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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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56
src/replicate.cpp
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@ -73,11 +73,13 @@ void Replicate::command(int narg, char **arg)
// maxtag = largest atom tag across all existing atoms
int maxtag = 0;
for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
int maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
maxtag = maxtag_all;
tagint maxtag = 0;
if (atom->tag_enable) {
for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxtag = maxtag_all;
}
// maxmol = largest molecule tag across all existing atoms
@ -124,25 +126,20 @@ void Replicate::command(int narg, char **arg)
atom->create_avec(old->atom_style,nstyles,keywords);
// check that new system will not be too large
// if molecular and N > MAXTAGINT, error
// if atomic and new N > MAXTAGINT, turn off tags for existing and new atoms
// new system cannot exceed MAXBIGINT
// NOTE: change these 2 to MAXTAGINT when allow tagint = bigint
// new tags cannot exceed MAXTAGINT
// new system sizes cannot exceed MAXBIGINT
if (atom->molecular &&
(nrep*old->natoms < 0 || nrep*old->natoms > MAXSMALLINT))
error->all(FLERR,"Replicated molecular system atom IDs are too big");
if (nrep*old->natoms < 0 || nrep*old->natoms > MAXSMALLINT)
atom->tag_enable = 0;
if (atom->tag_enable == 0)
for (int i = 0; i < atom->nlocal; i++)
atom->tag[i] = 0;
if (atom->tag_enable) {
bigint maxnewtag = maxtag + (nrep-1)*old->natoms;
if (maxnewtag < 0 || maxnewtag >= MAXTAGINT)
error->all(FLERR,"Replicated system atom IDs are too big");
}
if (nrep*old->natoms < 0 || nrep*old->natoms > MAXBIGINT ||
nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
nrep*old->nimpropers < 0 || nrep*old->nimpropers > MAXBIGINT)
if (nrep*old->natoms < 0 || nrep*old->natoms >= MAXBIGINT ||
nrep*old->nbonds < 0 || nrep*old->nbonds >= MAXBIGINT ||
nrep*old->nangles < 0 || nrep*old->nangles >= MAXBIGINT ||
nrep*old->ndihedrals < 0 || nrep*old->ndihedrals >= MAXBIGINT ||
nrep*old->nimpropers < 0 || nrep*old->nimpropers >= MAXBIGINT)
error->all(FLERR,"Replicated system is too big");
// assign atom and topology counts in new class from old one
@ -257,7 +254,8 @@ void Replicate::command(int narg, char **arg)
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
int ix,iy,iz,atom_offset,mol_offset;
int ix,iy,iz,mol_offset;
tagint atom_offset;
imageint image;
double x[3],lamda[3];
double *coord;
@ -393,13 +391,19 @@ void Replicate::command(int narg, char **arg)
}
}
// create global mapping and bond topology now that system is defined
// check that atom IDs are valid
if (atom->map_style) {
atom->nghost = 0;
atom->tag_check();
// if molecular system or user-requested, create global mapping of atoms
if (atom->molecular || atom->map_user) {
atom->map_init();
atom->map_set();
}
// create special bond lists for molecular systems
if (atom->molecular) {
Special special(lmp);
special.build();