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Adjust kernels to work with MxN loops

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-02 00:49:55 +01:00
parent 85e7954932
commit 5fd2d422ee
2 changed files with 11 additions and 5 deletions
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4
gromacs/force_lj.c
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@ -61,7 +61,7 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
for(int k = 0; k < numneighs; k++) { for(int k = 0; k < numneighs; k++) {
int cj = neighs[k]; int cj = neighs[k];
MD_FLOAT *cjptr = cluster_pos_ptr(cj); MD_FLOAT *cjptr = cluster_pos_ptr(cj);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) { for(int cii = 0; cii < CLUSTER_DIM_M; cii++) {
MD_FLOAT xtmp = cluster_x(ciptr, cii); MD_FLOAT xtmp = cluster_x(ciptr, cii);
MD_FLOAT ytmp = cluster_y(ciptr, cii); MD_FLOAT ytmp = cluster_y(ciptr, cii);
MD_FLOAT ztmp = cluster_z(ciptr, cii); MD_FLOAT ztmp = cluster_z(ciptr, cii);
@ -69,7 +69,7 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
MD_FLOAT fiy = 0; MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0; MD_FLOAT fiz = 0;
for(int cjj = 0; cjj < atom->clusters[cj].natoms; cjj++) { for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) {
if(ci != cj || cii != cjj) { if(ci != cj || cii != cjj) {
MD_FLOAT delx = xtmp - cluster_x(cjptr, cjj); MD_FLOAT delx = xtmp - cluster_x(cjptr, cjj);
MD_FLOAT dely = ytmp - cluster_y(cjptr, cjj); MD_FLOAT dely = ytmp - cluster_y(cjptr, cjj);

12
gromacs/pbc.c
View File

@ -44,7 +44,7 @@ void initPbc(Atom* atom) {
/* update coordinates of ghost atoms */ /* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */ /* uses mapping created in setupPbc */
void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) { void updatePbc(Atom *atom, Parameter *param, int firstUpdate) {
int *border_map = atom->border_map; int *border_map = atom->border_map;
int nlocal = atom->Nclusters_local; int nlocal = atom->Nclusters_local;
MD_FLOAT xprd = param->xprd; MD_FLOAT xprd = param->xprd;
@ -68,7 +68,7 @@ void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) {
cluster_y(cptr, cii) = ytmp; cluster_y(cptr, cii) = ytmp;
cluster_z(cptr, cii) = ztmp; cluster_z(cptr, cii) = ztmp;
if(updateBoundingBoxes) { if(firstUpdate) {
// TODO: To create the bounding boxes faster, we can use SIMD operations // TODO: To create the bounding boxes faster, we can use SIMD operations
if(bbminx > xtmp) { bbminx = xtmp; } if(bbminx > xtmp) { bbminx = xtmp; }
if(bbmaxx < xtmp) { bbmaxx = xtmp; } if(bbmaxx < xtmp) { bbmaxx = xtmp; }
@ -79,7 +79,13 @@ void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) {
} }
} }
if(updateBoundingBoxes) { if(firstUpdate) {
for(int cii = atom->clusters[ci].natoms; cii < CLUSTER_DIM_M; cii++) {
cluster_x(cptr, cii) = INFINITY;
cluster_y(cptr, cii) = INFINITY;
cluster_z(cptr, cii) = INFINITY;
}
atom->clusters[ci].bbminx = bbminx; atom->clusters[ci].bbminx = bbminx;
atom->clusters[ci].bbmaxx = bbmaxx; atom->clusters[ci].bbmaxx = bbmaxx;
atom->clusters[ci].bbminy = bbminy; atom->clusters[ci].bbminy = bbminy;