Add first working version with 4x8 config (ref kernel)

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>

gromacs/includes/atom.h

@@ -117,6 +117,7 @@ typedef struct {
     int *cl_type;
     Cluster *iclusters, *jclusters;
     int *icluster_bin;
+    int dummy_cj;
 } Atom;
 
 extern void initAtom(Atom*);

gromacs/includes/neighbor.h

@@ -40,6 +40,7 @@ extern void buildNeighbor(Atom*, Neighbor*);
 extern void pruneNeighbor(Parameter*, Atom*, Neighbor*);
 extern void sortAtom(Atom*);
 extern void buildClusters(Atom*);
+extern void defineJClusters(Atom*);
 extern void binClusters(Atom*);
 extern void updateSingleAtoms(Atom*);
 #endif