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Check all clusters in cell when building neighbor lists because ghost clusters may not be sorted

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-01 20:16:04 +01:00
parent 4a5216a177
commit 85e7954932
4 changed files with 77 additions and 46 deletions
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15
gromacs/force_lj.c
View File

@ -28,9 +28,11 @@
#include <parameter.h> #include <parameter.h>
#include <atom.h> #include <atom.h>
#include <stats.h> #include <stats.h>
#include <util.h>
double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) { double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
fprintf(stdout, "computeForceLJ begin\n"); DEBUG_MESSAGE("computeForceLJ begin\n");
int Nlocal = atom->Nlocal; int Nlocal = atom->Nlocal;
int* neighs; int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce; MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
@ -80,11 +82,6 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
fix += delx * force; fix += delx * force;
fiy += dely * force; fiy += dely * force;
fiz += delz * force; fiz += delz * force;
/*
if(force < -50.0 || force > 50.0) {
fprintf(stdout, "%d-%d/%d-%d: %f, %f, %f ---- %f, %f, %f, %f\n", ci, cii, cj, cjj, xtmp, ytmp, ztmp, fix, fiy, fiz, force);
}
*/
} }
} }
} }
@ -92,10 +89,6 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
cluster_x(cifptr, cii) += fix; cluster_x(cifptr, cii) += fix;
cluster_y(cifptr, cii) += fiy; cluster_y(cifptr, cii) += fiy;
cluster_z(cifptr, cii) += fiz; cluster_z(cifptr, cii) += fiz;
/*
if(fix < -100.0 || fix > 100.0 || fiy < -100.0 || fiy > 100.0 || fiz < -100.0 || fiz > 100.0) {
fprintf(stdout, "%d-%d: %f, %f, %f ---- %f, %f, %f\n", ci, cii, xtmp, ytmp, ztmp, fix, fiy, fiz);
}*/
} }
} }
@ -105,6 +98,6 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
LIKWID_MARKER_STOP("force"); LIKWID_MARKER_STOP("force");
double E = getTimeStamp(); double E = getTimeStamp();
fprintf(stdout, "computeForceLJ end\n"); DEBUG_MESSAGE("computeForceLJ end\n");
return E-S; return E-S;
} }

5
gromacs/includes/util.h
View File

@ -32,6 +32,11 @@
#ifndef ABS #ifndef ABS
#define ABS(a) ((a) >= 0 ? (a) : -(a)) #define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif #endif
#ifdef DEBUG
#define DEBUG_MESSAGE(msg) printf
#else
#define DEBUG_MESSAGE(msg)
#endif
#define FF_LJ 0 #define FF_LJ 0
#define FF_EAM 1 #define FF_EAM 1

12
gromacs/main.c
View File

@ -118,7 +118,8 @@ double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
} }
void initialIntegrate(Parameter *param, Atom *atom) { void initialIntegrate(Parameter *param, Atom *atom) {
fprintf(stdout, "initialIntegrate start\n"); DEBUG_MESSAGE("initialIntegrate start\n");
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *ciptr = cluster_pos_ptr(ci); MD_FLOAT *ciptr = cluster_pos_ptr(ci);
MD_FLOAT *civptr = cluster_velocity_ptr(ci); MD_FLOAT *civptr = cluster_velocity_ptr(ci);
@ -133,11 +134,13 @@ void initialIntegrate(Parameter *param, Atom *atom) {
cluster_z(ciptr, cii) += param->dt * cluster_z(civptr, cii); cluster_z(ciptr, cii) += param->dt * cluster_z(civptr, cii);
} }
} }
fprintf(stdout, "initialIntegrate end\n");
DEBUG_MESSAGE("initialIntegrate end\n");
} }
void finalIntegrate(Parameter *param, Atom *atom) { void finalIntegrate(Parameter *param, Atom *atom) {
fprintf(stdout, "finalIntegrate start\n"); DEBUG_MESSAGE("finalIntegrate start\n");
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *civptr = cluster_velocity_ptr(ci); MD_FLOAT *civptr = cluster_velocity_ptr(ci);
MD_FLOAT *cifptr = cluster_force_ptr(ci); MD_FLOAT *cifptr = cluster_force_ptr(ci);
@ -148,7 +151,8 @@ void finalIntegrate(Parameter *param, Atom *atom) {
cluster_z(civptr, cii) += param->dtforce * cluster_z(cifptr, cii); cluster_z(civptr, cii) += param->dtforce * cluster_z(cifptr, cii);
} }
} }
fprintf(stdout, "finalIntegrate end\n");
DEBUG_MESSAGE("finalIntegrate end\n");
} }
void printAtomState(Atom *atom) { void printAtomState(Atom *atom) {

91
gromacs/neighbor.c
View File

@ -202,7 +202,7 @@ int atomDistanceInRange(Atom *atom, int ci, int cj, MD_FLOAT rsq) {
} }
void buildNeighbor(Atom *atom, Neighbor *neighbor) { void buildNeighbor(Atom *atom, Neighbor *neighbor) {
printf("buildNeighbor start\n"); DEBUG_MESSAGE("buildNeighbor start\n");
int nall = atom->Nclusters_local + atom->Nclusters_ghost; int nall = atom->Nclusters_local + atom->Nclusters_ghost;
/* extend atom arrays if necessary */ /* extend atom arrays if necessary */
@ -240,17 +240,17 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
const int c = cluster_bincount[jbin]; const int c = cluster_bincount[jbin];
if(c > 0) { if(c > 0) {
do { //do {
m++; m++;
cj = loc_bin[m]; cj = loc_bin[m];
jbb_zmin = atom->clusters[cj].bbminz; jbb_zmin = atom->clusters[cj].bbminz;
jbb_zmax = atom->clusters[cj].bbmaxz; jbb_zmax = atom->clusters[cj].bbmaxz;
} while(m + 1 < c && (ibb_zmin - jbb_zmax) * (ibb_zmin - jbb_zmax) > cutneighsq); //} while(m + 1 < c && (ibb_zmin - jbb_zmax) * (ibb_zmin - jbb_zmax) > cutneighsq);
while(m < c) { while(m < c) {
if((jbb_zmin - ibb_zmax) * (jbb_zmin - ibb_zmax) > cutneighsq) { /*if((jbb_zmin - ibb_zmax) * (jbb_zmin - ibb_zmax) > cutneighsq) {
break; break;
} }*/
double d_bb_sq = getBoundingBoxDistanceSq(atom, ci, cj); double d_bb_sq = getBoundingBoxDistanceSq(atom, ci, cj);
if(d_bb_sq < cutneighsq) { if(d_bb_sq < cutneighsq) {
@ -280,7 +280,7 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
} }
if(resize) { if(resize) {
printf("RESIZE %d\n", neighbor->maxneighs); fprintf(stdout, "RESIZE %d\n", neighbor->maxneighs);
neighbor->maxneighs = new_maxneighs * 1.2; neighbor->maxneighs = new_maxneighs * 1.2;
free(neighbor->neighbors); free(neighbor->neighbors);
neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int)); neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int));
@ -288,28 +288,46 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor) {
} }
/* /*
printf("\ncutneighsq = %f, rbb_sq = %f\n", cutneighsq, rbb_sq); DEBUG_MESSAGE("\ncutneighsq = %f, rbb_sq = %f\n", cutneighsq, rbb_sq);
for(int ci = 0; ci < 6; ci++) { for(int ci = 0; ci < 6; ci++) {
MD_FLOAT *ciptr = cluster_pos_ptr(ci); MD_FLOAT *ciptr = cluster_pos_ptr(ci);
int* neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]); int* neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
printf("Cluster %d, bbx = {%f, %f}, bby = {%f, %f}, bbz = {%f, %f}\n", ci, atom->clusters[ci].bbminx, atom->clusters[ci].bbmaxx, atom->clusters[ci].bbminy, atom->clusters[ci].bbmaxy, atom->clusters[ci].bbminz, atom->clusters[ci].bbmaxz);
DEBUG_MESSAGE("Cluster %d, bbx = {%f, %f}, bby = {%f, %f}, bbz = {%f, %f}\n",
ci,
atom->clusters[ci].bbminx,
atom->clusters[ci].bbmaxx,
atom->clusters[ci].bbminy,
atom->clusters[ci].bbmaxy,
atom->clusters[ci].bbminz,
atom->clusters[ci].bbmaxz);
for(int cii = 0; cii < CLUSTER_DIM_N; cii++) { for(int cii = 0; cii < CLUSTER_DIM_N; cii++) {
fprintf(stdout, "%f, %f, %f\n", cluster_x(ciptr, cii), cluster_y(ciptr, cii), cluster_z(ciptr, cii)); DEBUG_MESSAGE("%f, %f, %f\n", cluster_x(ciptr, cii), cluster_y(ciptr, cii), cluster_z(ciptr, cii));
} }
printf("Neighbors:\n"); DEBUG_MESSAGE("Neighbors:\n");
for(int k = 0; k < neighbor->numneigh[ci]; k++) { for(int k = 0; k < neighbor->numneigh[ci]; k++) {
const int cj = neighptr[k]; const int cj = neighptr[k];
MD_FLOAT *cjptr = cluster_pos_ptr(cj); MD_FLOAT *cjptr = cluster_pos_ptr(cj);
printf(" Cluster %d, bbx = {%f, %f}, bby = {%f, %f}, bbz = {%f, %f}\n", cj, atom->clusters[cj].bbminx, atom->clusters[cj].bbmaxx, atom->clusters[cj].bbminy, atom->clusters[cj].bbmaxy, atom->clusters[cj].bbminz, atom->clusters[cj].bbmaxz);
DEBUG_MESSAGE(" Cluster %d, bbx = {%f, %f}, bby = {%f, %f}, bbz = {%f, %f}\n",
cj,
atom->clusters[cj].bbminx,
atom->clusters[cj].bbmaxx,
atom->clusters[cj].bbminy,
atom->clusters[cj].bbmaxy,
atom->clusters[cj].bbminz,
atom->clusters[cj].bbmaxz);
for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) { for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) {
fprintf(stdout, " %f, %f, %f\n", cluster_x(cjptr, cjj), cluster_y(cjptr, cjj), cluster_z(cjptr, cjj)); DEBUG_MESSAGE(" %f, %f, %f\n", cluster_x(cjptr, cjj), cluster_y(cjptr, cjj), cluster_z(cjptr, cjj));
} }
} }
} }
*/ */
printf("buildNeighbor end\n"); DEBUG_MESSAGE("buildNeighbor end\n");
} }
/* internal subroutines */ /* internal subroutines */
@ -376,7 +394,7 @@ void coord2bin2D(MD_FLOAT xin, MD_FLOAT yin, int *ix, int *iy) {
} }
void binAtoms(Atom *atom) { void binAtoms(Atom *atom) {
printf("binAtoms start\n"); DEBUG_MESSAGE("binAtoms start\n");
int resize = 1; int resize = 1;
while(resize > 0) { while(resize > 0) {
@ -388,7 +406,6 @@ void binAtoms(Atom *atom) {
for(int i = 0; i < atom->Nlocal; i++) { for(int i = 0; i < atom->Nlocal; i++) {
int ibin = coord2bin(atom_x(i), atom_y(i)); int ibin = coord2bin(atom_x(i), atom_y(i));
if(ibin < 0 || ibin > mbins) { fprintf(stderr, "%d: %f, %f\n", i, atom_x(i), atom_y(i)); }
if(bincount[ibin] < atoms_per_bin) { if(bincount[ibin] < atoms_per_bin) {
int ac = bincount[ibin]++; int ac = bincount[ibin]++;
bins[ibin * atoms_per_bin + ac] = i; bins[ibin * atoms_per_bin + ac] = i;
@ -403,12 +420,13 @@ void binAtoms(Atom *atom) {
bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int)); bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
} }
} }
printf("binAtoms end\n");
DEBUG_MESSAGE("binAtoms end\n");
} }
// TODO: Use pigeonhole sorting // TODO: Use pigeonhole sorting
void sortAtomsByZCoord(Atom *atom) { void sortAtomsByZCoord(Atom *atom) {
printf("sortAtomsByZCoord start\n"); DEBUG_MESSAGE("sortAtomsByZCoord start\n");
for(int bin = 0; bin < mbins; bin++) { for(int bin = 0; bin < mbins; bin++) {
int c = bincount[bin]; int c = bincount[bin];
int *bin_ptr = &bins[bin * atoms_per_bin]; int *bin_ptr = &bins[bin * atoms_per_bin];
@ -433,11 +451,12 @@ void sortAtomsByZCoord(Atom *atom) {
bin_ptr[min_ac] = i; bin_ptr[min_ac] = i;
} }
} }
printf("sortAtomsByZCoord end\n");
DEBUG_MESSAGE("sortAtomsByZCoord end\n");
} }
void buildClusters(Atom *atom) { void buildClusters(Atom *atom) {
printf("buildClusters start\n"); DEBUG_MESSAGE("buildClusters start\n");
atom->Nclusters_local = 0; atom->Nclusters_local = 0;
/* bin local atoms */ /* bin local atoms */
@ -506,20 +525,29 @@ void buildClusters(Atom *atom) {
} }
} }
printf("buildClusters end\n"); DEBUG_MESSAGE("buildClusters end\n");
} }
void binClusters(Atom *atom) { void binClusters(Atom *atom) {
printf("binClusters start\n"); DEBUG_MESSAGE("binClusters start\n");
/* /*
fprintf(stdout, "Nghost = %d\n", atom->Nclusters_ghost); DEBUG_MESSAGE("Nghost = %d\n", atom->Nclusters_ghost);
for(int ci = atom->Nclusters_local; ci < atom->Nclusters_local + 4; ci++) { for(int ci = atom->Nclusters_local; ci < atom->Nclusters_local + 4; ci++) {
MD_FLOAT *cptr = cluster_pos_ptr(ci); MD_FLOAT *cptr = cluster_pos_ptr(ci);
fprintf(stdout, "Cluster %d:\n", ci); DEBUG_MESSAGE("Cluster %d:\n", ci);
fprintf(stdout, "bin=%d, Natoms=%d, bbox={%f,%f},{%f,%f},{%f,%f}\n", atom->clusters[ci].bin, atom->clusters[ci].natoms, atom->clusters[ci].bbminx, atom->clusters[ci].bbmaxx, atom->clusters[ci].bbminy, atom->clusters[ci].bbmaxy, atom->clusters[ci].bbminz, atom->clusters[ci].bbmaxz); DEBUG_MESSAGE("bin=%d, Natoms=%d, bbox={%f,%f},{%f,%f},{%f,%f}\n",
atom->clusters[ci].bin,
atom->clusters[ci].natoms,
atom->clusters[ci].bbminx,
atom->clusters[ci].bbmaxx,
atom->clusters[ci].bbminy,
atom->clusters[ci].bbmaxy,
atom->clusters[ci].bbminz,
atom->clusters[ci].bbmaxz);
for(int cii = 0; cii < CLUSTER_DIM_N; cii++) { for(int cii = 0; cii < CLUSTER_DIM_N; cii++) {
fprintf(stdout, "%f, %f, %f\n", cluster_x(cptr, cii), cluster_y(cptr, cii), cluster_z(cptr, cii)); DEBUG_MESSAGE("%f, %f, %f\n", cluster_x(cptr, cii), cluster_y(cptr, cii), cluster_z(cptr, cii));
} }
} }
*/ */
@ -590,16 +618,16 @@ void binClusters(Atom *atom) {
} }
/* /*
fprintf(stdout, "cluster_bincount\n"); DEBUG_MESSAGE("cluster_bincount\n");
for(int i = 0; i < mbins; i++) { fprintf(stdout, "%d, ", cluster_bincount[i]); } for(int i = 0; i < mbins; i++) { DEBUG_MESSAGE("%d, ", cluster_bincount[i]); }
fprintf(stdout, "\n"); DEBUG_MESSAGE("\n");
*/ */
printf("binClusters stop\n"); DEBUG_MESSAGE("binClusters stop\n");
} }
void updateSingleAtoms(Atom *atom) { void updateSingleAtoms(Atom *atom) {
printf("updateSingleAtoms start\n"); DEBUG_MESSAGE("updateSingleAtoms start\n");
int Natom = 0; int Natom = 0;
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
@ -620,5 +648,6 @@ void updateSingleAtoms(Atom *atom) {
if(Natom != atom->Nlocal) { if(Natom != atom->Nlocal) {
fprintf(stderr, "updateSingleAtoms(): Number of atoms changed!\n"); fprintf(stderr, "updateSingleAtoms(): Number of atoms changed!\n");
} }
printf("updateSingleAtoms stop\n");
DEBUG_MESSAGE("updateSingleAtoms stop\n");
} }