wien2k: updates and parsing charge distances between two interations

parser/parser-wien2k/wien2k_parser.py

@@ -121,10 +121,10 @@ mainFileDescription = SM(
                       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":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<x_wien2k_total_ene>[-+0-9.]+)"),
+                      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)
-
+                      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),
+                      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.]+)")
                   ]
               )
            ]

parser/parser-wien2k/wien2k_parser_struct.py

@@ -3,7 +3,8 @@ 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
+import os, sys, json, logging
+import numpy as np
 
 class Wien2kStructContext(object):
     """context for wien2k struct parser"""
@@ -21,6 +22,25 @@ class Wien2kStructContext(object):
         # 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"]
+            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():
@@ -66,6 +86,7 @@ def get_cachingLevelForMetaName(metaInfoEnv, 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

src/main/scala/eu/nomad_lab/parsers/Wien2kParser.scala

@@ -30,6 +30,8 @@ object Wien2kParser extends SimpleExternalParserGenerator(
     "parser-wien2k/wien2k_parser_in0.py",
     "parser-wien2k/wien2k_parser_in1c.py",
     "parser-wien2k/wien2k_parser_in2c.py",
+    "parser-wien2k/wien2k_parser_in1.py",
+    "parser-wien2k/wien2k_parser_in2.py",
     "parser-wien2k/wien2k_parser_struct.py",
     "parser-wien2k/setup_paths.py",
     "nomad_meta_info/public.nomadmetainfo.json",