Remove segfaults

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

gromacs/includes/atom.h

@@ -61,7 +61,7 @@ extern int readAtom(Atom*, Parameter*);
 extern void growAtom(Atom*);
 extern void growClusters(Atom*);
 
-#define cluster_ptr(ci)     &(atom->cl_x[ci * CLUSTER_DIM_N * 3])
+#define cluster_ptr(ci)     &(atom->cl_x[(ci) * CLUSTER_DIM_N * 3])
 
 #ifdef AOS
 #define POS_DATA_LAYOUT     "AoS"

gromacs/neighbor.c

@@ -102,11 +102,6 @@ void setupNeighbor(Parameter *param, Atom *atom) {
     bininvx = 1.0 / binsizex;
     bininvy = 1.0 / binsizey;
 
-    printf("hi = %f, %f\n", xhi, yhi);
-    printf("atom_density = %f\n", atom_density);
-    printf("atoms_in_cell = %f\n", atoms_in_cell);
-    printf("binsize = %f, %f\n", binsizex, binsizey);
-    printf("nbin = %d, %d\n", nbinx, nbiny);
     coord = xlo - cutneigh - SMALL * xprd;
     mbinxlo = (int) (coord * bininvx);
     if (coord < 0.0) {
@@ -207,7 +202,6 @@ int atomDistanceInRange(Atom *atom, int ci, int cj, MD_FLOAT rsq) {
 }
 
 void buildNeighbor(Atom *atom, Neighbor *neighbor) {
-    printf("buildNeighbor start\n");
     int nall = atom->Nclusters_local + atom->Nclusters_ghost;
 
     /* extend atom arrays if necessary */
@@ -272,7 +266,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
             }
 
             neighbor->numneigh[ci] = n;
-
             if(n >= neighbor->maxneighs) {
                 resize = 1;
 
@@ -289,7 +282,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
             neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int));
         }
     }
-    printf("buildNeighbor end\n");
 }
 
 /* internal subroutines */
@@ -356,7 +348,6 @@ void coord2bin2D(MD_FLOAT xin, MD_FLOAT yin, int *ix, int *iy) {
 }
 
 void binAtoms(Atom *atom) {
-    printf("binatoms start\n");
     int nall = atom->Nlocal + atom->Nghost;
     int resize = 1;
 
@@ -369,7 +360,6 @@ void binAtoms(Atom *atom) {
 
         for(int i = 0; i < nall; i++) {
             int ibin = coord2bin(atom_x(i), atom_y(i));
-
             if(bincount[ibin] < atoms_per_bin) {
                 int ac = bincount[ibin]++;
                 bins[ibin * atoms_per_bin + ac] = i;
@@ -384,7 +374,6 @@ void binAtoms(Atom *atom) {
             bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
         }
     }
-    printf("binatoms end\n");
 }
 
 // TODO: Use pigeonhole sorting
@@ -416,7 +405,6 @@ void sortAtomsByZCoord(Atom *atom) {
 }
 
 void buildClusters(Atom *atom) {
-    printf("buildClusters start\n");
     atom->Nclusters_local = 0;
 
     /* bin local atoms */
@@ -480,12 +468,9 @@ void buildClusters(Atom *atom) {
             atom->Nclusters_local++;
         }
     }
-
-    printf("buildClusters end\n");
 }
 
 void binClusters(Atom *atom) {
-    printf("binClusters start\n");
     const int nlocal = atom->Nclusters_local;
     int resize = 1;
 
@@ -496,7 +481,6 @@ void binClusters(Atom *atom) {
             cluster_bincount[bin] = 0;
         }
 
-        printf("local\n");
         for(int ci = 0; ci < nlocal && !resize; ci++) {
             int bin = atom->clusters[ci].bin;
             int c = cluster_bincount[bin];
@@ -508,7 +492,6 @@ void binClusters(Atom *atom) {
             }
         }
 
-        printf("ghost\n");
         for(int ci = 0; ci < atom->Nclusters_ghost && !resize; ci++) {
             MD_FLOAT *cptr = cluster_ptr(nlocal + ci);
             MD_FLOAT xtmp, ytmp;
@@ -517,12 +500,15 @@ void binClusters(Atom *atom) {
             xtmp = cluster_x(cptr, 0);
             ytmp = cluster_y(cptr, 0);
             coord2bin2D(xtmp, ytmp, &ix, &iy);
-
+            ix = MAX(MIN(ix, nbinx - 1), 0);
+            iy = MAX(MIN(iy, nbiny - 1), 0);
             for(int cii = 1; cii < atom->clusters[ci].natoms; cii++) {
                 int nix, niy;
                 xtmp = cluster_x(cptr, cii);
                 ytmp = cluster_y(cptr, cii);
                 coord2bin2D(xtmp, ytmp, &nix, &niy);
+                nix = MAX(MIN(nix, nbinx - 1), 0);
+                niy = MAX(MIN(niy, nbiny - 1), 0);
                 // Always put the cluster on the bin of its innermost atom so
                 // the cluster should be closer to local clusters
                 if(atom->PBCx[ci] > 0 && ix > nix) { ix = nix; }
@@ -541,15 +527,12 @@ void binClusters(Atom *atom) {
             }
         }
 
-        printf("end\n");
         if(resize) {
             free(cluster_bins);
             clusters_per_bin *= 2;
             cluster_bins = (int*) malloc(mbins * clusters_per_bin * sizeof(int));
         }
     }
-
-    printf("binClusters end\n");
 }
 
 void updateSingleAtoms(Atom *atom) {

gromacs/pbc.c

@@ -44,7 +44,6 @@ void initPbc(Atom* atom) {
 /* update coordinates of ghost atoms */
 /* uses mapping created in setupPbc */
 void updatePbc(Atom *atom, Parameter *param) {
-    printf("updatePbc start\n");
     int *border_map = atom->border_map;
     int nlocal = atom->Nclusters_local;
     MD_FLOAT xprd = param->xprd;
@@ -61,13 +60,11 @@ void updatePbc(Atom *atom, Parameter *param) {
             cluster_z(cptr, cii) = cluster_z(bmap_cptr, cii) + atom->PBCz[ci] * zprd;
         }
     }
-    printf("updatePbc end\n");
 }
 
 /* relocate atoms that have left domain according
  * to periodic boundary conditions */
 void updateAtomsPbc(Atom *atom, Parameter *param) {
-    printf("updateAtomsPbc start\n");
     MD_FLOAT xprd = param->xprd;
     MD_FLOAT yprd = param->yprd;
     MD_FLOAT zprd = param->zprd;
@@ -91,7 +88,6 @@ void updateAtomsPbc(Atom *atom, Parameter *param) {
             atom_z(i) -= zprd;
         }
     }
-    printf("updateAtomsPbc end\n");
 }
 
 /* setup periodic boundary conditions by
@@ -124,7 +120,6 @@ void growPbc(Atom* atom) {
 }
 
 void setupPbc(Atom *atom, Parameter *param) {
-    printf("setupPbc start\n");
     int *border_map = atom->border_map;
     MD_FLOAT xprd = param->xprd;
     MD_FLOAT yprd = param->yprd;