move some more computes from EXTRA-COMPUTE back to src because of dependencies
This commit is contained in:
Axel Kohlmeyer
273
src/compute_cluster_atom.cpp
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273
src/compute_cluster_atom.cpp
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_cluster_atom.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "group.h"
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#include "memory.h"
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#include "modify.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "neighbor.h"
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#include "pair.h"
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#include "update.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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enum{CLUSTER,MASK,COORDS};
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/* ---------------------------------------------------------------------- */
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ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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clusterID(nullptr)
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{
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if (narg != 4) error->all(FLERR,"Illegal compute cluster/atom command");
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double cutoff = utils::numeric(FLERR,arg[3],false,lmp);
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cutsq = cutoff*cutoff;
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peratom_flag = 1;
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size_peratom_cols = 0;
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comm_forward = 3;
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nmax = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeClusterAtom::~ComputeClusterAtom()
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{
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memory->destroy(clusterID);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeClusterAtom::init()
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{
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if (atom->tag_enable == 0)
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error->all(FLERR,"Cannot use compute cluster/atom unless atoms have IDs");
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if (force->pair == nullptr)
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error->all(FLERR,"Compute cluster/atom requires a pair style to be defined");
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if (sqrt(cutsq) > force->pair->cutforce)
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error->all(FLERR,
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"Compute cluster/atom cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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// full required so that pair of atoms on 2 procs both set their clusterID
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->compute = 1;
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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neighbor->requests[irequest]->occasional = 1;
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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if (strcmp(modify->compute[i]->style,"cluster/atom") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute cluster/atom");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeClusterAtom::init_list(int /*id*/, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeClusterAtom::compute_peratom()
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{
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int i,j,ii,jj,inum,jnum;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *ilist,*jlist,*numneigh,**firstneigh;
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invoked_peratom = update->ntimestep;
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// grow clusterID array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(clusterID);
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nmax = atom->nmax;
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memory->create(clusterID,nmax,"cluster/atom:clusterID");
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vector_atom = clusterID;
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}
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// invoke full neighbor list (will copy or build if necessary)
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// on the first step of a run, set preflag to one in neighbor->build_one(...)
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if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
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else neighbor->build_one(list);
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// if update->post_integrate set:
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// a dynamic group in FixGroup is invoking a variable with this compute
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// thus ghost atom coords need to be up-to-date after initial_integrate()
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if (update->post_integrate) {
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commflag = COORDS;
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comm->forward_comm_compute(this);
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}
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// if group is dynamic, insure ghost atom masks are current
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if (group->dynamic[igroup]) {
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commflag = MASK;
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comm->forward_comm_compute(this);
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}
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// every atom starts in its own cluster, with clusterID = atomID
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tagint *tag = atom->tag;
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int *mask = atom->mask;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) clusterID[i] = tag[i];
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else clusterID[i] = 0;
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}
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// loop until no more changes on any proc:
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// acquire clusterIDs of ghost atoms
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// loop over my atoms, checking distance to neighbors
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// if both atoms are in cluster, assign lowest clusterID to both
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// iterate until no changes in my atoms
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// then check if any proc made changes
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commflag = CLUSTER;
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double **x = atom->x;
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int change,done,anychange;
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while (1) {
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comm->forward_comm_compute(this);
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change = 0;
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while (1) {
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done = 1;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (!(mask[i] & groupbit)) continue;
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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if (!(mask[j] & groupbit)) continue;
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if (clusterID[i] == clusterID[j]) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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clusterID[i] = clusterID[j] = MIN(clusterID[i],clusterID[j]);
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done = 0;
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}
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}
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}
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if (!done) change = 1;
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if (done) break;
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}
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// stop if all procs are done
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MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
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if (!anychange) break;
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
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int /*pbc_flag*/, int * /*pbc*/)
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{
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int i,j,m;
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m = 0;
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if (commflag == CLUSTER) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = clusterID[j];
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}
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} else if (commflag == MASK) {
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int *mask = atom->mask;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = ubuf(mask[j]).d;
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}
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} else if (commflag == COORDS) {
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double **x = atom->x;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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if (commflag == CLUSTER) {
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for (i = first; i < last; i++) clusterID[i] = buf[m++];
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} else if (commflag == MASK) {
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int *mask = atom->mask;
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for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
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} else if (commflag == COORDS) {
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double **x = atom->x;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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}
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double ComputeClusterAtom::memory_usage()
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{
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double bytes = (double)nmax * sizeof(double);
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return bytes;
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}
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