/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   www.cs.sandia.gov/~sjplimp/lammps.html
   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   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: Paul Crozier (SNL)
------------------------------------------------------------------------- */

#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"

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

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

PairLJCut::PairLJCut()
{
  respa_enable = 1;
}

/* ----------------------------------------------------------------------
   free all arrays 
------------------------------------------------------------------------- */

PairLJCut::~PairLJCut()
{
  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(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(offset);
  }
}

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

void PairLJCut::compute(int eflag, int vflag)
{
  int i,j,k,numneigh,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz;
  double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
  int *neighs;
  double **f;

  eng_vdwl = 0.0;
  if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;

  if (vflag == 2) f = update->f_pair;
  else f = atom->f;
  double **x = atom->x;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = atom->nlocal + atom->nghost;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  // loop over neighbors of my atoms

  for (i = 0; i < nlocal; i++) {
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    neighs = neighbor->firstneigh[i];
    numneigh = neighbor->numneigh[i];

    for (k = 0; k < numneigh; k++) {
      j = neighs[k];

      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]);
	fforce = factor_lj*forcelj*r2inv;

	f[i][0] += delx*fforce;
	f[i][1] += dely*fforce;
	f[i][2] += delz*fforce;
	if (newton_pair || j < nlocal) {
	  f[j][0] -= delx*fforce;
	  f[j][1] -= dely*fforce;
	  f[j][2] -= delz*fforce;
	}

	if (eflag) {
	  philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
	    offset[itype][jtype];
	  if (newton_pair || j < nlocal) eng_vdwl += factor_lj*philj;
	  else eng_vdwl += 0.5*factor_lj*philj;
	}

	if (vflag == 1) {
	  if (newton_pair || j < nlocal) {
	    virial[0] += delx*delx*fforce;
	    virial[1] += dely*dely*fforce;
	    virial[2] += delz*delz*fforce;
	    virial[3] += delx*dely*fforce;
	    virial[4] += delx*delz*fforce;
	    virial[5] += dely*delz*fforce;
	  } else {
	    virial[0] += 0.5*delx*delx*fforce;
	    virial[1] += 0.5*dely*dely*fforce;
	    virial[2] += 0.5*delz*delz*fforce;
	    virial[3] += 0.5*delx*dely*fforce;
	    virial[4] += 0.5*delx*delz*fforce;
	    virial[5] += 0.5*dely*delz*fforce;
	  }
	}
      }
    }
  }
  if (vflag == 2) virial_compute();
}

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

void PairLJCut::compute_inner()
{
  int i,j,k,numneigh,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz;
  double rsq,r2inv,r6inv,forcelj,fforce,factor_lj;
  double rsw;
  int *neighs;
  double **f;

  f = atom->f;
  double **x = atom->x;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = atom->nlocal + atom->nghost;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;
  
  double cut_out_on = cut_respa[0];
  double cut_out_off = cut_respa[1];
  
  double cut_out_diff = cut_out_off - cut_out_on;
  double cut_out_on_sq = cut_out_on*cut_out_on;
  double cut_out_off_sq = cut_out_off*cut_out_off;
  
  // loop over neighbors of my atoms

  for (i = 0; i < nlocal; i++) {
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    neighs = neighbor->firstneigh_inner[i];
    numneigh = neighbor->numneigh_inner[i];

    for (k = 0; k < numneigh; k++) {
      j = neighs[k];
      
      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;

      if (rsq < cut_out_off_sq) {
	r2inv = 1.0/rsq;
	r6inv = r2inv*r2inv*r2inv;
	jtype = type[j];
	forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
	fforce = factor_lj*forcelj*r2inv;
        if (rsq > cut_out_on_sq) {
	  rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; 
	  fforce *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
	}

	f[i][0] += delx*fforce;
	f[i][1] += dely*fforce;
	f[i][2] += delz*fforce;
	if (newton_pair || j < nlocal) {
	  f[j][0] -= delx*fforce;
	  f[j][1] -= dely*fforce;
	  f[j][2] -= delz*fforce;
	}
      }
    }
  }
}

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

void PairLJCut::compute_middle()
{
  int i,j,k,numneigh,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz;
  double rsq,r2inv,r6inv,forcelj,fforce,factor_lj;
  double rsw;
  int *neighs;
  double **f;

  f = atom->f;
  double **x = atom->x;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = atom->nlocal + atom->nghost;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  double cut_in_off = cut_respa[0];
  double cut_in_on = cut_respa[1];
  double cut_out_on = cut_respa[2];
  double cut_out_off = cut_respa[3];

  double cut_in_diff = cut_in_on - cut_in_off;
  double cut_out_diff = cut_out_off - cut_out_on;
  double cut_in_off_sq = cut_in_off*cut_in_off;
  double cut_in_on_sq = cut_in_on*cut_in_on;
  double cut_out_on_sq = cut_out_on*cut_out_on;
  double cut_out_off_sq = cut_out_off*cut_out_off;

  // loop over neighbors of my atoms

  for (i = 0; i < nlocal; i++) {
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    neighs = neighbor->firstneigh_middle[i];
    numneigh = neighbor->numneigh_middle[i];

    for (k = 0; k < numneigh; k++) {
      j = neighs[k];

      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;

      if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
	r2inv = 1.0/rsq;
	r6inv = r2inv*r2inv*r2inv;
	jtype = type[j];
	forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
	fforce = factor_lj*forcelj*r2inv;
        if (rsq < cut_in_on_sq) {
	  rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; 
	  fforce *= rsw*rsw*(3.0 - 2.0*rsw);
	}
        if (rsq > cut_out_on_sq) {
	  rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; 
	  fforce *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
	}

	f[i][0] += delx*fforce;
	f[i][1] += dely*fforce;
	f[i][2] += delz*fforce;
	if (newton_pair || j < nlocal) {
	  f[j][0] -= delx*fforce;
	  f[j][1] -= dely*fforce;
	  f[j][2] -= delz*fforce;
	}
      }
    }
  }
}

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

void PairLJCut::compute_outer(int eflag, int vflag)
{
  int i,j,k,numneigh,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz;
  double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
  double rsw;
  int *neighs;
  double **f;

  eng_vdwl = 0.0;
  if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;

  f = atom->f;
  double **x = atom->x;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = atom->nlocal + atom->nghost;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  double cut_in_off = cut_respa[2];
  double cut_in_on = cut_respa[3];

  double cut_in_diff = cut_in_on - cut_in_off;
  double cut_in_off_sq = cut_in_off*cut_in_off;
  double cut_in_on_sq = cut_in_on*cut_in_on;

  // loop over neighbors of my atoms

  for (i = 0; i < nlocal; i++) {
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    neighs = neighbor->firstneigh[i];
    numneigh = neighbor->numneigh[i];

    for (k = 0; k < numneigh; k++) {
      j = neighs[k];

      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]) {
	if (rsq > cut_in_off_sq) {
	  r2inv = 1.0/rsq;
	  r6inv = r2inv*r2inv*r2inv;
	  forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
	  fforce = factor_lj*forcelj*r2inv;
          if (rsq < cut_in_on_sq) {
	    rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; 
	    fforce *= rsw*rsw*(3.0 - 2.0*rsw);
	  }

	  f[i][0] += delx*fforce;
	  f[i][1] += dely*fforce;
	  f[i][2] += delz*fforce;
	  if (newton_pair || j < nlocal) {
	    f[j][0] -= delx*fforce;
	    f[j][1] -= dely*fforce;
	    f[j][2] -= delz*fforce;
	  }
	}

	if (eflag) {
	  r2inv = 1.0/rsq;
	  r6inv = r2inv*r2inv*r2inv;
	  philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
	    offset[itype][jtype];
	  if (newton_pair || j < nlocal) eng_vdwl += factor_lj*philj;
	  else eng_vdwl += 0.5*factor_lj*philj;
	}

	if (vflag) {
	  if (rsq <= cut_in_off_sq) {
	    r2inv = 1.0/rsq;
	    r6inv = r2inv*r2inv*r2inv;
	    forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
	    fforce = factor_lj*forcelj*r2inv;
	  } else if (rsq < cut_in_on_sq)
	    fforce = factor_lj*forcelj*r2inv;

	  if (newton_pair || j < nlocal) {
	    virial[0] += delx*delx*fforce;
	    virial[1] += dely*dely*fforce;
	    virial[2] += delz*delz*fforce;
	    virial[3] += delx*dely*fforce;
	    virial[4] += delx*delz*fforce;
	    virial[5] += dely*delz*fforce;
	  } else {
	    virial[0] += 0.5*delx*delx*fforce;
	    virial[1] += 0.5*dely*dely*fforce;
	    virial[2] += 0.5*delz*delz*fforce;
	    virial[3] += 0.5*delx*dely*fforce;
	    virial[4] += 0.5*delx*delz*fforce;
	    virial[5] += 0.5*dely*delz*fforce;
	  }
	}
      }
    }
  }
}

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

void PairLJCut::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");
  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");
  offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}

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

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

  cut_global = atof(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 PairLJCut::coeff(int narg, char **arg)
{
  if (narg < 4 || narg > 5) 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_one = cut_global;
  if (narg == 5) cut_one = atof(arg[4]);

  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[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 PairLJCut::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[i][j] = mix_distance(cut[i][i],cut[j][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);
     
  if (offset_flag) {
    double ratio = sigma[i][j] / cut[i][j];
    offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
  } else offset[i][j] = 0.0;

  lj1[j][i] = lj1[i][j];
  lj2[j][i] = lj2[i][j];
  lj3[j][i] = lj3[i][j];
  lj4[j][i] = lj4[i][j];
  offset[j][i] = offset[i][j];

  // set & error check interior rRESPA cutoff

  if (strcmp(update->integrate_style,"respa") == 0) {
    if (((Respa *) update->integrate)->level_inner >= 0) {
      cut_respa = ((Respa *) update->integrate)->cutoff;
      if (cut[i][j] < cut_respa[3])
	error->all("Pair cutoff < Respa interior cutoff");
    }
  } else cut_respa = NULL;

  // compute I,J contribution to long-range tail correction
  // count total # of atoms of type I and J via Allreduce

  if (tail_flag) {
    int *type = atom->type;
    int nlocal = atom->nlocal;

    double count[2],all[2];
    count[0] = count[1] = 0.0;
    for (int k = 0; k < nlocal; k++) {
      if (type[k] == i) count[0] += 1.0;
      if (type[k] == j) count[1] += 1.0;
    }
    MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
        
    double PI = 4.0*atan(1.0);
    double sig2 = sigma[i][j]*sigma[i][j];
    double sig6 = sig2*sig2*sig2;
    double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
    double rc6 = rc3*rc3;
    double rc9 = rc3*rc6;
    etail_ij = 8.0*PI*all[0]*all[1]*epsilon[i][j] * 
      sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); 
    ptail_ij = 16.0*PI*all[0]*all[1]*epsilon[i][j] * 
      sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); 
  } 

  return cut[i][j];
}

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

void PairLJCut::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[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairLJCut::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[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[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

void PairLJCut::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 PairLJCut::read_restart_settings(FILE *fp)
{
  int me = comm->me;
  if (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);
}

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

void PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
		       double factor_coul, double factor_lj, int eflag,
		       One &one)
{
  double r2inv,r6inv,forcelj,philj;

  r2inv = 1.0/rsq;
  r6inv = r2inv*r2inv*r2inv;
  forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
  one.fforce = factor_lj*forcelj*r2inv;

  if (eflag) {
    philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
      offset[itype][jtype];
    one.eng_vdwl = factor_lj*philj;
    one.eng_coul = 0.0;
  }
}