nexus: more species querying support

git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6575 e5b18d87-469d-4833-9cc0-8cdfa06e9491

nexus/library/physical_system.py

@@ -562,6 +562,19 @@ class PhysicalSystem(Matter):
         #end for
         return elem
     #end def large_Zeff_elem
+
+
+    def ae_pp_species(self):
+        species = set(self.structure.elem)
+        if self.pseudized:
+            pp_species = set(self.valency.keys())
+            ae_species = species-pp_species
+        else:
+            pp_species = set()
+            ae_species = species
+        #end if
+        return ae_species,pp_species
+    #end def ae_pp_species
 #end class PhysicalSystem
 
 

nexus/library/structure.py

@@ -1187,6 +1187,36 @@ class Structure(Sobj):
         #end if
     #end def species
 
+        
+    def ordered_species(self,symbol=False):
+        speclab_set    = set()
+        species_labels = []
+        if not symbol:
+            for e in self.elem:
+                if e not in speclab_set:
+                    speclab_set.add(e)
+                    species_labels.append(e)
+                #end if
+            #end for
+            return species_labels
+        else:
+            species  = []
+            spec_set = set()
+            for e in self.elem:
+                is_elem,symbol = is_element(e,symbol=True)
+                if e not in speclab_set:
+                    speclab_set.add(e)
+                    species_labels.append(e)
+                #end if
+                if symbol not in spec_set:
+                    spec_set.add(symbol)
+                    species.append(symbol)
+                #end if
+            #end for
+            return species_labels,species
+        #end if
+    #end def ordered_species
+
 
     def order_by_species(self,folded=False):
         species        = []