Commit 5685131f authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

add USER-OMP version of pair style agni

parent 22fc92f9

src/USER-OMP/pair_agni_omp.cpp

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+171 −0
Original line number Diff line number Diff line 
/* ----------------------------------------------------------------------

   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 <string.h>

#include "pair_agni_omp.h"

#include "atom.h"

#include "comm.h"

#include "force.h"

#include "memory.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "math_special.h"

#include "math_const.h"



#include "suffix.h"

using namespace LAMMPS_NS;

using namespace MathSpecial;



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



PairAGNIOMP::PairAGNIOMP(LAMMPS *lmp) :

  PairAGNI(lmp), ThrOMP(lmp, THR_PAIR)

{

  suffix_flag |= Suffix::OMP;

  respa_enable = 0;

}



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



void PairAGNIOMP::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);

    ThrData *thr = fix->get_thr(tid);

    thr->timer(Timer::START);

    ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);



    if (evflag) eval<1>(ifrom, ito, thr);

    else eval<0>(ifrom, ito, thr);



    thr->timer(Timer::PAIR);

    reduce_thr(this, eflag, vflag, thr);

  } // end of omp parallel region

}



template <int EVFLAG>

void PairAGNIOMP::eval(int iifrom, int iito, ThrData * const thr)

{

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

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

  double rsq;

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



  const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];

  dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];

  const int * _noalias const type = atom->type;



  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  double fxtmp,fytmp,fztmp;

  dbl3_t *V;



  // loop over full neighbor list of my atoms



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



    i = ilist[ii];

    itype = map[type[i]];

    xtmp = x[i].x;

    ytmp = x[i].y;

    ztmp = x[i].z;

    fxtmp = fytmp = fztmp = 0.0;



    const Param &iparam = params[elem2param[itype]];

    V = new dbl3_t[iparam.numeta];

    memset(V,0,iparam.numeta *sizeof(dbl3_t));



    jlist = firstneigh[i];

    jnum = numneigh[i];



    for (jj = 0; jj < jnum; jj++) {

      j = jlist[jj];

      j &= NEIGHMASK;



      delx = xtmp - x[j].x;

      dely = ytmp - x[j].y;

      delz = ztmp - x[j].z;

      rsq = delx*delx + dely*dely + delz*delz;



      if ((rsq > 0.0) && (rsq < iparam.cutsq)) {

        const double r = sqrt(rsq);

        const double cF = 0.5*(cos((MathConst::MY_PI*r)/iparam.cut)+1.0);

        const double wX = cF*delx/r;

        const double wY = cF*dely/r;

        const double wZ = cF*delz/r;

        

        for (k = 0; k < iparam.numeta; ++k) {

          const double e = exp(-(iparam.eta[k]*rsq));

          V[k].x += wX*e;

          V[k].y += wY*e;

          V[k].z += wZ*e;

        }

      }

    }



    for (j = 0; j < iparam.numtrain; ++j) {

      double kx = 0.0;

      double ky = 0.0;

      double kz = 0.0;    



      for(int k = 0; k < iparam.numeta; ++k) {

        const double xu = iparam.xU[k][j];

        kx += square(V[k].x - xu);  

        ky += square(V[k].y - xu);

        kz += square(V[k].z - xu);        

      }

      const double e = -0.5/(square(iparam.sigma));

      fxtmp += iparam.alpha[j]*exp(kx*e);

      fytmp += iparam.alpha[j]*exp(ky*e);

      fztmp += iparam.alpha[j]*exp(kz*e);

    }

    fxtmp += iparam.b;

    fytmp += iparam.b;

    fztmp += iparam.b;

    f[i].x += fxtmp;

    f[i].y += fytmp;

    f[i].z += fztmp;



    if (EVFLAG) ev_tally_xyz_full_thr(this,i,0.0,0.0,

                                      fxtmp,fytmp,fztmp,

                                      delx,dely,delz,thr);

    delete [] V;

  }

}



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



double PairAGNIOMP::memory_usage()

{

  double bytes = memory_usage_thr();

  bytes += PairAGNI::memory_usage();



  return bytes;

}

src/USER-OMP/pair_agni_omp.h

0 → 100644
+48 −0
Original line number Diff line number Diff line 
/* -*- 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(agni/omp,PairAGNIOMP)



#else



#ifndef LMP_PAIR_AGNI_OMP_H

#define LMP_PAIR_AGNI_OMP_H



#include "pair_agni.h"

#include "thr_omp.h"



namespace LAMMPS_NS {



class PairAGNIOMP : public PairAGNI, public ThrOMP {



 public:

  PairAGNIOMP(class LAMMPS *);



  virtual void compute(int, int);

  virtual double memory_usage();



 private:

  template <int EVFLAG>

  void eval(int ifrom, int ito, ThrData * const thr);

};



}



#endif

#endif

src/USER-OMP/thr_omp.cpp

+31 −0
Original line number Diff line number Diff line
@@ -557,6 +557,37 @@ void ThrOMP::ev_tally_xyz_thr(Pair * const pair, const int i, const int j, 
  }

}





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

   tally eng_vdwl and virial into global and per-atom accumulators

   for virial, have delx,dely,delz and fx,fy,fz

   called when using full neighbor lists

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



void ThrOMP::ev_tally_xyz_full_thr(Pair * const pair, const int i,

                                   const double evdwl, const double ecoul,

                                   const double fx, const double fy,

                                   const double fz, const double delx,

                                   const double dely, const double delz,

                                   ThrData * const thr)

{



  if (pair->eflag_either)

    e_tally_thr(pair,i,i,i+1,0,0.5*evdwl,ecoul,thr);



  if (pair->vflag_either) {

    double v[6];

    v[0] = 0.5*delx*fx;

    v[1] = 0.5*dely*fy;

    v[2] = 0.5*delz*fz;

    v[3] = 0.5*delx*fy;

    v[4] = 0.5*delx*fz;

    v[5] = 0.5*dely*fz;



    v_tally_thr(pair,i,i,i+1,0,v,thr);

  }

}



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

   tally eng_vdwl and virial into global and per-atom accumulators

   called by SW and hbond potentials, newton_pair is always on

src/USER-OMP/thr_omp.h

+3 −0
Original line number Diff line number Diff line
@@ -118,6 +118,9 @@ class ThrOMP { 
                        const int, const double, const double, const double,

                        const double, const double, const double,

                        const double, const double, ThrData * const);

  void ev_tally_xyz_full_thr(Pair * const, const int, const double, const double,

                             const double, const double, const double,

                             const double, const double, const double, ThrData * const);

  void ev_tally3_thr(Pair * const, const int, const int, const int, const double,

                     const double, const double * const, const double * const,

                     const double * const, const double * const, ThrData * const);

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