lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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 <cmath>
#include "pair_hbond_dreiding_morse_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"

#include "math_const.h"
#include "math_special.h"

#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;

#define SMALL 0.001

/* ---------------------------------------------------------------------- */

PairHbondDreidingMorseOMP::PairHbondDreidingMorseOMP(LAMMPS *lmp) :
  PairHbondDreidingMorse(lmp), ThrOMP(lmp, THR_PAIR)
{
  suffix_flag |= Suffix::OMP;
  respa_enable = 0;
  hbcount_thr = hbeng_thr = NULL;
}

/* ---------------------------------------------------------------------- */

PairHbondDreidingMorseOMP::~PairHbondDreidingMorseOMP()
{
  if (hbcount_thr) {
    delete[] hbcount_thr;
    delete[] hbeng_thr;
  }
}

/* ---------------------------------------------------------------------- */

void PairHbondDreidingMorseOMP::compute(int eflag, int vflag)
{
  ev_init(eflag,vflag);

  const int nall = atom->nlocal + atom->nghost;
  const int nthreads = comm->nthreads;
  const int inum = list->inum;

  if (!hbcount_thr) {
    hbcount_thr = new double[nthreads];
    hbeng_thr = new double[nthreads];
  }

  for (int i=0; i < nthreads; ++i) {
    hbcount_thr[i] = 0.0;
    hbeng_thr[i] = 0.0;
  }

#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

  // reduce per thread hbond data
  if (eflag_global) {
    pvector[0] = 0.0;
    pvector[1] = 0.0;
    for (int i=0; i < nthreads; ++i) {
      pvector[0] += hbcount_thr[i];
      pvector[1] += hbeng_thr[i];
    }
  }
}

template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
{
  int i,j,k,m,ii,jj,kk,jnum,knum,itype,jtype,ktype,imol,iatom;
  tagint tagprev;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq,rsq1,rsq2,r1,r2;
  double factor_hb,force_angle,force_kernel,evdwl;
  double c,s,a,b,ac,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;
  double fi[3],fj[3],delr1[3],delr2[3];
  double r,dr,dexp,eng_morse,switch1,switch2;
  int *ilist,*jlist,*numneigh,**firstneigh;
  const tagint *klist;

  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 tagint * _noalias const tag = atom->tag;
  const int * _noalias const type = atom->type;
  const int * _noalias const molindex = atom->molindex;
  const int * _noalias const molatom = atom->molatom;
  const double * _noalias const special_lj = force->special_lj;
  const int * const * const nspecial = atom->nspecial;
  const tagint * const * const special = atom->special;
  const int molecular = atom->molecular;
  Molecule * const * const onemols = atom->avec->onemols;
  double fxtmp,fytmp,fztmp;

  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

  // ii = loop over donors
  // jj = loop over acceptors
  // kk = loop over hydrogens bonded to donor

  int hbcount = 0;
  double hbeng = 0.0;

  for (ii = iifrom; ii < iito; ++ii) {

    i = ilist[ii];
    itype = type[i];
    if (!donor[itype]) continue;
    if (molecular == 1) {
      klist = special[i];
      knum = nspecial[i][0];
    } else {
      if (molindex[i] < 0) continue;
      imol = molindex[i];
      iatom = molatom[i];
      klist = onemols[imol]->special[iatom];
      knum = onemols[imol]->nspecial[iatom][0];
      tagprev = tag[i] - iatom - 1;
    }
    jlist = firstneigh[i];
    jnum = numneigh[i];
    fxtmp=fytmp=fztmp=0.0;

    xtmp = x[i].x;
    ytmp = x[i].y;
    ztmp = x[i].z;

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      factor_hb = special_lj[sbmask(j)];
      j &= NEIGHMASK;

      jtype = type[j];
      if (!acceptor[jtype]) continue;

      delx = xtmp - x[j].x;
      dely = ytmp - x[j].y;
      delz = ztmp - x[j].z;
      rsq = delx*delx + dely*dely + delz*delz;

      for (kk = 0; kk < knum; kk++) {
        if (molecular == 1) k = atom->map(klist[kk]);
        else k = atom->map(klist[kk]+tagprev);
        if (k < 0) continue;
        ktype = type[k];
        m = type2param[itype][jtype][ktype];
        if (m < 0) continue;
        const Param &pm = params[m];

        if (rsq < pm.cut_outersq) {
          delr1[0] = xtmp - x[k].x;
          delr1[1] = ytmp - x[k].y;
          delr1[2] = ztmp - x[k].z;
          domain->minimum_image(delr1);
          rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
          r1 = sqrt(rsq1);

          delr2[0] = x[j].x - x[k].x;
          delr2[1] = x[j].y - x[k].y;
          delr2[2] = x[j].z - x[k].z;
          domain->minimum_image(delr2);
          rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
          r2 = sqrt(rsq2);

          // angle (cos and sin)

          c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
          c /= r1*r2;
          if (c > 1.0) c = 1.0;
          if (c < -1.0) c = -1.0;
          ac = acos(c);

          if (ac > pm.cut_angle && ac < (2.0*MY_PI - pm.cut_angle)) {
            s = sqrt(1.0 - c*c);
            if (s < SMALL) s = SMALL;

            // Morse-specific kernel

            r = sqrt(rsq);
            dr = r - pm.r0;
            dexp = exp(-pm.alpha * dr);
            eng_morse = pm.d0 * (dexp*dexp - 2.0*dexp);
            force_kernel = pm.morse1*(dexp*dexp - dexp)/r * powint(c,pm.ap);
            force_angle = pm.ap * eng_morse * powint(c,pm.ap-1)*s;

            if (rsq > pm.cut_innersq) {
              switch1 = (pm.cut_outersq-rsq) * (pm.cut_outersq-rsq) *
                        (pm.cut_outersq + 2.0*rsq - 3.0*pm.cut_innersq) /
                        pm.denom_vdw;
              switch2 = 12.0*rsq * (pm.cut_outersq-rsq) *
                        (rsq-pm.cut_innersq) / pm.denom_vdw;
              force_kernel = force_kernel*switch1 + eng_morse*switch2/rsq;
              force_angle  *= switch1;
              eng_morse    *= switch1;
            }

            if (EFLAG) {
              evdwl = eng_morse * powint(c,pm.ap);
              evdwl *= factor_hb;
            }

            a = factor_hb*force_angle/s;
            b = factor_hb*force_kernel;

            a11 = a*c / rsq1;
            a12 = -a / (r1*r2);
            a22 = a*c / rsq2;

            vx1 = a11*delr1[0] + a12*delr2[0];
            vx2 = a22*delr2[0] + a12*delr1[0];
            vy1 = a11*delr1[1] + a12*delr2[1];
            vy2 = a22*delr2[1] + a12*delr1[1];
            vz1 = a11*delr1[2] + a12*delr2[2];
            vz2 = a22*delr2[2] + a12*delr1[2];

            fi[0] = vx1 + b*delx;
            fi[1] = vy1 + b*dely;
            fi[2] = vz1 + b*delz;
            fj[0] = vx2 - b*delx;
            fj[1] = vy2 - b*dely;
            fj[2] = vz2 - b*delz;

            fxtmp += fi[0];
            fytmp += fi[1];
            fztmp += fi[2];

            f[j].x += fj[0];
            f[j].y += fj[1];
            f[j].z += fj[2];

            f[k].x -= vx1 + vx2;
            f[k].y -= vy1 + vy2;
            f[k].z -= vz1 + vz2;

            // KIJ instead of IJK b/c delr1/delr2 are both with respect to k

            if (EVFLAG) ev_tally3_thr(this,k,i,j,evdwl,0.0,fi,fj,delr1,delr2,thr);
            if (EFLAG) {
              hbcount++;
              hbeng += evdwl;
            }
          }
        }
      }
    }
    f[i].x += fxtmp;
    f[i].y += fytmp;
    f[i].z += fztmp;
  }
  const int tid = thr->get_tid();
  hbcount_thr[tid] = static_cast<double>(hbcount);
  hbeng_thr[tid] = hbeng;
}

/* ---------------------------------------------------------------------- */

double PairHbondDreidingMorseOMP::memory_usage()
{
  double bytes = memory_usage_thr();
  bytes += comm->nthreads * 2 * sizeof(double);
  bytes += PairHbondDreidingMorse::memory_usage();

  return bytes;
}