shock srd xtc

PACKUSER = user-misc user-atc user-awpmd user-cg-cmm \

	   user-cuda user-eff user-ewaldn user-reaxc

	   user-cuda user-eff user-ewaldn user-omp user-reaxc

PACKALL = $(PACKAGE) $(PACKUSER)

# Install/unInstall package files in LAMMPS

# do not install child files if parent does not exist

if (test $1 = 1) then

#  if (test -e ../pair_lj_cut_coul_long.cpp) then

#    cp pair_lj_cut_coul_long_omp.cpp ..

#    cp pair_lj_cut_coul_long_omp.h ..

#  fi

  cp pair_lj_cut_omp.cpp ..

  cp thr_omp.cpp ..

  cp pair_lj_cut_omp.h ..

  cp thr_omp.h ..

elif (test $1 = 0) then

#  rm -f ../pair_lj_cut_coul_long_omp.cpp

  rm -f ../pair_lj_cut_omp.cpp

  rm -f ../thr_omp.cpp

#  rm -f ../pair_lj_cut_coul_long_omp.h

  rm -f ../pair_lj_cut_omp.h

  rm -f ../thr_omp.h

fi

#/bin/sh

# Update package files in LAMMPS

# copy package file to src if it doesn't exists or is different

# do not copy gayberne files if non-GPU version does not exist

for file in *_omp.cpp *_omp.h; do

  # let us see if the "rain man" can count the toothpicks...

  ofile=`echo $file | sed -e s,\\\\\\(.\\*\\\\\\)_omp\\\\.\\\\\\(h\\\\\\|cpp\\\\\\),\\\\1.\\\\2,`

  if (test $file = "thr_omp.h") || (test $file = "thr_omp.cpp") then

    :  # do check for those files.

  elif (test ! -e ../$ofile) then

    continue

  fi

  if (test ! -e ../$file) then

    echo "  creating src/$file"

    cp $file ..

  elif ! cmp -s $file ../$file ; then

    echo "  updating src/$file"

    cp $file ..

  fi

done

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

   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_omp.h"

#include "atom.h"

#include "comm.h"

#include "force.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "neigh_request.h"

#include "memory.h"

#include "error.h"

using namespace LAMMPS_NS;

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

PairLJCutOMP::PairLJCutOMP(LAMMPS *lmp) :

  PairLJCut(lmp), ThrOMP(lmp, PAIR)

{

  respa_enable = 0;

}

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

void PairLJCutOMP::compute(int eflag, int vflag)

{

  if (eflag || vflag) {

    ev_setup(eflag,vflag);

    ev_setup_thr(this);

  } 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(shared)

#endif

  {

    int ifrom, ito, tid;

    double **f;

    f = loop_setup_thr(atom->f, ifrom, ito, tid, inum, nall, nthreads);

    if (evflag) {

      if (eflag) {

	if (force->newton_pair) eval<1,1,1>(f, ifrom, ito, tid);

	else eval<1,1,0>(f, ifrom, ito, tid);

      } else {

	if (force->newton_pair) eval<1,0,1>(f, ifrom, ito, tid);

	else eval<1,0,0>(f, ifrom, ito, tid);

      }

    } else {

      if (force->newton_pair) eval<0,0,1>(f, ifrom, ito, tid);

      else eval<0,0,0>(f, ifrom, ito, tid);

    }

    // reduce per thread forces into global force array.

    force_reduce_thr(&(atom->f[0][0]), nall, nthreads, tid);

  } // end of omp parallel region

  // reduce per thread energy and virial, if requested.

  if (evflag) ev_reduce_thr(this);

  if (vflag_fdotr) virial_fdotr_compute();

}

template <int EVFLAG, int EFLAG, int NEWTON_PAIR>

void PairLJCutOMP::eval(double **f, int iifrom, int iito, int tid)

{

  int i,j,ii,jj,jnum,itype,jtype;

  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

  double rsq,r2inv,r6inv,forcelj,factor_lj;

  int *ilist,*jlist,*numneigh,**firstneigh;

  evdwl = 0.0;

  double **x = atom->x;

  int *type = atom->type;

  int nlocal = atom->nlocal;

  double *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][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)];

      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;

	r6inv = r2inv*r2inv*r2inv;

	forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);

	fpair = factor_lj*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) {

	  evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])

	    - offset[itype][jtype];

	  evdwl *= factor_lj;

	}

	if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,

				 evdwl,0.0,fpair,delx,dely,delz,tid);

      }

    }

    f[i][0] += fxtmp;

    f[i][1] += fytmp;

    f[i][2] += fztmp;

  }

}

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

double PairLJCutOMP::memory_usage()

{

  double bytes = memory_usage_thr();

  bytes += PairLJCut::memory_usage();

  return bytes;

}

/* -*- 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/omp,PairLJCutOMP)

#else

#ifndef LMP_PAIR_LJ_CUT_OMP_H

#define LMP_PAIR_LJ_CUT_OMP_H

#include "pair_lj_cut.h"

#include "thr_omp.h"

namespace LAMMPS_NS {

class PairLJCutOMP : public PairLJCut, public ThrOMP {

 public:

  PairLJCutOMP(class LAMMPS *);

  virtual void compute(int, int);

  virtual double memory_usage();

 private:

  template <int EVFLAG, int EFLAG, int NEWTON_PAIR>

  void eval(double **f, int ifrom, int ito, int tid);

};

}

#endif

#endif