/* ----------------------------------------------------------------------
   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: Mark Stevens (SNL)
------------------------------------------------------------------------- */

#include "dihedral_opls.h"

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

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;

static constexpr double TOLERANCE = 0.05;
static constexpr double SMALL = 0.001;
static constexpr double SMALLER = 0.00001;

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

DihedralOPLS::DihedralOPLS(LAMMPS *_lmp) : Dihedral(_lmp)
{
  writedata = 1;
  born_matrix_enable = 1;
}

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

DihedralOPLS::~DihedralOPLS()
{
  if (allocated && !copymode) {
    memory->destroy(setflag);
    memory->destroy(k1);
    memory->destroy(k2);
    memory->destroy(k3);
    memory->destroy(k4);
  }
}

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

void DihedralOPLS::compute(int eflag, int vflag)
{
  int i1, i2, i3, i4, n, type;
  double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
  double edihedral, f1[3], f2[3], f3[3], f4[3];
  double sb1, sb2, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2;
  double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2;
  double c2mag, sc1, sc2, s1, s12, c, p, pd, a, a11, a22;
  double a33, a12, a13, a23, sx2, sy2, sz2;
  double s2, cx, cy, cz, cmag, dx, phi, si, siinv, sin2;

  edihedral = 0.0;
  ev_init(eflag, vflag);

  double **x = atom->x;
  double **f = atom->f;
  int **dihedrallist = neighbor->dihedrallist;
  int ndihedrallist = neighbor->ndihedrallist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  for (n = 0; n < ndihedrallist; n++) {
    i1 = dihedrallist[n][0];
    i2 = dihedrallist[n][1];
    i3 = dihedrallist[n][2];
    i4 = dihedrallist[n][3];
    type = dihedrallist[n][4];

    // 1st bond

    vb1x = x[i1][0] - x[i2][0];
    vb1y = x[i1][1] - x[i2][1];
    vb1z = x[i1][2] - x[i2][2];

    // 2nd bond

    vb2x = x[i3][0] - x[i2][0];
    vb2y = x[i3][1] - x[i2][1];
    vb2z = x[i3][2] - x[i2][2];

    vb2xm = -vb2x;
    vb2ym = -vb2y;
    vb2zm = -vb2z;

    // 3rd bond

    vb3x = x[i4][0] - x[i3][0];
    vb3y = x[i4][1] - x[i3][1];
    vb3z = x[i4][2] - x[i3][2];

    // c0 calculation

    sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
    sb2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
    sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);

    rb1 = sqrt(sb1);
    rb3 = sqrt(sb3);

    c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;

    // 1st and 2nd angle

    b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z;
    b1mag = sqrt(b1mag2);
    b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z;
    b2mag = sqrt(b2mag2);
    b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
    b3mag = sqrt(b3mag2);

    ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z;
    r12c1 = 1.0 / (b1mag * b2mag);
    c1mag = ctmp * r12c1;

    ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z;
    r12c2 = 1.0 / (b2mag * b3mag);
    c2mag = ctmp * r12c2;

    // cos and sin of 2 angles and final c

    sin2 = MAX(1.0 - c1mag * c1mag, 0.0);
    sc1 = sqrt(sin2);
    if (sc1 < SMALL) sc1 = SMALL;
    sc1 = 1.0 / sc1;

    sin2 = MAX(1.0 - c2mag * c2mag, 0.0);
    sc2 = sqrt(sin2);
    if (sc2 < SMALL) sc2 = SMALL;
    sc2 = 1.0 / sc2;

    s1 = sc1 * sc1;
    s2 = sc2 * sc2;
    s12 = sc1 * sc2;
    c = (c0 + c1mag * c2mag) * s12;

    cx = vb1y * vb2z - vb1z * vb2y;
    cy = vb1z * vb2x - vb1x * vb2z;
    cz = vb1x * vb2y - vb1y * vb2x;
    cmag = sqrt(cx * cx + cy * cy + cz * cz);
    dx = (cx * vb3x + cy * vb3y + cz * vb3z) / cmag / b3mag;

    // error check

    if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);

    if (c > 1.0) c = 1.0;
    if (c < -1.0) c = -1.0;

    // force & energy
    // p = sum (i=1,4) k_i * (1 + (-1)**(i+1)*cos(i*phi) )
    // pd = dp/dc

    phi = acos(c);
    if (dx < 0.0) phi *= -1.0;
    si = sin(phi);
    if (fabs(si) < SMALLER) si = SMALLER;
    siinv = 1.0 / si;

    p = k1[type] * (1.0 + c) + k2[type] * (1.0 - cos(2.0 * phi)) +
        k3[type] * (1.0 + cos(3.0 * phi)) + k4[type] * (1.0 - cos(4.0 * phi));
    pd = k1[type] - 2.0 * k2[type] * sin(2.0 * phi) * siinv +
        3.0 * k3[type] * sin(3.0 * phi) * siinv - 4.0 * k4[type] * sin(4.0 * phi) * siinv;

    if (eflag) edihedral = p;

    a = pd;
    c = c * a;
    s12 = s12 * a;
    a11 = c * sb1 * s1;
    a22 = -sb2 * (2.0 * c0 * s12 - c * (s1 + s2));
    a33 = c * sb3 * s2;
    a12 = -r12c1 * (c1mag * c * s1 + c2mag * s12);
    a13 = -rb1 * rb3 * s12;
    a23 = r12c2 * (c2mag * c * s2 + c1mag * s12);

    sx2 = a12 * vb1x + a22 * vb2x + a23 * vb3x;
    sy2 = a12 * vb1y + a22 * vb2y + a23 * vb3y;
    sz2 = a12 * vb1z + a22 * vb2z + a23 * vb3z;

    f1[0] = a11 * vb1x + a12 * vb2x + a13 * vb3x;
    f1[1] = a11 * vb1y + a12 * vb2y + a13 * vb3y;
    f1[2] = a11 * vb1z + a12 * vb2z + a13 * vb3z;

    f2[0] = -sx2 - f1[0];
    f2[1] = -sy2 - f1[1];
    f2[2] = -sz2 - f1[2];

    f4[0] = a13 * vb1x + a23 * vb2x + a33 * vb3x;
    f4[1] = a13 * vb1y + a23 * vb2y + a33 * vb3y;
    f4[2] = a13 * vb1z + a23 * vb2z + a33 * vb3z;

    f3[0] = sx2 - f4[0];
    f3[1] = sy2 - f4[1];
    f3[2] = sz2 - f4[2];

    // 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, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
               vb2y, vb2z, vb3x, vb3y, vb3z);
  }
}

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

void DihedralOPLS::allocate()
{
  allocated = 1;
  const int np1 = atom->ndihedraltypes + 1;

  memory->create(k1, np1, "dihedral:k1");
  memory->create(k2, np1, "dihedral:k2");
  memory->create(k3, np1, "dihedral:k3");
  memory->create(k4, np1, "dihedral:k4");

  memory->create(setflag, np1, "dihedral:setflag");
  for (int i = 1; i < np1; i++) setflag[i] = 0;
}

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

void DihedralOPLS::coeff(int narg, char **arg)
{
  if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients" + utils::errorurl(21));
  if (!allocated) allocate();

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

  double k1_one = utils::numeric(FLERR, arg[1], false, lmp);
  double k2_one = utils::numeric(FLERR, arg[2], false, lmp);
  double k3_one = utils::numeric(FLERR, arg[3], false, lmp);
  double k4_one = utils::numeric(FLERR, arg[4], false, lmp);

  // store 1/2 factor with prefactor

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    k1[i] = 0.5 * k1_one;
    k2[i] = 0.5 * k2_one;
    k3[i] = 0.5 * k3_one;
    k4[i] = 0.5 * k4_one;
    setflag[i] = 1;
    count++;
  }

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

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

void DihedralOPLS::write_restart(FILE *fp)
{
  fwrite(&k1[1], sizeof(double), atom->ndihedraltypes, fp);
  fwrite(&k2[1], sizeof(double), atom->ndihedraltypes, fp);
  fwrite(&k3[1], sizeof(double), atom->ndihedraltypes, fp);
  fwrite(&k4[1], sizeof(double), atom->ndihedraltypes, fp);
}

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

void DihedralOPLS::read_restart(FILE *fp)
{
  allocate();

  if (comm->me == 0) {
    utils::sfread(FLERR, &k1[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
    utils::sfread(FLERR, &k2[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
    utils::sfread(FLERR, &k3[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
    utils::sfread(FLERR, &k4[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
  }
  MPI_Bcast(&k1[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&k2[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&k3[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&k4[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);

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

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

void DihedralOPLS::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ndihedraltypes; i++)
    fprintf(fp, "%d %g %g %g %g\n", i, 2.0 * k1[i], 2.0 * k2[i], 2.0 * k3[i], 2.0 * k4[i]);
}

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

void DihedralOPLS::born_matrix(int nd, int i1, int i2, int i3, int i4, double &du, double &du2)
{
  double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
  double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2;
  double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2;
  double c2mag, sc1, sc2, s12, c;
  double cx, cy, cz, cmag, dx, phi, si, sin2;

  double **x = atom->x;
  int **dihedrallist = neighbor->dihedrallist;

  int type = dihedrallist[nd][4];

  // 1st bond
  vb1x = x[i1][0] - x[i2][0];
  vb1y = x[i1][1] - x[i2][1];
  vb1z = x[i1][2] - x[i2][2];

  // 2nd bond
  vb2x = x[i3][0] - x[i2][0];
  vb2y = x[i3][1] - x[i2][1];
  vb2z = x[i3][2] - x[i2][2];

  vb2xm = -vb2x;
  vb2ym = -vb2y;
  vb2zm = -vb2z;

  // 3rd bond
  vb3x = x[i4][0] - x[i3][0];
  vb3y = x[i4][1] - x[i3][1];
  vb3z = x[i4][2] - x[i3][2];

  // c0 calculation
  sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
  sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);

  rb1 = sqrt(sb1);
  rb3 = sqrt(sb3);

  c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;

  // 1st and 2nd angle
  b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z;
  b1mag = sqrt(b1mag2);
  b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z;
  b2mag = sqrt(b2mag2);
  b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
  b3mag = sqrt(b3mag2);

  ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z;
  r12c1 = 1.0 / (b1mag * b2mag);
  c1mag = ctmp * r12c1;

  ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z;
  r12c2 = 1.0 / (b2mag * b3mag);
  c2mag = ctmp * r12c2;

  // cos and sin of 2 angles and final c
  sin2 = MAX(1.0 - c1mag * c1mag, 0.0);
  sc1 = sqrt(sin2);
  if (sc1 < SMALL) sc1 = SMALL;
  sc1 = 1.0 / sc1;

  sin2 = MAX(1.0 - c2mag * c2mag, 0.0);
  sc2 = sqrt(sin2);
  if (sc2 < SMALL) sc2 = SMALL;
  sc2 = 1.0 / sc2;

  s12 = sc1 * sc2;
  c = (c0 + c1mag * c2mag) * s12;

  cx = vb1y * vb2z - vb1z * vb2y;
  cy = vb1z * vb2x - vb1x * vb2z;
  cz = vb1x * vb2y - vb1y * vb2x;
  cmag = sqrt(cx * cx + cy * cy + cz * cz);
  dx = (cx * vb3x + cy * vb3y + cz * vb3z) / cmag / b3mag;

  // error check
  if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);

  if (c > 1.0) c = 1.0;
  if (c < -1.0) c = -1.0;

  phi = acos(c);
  if (dx < 0.0) phi *= -1.0;
  si = sin(phi);
  if (fabs(si) < SMALLER) si = SMALLER;

  du = k1[type] - 2.0 * k2[type] * sin(2.0 * phi) / si + 3.0 * k3[type] * sin(3.0 * phi) / si -
      4.0 * k4[type] * sin(4.0 * phi) / si;
  du2 = (4.0 * k2[type] * si * cos(2.0 * phi) - 2.0 * k2[type] * sin(2.0 * phi) -
         9.0 * k3[type] * si * cos(3.0 * phi) + 3.0 * k3[type] * sin(3.0 * phi) +
         16.0 * k4[type] * si * cos(4.0 * phi) - 4.0 * k4[type] * sin(4.0 * phi)) /
      (si * si * si);
}

/* ----------------------------------------------------------------------
   return ptr to internal members upon request
------------------------------------------------------------------------ */

void *DihedralOPLS::extract(const char *str, int &dim)
{
  dim = 1;
  if (strcmp(str, "k1") == 0) return (void *) k1;
  if (strcmp(str, "k2") == 0) return (void *) k2;
  if (strcmp(str, "k3") == 0) return (void *) k3;
  if (strcmp(str, "k4") == 0) return (void *) k4;
  return nullptr;
}
