/* ----------------------------------------------------------------------
   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 authors: Kristen Fichthorn, Tonnam Balankura,
                         Ya Zhou (Penn State University)
------------------------------------------------------------------------- */

#include <cmath>
#include <cstdio>
#include <cstdlib>
#include "pair_momb.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"

using namespace LAMMPS_NS;

static const char cite_momb[] =
  "Pair style momb:\n\n"
  "@Article{pair_momb_2015,\n"
  "title = {A force field for describing the polyvinylpyrrolidone-mediated"
       " solution-phase synthesis of shape-selective Ag nanoparticles.},\n"
  "volume = {118},\n"
  "number = {6},\n"
  "url = {http://dx.doi.org/10.1021/jp412098n},\n"
  "doi = {10.1021/jp412098n},\n"
  "journal = {J. Phys. Chem. C},\n"
  "author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n"
  "year = {2014},\n"
  "pages = {3366--3374}\n"
  "}\n\n";

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

PairMomb::PairMomb(LAMMPS *lmp) : Pair(lmp)
{
  if (lmp->citeme) lmp->citeme->add(cite_momb);
}

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

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

    memory->destroy(cut);
    memory->destroy(d0);
    memory->destroy(alpha);
    memory->destroy(r0);
    memory->destroy(c);
    memory->destroy(rr);
    memory->destroy(morse1);
    memory->destroy(offset);
  }
}

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

void PairMomb::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,r2inv,r6inv,ddexp,invexp;
  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]) {
        r2inv = 1.0/rsq;
        r6inv = r2inv*r2inv*r2inv;
        r = sqrt(rsq);
        dr = r - r0[itype][jtype];
        dexp = exp(-alpha[itype][jtype] * dr);
        ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0));
        invexp = 1.0/(1+ddexp);
        fpair = morse1[itype][jtype] * (dexp*dexp - dexp) / r;
        fpair -= sscale*c[itype][jtype]
          * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r;
        fpair -= sscale*c[itype][jtype] * (6.0 * invexp * r6inv * r2inv);
        fpair *= factor_lj;

        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 - 2.0*dexp) -
            sscale*c[itype][jtype]*r6inv*invexp  - 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 PairMomb::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(c,n+1,n+1,"pair:c");
  memory->create(rr,n+1,n+1,"pair:rr");
  memory->create(morse1,n+1,n+1,"pair:morse1");
  memory->create(offset,n+1,n+1,"pair:offset");
}

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

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

  cut_global = force->numeric(FLERR,arg[0]);
  sscale = force->numeric(FLERR,arg[1]);
  dscale = force->numeric(FLERR,arg[2]);

  // 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 PairMomb::coeff(int narg, char **arg)
{
  if (narg < 7 || narg > 8)
    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 c_one = force->numeric(FLERR,arg[5]);
  double rr_one = force->numeric(FLERR,arg[6]);

  double cut_one = cut_global;
  if (narg == 8) 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;
      c[i][j] = c_one;
      rr[i][j] = rr_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 PairMomb::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];
  c[j][i] = c[i][j];
  rr[j][i] = rr[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 PairMomb::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(&c[i][j],sizeof(double),1,fp);
        fwrite(&rr[i][j],sizeof(double),1,fp);
        fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairMomb::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(&c[i][j],sizeof(double),1,fp);
          fread(&rr[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(&c[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&rr[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

void PairMomb::write_restart_settings(FILE *fp)
{
  fwrite(&cut_global,sizeof(double),1,fp);
  fwrite(&sscale,sizeof(double),1,fp);
  fwrite(&dscale,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 PairMomb::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    fread(&cut_global,sizeof(double),1,fp);
    fread(&sscale,sizeof(double),1,fp);
    fread(&dscale,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(&sscale,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&dscale,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}

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

double PairMomb::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
                         double /*factor_coul*/, double factor_lj,
                         double &fforce)
{
  double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp;

  r2inv = 1.0/rsq;
  r6inv = r2inv*r2inv*r2inv;
  r = sqrt(rsq);
  dr = r - r0[itype][jtype];
  dexp = exp(-alpha[itype][jtype] * dr);
  ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0));
  invexp = 1.0/(1+ddexp);
  fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
  fforce -= factor_lj * sscale* c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r;
  fforce -= factor_lj * sscale* c[itype][jtype] * (6.0 * invexp * r6inv * r2inv);

  phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - sscale*c[itype][jtype]*r6inv*invexp - offset[itype][jtype];
  return factor_lj*phi;
}