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Add first version of force calculation with cluster scheme

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-01-28 18:07:41 +01:00
parent eedcc97e4a
commit 6691803910
8 changed files with 85 additions and 85 deletions
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8
gromacs/atom.c
View File

@ -45,8 +45,9 @@ void initAtom(Atom *atom)
{
atom->x = NULL; atom->y = NULL; atom->z = NULL;
atom->vx = NULL; atom->vy = NULL; atom->vz = NULL;
atom->fx = NULL; atom->fy = NULL; atom->fz = NULL;
atom->cl_x = NULL;
atom->cl_v = NULL;
atom->cl_f = NULL;
atom->Natoms = 0;
atom->Nlocal = 0;
atom->Nghost = 0;
@ -275,9 +276,6 @@ void growAtom(Atom *atom)
atom->vx = (MD_FLOAT*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vy = (MD_FLOAT*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vz = (MD_FLOAT*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fx = (MD_FLOAT*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fy = (MD_FLOAT*) reallocate(atom->fy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fz = (MD_FLOAT*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int));
}
@ -287,4 +285,6 @@ void growClusters(Atom *atom)
atom->Nclusters_max += DELTA;
atom->clusters = (Cluster*) reallocate(atom->clusters, ALIGNMENT, atom->Nclusters_max * sizeof(Cluster), nold * sizeof(Cluster));
atom->cl_x = (MD_FLOAT*) reallocate(atom->cl_x, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT));
atom->cl_f = (MD_FLOAT*) reallocate(atom->cl_f, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT));
atom->cl_v = (MD_FLOAT*) reallocate(atom->cl_v, ALIGNMENT, atom->Nclusters_max * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT), nold * CLUSTER_DIM_N * 3 * sizeof(MD_FLOAT));
}

4
gromacs/force_eam.c
View File

@ -33,6 +33,7 @@
#include <util.h>
double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbor, Stats *stats) {
/*
if(eam->nmax < atom->Nmax) {
eam->nmax = atom->Nmax;
if(eam->fp != NULL) { free(eam->fp); }
@ -45,9 +46,11 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline;
MD_FLOAT rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; MD_FLOAT rdrho = eam->rdrho;
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot;
*/
double S = getTimeStamp();
LIKWID_MARKER_START("force_eam_fp");
/*
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
@ -207,6 +210,7 @@ double computeForceEam(Eam* eam, Parameter* param, Atom *atom, Neighbor *neighbo
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
*/
LIKWID_MARKER_STOP("force_eam");
double E = getTimeStamp();
return E-S;

84
gromacs/force_lj.c
View File

@ -31,69 +31,61 @@
double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx;
MD_FLOAT* fy = atom->fy;
MD_FLOAT* fz = atom->fz;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *fptr = cluster_force_ptr(ci);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
cluster_x(fptr, cii) = 0.0;
cluster_y(fptr, cii) = 0.0;
cluster_z(fptr, cii) = 0.0;
}
}
double S = getTimeStamp();
LIKWID_MARKER_START("force");
#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);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *ciptr = cluster_pos_ptr(ci);
MD_FLOAT *cifptr = cluster_force_ptr(ci);
neighs = &neighbor->neighbors[ci * neighbor->maxneighs];
int numneighs = neighbor->numneigh[ci];
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;
int cj = neighs[k];
MD_FLOAT *cjptr = cluster_pos_ptr(cj);
for(int cii = 0; cii < CLUSTER_DIM_M; cii++) {
MD_FLOAT xtmp = cluster_x(ciptr, cii);
MD_FLOAT ytmp = cluster_y(ciptr, cii);
MD_FLOAT ztmp = cluster_z(ciptr, cii);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) {
MD_FLOAT delx = xtmp - cluster_x(cjptr, cjj);
MD_FLOAT dely = ytmp - cluster_y(cjptr, cjj);
MD_FLOAT delz = ztmp - cluster_z(cjptr, cjj);
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;
cluster_x(cifptr, cii) += fix;
cluster_y(cifptr, cii) += fiy;
cluster_z(cifptr, cii) += fiz;
}
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}

7
gromacs/includes/atom.h
View File

@ -42,8 +42,9 @@ typedef struct {
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *fx, *fy, *fz;
MD_FLOAT *cl_x;
MD_FLOAT *cl_v;
MD_FLOAT *cl_f;
int *border_map;
int *type;
int ntypes;
@ -61,7 +62,9 @@ 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_pos_ptr(ci) &(atom->cl_x[(ci) * CLUSTER_DIM_N * 3])
#define cluster_velocity_ptr(ci) &(atom->cl_v[(ci) * CLUSTER_DIM_N * 3])
#define cluster_force_ptr(ci) &(atom->cl_f[(ci) * CLUSTER_DIM_N * 3])
#ifdef AOS
#define POS_DATA_LAYOUT "AoS"

49
gromacs/main.c
View File

@ -129,30 +129,33 @@ double reneighbour(
return E-S;
}
void initialIntegrate(Parameter *param, Atom *atom)
{
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
void initialIntegrate(Parameter *param, Atom *atom) {
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *ciptr = cluster_pos_ptr(ci);
MD_FLOAT *civptr = cluster_velocity_ptr(ci);
MD_FLOAT *cifptr = cluster_force_ptr(ci);
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i];
vz[i] += param->dtforce * fz[i];
atom_x(i) = atom_x(i) + param->dt * vx[i];
atom_y(i) = atom_y(i) + param->dt * vy[i];
atom_z(i) = atom_z(i) + param->dt * vz[i];
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
cluster_x(civptr, cii) += param->dtforce * cluster_x(cifptr, cii);
cluster_y(civptr, cii) += param->dtforce * cluster_y(cifptr, cii);
cluster_z(civptr, cii) += param->dtforce * cluster_z(cifptr, cii);
cluster_x(ciptr, cii) += param->dt * cluster_x(civptr, cii);
cluster_y(ciptr, cii) += param->dt * cluster_y(civptr, cii);
cluster_z(ciptr, cii) += param->dt * cluster_z(civptr, cii);
}
}
}
void finalIntegrate(Parameter *param, Atom *atom)
{
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
void finalIntegrate(Parameter *param, Atom *atom) {
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *civptr = cluster_velocity_ptr(ci);
MD_FLOAT *cifptr = cluster_force_ptr(ci);
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i];
vz[i] += param->dtforce * fz[i];
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
cluster_x(civptr, cii) += param->dtforce * cluster_x(cifptr, cii);
cluster_y(civptr, cii) += param->dtforce * cluster_y(cifptr, cii);
cluster_z(civptr, cii) += param->dtforce * cluster_z(cifptr, cii);
}
}
}
@ -257,13 +260,11 @@ int main(int argc, char** argv)
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
/*
if(param.force_field == FF_EAM) {
timer[FORCE] = computeForceEam(&eam, &param, &atom, &neighbor, &stats);
} else {
timer[FORCE] = computeForceLJ(&param, &atom, &neighbor, &stats);
}
*/
timer[NEIGH] = 0.0;
timer[TOTAL] = getTimeStamp();
@ -273,7 +274,7 @@ int main(int argc, char** argv)
}
for(int n = 0; n < param.ntimes; n++) {
//initialIntegrate(&param, &atom);
initialIntegrate(&param, &atom);
if((n + 1) % param.every) {
updatePbc(&atom, &param);
@ -285,15 +286,13 @@ int main(int argc, char** argv)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
/*
if(param.force_field == FF_EAM) {
timer[FORCE] += computeForceEam(&eam, &param, &atom, &neighbor, &stats);
} else {
timer[FORCE] += computeForceLJ(&param, &atom, &neighbor, &stats);
}
*/
//finalIntegrate(&param, &atom);
finalIntegrate(&param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
computeThermo(n + 1, &param, &atom);

10
gromacs/neighbor.c
View File

@ -184,8 +184,8 @@ MD_FLOAT getBoundingBoxDistanceSq(Atom *atom, int ci, int cj) {
}
int atomDistanceInRange(Atom *atom, int ci, int cj, MD_FLOAT rsq) {
MD_FLOAT *ciptr = cluster_ptr(ci);
MD_FLOAT *cjptr = cluster_ptr(cj);
MD_FLOAT *ciptr = cluster_pos_ptr(ci);
MD_FLOAT *cjptr = cluster_pos_ptr(cj);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
for(int cjj = 0; cjj < atom->clusters[cj].natoms; cjj++) {
@ -422,7 +422,7 @@ void buildClusters(Atom *atom) {
growClusters(atom);
}
MD_FLOAT *cptr = cluster_ptr(ci);
MD_FLOAT *cptr = cluster_pos_ptr(ci);
MD_FLOAT bbminx = INFINITY, bbmaxx = -INFINITY;
MD_FLOAT bbminy = INFINITY, bbmaxy = -INFINITY;
MD_FLOAT bbminz = INFINITY, bbmaxz = -INFINITY;
@ -493,7 +493,7 @@ void binClusters(Atom *atom) {
}
for(int ci = 0; ci < atom->Nclusters_ghost && !resize; ci++) {
MD_FLOAT *cptr = cluster_ptr(nlocal + ci);
MD_FLOAT *cptr = cluster_pos_ptr(nlocal + ci);
MD_FLOAT xtmp, ytmp;
int ix = -1, iy = -1;
@ -539,7 +539,7 @@ void updateSingleAtoms(Atom *atom) {
int Natom = 0;
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *cptr = cluster_ptr(ci);
MD_FLOAT *cptr = cluster_pos_ptr(ci);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
atom_x(Natom) = cluster_x(cptr, cii);

4
gromacs/pbc.c
View File

@ -51,8 +51,8 @@ void updatePbc(Atom *atom, Parameter *param) {
MD_FLOAT zprd = param->zprd;
for(int ci = 0; ci < atom->Nclusters_ghost; ci++) {
MD_FLOAT *cptr = cluster_ptr(nlocal + ci);
MD_FLOAT *bmap_cptr = cluster_ptr(border_map[ci]);
MD_FLOAT *cptr = cluster_pos_ptr(nlocal + ci);
MD_FLOAT *bmap_cptr = cluster_pos_ptr(border_map[ci]);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
cluster_x(cptr, cii) = cluster_x(bmap_cptr, cii) + atom->PBCx[ci] * xprd;

4
gromacs/tracing.c
View File

@ -30,7 +30,7 @@ void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timest
INDEX_TRACER_INIT;
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
//MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
INDEX_TRACE_NATOMS(Nlocal, atom->Nghost, neighbor->maxneighs);
for(int i = 0; i < Nlocal; i++) {
@ -60,12 +60,14 @@ void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timest
#endif
}
/*
MEM_TRACE(fx[i], 'R');
MEM_TRACE(fx[i], 'W');
MEM_TRACE(fy[i], 'R');
MEM_TRACE(fy[i], 'W');
MEM_TRACE(fz[i], 'R');
MEM_TRACE(fz[i], 'W');
*/
}
INDEX_TRACER_END;