9.eEdD]{9})\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+0-9.eEdD]{9})\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+0-9.eEdD]+)"),
- SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_b>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_unit_cell_param_c>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
- SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
- repeats=True,
- sections=["x_wien2k_section_equiv_atoms"],
- subMatchers=[
- SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
- repeats=True
- ),
- # SM(r"\s*(?P<atom>.{10})\s*NPT=\s*(?P<NPT>[0-9]+)\s*R0=(?P<r0>[0-9.]+)\s*RMT=\s*(?P<rmt>[0-9.]+)\s*Z:\s*(?P<z>[0-9.]+)",)
- SM(r"\s*(?P<x_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_wien2k_NPT>[0-9]+)\s*R0=(?P<x_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_wien2k_atomic_number_Z>[0-9.]+)",)
- ]
- )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_system': CachingLvl
- }
- cachingLevelForMetaName["x_wien2k_system_nameIn"] = CachingLevel.ForwardAndCache
- cachingLevelForMetaName["x_wien2k_section_equiv_atoms"] = CachingLevel.ForwardAndCache
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct_old.py b/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct_old.py
deleted file mode 100644
index fb10a7e..0000000
--- a/parser/parser-wien2k/wien2k_parser_backups/wien2k_parser_struct_old.py
+++ /dev/null
@@ -1,66 +0,0 @@
-from builtins import object
-import setup_paths
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json
-
-class Wien2kStructContext(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
-
-# description of the input
-def buildStructureMatchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_system"],
- subMatchers = [
- SM(name = 'systemName',
- startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
- SM(r"\w+\s*LATTICE,NONEQUIV\.ATOMS:\s*(?P<x_wien2k_nonequiv_atoms>[0-9]+)"),
- SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
- repeats=True,
- sections=["x_wien2k_section_equiv_atoms"],
- subMatchers=[
- SM(r"\s*[-0-9]+:\s*X=(?P<x_wien2k_atom_pos_x>[-+0-9.eEdD]+)\s*Y=(?P<x_wien2k_atom_pos_y>[-+0-9.eEdD]+)\s*Z=(?P<x_wien2k_atom_pos_z>[-+0-9.eEdD]+)",
- repeats=True
- )
- ]
- )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_system': CachingLvl
- }
- cachingLevelForMetaName["x_wien2k_system_nameIn"] = CachingLevel.ForwardAndCache
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
--
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