// clang-format off
/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

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

#include "pair_lj_cut_thole_long.h"

#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_drude.h"
#include "force.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neighbor.h"

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;
using namespace MathConst;

static constexpr double EWALD_F =  1.12837917;
static constexpr double EWALD_P =  9.95473818e-1;
static constexpr double B0      = -0.1335096380159268;
static constexpr double B1      = -2.57839507e-1;
static constexpr double B2      = -1.37203639e-1;
static constexpr double B3      = -8.88822059e-3;
static constexpr double B4      = -5.80844129e-3;
static constexpr double B5      =  1.14652755e-1;

static constexpr double EPSILON = 1.0e-20;
static constexpr double EPS_EWALD = 1.0e-6;
static constexpr double EPS_EWALD_SQR = 1.0e-12;

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

PairLJCutTholeLong::PairLJCutTholeLong(LAMMPS *lmp) : Pair(lmp)
{
  ewaldflag = pppmflag = 1;
  single_enable = 0;
  writedata = 1;
  ftable = nullptr;
  qdist = 0.0;
  fix_drude = nullptr;
}

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

PairLJCutTholeLong::~PairLJCutTholeLong()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);
    memory->destroy(polar);
    memory->destroy(thole);
    memory->destroy(ascreen);
    memory->destroy(cut_lj);
    memory->destroy(cut_ljsq);
    memory->destroy(scale);
    memory->destroy(epsilon);
    memory->destroy(sigma);
    memory->destroy(lj1);
    memory->destroy(lj2);
    memory->destroy(lj3);
    memory->destroy(lj4);
    memory->destroy(offset);
  }
  if (ftable) free_tables();
}

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

void PairLJCutTholeLong::compute(int eflag, int vflag)
{
  int i,j,ii,jj,inum,jnum,itype,jtype,itable;
  double qi,qj,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,evdwl;
  double r,rsq,r2inv,forcecoul,factor_coul,forcelj,factor_lj,r6inv;
  double fraction,table;
  double grij,expm2,prefactor,t,erfc,u;
  int *ilist,*jlist,*numneigh,**firstneigh;
  double factor_f,factor_e;
  int di,dj;
  double dqi,dqj,dcoul,asr,exp_asr;
  int di_closest;

  evdwl = ecoul = 0.0;
  ev_init(eflag,vflag);

  double **x = atom->x;
  double **f = atom->f;
  double *q = atom->q;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  double *special_coul = force->special_coul;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;
  double qqrd2e = force->qqrd2e;
  int *drudetype = fix_drude->drudetype;
  tagint *drudeid = fix_drude->drudeid;

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

    if (drudetype[type[i]] != NOPOL_TYPE) {
      di = atom->map(drudeid[i]);
      if (di < 0) error->all(FLERR, "Drude partner not found");
      di_closest = domain->closest_image(i, di);
      if (drudetype[type[i]] == CORE_TYPE)
        dqi = -q[di];
      else
        dqi = qi;
    }

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      factor_lj = special_lj[sbmask(j)];
      factor_coul = special_coul[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]) {
         rsq += EPSILON; // Add Epsilon for case: r = 0; DC-DP 1-1 interaction must be removed by special bond;
         r2inv = 1.0/rsq;

        if (rsq < cut_coulsq) {
          qj = q[j];
          r = sqrt(rsq);

          if (!ncoultablebits || rsq <= tabinnersq) {
            grij = g_ewald * (r + EPS_EWALD);
            expm2 = exp(-grij*grij);
            t = 1.0 / (1.0 + EWALD_P*grij);
            u = 1. - t;
            erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
            prefactor = qqrd2e * qi*qj/(r + EPS_EWALD);
            forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
            if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
            r2inv = 1.0/(rsq + EPS_EWALD_SQR);
          } else {
            union_int_float_t rsq_lookup;
            rsq_lookup.f = rsq;
            itable = rsq_lookup.i & ncoulmask;
            itable >>= ncoulshiftbits;
            fraction = ((double) rsq_lookup.f - rtable[itable]) * drtable[itable];
            table = ftable[itable] + fraction*dftable[itable];
            forcecoul = qi*qj * table;
            if (factor_coul < 1.0) {
              table = ctable[itable] + fraction*dctable[itable];
              prefactor = qi*qj * table;
              forcecoul -= (1.0-factor_coul)*prefactor;
            }
          }

          if (drudetype[type[i]] != NOPOL_TYPE &&
              drudetype[type[j]] != NOPOL_TYPE) {
            if (j != di_closest) {
              if (drudetype[type[j]] == CORE_TYPE) {
                dj = atom->map(drudeid[j]);
                dqj = -q[dj];
              } else dqj = qj;
              asr = ascreen[type[i]][type[j]] * r;
              exp_asr = exp(-asr);
              dcoul = qqrd2e * dqi * dqj / r;
              factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr))))
                  - factor_coul;
              if (eflag) factor_e = 0.5*(2. - (exp_asr * (2. + asr)))
                             - factor_coul;
              forcecoul += factor_f * dcoul;
            }
          }
        } else forcecoul = 0.0;

        if (rsq < cut_ljsq[itype][jtype]) {
          r6inv = r2inv*r2inv*r2inv;
          forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
        } else forcelj = 0.0;

        fpair = (forcecoul + factor_lj*forcelj) * 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) {
          if (rsq < cut_coulsq) {
            if (!ncoultablebits || rsq <= tabinnersq)
              ecoul = prefactor*erfc;
            else {
              table = etable[itable] + fraction*detable[itable];
              ecoul = qi*qj * table;
            }
            if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
            if (drudetype[type[i]] != NOPOL_TYPE &&
                drudetype[type[j]] != NOPOL_TYPE && j != di_closest) {
              ecoul += factor_e * dcoul;
            }
          } else ecoul = 0.0;

          if (rsq < cut_ljsq[itype][jtype]) {
            evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
              offset[itype][jtype];
            evdwl *= factor_lj;
          } else evdwl = 0.0;
        }

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

  if (vflag_fdotr) virial_fdotr_compute();
}

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

void PairLJCutTholeLong::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_lj,n+1,n+1,"pair:cut_lj");
  memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
  memory->create(scale,n+1,n+1,"pair:scale");
  memory->create(ascreen,n+1,n+1,"pair:ascreen");
  memory->create(thole,n+1,n+1,"pair:thole");
  memory->create(polar,n+1,n+1,"pair:polar");
  memory->create(epsilon,n+1,n+1,"pair:epsilon");
  memory->create(sigma,n+1,n+1,"pair:sigma");
  memory->create(lj1,n+1,n+1,"pair:lj1");
  memory->create(lj2,n+1,n+1,"pair:lj2");
  memory->create(lj3,n+1,n+1,"pair:lj3");
  memory->create(lj4,n+1,n+1,"pair:lj4");
  memory->create(offset,n+1,n+1,"pair:offset");
}

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

void PairLJCutTholeLong::settings(int narg, char **arg)
{
 if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");

  thole_global = utils::numeric(FLERR,arg[0],false,lmp);
  cut_lj_global = utils::numeric(FLERR,arg[1],false,lmp);
  if (narg == 2) cut_coul = cut_lj_global;
  else cut_coul = utils::numeric(FLERR,arg[2],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]) {
          thole[i][j] = thole_global;
          cut_lj[i][j] = cut_lj_global;
        }
  }
}

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

void PairLJCutTholeLong::coeff(int narg, char **arg)
{
  if (narg < 5 || narg > 7)
    error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21));
  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 polar_one = utils::numeric(FLERR,arg[4],false,lmp);
  double thole_one = thole_global;
  if (narg >=6) thole_one = utils::numeric(FLERR,arg[5],false,lmp);

  double cut_lj_one = cut_lj_global;
  if (narg == 7) cut_lj_one = utils::numeric(FLERR,arg[6],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;
      polar[i][j] = polar_one;
      thole[i][j] = thole_one;
      ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
      cut_lj[i][j] = cut_lj_one;
      scale[i][j] = 1.0;
      setflag[i][j] = 1;
      count++;
    }
  }

  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients" + utils::errorurl(21));
}

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

void PairLJCutTholeLong::init_style()
{
  if (!atom->q_flag)
    error->all(FLERR,"Pair style lj/cut/thole/long requires atom attribute q");
  int ifix;
  for (ifix = 0; ifix < modify->nfix; ifix++)
    if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
  if (ifix == modify->nfix)
      error->all(FLERR, "Pair style lj/cut/thole/long requires fix drude");
  fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);

  neighbor->add_request(this);

  cut_coulsq = cut_coul * cut_coul;

  // set rRESPA cutoffs

  cut_respa = nullptr;

  // ensure use of KSpace long-range solver, set g_ewald

  if (force->kspace == nullptr)
    error->all(FLERR,"Pair style requires a KSpace style");
  g_ewald = force->kspace->g_ewald;

  // setup force tables

  if (ncoultablebits) init_tables(cut_coul,cut_respa);
}

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

double PairLJCutTholeLong::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_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
    polar[i][j] = sqrt(polar[i][i] * polar[j][j]);
    thole[i][j] = 0.5 * (thole[i][i] + thole[j][j]);
    ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
  }

  // include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P

  double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
  cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][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_lj[i][j] > 0.0)) {
    double ratio = sigma[i][j] / cut_lj[i][j];
    offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
  } else offset[i][j] = 0.0;

  cut_ljsq[j][i] = cut_ljsq[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];
  polar[j][i] = polar[i][j];
  thole[j][i] = thole[i][j];
  ascreen[j][i] = ascreen[i][j];
  scale[j][i] = scale[i][j];

  // check interior rRESPA cutoff

  if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
    error->all(FLERR,"Pair cutoff < Respa interior cutoff");

  // 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 sig2 = sigma[i][j]*sigma[i][j];
    double sig6 = sig2*sig2*sig2;
    double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
    double rc6 = rc3*rc3;
    double rc9 = rc3*rc6;
    etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
      sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
    ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
      sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
  }

  return cut;
}

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

void PairLJCutTholeLong::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(&polar[i][j],sizeof(double),1,fp);
        fwrite(&thole[i][j],sizeof(double),1,fp);
        fwrite(&cut_lj[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairLJCutTholeLong::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);
      if (setflag[i][j]) {
        if (me == 0) {
          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error);
          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error);
          utils::sfread(FLERR,&polar[i][j],sizeof(double),1,fp,nullptr,error);
          utils::sfread(FLERR,&thole[i][j],sizeof(double),1,fp,nullptr,error);
          ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
          utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,nullptr,error);
        }
        MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&polar[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&thole[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&ascreen[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

void PairLJCutTholeLong::write_restart_settings(FILE *fp)
{
  fwrite(&cut_lj_global,sizeof(double),1,fp);
  fwrite(&cut_coul,sizeof(double),1,fp);
  fwrite(&thole_global,sizeof(double),1,fp);
  fwrite(&cut_global,sizeof(double),1,fp);
  fwrite(&offset_flag,sizeof(int),1,fp);
  fwrite(&mix_flag,sizeof(int),1,fp);
  fwrite(&tail_flag,sizeof(int),1,fp);
  fwrite(&ncoultablebits,sizeof(int),1,fp);
  fwrite(&tabinner,sizeof(double),1,fp);
}

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

void PairLJCutTholeLong::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,nullptr,error);
    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,nullptr,error);
    utils::sfread(FLERR,&thole_global,sizeof(double),1,fp,nullptr,error);
    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);
    utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error);
    utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,nullptr,error);
    utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,nullptr,error);
  }
  MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&thole_global,1,MPI_DOUBLE,0,world);
  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);
  MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
  MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
  MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}


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

void PairLJCutTholeLong::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    fprintf(fp,"%d %g %g %g %g\n",i,epsilon[i][i],sigma[i][i],polar[i][i],thole[i][i]);
}

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

void PairLJCutTholeLong::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 %g %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],polar[i][j],thole[i][j],cut_lj[i][j]);
}

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

// No point in having single() since it  has no information about topology or Drude particles.
// Charges qi and qj are defined by the user (or 1.0 by default)

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

void *PairLJCutTholeLong::extract(const char *str, int &dim)
{
  dim = 0;
  if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
  dim = 2;
  if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
  if (strcmp(str,"sigma") == 0) return (void *) sigma;
  if (strcmp(str,"scale") == 0) return (void *) scale;
  if (strcmp(str,"polar") == 0) return (void *) polar;
  if (strcmp(str,"thole") == 0) return (void *) thole;
  if (strcmp(str,"ascreen") == 0) return (void *) ascreen;
  return nullptr;
}
