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Merge master branch into stub

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2021-04-15 20:12:36 +02:00
parent a0699dde4c 06ba3b2726
commit 78e6e5c773
6 changed files with 60 additions and 49 deletions
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65
src/force.c
View File

@@ -40,9 +40,8 @@ double computeForce(
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT S, E;
double S, E;
S = getTimeStamp();
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
@@ -50,49 +49,47 @@ double computeForce(
}
if(profile) {
LIKWID_MARKER_START("force");
// LIKWID_MARKER_START("force");
}
for(int t = 0; t < ntimes; t++) {
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
// printf("%d: %d\n", i, numneighs);
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
}
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
}
if(profile) {
LIKWID_MARKER_STOP("force");
// LIKWID_MARKER_STOP("force");
}
E = getTimeStamp();
return E-S;
return 0.0;
}

26
src/main-stub.c
View File

@@ -158,11 +158,17 @@ int main(int argc, const char *argv[]) {
}
}
const double estim_volume = (double)(atom->Nlocal * 6 * sizeof(MD_FLOAT) + atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0;
const double estim_volume = (double)
(atom->Nlocal * 6 * sizeof(MD_FLOAT) +
atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0;
printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz);
printf("Atoms per unit cell: %d\n", atoms_per_unit_cell);
printf("Total number of atoms: %d\n", atom->Nlocal);
printf("Estimated memory volume (kB): %.4f\n", estim_volume);
printf("Estimated total data volume (kB): %.4f\n", estim_volume );
printf("Estimated atom data volume (kB): %.4f\n",
(double)(atom->Nlocal * 3 * sizeof(MD_FLOAT) / 1000.0));
printf("Estimated neighborlist data volume (kB): %.4f\n",
(double)(atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0);
DEBUG("Initializing neighbor lists...\n");
initNeighbor(&neighbor, &param);
@@ -171,10 +177,20 @@ int main(int argc, const char *argv[]) {
DEBUG("Building neighbor lists...\n");
buildNeighbor(atom, &neighbor);
DEBUG("Computing forces...\n");
computeForce(&param, atom, &neighbor, 0, 1);
computeForce(&param, atom, &neighbor, 0);
double T_accum = computeForce(&param, atom, &neighbor, 1, param.ntimes);
printf("Total time: %.4f, Time/force: %.4f\n", T_accum, T_accum / param.ntimes);
double S, E;
S = getTimeStamp();
LIKWID_MARKER_START("force");
for(int i = 0; i < param.ntimes; i++) {
computeForce(&param, atom, &neighbor, 1);
}
LIKWID_MARKER_STOP("force");
E = getTimeStamp();
double T_accum = E-S;
printf("Total time: %.4f, Mega atom updates/s: %.4f\n",
T_accum, atom->Nlocal * param.ntimes/T_accum/1.E6);
LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS;
}