(1) xml file

    If we have 'LoadCmd: loading from *' in *.r file, we first search for this file and give a warning:
       " This output showed this calculation need to load xml file, so we need this xml file ('../si2gs/test.xml') to read geometry information"

      If this file exit, we will parser this file with QboxXMLParser.py,
      else we give another warning:
         " Could not find xml file in directory *."

(2) We add LDA default by open qbox_section_functionals at header part,

    So when grep 'qbox_section_functionals' out, we could get:
    4 times when we have 'set xc PBE' in *.r file
    2 times when we do not have 'set xc' in *.r file