347 lines
9.7 KiB
C++
347 lines
9.7 KiB
C++
/* ----------------------------------------------------------------------
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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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#include "compute_coord_atom.h"
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#include "atom.h"
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#include "comm.h"
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#include "compute_orientorder_atom.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 "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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/* ---------------------------------------------------------------------- */
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ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), typelo(nullptr), typehi(nullptr), cvec(nullptr), carray(nullptr),
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group2(nullptr), id_orientorder(nullptr), normv(nullptr)
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{
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if (narg < 5) error->all(FLERR, "Illegal compute coord/atom command");
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jgroupbit = group->get_bitmask_by_id(FLERR, "all", "compute coord/atom");
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cstyle = NONE;
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if (strcmp(arg[3], "cutoff") == 0) {
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cstyle = CUTOFF;
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double cutoff = utils::numeric(FLERR, arg[4], false, lmp);
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cutsq = cutoff * cutoff;
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int iarg = 5;
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if ((narg > 6) && (strcmp(arg[5], "group") == 0)) {
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delete[] group2;
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group2 = utils::strdup(arg[6]);
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iarg += 2;
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jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute coord/atom");
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}
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ncol = narg - iarg + 1;
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int ntypes = atom->ntypes;
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typelo = new int[ncol];
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typehi = new int[ncol];
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if (narg == iarg) {
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ncol = 1;
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typelo[0] = 1;
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typehi[0] = ntypes;
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} else {
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ncol = 0;
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while (iarg < narg) {
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utils::bounds(FLERR, arg[iarg], 1, ntypes, typelo[ncol], typehi[ncol], error);
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if (typelo[ncol] > typehi[ncol]) error->all(FLERR, "Illegal compute coord/atom command");
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ncol++;
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iarg++;
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}
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}
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} else if (strcmp(arg[3], "orientorder") == 0) {
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cstyle = ORIENT;
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if (narg != 6) error->all(FLERR, "Illegal compute coord/atom command");
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id_orientorder = utils::strdup(arg[4]);
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auto iorientorder = modify->get_compute_by_id(id_orientorder);
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if (!iorientorder)
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error->all(FLERR, "Could not find compute coord/atom compute ID {}", id_orientorder);
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if (!utils::strmatch(iorientorder->style, "^orientorder/atom"))
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error->all(FLERR, "Compute coord/atom compute ID {} is not orientorder/atom", id_orientorder);
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threshold = utils::numeric(FLERR, arg[5], false, lmp);
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if (threshold <= -1.0 || threshold >= 1.0)
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error->all(FLERR, "Compute coord/atom threshold not between -1 and 1");
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ncol = 1;
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typelo = new int[ncol];
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typehi = new int[ncol];
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typelo[0] = 1;
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typehi[0] = atom->ntypes;
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} else
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error->all(FLERR, "Invalid cstyle in compute coord/atom");
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peratom_flag = 1;
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if (ncol == 1)
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size_peratom_cols = 0;
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else
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size_peratom_cols = ncol;
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nmax = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeCoordAtom::~ComputeCoordAtom()
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{
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if (copymode) return;
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delete[] group2;
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delete[] typelo;
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delete[] typehi;
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memory->destroy(cvec);
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memory->destroy(carray);
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delete[] id_orientorder;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::init()
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{
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if (cstyle == ORIENT) {
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c_orientorder =
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dynamic_cast<ComputeOrientOrderAtom *>(modify->get_compute_by_id(id_orientorder));
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if (!c_orientorder)
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error->all(FLERR, "Could not find compute coord/atom compute ID {}", id_orientorder);
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cutsq = c_orientorder->cutsq;
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l = c_orientorder->qlcomp;
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// communicate real and imaginary 2*l+1 components of the normalized vector
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comm_forward = 2 * (2 * l + 1);
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if (!(c_orientorder->qlcompflag))
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error->all(FLERR,
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"Compute coord/atom requires components option in compute orientorder/atom");
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}
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if (force->pair == nullptr)
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error->all(FLERR, "Compute coord/atom requires a pair style be defined");
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if (sqrt(cutsq) > force->pair->cutforce)
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error->all(FLERR, "Compute coord/atom cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::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 ComputeCoordAtom::compute_peratom()
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{
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int i, j, m, ii, jj, inum, jnum, jtype, n;
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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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double *count;
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invoked_peratom = update->ntimestep;
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// grow coordination array if necessary
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if (atom->nmax > nmax) {
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if (ncol == 1) {
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memory->destroy(cvec);
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nmax = atom->nmax;
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memory->create(cvec, nmax, "coord/atom:cvec");
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vector_atom = cvec;
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} else {
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memory->destroy(carray);
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nmax = atom->nmax;
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memory->create(carray, nmax, ncol, "coord/atom:carray");
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array_atom = carray;
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}
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}
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if (cstyle == ORIENT) {
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if (!(c_orientorder->invoked_flag & Compute::INVOKED_PERATOM)) {
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c_orientorder->compute_peratom();
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c_orientorder->invoked_flag |= Compute::INVOKED_PERATOM;
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}
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nqlist = c_orientorder->nqlist;
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normv = c_orientorder->array_atom;
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comm->forward_comm(this);
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}
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// invoke full 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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// compute coordination number(s) for each atom in group
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// use full neighbor list to count atoms less than cutoff
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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if (cstyle == CUTOFF) {
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if (ncol == 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) {
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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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n = 0;
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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] & jgroupbit) {
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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 (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) n++;
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}
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}
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cvec[i] = n;
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} else
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cvec[i] = 0.0;
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}
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} else {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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count = carray[i];
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for (m = 0; m < ncol; m++) count[m] = 0.0;
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if (mask[i] & groupbit) {
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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] & jgroupbit) {
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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 (rsq < cutsq) {
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for (m = 0; m < ncol; m++)
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if (jtype >= typelo[m] && jtype <= typehi[m]) count[m] += 1.0;
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}
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}
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}
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}
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}
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}
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} else if (cstyle == ORIENT) {
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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) {
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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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n = 0;
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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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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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double dot_product = 0.0;
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for (m = 0; m < 2 * (2 * l + 1); m++) {
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dot_product += normv[i][nqlist + m] * normv[j][nqlist + m];
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}
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if (dot_product > threshold) n++;
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}
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}
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cvec[i] = n;
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} else
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cvec[i] = 0.0;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
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int * /*pbc*/)
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{
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int i, m = 0, j;
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for (i = 0; i < n; ++i) {
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for (j = nqlist; j < nqlist + 2 * (2 * l + 1); ++j) { buf[m++] = normv[list[i]][j]; }
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
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{
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int i, last, m = 0, j;
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last = first + n;
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for (i = first; i < last; ++i) {
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for (j = nqlist; j < nqlist + 2 * (2 * l + 1); ++j) { normv[i][j] = buf[m++]; }
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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 ComputeCoordAtom::memory_usage()
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{
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double bytes = (double) ncol * nmax * sizeof(double);
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return bytes;
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}
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