git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14776 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
266
src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
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266
src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
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@ -0,0 +1,266 @@
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/* ----------------------------------------------------------------------
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||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
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||||
|
||||
/* ----------------------------------------------------------------------
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||||
Contributing author: Paul Crozier (SNL)
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||||
------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "pair_lj_cut_thole_long_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 "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "math_const.h"
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#include "error.h"
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#include "suffix.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define EWALD_F 1.12837917
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#define EWALD_P 9.95473818e-1
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#define B0 -0.1335096380159268
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#define B1 -2.57839507e-1
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#define B2 -1.37203639e-1
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#define B3 -8.88822059e-3
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#define B4 -5.80844129e-3
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#define B5 1.14652755e-1
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/* ---------------------------------------------------------------------- */
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PairLJCutTholeLongOMP::PairLJCutTholeLongOMP(LAMMPS *lmp) :
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PairLJCutTholeLong(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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cut_respa = NULL;
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCutTholeLongOMP::compute(int eflag, int vflag)
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{
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if (eflag || vflag) {
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ev_setup(eflag,vflag);
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} else evflag = vflag_fdotr = 0;
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const int nall = atom->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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#if defined(_OPENMP)
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#pragma omp parallel default(none) 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, thr);
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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 PairLJCutTholeLongOMP::eval(int iifrom, int iito, ThrData * const thr)
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{
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const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
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dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
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const double * const q = atom->q;
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const int * _noalias const type = atom->type;
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const double * _noalias const special_lj = force->special_lj;
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const double * _noalias const special_coul = force->special_coul;
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const int * _noalias const ilist = list->ilist;
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const int * _noalias const numneigh = list->numneigh;
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const int * const * const firstneigh = list->firstneigh;
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const int * _noalias const drudetype = fix_drude->drudetype;
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const tagint * _noalias const drudeid = fix_drude->drudeid;
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double xtmp,ytmp,ztmp,delx,dely,delz,fxtmp,fytmp,fztmp;
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const int nlocal = atom->nlocal;
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int j,jj,jnum,jtype,itable;
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double ecoul,fpair,evdwl;
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double r,rsq,r2inv,forcecoul,factor_coul,forcelj,factor_lj,r6inv;
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double fraction,table;
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double grij,expm2,prefactor,t,erfc,u;
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double factor_f,factor_e;
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int di,dj;
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double qj,dqi,dqj,dcoul,asr,exp_asr;
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int di_closest;
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const double qqrd2e = force->qqrd2e;
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evdwl = ecoul = 0.0;
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// loop over neighbors of my atoms
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for (int ii = iifrom; ii < iito; ii++) {
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const int i = ilist[ii];
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const double qi = q[i];
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const int itype = type[i];
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const int * _noalias const jlist = firstneigh[i];
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const double * _noalias const cutsqi = cutsq[itype];
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const double * _noalias const cut_ljsqi = cut_ljsq[itype];
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const double * _noalias const offseti = offset[itype];
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const double * _noalias const lj1i = lj1[itype];
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const double * _noalias const lj2i = lj2[itype];
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const double * _noalias const lj3i = lj3[itype];
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const double * _noalias const lj4i = lj4[itype];
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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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jnum = numneigh[i];
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fxtmp=fytmp=fztmp=0.;
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if (drudetype[type[i]] != NOPOL_TYPE){
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di = atom->map(drudeid[i]);
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if (di < 0) error->all(FLERR, "Drude partner not found");
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di_closest = domain->closest_image(i, di);
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if (drudetype[type[i]] == CORE_TYPE)
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dqi = -q[di];
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else
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dqi = qi;
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}
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_lj = special_lj[sbmask(j)];
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factor_coul = special_coul[sbmask(j)];
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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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jtype = type[j];
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if (rsq < cutsqi[jtype]) {
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r2inv = 1.0/rsq;
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if (rsq < cut_coulsq) {
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qj = q[j];
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r = sqrt(rsq);
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if (!ncoultablebits || rsq <= tabinnersq) {
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grij = g_ewald * r;
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expm2 = exp(-grij*grij);
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t = 1.0 / (1.0 + EWALD_P*grij);
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u = 1. - t;
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erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
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prefactor = qqrd2e * qi*qj/r;
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forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
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} else {
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union_int_float_t rsq_lookup;
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rsq_lookup.f = rsq;
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itable = rsq_lookup.i & ncoulmask;
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itable >>= ncoulshiftbits;
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fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
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table = ftable[itable] + fraction*dftable[itable];
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forcecoul = qi*qj * table;
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if (factor_coul < 1.0) {
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table = ctable[itable] + fraction*dctable[itable];
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prefactor = qi*qj * table;
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forcecoul -= (1.0-factor_coul)*prefactor;
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}
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}
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if (drudetype[type[i]] != NOPOL_TYPE &&
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drudetype[type[j]] != NOPOL_TYPE){
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if (j != di_closest){
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if (drudetype[type[j]] == CORE_TYPE){
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dj = atom->map(drudeid[j]);
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dqj = -q[dj];
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} else dqj = qj;
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asr = ascreen[type[i]][type[j]] * r;
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exp_asr = exp(-asr);
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dcoul = qqrd2e * dqi * dqj / r;
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factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr))))
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- factor_coul;
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if (EFLAG) factor_e = 0.5*(2. - (exp_asr * (2. + asr)))
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- factor_coul;
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forcecoul += factor_f * dcoul;
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}
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}
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} else forcecoul = 0.0;
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if (rsq < cut_ljsqi[jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1i[jtype]*r6inv - lj2i[jtype]);
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} else forcelj = 0.0;
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fpair = (forcecoul + factor_lj*forcelj) * r2inv;
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fxtmp += delx*fpair;
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fytmp += dely*fpair;
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fztmp += delz*fpair;
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if (NEWTON_PAIR || j < nlocal) {
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f[j].x -= delx*fpair;
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f[j].y -= dely*fpair;
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f[j].z -= delz*fpair;
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}
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if (EFLAG) {
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if (rsq < cut_coulsq) {
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if (!ncoultablebits || rsq <= tabinnersq)
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ecoul = prefactor*erfc;
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else {
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table = etable[itable] + fraction*detable[itable];
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ecoul = qi*qj * table;
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}
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if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
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if (drudetype[type[i]] != NOPOL_TYPE &&
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drudetype[type[j]] != NOPOL_TYPE && j != di_closest){
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ecoul += factor_e * dcoul;
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}
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} else ecoul = 0.0;
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||||
|
||||
if (rsq < cut_ljsqi[jtype]) {
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evdwl = r6inv*(lj3i[jtype]*r6inv-lj4i[jtype]) -
|
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offseti[jtype];
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evdwl *= factor_lj;
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} else evdwl = 0.0;
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}
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if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
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evdwl,ecoul,fpair,delx,dely,delz,thr);
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}
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}
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f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
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}
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||||
}
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||||
|
||||
70
src/USER-OMP/pair_lj_cut_thole_long_omp.h
Normal file
70
src/USER-OMP/pair_lj_cut_thole_long_omp.h
Normal file
@ -0,0 +1,70 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/thole/long/omp,PairLJCutTholeLongOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H
|
||||
|
||||
#include "pair.h"
|
||||
#include "pair_lj_cut_thole_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutTholeLongOMP : public PairLJCutTholeLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutTholeLongOMP(class LAMMPS *);
|
||||
virtual void compute(int, int);
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style lj/cut/coul/long requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: Pair style requires a KSpace style
|
||||
|
||||
No kspace style is defined.
|
||||
|
||||
E: Pair cutoff < Respa interior cutoff
|
||||
|
||||
One or more pairwise cutoffs are too short to use with the specified
|
||||
rRESPA cutoffs.
|
||||
|
||||
*/
|
||||
169
src/USER-OMP/pair_morse_smooth_linear_omp.cpp
Normal file
169
src/USER-OMP/pair_morse_smooth_linear_omp.cpp
Normal file
@ -0,0 +1,169 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Stefan Paquay (Eindhoven University of Technology)
|
||||
Most code borrowed from pair_morse_omp.cpp
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include "pair_morse_smooth_linear_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairMorseSmoothLinearOMP::PairMorseSmoothLinearOMP(LAMMPS *lmp) :
|
||||
PairMorseSmoothLinear(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSmoothLinearOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) {
|
||||
ev_setup(eflag,vflag);
|
||||
} else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else {
|
||||
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
|
||||
else eval<0,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
|
||||
thr->timer(Timer::PAIR);
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairMorseSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpartial;
|
||||
double rsq,r,dr,dexp,factor_lj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const int * _noalias const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * _noalias const special_lj = force->special_lj;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[itype][jtype];
|
||||
dexp = exp(-alpha[itype][jtype] * dr);
|
||||
|
||||
fpartial = morse1[itype][jtype] * (dexp*dexp - dexp) / r;
|
||||
fpair = factor_lj * ( fpartial - der_at_cutoff[itype][jtype] / r);
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j].x -= delx*fpair;
|
||||
f[j].y -= dely*fpair;
|
||||
f[j].z -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
|
||||
offset[itype][jtype];
|
||||
evdwl += ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,0.0,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairMorseSmoothLinearOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairMorseSmoothLinear::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
62
src/USER-OMP/pair_morse_smooth_linear_omp.h
Normal file
62
src/USER-OMP/pair_morse_smooth_linear_omp.h
Normal file
@ -0,0 +1,62 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(morse/smooth/linear/omp,PairMorseSmoothLinearOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_MORSE_SMOOTH_LINEAR_OMP_H
|
||||
#define LMP_PAIR_MORSE_SMOOTH_LINEAR_OMP_H
|
||||
|
||||
#include "pair_morse_smooth_linear.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairMorseSmoothLinearOMP : public PairMorseSmoothLinear, public ThrOMP {
|
||||
public:
|
||||
PairMorseSmoothLinearOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval( int ifrom, int ito, ThrData * const thr );
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user