text: /* ----------------------------------------------------------------------
     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_gran_hooke_omp.h"
  #include "atom.h"
  #include "comm.h"
  #include "fix.h"
  #include "force.h"
  #include "memory.h"
  #include "neighbor.h"
  #include "neigh_list.h"
  
  #include "suffix.h"
  using namespace LAMMPS_NS;
  
  /* ---------------------------------------------------------------------- */
  
  PairGranHookeOMP::PairGranHookeOMP(LAMMPS *lmp) :
    PairGranHooke(lmp), ThrOMP(lmp, THR_PAIR)
  {
    suffix_flag |= Suffix::OMP;
    respa_enable = 0;
  }
  
  /* ---------------------------------------------------------------------- */
  
  void PairGranHookeOMP::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;
  
    // update rigid body info for owned & ghost atoms if using FixRigid masses
    // body[i] = which body atom I is in, -1 if none
    // mass_body = mass of each rigid body
  
    if (fix_rigid && neighbor->ago == 0) {
      int tmp;
      int *body = (int *) fix_rigid->extract("body",tmp);
      double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
      if (atom->nmax > nmax) {
        memory->destroy(mass_rigid);
        nmax = atom->nmax;
        memory->create(mass_rigid,nmax,"pair:mass_rigid");
      }
      int nlocal = atom->nlocal;
      for (int i = 0; i < nlocal; i++)
        if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
        else mass_rigid[i] = 0.0;
      comm->forward_comm_pair(this);
    }
  
  #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 (force->newton_pair) eval<1,1>(ifrom, ito, thr);
        else eval<1,0>(ifrom, ito, thr);
      else
        if (force->newton_pair) eval<0,1>(ifrom, ito, thr);
        else eval<0,0>(ifrom, ito, thr);
  
      thr->timer(Timer::PAIR);
      reduce_thr(this, eflag, vflag, thr);
    } // end of omp parallel region
  }
  
  template <int EVFLAG, int NEWTON_PAIR>
  void PairGranHookeOMP::eval(int iifrom, int iito, ThrData * const thr)
  {
    int i,j,ii,jj,jnum;
    double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
    double radi,radj,radsum,rsq,r,rinv,rsqinv;
    double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
    double wr1,wr2,wr3;
    double vtr1,vtr2,vtr3,vrel;
    double mi,mj,meff,damp,ccel,tor1,tor2,tor3;
    double fn,fs,ft,fs1,fs2,fs3;
    int *ilist,*jlist,*numneigh,**firstneigh;
  
    const double * const * const x = atom->x;
    const double * const * const v = atom->v;
    const double * const * const omega = atom->omega;
    const double * const radius = atom->radius;
    const double * const rmass = atom->rmass;
    const double * const mass = atom->mass;
    double * const * const f = thr->get_f();
    double * const * const torque = thr->get_torque();
    const int * const type = atom->type;
    const int * const mask = atom->mask;
    const int nlocal = atom->nlocal;
    double fxtmp,fytmp,fztmp;
    double t1tmp,t2tmp,t3tmp;
  
    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][0];
      ytmp = x[i][1];
      ztmp = x[i][2];
      radi = radius[i];
      jlist = firstneigh[i];
      jnum = numneigh[i];
      fxtmp=fytmp=fztmp=t1tmp=t2tmp=t3tmp=0.0;
  
      for (jj = 0; jj < jnum; jj++) {
        j = jlist[jj];
        j &= NEIGHMASK;
  
        delx = xtmp - x[j][0];
        dely = ytmp - x[j][1];
        delz = ztmp - x[j][2];
        rsq = delx*delx + dely*dely + delz*delz;
        radj = radius[j];
        radsum = radi + radj;
  
        if (rsq < radsum*radsum) {
          r = sqrt(rsq);
          rinv = 1.0/r;
          rsqinv = 1.0/rsq;
  
          // relative translational velocity
  
          vr1 = v[i][0] - v[j][0];
          vr2 = v[i][1] - v[j][1];
          vr3 = v[i][2] - v[j][2];
  
          // normal component
  
          vnnr = vr1*delx + vr2*dely + vr3*delz;
          vn1 = delx*vnnr * rsqinv;
          vn2 = dely*vnnr * rsqinv;
          vn3 = delz*vnnr * rsqinv;
  
          // tangential component
  
          vt1 = vr1 - vn1;
          vt2 = vr2 - vn2;
          vt3 = vr3 - vn3;
  
          // relative rotational velocity
  
          wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
          wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
          wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
  
          // meff = effective mass of pair of particles
          // if I or J part of rigid body, use body mass
          // if I or J is frozen, meff is other particle
  
          if (rmass) {
            mi = rmass[i];
            mj = rmass[j];
          } else {
            mi = mass[type[i]];
            mj = mass[type[j]];
          }
          if (fix_rigid) {
            if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
            if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
          }
  
          meff = mi*mj / (mi+mj);
          if (mask[i] & freeze_group_bit) meff = mj;
          if (mask[j] & freeze_group_bit) meff = mi;
  
          // normal forces = Hookian contact + normal velocity damping
  
          damp = meff*gamman*vnnr*rsqinv;
          ccel = kn*(radsum-r)*rinv - damp;
  
          // relative velocities
  
          vtr1 = vt1 - (delz*wr2-dely*wr3);
          vtr2 = vt2 - (delx*wr3-delz*wr1);
          vtr3 = vt3 - (dely*wr1-delx*wr2);
          vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
          vrel = sqrt(vrel);
  
          // force normalization
  
          fn = xmu * fabs(ccel*r);
          fs = meff*gammat*vrel;
          if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
          else ft = 0.0;
  
          // tangential force due to tangential velocity damping
  
          fs1 = -ft*vtr1;
          fs2 = -ft*vtr2;
          fs3 = -ft*vtr3;
  
          // forces & torques
  
          fx = delx*ccel + fs1;
          fy = dely*ccel + fs2;
          fz = delz*ccel + fs3;
          fxtmp  += fx;
          fytmp  += fy;
          fztmp  += fz;
  
          tor1 = rinv * (dely*fs3 - delz*fs2);
          tor2 = rinv * (delz*fs1 - delx*fs3);
          tor3 = rinv * (delx*fs2 - dely*fs1);
          t1tmp -= radi*tor1;
          t2tmp -= radi*tor2;
          t3tmp -= radi*tor3;
  
          if (NEWTON_PAIR || j < nlocal) {
            f[j][0] -= fx;
            f[j][1] -= fy;
            f[j][2] -= fz;
            torque[j][0] -= radj*tor1;
            torque[j][1] -= radj*tor2;
            torque[j][2] -= radj*tor3;
          }
  
          if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
                                       0.0,0.0,fx,fy,fz,delx,dely,delz,thr);
  
        }
      }
      f[i][0] += fxtmp;
      f[i][1] += fytmp;
      f[i][2] += fztmp;
      torque[i][0] += t1tmp;
      torque[i][1] += t2tmp;
      torque[i][2] += t3tmp;
    }
  }
  
  /* ---------------------------------------------------------------------- */
  
  double PairGranHookeOMP::memory_usage()
  {
    double bytes = memory_usage_thr();
    bytes += PairGranHooke::memory_usage();
  
    return bytes;
  }
  