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Merge branch 'develop' into BPM

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This commit is contained in:
jtclemm
2022-01-12 10:52:11 -07:00
committed by GitHub
parent 744e615dbb 878557dd48
commit 19abc5d329
884 changed files with 39864 additions and 18216 deletions
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64
src/dump.cpp
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@ -128,8 +128,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
char *ptr;
if ((ptr = strchr(filename,'%'))) {
if (strstr(style,"mpiio"))
error->all(FLERR,
"Dump file MPI-IO output not allowed with % in filename");
error->all(FLERR,"Dump file MPI-IO output not allowed with % in filename");
multiproc = 1;
nclusterprocs = 1;
filewriter = 1;
@ -228,7 +227,7 @@ 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 +236,6 @@ 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 +265,7 @@ 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 +281,7 @@ void Dump::init()
else if (me+1 != hi) idhi++;
nme_reorder = idhi-idlo;
ntotal_reorder = isize;
ntotal_reorder = size;
}
}
}
@ -369,16 +366,6 @@ 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 +418,19 @@ 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
@ -918,11 +918,6 @@ void Dump::modify_params(int narg, char **arg)
else delay_flag = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"header") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
write_header_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
int idump;
@ -937,9 +932,28 @@ void Dump::modify_params(int narg, char **arg)
n = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (n <= 0) error->all(FLERR,"Illegal dump_modify command");
}
output->mode_dump[idump] = 0;
output->every_dump[idump] = n;
iarg += 2;
} else if (strcmp(arg[iarg],"every/time") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
double delta;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete [] output->var_dump[idump];
output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
delta = 0.0;
} else {
delta = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (delta <= 0.0) error->all(FLERR,"Illegal dump_modify command");
}
output->mode_dump[idump] = 1;
output->every_time_dump[idump] = delta;
iarg += 2;
} else if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
@ -1007,6 +1021,11 @@ void Dump::modify_params(int narg, char **arg)
iarg += n;
}
} else if (strcmp(arg[iarg],"header") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
write_header_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"maxfiles") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multifile)
@ -1113,6 +1132,7 @@ double Dump::compute_time()
{
return update->atime + (update->ntimestep - update->atimestep)*update->dt;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */