/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_push.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "atom_vec_ellipsoid.h"

#include <iostream>


using namespace LAMMPS_NS;

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

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

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

PairPush::~PairPush()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);

    memory->destroy(cut);
    memory->destroy(d0);
    memory->destroy(alpha);
    memory->destroy(fmag);
    memory->destroy(morse1);
    memory->destroy(offset);
  }
}

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

void PairPush::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,r,dr,dexp,factor_lj;
  int *ilist,*jlist,*numneigh,**firstneigh;

  evdwl = 0.0;
  if (eflag || vflag) ev_setup(eflag,vflag);
  else evflag = vflag_fdotr = 0;

  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
  int *ellipsoid = atom->ellipsoid;
  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  double *quat;
  int i_is_elip,j_is_elip;
  double fvecx,fvecy,fvecz,
    signed_fmag,
    ftotx,ftoty,ftotz,
    dexp2;

  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];

    if (ellipsoid[i] >= 0) { i_is_elip=1; } else { i_is_elip=0; }

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      factor_lj = special_lj[sbmask(j)];
      j &= NEIGHMASK;

      if (ellipsoid[j] >= 0) { j_is_elip=1; } else { j_is_elip=0; }

      if ( i_is_elip != j_is_elip ) {

	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 ( i_is_elip > j_is_elip ) { // i is the ellipse
	  quat = bonus[ellipsoid[i]].quat;
	  signed_fmag = -fmag[itype][jtype]; 
	} else { // j is the ellipse
	  quat = bonus[ellipsoid[j]].quat;
	  signed_fmag = fmag[itype][jtype];
	}
	fvecx = 2.0 * (quat[1]*quat[3] + quat[0]*quat[2]);
	fvecy = 2.0 * (quat[2]*quat[3] - quat[0]*quat[1]);
	fvecz = quat[0]*quat[0] - quat[1]*quat[1] - quat[2]*quat[2] + quat[3]*quat[3]; 

	if (rsq < cutsq[itype][jtype]) {

	  r = sqrt(rsq);
	  dr = r;
	  dexp = exp(-alpha[itype][jtype] * dr);
	  dexp2=dexp*dexp;
	  fpair = factor_lj * morse1[itype][jtype] * (dexp2 - dexp) / r;

	  ftotx = delx*fpair;
	  ftoty = dely*fpair;
	  ftotz = delz*fpair;

	  //if (r<0.5) {
	    ftotx += fvecx*signed_fmag*dexp2; // add non equilibrium bit
	    ftoty += fvecy*signed_fmag*dexp2;
	    ftotz += fvecz*signed_fmag*dexp2;
	    //}

	  f[i][0] += ftotx;
	  f[i][1] += ftoty;
	  f[i][2] += ftotz;
	  if (newton_pair || j < nlocal) {
	    f[j][0] -= ftotx;
	    f[j][1] -= ftoty;
	    f[j][2] -= ftotz;
	  }

	  if (eflag) {
	    evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
	      offset[itype][jtype];
	    evdwl *= factor_lj;
	  }

	  if (evflag) ev_tally(i,j,nlocal,newton_pair,
			       evdwl,0.0,fpair,delx,dely,delz);
	}

      } else {
	error->all(FLERR,"Push interaction between two ellipsoids or two non-ellipsoids");
      }

    }
  }

  if (vflag_fdotr) virial_fdotr_compute();
}

/* ----------------------------------------------------------------------
   allocate all arrays
------------------------------------------------------------------------- */

void PairPush::allocate()
{

  avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
  if (!avec) error->all(FLERR,"Pair push requires atom style ellipsoid");

  allocated = 1;
  int n = atom->ntypes;

  memory->create(setflag,n+1,n+1,"pair:setflag");
  for (int i = 1; i <= n; i++)
    for (int j = i; j <= n; j++)
      setflag[i][j] = 0;

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

  memory->create(cut,n+1,n+1,"pair:cut");
  memory->create(d0,n+1,n+1,"pair:d0");
  memory->create(alpha,n+1,n+1,"pair:alpha");
  memory->create(fmag,n+1,n+1,"pair:fmag");  
  memory->create(morse1,n+1,n+1,"pair:morse1");
  memory->create(offset,n+1,n+1,"pair:offset");
}

/* ----------------------------------------------------------------------
   global settings
------------------------------------------------------------------------- */

void PairPush::settings(int narg, char **arg)
{
  if (narg != 1) error->all(FLERR,"Illegal pair_style command");

  cut_global = force->numeric(FLERR,arg[0]);

  // 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[i][j] = cut_global;
  }
}

/* ----------------------------------------------------------------------
   set coeffs for one or more type pairs
------------------------------------------------------------------------- */

void PairPush::coeff(int narg, char **arg)
{
  if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

  int ilo,ihi,jlo,jhi;
  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);

  double d0_one = force->numeric(FLERR,arg[2]);
  double alpha_one = force->numeric(FLERR,arg[3]);
  //double r0_one = force->numeric(FLERR,arg[4]);
  double fmag_one = force->numeric(FLERR,arg[4]);

  double cut_one = cut_global;
  if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      d0[i][j] = d0_one;
      alpha[i][j] = alpha_one;
      //r0[i][j] = r0_one;
      fmag[i][j] = fmag_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
      count++;
    }
  }

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


/* ----------------------------------------------------------------------
   init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

double PairPush::init_one(int i, int j)
{

  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

  morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];

  if (offset_flag) {
    double alpha_dr = -alpha[i][j] * (cut[i][j] ); //- r0[i][j]);  // r0=0 in push
    offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
  } else offset[i][j] = 0.0;

  d0[j][i] = d0[i][j];
  alpha[j][i] = alpha[i][j];
  fmag[j][i] = fmag[i][j];
  morse1[j][i] = morse1[i][j];
  offset[j][i] = offset[i][j];

  return cut[i][j];
}

/* ----------------------------------------------------------------------
   proc 0 writes to restart file
------------------------------------------------------------------------- */

void PairPush::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(&d0[i][j],sizeof(double),1,fp);
        fwrite(&alpha[i][j],sizeof(double),1,fp);
        fwrite(&fmag[i][j],sizeof(double),1,fp);
	//  fwrite(&r0[i][j],sizeof(double),1,fp);
        fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

/* ----------------------------------------------------------------------
   proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */

void PairPush::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(&d0[i][j],sizeof(double),1,fp);
          fread(&alpha[i][j],sizeof(double),1,fp);
	  fread(&fmag[i][j],sizeof(double),1,fp);
	  //   fread(&r0[i][j],sizeof(double),1,fp);
          fread(&cut[i][j],sizeof(double),1,fp);
        }
        MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&fmag[i][j],1,MPI_DOUBLE,0,world);
    //        MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

/* ----------------------------------------------------------------------
   proc 0 writes to restart file
------------------------------------------------------------------------- */

void PairPush::write_restart_settings(FILE *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 PairPush::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    fread(&cut_global,sizeof(double),1,fp);
    fread(&offset_flag,sizeof(int),1,fp);
    fread(&mix_flag,sizeof(int),1,fp);
  }
  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 PairPush::single(int i, int j, int itype, int jtype, double rsq,
                         double factor_coul, double factor_lj,
                         double &fforce)
{
  double r,dr,dexp,phi;

  r = sqrt(rsq);
  dr = r ;// - r0[itype][jtype];    // r0=0 for push
  dexp = exp(-alpha[itype][jtype] * dr);
  fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;

  phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
  return factor_lj*phi;
}