/* ----------------------------------------------------------------------
   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: Kurt Smith (U Pittsburgh)
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Modified by Stephen Weitzner (Penn State).

   Force calculations adapted to reflect gaussian well potential 
   discussed in:
   
    J. Magee & F. Siperstein "Formation of Ordered Mesoporous Materials
    Under Slow Aggregation Conditions" J. Phys. Chem. C 2009 113 (5),
    1680-1685.

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


#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_dpd_mod.h" // SW
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

#define EPSILON 1.0e-10

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

PairDPDmod::PairDPDmod(LAMMPS *lmp) : Pair(lmp) // SW
{
  random = NULL;
}

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

PairDPDmod::~PairDPDmod() // SW
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);

    memory->destroy(cut);
    memory->destroy(a0);
    memory->destroy(gamma);
    memory->destroy(sigma);

    memory->destroy(well_width);  // SW
    memory->destroy(well_center); // SW
    memory->destroy(well_depth);  // SW
  }

  if (random) delete random;
}

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

void PairDPDmod::compute(int eflag, int vflag) // SW
{
  int i,j,ii,jj,inum,jnum,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
  double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
  double rsq,r,rinv,dot,wd,randnum,factor_dpd,bp,widthsq; // SW
  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 **v = atom->v;
  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 dtinvsqrt = 1.0/sqrt(update->dt);

  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];
    vxtmp = v[i][0];
    vytmp = v[i][1];
    vztmp = v[i][2];
    itype = type[i];
    jlist = firstneigh[i];
    jnum = numneigh[i];

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      factor_dpd = 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);
	if (r < EPSILON) continue;     // r can be 0.0 in DPD systems
	rinv = 1.0/r;
	delvx = vxtmp - v[j][0];
	delvy = vytmp - v[j][1];
	delvz = vztmp - v[j][2];
	dot = delx*delvx + dely*delvy + delz*delvz;
	wd = 1.0 - r/cut[itype][jtype];
        bp = r - well_center[itype][jtype]; // SW added line
        widthsq = pow(well_width[itype][jtype],2); // SW added line
	randnum = random->gaussian();

	// conservative force = a0 * wd
	// drag force = -gamma * wd^2 * (delx dot delv) / r
	// random force = sigma * wd * rnd * dtinvsqrt;

	fpair = a0[itype][jtype]*wd;
        /*----------------------------------------------------
          SW: The next update to fpair establishes the 
              gaussian well component of the conservative 
              force.
        ------------------------------------------------------*/
	fpair -= (2*well_depth[itype][jtype]*bp/widthsq)*exp(-1*pow(bp,2)/widthsq); // SW

	fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
	fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
	fpair *= factor_dpd*rinv;	

	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) {
          // unshifted eng of conservative term:
	  // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
	  // eng shifted to 0.0 at cutoff
	  evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
	  evdwl *= factor_dpd;
	}

	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 PairDPDmod::allocate() // SW
{ 
  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(a0,n+1,n+1,"pair:a0");
  memory->create(gamma,n+1,n+1,"pair:gamma");
  memory->create(sigma,n+1,n+1,"pair:sigma");

  memory->create(well_width,n+1,n+1,"pair:well_width");  // SW
  memory->create(well_center,n+1,n+1,"pair:well_center");  // SW
  memory->create(well_depth,n+1,n+1,"pair:well_depth"); // SW

}

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

void PairDPDmod::settings(int narg, char **arg) // SW
{
  if (narg != 3) error->all(FLERR,"Illegal pair_style command");

  temperature = force->numeric(arg[0]);
  cut_global = force->numeric(arg[1]);
  seed = force->inumeric(arg[2]);

  // initialize Marsaglia RNG with processor-unique seed

  if (seed <= 0) error->all(FLERR,"Illegal pair_style command");
  delete random;
  random = new RanMars(lmp,seed + comm->me);

  // 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 PairDPDmod::coeff(int narg, char **arg) // SW
{
  if (narg < 4 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); // SW 8 replaced 5
  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 a0_one = force->numeric(arg[2]);
  double gamma_one = force->numeric(arg[3]);
  double cut_one = force->numeric(arg[4]); // SW now cut-off MUST be defined
  
  double well_width_one = force->numeric(arg[5]);  // SW
  double well_center_one = force->numeric(arg[6]); // SW
  double well_depth_one = force->numeric(arg[7]);  // SW
  
  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      a0[i][j] = a0_one;
      gamma[i][j] = gamma_one;
      cut[i][j] = cut_one;

      well_width[i][j] = well_width_one;  // SW
      well_center[i][j] = well_center_one;  // SW
      well_depth[i][j] = well_depth_one;  // SW
      
      setflag[i][j] = 1;
      count++;
    }
  }

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

/* ----------------------------------------------------------------------
   init specific to this pair style
------------------------------------------------------------------------- */

void PairDPDmod::init_style() // SW
{
  if (comm->ghost_velocity == 0)
    error->all(FLERR,"Pair dpd requires ghost atoms store velocity");

  // if newton off, forces between atoms ij will be double computed
  // using different random numbers

  if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR,
      "Pair dpd needs newton pair on for momentum conservation");

  neighbor->request(this);
}

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

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

  sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
     
  cut[j][i] = cut[i][j];
  a0[j][i] = a0[i][j];
  gamma[j][i] = gamma[i][j];
  sigma[j][i] = sigma[i][j];
  
  well_width[j][i] = well_width[i][j];  // SW
  well_center[j][i] = well_center[i][j];  // SW
  well_depth[j][i] = well_depth[i][j]; // SW

  return cut[i][j];
}

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

void PairDPDmod::write_restart(FILE *fp) // SW
{
  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(&a0[i][j],sizeof(double),1,fp);
	fwrite(&gamma[i][j],sizeof(double),1,fp);
	fwrite(&cut[i][j],sizeof(double),1,fp);

        fwrite(&well_width[i][j],sizeof(double),1,fp);  // SW
        fwrite(&well_center[i][j],sizeof(double),1,fp);  // SW
        fwrite(&well_depth[i][j],sizeof(double),1,fp);  // SW

      }
    }
}

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

void PairDPDmod::read_restart(FILE *fp) // SW
{
  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(&a0[i][j],sizeof(double),1,fp);
	  fread(&gamma[i][j],sizeof(double),1,fp);
	  fread(&cut[i][j],sizeof(double),1,fp);

          fread(&well_width[i][j],sizeof(double),1,fp);  // SW
	  fread(&well_center[i][j],sizeof(double),1,fp);  // SW
	  fread(&well_depth[i][j],sizeof(double),1,fp);  // SW

	}
	MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
   
	MPI_Bcast(&well_width[i][j],1,MPI_DOUBLE,0,world);  // SW
	MPI_Bcast(&well_center[i][j],1,MPI_DOUBLE,0,world);  // SW
	MPI_Bcast(&well_depth[i][j],1,MPI_DOUBLE,0,world);  // SW

      }
    }
}

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

void PairDPDmod::write_restart_settings(FILE *fp) // SW
{
  fwrite(&temperature,sizeof(double),1,fp);
  fwrite(&cut_global,sizeof(double),1,fp);
  fwrite(&seed,sizeof(int),1,fp);
  fwrite(&mix_flag,sizeof(int),1,fp);
}

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

void PairDPDmod::read_restart_settings(FILE *fp) // SW
{
  if (comm->me == 0) {
    fread(&temperature,sizeof(double),1,fp);
    fread(&cut_global,sizeof(double),1,fp);
    fread(&seed,sizeof(int),1,fp);
    fread(&mix_flag,sizeof(int),1,fp);
  }
  MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&seed,1,MPI_INT,0,world);
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

  // initialize Marsaglia RNG with processor-unique seed
  // same seed that pair_style command initially specified

  if (random) delete random;
  random = new RanMars(lmp,seed + comm->me);
}

/* ---------------------------------------------------------------------- */
//http://lammps.sandia.gov/doc/compute_pair_local.html
//+  It looks like this member fxn is only called when compute pair/local
//+  is used

double PairDPDmod::single(int i, int j, int itype, int jtype, double rsq,
			  double factor_coul, double factor_dpd, double &fforce) // SW
{
  double r,rinv,wd,phi;

  r = sqrt(rsq);
  if (r < EPSILON) {
    fforce = 0.0;
    return 0.0;
  }

  rinv = 1.0/r;
  wd = 1.0 - r/cut[itype][jtype];
  fforce = a0[itype][jtype]*wd * factor_dpd*rinv; // SW what is this?

  phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; // SW what is this?
  return factor_dpd*phi;
}