/* ----------------------------------------------------------------------
   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_ctm.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

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

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

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

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

    memory->destroy(cut);
    memory->destroy(d0);
    memory->destroy(alpha);
    memory->destroy(r0);
    memory->destroy(ctm1);
    memory->destroy(offset);
    memory->destroy(paras);
    memory->destroy(beta1);
    memory->destroy(Ba);
    memory->destroy(Nc);

  }
}

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

void PairCtm::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,dexpa;
  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;
  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;

  // 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];
      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]) {
        r = sqrt(rsq);
        dr = r - r0[itype][jtype];
        dexp = exp(-alpha[itype][jtype] * dr);
        dexpa = exp(-beta1[itype][jtype]*beta1[itype][jtype]/alpha[itype][jtype]*dr);
        fpair = factor_lj * ctm1[itype][jtype] * (dexp*dexp - Ba[itype]*paras[itype][jtype]*beta1[itype][jtype]*beta1[itype][jtype]/(2*alhpa[itype][jtype]*alpha[itype][jtype])*dexpa) / r;

        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 = d0[itype][jtype] * (dexp*dexp - Ba[itype]*paras[itype][jtype]*dexpa) -
            offset[itype][jtype];
          evdwl *= factor_lj;
        }

        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 PairCtm::allocate()
{
  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(r0,n+1,n+1,"pair:r0");
  memory->create(ctm1,n+1,n+1,"pair:ctm1");
  memory->create(offset,n+1,n+1,"pair:offset");
  memory->create(paras,n+1,n+1,"pair:paras");
  memory->create(beta1,n+1,n+1,"pair:beta1");
  memory->create(Ba,n+1,"pair:Ba");
  memory->create(Nc,n+1,"pair:Nc");
}

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

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

  cut_global = force->numeric(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 PairCtm::coeff(int narg, char **arg)
{
  if (narg < 10 || narg > 11) error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

  int ilo,ihi,jlo,jhi,cutff,Ncc;
  double Nc;

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

  double de_one = force->numeric(arg[2]);
  double paras_one = force->numeric(arg[3]);
  double beta1_one = force->numeric(arg[4]);
  double r0_one = force->numeric(arg[5]);
  double r1_one = force->numeric(arg[6]);
  double r2_one = force->numeric(arg[7]);
  double parab_one = force->numeric(arg[8]);
  double paradel_one = force->numeric(arg[9]);


  double cut_one = cut_global;
  if (narg == 11) cut_one = force->numeric(arg[10]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
        Ncc = 0;
    for (int j = MAX(jlo,i); j <= jhi; j++) {
        if (r < r1_one) {cutff = 1;}
        else if (r > r2_one) {cutff = 0;}
        else {cutff = (1+cos((r-r1_one)/(r2_one-r1_one)*pi))/2;}
      Ncc += cutff;
      d0[i][j] = de_one/(paras_one-1);
      paras[i][j] = paras_one;
      alpha[i][j] = beta1_one*sqrt(2*paras_one)/2;
      r0[i][j] = r0_one;
      r1[i][j] = r1_one;
      r2[i][j] = r2_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
      count++;
    }
    Nc[i] = 1+Ncc;
    Ba[i] = pow(1+parab_one*(Nc[i]-1),paradel_one);
  }

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


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

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

  ctm1[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) - Ba[i]*paras[i][j]*exp(beta1[i][j]*beta1[i][j]/(alpha[i][j]*alpha[i][j])*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];
  r1[j][i] = r1[i][j];
  r2[j][i] = r2[i][j];
  ctm1[j][i] = ctm1[i][j];
  offset[j][i] = offset[i][j];
  beta1[j][i] = beta1[i][j];
  paras[j][i] = paras[i][j];

  return cut[i][j];
}

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

void PairCtm::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(&paras[i][j],sizeof(double),1,fp);
        fwrite(&alpha[i][j],sizeof(double),1,fp);
        fwrite(&r0[i][j],sizeof(double),1,fp);
        fwrite(&r1[i][j],sizeof(double),1,fp);
        fwrite(&r2[i][j],sizeof(double),1,fp);
        fwrite(&Ba[i],sizeof(double),1,fp);
        fwrite(&Nc[i],sizeof(double),1,fp);
        fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairCtm::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(&paras[i][j],sizeof(double),1,fp);
          fread(&alpha[i][j],sizeof(double),1,fp);
          fread(&r0[i][j],sizeof(double),1,fp);
          fread(&r1[i][j],sizeof(double),1,fp);
          fread(&r2[i][j],sizeof(double),1,fp);
          fread(&Ba[i],sizeof(int),1,fp);
          fread(&Nc[i],sizeof(int),1,fp);
          fread(&cut[i][j],sizeof(double),1,fp);

        }
        MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&paras[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(&r1[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&r2[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&Ba[i],1,MPI_INT,0,world);
        MPI_Bcast(&Nc[i],1,MPI_INT,0,world);
        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);

      }
    }
}

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

void PairCtm::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 PairCtm::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 PairCtm::single(int i, int j, int itype, int jtype, double rsq,
                         double factor_coul, double factor_lj,
                         double &fforce)
{
  double r,dr,dexp,phi,dexpa;

  r = sqrt(rsq);
  dr = r - r0[itype][jtype];
  dexp = exp(-alpha[itype][jtype] * dr);
  dexpa = exp(-beta1[itype][jtype]*beta1[itype][jtype]/alpha[itype][jtype]*dr);
  fforce = factor_lj * ctm1[itype][jtype] * (dexp*dexp - Ba[itype]*paras[itype][jtype]*beta1[itype][jtype]*beta1[itype][jtype]/(2*alhpa[itype][jtype]*alpha[itype][jtype])*dexpa) / r;

  phi = d0[itype][jtype] * (exp(2.0*alpha_dr) - Ba[itype]*paras[itype][jtype]*exp(beta1[itype][jtype]*beta1[itype][jtype]/(alpha[itype][jtype]*alpha[itype][jtype])*alpha_dr)) - offset[itype][jtype];
  return factor_lj*phi;
}