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This commit is contained in:
Steve Plimpton
2022-11-07 16:18:40 -07:00
parent e6da584a76
commit 90b54300e9
22 changed files with 222 additions and 222 deletions
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102
src/grid2d.cpp
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@ -2,7 +2,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
LAMMPS Development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -58,7 +58,7 @@ Grid2d::Grid2d(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny) : Pointers(lmp)
// default settings, can be overridden by set() methods
// these affect assignment of owned and ghost cells
maxdist = 0.0;
stencil_grid_lo = stencil_grid_hi = 0;
stencil_atom_lo = stencil_atom_hi = 0;
@ -94,7 +94,7 @@ Grid2d::Grid2d(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny,
ny = gny;
// store owned/ghost indices provided by caller
inxlo = ixlo;
inxhi = ixhi;
inylo = iylo;
@ -142,14 +142,14 @@ Grid2d::~Grid2d()
memory->destroy(copy[i].unpacklist);
}
memory->sfree(copy);
delete [] requests;
delete [] requests_remap;
memory->sfree(rcbinfo);
// remap data structs
deallocate_remap();
}
@ -328,9 +328,9 @@ void Grid2d::setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi,
{
// owned grid cells = those whose grid point is within proc subdomain
// shift_grid = 0.5 for grid point at cell center, 0.0 for lower-left corner
double fraclo,frachi;
if (comm->layout != Comm::LAYOUT_TILED) {
fraclo = comm->xsplit[comm->myloc[0]];
frachi = comm->xsplit[comm->myloc[0]+1];
@ -355,9 +355,9 @@ void Grid2d::setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi,
// other constructor invokes this directly
initialize();
// return values
ixlo = inxlo;
ixhi = inxhi;
iylo = inylo;
@ -384,7 +384,7 @@ void Grid2d::initialize()
// default = caller grid is allocated to ghost grid
// used when computing pack/unpack lists in indices()
// these values can be overridden using set_caller_grid()
fullxlo = outxlo;
fullxhi = outxhi;
fullylo = outylo;
@ -476,7 +476,7 @@ void Grid2d::ghost_grid()
}
// for triclinic, maxdist = different value in each orthogonal direction
double dist[3] = {0.0,0.0,0.0};
if (triclinic == 0) dist[0] = dist[1] = dist[2] = maxdist;
else MathExtra::tribbox(domain->h,maxdist,&dist[0]);
@ -488,11 +488,11 @@ void Grid2d::ghost_grid()
// ghost cell layers needed in each dim/dir = max of two extension effects
// OFFSET allows generation of negative indices with static_cast
// out xyz lo/hi = index range of owned + ghost cells
double dxinv = nx / prd[0];
double dyinv = ny / prd[1];
double dyinv_slab = ny / (prd[1] * yfactor);
int lo, hi;
lo = static_cast<int>((sublo[0]-dist[0]-boxlo[0]) * dxinv + shift_atom_lo + OFFSET) - OFFSET;
@ -571,7 +571,7 @@ void Grid2d::extract_comm_info()
ysplit = new double[comm->procgrid[1]+1];
memcpy(xsplit,comm->xsplit,(comm->procgrid[0]+1)*sizeof(double));
memcpy(ysplit,comm->ysplit,(comm->procgrid[1]+1)*sizeof(double));
memory->create(grid2proc,comm->procgrid[0],comm->procgrid[1],comm->procgrid[2],
"grid3d:grid2proc");
memcpy(&grid2proc[0][0][0],&comm->grid2proc[0][0][0],
@ -593,7 +593,7 @@ void Grid2d::extract_comm_info()
if (rcbone.dim <= 0) rcbone.cut = inxlo;
else if (rcbone.dim == 1) rcbone.cut = inylo;
MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR,
rcbinfo,sizeof(RCBinfo),MPI_CHAR,gridcomm);
rcbinfo,sizeof(RCBinfo),MPI_CHAR,gridcomm);
}
}
@ -866,7 +866,7 @@ void Grid2d::setup_comm_tiled(int &nbuf1, int &nbuf2)
// content: me, index of my overlap, box that overlaps with its owned cells
// ncopy = # of overlaps with myself, across a periodic boundary
// skip copy to self when non-PBC
int *proclist;
memory->create(proclist,noverlap,"grid2d:proclist");
srequest = (Request *)
@ -955,7 +955,7 @@ void Grid2d::setup_comm_tiled(int &nbuf1, int &nbuf2)
// create Copy data struct from overlaps with self
// skip copy to self when non-PBC
copy = (Copy *) memory->smalloc(ncopy*sizeof(Copy),"grid2d:copy");
ncopy = 0;
@ -1088,13 +1088,13 @@ void Grid2d::forward_comm(int caller, void *ptr, int nper, int nbyte, int which,
if (layout != Comm::LAYOUT_TILED) {
if (caller == KSPACE)
forward_comm_brick<KSpace>((KSpace *) ptr,nper,nbyte,which,
buf1,buf2,datatype);
buf1,buf2,datatype);
else if (caller == PAIR)
forward_comm_brick<Pair>((Pair *) ptr,nper,nbyte,which,
buf1,buf2,datatype);
buf1,buf2,datatype);
else if (caller == FIX)
forward_comm_brick<Fix>((Fix *) ptr,nper,nbyte,which,
buf1,buf2,datatype);
buf1,buf2,datatype);
} else {
if (caller == KSPACE)
forward_comm_tiled<KSpace>((KSpace *) ptr,nper,nbyte,which,
@ -1115,7 +1115,7 @@ void Grid2d::forward_comm(int caller, void *ptr, int nper, int nbyte, int which,
template < class T >
void Grid2d::
forward_comm_brick(T *ptr, int nper, int /*nbyte*/, int which,
void *buf1, void *buf2, MPI_Datatype datatype)
void *buf1, void *buf2, MPI_Datatype datatype)
{
int m;
MPI_Request request;
@ -1193,13 +1193,13 @@ void Grid2d::reverse_comm(int caller, void *ptr, int nper, int nbyte, int which,
if (layout != Comm::LAYOUT_TILED) {
if (caller == KSPACE)
reverse_comm_brick<KSpace>((KSpace *) ptr,nper,nbyte,which,
buf1,buf2,datatype);
buf1,buf2,datatype);
else if (caller == PAIR)
reverse_comm_brick<Pair>((Pair *) ptr,nper,nbyte,which,
buf1,buf2,datatype);
buf1,buf2,datatype);
else if (caller == FIX)
reverse_comm_brick<Fix>((Fix *) ptr,nper,nbyte,which,
buf1,buf2,datatype);
buf1,buf2,datatype);
} else {
if (caller == KSPACE)
reverse_comm_tiled<KSpace>((KSpace *) ptr,nper,nbyte,which,
@ -1220,7 +1220,7 @@ void Grid2d::reverse_comm(int caller, void *ptr, int nper, int nbyte, int which,
template < class T >
void Grid2d::
reverse_comm_brick(T *ptr, int nper, int /*nbyte*/, int which,
void *buf1, void *buf2, MPI_Datatype datatype)
void *buf1, void *buf2, MPI_Datatype datatype)
{
int m;
MPI_Request request;
@ -1311,7 +1311,7 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
int *box;
// deallocated existing remap data structs
deallocate_remap();
// set layout to current Comm layout
@ -1331,7 +1331,7 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
// use overlap_old to construct send and copy lists
// skip overlaps that contain no grid cells
self_remap = 0;
nsend_remap = 0;
@ -1343,19 +1343,19 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
}
send_remap = new Send[nsend_remap];
nsend_remap = 0;
for (m = 0; m < noverlap_old; m++) {
box = overlap_old[m].box;
if (box[0] > box[1] || box[2] > box[3]) continue;
if (overlap_old[m].proc == me) {
copy_remap.npack =
old->indices(copy_remap.packlist,box[0],box[1],box[2],box[3]);
old->indices(copy_remap.packlist,box[0],box[1],box[2],box[3]);
} else {
send_remap[nsend_remap].proc = overlap_old[m].proc;
send_remap[nsend_remap].npack =
old->indices(send_remap[nsend_remap].packlist,
box[0],box[1],box[2],box[3]);
old->indices(send_remap[nsend_remap].packlist,
box[0],box[1],box[2],box[3]);
nsend_remap++;
}
}
@ -1381,7 +1381,7 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
if (box[0] > box[1] || box[2] > box[3]) continue;
if (overlap_new[m].proc != me) nrecv_remap++;
}
recv_remap = new Recv[nrecv_remap];
nrecv_remap = 0;
@ -1390,12 +1390,12 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
if (box[0] > box[1] || box[2] > box[3]) continue;
if (overlap_new[m].proc == me) {
copy_remap.nunpack =
indices(copy_remap.unpacklist,box[0],box[1],box[2],box[3]);
indices(copy_remap.unpacklist,box[0],box[1],box[2],box[3]);
} else {
recv_remap[nrecv_remap].proc = overlap_new[m].proc;
recv_remap[nrecv_remap].nunpack =
indices(recv_remap[nrecv_remap].unpacklist,
box[0],box[1],box[2],box[3]);
indices(recv_remap[nrecv_remap].unpacklist,
box[0],box[1],box[2],box[3]);
nrecv_remap++;
}
}
@ -1417,7 +1417,7 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
clean_overlap();
old->clean_overlap();
// nremap_buf1 = largest pack or unpack in any Send or Recv or Copy
// nremap_buf2 = sum of all unpacks in Recv
@ -1444,7 +1444,7 @@ void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2)
------------------------------------------------------------------------- */
void Grid2d::remap(int caller, void *ptr, int nper, int nbyte,
void *buf1, void *buf2, MPI_Datatype datatype)
void *buf1, void *buf2, MPI_Datatype datatype)
{
if (caller == FIX) remap_style<Fix>((Fix *) ptr,nper,nbyte,buf1,buf2,datatype);
}
@ -1453,7 +1453,7 @@ void Grid2d::remap(int caller, void *ptr, int nper, int nbyte,
template < class T >
void Grid2d::remap_style(T *ptr, int nper, int nbyte,
void *buf1, void *vbuf2, MPI_Datatype datatype)
void *buf1, void *vbuf2, MPI_Datatype datatype)
{
int i,m,offset;
@ -1487,7 +1487,7 @@ void Grid2d::remap_style(T *ptr, int nper, int nbyte,
MPI_Waitany(nrecv_remap,requests_remap,&m,MPI_STATUS_IGNORE);
offset = nper * recv_remap[m].offset * nbyte;
ptr->unpack_remap_grid((void *) &buf2[offset],
recv_remap[m].nunpack,recv_remap[m].unpacklist);
recv_remap[m].nunpack,recv_remap[m].unpacklist);
}
}
@ -1535,7 +1535,7 @@ void Grid2d::read_file_style(T *ptr, FILE *fp, int nchunk, int maxline)
------------------------------------------------------------------------- */
void Grid2d::write_file(int caller, void *ptr, int which,
int nper, int nbyte, MPI_Datatype datatype)
int nper, int nbyte, MPI_Datatype datatype)
{
if (caller == FIX)
write_file_style<Fix>((Fix *) ptr, which, nper, nbyte, datatype);
@ -1550,7 +1550,7 @@ void Grid2d::write_file(int caller, void *ptr, int which,
template < class T >
void Grid2d::write_file_style(T *ptr, int which,
int nper, int nbyte, MPI_Datatype datatype)
int nper, int nbyte, MPI_Datatype datatype)
{
// maxsize = max size of grid data owned by any proc
@ -1603,7 +1603,7 @@ void Grid2d::write_file_style(T *ptr, int which,
}
// clean up
memory->destroy(onebuf);
}
@ -1640,7 +1640,7 @@ void Grid2d::write_file_style(T *ptr, int which,
int Grid2d::compute_overlap(int ghostflag, int *box, int *pbc, Overlap *&overlap)
{
int obox[4];
memory->create(overlap_procs,nprocs,"grid2d:overlap_procs");
noverlap_list = maxoverlap_list = 0;
overlap_list = nullptr;
@ -1653,11 +1653,11 @@ int Grid2d::compute_overlap(int ghostflag, int *box, int *pbc, Overlap *&overlap
}
// test obox against appropriate layout
if (layout != Comm::LAYOUT_TILED) {
// find comm->procgrid indices in each dim for box bounds
int iproclo = proc_index_uniform(box[0],nx,shift_grid,0,xsplit);
int iprochi = proc_index_uniform(box[1],nx,shift_grid,0,xsplit);
int jproclo = proc_index_uniform(box[2],ny,shift_grid,1,ysplit);
@ -1690,12 +1690,12 @@ int Grid2d::compute_overlap(int ghostflag, int *box, int *pbc, Overlap *&overlap
obox[1] = nx-1;
obox[2] = 0;
obox[3] = ny-1;
partition_tiled(overlap_list[m].proc,0,nprocs-1,obox);
if (me == 1) printf("OBOX: proc %d obox %d %d: %d %d\n",
overlap_list[m].proc,obox[0],obox[1],obox[2],obox[3]);
overlap_list[m].box[0] = MAX(box[0],obox[0]);
overlap_list[m].box[1] = MIN(box[1],obox[1]);
overlap_list[m].box[2] = MAX(box[2],obox[2]);
@ -1860,7 +1860,7 @@ void Grid2d::deallocate_remap()
for (int i = 0; i < nsend_remap; i++)
memory->destroy(send_remap[i].packlist);
delete [] send_remap;
for (int i = 0; i < nrecv_remap; i++)
memory->destroy(recv_remap[i].unpacklist);
delete [] recv_remap;
@ -1913,12 +1913,12 @@ int Grid2d::proc_index_uniform(int igrid, int n, double shift, int dim, double *
// compute the grid bounds for that proc
// if igrid falls within those bounds, return m = proc index
// same logic as in partition_grid()
int m;
for (m = 0; m < comm->procgrid[dim]; m++) {
fraclo = split[m];
frachi = split[m+1];
lo = static_cast<int> (fraclo * n);
while (lo+shift < fraclo*n) lo++;
hi = static_cast<int> (frachi * n);
@ -1953,7 +1953,7 @@ void Grid2d::partition_tiled(int proc, int proclower, int procupper, int *box)
int cut = rcbinfo[procmid].cut;
// adjust box to reflect which half of partition the proc is in
if (proc < procmid) {
box[2*dim+1] = cut-1;
partition_tiled(proc,proclower,procmid-1,box);