fixed bug with atomic positions

parser/parser-exciting/parser_exciting.py

@@ -5,7 +5,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 from nomadcore.caching_backend import CachingLevel
 from nomadcore.unit_conversion import unit_conversion
-import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_input
+import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure #, exciting_parser_input
 
 class ExcitingParserContext(object):
 
@@ -56,11 +56,11 @@ class ExcitingParserContext(object):
     bandFile = os.path.join(dirPath, "bandstructure.xml")
     eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
     fermiSurfFile = os.path.join(dirPath, "FERMISURF.bxsf")
-    inputFile = os.path.join(dirPath, "input.xml")
+#    inputFile = os.path.join(dirPath, "input.xml")
 ############# reading input file for atom positions##############
-    if os.path.exists(inputFile):
-      with open(inputFile) as f:
-        exciting_parser_input.parseInput(f, backend)
+#    if os.path.exists(inputFile):
+#      with open(inputFile) as f:
+#        exciting_parser_input.parseInput(f, backend)
     if os.path.exists(dosFile):
       with open(dosFile) as f:
         exciting_parser_dos.parseDos(f, backend)
@@ -187,7 +187,19 @@ class ExcitingParserContext(object):
 #    if os.path.exists(inputFile):
 #      with open(inputFile) as f:
 #        exciting_parser_input.parseInput(f, backend)
+    self.secSystemDescriptionIndex = gIndex
 
+    atom_pos = []
+    for i in ['x', 'y', 'z']:
+       api = section['x_exciting_geometry_atom_positions_' + i]
+       if api is not None:
+          atom_pos.append(api)
+    if atom_pos:
+       backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
+#       print("atom_positions==",atom_pos)
+    atom_labels = section['x_exciting_geometry_atom_labels']
+    if atom_labels is not None:
+       backend.addArrayValues('atom_labels', np.asarray(atom_labels))
 
 mainFileDescription = \
     SM(name = "root matcher",