forked from lijiext/lammps
Merge pull request #723 from lammps/replicate_bbox
Add bounding box to Replicate command
This commit is contained in:
Steve Plimpton
GitHub
commit
f2dc764d1d
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@ -10,9 +10,11 @@ replicate command :h3
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[Syntax:]
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replicate nx ny nz :pre
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replicate nx ny nz {keyword} :pre
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nx,ny,nz = replication factors in each dimension :ul
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nx,ny,nz = replication factors in each dimension :ulb
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optional {keyword} = {bbox} :l
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{bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule
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[Examples:]
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@ -43,6 +45,12 @@ file that crosses a periodic boundary should be between two atoms with
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image flags that differ by 1. This will allow the bond to be
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unwrapped appropriately.
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The optional keyword {bbox} uses a bounding box to only check atoms
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in replicas that overlap with a processor's subdomain when assigning
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atoms to processors, and thus can result in substantial speedups for
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calculations using a large number of processors. It does require
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temporarily using more memory.
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[Restrictions:]
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A 2d simulation cannot be replicated in the z dimension.
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@ -44,7 +44,7 @@ void Replicate::command(int narg, char **arg)
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if (domain->box_exist == 0)
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error->all(FLERR,"Replicate command before simulation box is defined");
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if (narg != 3) error->all(FLERR,"Illegal replicate command");
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if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
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int me = comm->me;
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int nprocs = comm->nprocs;
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@ -58,6 +58,10 @@ void Replicate::command(int narg, char **arg)
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int nz = force->inumeric(FLERR,arg[2]);
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int nrep = nx*ny*nz;
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int bbox_flag = 0;
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if (narg == 4)
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if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1;
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// error and warning checks
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if (nx <= 0 || ny <= 0 || nz <= 0)
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@ -99,6 +103,37 @@ void Replicate::command(int narg, char **arg)
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maxmol = maxmol_all;
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}
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// check image flags maximum extent; only efficient small image flags compared to new system
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int _imagelo[3], _imagehi[3];
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_imagelo[0] = 0;
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_imagelo[1] = 0;
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_imagelo[2] = 0;
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_imagehi[0] = 0;
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_imagehi[1] = 0;
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_imagehi[2] = 0;
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if (bbox_flag) {
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for (i=0; i<atom->nlocal; ++i) {
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imageint image = atom->image[i];
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int xbox = (image & IMGMASK) - IMGMAX;
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int ybox = (image >> IMGBITS & IMGMASK) - IMGMAX;
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int zbox = (image >> IMG2BITS) - IMGMAX;
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if (xbox < _imagelo[0]) _imagelo[0] = xbox;
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if (ybox < _imagelo[1]) _imagelo[1] = ybox;
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if (zbox < _imagelo[2]) _imagelo[2] = zbox;
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if (xbox > _imagehi[0]) _imagehi[0] = xbox;
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if (ybox > _imagehi[1]) _imagehi[1] = ybox;
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if (zbox > _imagehi[2]) _imagehi[2] = zbox;
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}
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MPI_Allreduce(MPI_IN_PLACE, &(_imagelo[0]), 3, MPI_INT, MPI_MIN, world);
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MPI_Allreduce(MPI_IN_PLACE, &(_imagehi[0]), 3, MPI_INT, MPI_MAX, world);
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}
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// unmap existing atoms via image flags
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for (i = 0; i < atom->nlocal; i++)
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@ -280,93 +315,392 @@ void Replicate::command(int narg, char **arg)
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double *coord;
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int tag_enable = atom->tag_enable;
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for (int iproc = 0; iproc < nprocs; iproc++) {
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if (me == iproc) {
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n = 0;
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for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);
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if (bbox_flag) {
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// allgather size of buf on each proc
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n = 0;
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for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);
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int * size_buf_rnk;
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memory->create(size_buf_rnk, nprocs, "replicate:size_buf_rnk");
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MPI_Allgather(&n, 1, MPI_INT, size_buf_rnk, 1, MPI_INT, world);
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// size of buf_all
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int size_buf_all = 0;
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MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world);
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if (me == 0 && screen) {
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fprintf(screen," bounding box image = (%i %i %i) to (%i %i %i)\n",
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_imagelo[0],_imagelo[1],_imagelo[2],_imagehi[0],_imagehi[1],_imagehi[2]);
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fprintf(screen," bounding box extra memory = %.2f MB\n",
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(double)size_buf_all*sizeof(double)/1024/1024);
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}
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MPI_Bcast(&n,1,MPI_INT,iproc,world);
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MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world);
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// rnk offsets
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int * disp_buf_rnk;
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memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk");
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disp_buf_rnk[0] = 0;
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for (i=1; i<nprocs; ++i) disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1];
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// allgather buf_all
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double * buf_all;
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memory->create(buf_all, size_buf_all, "replicate:buf_all");
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MPI_Allgatherv(buf, n, MPI_DOUBLE, buf_all, size_buf_rnk, disp_buf_rnk, MPI_DOUBLE, world);
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// bounding box of original unwrapped system
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double _orig_lo[3], _orig_hi[3];
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if (triclinic) {
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_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz;
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_orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd + _imagelo[2] * old_yz;
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_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;
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_orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd + (_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz;
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_orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz;
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_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
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} else {
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_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd;
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_orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd;
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_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;
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_orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd;
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_orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd;
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_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
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}
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double _lo[3], _hi[3];
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int num_replicas_added = 0;
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for (ix = 0; ix < nx; ix++) {
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for (iy = 0; iy < ny; iy++) {
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for (iz = 0; iz < nz; iz++) {
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// domain->remap() overwrites coordinates, so always recompute here
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if (triclinic) {
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_lo[0] = _orig_lo[0] + ix * old_xprd + iy * old_xy + iz * old_xz;
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_hi[0] = _orig_hi[0] + ix * old_xprd + iy * old_xy + iz * old_xz;
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_lo[1] = _orig_lo[1] + iy * old_yprd + iz * old_yz;
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_hi[1] = _orig_hi[1] + iy * old_yprd + iz * old_yz;
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_lo[2] = _orig_lo[2] + iz * old_zprd;
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_hi[2] = _orig_hi[2] + iz * old_zprd;
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} else {
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_lo[0] = _orig_lo[0] + ix * old_xprd;
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_hi[0] = _orig_hi[0] + ix * old_xprd;
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_lo[1] = _orig_lo[1] + iy * old_yprd;
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_hi[1] = _orig_hi[1] + iy * old_yprd;
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_lo[2] = _orig_lo[2] + iz * old_zprd;
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_hi[2] = _orig_hi[2] + iz * old_zprd;
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}
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// test if bounding box of shifted replica overlaps sub-domain of proc
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// if not, then skip testing atoms
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int xoverlap = 1;
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int yoverlap = 1;
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int zoverlap = 1;
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if (triclinic) {
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double _llo[3];
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domain->x2lamda(_lo,_llo);
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double _lhi[3];
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domain->x2lamda(_hi,_lhi);
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if (_llo[0] > (subhi[0] - EPSILON)
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|| _lhi[0] < (sublo[0] + EPSILON) ) xoverlap = 0;
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if (_llo[1] > (subhi[1] - EPSILON)
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|| _lhi[1] < (sublo[1] + EPSILON) ) yoverlap = 0;
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if (_llo[2] > (subhi[2] - EPSILON)
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|| _lhi[2] < (sublo[2] + EPSILON) ) zoverlap = 0;
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} else {
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if (_lo[0] > (subhi[0] - EPSILON)
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|| _hi[0] < (sublo[0] + EPSILON) ) xoverlap = 0;
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if (_lo[1] > (subhi[1] - EPSILON)
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|| _hi[1] < (sublo[1] + EPSILON) ) yoverlap = 0;
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if (_lo[2] > (subhi[2] - EPSILON)
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|| _hi[2] < (sublo[2] + EPSILON) ) zoverlap = 0;
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}
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int overlap = 0;
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if (xoverlap && yoverlap && zoverlap) overlap = 1;
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// if no overlap, test if bounding box wrapped back into new system
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if (!overlap) {
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// wrap back into cell
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imageint imagelo = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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domain->remap(&(_lo[0]), imagelo);
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int xboxlo = (imagelo & IMGMASK) - IMGMAX;
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int yboxlo = (imagelo >> IMGBITS & IMGMASK) - IMGMAX;
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int zboxlo = (imagelo >> IMG2BITS) - IMGMAX;
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imageint imagehi = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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domain->remap(&(_hi[0]), imagehi);
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int xboxhi = (imagehi & IMGMASK) - IMGMAX;
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int yboxhi = (imagehi >> IMGBITS & IMGMASK) - IMGMAX;
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int zboxhi = (imagehi >> IMG2BITS) - IMGMAX;
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if (triclinic) {
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double _llo[3];
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_llo[0] = _lo[0]; _llo[1] = _lo[1]; _llo[2] = _lo[2];
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domain->x2lamda(_llo,_lo);
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double _lhi[3];
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_lhi[0] = _hi[0]; _lhi[1] = _hi[1]; _lhi[2] = _hi[2];
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domain->x2lamda(_lhi,_hi);
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}
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// test all fragments for any overlap; ok to include false positives
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int _xoverlap1 = 0;
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int _xoverlap2 = 0;
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if (!xoverlap) {
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if (xboxlo < 0) {
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_xoverlap1 = 1;
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if ( _lo[0] > (subhi[0] - EPSILON) ) _xoverlap1 = 0;
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}
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if (xboxhi > 0) {
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_xoverlap2 = 1;
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if ( _hi[0] < (sublo[0] + EPSILON) ) _xoverlap2 = 0;
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}
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if (_xoverlap1 || _xoverlap2) xoverlap = 1;
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}
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int _yoverlap1 = 0;
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int _yoverlap2 = 0;
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if (!yoverlap) {
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if (yboxlo < 0) {
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_yoverlap1 = 1;
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if ( _lo[1] > (subhi[1] - EPSILON) ) _yoverlap1 = 0;
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}
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if (yboxhi > 0) {
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_yoverlap2 = 1;
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if ( _hi[1] < (sublo[1] + EPSILON) ) _yoverlap2 = 0;
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}
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if (_yoverlap1 || _yoverlap2) yoverlap = 1;
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}
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int _zoverlap1 = 0;
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int _zoverlap2 = 0;
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if (!zoverlap) {
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if (zboxlo < 0) {
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_zoverlap1 = 1;
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if ( _lo[2] > (subhi[2] - EPSILON) ) _zoverlap1 = 0;
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}
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if (zboxhi > 0) {
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_zoverlap2 = 1;
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if ( _hi[2] < (sublo[2] + EPSILON) ) _zoverlap2 = 0;
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}
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if (_zoverlap1 || _zoverlap2) zoverlap = 1;
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}
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// does either fragment overlap w/ sub-domain
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if (xoverlap && yoverlap && zoverlap) overlap = 1;
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}
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// while loop over one proc's atom list
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m = 0;
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while (m < n) {
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image = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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if (triclinic == 0) {
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x[0] = buf[m+1] + ix*old_xprd;
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x[1] = buf[m+2] + iy*old_yprd;
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x[2] = buf[m+3] + iz*old_zprd;
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} else {
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x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
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x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
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x[2] = buf[m+3] + iz*old_zprd;
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}
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domain->remap(x,image);
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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if (overlap) {
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num_replicas_added++;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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m += avec->unpack_restart(&buf[m]);
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i = atom->nlocal - 1;
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if (tag_enable)
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atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
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else atom_offset = 0;
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mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
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atom->x[i][0] = x[0];
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atom->x[i][1] = x[1];
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atom->x[i][2] = x[2];
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atom->tag[i] += atom_offset;
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atom->image[i] = image;
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if (atom->molecular) {
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if (atom->molecule[i] > 0)
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atom->molecule[i] += mol_offset;
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if (atom->molecular == 1) {
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if (atom->avec->bonds_allow)
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for (j = 0; j < atom->num_bond[i]; j++)
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atom->bond_atom[i][j] += atom_offset;
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if (atom->avec->angles_allow)
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for (j = 0; j < atom->num_angle[i]; j++) {
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atom->angle_atom1[i][j] += atom_offset;
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atom->angle_atom2[i][j] += atom_offset;
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atom->angle_atom3[i][j] += atom_offset;
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}
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if (atom->avec->dihedrals_allow)
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for (j = 0; j < atom->num_dihedral[i]; j++) {
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atom->dihedral_atom1[i][j] += atom_offset;
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atom->dihedral_atom2[i][j] += atom_offset;
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atom->dihedral_atom3[i][j] += atom_offset;
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atom->dihedral_atom4[i][j] += atom_offset;
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}
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if (atom->avec->impropers_allow)
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for (j = 0; j < atom->num_improper[i]; j++) {
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atom->improper_atom1[i][j] += atom_offset;
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atom->improper_atom2[i][j] += atom_offset;
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atom->improper_atom3[i][j] += atom_offset;
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atom->improper_atom4[i][j] += atom_offset;
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}
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}
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m = 0;
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while (m < size_buf_all) {
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image = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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if (triclinic == 0) {
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x[0] = buf_all[m+1] + ix*old_xprd;
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x[1] = buf_all[m+2] + iy*old_yprd;
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x[2] = buf_all[m+3] + iz*old_zprd;
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} else {
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x[0] = buf_all[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
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x[1] = buf_all[m+2] + iy*old_yprd + iz*old_yz;
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x[2] = buf_all[m+3] + iz*old_zprd;
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}
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} else m += static_cast<int> (buf[m]);
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domain->remap(x,image);
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
|
||||
|
||||
m += avec->unpack_restart(&buf_all[m]);
|
||||
|
||||
i = atom->nlocal - 1;
|
||||
if (tag_enable)
|
||||
atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
|
||||
else atom_offset = 0;
|
||||
mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
|
||||
|
||||
atom->x[i][0] = x[0];
|
||||
atom->x[i][1] = x[1];
|
||||
atom->x[i][2] = x[2];
|
||||
|
||||
atom->tag[i] += atom_offset;
|
||||
atom->image[i] = image;
|
||||
|
||||
if (atom->molecular) {
|
||||
if (atom->molecule[i] > 0)
|
||||
atom->molecule[i] += mol_offset;
|
||||
if (atom->molecular == 1) {
|
||||
if (atom->avec->bonds_allow)
|
||||
for (j = 0; j < atom->num_bond[i]; j++)
|
||||
atom->bond_atom[i][j] += atom_offset;
|
||||
if (atom->avec->angles_allow)
|
||||
for (j = 0; j < atom->num_angle[i]; j++) {
|
||||
atom->angle_atom1[i][j] += atom_offset;
|
||||
atom->angle_atom2[i][j] += atom_offset;
|
||||
atom->angle_atom3[i][j] += atom_offset;
|
||||
}
|
||||
if (atom->avec->dihedrals_allow)
|
||||
for (j = 0; j < atom->num_dihedral[i]; j++) {
|
||||
atom->dihedral_atom1[i][j] += atom_offset;
|
||||
atom->dihedral_atom2[i][j] += atom_offset;
|
||||
atom->dihedral_atom3[i][j] += atom_offset;
|
||||
atom->dihedral_atom4[i][j] += atom_offset;
|
||||
}
|
||||
if (atom->avec->impropers_allow)
|
||||
for (j = 0; j < atom->num_improper[i]; j++) {
|
||||
atom->improper_atom1[i][j] += atom_offset;
|
||||
atom->improper_atom2[i][j] += atom_offset;
|
||||
atom->improper_atom3[i][j] += atom_offset;
|
||||
atom->improper_atom4[i][j] += atom_offset;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else m += static_cast<int> (buf_all[m]);
|
||||
}
|
||||
} // if (overlap)
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
memory->destroy(size_buf_rnk);
|
||||
memory->destroy(disp_buf_rnk);
|
||||
memory->destroy(buf_all);
|
||||
|
||||
int sum = 0;
|
||||
MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world);
|
||||
double avg = (double) sum / nprocs;
|
||||
if (me == 0 && screen)
|
||||
fprintf(screen," average # of replicas added to proc = %.2f out of %i (%.2f %%)\n",
|
||||
avg,nx*ny*nz,avg/(nx*ny*nz)*100.0);
|
||||
|
||||
} else {
|
||||
|
||||
for (int iproc = 0; iproc < nprocs; iproc++) {
|
||||
if (me == iproc) {
|
||||
n = 0;
|
||||
for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);
|
||||
}
|
||||
MPI_Bcast(&n,1,MPI_INT,iproc,world);
|
||||
MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world);
|
||||
|
||||
for (ix = 0; ix < nx; ix++) {
|
||||
for (iy = 0; iy < ny; iy++) {
|
||||
for (iz = 0; iz < nz; iz++) {
|
||||
|
||||
// while loop over one proc's atom list
|
||||
|
||||
m = 0;
|
||||
while (m < n) {
|
||||
image = ((imageint) IMGMAX << IMG2BITS) |
|
||||
((imageint) IMGMAX << IMGBITS) | IMGMAX;
|
||||
if (triclinic == 0) {
|
||||
x[0] = buf[m+1] + ix*old_xprd;
|
||||
x[1] = buf[m+2] + iy*old_yprd;
|
||||
x[2] = buf[m+3] + iz*old_zprd;
|
||||
} else {
|
||||
x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
|
||||
x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
|
||||
x[2] = buf[m+3] + iz*old_zprd;
|
||||
}
|
||||
domain->remap(x,image);
|
||||
if (triclinic) {
|
||||
domain->x2lamda(x,lamda);
|
||||
coord = lamda;
|
||||
} else coord = x;
|
||||
|
||||
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
|
||||
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
|
||||
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
|
||||
|
||||
m += avec->unpack_restart(&buf[m]);
|
||||
|
||||
i = atom->nlocal - 1;
|
||||
if (tag_enable)
|
||||
atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
|
||||
else atom_offset = 0;
|
||||
mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
|
||||
|
||||
atom->x[i][0] = x[0];
|
||||
atom->x[i][1] = x[1];
|
||||
atom->x[i][2] = x[2];
|
||||
|
||||
atom->tag[i] += atom_offset;
|
||||
atom->image[i] = image;
|
||||
|
||||
if (atom->molecular) {
|
||||
if (atom->molecule[i] > 0)
|
||||
atom->molecule[i] += mol_offset;
|
||||
if (atom->molecular == 1) {
|
||||
if (atom->avec->bonds_allow)
|
||||
for (j = 0; j < atom->num_bond[i]; j++)
|
||||
atom->bond_atom[i][j] += atom_offset;
|
||||
if (atom->avec->angles_allow)
|
||||
for (j = 0; j < atom->num_angle[i]; j++) {
|
||||
atom->angle_atom1[i][j] += atom_offset;
|
||||
atom->angle_atom2[i][j] += atom_offset;
|
||||
atom->angle_atom3[i][j] += atom_offset;
|
||||
}
|
||||
if (atom->avec->dihedrals_allow)
|
||||
for (j = 0; j < atom->num_dihedral[i]; j++) {
|
||||
atom->dihedral_atom1[i][j] += atom_offset;
|
||||
atom->dihedral_atom2[i][j] += atom_offset;
|
||||
atom->dihedral_atom3[i][j] += atom_offset;
|
||||
atom->dihedral_atom4[i][j] += atom_offset;
|
||||
}
|
||||
if (atom->avec->impropers_allow)
|
||||
for (j = 0; j < atom->num_improper[i]; j++) {
|
||||
atom->improper_atom1[i][j] += atom_offset;
|
||||
atom->improper_atom2[i][j] += atom_offset;
|
||||
atom->improper_atom3[i][j] += atom_offset;
|
||||
atom->improper_atom4[i][j] += atom_offset;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else m += static_cast<int> (buf[m]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
} // if (bbox_flag)
|
||||
|
||||
// free communication buffer and old atom class
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue