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Remove segfaults

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-01-28 15:18:54 +01:00
parent a119fcdfdd
commit eedcc97e4a
3 changed files with 5 additions and 27 deletions
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2
gromacs/includes/atom.h
View File

@ -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"

25
gromacs/neighbor.c
View File

@ -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) {

5
gromacs/pbc.c
View File

@ -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;