Moved null.dx into 'potentials' directory

mrdna/model/arbdmodel.py

@@ -733,7 +733,7 @@ class ArbdModel(PdbModel):
 
     def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000):
         ## TODO: save and reference directories and prefixes using member data
-        d = "potentials"
+        d = self.potential_directory = "potentials"
         if not os.path.exists(d):
             os.makedirs(d)
         self._bond_filename = "%s/%s.bonds.txt" % (d, prefix)
@@ -834,7 +834,7 @@ diffusion {diffusivity}
                     fh.write("gridFileScale {}\n".format(gridFileScale))
 
                 else:
-                    fh.write("gridFile null.dx\n")
+                    fh.write("gridFile {}/null.dx\n".format(self.potential_directory))
 
             ## Write coordinates and interactions
             fh.write("""
@@ -876,7 +876,8 @@ tabulatedPotential  1
         write_null_dx = False
         for pt,num in self.getParticleTypesAndCounts():
             if "grid" not in pt.__dict__: 
-                with open("null.dx",'w') as fh:
+                gridfile = "{}/null.dx".format(self.potential_directory)
+                with open(gridfile, 'w') as fh:
                     fh.write("""object 1 class gridpositions counts  2 2 2
 origin {originX} {originY} {originZ}
 delta  {dimX} 0.000000 0.000000