lammps/src/MOLECULE/bond_fene_expand.cpp

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

#include "bond_fene_expand.h"

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

#include <cmath>

using namespace LAMMPS_NS;
using MathConst::MY_CUBEROOT2;

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

BondFENEExpand::~BondFENEExpand()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(k);
    memory->destroy(r0);
    memory->destroy(epsilon);
    memory->destroy(sigma);
    memory->destroy(shift);
  }
}

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

void BondFENEExpand::compute(int eflag, int vflag)
{
  int i1, i2, n, type;
  double delx, dely, delz, ebond, fbond;
  double rsq, r0sq, rlogarg, sr2, sr6;
  double r, rshift, rshiftsq;

  ebond = sr6 = 0.0;
  ev_init(eflag, vflag);

  double **x = atom->x;
  double **f = atom->f;
  int **bondlist = neighbor->bondlist;
  int nbondlist = neighbor->nbondlist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  for (n = 0; n < nbondlist; n++) {
    i1 = bondlist[n][0];
    i2 = bondlist[n][1];
    type = bondlist[n][2];

    delx = x[i1][0] - x[i2][0];
    dely = x[i1][1] - x[i2][1];
    delz = x[i1][2] - x[i2][2];

    // force from log term

    rsq = delx * delx + dely * dely + delz * delz;
    r = sqrt(rsq);
    rshift = r - shift[type];
    rshiftsq = rshift * rshift;
    r0sq = r0[type] * r0[type];
    rlogarg = 1.0 - rshiftsq / r0sq;

    // if r -> r0, then rlogarg < 0.0 which is an error
    // issue a warning and reset rlogarg = epsilon
    // if r > 2*r0 something serious is wrong, abort

    if (rlogarg < 0.1) {
      error->warning(FLERR, "FENE bond too long: {} {} {} {:.8}", update->ntimestep, atom->tag[i1],
                     atom->tag[i2], sqrt(rsq));
      if (rlogarg <= -3.0) error->one(FLERR, "Bad FENE bond");
      rlogarg = 0.1;
    }

    fbond = -k[type] * rshift / rlogarg / r;

    // force from LJ term

    if (rshiftsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) {
      sr2 = sigma[type] * sigma[type] / rshiftsq;
      sr6 = sr2 * sr2 * sr2;
      fbond += 48.0 * epsilon[type] * sr6 * (sr6 - 0.5) / rshift / r;
    }

    // energy

    if (eflag) {
      ebond = -0.5 * k[type] * r0sq * log(rlogarg);
      if (rshiftsq < MY_CUBEROOT2 * sigma[type] * sigma[type])
        ebond += 4.0 * epsilon[type] * sr6 * (sr6 - 1.0) + epsilon[type];
    }

    // apply force to each of 2 atoms

    if (newton_bond || i1 < nlocal) {
      f[i1][0] += delx * fbond;
      f[i1][1] += dely * fbond;
      f[i1][2] += delz * fbond;
    }

    if (newton_bond || i2 < nlocal) {
      f[i2][0] -= delx * fbond;
      f[i2][1] -= dely * fbond;
      f[i2][2] -= delz * fbond;
    }

    if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
  }
}

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

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

  memory->create(k, np1, "bond:k");
  memory->create(r0, np1, "bond:r0");
  memory->create(epsilon, np1, "bond:epsilon");
  memory->create(sigma, np1, "bond:sigma");
  memory->create(shift, np1, "bond:shift");
  memory->create(setflag, np1, "bond:setflag");
  for (int i = 1; i < np1; i++) setflag[i] = 0;
}

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

void BondFENEExpand::coeff(int narg, char **arg)
{
  if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients");
  if (!allocated) allocate();

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

  double k_one = utils::numeric(FLERR, arg[1], false, lmp);
  double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
  double epsilon_one = utils::numeric(FLERR, arg[3], false, lmp);
  double sigma_one = utils::numeric(FLERR, arg[4], false, lmp);
  double shift_one = utils::numeric(FLERR, arg[5], false, lmp);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    k[i] = k_one;
    r0[i] = r0_one;
    epsilon[i] = epsilon_one;
    sigma[i] = sigma_one;
    shift[i] = shift_one;
    setflag[i] = 1;
    count++;
  }

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

/* ----------------------------------------------------------------------
   check if special_bond settings are valid
------------------------------------------------------------------------- */

void BondFENEExpand::init_style()
{
  // special bonds should be 0 1 1

  if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) {
    if (comm->me == 0)
      error->warning(FLERR, "Use special bonds = 0,1,1 with bond style fene/expand");
  }
}

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

double BondFENEExpand::equilibrium_distance(int i)
{
  return 0.97 * sigma[i] + shift[i];
}

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

void BondFENEExpand::write_restart(FILE *fp)
{
  fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
  fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
  fwrite(&epsilon[1], sizeof(double), atom->nbondtypes, fp);
  fwrite(&sigma[1], sizeof(double), atom->nbondtypes, fp);
  fwrite(&shift[1], sizeof(double), atom->nbondtypes, fp);
}

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

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

  if (comm->me == 0) {
    utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
    utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
    utils::sfread(FLERR, &epsilon[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
    utils::sfread(FLERR, &sigma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
    utils::sfread(FLERR, &shift[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
  }
  MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&epsilon[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&sigma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
  MPI_Bcast(&shift[1], atom->nbondtypes, MPI_DOUBLE, 0, world);

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

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

void BondFENEExpand::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->nbondtypes; i++)
    fprintf(fp, "%d %g %g %g %g %g\n", i, k[i], r0[i], epsilon[i], sigma[i], shift[i]);
}

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

double BondFENEExpand::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
{
  double r = sqrt(rsq);
  double rshift = r - shift[type];
  double rshiftsq = rshift * rshift;
  double r0sq = r0[type] * r0[type];
  double rlogarg = 1.0 - rshiftsq / r0sq;

  // if r -> r0, then rlogarg < 0.0 which is an error
  // issue a warning and reset rlogarg = epsilon
  // if r > 2*r0 something serious is wrong, abort

  if (rlogarg < 0.1) {
    error->warning(FLERR, "FENE bond too long: {} {:.8}", update->ntimestep, sqrt(rsq));
    if (rlogarg <= -3.0) error->one(FLERR, "Bad FENE bond");
    rlogarg = 0.1;
  }

  double eng = -0.5 * k[type] * r0sq * log(rlogarg);
  fforce = -k[type] * rshift / rlogarg / r;
  if (rshiftsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) {
    double sr2, sr6;
    sr2 = sigma[type] * sigma[type] / rshiftsq;
    sr6 = sr2 * sr2 * sr2;
    eng += 4.0 * epsilon[type] * sr6 * (sr6 - 1.0) + epsilon[type];
    fforce += 48.0 * epsilon[type] * sr6 * (sr6 - 0.5) / rshift / r;
  }

  return eng;
}