Neighbor list preparation

gromacs/includes/atom.h

@@ -149,7 +149,6 @@ typedef struct {
 } Cluster;
 
 typedef struct {
-    //int *iclusters;
     int nclusters;
     MD_FLOAT bbminx, bbmaxx;
     MD_FLOAT bbminy, bbmaxy;

gromacs/includes/pbc.h

@@ -16,5 +16,8 @@ extern void setupPbc(Atom*, Parameter*);
 
 #ifdef CUDA_TARGET
 extern void cudaUpdatePbc(Atom*, Parameter*, int);
+#if defined(USE_SUPER_CLUSTERS)
+extern void setupPbcGPU(Atom*, Parameter*);
+#endif //defined(USE_SUPER_CLUSTERS)
 #endif
 #endif

gromacs/includes/utils.h

@@ -6,12 +6,14 @@
 #define MD_BENCH_UTILS_H
 
 #include <atom.h>
+#include <neighbor.h>
 
 #ifdef USE_SUPER_CLUSTERS
 void verifyClusters(Atom *atom);
 void verifyLayout(Atom *atom);
 void checkAlignment(Atom *atom);
 void showSuperclusters(Atom *atom);
+void printNeighs(Atom *atom, Neighbor *neighbor);
 #endif //USE_SUPER_CLUSTERS
 
 #endif //MD_BENCH_UTILS_H