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

   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)
------------------------------------------------------------------------- */

#include <cmath>
#include "improper_fourier_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "timer.h"
#include "force.h"
#include "update.h"
#include "error.h"

#include "suffix.h"
using namespace LAMMPS_NS;

#define TOLERANCE 0.05
#define SMALL     0.001

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

ImproperFourierOMP::ImproperFourierOMP(class LAMMPS *lmp)
  : ImproperFourier(lmp), ThrOMP(lmp,THR_IMPROPER)
{
  suffix_flag |= Suffix::OMP;
}

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

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

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

#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 (inum > 0) {
      if (evflag) {
        if (eflag) {
          if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
          else eval<1,1,0>(ifrom, ito, thr);
        } else {
          if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
          else eval<1,0,0>(ifrom, ito, thr);
        }
      } else {
        if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
        else eval<0,0,0>(ifrom, ito, thr);
      }
    }
    thr->timer(Timer::BOND);
    reduce_thr(this, eflag, vflag, thr);
  } // end of omp parallel region
}

template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
{
  int i1,i2,i3,i4,n,type;
  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;

  const double * const * const x = atom->x;
  const int * const * const improperlist = neighbor->improperlist;

  for (n = nfrom; n < nto; n++) {
    i1 = improperlist[n][0];
    i2 = improperlist[n][1];
    i3 = improperlist[n][2];
    i4 = improperlist[n][3];
    type = improperlist[n][4];

    // 1st bond

    vb1x = x[i2][0] - x[i1][0];
    vb1y = x[i2][1] - x[i1][1];
    vb1z = x[i2][2] - x[i1][2];

    // 2nd bond

    vb2x = x[i3][0] - x[i1][0];
    vb2y = x[i3][1] - x[i1][1];
    vb2z = x[i3][2] - x[i1][2];

    // 3rd bond

    vb3x = x[i4][0] - x[i1][0];
    vb3y = x[i4][1] - x[i1][1];
    vb3z = x[i4][2] - x[i1][2];

    add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i2,i3,i4,type,
                                       vb1x,vb1y,vb1z,
                                       vb2x,vb2y,vb2z,
                                       vb3x,vb3y,vb3z,thr);
    if ( all[type] ) {
      add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i4,i2,i3,type,
                                         vb3x,vb3y,vb3z,
                                         vb1x,vb1y,vb1z,
                                         vb2x,vb2y,vb2z,thr);
      add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i3,i4,i2,type,
                                         vb2x,vb2y,vb2z,
                                         vb3x,vb3y,vb3z,
                                         vb1x,vb1y,vb1z,thr);
    }
  }
}

template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperFourierOMP::add1_thr(const int i1,const int i2,
                               const int i3,const int i4,
                               const int type,
                               const double &vb1x,
                               const double &vb1y,
                               const double &vb1z,
                               const double &vb2x,
                               const double &vb2y,
                               const double &vb2z,
                               const double &vb3x,
                               const double &vb3y,
                               const double &vb3z,
                               ThrData * const thr)
{
  double eimproper,f1[3],f2[3],f3[3],f4[3];
  double c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
  double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz;

  double * const * const f = thr->get_f();
  const int nlocal = atom->nlocal;

  eimproper = 0.0;

  // c0 calculation
  // A = vb1 X vb2 is perpendicular to IJK plane

  ax = vb1y*vb2z-vb1z*vb2y;
  ay = vb1z*vb2x-vb1x*vb2z;
  az = vb1x*vb2y-vb1y*vb2x;
  ra2 = ax*ax+ay*ay+az*az;
  rh2 = vb3x*vb3x+vb3y*vb3y+vb3z*vb3z;
  ra = sqrt(ra2);
  rh = sqrt(rh2);
  if (ra < SMALL) ra = SMALL;
  if (rh < SMALL) rh = SMALL;

  rar = 1/ra;
  rhr = 1/rh;
  arx = ax*rar;
  ary = ay*rar;
  arz = az*rar;
  hrx = vb3x*rhr;
  hry = vb3y*rhr;
  hrz = vb3z*rhr;

  c = arx*hrx+ary*hry+arz*hrz;

  // error check

  if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
    int me = comm->me;

    if (screen) {
      char str[128];
      sprintf(str,
              "Improper problem: %d/%d " BIGINT_FORMAT " "
                TAGINT_FORMAT " " TAGINT_FORMAT " "
                TAGINT_FORMAT " " TAGINT_FORMAT,
              me,thr->get_tid(),update->ntimestep,
              atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
      error->warning(FLERR,str,0);
      fprintf(screen,"  1st atom: %d %g %g %g\n",
              me,atom->x[i1][0],atom->x[i1][1],atom->x[i1][2]);
      fprintf(screen,"  2nd atom: %d %g %g %g\n",
              me,atom->x[i2][0],atom->x[i2][1],atom->x[i2][2]);
      fprintf(screen,"  3rd atom: %d %g %g %g\n",
              me,atom->x[i3][0],atom->x[i3][1],atom->x[i3][2]);
      fprintf(screen,"  4th atom: %d %g %g %g\n",
              me,atom->x[i4][0],atom->x[i4][1],atom->x[i4][2]);
    }
  }

  if (c > 1.0) c = 1.0;
  if (c < -1.0) c = -1.0;

  s = sqrt(1.0 - c*c);
  if (s < SMALL) s = SMALL;
  cotphi = c/s;

  projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
    sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
  projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
    sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
  if (projhfg > 0.0) {
    s *= -1.0;
    cotphi *= -1.0;
  }

  //  force and energy
  //  E = k ( C0 + C1 cos(w) + C2 cos(w)

  c2 = 2.0*s*s-1.0;
  if (EFLAG) eimproper =  k[type]*(C0[type]+C1[type]*s+C2[type]*c2);

  // dhax = diffrence between H and A in X direction, etc

  a = k[type]*(C1[type]+4.0*C2[type]*s)*cotphi;
  dhax = hrx-c*arx;
  dhay = hry-c*ary;
  dhaz = hrz-c*arz;

  dahx = arx-c*hrx;
  dahy = ary-c*hry;
  dahz = arz-c*hrz;

  f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
  f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
  f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;

  f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
  f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
  f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;

  f4[0] = dahx*rhr*a;
  f4[1] = dahy*rhr*a;
  f4[2] = dahz*rhr*a;

  f1[0] = -(f2[0] + f3[0] + f4[0]);
  f1[1] = -(f2[1] + f3[1] + f4[1]);
  f1[2] = -(f2[2] + f3[2] + f4[2]);

  // apply force to each of 4 atoms

  if (NEWTON_BOND || i1 < nlocal) {
    f[i1][0] += f1[0];
    f[i1][1] += f1[1];
    f[i1][2] += f1[2];
  }

  if (NEWTON_BOND || i2 < nlocal) {
    f[i2][0] += f3[0];
    f[i2][1] += f3[1];
    f[i2][2] += f3[2];
  }

  if (NEWTON_BOND || i3 < nlocal) {
    f[i3][0] += f2[0];
    f[i3][1] += f2[1];
    f[i3][2] += f2[2];
  }

  if (NEWTON_BOND || i4 < nlocal) {
    f[i4][0] += f4[0];
    f[i4][1] += f4[1];
    f[i4][2] += f4[2];
  }

  if (EVFLAG)
    ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4,
                 -vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z,thr);

}