jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

a few bug fixes for support for multi and triclinic in CommTiled

This commit is contained in:
Steve Plimpton 2020-08-05 15:44:02 -06:00
parent c2ed040529
commit 304d6876f4
2 changed files with 41 additions and 33 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
src/atom_vec.cpp
View File

@ -1096,8 +1096,9 @@ void AtomVec::unpack_border(int n, int first, double *buf)
m = 0;
last = first + n;
while (last > nmax) grow(0);
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
@ -1165,8 +1166,9 @@ void AtomVec::unpack_border_vel(int n, int first, double *buf)
m = 0;
last = first + n;
while (last > nmax) grow(0);
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];

68
src/comm_tiled.cpp
View File

@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author (multi) : Adrian Diaz (University of Florida)
Contributing author (multi and triclinic support):
Adrian Diaz (University of Florida)
------------------------------------------------------------------------- */
#include "comm_tiled.h"
@ -99,7 +100,6 @@ void CommTiled::init_buffers()
sendbox_multi = NULL;
maxswap = 6;
nswap = 2*domain->dimension;
allocate_swap(maxswap);
}
@ -109,6 +109,11 @@ void CommTiled::init()
{
Comm::init();
// cannot set nswap in init_buffers() b/c
// dimension command can be after comm_style command
nswap = 2*domain->dimension;
memory->destroy(cutghostmulti);
if (mode == Comm::MULTI)
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
@ -374,21 +379,23 @@ void CommTiled::setup()
if (idir == 0) {
sbox[idim] = sublo[idim];
if (i < noverlap1) sbox[3+idim] = MIN(sbox[3+idim]+cut,subhi[idim]);
else sbox[3+idim] = MIN(sbox[3+idim]-prd[idim]+cut,subhi[idim]);
if (i < noverlap1)
sbox[3+idim] = MIN(sbox[3+idim]+cutghost[idim],subhi[idim]);
else
sbox[3+idim] = MIN(sbox[3+idim]-prd[idim]+cutghost[idim],subhi[idim]);
} else {
if (i < noverlap1) sbox[idim] = MAX(sbox[idim]-cut,sublo[idim]);
else sbox[idim] = MAX(sbox[idim]+prd[idim]-cut,sublo[idim]);
if (i < noverlap1) sbox[idim] = MAX(sbox[idim]-cutghost[idim],sublo[idim]);
else sbox[idim] = MAX(sbox[idim]+prd[idim]-cutghost[idim],sublo[idim]);
sbox[3+idim] = subhi[idim];
}
if (idim >= 1) {
if (sbox[0] == oboxlo[0]) sbox[0] -= cut;
if (sbox[3] == oboxhi[0]) sbox[3] += cut;
if (sbox[0] == oboxlo[0]) sbox[0] -= cutghost[0];
if (sbox[3] == oboxhi[0]) sbox[3] += cutghost[0];
}
if (idim == 2) {
if (sbox[1] == oboxlo[1]) sbox[1] -= cut;
if (sbox[4] == oboxhi[1]) sbox[4] += cut;
if (sbox[1] == oboxlo[1]) sbox[1] -= cutghost[1];
if (sbox[4] == oboxhi[1]) sbox[4] += cutghost[1];
}
memcpy(sendbox[iswap][i],sbox,6*sizeof(double));
@ -1074,9 +1081,8 @@ void CommTiled::borders()
if (rmaxall*size_border > maxrecv) grow_recv(rmaxall*size_border);
// swap atoms with other procs using pack_border(), unpack_border()
// use Waitall() instead of Waitany() because calls to unpack_border()
// must increment per-atom arrays in ascending order
// For the same reason, sendself unpacks must occur after recvother unpacks
// can use Waitany() because calls to unpack_border()
// increment per-atom arrays as much as needed
if (ghost_velocity) {
if (recvother[iswap]) {
@ -1092,13 +1098,6 @@ void CommTiled::borders()
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][m],0,world);
}
}
if (recvother[iswap]) {
MPI_Waitall(nrecv,requests,MPI_STATUS_IGNORE);
for (m = 0; m < nrecv; m++)
avec->unpack_border_vel(recvnum[iswap][m],firstrecv[iswap][m],
&buf_recv[size_border*
forward_recv_offset[iswap][m]]);
}
if (sendself[iswap]) {
avec->pack_border_vel(sendnum[iswap][nsend],sendlist[iswap][nsend],
buf_send,pbc_flag[iswap][nsend],
@ -1106,6 +1105,14 @@ void CommTiled::borders()
avec->unpack_border_vel(recvnum[iswap][nrecv],firstrecv[iswap][nrecv],
buf_send);
}
if (recvother[iswap]) {
for (i = 0; i < nrecv; i++) {
MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE);
avec->unpack_border_vel(recvnum[iswap][m],firstrecv[iswap][m],
&buf_recv[size_border*
forward_recv_offset[iswap][m]]);
}
}
} else {
if (recvother[iswap]) {
@ -1121,19 +1128,20 @@ void CommTiled::borders()
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][m],0,world);
}
}
if (recvother[iswap]) {
MPI_Waitall(nrecv,requests,MPI_STATUS_IGNORE);
for (m = 0; m < nrecv; m++)
avec->unpack_border(recvnum[iswap][m],firstrecv[iswap][m],
&buf_recv[size_border*
forward_recv_offset[iswap][m]]);
}
if (sendself[iswap]) {
avec->pack_border(sendnum[iswap][nsend],sendlist[iswap][nsend],
buf_send,pbc_flag[iswap][nsend],pbc[iswap][nsend]);
avec->unpack_border(recvnum[iswap][nrecv],firstrecv[iswap][nrecv],
buf_send);
}
if (recvother[iswap]) {
for (i = 0; i < nrecv; i++) {
MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE);
avec->unpack_border(recvnum[iswap][m],firstrecv[iswap][m],
&buf_recv[size_border*
forward_recv_offset[iswap][m]]);
}
}
}
// increment ghost atoms
@ -1636,11 +1644,9 @@ 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: these error messages are internal sanity checks
// should not occur, can be removed at some point
int dir;
int index = -1;
int index=-1,dir;
if (hi[idim] == sublo[idim]) {
index = myloc[idim] - 1;
dir = -1;