313 lines
8.3 KiB
C++
313 lines
8.3 KiB
C++
// 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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LAMMPS development team: developers@lammps.org
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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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/* ----------------------------------------------------------------------
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Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
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------------------------------------------------------------------------- */
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#include "compute_rattlers_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 "memory.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 { TYPE, RADIUS };
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/* ---------------------------------------------------------------------- */
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ComputeRattlersAtom::ComputeRattlersAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), ncontacts(nullptr), rattler(nullptr)
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{
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if (narg != 6) error->all(FLERR, "Illegal compute rattlers/atom command");
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if (strcmp(arg[3], "type") == 0)
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cutstyle = TYPE;
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else if (strcmp(arg[3], "radius") == 0)
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cutstyle = RADIUS;
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else
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error->all(FLERR, "Illegal compute rattlers/atom command");
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if (cutstyle == RADIUS && !atom->radius_flag)
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error->all(FLERR, "Compute rattlers/atom radius style requires atom attribute radius");
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ncontacts_rattler = utils::inumeric(FLERR, arg[4], false, lmp);
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max_tries = utils::inumeric(FLERR, arg[5], false, lmp);
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nmax = 0;
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invoked_peratom = -1;
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scalar_flag = 1;
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extscalar = 1;
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peratom_flag = 1;
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size_peratom_cols = 0;
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comm_forward = 1;
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comm_reverse = 1;
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}
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/* ---------------------------------------------------------------------- */
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ComputeRattlersAtom::~ComputeRattlersAtom()
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{
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memory->destroy(ncontacts);
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memory->destroy(rattler);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeRattlersAtom::init()
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{
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if (force->pair == nullptr) error->all(FLERR, "No pair style is defined for compute rattlers");
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// Cannot calculate distance from radii for JKR/DMT
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if (force->pair->beyond_contact)
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error->all(FLERR, "Compute rattlers does not currently support pair styles that extend beyond contact");
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// need an occasional half neighbor list
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// set size to same value as request made by force->pair
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// this should enable it to always be a copy list (e.g. for granular pstyle)
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auto pairrequest = neighbor->find_request(force->pair);
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if (pairrequest && pairrequest->get_size())
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neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL);
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else
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neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeRattlersAtom::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 ComputeRattlersAtom::compute_peratom()
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{
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if (invoked_peratom == update->ntimestep) return;
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invoked_peratom = update->ntimestep;
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int i, j, ii, jj, inum, jnum, itype, jtype, tmp_flag;
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tagint itag, jtag;
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double xtmp, ytmp, ztmp, delx, dely, delz;
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double rsq, radsum;
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if (nmax < atom->nmax) {
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nmax = atom->nmax;
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memory->destroy(ncontacts);
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memory->destroy(rattler);
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memory->create(ncontacts, nmax, "rattlers:ncontacts");
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memory->create(rattler, nmax, "rattlers:rattler");
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vector_atom = rattler;
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}
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for (i = 0; i < nmax; i++) rattler[i] = 0;
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int *ilist, *jlist, *numneigh, **firstneigh;
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double **x = atom->x;
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double *radius = atom->radius;
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tagint *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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// invoke half neighbor list (will copy or build if necessary)
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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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Pair *pair = force->pair;
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double **cutsq = force->pair->cutsq;
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int change_flag = 1;
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int ntry = 0;
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while (ntry < max_tries) {
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change_flag = 0;
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for (i = 0; i < nmax; i++) ncontacts[i] = 0;
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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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if (rattler[i] == 1) 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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itag = tag[i];
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itype = type[i];
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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 (rattler[j] == 1) continue;
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// itag = jtag is possible for long cutoffs that include images of self
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if (newton_pair == 0 && j >= nlocal) {
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag + jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag + jtag) % 2 == 1) continue;
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} else {
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp) {
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if (x[j][1] < ytmp) continue;
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if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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}
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}
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jtype = type[j];
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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 (cutstyle == TYPE) {
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if (rsq >= cutsq[itype][jtype]) continue;
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} else {
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radsum = radius[i] + radius[j];
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if (rsq >= radsum * radsum) continue;
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}
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ncontacts[i] += 1;
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if (newton_pair || j < nlocal)
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ncontacts[j] += 1;
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}
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}
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// add contributions from ghosts
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if (force->newton_pair) comm->reverse_comm(this);
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// Set flags for rattlers
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for (i = 0; i < atom->nlocal; i++) {
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if (ncontacts[i] < ncontacts_rattler && rattler[i] == 0) {
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rattler[i] = 1;
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change_flag = 1;
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}
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}
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comm->forward_comm(this);
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MPI_Allreduce(&change_flag, &tmp_flag, 1, MPI_INT, MPI_MAX, world);
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change_flag = tmp_flag;
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if (change_flag == 0) break;
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ntry += 1;
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}
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if (change_flag == 1)
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error->warning(FLERR, "Rattler calculation failed to converge within max tries");
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}
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/* ---------------------------------------------------------------------- */
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double ComputeRattlersAtom::compute_scalar()
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{
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if (invoked_peratom != update->ntimestep)
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compute_peratom();
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invoked_scalar = update->ntimestep;
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double total_rattlers = 0;
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for (int i = 0; i < atom->nlocal; i++) {
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if (rattler[i] == 1) {
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total_rattlers += 1;
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}
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}
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//Total across processors
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MPI_Allreduce(&total_rattlers, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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int ComputeRattlersAtom::pack_reverse_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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for (i = first; i < last; i++) {
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buf[m++] = ubuf(ncontacts[i]).d;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeRattlersAtom::unpack_reverse_comm(int n, int *list, double *buf)
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{
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int i, j, m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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ncontacts[j] += (int) ubuf(buf[m++]).i;
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeRattlersAtom::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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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = rattler[j];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeRattlersAtom::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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for (i = first; i < last; i++) {
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rattler[i] = buf[m++];
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}
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}
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