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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12285 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-08-08 17:55:44 +00:00
parent 9026afed5c
commit c1e12f9508
22 changed files with 299 additions and 316 deletions
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213
src/balance.cpp
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@ -268,7 +268,7 @@ void Balance::command(int narg, char **arg)
// debug output of initial state
#ifdef BALANCE_DEBUG
if (me == 0 && fp) dumpout(update->ntimestep,fp);
if (outflag) dumpout(update->ntimestep,fp);
#endif
int niter = 0;
@ -328,7 +328,7 @@ void Balance::command(int narg, char **arg)
// output of final result
if (outflag && me == 0) dumpout(update->ntimestep,fp);
if (outflag) dumpout(update->ntimestep,fp);
// reset proc sub-domains
// for either brick or tiled comm style
@ -475,19 +475,59 @@ int *Balance::bisection(int sortflag)
{
if (!rcb) rcb = new RCB(lmp);
// NOTE: lo/hi args could be simulation box or particle bounding box
// if particle bbox, then mysplit needs to be reset to sim box
// NOTE: triclinic needs to be in lamda coords
// NOTE: this logic is specific to orthogonal boxes, not triclinic
int dim = domain->dimension;
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
rcb->compute(dim,atom->nlocal,atom->x,NULL,boxlo,boxhi);
// shrink-wrap simulation box around atoms for input to RCB
// leads to better-shaped sub-boxes when atoms are far from box boundaries
double shrink[6],shrinkall[6];
shrink[0] = boxhi[0]; shrink[1] = boxhi[1]; shrink[2] = boxhi[2];
shrink[3] = boxlo[0]; shrink[4] = boxlo[1]; shrink[5] = boxlo[2];
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
shrink[0] = MIN(shrink[0],x[i][0]);
shrink[1] = MIN(shrink[1],x[i][1]);
shrink[2] = MIN(shrink[2],x[i][2]);
shrink[3] = MAX(shrink[3],x[i][0]);
shrink[4] = MAX(shrink[4],x[i][1]);
shrink[5] = MAX(shrink[5],x[i][2]);
}
shrink[3] = -shrink[3]; shrink[4] = -shrink[4]; shrink[5] = -shrink[5];
MPI_Allreduce(shrink,shrinkall,6,MPI_DOUBLE,MPI_MIN,world);
shrinkall[3] = -shrinkall[3];
shrinkall[4] = -shrinkall[4];
shrinkall[5] = -shrinkall[5];
double *shrinklo = &shrinkall[0];
double *shrinkhi = &shrinkall[3];
// invoke RCB
// then invert() to create list of proc assignements for my atoms
//rcb->compute(dim,atom->nlocal,atom->x,NULL,boxlo,boxhi);
rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
rcb->invert(sortflag);
// reset RCB lo/hi bounding box to full simulation box as needed
// NOTE: this logic is specific to orthogonal boxes, not triclinic
double *lo = rcb->lo;
double *hi = rcb->hi;
if (lo[0] == shrinklo[0]) lo[0] = boxlo[0];
if (lo[1] == shrinklo[1]) lo[1] = boxlo[1];
if (lo[2] == shrinklo[2]) lo[2] = boxlo[2];
if (hi[0] == shrinkhi[0]) hi[0] = boxhi[0];
if (hi[1] == shrinkhi[1]) hi[1] = boxhi[1];
if (hi[2] == shrinkhi[2]) hi[2] = boxhi[2];
// store RCB cut, dim, lo/hi box in CommTiled
// cut and lo/hi need to be in fractional form so can
@ -502,18 +542,18 @@ int *Balance::bisection(int sortflag)
comm->rcbcutdim = idim;
double (*mysplit)[2] = comm->mysplit;
mysplit[0][0] = (lo[0] - boxlo[0]) / prd[0];
if (hi[0] == boxhi[0]) mysplit[0][1] = 1.0;
else mysplit[0][1] = (hi[0] - boxlo[0]) / prd[0];
mysplit[0][0] = (rcb->lo[0] - boxlo[0]) / prd[0];
if (rcb->hi[0] == boxhi[0]) mysplit[0][1] = 1.0;
else mysplit[0][1] = (rcb->hi[0] - boxlo[0]) / prd[0];
mysplit[1][0] = (lo[1] - boxlo[1]) / prd[1];
if (hi[1] == boxhi[1]) mysplit[1][1] = 1.0;
else mysplit[1][1] = (hi[1] - boxlo[1]) / prd[1];
mysplit[1][0] = (rcb->lo[1] - boxlo[1]) / prd[1];
if (rcb->hi[1] == boxhi[1]) mysplit[1][1] = 1.0;
else mysplit[1][1] = (rcb->hi[1] - boxlo[1]) / prd[1];
mysplit[2][0] = (rcb->lo[2] - boxlo[2]) / prd[2];
if (rcb->hi[2] == boxhi[2]) mysplit[2][1] = 1.0;
else mysplit[2][1] = (rcb->hi[2] - boxlo[2]) / prd[2];
mysplit[2][0] = (lo[2] - boxlo[2]) / prd[2];
if (hi[2] == boxhi[2]) mysplit[2][1] = 1.0;
else mysplit[2][1] = (hi[2] - boxlo[2]) / prd[2];
// return list of procs to send my atoms to
@ -669,7 +709,7 @@ int Balance::shift()
#ifdef BALANCE_DEBUG
if (me == 0) debug_shift_output(idim,m+1,np,split);
if (me == 0 && fp) dumpout(update->ntimestep,fp);
if (outflag) dumpout(update->ntimestep,fp);
#endif
// stop if no change in splits, b/c all targets are met exactly
@ -873,89 +913,36 @@ int Balance::binary(double value, int n, double *vec)
write xy lines around each proc's sub-domain for 2d
write xyz cubes around each proc's sub-domain for 3d
only called by proc 0
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
void Balance::dumpout(bigint tstep, FILE *bfp)
void Balance::dumpout(bigint tstep, FILE *fp)
{
int dimension = domain->dimension;
// write out one square/cube per processor for 2d/3d
// only write once since topology is static
// write out nodal coords
// some will be duplicates
if (firststep) {
firststep = 0;
fprintf(bfp,"ITEM: TIMESTEP\n");
fprintf(bfp,BIGINT_FORMAT "\n",tstep);
if (dimension == 2) fprintf(bfp,"ITEM: NUMBER OF SQUARES\n");
else fprintf(bfp,"ITEM: NUMBER OF CUBES\n");
fprintf(bfp,"%d\n",nprocs);
if (dimension == 2) fprintf(bfp,"ITEM: SQUARES\n");
else fprintf(bfp,"ITEM: CUBES\n");
/*
double *sublo = domain->sublo;
double *subhi = domain->subhi;
int nx = comm->procgrid[0] + 1;
int ny = comm->procgrid[1] + 1;
int nz = comm->procgrid[2] + 1;
if (dimension == 2) {
int m = 0;
for (int j = 0; j < comm->procgrid[1]; j++)
for (int i = 0; i < comm->procgrid[0]; i++) {
int c1 = j*nx + i + 1;
int c2 = c1 + 1;
int c3 = c2 + nx;
int c4 = c3 - 1;
fprintf(bfp,"%d %d %d %d %d %d\n",m+1,m+1,c1,c2,c3,c4);
m++;
}
} else {
int m = 0;
for (int k = 0; k < comm->procgrid[2]; k++)
for (int j = 0; j < comm->procgrid[1]; j++)
for (int i = 0; i < comm->procgrid[0]; i++) {
int c1 = k*ny*nx + j*nx + i + 1;
int c2 = c1 + 1;
int c3 = c2 + nx;
int c4 = c3 - 1;
int c5 = c1 + ny*nx;
int c6 = c2 + ny*nx;
int c7 = c3 + ny*nx;
int c8 = c4 + ny*nx;
fprintf(bfp,"%d %d %d %d %d %d %d %d %d %d\n",
m+1,m+1,c1,c2,c3,c4,c5,c6,c7,c8);
m++;
}
}
}
// write out nodal coords, can be different every call
// scale xsplit,ysplit,zsplit values to full box
// only implmented for orthogonal boxes, not triclinic
int nx = comm->procgrid[0] + 1;
int ny = comm->procgrid[1] + 1;
int nz = comm->procgrid[2] + 1;
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
fprintf(bfp,"ITEM: TIMESTEP\n");
fprintf(bfp,BIGINT_FORMAT "\n",tstep);
fprintf(bfp,"ITEM: NUMBER OF NODES\n");
if (dimension == 2) fprintf(bfp,"%d\n",nx*ny);
else fprintf(bfp,"%d\n",nx*ny*nz);
fprintf(bfp,"ITEM: BOX BOUNDS\n");
fprintf(bfp,"%g %g\n",boxlo[0],boxhi[0]);
fprintf(bfp,"%g %g\n",boxlo[1],boxhi[1]);
fprintf(bfp,"%g %g\n",boxlo[2],boxhi[2]);
fprintf(bfp,"ITEM: NODES\n");
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",tstep);
fprintf(fp,"ITEM: NUMBER OF NODES\n");
if (dimension == 2) fprintf(fp,"%d\n",4*nprocs);
else fprintf(fp,"%d\n",8*nprocs);
fprintf(fp,"ITEM: BOX BOUNDS\n");
fprintf(fp,"%g %g\n",boxlo[0],boxhi[0]);
fprintf(fp,"%g %g\n",boxlo[1],boxhi[1]);
fprintf(fp,"%g %g\n",boxlo[2],boxhi[2]);
fprintf(fp,"ITEM: NODES\n");
if (dimension == 2) {
int m = 0;
for (int j = 0; j < ny; j++)
for (int i = 0; i < nx; i++) {
fprintf(bfp,"%d %d %g %g %g\n",m+1,1,
fprintf(fp,"%d %d %g %g %g\n",m+1,1,
boxlo[0] + prd[0]*comm->xsplit[i],
boxlo[1] + prd[1]*comm->ysplit[j],
0.0);
@ -966,13 +953,59 @@ void Balance::dumpout(bigint tstep, FILE *bfp)
for (int k = 0; k < nz; k++)
for (int j = 0; j < ny; j++)
for (int i = 0; i < nx; i++) {
fprintf(bfp,"%d %d %g %g %g\n",m+1,1,
fprintf(fp,"%d %d %g %g %g\n",m+1,1,
boxlo[0] + prd[0]*comm->xsplit[i],
boxlo[1] + prd[1]*comm->ysplit[j],
boxlo[2] + prd[2]*comm->zsplit[k]);
m++;
}
}
// write out one square/cube per processor for 2d/3d
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",tstep);
if (dimension == 2) fprintf(fp,"ITEM: NUMBER OF SQUARES\n");
else fprintf(fp,"ITEM: NUMBER OF CUBES\n");
fprintf(fp,"%d\n",nprocs);
if (dimension == 2) fprintf(fp,"ITEM: SQUARES\n");
else fprintf(fp,"ITEM: CUBES\n");
int nx = comm->procgrid[0] + 1;
int ny = comm->procgrid[1] + 1;
int nz = comm->procgrid[2] + 1;
if (dimension == 2) {
int m = 0;
for (int j = 0; j < comm->procgrid[1]; j++)
for (int i = 0; i < comm->procgrid[0]; i++) {
int c1 = j*nx + i + 1;
int c2 = c1 + 1;
int c3 = c2 + nx;
int c4 = c3 - 1;
fprintf(fp,"%d %d %d %d %d %d\n",m+1,m+1,c1,c2,c3,c4);
m++;
}
} else {
int m = 0;
for (int k = 0; k < comm->procgrid[2]; k++)
for (int j = 0; j < comm->procgrid[1]; j++)
for (int i = 0; i < comm->procgrid[0]; i++) {
int c1 = k*ny*nx + j*nx + i + 1;
int c2 = c1 + 1;
int c3 = c2 + nx;
int c4 = c3 - 1;
int c5 = c1 + ny*nx;
int c6 = c2 + ny*nx;
int c7 = c3 + ny*nx;
int c8 = c4 + ny*nx;
fprintf(fp,"%d %d %d %d %d %d %d %d %d %d\n",
m+1,m+1,c1,c2,c3,c4,c5,c6,c7,c8);
m++;
}
}
*/
}
/* ----------------------------------------------------------------------