Fixed some issues with formatting, the band tructure parser is currently...

Fixed some issues with formatting, the band tructure parser is currently disabled and the 'debug' mode is enabled in parser_exciting.py

parser/parser-exciting/exciting_parser_bandstructure.py

@@ -14,9 +14,9 @@ class BandHandler(xml.sax.handler.ContentHandler):
         if name == "bandstructure":
             self.bandSectionGIndex = self.backend.openSection("x_exciting_section_bandstructure")
             self.inBand = True
-        elif name == "point" and self.inBand:
-            self.backend.addValue("x_exciting_band_value",float(attrs.getValue('eval')))
-            self.backend.addValue("x_exciting_band_k",float(attrs.getValue('distance')))
+        # elif name == "point" and self.inBand:
+            # self.backend.addValue("x_exciting_band_value",float(attrs.getValue('eval')))
+            # self.backend.addValue("x_exciting_band_k",float(attrs.getValue('distance')))
         # attrDict={}
         # for name in attrs.getNames():
         #     attrDict[name] = attrs.getValue(name)

parser/parser-exciting/parser_exciting.py

@@ -5,6 +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
+from nomadcore.local_backend import LocalBackend
 import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_input
 
 class ExcitingParserContext(object):
@@ -18,19 +19,19 @@ class ExcitingParserContext(object):
     latticeX = section["x_exciting_geometry_lattice_vector_x"]
     latticeY = section["x_exciting_geometry_lattice_vector_y"]
     latticeZ = section["x_exciting_geometry_lattice_vector_z"]
-    cell = [[latticeX[0],latticeY[0],latticeZ[0]],
+    cell = np.array([[latticeX[0],latticeY[0],latticeZ[0]],
             [latticeX[1],latticeY[1],latticeZ[1]],
-            [latticeX[2],latticeY[2],latticeZ[2]]]
-    backend.addValue("simulation_cell", cell)
+            [latticeX[2],latticeY[2],latticeZ[2]]])
+    backend.addArrayValues("simulation_cell", cell)
 
   def onClose_x_exciting_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
     recLatticeX = section["x_exciting_geometry_reciprocal_lattice_vector_x"]
     recLatticeY = section["x_exciting_geometry_reciprocal_lattice_vector_y"]
     recLatticeZ = section["x_exciting_geometry_reciprocal_lattice_vector_z"]
-    recCell = [[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
+    recCell = np.array([[recLatticeX[0],recLatticeY[0],recLatticeZ[0]],
             [recLatticeX[1],recLatticeY[1],recLatticeZ[1]],
-            [recLatticeX[2],recLatticeY[2],recLatticeZ[2]]]
-    backend.addValue("x_exciting_simulation_reciprocal_cell", recCell)
+            [recLatticeX[2],recLatticeY[2],recLatticeZ[2]]])
+    backend.addArrayValues("x_exciting_simulation_reciprocal_cell", recCell)
 
   def onClose_x_exciting_section_xc(self, backend, gIndex, section):
     xcNr = section["x_exciting_xc_functional"][0]
@@ -153,7 +154,7 @@ class ExcitingParserContext(object):
             else:
               values[-1].append(float(st[0]))
           elif len(s) < 5 and len(st) == 1:
-            number_of_bands = st[0]  
+            number_of_bands = st[0]
         mesh_size = grid[0]*grid[1]*grid[2]
         origin.append(all_vectors[0])
         vectors.append(all_vectors[1:])
@@ -179,7 +180,7 @@ class ExcitingParserContext(object):
         atom_forces[1].append([])
         for j in range (3,6):
           atom_forces[1][-1].append(float(f_st[i][j]))
-      backend.addArrayValues("x_exciting_atom_forces",np.asarray(f_st))      
+      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)
@@ -195,9 +196,9 @@ class ExcitingParserContext(object):
        backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
     self.atom_pos = []
     if self.atom_labels is not None:
-       backend.addArrayValues('atom_labels', np.asarray(self.atom_labels))
+        backend.addArrayValues('atom_labels', np.asarray(self.atom_labels, dtype=np.str))
     self.atom_labels = []
-    
+
 
   def onClose_x_exciting_section_atoms_group(self, backend, gIndex, section):
     pos = [section['x_exciting_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
@@ -360,7 +361,7 @@ mainFileDescription = \
 #                     SM(r"\s*(?P<x_exciting_store_total_forces>\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)"),
 #                     SM(r"\s*(?P<x_exciting_store_total_forces>\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)")
 #                     SM(r"\s*(?P<x_exciting_store_total_forces>\s*\:+\s*[-\d\.]+\s*[-\d\.]+\s*[-\d\.]+\s*[A-Za-z]+\s*[A-Za-z]+)"),
-#                   ] 
+#                   ]
 #                    )
                    ])
                ]
@@ -393,4 +394,15 @@ cachingLevelForMetaName = {
 if __name__ == "__main__":
 #    for name in metaInfoEnv.infoKinds:
 #        print 'nameo', name
-    mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext())
+
+    # Production
+    # mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext())
+
+    # Debug
+    local_backend = LocalBackend(metaInfoEnv)
+    mainFunction(mainFileDescription, metaInfoEnv, parserInfo, outF=local_backend.fileOut, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ExcitingParserContext(), superBackend=local_backend)
+    results = local_backend.results
+    program_name = results["program_name"]
+    atom_labels = results["atom_labels"]
+    print(program_name)
+    print(atom_labels)