Fix to productpotential

mrdna/arbdmodel/__init__.py

@@ -157,9 +157,9 @@ class Parent():
         # for b in (i,j): assert(b in beads)
         self.bond_angles.append( (i,j,k,l, bond_angle) )
 
-    def add_product_potential_angle(self, potential_list):
+    def add_product_potential(self, potential_list):
         """ potential_list: list of tuples of form (particle_i, particle_j,..., TabulatedPotential) """
-        if len(terms) < 2: raise ValueError("Too few potentials")
+        if len(potential_list) < 2: raise ValueError("Too few potentials")
         for elem in potential_list:
             beads = elem[:-1]
             pot = elem[-1]
@@ -1272,20 +1272,23 @@ component "data" value 3
     def _writeArbdProductPotentialFile( self ):
         if len(self.product_potentials) > 0:
             with open(self._product_potential_filename,'w') as fh:
-                for ijk_tb in self.get_product_potentials():
-                    ijk = ijk_b[:-1]
+                for pot in self.get_product_potentials():
+                    line = "PRODUCTPOTENTIAL "
+                    for ijk_tb in pot:
+                        ijk = ijk_tb[:-1]
                         tb = ijk_tb[-1]
-                    if not (type(tb) is tuple or type(tb) is list):
+                        if type(tb) is tuple or type(tb) is list:
                             if len(tb) != 2: raise ValueError("Invalid product potential")
                             type_,b = tb
                             if type(type_) is not str: raise ValueError("Invalid product potential: unrecognized specification of potential type")
                         else:
                             type_ = ""
                             b = tb
-
                         if type(b) is not str and not isinstance(b, Path):
                             b.write_file()
-                    fh.write("PRODUCTPOTENTIAL "+" ".join([str(x) for x in ijk+[type_,b] if x != ""]))
+                        line = line+" ".join([str(x.idx) for x in ijk])+" "
+                        line = line+" ".join([str(x) for x in [type_,b] if x != ""])+" "
+                    fh.write(line)
 
 
     def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):