395 lines
12 KiB
C++
395 lines
12 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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This software is distributed under 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: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "pair_adp_omp.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include "suffix.h"
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#include <cmath>
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#include "omp_compat.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairADPOMP::PairADPOMP(LAMMPS *lmp) :
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PairADP(lmp), ThrOMP(lmp, THR_PAIR)
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{
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suffix_flag |= Suffix::OMP;
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respa_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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void PairADPOMP::compute(int eflag, int vflag)
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{
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ev_init(eflag,vflag);
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const int nlocal = atom->nlocal;
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const int nall = nlocal + atom->nghost;
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const int nthreads = comm->nthreads;
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const int inum = list->inum;
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// grow energy and fp 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,nthreads*nmax,"pair:rho");
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memory->create(fp,nmax,"pair:fp");
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memory->create(mu,nthreads*nmax,3,"pair:mu");
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memory->create(lambda,nthreads*nmax,6,"pair:lambda");
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}
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#if defined(_OPENMP)
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#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag)
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#endif
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{
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int ifrom, ito, tid;
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loop_setup_thr(ifrom, ito, tid, inum, nthreads);
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ThrData *thr = fix->get_thr(tid);
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thr->timer(Timer::START);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
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if (force->newton_pair)
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thr->init_adp(nall, rho, mu, lambda);
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else
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thr->init_adp(nlocal, rho, mu, lambda);
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if (evflag) {
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if (eflag) {
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if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
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else eval<1,1,0>(ifrom, ito, thr);
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} else {
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if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
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else eval<1,0,0>(ifrom, ito, thr);
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}
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} else {
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if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
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else eval<0,0,0>(ifrom, ito, thr);
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}
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thr->timer(Timer::PAIR);
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reduce_thr(this, eflag, vflag, thr);
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} // end of omp parallel region
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}
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
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{
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int i,j,ii,jj,m,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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const auto * _noalias const x = (dbl3_t *) atom->x[0];
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auto * _noalias const f = (dbl3_t *) thr->get_f()[0];
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double * const rho_t = thr->get_rho();
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double * const * const mu_t = thr->get_mu();
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double * const * const lambda_t = thr->get_lambda();
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const int tid = thr->get_tid();
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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double fxtmp,fytmp,fztmp;
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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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// rho = density at each atom
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// loop over neighbors of my atoms
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for (ii = iifrom; ii < iito; ii++) {
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i = ilist[ii];
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xtmp = x[i].x;
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ytmp = x[i].y;
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ztmp = x[i].z;
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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].x;
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dely = ytmp - x[j].y;
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delz = ztmp - x[j].z;
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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_t[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_t[i][0] += u2*delx;
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mu_t[i][1] += u2*dely;
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mu_t[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_t[i][0] += w2*delx*delx;
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lambda_t[i][1] += w2*dely*dely;
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lambda_t[i][2] += w2*delz*delz;
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lambda_t[i][3] += w2*dely*delz;
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lambda_t[i][4] += w2*delx*delz;
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lambda_t[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_t[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_t[j][0] -= u2*delx;
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mu_t[j][1] -= u2*dely;
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mu_t[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_t[j][0] += w2*delx*delx;
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lambda_t[j][1] += w2*dely*dely;
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lambda_t[j][2] += w2*delz*delz;
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lambda_t[j][3] += w2*dely*delz;
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lambda_t[j][4] += w2*delx*delz;
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lambda_t[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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// wait until all threads are done with computation
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sync_threads();
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// communicate and sum densities
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if (NEWTON_PAIR) {
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// reduce per thread density
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thr->timer(Timer::PAIR);
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data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid);
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data_reduce_thr(&(mu[0][0]), nall, comm->nthreads, 3, tid);
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data_reduce_thr(&(lambda[0][0]), nall, comm->nthreads, 6, tid);
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// wait until reduction is complete
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sync_threads();
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#if defined(_OPENMP)
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#pragma omp master
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#endif
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{ comm->reverse_comm(this); }
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// wait until master thread is done with communication
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sync_threads();
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} else {
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// reduce per thread density
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thr->timer(Timer::PAIR);
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data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid);
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data_reduce_thr(&(mu[0][0]), nlocal, comm->nthreads, 3, tid);
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data_reduce_thr(&(lambda[0][0]), nlocal, comm->nthreads, 6, tid);
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// wait until reduction is complete
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sync_threads();
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}
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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 = iifrom; ii < iito; 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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e_tally_thr(this,i,i,nlocal,/* newton_pair */ 1, phi, 0.0, thr);
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}
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}
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// wait until all theads are done with computation
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sync_threads();
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// communicate derivative of embedding function
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// MPI communication only on master thread
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#if defined(_OPENMP)
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#pragma omp master
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#endif
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{ comm->forward_comm(this); }
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// wait until master thread is done with communication
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sync_threads();
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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 = iifrom; ii < iito; ii++) {
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i = ilist[ii];
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xtmp = x[i].x;
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ytmp = x[i].y;
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ztmp = x[i].z;
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itype = type[i];
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fxtmp = fytmp = fztmp = 0.0;
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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].x;
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dely = ytmp - x[j].y;
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delz = ztmp - x[j].z;
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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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fxtmp += fx;
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fytmp += fy;
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fztmp += fz;
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if (NEWTON_PAIR || j < nlocal) {
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f[j].x -= fx;
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f[j].y -= fy;
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f[j].z -= fz;
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}
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if (EFLAG) evdwl = phi;
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if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,evdwl,0.0,
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fx,fy,fz,delx,dely,delz,thr);
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}
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}
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f[i].x += fxtmp;
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f[i].y += fytmp;
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f[i].z += fztmp;
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairADPOMP::memory_usage()
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{
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double bytes = memory_usage_thr();
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bytes += (double)PairADP::memory_usage();
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bytes += (double)(comm->nthreads-1) * nmax * (10*sizeof(double) + 3*sizeof(double *));
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return bytes;
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}
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