// 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.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: Georgios G. Vogiatzis (CoMSE, NTU Athens),
     gvog@chemeng.ntua.gr
------------------------------------------------------------------------- */

#include "improper_cossq.h"

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

#include <cmath>

using namespace LAMMPS_NS;
using namespace MathConst;

#define TOLERANCE 0.05
#define SMALL     0.001

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

ImproperCossq::ImproperCossq(LAMMPS *lmp) : Improper(lmp) {}

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

ImproperCossq::~ImproperCossq()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(k);
    memory->destroy(chi);
  }
}

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

void ImproperCossq::compute(int eflag, int vflag)
{
  int i1,i2,i3,i4,n,type;
  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z ;
  double eimproper,f1[3],f2[3],f3[3],f4[3];
  double rjisq, rji, rlksq, rlk, cosphi, angfac;
  double cjiji, clkji, clklk, cfact1, cfact2, cfact3;

  eimproper = 0.0;
  ev_init(eflag,vflag);

  double **x = atom->x;
  double **f = atom->f;
  int **improperlist = neighbor->improperlist;
  int nimproperlist = neighbor->nimproperlist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  for (n = 0; n < nimproperlist; n++) {
    /* Ask the improper list for the atom types. */
    i1 = improperlist[n][0];
    i2 = improperlist[n][1];
    i3 = improperlist[n][2];
    i4 = improperlist[n][3];
    type = improperlist[n][4];

    /* separation vector between i1 and i2, (i2-i1) */
    vb1x = x[i2][0] - x[i1][0];
    vb1y = x[i2][1] - x[i1][1];
    vb1z = x[i2][2] - x[i1][2];
    rjisq = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z ;
    rji = sqrt(rjisq);

    /* separation vector between i2 and i3 (i3-i2) */
    vb2x = x[i3][0] - x[i2][0];
    vb2y = x[i3][1] - x[i2][1];
    vb2z = x[i3][2] - x[i2][2];

    /* separation vector between i3 and i4, (i4-i3) */
    vb3x = x[i4][0] - x[i3][0];
    vb3y = x[i4][1] - x[i3][1];
    vb3z = x[i4][2] - x[i3][2];
    rlksq = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z ;
    rlk = sqrt(rlksq);

    cosphi = (vb3x*vb1x + vb3y*vb1y + vb3z*vb1z)/(rji * rlk);

    /* Check that cos(phi) is in the correct limits. */
    if (cosphi > 1.0 + TOLERANCE || cosphi < (-1.0 - TOLERANCE))
      problem(FLERR, i1, i2, i3, i4);

    /* Apply corrections to round-off errors. */
    if (cosphi > 1.0)  cosphi -= SMALL;
    if (cosphi < -1.0) cosphi += SMALL;

    /* Calculate the angle: */
    double torangle = acos(cosphi);
    cosphi = cos(torangle - chi[type]);

    if (eflag) eimproper = 0.5 * k[type] * cosphi * cosphi;

    /*
      printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
      printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
      printf("The cosine of the angle: %-1.16e.\n", cosphi);
      printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
    */

    /* Work out forces. */
    angfac = - k[type] * cosphi;

    cjiji = rjisq;
    clklk = rlksq;
    /*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
    clkji = vb3x*vb1x + vb3y*vb1y + vb3z*vb1z;

    /*CFACT1 = CLKLK * CJIJI
      CFACT1 = SQRT(CFACT1)
      CFACT1 = ANGFAC / CFACT1*/
    cfact1 = angfac / sqrt(clklk * cjiji);
    /*CFACT2 = CLKJI / CLKLK*/
    cfact2 = clkji / clklk;
    /*CFACT3 = CLKJI / CJIJI*/
    cfact3 = clkji / cjiji;

    /*FIX = -RXLK + CFACT3 * RXJI
      FIY = -RYLK + CFACT3 * RYJI
      FIZ = -RZLK + CFACT3 * RZJI*/
    f1[0] = - vb3x + cfact3 * vb1x;
    f1[1] = - vb3y + cfact3 * vb1y;
    f1[2] = - vb3z + cfact3 * vb1z;

    /*FJX = -FIX
      FJY = -FIY
      FJZ = -FIZ*/
    f2[0] = - f1[0];
    f2[1] = - f1[1];
    f2[2] = - f1[2];

    /*FKX = CFACT2 * RXLK - RXJI
      FKY = CFACT2 * RYLK - RYJI
      FKZ = CFACT2 * RZLK - RZJI*/
    f3[0] = cfact2 * vb3x - vb1x;
    f3[1] = cfact2 * vb3y - vb1y;
    f3[2] = cfact2 * vb3z - vb1z;

    /*FLX = -FKX
      FLY = -FKY
      FLZ = -FKZ*/
    f4[0] = - f3[0];
    f4[1] = - f3[1];
    f4[2] = - f3[2];

    /*FIX = FIX * CFACT1
      FIY = FIY * CFACT1
      FIZ = FIZ * CFACT1*/
    f1[0] *= cfact1;
    f1[1] *= cfact1;
    f1[2] *= cfact1;

    /*FJX = FJX * CFACT1
      FJY = FJY * CFACT1
      FJZ = FJZ * CFACT1*/
    f2[0] *= cfact1;
    f2[1] *= cfact1;
    f2[2] *= cfact1;

    /*FKX = FKX * CFACT1
      FKY = FKY * CFACT1
      FKZ = FKZ * CFACT1*/
    f3[0] *= cfact1;
    f3[1] *= cfact1;
    f3[2] *= cfact1;

    /*FLX = FLX * CFACT1
      FLY = FLY * CFACT1
      FLZ = FLZ * CFACT1*/
    f4[0] *= cfact1;
    f4[1] *= cfact1;
    f4[2] *= cfact1;

    /* Apply force to each of 4 atoms */
    if (newton_bond || i1 < nlocal) {
      f[i1][0] += f1[0];
      f[i1][1] += f1[1];
      f[i1][2] += f1[2];
    }

    if (newton_bond || i2 < nlocal) {
      f[i2][0] += f2[0];
      f[i2][1] += f2[1];
      f[i2][2] += f2[2];
    }

    if (newton_bond || i3 < nlocal) {
      f[i3][0] += f3[0];
      f[i3][1] += f3[1];
      f[i3][2] += f3[2];
    }

    if (newton_bond || i4 < nlocal) {
      f[i4][0] += f4[0];
      f[i4][1] += f4[1];
      f[i4][2] += f4[2];
    }

    if (evflag)
      ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
               -vb1x,-vb1y,-vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
  }
}

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

void ImproperCossq::allocate()
{
  allocated = 1;
  int n = atom->nimpropertypes;

  memory->create(k,n+1,"improper:k");
  memory->create(chi,n+1,"improper:chi");

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

/* ----------------------------------------------------------------------
   set coeffs for one type
------------------------------------------------------------------------- */

void ImproperCossq::coeff(int narg, char **arg)
{
   /* Check whether there exist sufficient number of arguments.
      0: type of improper to be applied to
      1: energetic constant
      2: equilibrium angle in degrees */
   if (narg != 3) error->all(FLERR,"Incorrect args for cossq improper coefficients");
   if (!allocated) allocate();

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

   double k_one = utils::numeric(FLERR,arg[1],false,lmp);
   double chi_one = utils::numeric(FLERR,arg[2],false,lmp);

   int count = 0;
   for (int i = ilo; i <= ihi; i++) {
      k[i] = k_one;
      chi[i] = ((chi_one * MY_PI)/180.0);
      setflag[i] = 1;
      count++;
   }

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

/* ----------------------------------------------------------------------
   proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperCossq::write_restart(FILE *fp)
{
   fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
   fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}

/* ----------------------------------------------------------------------
   proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperCossq::read_restart(FILE *fp)
{
  allocate();

  if (comm->me == 0) {
    utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,nullptr,error);
    utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,nullptr,error);
  }
  MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
  MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);

  for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}

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

void ImproperCossq::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->nimpropertypes; i++)
    fprintf(fp,"%d %g %g\n",i,k[i],chi[i]/MY_PI*180.0);
}
