152 lines
4.9 KiB
C++
152 lines
4.9 KiB
C++
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
http://lammps.sandia.gov, Sandia National Laboratories
|
|
Steve Plimpton, sjplimp@sandia.gov
|
|
|
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
certain rights in this software. This software is distributed under
|
|
the GNU General Public License.
|
|
|
|
See the README file in the top-level LAMMPS directory.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing author: Jacob Gissinger (jacob.gissinger@colorado.edu)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "reset_mol_ids.h"
|
|
#include <mpi.h>
|
|
#include <string>
|
|
#include "atom.h"
|
|
#include "domain.h"
|
|
#include "comm.h"
|
|
#include "group.h"
|
|
#include "modify.h"
|
|
#include "compute_fragment_atom.h"
|
|
#include "compute_chunk_atom.h"
|
|
#include "utils.h"
|
|
#include "error.h"
|
|
#include "fmt/format.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) {}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ResetMolIDs::command(int narg, char **arg)
|
|
{
|
|
if (domain->box_exist == 0)
|
|
error->all(FLERR,"Reset_mol_ids command before simulation box is defined");
|
|
if (atom->tag_enable == 0)
|
|
error->all(FLERR,"Cannot use reset_mol_ids unless atoms have IDs");
|
|
if (atom->molecular != 1)
|
|
error->all(FLERR,"Can only use reset_mol_ids on molecular systems");
|
|
|
|
// process args
|
|
|
|
if (narg < 1) error->all(FLERR,"Illegal reset_mol_ids command");
|
|
int igroup = group->find(arg[0]);
|
|
if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID");
|
|
int groupbit = group->bitmask[igroup];
|
|
|
|
bigint offset = 0;
|
|
|
|
int iarg = 1;
|
|
while (iarg < narg) {
|
|
if (strcmp(arg[iarg],"offset") == 0) {
|
|
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
|
|
offset = utils::tnumeric(FLERR,arg[iarg+1],1,lmp);
|
|
if (offset < 0) error->all(FLERR,"Illegal reset_mol_ids command");
|
|
iarg += 2;
|
|
} else error->all(FLERR,"Illegal reset_mol_ids command");
|
|
}
|
|
|
|
if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n");
|
|
|
|
// record wall time for resetting molecule IDs
|
|
|
|
MPI_Barrier(world);
|
|
double time1 = MPI_Wtime();
|
|
|
|
// create instances of compute fragment/atom and compute chunk/atom
|
|
// both use the group-ID for this command
|
|
|
|
const std::string idfrag = "reset_mol_ids_FRAGMENT_ATOM";
|
|
modify->add_compute(fmt::format("{} {} fragment/atom",idfrag,arg[0]));
|
|
|
|
const std::string idchunk = "reset_mol_ids_CHUNK_ATOM";
|
|
modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes",
|
|
idchunk,arg[0]));
|
|
|
|
// initialize system since comm->borders() will be invoked
|
|
|
|
lmp->init();
|
|
|
|
// setup domain, communication
|
|
// exchange will clear map, borders will reset
|
|
// this is the map needed to lookup current global IDs for bond topology
|
|
|
|
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
|
domain->pbc();
|
|
domain->reset_box();
|
|
comm->setup();
|
|
comm->exchange();
|
|
comm->borders();
|
|
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
|
|
|
|
// invoke peratom method of compute fragment/atom
|
|
// walks bond connectivity and assigns each atom a fragment ID
|
|
|
|
int icompute = modify->find_compute(idfrag);
|
|
ComputeFragmentAtom *cfa = (ComputeFragmentAtom *) modify->compute[icompute];
|
|
cfa->compute_peratom();
|
|
double *ids = cfa->vector_atom;
|
|
|
|
// copy fragmentID to molecule ID
|
|
// only for atoms in the group
|
|
|
|
tagint *molecule = atom->molecule;
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit)
|
|
molecule[i] = static_cast<tagint> (ids[i]);
|
|
|
|
// invoke peratom method of compute chunk/atom
|
|
// compress new molecule IDs to be contiguous 1 to Nmol
|
|
// NOTE: use of compute chunk/atom limits # of molecules to 32-bit int
|
|
|
|
icompute = modify->find_compute(idchunk);
|
|
ComputeChunkAtom *cca = (ComputeChunkAtom *) modify->compute[icompute];
|
|
cca->compute_peratom();
|
|
ids = cca->vector_atom;
|
|
int nchunk = cca->nchunk;
|
|
|
|
// copy chunkID to molecule ID + offset
|
|
// only for atoms in the group
|
|
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit)
|
|
molecule[i] = static_cast<tagint> (ids[i]) + offset;
|
|
|
|
// clean up
|
|
|
|
modify->delete_compute(idchunk);
|
|
modify->delete_compute(idfrag);
|
|
|
|
// total time
|
|
|
|
MPI_Barrier(world);
|
|
|
|
if (comm->me == 0) {
|
|
utils::logmesg(lmp,fmt::format(" number of new molecule IDs = {}\n",nchunk));
|
|
utils::logmesg(lmp,fmt::format(" reset_mol_ids CPU = {:.3f} seconds\n",
|
|
MPI_Wtime()-time1));
|
|
}
|
|
}
|