1031 lines
30 KiB
C++
1031 lines
30 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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/* ----------------------------------------------------------------------
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Contributing authors: Christopher Weinberger (SNL), Stephen Foiles (SNL),
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Chandra Veer Singh (Cornell)
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------------------------------------------------------------------------- */
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#include "pair_adp.h"
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#include <mpi.h>
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#include <cmath>
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#include <cstdlib>
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#include <cstring>
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#include "atom.h"
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#include "force.h"
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#include "comm.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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#include "utils.h"
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#include "tokenizer.h"
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#include "potential_file_reader.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairADP::PairADP(LAMMPS *lmp) : Pair(lmp)
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{
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restartinfo = 0;
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nmax = 0;
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rho = NULL;
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fp = NULL;
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mu = NULL;
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lambda = NULL;
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map = NULL;
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setfl = NULL;
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frho = NULL;
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rhor = NULL;
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z2r = NULL;
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u2r = NULL;
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w2r = NULL;
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frho_spline = NULL;
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rhor_spline = NULL;
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z2r_spline = NULL;
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u2r_spline = NULL;
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w2r_spline = NULL;
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// set comm size needed by this Pair
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comm_forward = 10;
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comm_reverse = 10;
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single_enable = 0;
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one_coeff = 1;
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manybody_flag = 1;
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}
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/* ----------------------------------------------------------------------
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check if allocated, since class can be destructed when incomplete
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------------------------------------------------------------------------- */
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PairADP::~PairADP()
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{
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memory->destroy(rho);
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memory->destroy(fp);
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memory->destroy(mu);
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memory->destroy(lambda);
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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delete [] map;
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delete [] type2frho;
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memory->destroy(type2rhor);
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memory->destroy(type2z2r);
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memory->destroy(type2u2r);
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memory->destroy(type2w2r);
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}
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if (setfl) {
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for (int i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
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delete [] setfl->elements;
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memory->destroy(setfl->mass);
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memory->destroy(setfl->frho);
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memory->destroy(setfl->rhor);
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memory->destroy(setfl->z2r);
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memory->destroy(setfl->u2r);
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memory->destroy(setfl->w2r);
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delete setfl;
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}
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memory->destroy(frho);
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memory->destroy(rhor);
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memory->destroy(z2r);
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memory->destroy(u2r);
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memory->destroy(w2r);
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memory->destroy(frho_spline);
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memory->destroy(rhor_spline);
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memory->destroy(z2r_spline);
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memory->destroy(u2r_spline);
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memory->destroy(w2r_spline);
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}
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/* ---------------------------------------------------------------------- */
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void PairADP::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,m,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r,p,rhoip,rhojp,z2,z2p,recip,phip,psip,phi;
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double u2,u2p,w2,w2p,nu;
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double *coeff;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double delmux,delmuy,delmuz,trdelmu,tradellam;
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double adpx,adpy,adpz,fx,fy,fz;
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double sumlamxx,sumlamyy,sumlamzz,sumlamyz,sumlamxz,sumlamxy;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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// grow local arrays if necessary
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// need to be atom->nmax in length
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if (atom->nmax > nmax) {
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memory->destroy(rho);
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memory->destroy(fp);
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memory->destroy(mu);
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memory->destroy(lambda);
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nmax = atom->nmax;
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memory->create(rho,nmax,"pair:rho");
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memory->create(fp,nmax,"pair:fp");
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memory->create(mu,nmax,3,"pair:mu");
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memory->create(lambda,nmax,6,"pair:lambda");
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}
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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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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// zero out density
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if (newton_pair) {
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m = nlocal + atom->nghost;
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for (i = 0; i < m; i++) {
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rho[i] = 0.0;
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mu[i][0] = 0.0; mu[i][1] = 0.0; mu[i][2] = 0.0;
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lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
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lambda[i][3] = 0.0; lambda[i][4] = 0.0; lambda[i][5] = 0.0;
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}
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} else {
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for (i = 0; i < nlocal; i++) {
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rho[i] = 0.0;
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mu[i][0] = 0.0; mu[i][1] = 0.0; mu[i][2] = 0.0;
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lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
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lambda[i][3] = 0.0; lambda[i][4] = 0.0; lambda[i][5] = 0.0;
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}
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}
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// rho = density at each atom
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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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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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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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 < cutforcesq) {
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jtype = type[j];
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p = sqrt(rsq)*rdr + 1.0;
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m = static_cast<int> (p);
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m = MIN(m,nr-1);
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p -= m;
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p = MIN(p,1.0);
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coeff = rhor_spline[type2rhor[jtype][itype]][m];
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rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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coeff = u2r_spline[type2u2r[jtype][itype]][m];
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u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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mu[i][0] += u2*delx;
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mu[i][1] += u2*dely;
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mu[i][2] += u2*delz;
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coeff = w2r_spline[type2w2r[jtype][itype]][m];
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w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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lambda[i][0] += w2*delx*delx;
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lambda[i][1] += w2*dely*dely;
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lambda[i][2] += w2*delz*delz;
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lambda[i][3] += w2*dely*delz;
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lambda[i][4] += w2*delx*delz;
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lambda[i][5] += w2*delx*dely;
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if (newton_pair || j < nlocal) {
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// verify sign difference for mu and lambda
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coeff = rhor_spline[type2rhor[itype][jtype]][m];
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rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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coeff = u2r_spline[type2u2r[itype][jtype]][m];
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u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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mu[j][0] -= u2*delx;
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mu[j][1] -= u2*dely;
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mu[j][2] -= u2*delz;
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coeff = w2r_spline[type2w2r[itype][jtype]][m];
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w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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lambda[j][0] += w2*delx*delx;
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lambda[j][1] += w2*dely*dely;
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lambda[j][2] += w2*delz*delz;
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lambda[j][3] += w2*dely*delz;
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lambda[j][4] += w2*delx*delz;
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lambda[j][5] += w2*delx*dely;
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}
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}
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}
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}
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// communicate and sum densities
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if (newton_pair) comm->reverse_comm_pair(this);
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// fp = derivative of embedding energy at each atom
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// phi = embedding energy at each atom
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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p = rho[i]*rdrho + 1.0;
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m = static_cast<int> (p);
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m = MAX(1,MIN(m,nrho-1));
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p -= m;
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p = MIN(p,1.0);
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coeff = frho_spline[type2frho[type[i]]][m];
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fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
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if (eflag) {
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phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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phi += 0.5*(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]);
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phi += 0.5*(lambda[i][0]*lambda[i][0]+lambda[i][1]*
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lambda[i][1]+lambda[i][2]*lambda[i][2]);
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phi += 1.0*(lambda[i][3]*lambda[i][3]+lambda[i][4]*
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lambda[i][4]+lambda[i][5]*lambda[i][5]);
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phi -= 1.0/6.0*(lambda[i][0]+lambda[i][1]+lambda[i][2])*
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(lambda[i][0]+lambda[i][1]+lambda[i][2]);
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if (eflag_global) eng_vdwl += phi;
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if (eflag_atom) eatom[i] += phi;
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}
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}
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// communicate derivative of embedding function
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comm->forward_comm_pair(this);
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// compute forces on each atom
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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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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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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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 < cutforcesq) {
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jtype = type[j];
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r = sqrt(rsq);
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p = r*rdr + 1.0;
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m = static_cast<int> (p);
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m = MIN(m,nr-1);
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p -= m;
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p = MIN(p,1.0);
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// rhoip = derivative of (density at atom j due to atom i)
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// rhojp = derivative of (density at atom i due to atom j)
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// phi = pair potential energy
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// phip = phi'
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// z2 = phi * r
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// z2p = (phi * r)' = (phi' r) + phi
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// u2 = u
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// u2p = u'
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// w2 = w
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// w2p = w'
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// psip needs both fp[i] and fp[j] terms since r_ij appears in two
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// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
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// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
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coeff = rhor_spline[type2rhor[itype][jtype]][m];
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rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
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coeff = rhor_spline[type2rhor[jtype][itype]][m];
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rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
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coeff = z2r_spline[type2z2r[itype][jtype]][m];
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z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
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z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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coeff = u2r_spline[type2u2r[itype][jtype]][m];
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u2p = (coeff[0]*p + coeff[1])*p + coeff[2];
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u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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coeff = w2r_spline[type2w2r[itype][jtype]][m];
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w2p = (coeff[0]*p + coeff[1])*p + coeff[2];
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w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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recip = 1.0/r;
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phi = z2*recip;
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phip = z2p*recip - phi*recip;
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psip = fp[i]*rhojp + fp[j]*rhoip + phip;
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fpair = -psip*recip;
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delmux = mu[i][0]-mu[j][0];
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delmuy = mu[i][1]-mu[j][1];
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delmuz = mu[i][2]-mu[j][2];
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trdelmu = delmux*delx+delmuy*dely+delmuz*delz;
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sumlamxx = lambda[i][0]+lambda[j][0];
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sumlamyy = lambda[i][1]+lambda[j][1];
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sumlamzz = lambda[i][2]+lambda[j][2];
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sumlamyz = lambda[i][3]+lambda[j][3];
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sumlamxz = lambda[i][4]+lambda[j][4];
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sumlamxy = lambda[i][5]+lambda[j][5];
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tradellam = sumlamxx*delx*delx+sumlamyy*dely*dely+
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sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
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2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
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nu = sumlamxx+sumlamyy+sumlamzz;
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adpx = delmux*u2 + trdelmu*u2p*delx*recip +
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2.0*w2*(sumlamxx*delx+sumlamxy*dely+sumlamxz*delz) +
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w2p*delx*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delx;
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adpy = delmuy*u2 + trdelmu*u2p*dely*recip +
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2.0*w2*(sumlamxy*delx+sumlamyy*dely+sumlamyz*delz) +
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w2p*dely*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*dely;
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adpz = delmuz*u2 + trdelmu*u2p*delz*recip +
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2.0*w2*(sumlamxz*delx+sumlamyz*dely+sumlamzz*delz) +
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w2p*delz*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delz;
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adpx*=-1.0; adpy*=-1.0; adpz*=-1.0;
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fx = delx*fpair+adpx;
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fy = dely*fpair+adpy;
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fz = delz*fpair+adpz;
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f[i][0] += fx;
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f[i][1] += fy;
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f[i][2] += fz;
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if (newton_pair || j < nlocal) {
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f[j][0] -= fx;
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f[j][1] -= fy;
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f[j][2] -= fz;
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}
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if (eflag) evdwl = phi;
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if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,
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fx,fy,fz,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairADP::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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map = new int[n+1];
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for (int i = 1; i <= n; i++) map[i] = -1;
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type2frho = new int[n+1];
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memory->create(type2rhor,n+1,n+1,"pair:type2rhor");
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memory->create(type2z2r,n+1,n+1,"pair:type2z2r");
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memory->create(type2u2r,n+1,n+1,"pair:type2u2r");
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memory->create(type2w2r,n+1,n+1,"pair:type2w2r");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairADP::settings(int narg, char **/*arg*/)
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{
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if (narg > 0) error->all(FLERR,"Illegal pair_style command");
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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read concatenated *.plt file
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------------------------------------------------------------------------- */
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void PairADP::coeff(int narg, char **arg)
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{
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int i,j;
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if (!allocated) allocate();
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if (narg != 3 + atom->ntypes)
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error->all(FLERR,"Incorrect args for pair coefficients");
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// insure I,J args are * *
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|
|
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
|
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
|
|
|
// read ADP parameter file
|
|
|
|
if (setfl) {
|
|
for (i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
|
|
delete [] setfl->elements;
|
|
memory->destroy(setfl->mass);
|
|
memory->destroy(setfl->frho);
|
|
memory->destroy(setfl->rhor);
|
|
memory->destroy(setfl->z2r);
|
|
memory->destroy(setfl->u2r);
|
|
memory->destroy(setfl->w2r);
|
|
delete setfl;
|
|
}
|
|
setfl = new Setfl();
|
|
read_file(arg[2]);
|
|
|
|
// read args that map atom types to elements in potential file
|
|
// map[i] = which element the Ith atom type is, -1 if NULL
|
|
|
|
for (i = 3; i < narg; i++) {
|
|
if (strcmp(arg[i],"NULL") == 0) {
|
|
map[i-2] = -1;
|
|
continue;
|
|
}
|
|
for (j = 0; j < setfl->nelements; j++)
|
|
if (strcmp(arg[i],setfl->elements[j]) == 0) break;
|
|
if (j < setfl->nelements) map[i-2] = j;
|
|
else error->all(FLERR,"No matching element in ADP potential file");
|
|
}
|
|
|
|
// clear setflag since coeff() called once with I,J = * *
|
|
|
|
int n = atom->ntypes;
|
|
for (i = 1; i <= n; i++)
|
|
for (j = i; j <= n; j++)
|
|
setflag[i][j] = 0;
|
|
|
|
// set setflag i,j for type pairs where both are mapped to elements
|
|
// set mass of atom type if i = j
|
|
|
|
int count = 0;
|
|
for (i = 1; i <= n; i++) {
|
|
for (j = i; j <= n; j++) {
|
|
if (map[i] >= 0 && map[j] >= 0) {
|
|
setflag[i][j] = 1;
|
|
if (i == j) atom->set_mass(FLERR,i,setfl->mass[map[i]]);
|
|
count++;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
|
}
|
|
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init specific to this pair style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairADP::init_style()
|
|
{
|
|
// convert read-in file(s) to arrays and spline them
|
|
|
|
file2array();
|
|
array2spline();
|
|
|
|
neighbor->request(this,instance_me);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init for one type pair i,j and corresponding j,i
|
|
------------------------------------------------------------------------- */
|
|
|
|
double PairADP::init_one(int /*i*/, int /*j*/)
|
|
{
|
|
// single global cutoff = max of cut from all files read in
|
|
// for funcfl could be multiple files
|
|
// for setfl or fs, just one file
|
|
|
|
if (setfl) cutmax = setfl->cut;
|
|
cutforcesq = cutmax*cutmax;
|
|
|
|
return cutmax;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read potential values from a DYNAMO single element funcfl file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairADP::read_file(char *filename)
|
|
{
|
|
Setfl *file = setfl;
|
|
|
|
// read potential file
|
|
if(comm->me == 0) {
|
|
PotentialFileReader reader(lmp, filename, "ADP");
|
|
|
|
try {
|
|
reader.skip_line();
|
|
reader.skip_line();
|
|
reader.skip_line();
|
|
|
|
// extract element names from nelements line
|
|
ValueTokenizer values = reader.next_values(1);
|
|
file->nelements = values.next_int();
|
|
|
|
if (values.count() != file->nelements + 1)
|
|
error->one(FLERR,"Incorrect element names in ADP potential file");
|
|
|
|
file->elements = new char*[file->nelements];
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
const std::string word = values.next_string();
|
|
const int n = word.length() + 1;
|
|
file->elements[i] = new char[n];
|
|
strcpy(file->elements[i], word.c_str());
|
|
}
|
|
|
|
//
|
|
|
|
values = reader.next_values(5);
|
|
file->nrho = values.next_int();
|
|
file->drho = values.next_double();
|
|
file->nr = values.next_int();
|
|
file->dr = values.next_double();
|
|
file->cut = values.next_double();
|
|
|
|
if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
|
|
error->one(FLERR,"Invalid EAM potential file");
|
|
|
|
memory->create(file->mass, file->nelements, "pair:mass");
|
|
memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
|
|
memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
|
|
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
|
|
memory->create(file->u2r, file->nelements, file->nelements, file->nr + 1, "pair:u2r");
|
|
memory->create(file->w2r, file->nelements, file->nelements, file->nr + 1, "pair:w2r");
|
|
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
values = reader.next_values(2);
|
|
values.next_int(); // ignore
|
|
file->mass[i] = values.next_double();
|
|
|
|
reader.next_dvector(file->nrho, &file->frho[i][1]);
|
|
reader.next_dvector(file->nr, &file->rhor[i][1]);
|
|
}
|
|
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
for (int j = 0; j <= i; j++) {
|
|
reader.next_dvector(file->nr, &file->z2r[i][j][1]);
|
|
}
|
|
}
|
|
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
for (int j = 0; j <= i; j++) {
|
|
reader.next_dvector(file->nr, &file->u2r[i][j][1]);
|
|
}
|
|
}
|
|
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
for (int j = 0; j <= i; j++) {
|
|
reader.next_dvector(file->nr, &file->w2r[i][j][1]);
|
|
}
|
|
}
|
|
} catch (TokenizerException & e) {
|
|
error->one(FLERR, e.what());
|
|
}
|
|
}
|
|
|
|
// broadcast potential information
|
|
MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
|
|
|
|
MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
|
|
MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
|
|
MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
|
|
MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
|
|
MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
|
|
|
|
// allocate memory on other procs
|
|
if (comm->me != 0) {
|
|
file->elements = new char*[file->nelements];
|
|
for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
|
|
memory->create(file->mass, file->nelements, "pair:mass");
|
|
memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
|
|
memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
|
|
memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
|
|
memory->create(file->u2r, file->nelements, file->nelements, file->nr + 1, "pair:u2r");
|
|
memory->create(file->w2r, file->nelements, file->nelements, file->nr + 1, "pair:w2r");
|
|
}
|
|
|
|
// broadcast file->elements string array
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
int n;
|
|
if (comm->me == 0) n = strlen(file->elements[i]) + 1;
|
|
MPI_Bcast(&n, 1, MPI_INT, 0, world);
|
|
if (comm->me != 0) file->elements[i] = new char[n];
|
|
MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
|
|
}
|
|
|
|
// broadcast file->mass, frho, rhor
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
|
|
}
|
|
|
|
// broadcast file->z2r, u2r, w2r
|
|
for (int i = 0; i < file->nelements; i++) {
|
|
for (int j = 0; j <= i; j++) {
|
|
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&file->u2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&file->w2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
convert read-in funcfl potential(s) to standard array format
|
|
interpolate all file values to a single grid and cutoff
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairADP::file2array()
|
|
{
|
|
int i,j,m,n;
|
|
int ntypes = atom->ntypes;
|
|
|
|
// set function params directly from setfl file
|
|
|
|
nrho = setfl->nrho;
|
|
nr = setfl->nr;
|
|
drho = setfl->drho;
|
|
dr = setfl->dr;
|
|
|
|
// ------------------------------------------------------------------
|
|
// setup frho arrays
|
|
// ------------------------------------------------------------------
|
|
|
|
// allocate frho arrays
|
|
// nfrho = # of setfl elements + 1 for zero array
|
|
|
|
nfrho = setfl->nelements + 1;
|
|
memory->destroy(frho);
|
|
memory->create(frho,nfrho,nrho+1,"pair:frho");
|
|
|
|
// copy each element's frho to global frho
|
|
|
|
for (i = 0; i < setfl->nelements; i++)
|
|
for (m = 1; m <= nrho; m++) frho[i][m] = setfl->frho[i][m];
|
|
|
|
// add extra frho of zeroes for non-ADP types to point to (pair hybrid)
|
|
// this is necessary b/c fp is still computed for non-ADP atoms
|
|
|
|
for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
|
|
|
|
// type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
|
|
// if atom type doesn't point to element (non-ADP atom in pair hybrid)
|
|
// then map it to last frho array of zeroes
|
|
|
|
for (i = 1; i <= ntypes; i++)
|
|
if (map[i] >= 0) type2frho[i] = map[i];
|
|
else type2frho[i] = nfrho-1;
|
|
|
|
// ------------------------------------------------------------------
|
|
// setup rhor arrays
|
|
// ------------------------------------------------------------------
|
|
|
|
// allocate rhor arrays
|
|
// nrhor = # of setfl elements
|
|
|
|
nrhor = setfl->nelements;
|
|
memory->destroy(rhor);
|
|
memory->create(rhor,nrhor,nr+1,"pair:rhor");
|
|
|
|
// copy each element's rhor to global rhor
|
|
|
|
for (i = 0; i < setfl->nelements; i++)
|
|
for (m = 1; m <= nr; m++) rhor[i][m] = setfl->rhor[i][m];
|
|
|
|
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
|
|
// for setfl files, I,J mapping only depends on I
|
|
// OK if map = -1 (non-APD atom in pair hybrid) b/c type2rhor not used
|
|
|
|
for (i = 1; i <= ntypes; i++)
|
|
for (j = 1; j <= ntypes; j++)
|
|
type2rhor[i][j] = map[i];
|
|
|
|
// ------------------------------------------------------------------
|
|
// setup z2r arrays
|
|
// ------------------------------------------------------------------
|
|
|
|
// allocate z2r arrays
|
|
// nz2r = N*(N+1)/2 where N = # of setfl elements
|
|
|
|
nz2r = setfl->nelements * (setfl->nelements+1) / 2;
|
|
memory->destroy(z2r);
|
|
memory->create(z2r,nz2r,nr+1,"pair:z2r");
|
|
|
|
// copy each element pair z2r to global z2r, only for I >= J
|
|
|
|
n = 0;
|
|
for (i = 0; i < setfl->nelements; i++)
|
|
for (j = 0; j <= i; j++) {
|
|
for (m = 1; m <= nr; m++) z2r[n][m] = setfl->z2r[i][j][m];
|
|
n++;
|
|
}
|
|
|
|
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
|
|
// set of z2r arrays only fill lower triangular Nelement matrix
|
|
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
|
|
// swap indices when irow < icol to stay lower triangular
|
|
// OK if map = -1 (non-ADP atom in pair hybrid) b/c type2z2r not used
|
|
|
|
int irow,icol;
|
|
for (i = 1; i <= ntypes; i++) {
|
|
for (j = 1; j <= ntypes; j++) {
|
|
irow = map[i];
|
|
icol = map[j];
|
|
if (irow == -1 || icol == -1) continue;
|
|
if (irow < icol) {
|
|
irow = map[j];
|
|
icol = map[i];
|
|
}
|
|
n = 0;
|
|
for (m = 0; m < irow; m++) n += m + 1;
|
|
n += icol;
|
|
type2z2r[i][j] = n;
|
|
}
|
|
}
|
|
|
|
// ------------------------------------------------------------------
|
|
// setup u2r arrays
|
|
// ------------------------------------------------------------------
|
|
|
|
// allocate u2r arrays
|
|
// nu2r = N*(N+1)/2 where N = # of setfl elements
|
|
|
|
nu2r = setfl->nelements * (setfl->nelements+1) / 2;
|
|
memory->destroy(u2r);
|
|
memory->create(u2r,nu2r,nr+1,"pair:u2r");
|
|
|
|
// copy each element pair z2r to global z2r, only for I >= J
|
|
|
|
n = 0;
|
|
for (i = 0; i < setfl->nelements; i++)
|
|
for (j = 0; j <= i; j++) {
|
|
for (m = 1; m <= nr; m++) u2r[n][m] = setfl->u2r[i][j][m];
|
|
n++;
|
|
}
|
|
|
|
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
|
|
// set of z2r arrays only fill lower triangular Nelement matrix
|
|
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
|
|
// swap indices when irow < icol to stay lower triangular
|
|
// OK if map = -1 (non-ADP atom in pair hybrid) b/c type2z2r not used
|
|
|
|
for (i = 1; i <= ntypes; i++) {
|
|
for (j = 1; j <= ntypes; j++) {
|
|
irow = map[i];
|
|
icol = map[j];
|
|
if (irow == -1 || icol == -1) continue;
|
|
if (irow < icol) {
|
|
irow = map[j];
|
|
icol = map[i];
|
|
}
|
|
n = 0;
|
|
for (m = 0; m < irow; m++) n += m + 1;
|
|
n += icol;
|
|
type2u2r[i][j] = n;
|
|
}
|
|
}
|
|
|
|
// ------------------------------------------------------------------
|
|
// setup w2r arrays
|
|
// ------------------------------------------------------------------
|
|
|
|
// allocate w2r arrays
|
|
// nw2r = N*(N+1)/2 where N = # of setfl elements
|
|
|
|
nw2r = setfl->nelements * (setfl->nelements+1) / 2;
|
|
memory->destroy(w2r);
|
|
memory->create(w2r,nw2r,nr+1,"pair:w2r");
|
|
|
|
// copy each element pair z2r to global z2r, only for I >= J
|
|
|
|
n = 0;
|
|
for (i = 0; i < setfl->nelements; i++)
|
|
for (j = 0; j <= i; j++) {
|
|
for (m = 1; m <= nr; m++) w2r[n][m] = setfl->w2r[i][j][m];
|
|
n++;
|
|
}
|
|
|
|
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
|
|
// set of z2r arrays only fill lower triangular Nelement matrix
|
|
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
|
|
// swap indices when irow < icol to stay lower triangular
|
|
// OK if map = -1 (non-ADP atom in pair hybrid) b/c type2z2r not used
|
|
|
|
for (i = 1; i <= ntypes; i++) {
|
|
for (j = 1; j <= ntypes; j++) {
|
|
irow = map[i];
|
|
icol = map[j];
|
|
if (irow == -1 || icol == -1) continue;
|
|
if (irow < icol) {
|
|
irow = map[j];
|
|
icol = map[i];
|
|
}
|
|
n = 0;
|
|
for (m = 0; m < irow; m++) n += m + 1;
|
|
n += icol;
|
|
type2w2r[i][j] = n;
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairADP::array2spline()
|
|
{
|
|
rdr = 1.0/dr;
|
|
rdrho = 1.0/drho;
|
|
|
|
memory->destroy(frho_spline);
|
|
memory->destroy(rhor_spline);
|
|
memory->destroy(z2r_spline);
|
|
memory->destroy(u2r_spline);
|
|
memory->destroy(w2r_spline);
|
|
|
|
memory->create(frho_spline,nfrho,nrho+1,7,"pair:frho");
|
|
memory->create(rhor_spline,nrhor,nr+1,7,"pair:rhor");
|
|
memory->create(z2r_spline,nz2r,nr+1,7,"pair:z2r");
|
|
memory->create(u2r_spline,nz2r,nr+1,7,"pair:u2r");
|
|
memory->create(w2r_spline,nz2r,nr+1,7,"pair:w2r");
|
|
|
|
for (int i = 0; i < nfrho; i++)
|
|
interpolate(nrho,drho,frho[i],frho_spline[i]);
|
|
|
|
for (int i = 0; i < nrhor; i++)
|
|
interpolate(nr,dr,rhor[i],rhor_spline[i]);
|
|
|
|
for (int i = 0; i < nz2r; i++)
|
|
interpolate(nr,dr,z2r[i],z2r_spline[i]);
|
|
|
|
for (int i = 0; i < nu2r; i++)
|
|
interpolate(nr,dr,u2r[i],u2r_spline[i]);
|
|
|
|
for (int i = 0; i < nw2r; i++)
|
|
interpolate(nr,dr,w2r[i],w2r_spline[i]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairADP::interpolate(int n, double delta, double *f, double **spline)
|
|
{
|
|
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
|
|
|
|
spline[1][5] = spline[2][6] - spline[1][6];
|
|
spline[2][5] = 0.5 * (spline[3][6]-spline[1][6]);
|
|
spline[n-1][5] = 0.5 * (spline[n][6]-spline[n-2][6]);
|
|
spline[n][5] = spline[n][6] - spline[n-1][6];
|
|
|
|
for (int m = 3; m <= n-2; m++)
|
|
spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
|
|
8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
|
|
|
|
for (int m = 1; m <= n-1; m++) {
|
|
spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
|
|
2.0*spline[m][5] - spline[m+1][5];
|
|
spline[m][3] = spline[m][5] + spline[m+1][5] -
|
|
2.0*(spline[m+1][6]-spline[m][6]);
|
|
}
|
|
|
|
spline[n][4] = 0.0;
|
|
spline[n][3] = 0.0;
|
|
|
|
for (int m = 1; m <= n; m++) {
|
|
spline[m][2] = spline[m][5]/delta;
|
|
spline[m][1] = 2.0*spline[m][4]/delta;
|
|
spline[m][0] = 3.0*spline[m][3]/delta;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int PairADP::pack_forward_comm(int n, int *list, double *buf,
|
|
int /*pbc_flag*/, int * /*pbc*/)
|
|
{
|
|
int i,j,m;
|
|
|
|
m = 0;
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = fp[j];
|
|
buf[m++] = mu[j][0];
|
|
buf[m++] = mu[j][1];
|
|
buf[m++] = mu[j][2];
|
|
buf[m++] = lambda[j][0];
|
|
buf[m++] = lambda[j][1];
|
|
buf[m++] = lambda[j][2];
|
|
buf[m++] = lambda[j][3];
|
|
buf[m++] = lambda[j][4];
|
|
buf[m++] = lambda[j][5];
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairADP::unpack_forward_comm(int n, int first, double *buf)
|
|
{
|
|
int i,m,last;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
fp[i] = buf[m++];
|
|
mu[i][0] = buf[m++];
|
|
mu[i][1] = buf[m++];
|
|
mu[i][2] = buf[m++];
|
|
lambda[i][0] = buf[m++];
|
|
lambda[i][1] = buf[m++];
|
|
lambda[i][2] = buf[m++];
|
|
lambda[i][3] = buf[m++];
|
|
lambda[i][4] = buf[m++];
|
|
lambda[i][5] = buf[m++];
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int PairADP::pack_reverse_comm(int n, int first, double *buf)
|
|
{
|
|
int i,m,last;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
buf[m++] = rho[i];
|
|
buf[m++] = mu[i][0];
|
|
buf[m++] = mu[i][1];
|
|
buf[m++] = mu[i][2];
|
|
buf[m++] = lambda[i][0];
|
|
buf[m++] = lambda[i][1];
|
|
buf[m++] = lambda[i][2];
|
|
buf[m++] = lambda[i][3];
|
|
buf[m++] = lambda[i][4];
|
|
buf[m++] = lambda[i][5];
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairADP::unpack_reverse_comm(int n, int *list, double *buf)
|
|
{
|
|
int i,j,m;
|
|
|
|
m = 0;
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
rho[j] += buf[m++];
|
|
mu[j][0] += buf[m++];
|
|
mu[j][1] += buf[m++];
|
|
mu[j][2] += buf[m++];
|
|
lambda[j][0] += buf[m++];
|
|
lambda[j][1] += buf[m++];
|
|
lambda[j][2] += buf[m++];
|
|
lambda[j][3] += buf[m++];
|
|
lambda[j][4] += buf[m++];
|
|
lambda[j][5] += buf[m++];
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
memory usage of local atom-based arrays
|
|
------------------------------------------------------------------------- */
|
|
|
|
double PairADP::memory_usage()
|
|
{
|
|
double bytes = Pair::memory_usage();
|
|
bytes += 21 * nmax * sizeof(double);
|
|
return bytes;
|
|
}
|