/* ----------------------------------------------------------------------
   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 <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_gupta.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

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

PairGupta::PairGupta(LAMMPS *lmp) : Pair(lmp)
{
  writedata = 1;
}

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

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

    memory->destroy(cut);
    memory->destroy(d0);
    memory->destroy(alpha);
    memory->destroy(r0);
    memory->destroy(morse1);
    memory->destroy(v_m);
    memory->destroy(dv_mm);
    memory->destroy(icutitoff);
    memory->destroy(offset);
  }
}

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

void PairGupta::compute(int eflag, int vflag)
{
  int i,j,ii,jj,kk,inum,jnum,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
  double rsq,r,dr,dexp,factor_lj;
//
 // double a_g,p_g,r0_g,xi_g,q_g;
  double xi2_g,rij,v_rij,dv_r_drij,dv_m_drij,v_mij ;
  double e_vm=0.0,e_vr=0.0, ev_to_kcal =96.48530898/4.184;
  double fx,fy,fz;
//
  int *ilist,*jlist,*numneigh,**firstneigh;

  evdwl = 0.0;
  ev_init(eflag,vflag);

  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;

  
  inum = list->inum;
  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

 // a_g  = 0.0855;
 // p_g  = 9.834 ;
 // r0_g = 2.579 ;
 // xi_g = 1.131 ;
 // q_g  = 2.549 ;
 //
 // substituted p_g --> p_g / r0_g in coeff
 // substituted q_g --> q_g / r0_g in coeff
 // substituted a_g --> a_g * 2.0  in coeff
 //
 //
   
  xi2_g =  xi_g*xi_g ;

  // loop over neighbors of my atoms
  for (i = 0; i < inum; i++) {
    v_m[i]  = 0.0;
   // printf("at i,x,y,z  = %d %g %g %g \n",i,x[i][0],x[i][1],x[i][2]);
  //  f[i][0] = 0.0;
  //  f[i][1] = 0.0;
  //  f[i][2] = 0.0;
  }

  for (i = 0; i < inum; i++) {
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];

    for (j = i+1; j < inum; j++) {

      delx = x[j][0] - xtmp;
      dely = x[j][1] - ytmp;
      delz = x[j][2] - ztmp;
      rsq = delx*delx + dely*dely + delz*delz;

      if (rsq < r2_cut) {
        rij = sqrt(rsq);
 //       jtype = type[j];
        v_rij =  a_g * exp( -p_g * ( rij - r0_g ) );
        e_vr  +=  v_rij ;

        dv_r_drij =  -p_g * v_rij / rij;
        fx =  dv_r_drij * delx ;
        fy =  dv_r_drij * dely ;
        fz =  dv_r_drij * delz ;
        f[i][0] +=  fx ;
        f[j][0] += -fx ;
        f[i][1] +=  fy ;
        f[j][1] += -fy ;
        f[i][2] +=  fz ;
        f[j][2] += -fz ;

        v_mij = xi2_g * exp( -2.0*q_g * ( rij - r0_g ) );
        v_m[i] += v_mij;
        v_m[j] += v_mij;

        dv_m_drij = -q_g * v_mij / rij;
        dv_mm[i][j][0] =  dv_m_drij * delx ;
        dv_mm[i][j][1] =  dv_m_drij * dely ;
        dv_mm[i][j][2] =  dv_m_drij * delz ;
        icutitoff[i][j] = 1;
      }
      else {
        icutitoff[i][j] = 0;
      }
    }
  }
  for (i = 0; i < inum; i++) {
    v_m[i] = sqrt(v_m[i]);
    e_vm += v_m[i];
  }
  for (i = 0; i < inum; i++) {
    for (j = i+1; j < inum; j++) {
      if ( icutitoff[i][j] == 1  ) {
        fx = dv_mm[i][j][0] / v_m[i] + dv_mm[i][j][0] / v_m[j];
        fy = dv_mm[i][j][1] / v_m[i] + dv_mm[i][j][1] / v_m[j];
        fz = dv_mm[i][j][2] / v_m[i] + dv_mm[i][j][2] / v_m[j];
        f[i][0] += -fx ;
        f[i][1] += -fy ;
        f[i][2] += -fz ;
        f[j][0] +=  fx ;
        f[j][1] +=  fy ;
        f[j][2] +=  fz ;
      }
    }
  }
 // for (i = 0; i < inum; i++) {
 //   f[i][0] *= ev_to_kcal ;
 //   f[i][1] *= ev_to_kcal ;
 //   f[i][2] *= ev_to_kcal ;
 // }


 //printf("vm,vr,Energy  = %g %g %g \n",e_vr, e_vm, e_vr - e_vm);
 // factor_lj = special_lj[sbmask(0)];
 // printf("factor_lj  = %g \n",factor_lj);
  if (eflag)   evdwl = e_vr - e_vm;

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

  if (vflag_fdotr) virial_fdotr_compute();
}

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

void PairGupta::allocate()
{
  allocated = 1;
  int n = atom->ntypes;
  int inum = atom->natoms;

  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(r0,n+1,n+1,"pair:r0");
  memory->create(morse1,n+1,n+1,"pair:morse1");
  memory->create(v_m   ,inum ,"pair:v_m");
 // printf("alloc inum = %d \n",inum);
  memory->create(dv_mm ,inum ,inum,3,"pair:dv_mm");
  memory->create(icutitoff ,inum ,inum,"pair:icutitoff");
  memory->create(offset,n+1,n+1,"pair:offset");
}

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

void PairGupta::settings(int narg, char **arg)
{
  if (narg != 1) error->all(FLERR,"Illegal OEPNV    e 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; j <= atom->ntypes; j++)
        if (setflag[i][j]) cut[i][j] = cut_global;
  }
}

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

void PairGupta::coeff(int narg, char **arg)
{
  if (narg < 6 || narg > 7)
    error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

  int ilo,ihi,jlo,jhi;

  a_g  = force->numeric(FLERR,arg[2]);
  p_g  = force->numeric(FLERR,arg[3]);
  r0_g = force->numeric(FLERR,arg[4]);
  xi_g = force->numeric(FLERR,arg[5]);
  q_g  = force->numeric(FLERR,arg[6]);
  printf("a_g   = %g \n",a_g  );
  printf("p_g   = %g \n",p_g  );
  printf("r0_g  = %g \n",r0_g );
  printf("xi_g  = %g \n",xi_g );
  printf("q_g   = %g \n",q_g  );
  
  q_g /= r0_g;
  p_g /= r0_g;
  a_g *= 2.0 ;

  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 cut_one = cut_global;
  r2_cut = cut_global*cut_global;
 // if (narg == 7) cut_one = force->numeric(FLERR,arg[7]);

  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;
      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 PairGupta::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]);
    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];
  r0[j][i] = r0[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 PairGupta::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(&r0[i][j],sizeof(double),1,fp);
        fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairGupta::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(&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(&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 PairGupta::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 PairGupta::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);
}

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

void PairGupta::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    fprintf(fp,"%d %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i]);
}

/* ----------------------------------------------------------------------
   proc 0 writes all pairs to data file
------------------------------------------------------------------------- */

void PairGupta::write_data_all(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    for (int j = i; j <= atom->ntypes; j++)
      fprintf(fp,"%d %d %g %g %g %g\n",
              i,j,d0[i][j],alpha[i][j],r0[i][j],cut[i][j]);
}

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

double PairGupta::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];
  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;
}

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

void *PairGupta::extract(const char *str, int &dim)
{
  dim = 2;
  if (strcmp(str,"d0") == 0) return (void *) d0;
  if (strcmp(str,"r0") == 0) return (void *) r0;
  if (strcmp(str,"alpha") == 0) return (void *) alpha;
  return NULL;
}