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Adapt stubbed version for new neighbor lists in GROMACS

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2023-03-29 21:54:33 +02:00
parent 59145644e3
commit 3eb7170a65
1 changed files with 18 additions and 8 deletions
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26
gromacs/main-stub.c
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@ -66,12 +66,13 @@ void init(Parameter *param) {
//#define DEBUG(msg) //#define DEBUG(msg)
void createNeighbors(Atom *atom, Neighbor *neighbor, int pattern, int nneighs, int nreps) { void createNeighbors(Atom *atom, Neighbor *neighbor, int pattern, int nneighs, int nreps, int masked) {
const int maxneighs = nneighs * nreps; const int maxneighs = nneighs * nreps;
const int jfac = MAX(1, CLUSTER_N / CLUSTER_M); const int jfac = MAX(1, CLUSTER_N / CLUSTER_M);
const int ncj = atom->Nclusters_local / jfac; const int ncj = atom->Nclusters_local / jfac;
const unsigned int imask = NBNXN_INTERACTION_MASK_ALL;
neighbor->numneigh = (int*) malloc(atom->Nclusters_max * sizeof(int)); neighbor->numneigh = (int*) malloc(atom->Nclusters_max * sizeof(int));
neighbor->neighbors = (int*) malloc(atom->Nclusters_max * maxneighs * sizeof(int)); neighbor->neighbors = (NeighborCluster*) malloc(atom->Nclusters_max * maxneighs * sizeof(int));
if(pattern == P_RAND && ncj <= nneighs) { if(pattern == P_RAND && ncj <= nneighs) {
fprintf(stderr, "Error: P_RAND: Number of j-clusters should be higher than number of j-cluster neighbors per i-cluster!\n"); fprintf(stderr, "Error: P_RAND: Number of j-clusters should be higher than number of j-cluster neighbors per i-cluster!\n");
@ -79,7 +80,7 @@ void createNeighbors(Atom *atom, Neighbor *neighbor, int pattern, int nneighs, i
} }
for(int ci = 0; ci < atom->Nclusters_local; ci++) { for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int *neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]); NeighborCluster *neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
int j = (pattern == P_SEQ) ? CJ0_FROM_CI(ci) : 0; int j = (pattern == P_SEQ) ? CJ0_FROM_CI(ci) : 0;
int m = (pattern == P_SEQ) ? ncj : nneighs; int m = (pattern == P_SEQ) ? ncj : nneighs;
int k = 0; int k = 0;
@ -89,27 +90,31 @@ void createNeighbors(Atom *atom, Neighbor *neighbor, int pattern, int nneighs, i
int found = 0; int found = 0;
do { do {
int cj = rand() % ncj; int cj = rand() % ncj;
neighptr[k] = cj; neighptr[k].cj = cj;
neighptr[k].imask = imask;
found = 0; found = 0;
for(int l = 0; l < k; l++) { for(int l = 0; l < k; l++) {
if(neighptr[l] == cj) { if(neighptr[l].cj == cj) {
found = 1; found = 1;
} }
} }
} while(found == 1); } while(found == 1);
} else { } else {
neighptr[k] = j; neighptr[k].cj = j;
neighptr[k].imask = imask;
j = (j + 1) % m; j = (j + 1) % m;
} }
} }
for(int r = 1; r < nreps; r++) { for(int r = 1; r < nreps; r++) {
for(int k = 0; k < nneighs; k++) { for(int k = 0; k < nneighs; k++) {
neighptr[r * nneighs + k] = neighptr[k]; neighptr[r * nneighs + k].cj = neighptr[k].cj;
neighptr[r * nneighs + k].imask = neighptr[k].imask;
} }
} }
neighbor->numneigh[ci] = nneighs * nreps; neighbor->numneigh[ci] = nneighs * nreps;
neighbor->numneigh_masked[ci] = (masked == 1) ? (nneighs * nreps) : 0;
} }
} }
@ -125,6 +130,7 @@ int main(int argc, const char *argv[]) {
int niclusters = 256; // Number of local i-clusters int niclusters = 256; // Number of local i-clusters
int iclusters_natoms = CLUSTER_M; // Number of valid atoms within i-clusters int iclusters_natoms = CLUSTER_M; // Number of valid atoms within i-clusters
int nneighs = 9; // Number of j-cluster neighbors per i-cluster int nneighs = 9; // Number of j-cluster neighbors per i-cluster
int masked = 0; // Use masked loop
int nreps = 1; int nreps = 1;
int csv = 0; int csv = 0;
@ -156,6 +162,10 @@ int main(int argc, const char *argv[]) {
param.eam_file = strdup(argv[++i]); param.eam_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-m") == 0)) {
masked = 1;
continue;
}
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) { if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
param.ntimes = atoi(argv[++i]); param.ntimes = atoi(argv[++i]);
continue; continue;
@ -286,7 +296,7 @@ int main(int argc, const char *argv[]) {
DEBUG("Initializing neighbor lists...\n"); DEBUG("Initializing neighbor lists...\n");
initNeighbor(&neighbor, &param); initNeighbor(&neighbor, &param);
DEBUG("Creating neighbor lists...\n"); DEBUG("Creating neighbor lists...\n");
createNeighbors(atom, &neighbor, pattern, nneighs, nreps); createNeighbors(atom, &neighbor, pattern, nneighs, nreps, masked);
DEBUG("Computing forces...\n"); DEBUG("Computing forces...\n");
double T_accum = 0.0; double T_accum = 0.0;