/* ----------------------------------------------------------------------
   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 "atom_vec_tri.h"

#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "math_const.h"
#include "math_eigen.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;
using MathConst::MY_PI;

static constexpr double EPSILON = 0.001;

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

AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
{
  molecular = Atom::ATOMIC;
  bonus_flag = 1;

  size_forward_bonus = 4;
  size_border_bonus = 17;
  size_restart_bonus_one = 17;
  size_data_bonus = 10;

  atom->tri_flag = 1;
  atom->molecule_flag = atom->rmass_flag = 1;
  atom->radius_flag = atom->omega_flag = atom->angmom_flag = 1;
  atom->torque_flag = 1;

  nlocal_bonus = nghost_bonus = nmax_bonus = 0;
  bonus = nullptr;

  // strings with peratom variables to include in each AtomVec method
  // strings cannot contain fields in corresponding AtomVec default strings
  // order of fields in a string does not matter
  // except: fields_data_atom & fields_data_vel must match data file

  fields_grow = {"molecule", "radius", "rmass", "omega", "angmom", "torque", "tri"};
  fields_copy = {"molecule", "radius", "rmass", "omega", "angmom"};
  fields_comm_vel = {"omega", "angmom"};
  fields_reverse = {"torque"};
  fields_border = {"molecule", "radius", "rmass"};
  fields_border_vel = {"molecule", "radius", "rmass", "omega"};
  fields_exchange = {"molecule", "radius", "rmass", "omega", "angmom"};
  fields_restart = {"molecule", "radius", "rmass", "omega", "angmom"};
  fields_create = {"molecule", "radius", "rmass", "omega", "angmom", "tri"};
  fields_data_atom = {"id", "molecule", "type", "tri", "rmass", "x"};
  fields_data_vel = {"id", "v", "omega", "angmom"};

  setup_fields();
}

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

AtomVecTri::~AtomVecTri()
{
  memory->sfree(bonus);
}

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

void AtomVecTri::init()
{
  AtomVec::init();

  if (domain->dimension != 3)
    error->all(FLERR, "Atom_style tri can only be used in 3d simulations");
}

/* ----------------------------------------------------------------------
   set local copies of all grow ptrs used by this class, except defaults
   needed in replicate when 2 atom classes exist and it calls pack_restart()
------------------------------------------------------------------------- */

void AtomVecTri::grow_pointers()
{
  tri = atom->tri;
  radius = atom->radius;
  rmass = atom->rmass;
  omega = atom->omega;
  angmom = atom->angmom;
}

/* ----------------------------------------------------------------------
   grow bonus data structure
------------------------------------------------------------------------- */

void AtomVecTri::grow_bonus()
{
  nmax_bonus = grow_nmax_bonus(nmax_bonus);
  if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");

  bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}

/* ----------------------------------------------------------------------
   copy atom I info to atom J
   if delflag and atom J has bonus data, then delete it
------------------------------------------------------------------------- */

void AtomVecTri::copy_bonus(int i, int j, int delflag)
{
  // if deleting atom J via delflag and J has bonus data, then delete it

  if (delflag && tri[j] >= 0) {
    copy_bonus_all(nlocal_bonus - 1, tri[j]);
    nlocal_bonus--;
  }

  // if atom I has bonus data, reset I's bonus.ilocal to loc J
  // do NOT do this if self-copy (I=J) since I's bonus data is already deleted

  if (tri[i] >= 0 && i != j) bonus[tri[i]].ilocal = j;
  tri[j] = tri[i];
}

/* ----------------------------------------------------------------------
   copy bonus data from I to J, effectively deleting the J entry
   also reset tri that points to I to now point to J
------------------------------------------------------------------------- */

void AtomVecTri::copy_bonus_all(int i, int j)
{
  tri[bonus[i].ilocal] = j;
  memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}

/* ----------------------------------------------------------------------
   clear ghost info in bonus data
   called before ghosts are recommunicated in comm and irregular
------------------------------------------------------------------------- */

void AtomVecTri::clear_bonus()
{
  nghost_bonus = 0;

  if (atom->nextra_grow)
    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
      modify->fix[atom->extra_grow[iextra]]->clear_bonus();
}

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

int AtomVecTri::pack_comm_bonus(int n, int *list, double *buf)
{
  int i, j, m;
  double *quat;

  m = 0;
  for (i = 0; i < n; i++) {
    j = list[i];
    if (tri[j] >= 0) {
      quat = bonus[tri[j]].quat;
      buf[m++] = quat[0];
      buf[m++] = quat[1];
      buf[m++] = quat[2];
      buf[m++] = quat[3];
    }
  }

  return m;
}

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

void AtomVecTri::unpack_comm_bonus(int n, int first, double *buf)
{
  int i, m, last;
  double *quat;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    if (tri[i] >= 0) {
      quat = bonus[tri[i]].quat;
      quat[0] = buf[m++];
      quat[1] = buf[m++];
      quat[2] = buf[m++];
      quat[3] = buf[m++];
    }
  }
}

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

int AtomVecTri::pack_border_bonus(int n, int *list, double *buf)
{
  int i, j, m;
  double *quat, *c1, *c2, *c3, *inertia;

  m = 0;
  for (i = 0; i < n; i++) {
    j = list[i];
    if (tri[j] < 0)
      buf[m++] = ubuf(0).d;
    else {
      buf[m++] = ubuf(1).d;
      quat = bonus[tri[j]].quat;
      c1 = bonus[tri[j]].c1;
      c2 = bonus[tri[j]].c2;
      c3 = bonus[tri[j]].c3;
      inertia = bonus[tri[j]].inertia;
      buf[m++] = quat[0];
      buf[m++] = quat[1];
      buf[m++] = quat[2];
      buf[m++] = quat[3];
      buf[m++] = c1[0];
      buf[m++] = c1[1];
      buf[m++] = c1[2];
      buf[m++] = c2[0];
      buf[m++] = c2[1];
      buf[m++] = c2[2];
      buf[m++] = c3[0];
      buf[m++] = c3[1];
      buf[m++] = c3[2];
      buf[m++] = inertia[0];
      buf[m++] = inertia[1];
      buf[m++] = inertia[2];
    }
  }

  return m;
}

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

int AtomVecTri::unpack_border_bonus(int n, int first, double *buf)
{
  int i, j, m, last;
  double *quat, *c1, *c2, *c3, *inertia;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    tri[i] = (int) ubuf(buf[m++]).i;
    if (tri[i] == 0)
      tri[i] = -1;
    else {
      j = nlocal_bonus + nghost_bonus;
      if (j == nmax_bonus) grow_bonus();
      quat = bonus[j].quat;
      c1 = bonus[j].c1;
      c2 = bonus[j].c2;
      c3 = bonus[j].c3;
      inertia = bonus[j].inertia;
      quat[0] = buf[m++];
      quat[1] = buf[m++];
      quat[2] = buf[m++];
      quat[3] = buf[m++];
      c1[0] = buf[m++];
      c1[1] = buf[m++];
      c1[2] = buf[m++];
      c2[0] = buf[m++];
      c2[1] = buf[m++];
      c2[2] = buf[m++];
      c3[0] = buf[m++];
      c3[1] = buf[m++];
      c3[2] = buf[m++];
      inertia[0] = buf[m++];
      inertia[1] = buf[m++];
      inertia[2] = buf[m++];
      bonus[j].ilocal = i;
      tri[i] = j;
      nghost_bonus++;
    }
  }

  return m;
}

/* ----------------------------------------------------------------------
   pack data for atom I for sending to another proc
   xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */

int AtomVecTri::pack_exchange_bonus(int i, double *buf)
{
  int m = 0;

  if (tri[i] < 0)
    buf[m++] = ubuf(0).d;
  else {
    buf[m++] = ubuf(1).d;
    int j = tri[i];
    double *quat = bonus[j].quat;
    double *c1 = bonus[j].c1;
    double *c2 = bonus[j].c2;
    double *c3 = bonus[j].c3;
    double *inertia = bonus[j].inertia;
    buf[m++] = quat[0];
    buf[m++] = quat[1];
    buf[m++] = quat[2];
    buf[m++] = quat[3];
    buf[m++] = c1[0];
    buf[m++] = c1[1];
    buf[m++] = c1[2];
    buf[m++] = c2[0];
    buf[m++] = c2[1];
    buf[m++] = c2[2];
    buf[m++] = c3[0];
    buf[m++] = c3[1];
    buf[m++] = c3[2];
    buf[m++] = inertia[0];
    buf[m++] = inertia[1];
    buf[m++] = inertia[2];
  }

  return m;
}

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

int AtomVecTri::unpack_exchange_bonus(int ilocal, double *buf)
{
  int m = 0;

  tri[ilocal] = (int) ubuf(buf[m++]).i;
  if (tri[ilocal] == 0)
    tri[ilocal] = -1;
  else {
    if (nlocal_bonus == nmax_bonus) grow_bonus();
    double *quat = bonus[nlocal_bonus].quat;
    double *c1 = bonus[nlocal_bonus].c1;
    double *c2 = bonus[nlocal_bonus].c2;
    double *c3 = bonus[nlocal_bonus].c3;
    double *inertia = bonus[nlocal_bonus].inertia;
    quat[0] = buf[m++];
    quat[1] = buf[m++];
    quat[2] = buf[m++];
    quat[3] = buf[m++];
    c1[0] = buf[m++];
    c1[1] = buf[m++];
    c1[2] = buf[m++];
    c2[0] = buf[m++];
    c2[1] = buf[m++];
    c2[2] = buf[m++];
    c3[0] = buf[m++];
    c3[1] = buf[m++];
    c3[2] = buf[m++];
    inertia[0] = buf[m++];
    inertia[1] = buf[m++];
    inertia[2] = buf[m++];
    bonus[nlocal_bonus].ilocal = ilocal;
    tri[ilocal] = nlocal_bonus++;
  }

  return m;
}

/* ----------------------------------------------------------------------
   size of restart data for all atoms owned by this proc
   include extra data stored by fixes
------------------------------------------------------------------------- */

int AtomVecTri::size_restart_bonus()
{
  int i;

  int n = 0;
  int nlocal = atom->nlocal;
  for (i = 0; i < nlocal; i++) {
    if (tri[i] >= 0)
      n += size_restart_bonus_one;
    else
      n++;
  }

  return n;
}

/* ----------------------------------------------------------------------
   unpack data for one atom from restart file including bonus data
------------------------------------------------------------------------- */

int AtomVecTri::pack_restart_bonus(int i, double *buf)
{
  int m = 0;

  if (tri[i] < 0)
    buf[m++] = ubuf(0).d;
  else {
    buf[m++] = ubuf(1).d;
    int j = tri[i];
    double *quat = bonus[j].quat;
    double *c1 = bonus[j].c1;
    double *c2 = bonus[j].c2;
    double *c3 = bonus[j].c3;
    double *inertia = bonus[j].inertia;
    buf[m++] = quat[0];
    buf[m++] = quat[1];
    buf[m++] = quat[2];
    buf[m++] = quat[3];
    buf[m++] = c1[0];
    buf[m++] = c1[1];
    buf[m++] = c1[2];
    buf[m++] = c2[0];
    buf[m++] = c2[1];
    buf[m++] = c2[2];
    buf[m++] = c3[0];
    buf[m++] = c3[1];
    buf[m++] = c3[2];
    buf[m++] = inertia[0];
    buf[m++] = inertia[1];
    buf[m++] = inertia[2];
  }

  return m;
}

/* ----------------------------------------------------------------------
   unpack data for one atom from restart file including bonus data
------------------------------------------------------------------------- */

int AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
{
  int m = 0;

  tri[ilocal] = (int) ubuf(buf[m++]).i;
  if (tri[ilocal] == 0)
    tri[ilocal] = -1;
  else {
    if (nlocal_bonus == nmax_bonus) grow_bonus();
    double *quat = bonus[nlocal_bonus].quat;
    double *c1 = bonus[nlocal_bonus].c1;
    double *c2 = bonus[nlocal_bonus].c2;
    double *c3 = bonus[nlocal_bonus].c3;
    double *inertia = bonus[nlocal_bonus].inertia;
    quat[0] = buf[m++];
    quat[1] = buf[m++];
    quat[2] = buf[m++];
    quat[3] = buf[m++];
    c1[0] = buf[m++];
    c1[1] = buf[m++];
    c1[2] = buf[m++];
    c2[0] = buf[m++];
    c2[1] = buf[m++];
    c2[2] = buf[m++];
    c3[0] = buf[m++];
    c3[1] = buf[m++];
    c3[2] = buf[m++];
    inertia[0] = buf[m++];
    inertia[1] = buf[m++];
    inertia[2] = buf[m++];
    bonus[nlocal_bonus].ilocal = ilocal;
    tri[ilocal] = nlocal_bonus++;
  }

  return m;
}

/* ----------------------------------------------------------------------
   unpack one line from Tris section of data file
------------------------------------------------------------------------- */

void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
{
  if (tri[m]) error->one(FLERR, "Assigning tri parameters to non-tri atom");

  if (nlocal_bonus == nmax_bonus) grow_bonus();

  double c1[3], c2[3], c3[3];
  int ivalue = 1;
  c1[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c1[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c1[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c2[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c2[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c2[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c3[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c3[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
  c3[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);

  // check for duplicate points

  if (c1[0] == c2[0] && c1[1] == c2[1] && c1[2] == c2[2])
    error->one(FLERR, "Invalid shape in Triangles section of data file");
  if (c1[0] == c3[0] && c1[1] == c3[1] && c1[2] == c3[2])
    error->one(FLERR, "Invalid shape in Triangles section of data file");
  if (c2[0] == c3[0] && c2[1] == c3[1] && c2[2] == c3[2])
    error->one(FLERR, "Invalid shape in Triangles section of data file");

  // size = length of one edge

  double c2mc1[3], c3mc1[3];
  MathExtra::sub3(c2, c1, c2mc1);
  MathExtra::sub3(c3, c1, c3mc1);
  double size = MAX(MathExtra::len3(c2mc1), MathExtra::len3(c3mc1));

  // convert c1,c2,c3 from general to restricted triclniic
  // x is already restricted triclinic

  if (domain->triclinic_general) {
    domain->general_to_restricted_coords(c1);
    domain->general_to_restricted_coords(c2);
    domain->general_to_restricted_coords(c3);
  }

  // remap corner points to be near x
  // necessary if atom x was remapped into periodic box

  domain->remap_near(c1,x[m]);
  domain->remap_near(c2,x[m]);
  domain->remap_near(c3,x[m]);

  // centroid = 1/3 of sum of vertices
  // error if centroid is not within EPSILON of atom x
  // reset atom x to centroid

  double centroid[3];
  centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
  centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
  centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;

  double dx = centroid[0] - x[m][0];
  double dy = centroid[1] - x[m][1];
  double dz = centroid[2] - x[m][2];
  double delta = sqrt(dx * dx + dy * dy + dz * dz);

  if (delta / size > EPSILON) error->one(FLERR, "Inconsistent triangle in data file");

  x[m][0] = centroid[0];
  x[m][1] = centroid[1];
  x[m][2] = centroid[2];

  // reset tri radius and mass
  // rmass currently holds density
  // tri area = 0.5 len(U x V), where U,V are edge vectors from one vertex

  double c4[3];
  MathExtra::sub3(c1, centroid, c4);
  radius[m] = MathExtra::lensq3(c4);
  MathExtra::sub3(c2, centroid, c4);
  radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
  MathExtra::sub3(c3, centroid, c4);
  radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
  radius[m] = sqrt(radius[m]);

  double norm[3];
  MathExtra::cross3(c2mc1, c3mc1, norm);
  double area = 0.5 * MathExtra::len3(norm);
  rmass[m] *= area;

  // inertia = inertia tensor of triangle as 6-vector in Voigt ordering

  double inertia[6];
  MathExtra::inertia_triangle(c1, c2, c3, rmass[m], inertia);

  // diagonalize inertia tensor via Jacobi rotations
  // bonus[].inertia = 3 eigenvalues = principal moments of inertia
  // evectors and exzy_space = 3 evectors = principal axes of triangle

  double tensor[3][3], evectors[3][3];
  tensor[0][0] = inertia[0];
  tensor[1][1] = inertia[1];
  tensor[2][2] = inertia[2];
  tensor[1][2] = tensor[2][1] = inertia[3];
  tensor[0][2] = tensor[2][0] = inertia[4];
  tensor[0][1] = tensor[1][0] = inertia[5];

  int ierror = MathEigen::jacobi3(tensor, bonus[nlocal_bonus].inertia, evectors);
  if (ierror) error->one(FLERR, "Insufficient Jacobi rotations for triangle");

  double ex_space[3], ey_space[3], ez_space[3];
  ex_space[0] = evectors[0][0];
  ex_space[1] = evectors[1][0];
  ex_space[2] = evectors[2][0];
  ey_space[0] = evectors[0][1];
  ey_space[1] = evectors[1][1];
  ey_space[2] = evectors[2][1];
  ez_space[0] = evectors[0][2];
  ez_space[1] = evectors[1][2];
  ez_space[2] = evectors[2][2];

  // enforce 3 orthogonal vectors as a right-handed coordinate system
  // flip 3rd vector if needed

  MathExtra::cross3(ex_space, ey_space, norm);
  if (MathExtra::dot3(norm, ez_space) < 0.0) MathExtra::negate3(ez_space);

  // create initial quaternion

  MathExtra::exyz_to_q(ex_space, ey_space, ez_space, bonus[nlocal_bonus].quat);

  // bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
  // in basis of principal axes

  double disp[3];
  MathExtra::sub3(c1, centroid, disp);
  MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c1);
  MathExtra::sub3(c2, centroid, disp);
  MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c2);
  MathExtra::sub3(c3, centroid, disp);
  MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c3);

  bonus[nlocal_bonus].ilocal = m;
  tri[m] = nlocal_bonus++;
}

/* ----------------------------------------------------------------------
   return # of bytes of allocated bonus memory
------------------------------------------------------------------------- */

double AtomVecTri::memory_usage_bonus()
{
  double bytes = 0;
  bytes += (double) nmax_bonus * sizeof(Bonus);
  return bytes;
}

/* ----------------------------------------------------------------------
   create one atom of itype at coord
   set other values to defaults
------------------------------------------------------------------------- */

void AtomVecTri::create_atom_post(int ilocal)
{
  double radius_one = 0.5;
  radius[ilocal] = radius_one;
  rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
  tri[ilocal] = -1;
}

/* ----------------------------------------------------------------------
   modify what AtomVec::data_atom() just unpacked
   or initialize other atom quantities
------------------------------------------------------------------------- */

void AtomVecTri::data_atom_post(int ilocal)
{
  tri_flag = tri[ilocal];
  if (tri_flag == 0)
    tri_flag = -1;
  else if (tri_flag == 1)
    tri_flag = 0;
  else
    error->one(FLERR, "Invalid tri flag in Atoms section of data file");
  tri[ilocal] = tri_flag;

  if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");

  if (tri_flag < 0) {
    double radius_one = 0.5;
    radius[ilocal] = radius_one;
    rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
  } else
    radius[ilocal] = 0.0;

  omega[ilocal][0] = 0.0;
  omega[ilocal][1] = 0.0;
  omega[ilocal][2] = 0.0;
  angmom[ilocal][0] = 0.0;
  angmom[ilocal][1] = 0.0;
  angmom[ilocal][2] = 0.0;
}

/* ----------------------------------------------------------------------
   modify values for AtomVec::pack_data() to pack
------------------------------------------------------------------------- */

void AtomVecTri::pack_data_pre(int ilocal)
{
  tri_flag = tri[ilocal];
  rmass_one = rmass[ilocal];

  if (tri_flag < 0)
    tri[ilocal] = 0;
  else
    tri[ilocal] = 1;

  if (tri_flag < 0) {
    double radius_one = radius[ilocal];
    rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
  } else {
    double c2mc1[3], c3mc1[3], norm[3];
    MathExtra::sub3(bonus[tri_flag].c2, bonus[tri_flag].c1, c2mc1);
    MathExtra::sub3(bonus[tri_flag].c3, bonus[tri_flag].c1, c3mc1);
    MathExtra::cross3(c2mc1, c3mc1, norm);
    double area = 0.5 * MathExtra::len3(norm);
    rmass[ilocal] /= area;
  }
}

/* ----------------------------------------------------------------------
   unmodify values packed by AtomVec::pack_data()
------------------------------------------------------------------------- */

void AtomVecTri::pack_data_post(int ilocal)
{
  tri[ilocal] = tri_flag;
  rmass[ilocal] = rmass_one;
}

/* ----------------------------------------------------------------------
   pack bonus tri info for writing to data file
   if buf is nullptr, just return buffer size
------------------------------------------------------------------------- */

int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
{
  int i, j;
  double xc, yc, zc;
  double dc1[3], dc2[3], dc3[3];
  double p[3][3];

  int triclinic_general = domain->triclinic_general;

  double **x_bonus;
  if (triclinic_general) x_bonus = x_hold;
  else x_bonus = x;

  tagint *tag = atom->tag;
  int nlocal = atom->nlocal;

  int m = 0;
  for (i = 0; i < nlocal; i++) {
    if (tri[i] < 0) continue;
    if (buf) {
      buf[m++] = ubuf(tag[i]).d;
      j = tri[i];
      MathExtra::quat_to_mat(bonus[j].quat, p);
      MathExtra::matvec(p, bonus[j].c1, dc1);
      MathExtra::matvec(p, bonus[j].c2, dc2);
      MathExtra::matvec(p, bonus[j].c3, dc3);

      xc = x_bonus[i][0];
      yc = x_bonus[i][1];
      zc = x_bonus[i][2];
      buf[m++] = xc + dc1[0];
      buf[m++] = yc + dc1[1];
      buf[m++] = zc + dc1[2];
      buf[m++] = xc + dc2[0];
      buf[m++] = yc + dc2[1];
      buf[m++] = zc + dc2[2];
      buf[m++] = xc + dc3[0];
      buf[m++] = yc + dc3[1];
      buf[m++] = zc + dc3[2];

      // if triclinic_general:
      // rotate 9 buf values from restricted to general triclinic
      // output by write_data_bonus() as c1,c2,c3

      if (triclinic_general) {
        domain->restricted_to_general_coords(&buf[m-9]);
        domain->restricted_to_general_coords(&buf[m-6]);
        domain->restricted_to_general_coords(&buf[m-3]);
      }

    } else
      m += size_data_bonus;
  }
  return m;
}

/* ----------------------------------------------------------------------
   write bonus tri info to data file
------------------------------------------------------------------------- */

void AtomVecTri::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
  int i = 0;
  while (i < n) {
    utils::print(fp, "{} {} {} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2],
               buf[i + 3], buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7], buf[i + 8], buf[i + 9]);
    i += size_data_bonus;
  }
}

/* ----------------------------------------------------------------------
   set equilateral tri of size in bonus data for particle I
   oriented symmetrically in xy plane
   this may create or delete entry in bonus data
------------------------------------------------------------------------- */

void AtomVecTri::set_equilateral(int i, double size)
{
  // also set radius = distance from center to corner-pt = len(c1)
  // unless size = 0.0, then set diameter = 1.0

  if (tri[i] < 0) {
    if (size == 0.0) return;
    if (nlocal_bonus == nmax_bonus) grow_bonus();
    double *quat = bonus[nlocal_bonus].quat;
    double *c1 = bonus[nlocal_bonus].c1;
    double *c2 = bonus[nlocal_bonus].c2;
    double *c3 = bonus[nlocal_bonus].c3;
    double *inertia = bonus[nlocal_bonus].inertia;
    quat[0] = 1.0;
    quat[1] = 0.0;
    quat[2] = 0.0;
    quat[3] = 0.0;
    c1[0] = -size / 2.0;
    c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
    c1[2] = 0.0;
    c2[0] = size / 2.0;
    c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
    c2[2] = 0.0;
    c3[0] = 0.0;
    c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
    c3[2] = 0.0;
    inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
    inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
    inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
    radius[i] = MathExtra::len3(c1);
    bonus[nlocal_bonus].ilocal = i;
    tri[i] = nlocal_bonus++;
  } else if (size == 0.0) {
    radius[i] = 0.5;
    copy_bonus_all(nlocal_bonus - 1, tri[i]);
    nlocal_bonus--;
    tri[i] = -1;
  } else {
    double *c1 = bonus[tri[i]].c1;
    double *c2 = bonus[tri[i]].c2;
    double *c3 = bonus[tri[i]].c3;
    double *inertia = bonus[tri[i]].inertia;
    c1[0] = -size / 2.0;
    c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
    c1[2] = 0.0;
    c2[0] = size / 2.0;
    c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
    c2[2] = 0.0;
    c3[0] = 0.0;
    c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
    c3[2] = 0.0;
    inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
    inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
    inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
    radius[i] = MathExtra::len3(c1);
  }
}
