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Fix atom sorting

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2023-04-09 01:19:12 +02:00
parent 1ad981a059
commit b6982d56f5
4 changed files with 30 additions and 14 deletions
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4
Makefile
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@ -30,6 +30,10 @@ ifneq ($(ASM_SYNTAX), ATT)
ASFLAGS += -masm=intel
endif
ifeq ($(strip $(SORT_ATOMS)),true)
DEFINES += -DSORT_ATOMS
endif
ifeq ($(strip $(EXPLICIT_TYPES)),true)
DEFINES += -DEXPLICIT_TYPES
endif

5
common/parameter.c
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@ -169,6 +169,11 @@ void printParameter(Parameter *param) {
printf("\tNumber of timesteps: %d\n", param->ntimes);
printf("\tReport stats every (timesteps): %d\n", param->nstat);
printf("\tReneighbor every (timesteps): %d\n", param->reneigh_every);
#ifdef SORT_ATOMS
printf("\tSort atoms when reneighboring: yes\n");
#else
printf("\tSort atoms when reneighboring: no\n");
#endif
printf("\tPrune every (timesteps): %d\n", param->prune_every);
printf("\tOutput positions every (timesteps): %d\n", param->x_out_every);
printf("\tOutput velocities every (timesteps): %d\n", param->v_out_every);

9
lammps/main.c
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@ -63,6 +63,10 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *
setupNeighbor(param);
setupThermo(param, atom->Natoms);
if(param->input_file == NULL) { adjustThermo(param, atom); }
#ifdef SORT_ATOMS
atom->Nghost = 0;
sortAtom(atom);
#endif
setupPbc(atom, param);
initDevice(atom, neighbor);
updatePbc(atom, param, true);
@ -76,9 +80,12 @@ double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
S = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param);
#ifdef SORT_ATOMS
atom->Nghost = 0;
sortAtom(atom);
#endif
setupPbc(atom, param);
updatePbc(atom, param, true);
//sortAtom(atom);
buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();

26
lammps/neighbor.c
View File

@ -326,45 +326,45 @@ void sortAtom(Atom* atom) {
int Nmax = atom->Nmax;
int* binpos = bincount;
for(int i=1; i<mbins; i++) {
binpos[i] += binpos[i-1];
for(int i = 1; i < mbins; i++) {
binpos[i] += binpos[i - 1];
}
#ifdef AOS
#ifdef AOS
MD_FLOAT* new_x = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT) * 3);
MD_FLOAT* new_vx = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT) * 3);
#else
#else
MD_FLOAT* new_x = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT));
MD_FLOAT* new_y = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT));
MD_FLOAT* new_z = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT));
MD_FLOAT* new_vx = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT));
MD_FLOAT* new_vy = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT));
MD_FLOAT* new_vz = (MD_FLOAT*) malloc(Nmax * sizeof(MD_FLOAT));
#endif
#endif
MD_FLOAT* old_x = atom->x; MD_FLOAT* old_y = atom->y; MD_FLOAT* old_z = atom->z;
MD_FLOAT* old_vx = atom->vx; MD_FLOAT* old_vy = atom->vy; MD_FLOAT* old_vz = atom->vz;
for(int mybin = 0; mybin<mbins; mybin++) {
int start = mybin>0?binpos[mybin-1]:0;
for(int mybin = 0; mybin < mbins; mybin++) {
int start = mybin > 0 ? binpos[mybin - 1] : 0;
int count = binpos[mybin] - start;
for(int k=0; k<count; k++) {
for(int k = 0; k < count; k++) {
int new_i = start + k;
int old_i = bins[mybin * atoms_per_bin + k];
#ifdef AOS
#ifdef AOS
new_x[new_i * 3 + 0] = old_x[old_i * 3 + 0];
new_x[new_i * 3 + 1] = old_x[old_i * 3 + 1];
new_x[new_i * 3 + 2] = old_x[old_i * 3 + 2];
new_vx[new_i * 3 + 0] = old_vx[old_i * 3 + 0];
new_vx[new_i * 3 + 1] = old_vx[old_i * 3 + 1];
new_vx[new_i * 3 + 2] = old_vx[old_i * 3 + 2];
#else
#else
new_x[new_i] = old_x[old_i];
new_y[new_i] = old_y[old_i];
new_z[new_i] = old_z[old_i];
new_vx[new_i] = old_vx[old_i];
new_vy[new_i] = old_vy[old_i];
new_vz[new_i] = old_vz[old_i];
#endif
#endif
}
}
@ -372,7 +372,7 @@ void sortAtom(Atom* atom) {
free(atom->vx);
atom->x = new_x;
atom->vx = new_vx;
#ifndef AOS
#ifndef AOS
free(atom->y);
free(atom->z);
free(atom->vy);
@ -381,5 +381,5 @@ void sortAtom(Atom* atom) {
atom->z = new_z;
atom->vy = new_vy;
atom->vz = new_vz;
#endif
#endif
}