Fix atom sorting

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

Makefile

@@ -30,6 +30,10 @@ ifneq ($(ASM_SYNTAX), ATT)
     ASFLAGS += -masm=intel
 endif
 
+ifeq ($(strip $(SORT_ATOMS)),true)
+    DEFINES += -DSORT_ATOMS
+endif
+
 ifeq ($(strip $(EXPLICIT_TYPES)),true)
     DEFINES += -DEXPLICIT_TYPES
 endif

common/parameter.c

@@ -169,6 +169,11 @@ void printParameter(Parameter *param) {
     printf("\tNumber of timesteps: %d\n", param->ntimes);
     printf("\tReport stats every (timesteps): %d\n", param->nstat);
     printf("\tReneighbor every (timesteps): %d\n", param->reneigh_every);
+    #ifdef SORT_ATOMS
+    printf("\tSort atoms when reneighboring: yes\n");
+    #else
+    printf("\tSort atoms when reneighboring: no\n");
+    #endif
     printf("\tPrune every (timesteps): %d\n", param->prune_every);
     printf("\tOutput positions every (timesteps): %d\n", param->x_out_every);
     printf("\tOutput velocities every (timesteps): %d\n", param->v_out_every);

lammps/main.c

@@ -63,6 +63,10 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *
     setupNeighbor(param);
     setupThermo(param, atom->Natoms);
     if(param->input_file == NULL) { adjustThermo(param, atom); }
+    #ifdef SORT_ATOMS
+    atom->Nghost = 0;
+    sortAtom(atom);
+    #endif
     setupPbc(atom, param);
     initDevice(atom, neighbor);
     updatePbc(atom, param, true);
@@ -76,9 +80,12 @@ double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
     S = getTimeStamp();
     LIKWID_MARKER_START("reneighbour");
     updateAtomsPbc(atom, param);
+    #ifdef SORT_ATOMS
+    atom->Nghost = 0;
+    sortAtom(atom);
+    #endif
     setupPbc(atom, param);
     updatePbc(atom, param, true);
-    //sortAtom(atom);
     buildNeighbor(atom, neighbor);
     LIKWID_MARKER_STOP("reneighbour");
     E = getTimeStamp();