// clang-format off
/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, 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 "pair_coul_exclude.h"

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

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;

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

PairCoulExclude::PairCoulExclude(LAMMPS *lmp) : Pair(lmp) {
  writedata = 1;
}

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

PairCoulExclude::~PairCoulExclude()
{
  if (copymode) return;

  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);
  }
}

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

void PairCoulExclude::compute(int eflag, int vflag)
{
  int i,j,ii,jj,inum,jnum;
  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
  double rsq,r2inv,rinv,forcecoul,factor_coul;
  int *ilist,*jlist,*numneigh,**firstneigh;

  ecoul = 0.0;
  ev_init(eflag,vflag);

  double **x = atom->x;
  double **f = atom->f;
  double *q = atom->q;
  int nlocal = atom->nlocal;
  double *special_coul = force->special_coul;
  int newton_pair = force->newton_pair;
  double qqrd2e = force->qqrd2e;

  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];
    qtmp = q[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    jlist = firstneigh[i];
    jnum = numneigh[i];

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];

      // skip over all non-excluded pairs and subtract excluded coulomb

      if (sbmask(j) == 0) continue;
      factor_coul = special_coul[sbmask(j)] - 1.0;

      j &= NEIGHMASK;

      delx = xtmp - x[j][0];
      dely = ytmp - x[j][1];
      delz = ztmp - x[j][2];
      rsq = delx*delx + dely*dely + delz*delz;

      r2inv = 1.0/rsq;
      rinv = sqrt(r2inv);
      forcecoul = qqrd2e * qtmp*q[j]*rinv;
      fpair = factor_coul*forcecoul * r2inv;

      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)
        ecoul = factor_coul * qqrd2e * qtmp*q[j]*rinv;

      if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,ecoul,fpair,delx,dely,delz);
    }
  }

  if (vflag_fdotr) virial_fdotr_compute();
}

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

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

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

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

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

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

/* ----------------------------------------------------------------------
   set coeffs for one or more type pairs
------------------------------------------------------------------------- */

void PairCoulExclude::coeff(int narg, char **arg)
{
  if (narg != 2)
    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);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      setflag[i][j] = 1;
      count++;
    }
  }

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


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

void PairCoulExclude::init_style()
{
  if (!atom->q_flag)
    error->all(FLERR,"Pair style coul/exclude requires atom attribute q");

  neighbor->request(this,instance_me);
}

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

double PairCoulExclude::init_one(int /*i*/, int /*j*/)
{
  return cut_global;
}

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

void PairCoulExclude::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);
    }
  }
}

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

void PairCoulExclude::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) {
        utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
      }
      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
    }
  }
}

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

void PairCoulExclude::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 PairCoulExclude::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
  }
  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);
}

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

void PairCoulExclude::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    fprintf(fp,"%d\n",i);
}

/* ----------------------------------------------------------------------
   proc 0 writes all pairs to data file
------------------------------------------------------------------------- */

void PairCoulExclude::write_data_all(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    for (int j = i; j <= atom->ntypes; j++)
      fprintf(fp,"%d %d\n",i,j);
}

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

double PairCoulExclude::single(int i, int j, int /*itype*/, int /*jtype*/,
                           double rsq, double factor_coul, double /*factor_lj*/,
                           double &fforce)
{
  double r2inv,rinv,forcecoul,phicoul;

  factor_coul -= 1.0; // we want to subtract the excluded coulomb
  r2inv = 1.0/rsq;
  rinv = sqrt(r2inv);
  forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*rinv;
  fforce = factor_coul*forcecoul * r2inv;

  phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*rinv;
  return factor_coul*phicoul;
}

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

void *PairCoulExclude::extract(const char *str, int &dim)
{
  dim = 0;
  if (strcmp(str,"cut_coul") == 0) return (void *) &cut_global;
  return nullptr;
}