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Merge pull request #1388 from lammps/tiled-bug 

bug fix for tiled communication at cutoffs near box size
This commit is contained in:
Axel Kohlmeyer 2019-03-28 13:45:41 -04:00 committed by GitHub
parent d71d12d2de 4aff7191e7
commit 93f531441a
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 20 additions and 19 deletions
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16
src/balance.cpp
View File

@ -1255,14 +1255,14 @@ void Balance::dumpout(bigint tstep)
int m = 0;
for (int i = 0; i < nprocs; i++) {
domain->lamda_box_corners(&boxall[i][0],&boxall[i][3]);
fprintf(fp,"%d %d %g %g %g\n",m+1,1,bc[0][0],bc[0][1],bc[0][1]);
fprintf(fp,"%d %d %g %g %g\n",m+2,1,bc[1][0],bc[1][1],bc[1][1]);
fprintf(fp,"%d %d %g %g %g\n",m+3,1,bc[2][0],bc[2][1],bc[2][1]);
fprintf(fp,"%d %d %g %g %g\n",m+4,1,bc[3][0],bc[3][1],bc[3][1]);
fprintf(fp,"%d %d %g %g %g\n",m+5,1,bc[4][0],bc[4][1],bc[4][1]);
fprintf(fp,"%d %d %g %g %g\n",m+6,1,bc[5][0],bc[5][1],bc[5][1]);
fprintf(fp,"%d %d %g %g %g\n",m+7,1,bc[6][0],bc[6][1],bc[6][1]);
fprintf(fp,"%d %d %g %g %g\n",m+8,1,bc[7][0],bc[7][1],bc[7][1]);
fprintf(fp,"%d %d %g %g %g\n",m+1,1,bc[0][0],bc[0][1],bc[0][2]);
fprintf(fp,"%d %d %g %g %g\n",m+2,1,bc[1][0],bc[1][1],bc[1][2]);
fprintf(fp,"%d %d %g %g %g\n",m+3,1,bc[2][0],bc[2][1],bc[2][2]);
fprintf(fp,"%d %d %g %g %g\n",m+4,1,bc[3][0],bc[3][1],bc[3][2]);
fprintf(fp,"%d %d %g %g %g\n",m+5,1,bc[4][0],bc[4][1],bc[4][2]);
fprintf(fp,"%d %d %g %g %g\n",m+6,1,bc[5][0],bc[5][1],bc[5][2]);
fprintf(fp,"%d %d %g %g %g\n",m+7,1,bc[6][0],bc[6][1],bc[6][2]);
fprintf(fp,"%d %d %g %g %g\n",m+8,1,bc[7][0],bc[7][1],bc[7][2]);
m += 8;
}
}

2
src/comm_tiled.cpp
View File

@ -512,7 +512,7 @@ void CommTiled::forward_comm(int /*dummy*/)
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
}
if (sendother[iswap]) {
for (i = 0; i < nsendproc[iswap]; i++) {
for (i = 0; i < nsend; i++) {
n = avec->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][i],0,world);

12
src/fix_ave_histo.cpp
View File

@ -46,9 +46,9 @@ enum{IGNORE,END,EXTRA};
FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
nvalues(0), which(NULL), argindex(NULL), value2index(NULL),
ids(NULL), fp(NULL), stats_list(NULL),
bin(NULL), bin_total(NULL), bin_all(NULL), bin_list(NULL),
bin(NULL), bin_total(NULL), bin_all(NULL), bin_list(NULL),
coord(NULL), vector(NULL)
{
if (narg < 10) error->all(FLERR,"Illegal fix ave/histo command");
@ -232,7 +232,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
if (ivariable < 0)
error->all(FLERR,"Fix ave/histo input is invalid variable");
// variables only produce one kind of output
if (input->variable->equalstyle(ivariable)) kindglobal = 1;
@ -247,13 +247,13 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
if (kindperatom) kind = PERATOM;
if (kindlocal) kind = LOCAL;
} else if (kind == GLOBAL) {
if (!kindglobal)
if (!kindglobal)
error->all(FLERR,"Fix ave/histo input kind is invalid");
} else if (kind == PERATOM) {
if (!kindperatom)
if (!kindperatom)
error->all(FLERR,"Fix ave/histo input kind is invalid");
} else if (kind == LOCAL) {
if (!kindlocal)
if (!kindlocal)
error->all(FLERR,"Fix ave/histo input kind is invalid");
}
}

9
src/fix_balance.cpp
View File

@ -274,10 +274,6 @@ void FixBalance::rebalance()
comm->layout = Comm::LAYOUT_TILED;
}
// output of new decomposition
if (balance->outflag) balance->dumpout(update->ntimestep);
// reset proc sub-domains
// check and warn if any proc's subbox is smaller than neigh skin
// since may lead to lost atoms in comm->exchange()
@ -286,12 +282,17 @@ void FixBalance::rebalance()
domain->set_local_box();
domain->subbox_too_small_check(neighbor->skin);
// output of new decomposition
if (balance->outflag) balance->dumpout(update->ntimestep);
// move atoms to new processors via irregular()
// for non-RCB only needed if migrate_check() says an atom moves too far
// else allow caller's comm->exchange() to do it
// set disable = 0, so weights migrate with atoms
// important to delay disable = 1 until after pre_neighbor imbfinal calc
// b/c atoms may migrate again in comm->exchange()
// NOTE: for reproducible debug runs, set 1st arg of migrate_atoms() to 1
if (domain->triclinic) domain->x2lamda(atom->nlocal);
if (wtflag) balance->fixstore->disable = 0;