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Fix some segfaults and add function to update single atoms

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-01-27 03:07:31 +01:00
parent aa0f4048d0
commit a119fcdfdd
5 changed files with 225 additions and 160 deletions
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2
gromacs/atom.c
View File

@ -286,5 +286,5 @@ void growClusters(Atom *atom)
int nold = atom->Nclusters_max;
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, nold * CLUSTER_DIM_N * 3);
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));
}

9
gromacs/includes/neighbor.h
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@ -34,10 +34,11 @@ typedef struct {
} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*);
extern void setupNeighbor(Parameter*, Atom*);
extern void binatoms(Atom*);
extern void buildNeighbor(Parameter*, Atom*, Neighbor*);
extern void buildNeighbor(Atom*, Neighbor*);
extern void sortAtom(Atom*);
extern void buildClusters(Parameter*, Atom*);
extern void binGhostClusters(Parameter*, Atom*);
extern void buildClusters(Atom*);
extern void binClusters(Atom*);
extern void updateSingleAtoms(Atom*);
#endif

20
gromacs/main.c
View File

@ -96,12 +96,13 @@ double setup(
} else {
readAtom(atom, param);
}
setupNeighbor(param);
setupNeighbor(param, atom);
setupThermo(param, atom->Natoms);
if(param->input_file == NULL) { adjustThermo(param, atom); }
buildClusters(atom);
setupPbc(atom, param);
buildClusters(param, atom);
buildNeighbor(param, atom, neighbor);
binClusters(atom);
buildNeighbor(atom, neighbor);
E = getTimeStamp();
return E-S;
@ -116,9 +117,12 @@ double reneighbour(
S = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateSingleAtoms(atom);
updateAtomsPbc(atom, param);
buildClusters(atom);
setupPbc(atom, param);
buildNeighbor(param, atom, neighbor);
binClusters(atom);
buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
@ -253,11 +257,13 @@ 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();
@ -267,7 +273,7 @@ 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);
@ -279,13 +285,15 @@ 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);

157
gromacs/neighbor.c
View File

@ -32,7 +32,7 @@
#define SMALL 1.0e-6
#define FACTOR 0.999
static MD_FLOAT xprd, yprd;
static MD_FLOAT xprd, yprd, zprd;
static MD_FLOAT bininvx, bininvy;
static int mbinxlo, mbinylo;
static int nbinx, nbiny;
@ -55,14 +55,12 @@ static int coord2bin(MD_FLOAT, MD_FLOAT);
static MD_FLOAT bindist(int, int);
/* exported subroutines */
void initNeighbor(Neighbor *neighbor, Parameter *param)
{
void initNeighbor(Neighbor *neighbor, Parameter *param) {
MD_FLOAT neighscale = 5.0 / 6.0;
xprd = param->nx * param->lattice;
yprd = param->ny * param->lattice;
zprd = param->nz * param->lattice;
cutneigh = param->cutneigh;
nbinx = neighscale * param->nx;
nbiny = neighscale * param->ny;
nmax = 0;
atoms_per_bin = 8;
clusters_per_bin = (atoms_per_bin / CLUSTER_DIM_N) + 4;
@ -76,7 +74,7 @@ void initNeighbor(Neighbor *neighbor, Parameter *param)
neighbor->neighbors = NULL;
}
void setupNeighbor(Parameter* param) {
void setupNeighbor(Parameter *param, Atom *atom) {
MD_FLOAT coord;
int mbinxhi, mbinyhi;
int nextx, nexty, nextz;
@ -84,30 +82,31 @@ void setupNeighbor(Parameter* param) {
if(param->input_file != NULL) {
xprd = param->xprd;
yprd = param->yprd;
zprd = param->zprd;
}
// TODO: update lo and hi for standard case and use them here instead
MD_FLOAT xlo = 0.0; MD_FLOAT xhi = xprd;
MD_FLOAT ylo = 0.0; MD_FLOAT yhi = yprd;
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = zprd;
MD_FLOAT atom_density = ((MD_FLOAT)(atom->Nlocal)) / ((xhi - xlo) * (yhi - ylo) * (zhi - zlo));
MD_FLOAT atoms_in_cell = MAX(CLUSTER_DIM_M, CLUSTER_DIM_N);
binsizex = cbrt(atoms_in_cell / atom_density);
binsizey = cbrt(atoms_in_cell / atom_density);
cutneighsq = cutneigh * cutneigh;
if(param->input_file != NULL) {
binsizex = cutneigh * 0.5;
binsizey = cutneigh * 0.5;
nbinx = (int)((param->xhi - param->xlo) / binsizex);
nbiny = (int)((param->yhi - param->ylo) / binsizey);
nbinx = (int)((xhi - xlo) / binsizex);
nbiny = (int)((yhi - ylo) / binsizey);
if(nbinx == 0) { nbinx = 1; }
if(nbiny == 0) { nbiny = 1; }
bininvx = nbinx / (param->xhi - param->xlo);
bininvy = nbiny / (param->yhi - param->ylo);
} else {
binsizex = xprd / nbinx;
binsizey = yprd / nbiny;
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
}
printf("hi = %f, %f\n", xhi, yhi);
printf("atom_density = %f\n", atom_density);
printf("atoms_in_cell = %f\n", atoms_in_cell);
printf("binsize = %f, %f\n", binsizex, binsizey);
printf("nbin = %d, %d\n", nbinx, nbiny);
coord = xlo - cutneigh - SMALL * xprd;
mbinxlo = (int) (coord * bininvx);
if (coord < 0.0) {
@ -207,8 +206,9 @@ int atomDistanceInRange(Atom *atom, int ci, int cj, MD_FLOAT rsq) {
return 0;
}
void buildNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
int nall = atom->Nlocal + atom->Nghost;
void buildNeighbor(Atom *atom, Neighbor *neighbor) {
printf("buildNeighbor start\n");
int nall = atom->Nclusters_local + atom->Nclusters_ghost;
/* extend atom arrays if necessary */
if(nall > nmax) {
@ -239,15 +239,17 @@ void buildNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
int *loc_bin = &cluster_bins[jbin * clusters_per_bin];
int cj, m = -1;
MD_FLOAT jbb_zmin, jbb_zmax;
const int c = cluster_bincount[jbin];
if(c > 0) {
do {
m++;
cj = loc_bin[m];
jbb_zmin = atom->clusters[cj].bbminz;
jbb_zmax = atom->clusters[cj].bbmaxz;
} while((ibb_zmin - jbb_zmax) * (ibb_zmin - jbb_zmax) > cutneighsq);
} while(m + 1 < c && (ibb_zmin - jbb_zmax) * (ibb_zmin - jbb_zmax) > cutneighsq);
while(m < cluster_bincount[jbin] && jbb_zmax - ibb_zmax < cutneighsq) {
while(m < c && jbb_zmax - ibb_zmax < cutneighsq) {
if((jbb_zmin - ibb_zmax) * (jbb_zmin - ibb_zmax) > cutneighsq) {
break;
}
@ -255,19 +257,19 @@ void buildNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
double d_bb_sq = getBoundingBoxDistanceSq(atom, ci, cj);
if(d_bb_sq < cutneighsq) {
if(d_bb_sq < rBB || atomDistanceInRange(atom, ci, cj, cutneighsq)) {
if(cj == ci) {
// Add to neighbor list with diagonal interaction mask
}
neighptr[n++] = cj;
}
}
m++;
if(m < c) {
cj = loc_bin[m];
jbb_zmin = atom->clusters[cj].bbminz;
jbb_zmax = atom->clusters[cj].bbmaxz;
}
}
}
}
neighbor->numneigh[ci] = n;
@ -287,6 +289,7 @@ void buildNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
neighbor->neighbors = (int*) malloc(atom->Nmax * neighbor->maxneighs * sizeof(int));
}
}
printf("buildNeighbor end\n");
}
/* internal subroutines */
@ -352,7 +355,8 @@ void coord2bin2D(MD_FLOAT xin, MD_FLOAT yin, int *ix, int *iy) {
}
}
void binatoms(Atom *atom) {
void binAtoms(Atom *atom) {
printf("binatoms start\n");
int nall = atom->Nlocal + atom->Nghost;
int resize = 1;
@ -380,10 +384,12 @@ void binatoms(Atom *atom) {
bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
}
}
printf("binatoms end\n");
}
// TODO: Use pigeonhole sorting
void sortBinAtomsByZCoord(Parameter *param, Atom *atom, int bin) {
void sortAtomsByZCoord(Atom *atom) {
for(int bin = 0; bin < mbins; bin++) {
int c = bincount[bin];
int *bin_ptr = &bins[bin * atoms_per_bin];
@ -407,26 +413,27 @@ void sortBinAtomsByZCoord(Parameter *param, Atom *atom, int bin) {
bin_ptr[min_ac] = i;
}
}
void buildClusters(Parameter *param, Atom *atom) {
/* bin local atoms */
binatoms(atom);
for(int bin = 0; bin < mbins; bin++) {
sortBinAtomsByZCoord(param, atom, bin);
}
int resize = 1;
while(resize > 0) {
resize = 0;
void buildClusters(Atom *atom) {
printf("buildClusters start\n");
atom->Nclusters_local = 0;
/* bin local atoms */
binAtoms(atom);
sortAtomsByZCoord(atom);
for(int bin = 0; bin < mbins; bin++) {
int c = bincount[bin];
int ac = 0;
const int nclusters = ((c + CLUSTER_DIM_N - 1) / CLUSTER_DIM_N);
if(nclusters < clusters_per_bin) {
for(int cl = 0; cl < nclusters; cl++) {
const int ci = atom->Nclusters_local;
if(ci >= atom->Nclusters_max) {
growClusters(atom);
}
MD_FLOAT *cptr = cluster_ptr(ci);
MD_FLOAT bbminx = INFINITY, bbmaxx = -INFINITY;
MD_FLOAT bbminy = INFINITY, bbmaxy = -INFINITY;
@ -463,7 +470,6 @@ void buildClusters(Parameter *param, Atom *atom) {
ac++;
}
cluster_bins[bin * clusters_per_bin + cl] = ci;
atom->clusters[ci].bin = bin;
atom->clusters[ci].bbminx = bbminx;
atom->clusters[ci].bbmaxx = bbmaxx;
@ -473,25 +479,37 @@ void buildClusters(Parameter *param, Atom *atom) {
atom->clusters[ci].bbmaxz = bbmaxz;
atom->Nclusters_local++;
}
}
cluster_bincount[bin] = nclusters;
printf("buildClusters end\n");
}
void binClusters(Atom *atom) {
printf("binClusters start\n");
const int nlocal = atom->Nclusters_local;
int resize = 1;
while(resize > 0) {
resize = 0;
for(int bin = 0; bin < mbins; bin++) {
cluster_bincount[bin] = 0;
}
printf("local\n");
for(int ci = 0; ci < nlocal && !resize; ci++) {
int bin = atom->clusters[ci].bin;
int c = cluster_bincount[bin];
if(c < clusters_per_bin) {
cluster_bins[bin * clusters_per_bin + c] = ci;
cluster_bincount[bin]++;
} else {
resize = 1;
}
}
if(resize) {
free(cluster_bins);
clusters_per_bin *= 2;
cluster_bins = (int*) malloc(mbins * clusters_per_bin * sizeof(int));
}
}
}
void binGhostClusters(Parameter *param, Atom *atom) {
int nlocal = atom->Nclusters_local;
for(int ci = 0; ci < atom->Nclusters_ghost; ci++) {
printf("ghost\n");
for(int ci = 0; ci < atom->Nclusters_ghost && !resize; ci++) {
MD_FLOAT *cptr = cluster_ptr(nlocal + ci);
MD_FLOAT xtmp, ytmp;
int ix = -1, iy = -1;
@ -515,7 +533,40 @@ void binGhostClusters(Parameter *param, Atom *atom) {
int bin = iy * mbinx + ix + 1;
int c = cluster_bincount[bin];
if(c < clusters_per_bin) {
cluster_bins[bin * clusters_per_bin + c] = nlocal + ci;
cluster_bincount[bin]++;
} else {
resize = 1;
}
}
printf("end\n");
if(resize) {
free(cluster_bins);
clusters_per_bin *= 2;
cluster_bins = (int*) malloc(mbins * clusters_per_bin * sizeof(int));
}
}
printf("binClusters end\n");
}
void updateSingleAtoms(Atom *atom) {
int Natom = 0;
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
MD_FLOAT *cptr = cluster_ptr(ci);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
atom_x(Natom) = cluster_x(cptr, cii);
atom_y(Natom) = cluster_y(cptr, cii);
atom_z(Natom) = cluster_z(cptr, cii);
Natom++;
}
}
if(Natom != atom->Nlocal) {
fprintf(stderr, "updateSingleAtoms(): Number of atoms changed!\n");
}
}

13
gromacs/pbc.c
View File

@ -44,6 +44,7 @@ void initPbc(Atom* atom) {
/* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */
void updatePbc(Atom *atom, Parameter *param) {
printf("updatePbc start\n");
int *border_map = atom->border_map;
int nlocal = atom->Nclusters_local;
MD_FLOAT xprd = param->xprd;
@ -60,11 +61,13 @@ void updatePbc(Atom *atom, Parameter *param) {
cluster_z(cptr, cii) = cluster_z(bmap_cptr, cii) + atom->PBCz[ci] * zprd;
}
}
printf("updatePbc end\n");
}
/* relocate atoms that have left domain according
* to periodic boundary conditions */
void updateAtomsPbc(Atom *atom, Parameter *param) {
printf("updateAtomsPbc start\n");
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
@ -88,6 +91,7 @@ void updateAtomsPbc(Atom *atom, Parameter *param) {
atom_z(i) -= zprd;
}
}
printf("updateAtomsPbc end\n");
}
/* setup periodic boundary conditions by
@ -120,6 +124,7 @@ void growPbc(Atom* atom) {
}
void setupPbc(Atom *atom, Parameter *param) {
printf("setupPbc start\n");
int *border_map = atom->border_map;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
@ -128,11 +133,11 @@ void setupPbc(Atom *atom, Parameter *param) {
int Nghost = -1;
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
if (atom->Nclusters_local + atom->Nclusters_ghost + 7 >= atom->Nclusters_max) {
if (atom->Nclusters_local + Nghost + 7 >= atom->Nclusters_max) {
growClusters(atom);
}
if (atom->Nclusters_ghost + 7 >= NmaxGhost) {
if (Nghost + 7 >= NmaxGhost) {
growPbc(atom);
border_map = atom->border_map;
}
@ -143,6 +148,7 @@ void setupPbc(Atom *atom, Parameter *param) {
MD_FLOAT bbmaxy = atom->clusters[ci].bbmaxy;
MD_FLOAT bbminz = atom->clusters[ci].bbminz;
MD_FLOAT bbmaxz = atom->clusters[ci].bbmaxz;
/* Setup ghost atoms */
/* 6 planes */
if (bbminx < Cutneigh) { ADDGHOST(+1,0,0); }
@ -179,7 +185,6 @@ void setupPbc(Atom *atom, Parameter *param) {
atom->Nclusters_ghost = Nghost + 1;
atom->Nclusters = atom->Nclusters_local + Nghost + 1;
// Update and bin created ghost clusters
// Update created ghost clusters positions
updatePbc(atom, param);
binGhostClusters(param, atom);
}