fixed problem with atom_positions

parser/parser-exciting/exciting_parser_input.py

+import xml.sax
+import logging
+
+class InputHandler(xml.sax.handler.ContentHandler):
+    def __init__(self, backend):
+        self.backend = backend
+        self.inputSectionGIndex = -1
+        self.inInput = False
+
+    def endDocument(self):
+        pass
+
+    def startElement(self, name, attrs):
+        if name == "structure":
+            self.inputSectionGIndex = self.backend.openSection("section_system")
+            self.inInput = True
+        elif name == "atom" and self.inInput:
+            g = attrs.getValue('coord')
+            print ("coord=", g)
+#            self.backend.addValue("atom_positions",float(attrs.getValue('coord')))
+#            self.backend.addValue("x_exciting_dos_energy",float(attrs.getValue('e')))
+        # attrDict={}
+        # for name in attrs.getNames():
+        #     attrDict[name] = attrs.getValue(name)
+        # logging.error("start element %s attr %s", name, attrDict)
+
+    def endElement(self, name):
+        if name == 'structure':
+            self.inInput = False
+            self.backend.closeSection("section_system",self.inputSectionGIndex)
+            self.inputSectionGIndex = -1
+        # logging.error("end element %s", name)
+
+#    def startElementNS(self, name, qname, attrs):
+#        attrDict={}
+#        for name in attrs.getNames():
+#            attrDict[name] = attrs.getValue(name)
+#        logging.error("start element %s ns %s attr %s", name, qname, attrDict)
+
+#    def endElementNS(self, name, qname):
+#        logging.error("end element %s ns %s", name, qname)
+
+#    def characters(self, content):
+#        pass
+
+def parseInput(inF, backend):
+    handler = InputHandler(backend)
+    logging.error("will parse")
+    xml.sax.parse(inF, handler)
+    logging.error("did parse")

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
+import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_input
 
 class ExcitingParserContext(object):
 
@@ -56,6 +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")
+############# 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(dosFile):
       with open(dosFile) as f:
         exciting_parser_dos.parseDos(f, backend)
@@ -169,7 +174,14 @@ class ExcitingParserContext(object):
       backend.addArrayValues("x_exciting_atom_forces",np.asarray(f_st))      
 
   def onClose_section_system(self, backend, gIndex, section):
+#    dirPath = os.path.dirname(self.parser.fIn.name)
     backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
+#    inputFile = os.path.join(dirPath, "input.xml")
+############# reading input file ##############
+#    if os.path.exists(inputFile):
+#      with open(inputFile) as f:
+#        exciting_parser_input.parseInput(f, backend)
+
 
 mainFileDescription = \
     SM(name = "root matcher",