Commit 3ad56870 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1805 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent f20c63d6

src/pair_lj_gromacs.cpp

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

   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: Mark Stevens (SNL)

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



#include "math.h"

#include "stdio.h"

#include "stdlib.h"

#include "string.h"

#include "pair_lj_gromacs.h"

#include "atom.h"

#include "comm.h"

#include "force.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "memory.h"

#include "error.h"



using namespace LAMMPS_NS;



#define MIN(a,b) ((a) < (b) ? (a) : (b))

#define MAX(a,b) ((a) > (b) ? (a) : (b))



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



PairLJGromacs::PairLJGromacs(LAMMPS *lmp) : Pair(lmp) {}



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



PairLJGromacs::~PairLJGromacs()

{

  if (allocated) {

    memory->destroy_2d_int_array(setflag);

    memory->destroy_2d_double_array(cutsq);



    memory->destroy_2d_double_array(cut);

    memory->destroy_2d_double_array(cut_inner);

    memory->destroy_2d_double_array(cut_inner_sq);

    memory->destroy_2d_double_array(epsilon);

    memory->destroy_2d_double_array(sigma);

    memory->destroy_2d_double_array(lj1);

    memory->destroy_2d_double_array(lj2);

    memory->destroy_2d_double_array(lj3);

    memory->destroy_2d_double_array(lj4);

    memory->destroy_2d_double_array(ljsw1);

    memory->destroy_2d_double_array(ljsw2);

    memory->destroy_2d_double_array(ljsw3);

    memory->destroy_2d_double_array(ljsw4);

    memory->destroy_2d_double_array(ljsw5);

  }

}



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



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

{

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

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

  double rsq,r2inv,r6inv,forcelj,factor_lj;

  double r,t,fswitch,eswitch;

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



  evdwl = 0.0;

  if (eflag || vflag) ev_setup(eflag,vflag);

  else evflag = vflag_fdotr = 0;



  double **x = atom->x;

  double **f = atom->f;

  double *q = atom->q;

  int *type = atom->type;

  int nlocal = atom->nlocal;

  int nall = nlocal + atom->nghost;

  double *special_lj = force->special_lj;

  int newton_pair = force->newton_pair;



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;

  

  // loop over neighbors of my atoms



  for (ii = 0; ii < inum; 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];



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

      j = jlist[jj];



      if (j < nall) factor_lj = 1.0;

      else {

	factor_lj = special_lj[j/nall];

	j %= nall;

      }



      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]);

        if (rsq > cut_inner_sq[itype][jtype]) {

          r = sqrt(rsq); 

	  t = r - cut_inner[itype][jtype];

	  fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);

	  forcelj += fswitch;

        }



	fpair = factor_lj*forcelj*r2inv;



	f[i][0] += delx*fpair;

	f[i][1] += dely*fpair;

	f[i][2] += 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]) + 

	    ljsw5[itype][jtype];

          if (rsq > cut_inner_sq[itype][jtype]) {

            eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);

            evdwl += eswitch;

          }

	  evdwl *= factor_lj;

	}



	if (evflag) ev_tally(i,j,nlocal,newton_pair,

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

      }

    }

  }



  if (vflag_fdotr) virial_compute();

}



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

   allocate all arrays

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



void PairLJGromacs::allocate()

{

  allocated = 1;

  int n = atom->ntypes;



  setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");

  for (int i = 1; i <= n; i++)

    for (int j = i; j <= n; j++)

      setflag[i][j] = 0;



  cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");



  cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");

  cut_inner = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner");

  cut_inner_sq = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner_sq");

  epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon");

  sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");

  lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");

  lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");

  lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");

  lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");

  ljsw1 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw1");

  ljsw2 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw2");

  ljsw3 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw3");

  ljsw4 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw4");

  ljsw5 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw5");

}



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

   global settings

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



void PairLJGromacs::settings(int narg, char **arg)

{

  if (narg != 2) error->all("Illegal pair_style command");



  cut_inner_global = atof(arg[0]);

  cut_global = atof(arg[1]);



  if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)

    error->all("Illegal pair_style command");



  // reset cutoffs that have been explicitly set



  if (allocated) {

    int i,j;

    for (i = 1; i <= atom->ntypes; i++)

      for (j = i+1; j <= atom->ntypes; j++)

	if (setflag[i][j]) {

	  cut_inner[i][j] = cut_inner_global;

	  cut[i][j] = cut_global;

	}

  }

}



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

   set coeffs for one or more type pairs

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



void PairLJGromacs::coeff(int narg, char **arg)

{

  if (narg != 4 && narg != 6)

    error->all("Incorrect args for pair coefficients");

  if (!allocated) allocate();



  int ilo,ihi,jlo,jhi;

  force->bounds(arg[0],atom->ntypes,ilo,ihi);

  force->bounds(arg[1],atom->ntypes,jlo,jhi);



  double epsilon_one = atof(arg[2]);

  double sigma_one = atof(arg[3]);



  double cut_inner_one = cut_inner_global;

  double cut_one = cut_global;

  if (narg == 6) {

    cut_inner_one = atof(arg[4]);

    cut_one = atof(arg[5]);

  }



  if (cut_inner_one <= 0.0 || cut_inner_one > cut_one)

    error->all("Incorrect args for pair coefficients");



  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    for (int j = MAX(jlo,i); j <= jhi; j++) {

      epsilon[i][j] = epsilon_one;

      sigma[i][j] = sigma_one;

      cut_inner[i][j] = cut_inner_one;

      cut[i][j] = cut_one;

      setflag[i][j] = 1;

      count++;

    }

  }



  if (count == 0) error->all("Incorrect args for pair coefficients");

}



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

   init for one type pair i,j and corresponding j,i

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



double PairLJGromacs::init_one(int i, int j)

{

  if (setflag[i][j] == 0) {

    epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],

			       sigma[i][i],sigma[j][j]);

    sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);

    cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);

    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);

  }



  cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];

  lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);

  lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);

  lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);

  lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);



  double r6inv = 1.0/pow(cut[i][j],6.0);

  double r8inv = 1.0/pow(cut[i][j],8.0);

  double t = cut[i][j] - cut_inner[i][j];

  double t2inv = 1.0/(t*t);

  double t3inv = t2inv/t;

  double t3 = 1.0/t3inv;

  double a6 = ( 7.0*cut_inner[i][j] - 10.0*cut[i][j])*r8inv*t2inv;

  double b6 = ( 9.0*cut[i][j] -  7.0*cut_inner[i][j])*r8inv*t3inv;

  double a12 = (13.0*cut_inner[i][j] - 16.0*cut[i][j])*r6inv*r8inv*t2inv;

  double b12 = (15.0*cut[i][j] - 13.0*cut_inner[i][j])*r6inv*r8inv*t3inv;

  double c6 = r6inv - t3*(a6/3.0 + b6*t/4.0);

  double c12 = r6inv*r6inv - t3*(a12/3.0 + b12*t/4.0);

  ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6;

  ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6;

  ljsw3[i][j] =-lj3[i][j]*a12/3.0 + lj4[i][j]*a6/3.0;

  ljsw4[i][j] =-lj3[i][j]*b12/4.0 + lj4[i][j]*b6/4.0;

  ljsw5[i][j] =-lj3[i][j]*c12 + lj4[i][j]*c6;



  cut_inner[j][i] = cut_inner[i][j];

  cut_inner_sq[j][i] = cut_inner_sq[i][j];

  lj1[j][i] = lj1[i][j];

  lj2[j][i] = lj2[i][j];

  lj3[j][i] = lj3[i][j];

  lj4[j][i] = lj4[i][j];

  ljsw1[j][i] = ljsw1[i][j];

  ljsw2[j][i] = ljsw2[i][j];

  ljsw3[j][i] = ljsw3[i][j];

  ljsw4[j][i] = ljsw4[i][j];

  ljsw5[j][i] = ljsw5[i][j];



  return cut[i][j];

}



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

  proc 0 writes to restart file

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



void PairLJGromacs::write_restart(FILE *fp)

{

  write_restart_settings(fp);



  int i,j;

  for (i = 1; i <= atom->ntypes; i++)

    for (j = i; j <= atom->ntypes; j++) {

      fwrite(&setflag[i][j],sizeof(int),1,fp);

      if (setflag[i][j]) {

	fwrite(&epsilon[i][j],sizeof(double),1,fp);

	fwrite(&sigma[i][j],sizeof(double),1,fp);

	fwrite(&cut_inner[i][j],sizeof(double),1,fp);

	fwrite(&cut[i][j],sizeof(double),1,fp);

      }

    }

}



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

  proc 0 reads from restart file, bcasts

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



void PairLJGromacs::read_restart(FILE *fp)

{

  read_restart_settings(fp);

  allocate();



  int i,j;

  int me = comm->me;

  for (i = 1; i <= atom->ntypes; i++)

    for (j = i; j <= atom->ntypes; j++) {

      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);

      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);

      if (setflag[i][j]) {

	if (me == 0) {

	  fread(&epsilon[i][j],sizeof(double),1,fp);

	  fread(&sigma[i][j],sizeof(double),1,fp);

	  fread(&cut_inner[i][j],sizeof(double),1,fp);

	  fread(&cut[i][j],sizeof(double),1,fp);

	}

	MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);

	MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);

	MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);

	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);

      }

    }

}



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

  proc 0 writes to restart file

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



void PairLJGromacs::write_restart_settings(FILE *fp)

{

  fwrite(&cut_inner_global,sizeof(double),1,fp);

  fwrite(&cut_global,sizeof(double),1,fp);

  fwrite(&offset_flag,sizeof(int),1,fp);

  fwrite(&mix_flag,sizeof(int),1,fp);

}



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

  proc 0 reads from restart file, bcasts

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



void PairLJGromacs::read_restart_settings(FILE *fp)

{

  int me = comm->me;

  if (me == 0) {

    fread(&cut_inner_global,sizeof(double),1,fp);

    fread(&cut_global,sizeof(double),1,fp);

    fread(&offset_flag,sizeof(int),1,fp);

    fread(&mix_flag,sizeof(int),1,fp);

  }

  MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);

  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);

  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

}



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



double PairLJGromacs::single(int i, int j, int itype, int jtype,

			     double rsq,

			     double factor_coul, double factor_lj,

			     double &fforce)

{

  double r2inv,r6inv,forcelj,philj;

  double r,t,fswitch,phiswitch;



  r2inv = 1.0/rsq;

  r6inv = r2inv*r2inv*r2inv;

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

  if (rsq > cut_inner_sq[itype][jtype]) {

    r = sqrt(rsq); 

    t = r - cut_inner[itype][jtype];

    fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);

    forcelj += fswitch;

  }

  fforce = factor_lj*forcelj*r2inv;



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

    ljsw5[itype][jtype];

  if (rsq > cut_inner_sq[itype][jtype]) {

    phiswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);

    philj += phiswitch;

  }



  return factor_lj*philj;

}

src/pair_lj_gromacs.h

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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



   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.

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



#ifndef PAIR_LJ_GROMACS_H

#define PAIR_LJ_GROMACS_H



#include "pair.h"



namespace LAMMPS_NS {



class PairLJGromacs : public Pair {

 public:

  PairLJGromacs(class LAMMPS *);

  virtual ~PairLJGromacs();

  virtual void compute(int, int);

  virtual void settings(int, char **);

  void coeff(int, char **);

  double init_one(int, int);

  void write_restart(FILE *);

  void read_restart(FILE *);

  virtual void write_restart_settings(FILE *);

  virtual void read_restart_settings(FILE *);

  virtual double single(int, int, int, int, double, double, double, double &);



 protected:

  double cut_inner_global,cut_global;

  double **cut,**cut_inner,**cut_inner_sq;

  double **epsilon,**sigma;

  double **lj1,**lj2,**lj3,**lj4;

  double **ljsw1,**ljsw2,**ljsw3,**ljsw4,**ljsw5;



  void allocate();

};



}



#endif

src/pair_lj_gromacs_coul_gromacs.cpp

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File added.

Preview size limit exceeded, changes collapsed.

src/pair_lj_gromacs_coul_gromacs.h

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+49 −0
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/* ----------------------------------------------------------------------

   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.

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



#ifndef PAIR_LJ_GROMACS_COUL_GROMACS_H

#define PAIR_LJ_GROMACS_COUL_GROMACS_H



#include "pair.h"



namespace LAMMPS_NS {



class PairLJGromacsCoulGromacs : public Pair {

 public:

  PairLJGromacsCoulGromacs(class LAMMPS *);

  virtual ~PairLJGromacsCoulGromacs();

  virtual void compute(int, int);

  virtual void settings(int, char **);

  void coeff(int, char **);

  void init_style();

  double init_one(int, int);

  void write_restart(FILE *);

  void read_restart(FILE *);

  virtual void write_restart_settings(FILE *);

  virtual void read_restart_settings(FILE *);

  virtual double single(int, int, int, int, double, double, double, double &);



 protected:

  double cut_lj_inner,cut_lj,cut_coul_inner,cut_coul;

  double cut_lj_innersq,cut_ljsq,cut_coul_innersq,cut_coulsq,cut_bothsq;

  double **epsilon,**sigma;

  double **lj1,**lj2,**lj3,**lj4;

  double **ljsw1,**ljsw2,**ljsw3,**ljsw4,**ljsw5;

  double coulsw1,coulsw2,coulsw3,coulsw4,coulsw5;



  void allocate();

};



}



#endif

src/style.h

+4 −0
Original line number Diff line number Diff line
@@ -300,6 +300,8 @@ MinimizeStyle(sd,MinSD) 
#include "pair_lj_cut_coul_cut.h"

#include "pair_lj_cut_coul_debye.h"

#include "pair_lj_expand.h"

#include "pair_lj_gromacs.h"

#include "pair_lj_gromacs_coul_gromacs.h"

#include "pair_lj_smooth.h"

#include "pair_morse.h"

#include "pair_soft.h"
@@ -318,6 +320,8 @@ PairStyle(lj/cut,PairLJCut) 
PairStyle(lj/cut/coul/cut,PairLJCutCoulCut)

PairStyle(lj/cut/coul/debye,PairLJCutCoulDebye)

PairStyle(lj/expand,PairLJExpand)

PairStyle(lj/gromacs,PairLJGromacs)

PairStyle(lj/gromacs/coul/gromacs,PairLJGromacsCoulGromacs)

PairStyle(lj/smooth,PairLJSmooth)

PairStyle(morse,PairMorse)

PairStyle(soft,PairSoft)

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