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Apply first changes to DEM kernel

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-07-13 02:34:33 +02:00
parent 99237241fb
commit 577955dfb7
3 changed files with 28 additions and 119 deletions
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140
lammps/force_dem.c
View File

@@ -37,9 +37,7 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
int* neighs; int* neighs;
MD_FLOAT k_s = param->k_s; MD_FLOAT k_s = param->k_s;
MD_FLOAT k_dn = param->k_dn; MD_FLOAT k_dn = param->k_dn;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
#endif
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
atom_fx(i) = 0.0; atom_fx(i) = 0.0;
@@ -50,7 +48,6 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
double S = getTimeStamp(); double S = getTimeStamp();
LIKWID_MARKER_START("force"); LIKWID_MARKER_START("force");
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs]; neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i]; int numneighs = neighbor->numneigh[i];
@@ -62,10 +59,6 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
MD_FLOAT fiy = 0; MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0; MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
for(int k = 0; k < numneighs; k++) { for(int k = 0; k < numneighs; k++) {
int j = neighs[k]; int j = neighs[k];
MD_FLOAT jrad = atom->radius[j]; MD_FLOAT jrad = atom->radius[j];
@@ -77,32 +70,11 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
MD_FLOAT delz = ztmp - zj; MD_FLOAT delz = ztmp - zj;
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
#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];
#endif
if(rsq < cutforcesq) { if(rsq < cutforcesq) {
MD_FLOAT r = sqrt(rsq); MD_FLOAT r = sqrt(rsq);
// penetration depth
MD_FLOAT p = irad + jrad - r; MD_FLOAT p = irad + jrad - r;
if(p >= 0) {
// contact position
//MD_FLOAT cterm = jrad / (irad + jrad);
//MD_FLOAT cx = xj + cterm * delx;
//MD_FLOAT cy = yj + cterm * dely;
//MD_FLOAT cz = zj + cterm * delz;
// delta contact and particle position if(p > 0) {
//MD_FLOAT delcx = cx - xtmp;
//MD_FLOAT delcy = cy - ytmp;
//MD_FLOAT delcz = cz - ztmp;
// contact velocity
//MD_FLOAT cvx = (atom_vx(i) + atom_avx(i) * delcx) - (atom_vx(j) + atom_avx(j) * (cx - xj));
//MD_FLOAT cvy = (atom_vy(i) + atom_avy(i) * delcy) - (atom_vy(j) + atom_avy(j) * (cy - yj));
//MD_FLOAT cvz = (atom_vz(i) + atom_avz(i) * delcz) - (atom_vz(j) + atom_avz(j) * (cz - zj));
MD_FLOAT delvx = atom_vx(i) - atom_vx(j); MD_FLOAT delvx = atom_vx(i) - atom_vx(j);
MD_FLOAT delvy = atom_vy(i) - atom_vy(j); MD_FLOAT delvy = atom_vy(i) - atom_vy(j);
MD_FLOAT delvz = atom_vz(i) - atom_vz(j); MD_FLOAT delvz = atom_vz(i) - atom_vz(j);
@@ -119,9 +91,28 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
MD_FLOAT nvz = delvz / vr; MD_FLOAT nvz = delvz / vr;
// forces // forces
fix += k_s * p * nx - k_dn * nvx; atom_fx(i) += k_s * p * nx - k_dn * nvx;
fiy += k_s * p * ny - k_dn * nvy; atom_fy(i) += k_s * p * ny - k_dn * nvy;
fiz += k_s * p * nz - k_dn * nvz; atom_fz(i) += k_s * p * nz - k_dn * nvz;
atom_fx(j) += -k_s * p * nx - k_dn * nvx;
atom_fy(j) += -k_s * p * ny - k_dn * nvy;
atom_fz(j) += -k_s * p * nz - k_dn * nvz;
// contact position
//MD_FLOAT cterm = jrad / (irad + jrad);
//MD_FLOAT cx = xj + cterm * delx;
//MD_FLOAT cy = yj + cterm * dely;
//MD_FLOAT cz = zj + cterm * delz;
// delta contact and particle position
//MD_FLOAT delcx = cx - xtmp;
//MD_FLOAT delcy = cy - ytmp;
//MD_FLOAT delcz = cz - ztmp;
// contact velocity
//MD_FLOAT cvx = (atom_vx(i) + atom_avx(i) * delcx) - (atom_vx(j) + atom_avx(j) * (cx - xj));
//MD_FLOAT cvy = (atom_vy(i) + atom_avy(i) * delcy) - (atom_vy(j) + atom_avy(j) * (cy - yj));
//MD_FLOAT cvz = (atom_vz(i) + atom_avz(i) * delcz) - (atom_vz(j) + atom_avz(j) * (cz - zj));
// tangential force // tangential force
//fix += MIN(kdt * vtsq, kf * fnx) * tx; //fix += MIN(kdt * vtsq, kf * fnx) * tx;
@@ -140,10 +131,6 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
} }
} }
atom_fx(i) += fix;
atom_fy(i) += fiy;
atom_fz(i) += fiz;
addStat(stats->total_force_neighs, numneighs); addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH); addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
} }
@@ -152,84 +139,3 @@ double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor
double E = getTimeStamp(); double E = getTimeStamp();
return E-S; return E-S;
} }
double computeForceDemHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;
int* neighs;
#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++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double S = getTimeStamp();
LIKWID_MARKER_START("forceLJ-halfneigh");
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
// Pragma required to vectorize the inner loop
#ifdef ENABLE_OMP_SIMD
#pragma omp simd reduction(+: fix,fiy,fiz)
#endif
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;
#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
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;
// We do not need to update forces for ghost atoms
if(j < Nlocal) {
atom_fx(j) -= delx * force;
atom_fy(j) -= dely * force;
atom_fz(j) -= delz * force;
}
}
}
atom_fx(i) += fix;
atom_fy(i) += fiy;
atom_fz(i) += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("forceLJ-halfneigh");
double E = getTimeStamp();
return E-S;
}

4
lammps/main.c
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@@ -50,7 +50,6 @@ extern double computeForceLJFullNeigh_simd(Parameter*, Atom*, Neighbor*, Stats*)
extern double computeForceLJHalfNeigh(Parameter*, Atom*, Neighbor*, Stats*); extern double computeForceLJHalfNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*); extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceDemFullNeigh(Parameter*, Atom*, Neighbor*, Stats*); extern double computeForceDemFullNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceDemHalfNeigh(Parameter*, Atom*, Neighbor*, Stats*);
#ifdef USE_SIMD_KERNEL #ifdef USE_SIMD_KERNEL
# define KERNEL_NAME "SIMD" # define KERNEL_NAME "SIMD"
@@ -135,7 +134,8 @@ double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor,
return computeForceEam(eam, param, atom, neighbor, stats); return computeForceEam(eam, param, atom, neighbor, stats);
} else if(param->force_field == FF_DEM) { } else if(param->force_field == FF_DEM) {
if(param->half_neigh) { if(param->half_neigh) {
return computeForceDemHalfNeigh(param, atom, neighbor, stats); fprintf(stderr, "Error: DEM cannot use half neighbor-lists!\n");
return 0.0;
} else { } else {
return computeForceDemFullNeigh(param, atom, neighbor, stats); return computeForceDemFullNeigh(param, atom, neighbor, stats);
} }

3
lammps/parameter.c
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@@ -130,6 +130,9 @@ void readParameter(Parameter *param, const char *filename) {
} }
} }
// Update dtforce
param->dtforce = 0.5 * param->dt;
// Update sigma6 parameter // Update sigma6 parameter
MD_FLOAT s2 = param->sigma * param->sigma; MD_FLOAT s2 = param->sigma * param->sigma;
param->sigma6 = s2 * s2 * s2; param->sigma6 = s2 * s2 * s2;