427 lines
11 KiB
C++
427 lines
11 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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/* ----------------------------------------------------------------------
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Contributing author: Michel Perez (U Lyon) for non-fcc lattices
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------------------------------------------------------------------------- */
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#include "compute_centro_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 "math_extra.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 <cstring>
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#include <utility>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), distsq(nullptr), nearest(nullptr), centro(nullptr)
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{
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if (narg < 4 || narg > 6) error->all(FLERR, "Illegal compute centro/atom command");
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if (strcmp(arg[3], "fcc") == 0)
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nnn = 12;
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else if (strcmp(arg[3], "bcc") == 0)
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nnn = 8;
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else
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nnn = utils::inumeric(FLERR, arg[3], false, lmp);
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// default values
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axes_flag = 0;
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// optional keywords
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int iarg = 4;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "axes") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute centro/atom command3");
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axes_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else
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error->all(FLERR, "Illegal compute centro/atom command1");
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}
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if (nnn <= 0 || nnn % 2)
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error->all(FLERR, "Illegal neighbor value for compute centro/atom command");
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peratom_flag = 1;
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if (!axes_flag)
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size_peratom_cols = 0;
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else
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size_peratom_cols = 10;
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nmax = 0;
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maxneigh = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeCentroAtom::~ComputeCentroAtom()
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{
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memory->destroy(centro);
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memory->destroy(distsq);
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memory->destroy(nearest);
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if (axes_flag) memory->destroy(array_atom);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCentroAtom::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR, "Compute centro/atom requires a pair style be defined");
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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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if (modify->get_compute_by_style(style).size() > 1)
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if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCentroAtom::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 ComputeCentroAtom::compute_peratom()
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{
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int i, j, k, ii, jj, kk, n, inum, jnum;
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double xtmp, ytmp, ztmp, delx, dely, delz, rsq, value;
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int *ilist, *jlist, *numneigh, **firstneigh;
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invoked_peratom = update->ntimestep;
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// grow centro array if necessary
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// grow array_atom array if axes_flag set
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if (atom->nmax > nmax) {
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if (!axes_flag) {
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memory->destroy(centro);
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nmax = atom->nmax;
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memory->create(centro, nmax, "centro/atom:centro");
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vector_atom = centro;
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} else {
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memory->destroy(centro);
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memory->destroy(array_atom);
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nmax = atom->nmax;
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memory->create(centro, nmax, "centro/atom:centro");
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memory->create(array_atom, nmax, size_peratom_cols, "centro/atom:array_atom");
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}
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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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// npairs = number of unique pairs
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int nhalf = nnn / 2;
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int npairs = nnn * (nnn - 1) / 2;
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auto pairs = new double[npairs];
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// compute centro-symmetry parameter for each atom in group
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// use full neighbor list
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double **x = atom->x;
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int *mask = atom->mask;
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double cutsq = force->pair->cutforce * force->pair->cutforce;
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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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// ensure distsq and nearest arrays are long enough
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if (jnum > maxneigh) {
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memory->destroy(distsq);
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memory->destroy(nearest);
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maxneigh = jnum;
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memory->create(distsq, maxneigh, "centro/atom:distsq");
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memory->create(nearest, maxneigh, "centro/atom:nearest");
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}
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// loop over list of all neighbors within force cutoff
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// distsq[] = distance sq to each
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// nearest[] = atom indices of neighbors
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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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distsq[n] = rsq;
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nearest[n++] = j;
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}
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}
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// check whether to include local crystal symmetry axes
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if (!axes_flag) {
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// if not nnn neighbors, centro = 0.0
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if (n < nnn) {
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centro[i] = 0.0;
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continue;
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}
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// store nnn nearest neighs in 1st nnn locations of distsq and nearest
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select2(nnn, n, distsq, nearest);
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// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
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// pairs = squared length of each R
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n = 0;
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for (j = 0; j < nnn; j++) {
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jj = nearest[j];
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for (k = j + 1; k < nnn; k++) {
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kk = nearest[k];
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delx = x[jj][0] + x[kk][0] - 2.0 * xtmp;
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dely = x[jj][1] + x[kk][1] - 2.0 * ytmp;
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delz = x[jj][2] + x[kk][2] - 2.0 * ztmp;
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pairs[n++] = delx * delx + dely * dely + delz * delz;
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}
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}
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} else {
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// calculate local crystal symmetry axes
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// rsq1, rsq2 are two smallest values of R^2
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// R1, R2 are corresponding vectors Ri - Rj
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// R3 is normal to R1, R2
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double rsq1, rsq2;
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double *r1 = &array_atom[i][1];
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double *r2 = &array_atom[i][4];
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double *r3 = &array_atom[i][7];
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if (n < nnn) {
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centro[i] = 0.0;
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MathExtra::zero3(r1);
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MathExtra::zero3(r2);
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MathExtra::zero3(r3);
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continue;
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}
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// store nnn nearest neighs in 1st nnn locations of distsq and nearest
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select2(nnn, n, distsq, nearest);
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n = 0;
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rsq1 = rsq2 = cutsq;
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for (j = 0; j < nnn; j++) {
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jj = nearest[j];
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for (k = j + 1; k < nnn; k++) {
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kk = nearest[k];
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delx = x[jj][0] + x[kk][0] - 2.0 * xtmp;
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dely = x[jj][1] + x[kk][1] - 2.0 * ytmp;
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delz = x[jj][2] + x[kk][2] - 2.0 * ztmp;
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rsq = delx * delx + dely * dely + delz * delz;
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pairs[n++] = rsq;
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if (rsq < rsq2) {
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if (rsq < rsq1) {
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rsq2 = rsq1;
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MathExtra::copy3(r1, r2);
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rsq1 = rsq;
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MathExtra::sub3(x[jj], x[kk], r1);
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} else {
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rsq2 = rsq;
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MathExtra::sub3(x[jj], x[kk], r2);
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}
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}
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}
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}
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MathExtra::cross3(r1, r2, r3);
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MathExtra::norm3(r1);
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MathExtra::norm3(r2);
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MathExtra::norm3(r3);
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}
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// store nhalf smallest pair distances in 1st nhalf locations of pairs
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select(nhalf, npairs, pairs);
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// centrosymmetry = sum of nhalf smallest squared values
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value = 0.0;
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for (j = 0; j < nhalf; j++) value += pairs[j];
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centro[i] = value;
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} else {
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centro[i] = 0.0;
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if (axes_flag) {
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MathExtra::zero3(&array_atom[i][1]);
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MathExtra::zero3(&array_atom[i][4]);
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MathExtra::zero3(&array_atom[i][7]);
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}
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}
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}
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delete[] pairs;
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if (axes_flag)
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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) array_atom[i][0] = centro[i];
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}
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}
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/* ----------------------------------------------------------------------
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2 select routines from Numerical Recipes (slightly modified)
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find k smallest values in array of length n
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2nd routine sorts auxiliary array at same time
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------------------------------------------------------------------------- */
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void ComputeCentroAtom::select(int k, int n, double *arr)
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{
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int i, ir, j, l, mid;
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double a;
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arr--;
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l = 1;
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ir = n;
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while (true) {
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if (ir <= l + 1) {
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if (ir == l + 1 && arr[ir] < arr[l]) std::swap(arr[l], arr[ir]);
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return;
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} else {
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mid = (l + ir) >> 1;
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std::swap(arr[mid], arr[l + 1]);
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if (arr[l] > arr[ir]) std::swap(arr[l], arr[ir]);
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if (arr[l + 1] > arr[ir]) std::swap(arr[l + 1], arr[ir]);
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if (arr[l] > arr[l + 1]) std::swap(arr[l], arr[l + 1]);
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i = l + 1;
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j = ir;
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a = arr[l + 1];
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while (true) {
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do i++;
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while (arr[i] < a);
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do j--;
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while (arr[j] > a);
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if (j < i) break;
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std::swap(arr[i], arr[j]);
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}
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arr[l + 1] = arr[j];
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arr[j] = a;
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if (j >= k) ir = j - 1;
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if (j <= k) l = i;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
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{
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int i, ir, j, l, mid, ia;
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double a;
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arr--;
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iarr--;
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l = 1;
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ir = n;
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while (true) {
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if (ir <= l + 1) {
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if (ir == l + 1 && arr[ir] < arr[l]) {
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std::swap(arr[l], arr[ir]);
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std::swap(iarr[l], iarr[ir]);
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}
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return;
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} else {
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mid = (l + ir) >> 1;
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std::swap(arr[mid], arr[l + 1]);
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std::swap(iarr[mid], iarr[l + 1]);
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if (arr[l] > arr[ir]) {
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std::swap(arr[l], arr[ir]);
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std::swap(iarr[l], iarr[ir]);
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}
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if (arr[l + 1] > arr[ir]) {
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std::swap(arr[l + 1], arr[ir]);
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std::swap(iarr[l + 1], iarr[ir]);
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}
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if (arr[l] > arr[l + 1]) {
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std::swap(arr[l], arr[l + 1]);
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std::swap(iarr[l], iarr[l + 1]);
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}
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i = l + 1;
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j = ir;
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a = arr[l + 1];
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ia = iarr[l + 1];
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while (true) {
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do i++;
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while (arr[i] < a);
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do j--;
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while (arr[j] > a);
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if (j < i) break;
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std::swap(arr[i], arr[j]);
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std::swap(iarr[i], iarr[j]);
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}
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arr[l + 1] = arr[j];
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arr[j] = a;
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iarr[l + 1] = iarr[j];
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iarr[j] = ia;
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if (j >= k) ir = j - 1;
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if (j <= k) l = i;
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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 ComputeCentroAtom::memory_usage()
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{
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double bytes = (double) nmax * sizeof(double);
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if (axes_flag) bytes += (double) size_peratom_cols * nmax * sizeof(double);
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return bytes;
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}
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