/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, Sandia National Laboratories
   LAMMPS development team: developers@lammps.org

   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 "pair_lj_cut_full.h"

#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "update.h"

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;
using namespace MathConst;

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

PairLJCutFull::PairLJCutFull(LAMMPS *lmp) : Pair(lmp)
{
  respa_enable = 0;
  single_enable = 0;
  writedata = 0;
  restartinfo = 0;
  no_virial_fdotr_compute = 1;
}

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

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

    memory->destroy(cut);
    memory->destroy(epsilon);
    memory->destroy(sigma);
    memory->destroy(lj1);
    memory->destroy(lj2);
    memory->destroy(lj3);
    memory->destroy(lj4);
    memory->destroy(offset);
  }
}

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

void PairLJCutFull::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, r2inv, r6inv, forcelj, factor_lj;
  double fxtmp, fytmp, fztmp;
  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;

  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];
    
    fxtmp = fytmp = fztmp = 0.0;
    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;
        forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
        fpair = factor_lj * forcelj * r2inv;

        fxtmp += delx * fpair;
        fytmp += dely * fpair;
        fztmp += delz * fpair;

        if (eflag) {
          evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
          evdwl *= factor_lj;
        }

        if (evflag) ev_tally(i, i, nlocal, 0, 0.5*evdwl, 0.0, 0.5*fpair, delx, dely, delz);
      }
    }
    f[i][0] += fxtmp;
    f[i][1] += fytmp;
    f[i][2] += fztmp;
  }

  if (vflag_fdotr) virial_fdotr_compute();
}

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

void PairLJCutFull::allocate()
{
  allocated = 1;
  int n = atom->ntypes + 1;

  memory->create(setflag, n, n, "pair:setflag");
  for (int i = 1; i < n; i++)
    for (int j = i; j < n; j++) setflag[i][j] = 0;

  memory->create(cutsq, n, n, "pair:cutsq");

  memory->create(cut, n, n, "pair:cut");
  memory->create(epsilon, n, n, "pair:epsilon");
  memory->create(sigma, n, n, "pair:sigma");
  memory->create(lj1, n, n, "pair:lj1");
  memory->create(lj2, n, n, "pair:lj2");
  memory->create(lj3, n, n, "pair:lj3");
  memory->create(lj4, n, n, "pair:lj4");
  memory->create(offset, n, n, "pair:offset");
}

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

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

  cut_global = utils::numeric(FLERR, arg[0], false, lmp);

  // 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 PairLJCutFull::coeff(int narg, char **arg)
{
  if (narg < 4 || narg > 5) error->all(FLERR, "Incorrect args for pair coefficients");
  if (!allocated) allocate();

  int ilo, ihi, jlo, jhi;
  utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
  utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);

  double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
  double sigma_one = utils::numeric(FLERR, arg[3], false, lmp);

  double cut_one = cut_global;
  if (narg == 5) cut_one = utils::numeric(FLERR, arg[4], false, lmp);

  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(FLERR, "Incorrect args for pair coefficients");
}

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

void PairLJCutFull::init_style()
{
  neighbor->add_request(this, NeighConst::REQ_FULL);
}

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

double PairLJCutFull::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 && (cut[i][j] > 0.0)) {
    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;

  epsilon[j][i] = epsilon[i][j];
  sigma[j][i] = epsilon[i][j];
  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];
  return cut[i][j];
}