278 lines
7.8 KiB
C++
278 lines
7.8 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://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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#include "compute_sna_atom.h"
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#include <cstring>
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#include <cstdlib>
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#include "sna.h"
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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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using namespace LAMMPS_NS;
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ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), cutsq(NULL), list(NULL), sna(NULL),
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radelem(NULL), wjelem(NULL)
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{
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double rmin0, rfac0;
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int twojmax, switchflag, bzeroflag;
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radelem = NULL;
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wjelem = NULL;
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int ntypes = atom->ntypes;
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int nargmin = 6+2*ntypes;
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if (narg < nargmin) error->all(FLERR,"Illegal compute sna/atom command");
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// default values
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rmin0 = 0.0;
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switchflag = 1;
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bzeroflag = 1;
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quadraticflag = 0;
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// offset by 1 to match up with types
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memory->create(radelem,ntypes+1,"sna/atom:radelem");
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memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
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rcutfac = atof(arg[3]);
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rfac0 = atof(arg[4]);
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twojmax = atoi(arg[5]);
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for(int i = 0; i < ntypes; i++)
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radelem[i+1] = atof(arg[6+i]);
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for(int i = 0; i < ntypes; i++)
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wjelem[i+1] = atof(arg[6+ntypes+i]);
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// construct cutsq
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double cut;
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cutmax = 0.0;
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memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq");
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for(int i = 1; i <= ntypes; i++) {
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cut = 2.0*radelem[i]*rcutfac;
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if (cut > cutmax) cutmax = cut;
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cutsq[i][i] = cut*cut;
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for(int j = i+1; j <= ntypes; j++) {
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cut = (radelem[i]+radelem[j])*rcutfac;
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cutsq[i][j] = cutsq[j][i] = cut*cut;
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}
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}
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// process optional args
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int iarg = nargmin;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"rmin0") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/atom command");
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rmin0 = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"switchflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/atom command");
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switchflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/atom command");
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bzeroflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/atom command");
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quadraticflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else error->all(FLERR,"Illegal compute sna/atom command");
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}
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snaptr = new SNA(lmp,rfac0,twojmax,
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rmin0,switchflag,bzeroflag);
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ncoeff = snaptr->ncoeff;
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size_peratom_cols = ncoeff;
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if (quadraticflag) size_peratom_cols += (ncoeff*(ncoeff+1))/2;
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peratom_flag = 1;
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nmax = 0;
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sna = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSNAAtom::~ComputeSNAAtom()
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{
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memory->destroy(sna);
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memory->destroy(radelem);
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memory->destroy(wjelem);
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memory->destroy(cutsq);
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delete snaptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAAtom::init()
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{
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if (force->pair == NULL)
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error->all(FLERR,"Compute sna/atom requires a pair style be defined");
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if (cutmax > force->pair->cutforce)
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error->all(FLERR,"Compute sna/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,"sna/atom") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute sna/atom");
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snaptr->init();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAAtom::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 ComputeSNAAtom::compute_peratom()
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{
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invoked_peratom = update->ntimestep;
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// grow sna array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(sna);
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nmax = atom->nmax;
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memory->create(sna,nmax,size_peratom_cols,"sna/atom:sna");
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array_atom = sna;
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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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const int inum = list->inum;
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const int* const ilist = list->ilist;
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const int* const numneigh = list->numneigh;
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int** const firstneigh = list->firstneigh;
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int * const type = atom->type;
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// compute sna for each atom in group
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// use full neighbor list to count atoms less than cutoff
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double** const x = atom->x;
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const int* const mask = atom->mask;
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for (int ii = 0; ii < inum; ii++) {
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const int i = ilist[ii];
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if (mask[i] & groupbit) {
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const double xtmp = x[i][0];
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const double ytmp = x[i][1];
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const double ztmp = x[i][2];
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const int itype = type[i];
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const double radi = radelem[itype];
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const int* const jlist = firstneigh[i];
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const int jnum = numneigh[i];
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// insure rij, inside, and typej are of size jnum
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snaptr->grow_rij(jnum);
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// rij[][3] = displacements between atom I and those neighbors
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// inside = indices of neighbors of I within cutoff
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// typej = types of neighbors of I within cutoff
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int ninside = 0;
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for (int jj = 0; jj < jnum; jj++) {
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int j = jlist[jj];
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j &= NEIGHMASK;
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const double delx = xtmp - x[j][0];
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const double dely = ytmp - x[j][1];
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const double delz = ztmp - x[j][2];
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const double rsq = delx*delx + dely*dely + delz*delz;
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int jtype = type[j];
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if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
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snaptr->rij[ninside][0] = delx;
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snaptr->rij[ninside][1] = dely;
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snaptr->rij[ninside][2] = delz;
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snaptr->inside[ninside] = j;
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snaptr->wj[ninside] = wjelem[jtype];
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snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
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ninside++;
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}
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}
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snaptr->compute_ui(ninside);
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snaptr->compute_zi();
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snaptr->compute_bi();
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for (int icoeff = 0; icoeff < ncoeff; icoeff++)
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sna[i][icoeff] = snaptr->blist[icoeff];
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if (quadraticflag) {
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int ncount = ncoeff;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bi = snaptr->blist[icoeff];
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// diagonal element of quadratic matrix
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sna[i][ncount++] = 0.5*bi*bi;
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// upper-triangular elements of quadratic matrix
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
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sna[i][ncount++] = bi*snaptr->blist[jcoeff];
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}
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}
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} else {
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for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++)
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sna[i][icoeff] = 0.0;
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}
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}
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}
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/* ----------------------------------------------------------------------
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memory usage
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------------------------------------------------------------------------- */
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double ComputeSNAAtom::memory_usage()
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{
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double bytes = nmax*size_peratom_cols * sizeof(double); // sna
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bytes += snaptr->memory_usage(); // SNA object
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return bytes;
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}
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