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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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This commit is contained in:
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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120
src/comm_tiled.cpp
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@ -46,8 +46,6 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
{
error->all(FLERR,"Comm_style tiled is not yet supported");
if (lmp->cuda)
error->all(FLERR,"USER-CUDA package does not yet support comm_style tiled");
if (lmp->kokkos)
@ -62,8 +60,6 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
CommTiled::CommTiled(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
{
error->all(FLERR,"Comm_style tiled is not yet supported");
if (lmp->cuda)
error->all(FLERR,"USER-CUDA package does not yet support comm_style tiled");
if (lmp->kokkos)
@ -92,6 +88,11 @@ CommTiled::~CommTiled()
void CommTiled::init_buffers()
{
// bufextra = max size of one exchanged atom
// = allowed overflow of sendbuf in exchange()
// atomvec, fix reset these 2 maxexchange values if needed
// only necessary if their size > BUFEXTRA
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
@ -617,10 +618,9 @@ void CommTiled::reverse_comm()
/* ----------------------------------------------------------------------
exchange: move atoms to correct processors
NOTE: need to re-doc this
atoms exchanged with all 6 stencil neighbors
atoms exchanged with procs that touch sub-box in each of 3 dims
send out atoms that have left my box, receive ones entering my box
atoms will be lost if not inside some proc's box
atoms will be lost if not inside a touching proc's box
can happen if atom moves outside of non-periodic bounary
or if atom moves more than one proc away
this routine called before every reneighboring
@ -645,6 +645,7 @@ void CommTiled::exchange()
atom->avec->clear_bonus();
// insure send buf is large enough for single atom
// bufextra = max size of one atom = allowed overflow of sendbuf
// fixes can change per-atom size requirement on-the-fly
int bufextra_old = bufextra;
@ -691,7 +692,7 @@ void CommTiled::exchange()
/*
// DEBUG:
// test if proc is not in exch list, means will lose atom
// could be that should lose atom
// could be that *should* lose atom
int flag = 0;
for (int k = 0; k < nexchproc[dim]; k++)
if (proc == exchproc[k]) flag = 1;
@ -774,7 +775,7 @@ void CommTiled::exchange()
void CommTiled::borders()
{
int i,m,n,irecv,nlast,nsend,nrecv,ncount,ncountall;
int i,m,n,irecv,nlast,nsend,nrecv,ngroup,ncount,ncountall;
double xlo,xhi,ylo,yhi,zlo,zhi;
double *bbox;
double **x;
@ -791,14 +792,13 @@ void CommTiled::borders()
for (int iswap = 0; iswap < nswap; iswap++) {
// find atoms within rectangles using >= and <
// find atoms within sendboxes using >= and <
// hi test with ">" is important b/c don't want to send an atom
// in lower dim (on boundary) that a proc will recv again in higher dim
// for x-dim swaps, check owned atoms
// for yz-dim swaps, check owned and ghost atoms
// store sent atom indices in list for use in future timesteps
// NOTE: assume SINGLE mode, add back in logic for MULTI mode later
// and for ngroup when bordergroup is set
// store sent atom indices in sendlist for use in future timesteps
// NOTE: assume SINGLE mode, add logic for MULTI mode later
x = atom->x;
if (iswap % 2 == 0) nlast = atom->nlocal + atom->nghost;
@ -811,12 +811,32 @@ void CommTiled::borders()
ncount = 0;
for (i = 0; i < nlast; i++) {
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
if (!bordergroup) {
for (i = 0; i < nlast; i++) {
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
} else {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
for (i = atom->nlocal; i < nlast; i++) {
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
}
@ -961,6 +981,7 @@ void CommTiled::borders()
/* ----------------------------------------------------------------------
forward communication invoked by a Pair
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommTiled::forward_comm_pair(Pair *pair)
@ -1007,7 +1028,7 @@ void CommTiled::forward_comm_pair(Pair *pair)
/* ----------------------------------------------------------------------
reverse communication invoked by a Pair
n = constant number of datums per atom
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_pair(Pair *pair)
@ -1053,15 +1074,20 @@ void CommTiled::reverse_comm_pair(Pair *pair)
/* ----------------------------------------------------------------------
forward communication invoked by a Fix
n = constant number of datums per atom
size/nsize used only to set recv buffer limit
size = 0 (default) -> use comm_forward from Fix
size > 0 -> Fix passes max size per atom
the latter is only useful if Fix does several comm modes,
some are smaller than max stored in its comm_forward
------------------------------------------------------------------------- */
void CommTiled::forward_comm_fix(Fix *fix)
void CommTiled::forward_comm_fix(Fix *fix, int size)
{
int i,irecv,n,nsend,nrecv;
int i,irecv,n,nsize,nsend,nrecv;
MPI_Status status;
int nsize = fix->comm_forward;
if (size) nsize = size;
else nsize = fix->comm_forward;
for (int iswap = 0; iswap < nswap; iswap++) {
nsend = nsendproc[iswap] - sendself[iswap];
@ -1100,15 +1126,20 @@ void CommTiled::forward_comm_fix(Fix *fix)
/* ----------------------------------------------------------------------
reverse communication invoked by a Fix
n = constant number of datums per atom
size/nsize used only to set recv buffer limit
size = 0 (default) -> use comm_forward from Fix
size > 0 -> Fix passes max size per atom
the latter is only useful if Fix does several comm modes,
some are smaller than max stored in its comm_forward
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_fix(Fix *fix)
void CommTiled::reverse_comm_fix(Fix *fix, int size)
{
int i,irecv,n,nsend,nrecv;
int i,irecv,n,nsize,nsend,nrecv;
MPI_Status status;
int nsize = fix->comm_reverse;
if (size) nsize = size;
else nsize = fix->comm_forward;
for (int iswap = nswap-1; iswap >= 0; iswap--) {
nsend = nsendproc[iswap] - sendself[iswap];
@ -1144,30 +1175,9 @@ void CommTiled::reverse_comm_fix(Fix *fix)
}
}
/* ----------------------------------------------------------------------
forward communication invoked by a Fix
n = total datums for all atoms, allows for variable number/atom
NOTE: complicated b/c don't know # to recv a priori
------------------------------------------------------------------------- */
void CommTiled::forward_comm_variable_fix(Fix *fix)
{
// NOTE: these two forward/reverse methods still need to be updated
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Fix
n = total datums for all atoms, allows for variable number/atom
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_variable_fix(Fix *fix)
{
}
/* ----------------------------------------------------------------------
forward communication invoked by a Compute
n = constant number of datums per atom
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommTiled::forward_comm_compute(Compute *compute)
@ -1216,7 +1226,7 @@ void CommTiled::forward_comm_compute(Compute *compute)
/* ----------------------------------------------------------------------
reverse communication invoked by a Compute
n = constant number of datums per atom
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_compute(Compute *compute)
@ -1263,7 +1273,7 @@ void CommTiled::reverse_comm_compute(Compute *compute)
/* ----------------------------------------------------------------------
forward communication invoked by a Dump
n = constant number of datums per atom
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommTiled::forward_comm_dump(Dump *dump)
@ -1311,7 +1321,7 @@ void CommTiled::forward_comm_dump(Dump *dump)
/* ----------------------------------------------------------------------
reverse communication invoked by a Dump
n = constant number of datums per atom
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_dump(Dump *dump)
@ -1444,8 +1454,8 @@ int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf)
void CommTiled::box_drop_brick(int idim, double *lo, double *hi, int &indexme)
{
// NOTE: this is not triclinic compatible
// NOTE: there error messages are internal - should not occur
// can remove at some point
// NOTE: these error messages are internal sanity checks
// should not occur, can be removed at some point
int index,dir;
if (hi[idim] == sublo[idim]) {