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://lammps.sandia.gov/, 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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/* ----------------------------------------------------------------------
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Contributing author: Aidan Thompson (SNL)
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------------------------------------------------------------------------- */
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#include "compute_hexorder_atom.h"
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#include <cmath>
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#include <cstring>
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#include <complex>
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "pair.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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#include "math_const.h"
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#ifdef DBL_EPSILON
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#define MY_EPSILON (10.0*DBL_EPSILON)
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#else
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#define MY_EPSILON (10.0*2.220446049250313e-16)
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#endif
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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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distsq(nullptr), nearest(nullptr), qnarray(nullptr)
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{
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if (narg < 3 ) error->all(FLERR,"Illegal compute hexorder/atom command");
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ndegree = 6;
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nnn = 6;
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cutsq = 0.0;
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// process optional args
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"degree") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
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ndegree = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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if (ndegree < 0)
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error->all(FLERR,"Illegal compute hexorder/atom command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"nnn") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
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if (strcmp(arg[iarg+1],"NULL") == 0)
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nnn = 0;
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else {
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nnn = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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if (nnn < 0)
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error->all(FLERR,"Illegal compute hexorder/atom command");
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"cutoff") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
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double cutoff = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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if (cutoff <= 0.0)
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error->all(FLERR,"Illegal compute hexorder/atom command");
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cutsq = cutoff*cutoff;
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iarg += 2;
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} else error->all(FLERR,"Illegal compute hexorder/atom command");
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}
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ncol = 2;
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peratom_flag = 1;
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size_peratom_cols = ncol;
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nmax = 0;
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maxneigh = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeHexOrderAtom::~ComputeHexOrderAtom()
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{
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memory->destroy(qnarray);
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memory->destroy(distsq);
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memory->destroy(nearest);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeHexOrderAtom::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Compute hexorder/atom requires a pair style be defined");
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if (cutsq == 0.0) cutsq = force->pair->cutforce * force->pair->cutforce;
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else if (sqrt(cutsq) > force->pair->cutforce)
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error->all(FLERR,
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"Compute hexorder/atom cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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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,"hexorder/atom") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute hexorder/atom");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeHexOrderAtom::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 ComputeHexOrderAtom::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 order parameter array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(qnarray);
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nmax = atom->nmax;
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memory->create(qnarray,nmax,ncol,"hexorder/atom:qnarray");
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array_atom = qnarray;
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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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// compute order parameter 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 *mask = atom->mask;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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double* qn = qnarray[i];
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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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// insure 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,"hexorder/atom:distsq");
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memory->create(nearest,maxneigh,"hexorder/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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int ncount = 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[ncount] = rsq;
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nearest[ncount++] = j;
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}
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}
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// if not nnn neighbors, order parameter = 0;
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if (ncount < nnn) {
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qn[0] = qn[1] = 0.0;
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continue;
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}
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// if nnn > 0, use only nearest nnn neighbors
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if (nnn > 0) {
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select2(nnn,ncount,distsq,nearest);
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ncount = nnn;
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}
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double usum = 0.0;
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double vsum = 0.0;
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for (jj = 0; jj < ncount; jj++) {
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j = nearest[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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double u, v;
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calc_qn_complex(delx, dely, u, v);
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usum += u;
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vsum += v;
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}
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qn[0] = usum/nnn;
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qn[1] = vsum/nnn;
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} else qn[0] = qn[1] = 0.0;
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}
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}
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// calculate order parameter using std::complex::pow function
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inline void ComputeHexOrderAtom::calc_qn_complex(double delx, double dely, double &u, double &v) {
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double rinv = 1.0/sqrt(delx*delx+dely*dely);
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double x = delx*rinv;
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double y = dely*rinv;
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std::complex<double> z(x, y);
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std::complex<double> zn = pow(z, ndegree);
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u = real(zn);
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v = imag(zn);
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}
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// calculate order parameter using trig functions
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// this is usually slower, but can be used if <complex> not available
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inline void ComputeHexOrderAtom::calc_qn_trig(double delx, double dely, double &u, double &v) {
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double ntheta;
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if (fabs(delx) <= MY_EPSILON) {
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if (dely > 0.0) ntheta = ndegree * MY_PI / 2.0;
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else ntheta = ndegree * 3.0 * MY_PI / 2.0;
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} else ntheta = ndegree * atan(dely / delx);
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u = cos(ntheta);
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v = sin(ntheta);
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}
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/* ----------------------------------------------------------------------
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select2 routine from Numerical Recipes (slightly modified)
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find k smallest values in array of length n
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sort auxiliary array at same time
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------------------------------------------------------------------------- */
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#define SWAP(a,b) tmp = a; a = b; b = tmp;
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#define ISWAP(a,b) itmp = a; a = b; b = itmp;
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/* ---------------------------------------------------------------------- */
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void ComputeHexOrderAtom::select2(int k, int n, double *arr, int *iarr)
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{
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int i,ir,j,l,mid,ia,itmp;
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double a,tmp;
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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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for (;;) {
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if (ir <= l+1) {
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if (ir == l+1 && arr[ir] < arr[l]) {
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SWAP(arr[l],arr[ir])
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ISWAP(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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SWAP(arr[mid],arr[l+1])
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ISWAP(iarr[mid],iarr[l+1])
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if (arr[l] > arr[ir]) {
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SWAP(arr[l],arr[ir])
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ISWAP(iarr[l],iarr[ir])
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}
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if (arr[l+1] > arr[ir]) {
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SWAP(arr[l+1],arr[ir])
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ISWAP(iarr[l+1],iarr[ir])
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}
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if (arr[l] > arr[l+1]) {
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SWAP(arr[l],arr[l+1])
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ISWAP(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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for (;;) {
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do i++; while (arr[i] < a);
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do j--; while (arr[j] > a);
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if (j < i) break;
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SWAP(arr[i],arr[j])
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ISWAP(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 ComputeHexOrderAtom::memory_usage()
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{
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double bytes = (double)ncol*nmax * sizeof(double);
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bytes += (double)maxneigh * sizeof(double);
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bytes += (double)maxneigh * sizeof(int);
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return bytes;
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}
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