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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13098 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-02-13 16:53:48 +00:00
parent 4682db87f2
commit 8f818715f4
31 changed files with 5531 additions and 1742 deletions
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103
src/compute.cpp
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@ -95,9 +95,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
ntime = maxtime = 0;
tlist = NULL;
// setup map for molecule IDs
molmap = NULL;
// data masks
datamask = ALL_MASK;
datamask_ext = ALL_MASK;
@ -114,9 +112,7 @@ Compute::~Compute()
{
delete [] id;
delete [] style;
memory->destroy(tlist);
memory->destroy(molmap);
}
/* ---------------------------------------------------------------------- */
@ -230,100 +226,3 @@ void Compute::clearstep()
{
ntime = 0;
}
/* ----------------------------------------------------------------------
identify molecule IDs with atoms in group
warn if any atom in group has molecule ID = 0
warn if any molecule has only some atoms in group
return Ncount = # of molecules with atoms in group
set molmap to NULL if molecule IDs include all in range from 1 to Ncount
else: molecule IDs range from idlo to idhi
set molmap to vector of length idhi-idlo+1
molmap[id-idlo] = index from 0 to Ncount-1
return idlo and idhi
------------------------------------------------------------------------- */
int Compute::molecules_in_group(tagint &idlo, tagint &idhi)
{
int i;
memory->destroy(molmap);
molmap = NULL;
// find lo/hi molecule ID for any atom in group
// warn if atom in group has ID = 0
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
tagint lo = BIG;
tagint hi = -BIG;
int flag = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (molecule[i] == 0) flag = 1;
lo = MIN(lo,molecule[i]);
hi = MAX(hi,molecule[i]);
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,"Atom with molecule ID = 0 included in "
"compute molecule group");
MPI_Allreduce(&lo,&idlo,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (idlo == BIG) return 0;
// molmap = vector of length nlen
// set to 1 for IDs that appear in group across all procs, else 0
tagint nlen_tag = idhi-idlo+1;
if (nlen_tag > MAXSMALLINT)
error->all(FLERR,"Too many molecules for compute");
int nlen = (int) nlen_tag;
memory->create(molmap,nlen,"compute:molmap");
for (i = 0; i < nlen; i++) molmap[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
molmap[molecule[i]-idlo] = 1;
int *molmapall;
memory->create(molmapall,nlen,"compute:molmapall");
MPI_Allreduce(molmap,molmapall,nlen,MPI_INT,MPI_MAX,world);
// nmolecules = # of non-zero IDs in molmap
// molmap[i] = index of molecule, skipping molecules not in group with -1
int nmolecules = 0;
for (i = 0; i < nlen; i++)
if (molmapall[i]) molmap[i] = nmolecules++;
else molmap[i] = -1;
memory->destroy(molmapall);
// warn if any molecule has some atoms in group and some not in group
flag = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) continue;
if (molecule[i] < idlo || molecule[i] > idhi) continue;
if (molmap[molecule[i]-idlo] >= 0) flag = 1;
}
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,
"One or more compute molecules has atoms not in group");
// if molmap simply stores 1 to Nmolecules, then free it
if (idlo == 1 && idhi == nmolecules && nlen == nmolecules) {
memory->destroy(molmap);
molmap = NULL;
}
return nmolecules;
}