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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11250 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-17 18:43:09 +00:00
parent 961be6ee48
commit bad19033d0
172 changed files with 2523 additions and 2184 deletions
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54
src/dump.cpp
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@ -34,7 +34,6 @@ using namespace LAMMPS_NS;
Dump *Dump::dumpptr;
#define BIG 1.0e20
#define IBIG 2147483647
#define EPSILON 1.0e-6
enum{ASCEND,DESCEND};
@ -77,7 +76,8 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
maxbuf = maxids = maxsort = maxproc = 0;
buf = bufsort = NULL;
ids = idsort = index = proclist = NULL;
ids = idsort = NULL;
index = proclist = NULL;
irregular = NULL;
maxsbuf = 0;
@ -177,7 +177,8 @@ void Dump::init()
maxids = maxsort = maxproc = 0;
bufsort = NULL;
ids = idsort = index = proclist = NULL;
ids = idsort = NULL;
index = proclist = NULL;
irregular = NULL;
}
@ -194,6 +195,7 @@ void Dump::init()
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
@ -202,32 +204,31 @@ void Dump::init()
reorderflag = 0;
if (sortcol == 0 && atom->tag_consecutive()) {
int *tag = atom->tag;
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int min = IBIG;
int max = 0;
tagint min = MAXTAGINT;
tagint max = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
min = MIN(min,tag[i]);
max = MAX(max,tag[i]);
}
int minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
int isize = static_cast<int> (size);
tagint minall,maxall;
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) {
reorderflag = 1;
double range = maxall-minall + EPSILON;
idlo = static_cast<int> (range*me/nprocs + minall);
int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
tagint idhi = static_cast<tagint> (range*(me+1)/nprocs + minall);
int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
int lo = static_cast<int> ((idlo-minall)/range * nprocs);
int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
int hi = static_cast<int> ((idhi-minall)/range * nprocs);
tagint lom1 = static_cast<tagint> ((idlo-1-minall)/range * nprocs);
tagint lo = static_cast<tagint> ((idlo-minall)/range * nprocs);
tagint him1 = static_cast<tagint> ((idhi-1-minall)/range * nprocs);
tagint hi = static_cast<tagint> ((idhi-minall)/range * nprocs);
if (me && me == lom1) idlo--;
else if (me && me != lo) idlo++;
if (me+1 == him1) idhi--;
@ -513,7 +514,7 @@ void Dump::sort()
bufsort = dptr;
if (sortcol == 0) {
int *iptr = ids;
tagint *iptr = ids;
ids = idsort;
idsort = iptr;
}
@ -533,16 +534,21 @@ void Dump::sort()
// proclist[i] = which proc Ith datum will be sent to
if (sortcol == 0) {
int min = IBIG;
int max = 0;
tagint min = MAXTAGINT;
tagint max = 0;
for (i = 0; i < nme; i++) {
min = MIN(min,ids[i]);
max = MAX(max,ids[i]);
}
int minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
double range = maxall-minall + EPSILON;
tagint minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
// use 0.5 instead of EPSILON since atom IDs are integers
// if use EPSILON, it can be lost if 64-bit maxall-minall is too big
// then iproc == nprocs for largest ID, causing irregular to crash
double range = maxall-minall + 0.5;
for (i = 0; i < nme; i++) {
iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
proclist[i] = iproc;
@ -589,7 +595,7 @@ void Dump::sort()
irregular->exchange_data((char *) buf,size_one*sizeof(double),
(char *) bufsort);
if (sortcol == 0)
irregular->exchange_data((char *) ids,sizeof(int),(char *) idsort);
irregular->exchange_data((char *) ids,sizeof(tagint),(char *) idsort);
irregular->destroy_data();
}
@ -645,7 +651,7 @@ void Dump::sort()
int Dump::idcompare(const void *pi, const void *pj)
{
int *idsort = dumpptr->idsort;
tagint *idsort = dumpptr->idsort;
int i = *((int *) pi);
int j = *((int *) pj);