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Merge branch 'develop' into time-dumps2

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This commit is contained in:
Axel Kohlmeyer
2021-12-23 14:29:04 -05:00
parent 6a442e1df4 09944f5d7a
commit 23f1c9de60
16 changed files with 759 additions and 27 deletions
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31
src/dump.cpp
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@ -228,7 +228,7 @@ void Dump::init()
if (sort_flag) {
if (multiproc > 1)
error->all(FLERR,
"Cannot dump sort when multiple dump files are written");
"Cannot dump sort when 'nfile' or 'fileper' keywords are set to non-default values");
if (sortcol == 0 && atom->tag_enable == 0)
error->all(FLERR,"Cannot dump sort on atom IDs with no atom IDs defined");
if (sortcol && sortcol > size_one)
@ -237,8 +237,6 @@ void Dump::init()
irregular = new Irregular(lmp);
bigint size = group->count(igroup);
if (size > MAXSMALLINT) error->all(FLERR,"Too many atoms to dump sort");
int isize = static_cast<int> (size);
// set reorderflag = 1 if can simply reorder local atoms rather than sort
// criteria: sorting by ID, atom IDs are consecutive from 1 to Natoms
@ -268,7 +266,7 @@ void Dump::init()
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (maxall-minall+1 == isize) {
if (maxall-minall+1 == size) {
reorderflag = 1;
double range = maxall-minall + EPSILON;
idlo = static_cast<tagint> (range*me/nprocs + minall);
@ -284,7 +282,7 @@ void Dump::init()
else if (me+1 != hi) idhi++;
nme_reorder = idhi-idlo;
ntotal_reorder = isize;
ntotal_reorder = size;
}
}
}
@ -369,16 +367,6 @@ void Dump::write()
if (multiproc != nprocs) MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
else nmax = nme;
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
bigint nheader = ntotal;
if (multiproc)
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
if (filewriter && write_header_flag) write_header(nheader);
// insure buf is sized for packing and communicating
// use nmax to insure filewriter proc can receive info from others
// limit nmax*size_one to int since used as arg in MPI calls
@ -431,6 +419,19 @@ void Dump::write()
else pack(nullptr);
if (sort_flag) sort();
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
// must come after sort, which can change nme
bigint nheader = ntotal;
if (multiproc) {
bnme = nme;
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
}
if (filewriter && write_header_flag) write_header(nheader);
// if buffering, convert doubles into strings
// insure sbuf is sized for communicating
// cannot buffer if output is to binary file