/* ----------------------------------------------------------------------
   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: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */

#include "angle_table.h"

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

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;
using MathConst::DEG2RAD;
using MathConst::MY_PI;
using MathConst::RAD2DEG;

enum { LINEAR, SPLINE };

static constexpr double SMALL = 0.001;
static constexpr double TINY = 1.E-10;

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

AngleTable::AngleTable(LAMMPS *_lmp) : Angle(_lmp)
{
  writedata = 0;
  ntables = 0;
  tables = nullptr;
}

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

AngleTable::~AngleTable()
{
  for (int m = 0; m < ntables; m++) free_table(&tables[m]);
  memory->sfree(tables);

  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(theta0);
    memory->destroy(tabindex);
  }
}

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

void AngleTable::compute(int eflag, int vflag)
{
  int i1, i2, i3, n, type;
  double eangle, f1[3], f3[3];
  double delx1, dely1, delz1, delx2, dely2, delz2;
  double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
  double theta, u, mdu;    //mdu: minus du, -du/dx=f

  eangle = 0.0;
  ev_init(eflag, vflag);

  double **x = atom->x;
  double **f = atom->f;
  int **anglelist = neighbor->anglelist;
  int nanglelist = neighbor->nanglelist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  for (n = 0; n < nanglelist; n++) {
    i1 = anglelist[n][0];
    i2 = anglelist[n][1];
    i3 = anglelist[n][2];
    type = anglelist[n][3];

    // 1st bond

    delx1 = x[i1][0] - x[i2][0];
    dely1 = x[i1][1] - x[i2][1];
    delz1 = x[i1][2] - x[i2][2];

    rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
    r1 = sqrt(rsq1);

    // 2nd bond

    delx2 = x[i3][0] - x[i2][0];
    dely2 = x[i3][1] - x[i2][1];
    delz2 = x[i3][2] - x[i2][2];

    rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
    r2 = sqrt(rsq2);

    // angle (cos and sin)

    c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
    c /= r1 * r2;

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

    s = sqrt(1.0 - c * c);
    if (s < SMALL) s = SMALL;
    s = 1.0 / s;

    // tabulated force & energy

    theta = acos(c);
    uf_lookup(type, theta, u, mdu);

    if (eflag) eangle = u;

    a = mdu * s;
    a11 = a * c / rsq1;
    a12 = -a / (r1 * r2);
    a22 = a * c / rsq2;

    f1[0] = a11 * delx1 + a12 * delx2;
    f1[1] = a11 * dely1 + a12 * dely2;
    f1[2] = a11 * delz1 + a12 * delz2;
    f3[0] = a22 * delx2 + a12 * delx1;
    f3[1] = a22 * dely2 + a12 * dely1;
    f3[2] = a22 * delz2 + a12 * delz1;

    // apply force to each of 3 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] -= f1[0] + f3[0];
      f[i2][1] -= f1[1] + f3[1];
      f[i2][2] -= f1[2] + f3[2];
    }

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

    if (evflag)
      ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
               delz2);
  }
}

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

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

  memory->create(theta0, np1, "angle:theta0");
  memory->create(tabindex, np1, "angle:tabindex");

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

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

void AngleTable::settings(int narg, char **arg)
{
  if (narg != 2) error->all(FLERR, "Illegal angle_style command: must have 2 arguments");

  if (strcmp(arg[0], "linear") == 0)
    tabstyle = LINEAR;
  else if (strcmp(arg[0], "spline") == 0)
    tabstyle = SPLINE;
  else
    error->all(FLERR, "Unknown table style {} in angle style table", arg[0]);

  tablength = utils::inumeric(FLERR, arg[1], false, lmp);
  if (tablength < 2) error->all(FLERR, "Illegal number of angle table entries: {}", arg[1]);

  // delete old tables, since cannot just change settings

  for (int m = 0; m < ntables; m++) free_table(&tables[m]);
  memory->sfree(tables);

  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(tabindex);
  }
  allocated = 0;

  ntables = 0;
  tables = nullptr;
}

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

void AngleTable::coeff(int narg, char **arg)
{
  if (narg != 3) error->all(FLERR, "Illegal angle_coeff command: must have 3 arguments");
  if (!allocated) allocate();

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

  int me;
  MPI_Comm_rank(world, &me);
  tables = (Table *) memory->srealloc(tables, (ntables + 1) * sizeof(Table), "angle:tables");
  Table *tb = &tables[ntables];
  null_table(tb);
  if (me == 0) read_table(tb, arg[1], arg[2]);
  bcast_table(tb);

  // error check on table parameters

  if (tb->ninput <= 1) error->one(FLERR, "Invalid angle table length: {}", tb->ninput);

  double alo, ahi;
  alo = tb->afile[0];
  ahi = tb->afile[tb->ninput - 1];
  if (fabs(alo - 0.0) > TINY || fabs(ahi - 180.0) > TINY)
    error->all(FLERR, "Angle table must range from 0 to 180 degrees");

  // convert theta from degrees to radians

  for (int i = 0; i < tb->ninput; i++) {
    tb->afile[i] *= DEG2RAD;
    tb->ffile[i] *= RAD2DEG;
  }

  // spline read-in and compute a,e,f vectors within table

  spline_table(tb);
  compute_table(tb);

  // store ptr to table in tabindex

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    tabindex[i] = ntables;
    setflag[i] = 1;
    theta0[i] = tb->theta0;
    count++;
  }
  ntables++;

  if (count == 0) error->all(FLERR, "Illegal angle_coeff command");
}

/* ----------------------------------------------------------------------
   return an equilbrium angle length
   should not be used, since don't know minimum of tabulated function
------------------------------------------------------------------------- */

double AngleTable::equilibrium_angle(int i)
{
  return theta0[i];
}

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

void AngleTable::write_restart(FILE *fp)
{
  write_restart_settings(fp);
}

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

void AngleTable::read_restart(FILE *fp)
{
  read_restart_settings(fp);
  allocate();
}

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

void AngleTable::write_restart_settings(FILE *fp)
{
  fwrite(&tabstyle, sizeof(int), 1, fp);
  fwrite(&tablength, sizeof(int), 1, fp);
}

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

void AngleTable::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    utils::sfread(FLERR, &tabstyle, sizeof(int), 1, fp, nullptr, error);
    utils::sfread(FLERR, &tablength, sizeof(int), 1, fp, nullptr, error);
  }
  MPI_Bcast(&tabstyle, 1, MPI_INT, 0, world);
  MPI_Bcast(&tablength, 1, MPI_INT, 0, world);
}

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

double AngleTable::single(int type, int i1, int i2, int i3)
{
  double **x = atom->x;

  double delx1 = x[i1][0] - x[i2][0];
  double dely1 = x[i1][1] - x[i2][1];
  double delz1 = x[i1][2] - x[i2][2];
  domain->minimum_image(FLERR, delx1, dely1, delz1);
  double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);

  double delx2 = x[i3][0] - x[i2][0];
  double dely2 = x[i3][1] - x[i2][1];
  double delz2 = x[i3][2] - x[i2][2];
  domain->minimum_image(FLERR, delx2, dely2, delz2);
  double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);

  double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
  c /= r1 * r2;
  if (c > 1.0) c = 1.0;
  if (c < -1.0) c = -1.0;

  double theta = acos(c);
  double u = 0.0;
  u_lookup(type, theta, u);
  return u;
}

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

void AngleTable::null_table(Table *tb)
{
  tb->afile = tb->efile = tb->ffile = nullptr;
  tb->e2file = tb->f2file = nullptr;
  tb->ang = tb->e = tb->de = nullptr;
  tb->f = tb->df = tb->e2 = tb->f2 = nullptr;
}

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

void AngleTable::free_table(Table *tb)
{
  memory->destroy(tb->afile);
  memory->destroy(tb->efile);
  memory->destroy(tb->ffile);
  memory->destroy(tb->e2file);
  memory->destroy(tb->f2file);

  memory->destroy(tb->ang);
  memory->destroy(tb->e);
  memory->destroy(tb->de);
  memory->destroy(tb->f);
  memory->destroy(tb->df);
  memory->destroy(tb->e2);
  memory->destroy(tb->f2);
}

/* ----------------------------------------------------------------------
   read table file, only called by proc 0
------------------------------------------------------------------------- */

void AngleTable::read_table(Table *tb, char *file, char *keyword)
{
  TableFileReader reader(lmp, file, "angle");

  char *line = reader.find_section_start(keyword);

  if (!line) error->one(FLERR, "Did not find keyword {} in table file", keyword);

  // read args on 2nd line of section
  // allocate table arrays for file values

  line = reader.next_line();
  param_extract(tb, line);
  memory->create(tb->afile, tb->ninput, "angle:afile");
  memory->create(tb->efile, tb->ninput, "angle:efile");
  memory->create(tb->ffile, tb->ninput, "angle:ffile");

  // read a,e,f table values from file

  reader.skip_line();
  for (int i = 0; i < tb->ninput; i++) {
    line = reader.next_line();
    if (!line)
      error->one(FLERR, "Data missing when parsing angle table '{}' line {} of {}.", keyword, i + 1,
                 tb->ninput);
    try {
      ValueTokenizer values(line);
      values.next_int();
      tb->afile[i] = values.next_double();
      tb->efile[i] = values.next_double();
      tb->ffile[i] = values.next_double();
    } catch (TokenizerException &e) {
      error->one(FLERR, "Error parsing angle table '{}' line {} of {}. {}\nLine was: {}", keyword,
                 i + 1, tb->ninput, e.what(), line);
    }
  }
}

/* ----------------------------------------------------------------------
   build spline representation of e,f over entire range of read-in table
   this function sets these values in e2file,f2file
------------------------------------------------------------------------- */

void AngleTable::spline_table(Table *tb)
{
  memory->create(tb->e2file, tb->ninput, "angle:e2file");
  memory->create(tb->f2file, tb->ninput, "angle:f2file");

  double ep0 = -tb->ffile[0];
  double epn = -tb->ffile[tb->ninput - 1];
  spline(tb->afile, tb->efile, tb->ninput, ep0, epn, tb->e2file);

  if (tb->fpflag == 0) {
    tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->afile[1] - tb->afile[0]);
    tb->fphi = (tb->ffile[tb->ninput - 1] - tb->ffile[tb->ninput - 2]) /
        (tb->afile[tb->ninput - 1] - tb->afile[tb->ninput - 2]);
  }

  double fp0 = tb->fplo;
  double fpn = tb->fphi;
  spline(tb->afile, tb->ffile, tb->ninput, fp0, fpn, tb->f2file);
}

/* ----------------------------------------------------------------------
   compute a,e,f vectors from splined values
------------------------------------------------------------------------- */

void AngleTable::compute_table(Table *tb)
{
  // delta = table spacing in angle for N-1 bins

  int tlm1 = tablength - 1;
  tb->delta = MY_PI / tlm1;
  tb->invdelta = 1.0 / tb->delta;
  tb->deltasq6 = tb->delta * tb->delta / 6.0;

  // N-1 evenly spaced bins in angle from 0 to PI
  // ang,e,f = value at lower edge of bin
  // de,df values = delta values of e,f
  // ang,e,f are N in length so de,df arrays can compute difference

  memory->create(tb->ang, tablength, "angle:ang");
  memory->create(tb->e, tablength, "angle:e");
  memory->create(tb->de, tablength, "angle:de");
  memory->create(tb->f, tablength, "angle:f");
  memory->create(tb->df, tablength, "angle:df");
  memory->create(tb->e2, tablength, "angle:e2");
  memory->create(tb->f2, tablength, "angle:f2");

  double a;
  for (int i = 0; i < tablength; i++) {
    a = i * tb->delta;
    tb->ang[i] = a;
    tb->e[i] = splint(tb->afile, tb->efile, tb->e2file, tb->ninput, a);
    tb->f[i] = splint(tb->afile, tb->ffile, tb->f2file, tb->ninput, a);
  }

  for (int i = 0; i < tlm1; i++) {
    tb->de[i] = tb->e[i + 1] - tb->e[i];
    tb->df[i] = tb->f[i + 1] - tb->f[i];
  }
  // get final elements from linear extrapolation
  tb->de[tlm1] = 2.0 * tb->de[tlm1 - 1] - tb->de[tlm1 - 2];
  tb->df[tlm1] = 2.0 * tb->df[tlm1 - 1] - tb->df[tlm1 - 2];

  double ep0 = -tb->f[0];
  double epn = -tb->f[tlm1];
  spline(tb->ang, tb->e, tablength, ep0, epn, tb->e2);
  spline(tb->ang, tb->f, tablength, tb->fplo, tb->fphi, tb->f2);
}

/* ----------------------------------------------------------------------
   extract attributes from parameter line in table section
   format of line: N value FP fplo fphi EQ theta0
   N is required, other params are optional
------------------------------------------------------------------------- */

void AngleTable::param_extract(Table *tb, char *line)
{
  tb->ninput = 0;
  tb->fpflag = 0;
  tb->theta0 = MY_PI;

  try {
    ValueTokenizer values(line);

    while (values.has_next()) {
      std::string word = values.next_string();

      if (word == "N") {
        tb->ninput = values.next_int();
      } else if (word == "FP") {
        tb->fpflag = 1;
        tb->fplo = values.next_double();
        tb->fphi = values.next_double();
        tb->fplo *= RAD2DEG * RAD2DEG;
        tb->fphi *= RAD2DEG * RAD2DEG;
      } else if (word == "EQ") {
        tb->theta0 = DEG2RAD * values.next_double();
      } else {
        error->one(FLERR, "Unknown keyword {} in angle table parameters", word);
      }
    }
  } catch (TokenizerException &e) {
    error->one(FLERR, e.what());
  }

  if (tb->ninput == 0) error->one(FLERR, "Angle table parameters did not set N");
}

/* ----------------------------------------------------------------------
   broadcast read-in table info from proc 0 to other procs
   this function communicates these values in Table:
     ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0
------------------------------------------------------------------------- */

void AngleTable::bcast_table(Table *tb)
{
  MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world);

  int me;
  MPI_Comm_rank(world, &me);
  if (me > 0) {
    memory->create(tb->afile, tb->ninput, "angle:afile");
    memory->create(tb->efile, tb->ninput, "angle:efile");
    memory->create(tb->ffile, tb->ninput, "angle:ffile");
  }

  MPI_Bcast(tb->afile, tb->ninput, MPI_DOUBLE, 0, world);
  MPI_Bcast(tb->efile, tb->ninput, MPI_DOUBLE, 0, world);
  MPI_Bcast(tb->ffile, tb->ninput, MPI_DOUBLE, 0, world);

  MPI_Bcast(&tb->fpflag, 1, MPI_INT, 0, world);
  if (tb->fpflag) {
    MPI_Bcast(&tb->fplo, 1, MPI_DOUBLE, 0, world);
    MPI_Bcast(&tb->fphi, 1, MPI_DOUBLE, 0, world);
  }
  MPI_Bcast(&tb->theta0, 1, MPI_DOUBLE, 0, world);
}

/* ----------------------------------------------------------------------
   spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */

void AngleTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2)
{
  int i, k;
  double p, qn, sig, un;
  auto *u = new double[n];

  if (yp1 > 0.99e300)
    y2[0] = u[0] = 0.0;
  else {
    y2[0] = -0.5;
    u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1);
  }
  for (i = 1; i < n - 1; i++) {
    sig = (x[i] - x[i - 1]) / (x[i + 1] - x[i - 1]);
    p = sig * y2[i - 1] + 2.0;
    y2[i] = (sig - 1.0) / p;
    u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]);
    u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p;
  }
  if (ypn > 0.99e300)
    qn = un = 0.0;
  else {
    qn = 0.5;
    un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2]));
  }
  y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0);
  for (k = n - 2; k >= 0; k--) y2[k] = y2[k] * y2[k + 1] + u[k];

  delete[] u;
}

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

double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x)
{
  int klo, khi, k;
  double h, b, a, y;

  klo = 0;
  khi = n - 1;
  while (khi - klo > 1) {
    k = (khi + klo) >> 1;
    if (xa[k] > x)
      khi = k;
    else
      klo = k;
  }
  h = xa[khi] - xa[klo];
  a = (xa[khi] - x) / h;
  b = (x - xa[klo]) / h;
  y = a * ya[klo] + b * ya[khi] +
      ((a * a * a - a) * y2a[klo] + (b * b * b - b) * y2a[khi]) * (h * h) / 6.0;
  return y;
}

/* ----------------------------------------------------------------------
   calculate potential u and force f at angle x
------------------------------------------------------------------------- */

void AngleTable::uf_lookup(int type, double x, double &u, double &f)
{
  if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); }

  double fraction, a, b;
  const Table *tb = &tables[tabindex[type]];

  // invdelta is based on tablength-1
  int itable = static_cast<int>(x * tb->invdelta);
  if (itable < 0) itable = 0;
  if (itable >= tablength) itable = tablength - 1;

  if (tabstyle == LINEAR) {
    fraction = (x - tb->ang[itable]) * tb->invdelta;
    u = tb->e[itable] + fraction * tb->de[itable];
    f = tb->f[itable] + fraction * tb->df[itable];
  } else if (tabstyle == SPLINE) {
    fraction = (x - tb->ang[itable]) * tb->invdelta;

    b = (x - tb->ang[itable]) * tb->invdelta;
    a = 1.0 - b;
    u = a * tb->e[itable] + b * tb->e[itable + 1] +
        ((a * a * a - a) * tb->e2[itable] + (b * b * b - b) * tb->e2[itable + 1]) * tb->deltasq6;
    f = a * tb->f[itable] + b * tb->f[itable + 1] +
        ((a * a * a - a) * tb->f2[itable] + (b * b * b - b) * tb->f2[itable + 1]) * tb->deltasq6;
  }
}

/* ----------------------------------------------------------------------
   calculate potential u at angle x
------------------------------------------------------------------------- */

void AngleTable::u_lookup(int type, double x, double &u)
{
  if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); }

  double fraction, a, b;
  const Table *tb = &tables[tabindex[type]];
  int itable = static_cast<int>(x * tb->invdelta);

  if (itable < 0) itable = 0;
  if (itable >= tablength) itable = tablength - 1;

  if (tabstyle == LINEAR) {
    fraction = (x - tb->ang[itable]) * tb->invdelta;
    u = tb->e[itable] + fraction * tb->de[itable];
  } else if (tabstyle == SPLINE) {
    fraction = (x - tb->ang[itable]) * tb->invdelta;

    b = (x - tb->ang[itable]) * tb->invdelta;
    a = 1.0 - b;
    u = a * tb->e[itable] + b * tb->e[itable + 1] +
        ((a * a * a - a) * tb->e2[itable] + (b * b * b - b) * tb->e2[itable + 1]) * tb->deltasq6;
  }
}
