moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Inline getBoundingBoxDistanceSq and avoid redundant loads from bbminz and bbmaxz

Browse Source 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-07 18:00:21 +01:00
parent cdb1d5b9f1
commit 0eacb2453e
1 changed files with 58 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

63
gromacs/neighbor.c
View File

@ -91,8 +91,8 @@ void setupNeighbor(Parameter *param, Atom *atom) {
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = zprd;
MD_FLOAT atom_density = ((MD_FLOAT)(atom->Nlocal)) / ((xhi - xlo) * (yhi - ylo) * (zhi - zlo));
//MD_FLOAT atoms_in_cell = MAX(CLUSTER_DIM_M, CLUSTER_DIM_N);
MD_FLOAT atoms_in_cell = CLUSTER_DIM_M;
MD_FLOAT atoms_in_cell = MAX(CLUSTER_DIM_M, CLUSTER_DIM_N);
//MD_FLOAT atoms_in_cell = CLUSTER_DIM_M;
binsizex = cbrt(atoms_in_cell / atom_density);
binsizey = cbrt(atoms_in_cell / atom_density);
cutneighsq = cutneigh * cutneigh;
@ -230,6 +230,10 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
int* neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
int n = 0;
int ibin = atom->clusters[ci].bin;
MD_FLOAT ibb_xmin = atom->clusters[ci].bbminx;
MD_FLOAT ibb_xmax = atom->clusters[ci].bbmaxx;
MD_FLOAT ibb_ymin = atom->clusters[ci].bbminy;
MD_FLOAT ibb_ymax = atom->clusters[ci].bbmaxy;
MD_FLOAT ibb_zmin = atom->clusters[ci].bbminz;
MD_FLOAT ibb_zmax = atom->clusters[ci].bbmaxz;
@ -237,13 +241,17 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
int jbin = ibin + stencil[k];
int *loc_bin = &cluster_bins[jbin * clusters_per_bin];
int cj, m = -1;
MD_FLOAT jbb_zmin, jbb_zmax;
MD_FLOAT jbb_xmin, jbb_xmax, jbb_ymin, jbb_ymax, jbb_zmin, jbb_zmax;
const int c = cluster_bincount[jbin];
if(c > 0) {
//do {
m++;
cj = loc_bin[m];
jbb_xmin = atom->clusters[cj].bbminx;
jbb_xmax = atom->clusters[cj].bbmaxx;
jbb_ymin = atom->clusters[cj].bbminy;
jbb_ymax = atom->clusters[cj].bbmaxy;
jbb_zmin = atom->clusters[cj].bbminz;
jbb_zmax = atom->clusters[cj].bbmaxz;
//} while(m + 1 < c && (ibb_zmin - jbb_zmax) * (ibb_zmin - jbb_zmax) > cutneighsq);
@ -253,7 +261,24 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
break;
}*/
double d_bb_sq = getBoundingBoxDistanceSq(atom, ci, cj);
MD_FLOAT dl = ibb_xmin - jbb_xmax;
MD_FLOAT dh = jbb_xmin - ibb_xmax;
MD_FLOAT dm = MAX(dl, dh);
MD_FLOAT dm0 = MAX(dm, 0.0);
MD_FLOAT d_bb_sq = dm0 * dm0;
dl = ibb_ymin - jbb_ymax;
dh = jbb_ymin - ibb_ymax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq += dm0 * dm0;
dl = ibb_zmin - jbb_zmax;
dh = jbb_zmin - ibb_zmax;
dm = MAX(dl, dh);
dm0 = MAX(dm, 0.0);
d_bb_sq += dm0 * dm0;
if(d_bb_sq < cutneighsq) {
if(d_bb_sq < rbb_sq || atomDistanceInRange(atom, ci, cj, cutneighsq)) {
neighptr[n++] = cj;
@ -263,6 +288,10 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
m++;
if(m < c) {
cj = loc_bin[m];
jbb_xmin = atom->clusters[cj].bbminx;
jbb_xmax = atom->clusters[cj].bbmaxx;
jbb_ymin = atom->clusters[cj].bbminy;
jbb_ymax = atom->clusters[cj].bbmaxy;
jbb_zmin = atom->clusters[cj].bbminz;
jbb_zmax = atom->clusters[cj].bbmaxz;
}
@ -583,6 +612,7 @@ void binClusters(Atom *atom) {
for(int cg = 0; cg < atom->Nclusters_ghost && !resize; cg++) {
const int ci = nlocal + cg;
MD_FLOAT *cptr = cluster_pos_ptr(ci);
MD_FLOAT ci_minz = atom->clusters[ci].bbminz;
MD_FLOAT xtmp, ytmp;
int ix = -1, iy = -1;
@ -598,6 +628,7 @@ void binClusters(Atom *atom) {
coord2bin2D(xtmp, ytmp, &nix, &niy);
nix = MAX(MIN(nix, mbinx - 1), 0);
niy = MAX(MIN(niy, mbiny - 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[cg] > 0 && ix > nix) { ix = nix; }
@ -609,8 +640,30 @@ void binClusters(Atom *atom) {
int bin = iy * mbinx + ix + 1;
int c = cluster_bincount[bin];
if(c < clusters_per_bin) {
// Insert the current ghost cluster in the bin keeping clusters
// sorted by z coordinate
int inserted = 0;
for(int i = 0; i < c; i++) {
int last_cl = cluster_bins[bin * clusters_per_bin + i];
if(atom->clusters[last_cl].bbminz > ci_minz) {
cluster_bins[bin * clusters_per_bin + i] = ci;
for(int j = i + 1; j <= c; j++) {
int tmp = cluster_bins[bin * clusters_per_bin + j];
cluster_bins[bin * clusters_per_bin + j] = last_cl;
last_cl = tmp;
}
inserted = 1;
break;
}
}
if(!inserted) {
cluster_bins[bin * clusters_per_bin + c] = ci;
}
atom->clusters[ci].bin = bin;
cluster_bins[bin * clusters_per_bin + c] = ci;
cluster_bincount[bin]++;
} else {
resize = 1;