forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8868 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
f47d2a82b6
commit
06e67b08df
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@ -1,261 +0,0 @@
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/* ----------------------------------------------------------------------
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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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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 "math.h"
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#include "pair_lj_charmm_coul_pppm_omp.h"
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#include "pppm_proxy.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.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 "update.h"
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#include <string.h>
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#include "suffix.h"
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using namespace LAMMPS_NS;
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#define EWALD_F 1.12837917
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#define EWALD_P 0.3275911
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#define A1 0.254829592
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#define A2 -0.284496736
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#define A3 1.421413741
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#define A4 -1.453152027
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#define A5 1.061405429
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/* ---------------------------------------------------------------------- */
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PairLJCharmmCoulPPPMOMP::PairLJCharmmCoulPPPMOMP(LAMMPS *lmp) :
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PairLJCharmmCoulLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
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{
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suffix_flag |= Suffix::OMP;
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respa_enable = 0;
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nproxy=1;
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kspace = NULL;
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulPPPMOMP::init_style()
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{
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if (comm->nthreads < 2)
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error->all(FLERR,"need at least two threads per MPI task for this pair style");
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if (strcmp(force->kspace_style,"pppm/proxy") != 0)
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error->all(FLERR,"kspace style pppm/proxy is required with this pair style");
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kspace = static_cast<PPPMProxy *>(force->kspace);
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PairLJCharmmCoulLong::init_style();
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulPPPMOMP::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, nproxy);
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ThrData *thr = fix->get_thr(tid);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
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// thread id 0 runs pppm, the rest the pair style
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if (tid < nproxy) {
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kspace->compute_proxy(eflag,vflag);
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} else {
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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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}
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sync_threads();
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reduce_thr(this, eflag, vflag, thr, nproxy);
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} // end of omp parallel region
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}
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/* ---------------------------------------------------------------------- */
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void PairLJCharmmCoulPPPMOMP::eval(int iifrom, int iito, ThrData * const thr)
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{
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int i,j,ii,jj,jnum,itype,jtype,itable;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double fraction,table;
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double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
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double grij,expm2,prefactor,t,erfc;
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double philj,switch1,switch2;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 0.0;
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const double * const * const x = atom->x;
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double * const * const f = thr->get_f();
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const double * const q = atom->q;
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const int * const type = atom->type;
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const int nlocal = atom->nlocal;
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const double * const special_coul = force->special_coul;
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const double * const special_lj = force->special_lj;
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const double qqrd2e = force->qqrd2e;
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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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// 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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qtmp = q[i];
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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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fxtmp=fytmp=fztmp=0.0;
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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][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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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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if (rsq < cut_coulsq) {
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if (!ncoultablebits || rsq <= tabinnersq) {
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r = sqrt(rsq);
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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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erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
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prefactor = qqrd2e * qtmp*q[j]/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 = qtmp*q[j] * 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 = qtmp*q[j] * table;
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forcecoul -= (1.0-factor_coul)*prefactor;
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}
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}
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} else forcecoul = 0.0;
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if (rsq < cut_ljsq) {
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r6inv = r2inv*r2inv*r2inv;
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jtype = type[j];
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
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(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
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switch2 = 12.0*rsq * (cut_ljsq-rsq) *
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(rsq-cut_lj_innersq) / denom_lj;
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philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
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forcelj = forcelj*switch1 + philj*switch2;
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}
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forcelj *= factor_lj;
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} else forcelj = 0.0;
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fpair = (forcecoul + 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][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= 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 = qtmp*q[j] * table;
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}
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if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
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} else ecoul = 0.0;
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if (rsq < cut_ljsq) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
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(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
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evdwl *= switch1;
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}
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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][0] += fxtmp;
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f[i][1] += fytmp;
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f[i][2] += fztmp;
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairLJCharmmCoulPPPMOMP::memory_usage()
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{
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double bytes = memory_usage_thr();
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bytes += PairLJCharmmCoulLong::memory_usage();
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return bytes;
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}
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@ -1,54 +0,0 @@
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/* -*- 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 author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(lj/charmm/coul/pppm/omp,PairLJCharmmCoulPPPMOMP)
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#else
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#ifndef LMP_PAIR_LJ_CHARMM_COUL_PPPM_OMP_H
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#define LMP_PAIR_LJ_CHARMM_COUL_PPPM_OMP_H
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#include "pair_lj_charmm_coul_long.h"
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#include "thr_omp.h"
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namespace LAMMPS_NS {
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class PairLJCharmmCoulPPPMOMP : public PairLJCharmmCoulLong, public ThrOMP {
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public:
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PairLJCharmmCoulPPPMOMP(class LAMMPS *);
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virtual ~PairLJCharmmCoulPPPMOMP() {};
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virtual void init_style();
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virtual void compute(int, int);
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virtual double memory_usage();
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private:
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void eval(int ifrom, int ito, ThrData * const thr);
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class PPPMProxy *kspace;
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int nproxy;
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};
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}
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#endif
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#endif
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@ -1,228 +0,0 @@
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/* ----------------------------------------------------------------------
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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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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 "math.h"
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#include "pair_lj_class2_coul_pppm_omp.h"
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#include "pppm_proxy.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.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 "update.h"
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#include <string.h>
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#include "suffix.h"
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using namespace LAMMPS_NS;
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#define EWALD_F 1.12837917
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#define EWALD_P 0.3275911
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#define A1 0.254829592
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#define A2 -0.284496736
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#define A3 1.421413741
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#define A4 -1.453152027
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#define A5 1.061405429
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/* ---------------------------------------------------------------------- */
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PairLJClass2CoulPPPMOMP::PairLJClass2CoulPPPMOMP(LAMMPS *lmp) :
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PairLJClass2CoulLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
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{
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suffix_flag |= Suffix::OMP;
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respa_enable = 0;
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nproxy=1;
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kspace = NULL;
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}
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/* ---------------------------------------------------------------------- */
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void PairLJClass2CoulPPPMOMP::init_style()
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{
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if (comm->nthreads < 2)
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error->all(FLERR,"need at least two threads per MPI task for this pair style");
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if (strcmp(force->kspace_style,"pppm/proxy") != 0)
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error->all(FLERR,"kspace style pppm/proxy is required with this pair style");
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kspace = static_cast<PPPMProxy *>(force->kspace);
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PairLJClass2CoulLong::init_style();
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}
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/* ---------------------------------------------------------------------- */
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void PairLJClass2CoulPPPMOMP::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, nproxy);
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ThrData *thr = fix->get_thr(tid);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
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// thread id 0 runs pppm, the rest the pair style
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if (tid < nproxy) {
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kspace->compute_proxy(eflag,vflag);
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} else {
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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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}
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sync_threads();
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reduce_thr(this, eflag, vflag, thr, nproxy);
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} // end of omp parallel region
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}
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/* ---------------------------------------------------------------------- */
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void PairLJClass2CoulPPPMOMP::eval(int iifrom, int iito, ThrData * const thr)
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{
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int i,j,ii,jj,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double r,rsq,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
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double grij,expm2,prefactor,t,erfc;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 0.0;
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const double * const * const x = atom->x;
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double * const * const f = thr->get_f();
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const double * const q = atom->q;
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const int * const type = atom->type;
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const int nlocal = atom->nlocal;
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||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
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];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
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)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
rinv = sqrt(r2inv);
|
||||
r3inv = r2inv*rinv;
|
||||
r6inv = r3inv*r3inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj;
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2CoulPPPMOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJClass2CoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -1,54 +0,0 @@
|
|||
/* -*- 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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/class2/coul/pppm/omp,PairLJClass2CoulPPPMOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CLASS2_COUL_PPPM_OMP_H
|
||||
#define LMP_PAIR_LJ_CLASS2_COUL_PPPM_OMP_H
|
||||
|
||||
#include "pair_lj_class2_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJClass2CoulPPPMOMP : public PairLJClass2CoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJClass2CoulPPPMOMP(class LAMMPS *);
|
||||
virtual ~PairLJClass2CoulPPPMOMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
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);
|
||||
|
||||
class PPPMProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -1,246 +0,0 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "pair_lj_cut_coul_pppm_omp.h"
|
||||
#include "pppm_proxy.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulPPPMOMP::PairLJCutCoulPPPMOMP(LAMMPS *lmp) :
|
||||
PairLJCutCoulLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
nproxy=1;
|
||||
|
||||
kspace = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulPPPMOMP::init_style()
|
||||
{
|
||||
if (comm->nthreads < 2)
|
||||
error->all(FLERR,"need at least two threads per MPI task for this pair style");
|
||||
|
||||
if (strcmp(force->kspace_style,"pppm/proxy") != 0)
|
||||
error->all(FLERR,"kspace style pppm/proxy is required with this pair style");
|
||||
|
||||
kspace = static_cast<PPPMProxy *>(force->kspace);
|
||||
|
||||
PairLJCutCoulLong::init_style();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulPPPMOMP::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, nproxy);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
// thread id 0 runs pppm, the rest the pair style
|
||||
if (tid < nproxy) {
|
||||
kspace->compute_proxy(eflag,vflag);
|
||||
} else {
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
||||
sync_threads();
|
||||
reduce_thr(this, eflag, vflag, thr, nproxy);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJCutCoulPPPMOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype,itable;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double fraction,table;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
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];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
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)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj;
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulPPPMOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutCoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -1,54 +0,0 @@
|
|||
/* -*- 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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/pppm/omp,PairLJCutCoulPPPMOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_PPPM_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_PPPM_OMP_H
|
||||
|
||||
#include "pair_lj_cut_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulPPPMOMP : public PairLJCutCoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutCoulPPPMOMP(class LAMMPS *);
|
||||
virtual ~PairLJCutCoulPPPMOMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
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);
|
||||
|
||||
class PPPMProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -1,542 +0,0 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "pair_lj_cut_coul_pppm_tip4p_omp.h"
|
||||
#include "pppm_tip4p_proxy.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulPPPMTIP4POMP::PairLJCutCoulPPPMTIP4POMP(LAMMPS *lmp) :
|
||||
PairLJCutCoulLongTIP4P(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
nproxy=1;
|
||||
|
||||
kspace = NULL;
|
||||
|
||||
// TIP4P cannot compute virial as F dot r
|
||||
// due to finding bonded H atoms which are not near O atom
|
||||
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulPPPMTIP4POMP::init_style()
|
||||
{
|
||||
if (comm->nthreads < 2)
|
||||
error->all(FLERR,"need at least two threads per MPI task for this pair style");
|
||||
|
||||
if (strcmp(force->kspace_style,"pppm/tip4p/proxy") != 0)
|
||||
error->all(FLERR,"kspace style pppm/tip4p/proxy is required with this pair style");
|
||||
|
||||
kspace = static_cast<PPPMTIP4PProxy *>(force->kspace);
|
||||
|
||||
PairLJCutCoulLongTIP4P::init_style();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulPPPMTIP4POMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
const int nall = nlocal + atom->nghost;
|
||||
|
||||
// reallocate hneigh & newsite if necessary
|
||||
// initialize hneigh[0] to -1 on steps when reneighboring occurred
|
||||
// initialize hneigh[2] to 0 every step
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
nmax = atom->nmax;
|
||||
memory->destroy(hneigh);
|
||||
memory->create(hneigh,nmax,3,"pair:hneigh");
|
||||
memory->destroy(newsite);
|
||||
memory->create(newsite,nmax,3,"pair:newsite");
|
||||
}
|
||||
|
||||
// XXX: this could be threaded, too.
|
||||
int i;
|
||||
if (neighbor->ago == 0)
|
||||
for (i = 0; i < nall; i++) hneigh[i][0] = -1;
|
||||
for (i = 0; i < nall; i++) hneigh[i][2] = 0;
|
||||
|
||||
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, nproxy);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
// thread id 0 runs pppm, the rest the pair style
|
||||
if (tid < nproxy) {
|
||||
kspace->compute_proxy(eflag,vflag);
|
||||
} else {
|
||||
if (!ncoultablebits) {
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<1,0,0,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
|
||||
else eval<0,1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
|
||||
else eval<0,1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<0,0,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
}
|
||||
|
||||
sync_threads();
|
||||
reduce_thr(this, eflag, vflag, thr, nproxy);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int CTABLE, int EVFLAG, int EFLAG, int VFLAG>
|
||||
void PairLJCutCoulPPPMTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype,itable;
|
||||
int n,vlist[6];
|
||||
int iH1,iH2,jH1,jH2;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
|
||||
double fraction,table;
|
||||
double delxOM,delyOM,delzOM;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
|
||||
double factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc,ddotf;
|
||||
double v[6],xH1[3],xH2[3];
|
||||
double fdx,fdy,fdz,f1x,f1y,f1z,fOx,fOy,fOz,fHx,fHy,fHz;
|
||||
const double *x1,*x2;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const int tid = thr->get_tid();
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
const double cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
|
||||
|
||||
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];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
|
||||
// if atom I = water O, set x1 = offset charge site
|
||||
// else x1 = x of atom I
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (itype == typeO) {
|
||||
if (hneigh[i][0] < 0) {
|
||||
iH1 = atom->map(atom->tag[i] + 1);
|
||||
iH2 = atom->map(atom->tag[i] + 2);
|
||||
if (iH1 == -1 || iH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite[i]);
|
||||
hneigh[i][2] = 1;
|
||||
hneigh[i][1] = iH2;
|
||||
hneigh[i][0] = iH1;
|
||||
} else {
|
||||
iH1 = hneigh[i][0];
|
||||
iH2 = hneigh[i][1];
|
||||
if (hneigh[i][2] == 0) {
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite[i]);
|
||||
hneigh[i][2] = 1;
|
||||
}
|
||||
}
|
||||
x1 = newsite[i];
|
||||
} else x1 = x[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)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
// LJ interaction based on true rsq
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj * r2inv;
|
||||
|
||||
fxtmp += delx*forcelj;
|
||||
fytmp += dely*forcelj;
|
||||
fztmp += delz*forcelj;
|
||||
f[j][0] -= delx*forcelj;
|
||||
f[j][1] -= dely*forcelj;
|
||||
f[j][2] -= delz*forcelj;
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
|
||||
evdwl,0.0,forcelj,delx,dely,delz,thr);
|
||||
}
|
||||
|
||||
// adjust rsq and delxyz for off-site O charge(s) if necessary
|
||||
// but only if they are within reach
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (rsq < cut_coulsqplus) {
|
||||
if (itype == typeO || jtype == typeO) {
|
||||
|
||||
// if atom J = water O, set x2 = offset charge site
|
||||
// else x2 = x of atom J
|
||||
|
||||
if (jtype == typeO) {
|
||||
if (hneigh[j][0] < 0) {
|
||||
jH1 = atom->map(atom->tag[j] + 1);
|
||||
jH2 = atom->map(atom->tag[j] + 2);
|
||||
if (jH1 == -1 || jH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite[j]);
|
||||
hneigh[j][2] = 1;
|
||||
hneigh[j][1] = jH2;
|
||||
hneigh[j][0] = jH1;
|
||||
} else {
|
||||
jH1 = hneigh[j][0];
|
||||
jH2 = hneigh[j][1];
|
||||
if (hneigh[j][2] == 0) {
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite[j]);
|
||||
hneigh[j][2] = 1;
|
||||
}
|
||||
}
|
||||
x2 = newsite[j];
|
||||
} else x2 = x[j];
|
||||
|
||||
delx = x1[0] - x2[0];
|
||||
dely = x1[1] - x2[1];
|
||||
delz = x1[2] - x2[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
|
||||
// Coulombic interaction based on modified rsq
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r2inv = 1 / rsq;
|
||||
if (CTABLE || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) {
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
|
||||
cforce = forcecoul * r2inv;
|
||||
|
||||
// if i,j are not O atoms, force is applied directly
|
||||
// if i or j are O atoms, force is on fictitious atom & partitioned
|
||||
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
|
||||
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
|
||||
// preserves total force and torque on water molecule
|
||||
// virial = sum(r x F) where each water's atoms are near xi and xj
|
||||
// vlist stores 2,4,6 atoms whose forces contribute to virial
|
||||
|
||||
n = 0;
|
||||
|
||||
if (itype != typeO) {
|
||||
fxtmp += delx * cforce;
|
||||
fytmp += dely * cforce;
|
||||
fztmp += delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = x[i][0] * delx * cforce;
|
||||
v[1] = x[i][1] * dely * cforce;
|
||||
v[2] = x[i][2] * delz * cforce;
|
||||
v[3] = x[i][0] * dely * cforce;
|
||||
v[4] = x[i][0] * delz * cforce;
|
||||
v[5] = x[i][1] * delz * cforce;
|
||||
vlist[n++] = i;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
fdx = delx*cforce;
|
||||
fdy = dely*cforce;
|
||||
fdz = delz*cforce;
|
||||
|
||||
delxOM = x[i][0] - x1[0];
|
||||
delyOM = x[i][1] - x1[1];
|
||||
delzOM = x[i][2] - x1[2];
|
||||
|
||||
ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
|
||||
(qdist*qdist);
|
||||
|
||||
f1x = alpha * (fdx - ddotf * delxOM);
|
||||
f1y = alpha * (fdy - ddotf * delyOM);
|
||||
f1z = alpha * (fdz - ddotf * delzOM);
|
||||
|
||||
fOx = fdx - f1x;
|
||||
fOy = fdy - f1y;
|
||||
fOz = fdz - f1z;
|
||||
|
||||
fHx = 0.5 * f1x;
|
||||
fHy = 0.5 * f1y;
|
||||
fHz = 0.5 * f1z;
|
||||
|
||||
fxtmp += fOx;
|
||||
fytmp += fOy;
|
||||
fztmp += fOz;
|
||||
|
||||
f[iH1][0] += fHx;
|
||||
f[iH1][1] += fHy;
|
||||
f[iH1][2] += fHz;
|
||||
|
||||
f[iH2][0] += fHx;
|
||||
f[iH2][1] += fHy;
|
||||
f[iH2][2] += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(x[i],x[iH1],xH1);
|
||||
domain->closest_image(x[i],x[iH2],xH2);
|
||||
|
||||
v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
|
||||
vlist[n++] = i;
|
||||
vlist[n++] = iH1;
|
||||
vlist[n++] = iH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (jtype != typeO) {
|
||||
f[j][0] -= delx * cforce;
|
||||
f[j][1] -= dely * cforce;
|
||||
f[j][2] -= delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] -= x[j][0] * delx * cforce;
|
||||
v[1] -= x[j][1] * dely * cforce;
|
||||
v[2] -= x[j][2] * delz * cforce;
|
||||
v[3] -= x[j][0] * dely * cforce;
|
||||
v[4] -= x[j][0] * delz * cforce;
|
||||
v[5] -= x[j][1] * delz * cforce;
|
||||
vlist[n++] = j;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
fdx = -delx*cforce;
|
||||
fdy = -dely*cforce;
|
||||
fdz = -delz*cforce;
|
||||
|
||||
delxOM = x[j][0] - x2[0];
|
||||
delyOM = x[j][1] - x2[1];
|
||||
delzOM = x[j][2] - x2[2];
|
||||
|
||||
ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
|
||||
(qdist*qdist);
|
||||
|
||||
f1x = alpha * (fdx - ddotf * delxOM);
|
||||
f1y = alpha * (fdy - ddotf * delyOM);
|
||||
f1z = alpha * (fdz - ddotf * delzOM);
|
||||
|
||||
fOx = fdx - f1x;
|
||||
fOy = fdy - f1y;
|
||||
fOz = fdz - f1z;
|
||||
|
||||
fHx = 0.5 * f1x;
|
||||
fHy = 0.5 * f1y;
|
||||
fHz = 0.5 * f1z;
|
||||
|
||||
f[j][0] += fOx;
|
||||
f[j][1] += fOy;
|
||||
f[j][2] += fOz;
|
||||
|
||||
f[jH1][0] += fHx;
|
||||
f[jH1][1] += fHy;
|
||||
f[jH1][2] += fHz;
|
||||
|
||||
f[jH2][0] += fHx;
|
||||
f[jH2][1] += fHy;
|
||||
f[jH2][2] += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(x[j],x[jH1],xH1);
|
||||
domain->closest_image(x[j],x[jH2],xH2);
|
||||
|
||||
v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
|
||||
vlist[n++] = j;
|
||||
vlist[n++] = jH1;
|
||||
vlist[n++] = jH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (CTABLE || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
compute position xM of fictitious charge site for O atom and 2 H atoms
|
||||
return it as xM
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulPPPMTIP4POMP::compute_newsite_thr(const double * xO,
|
||||
const double * xH1,
|
||||
const double * xH2,
|
||||
double * xM) const
|
||||
{
|
||||
double delx1 = xH1[0] - xO[0];
|
||||
double dely1 = xH1[1] - xO[1];
|
||||
double delz1 = xH1[2] - xO[2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
double delx2 = xH2[0] - xO[0];
|
||||
double dely2 = xH2[1] - xO[1];
|
||||
double delz2 = xH2[2] - xO[2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
const double prefac = alpha * 0.5;
|
||||
xM[0] = xO[0] + prefac * (delx1 + delx2);
|
||||
xM[1] = xO[1] + prefac * (dely1 + dely2);
|
||||
xM[2] = xO[2] + prefac * (delz1 + delz2);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulPPPMTIP4POMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutCoulLongTIP4P::memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -1,56 +0,0 @@
|
|||
/* -*- 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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/pppm/tip4p/omp,PairLJCutCoulPPPMTIP4POMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_PPPM_TIP4P_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_PPPM_TIP4P_OMP_H
|
||||
|
||||
#include "pair_lj_cut_coul_long_tip4p.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulPPPMTIP4POMP : public PairLJCutCoulLongTIP4P, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutCoulPPPMTIP4POMP(class LAMMPS *);
|
||||
virtual ~PairLJCutCoulPPPMTIP4POMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int, int, int, int>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
void compute_newsite_thr(const double *, const double *,
|
||||
const double *, double *) const;
|
||||
|
||||
class PPPMTIP4PProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue