lammps/src/EXTRA-PAIR/pair_lj_cubic.cpp

/* ----------------------------------------------------------------------
   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: Aidan Thompson (SNL)
------------------------------------------------------------------------- */

#include "pair_lj_cubic.h"

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

#include <cmath>

#include "pair_lj_cubic_const.h"

using namespace LAMMPS_NS;
using namespace PairLJCubicConstants;

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

PairLJCubic::PairLJCubic(LAMMPS *_lmp) : Pair(_lmp) {}

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

PairLJCubic::~PairLJCubic()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);

    memory->destroy(cut);
    memory->destroy(cut_inner);
    memory->destroy(cut_inner_sq);
    memory->destroy(epsilon);
    memory->destroy(sigma);
    memory->destroy(lj1);
    memory->destroy(lj2);
    memory->destroy(lj3);
    memory->destroy(lj4);
  }
}

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

void PairLJCubic::compute(int eflag, int vflag)
{
  int i, j, ii, jj, inum, jnum, itype, jtype;
  double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
  double rsq, r2inv, r6inv, forcelj, factor_lj;
  double r, t, rmin;
  int *ilist, *jlist, *numneigh, **firstneigh;

  evdwl = 0.0;
  ev_init(eflag, vflag);

  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  inum = list->inum;
  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

  // loop over neighbors of my atoms

  for (ii = 0; ii < inum; ii++) {
    i = ilist[ii];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    jlist = firstneigh[i];
    jnum = numneigh[i];

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      factor_lj = special_lj[sbmask(j)];
      j &= NEIGHMASK;

      delx = xtmp - x[j][0];
      dely = ytmp - x[j][1];
      delz = ztmp - x[j][2];
      rsq = delx * delx + dely * dely + delz * delz;
      jtype = type[j];

      if (rsq < cutsq[itype][jtype]) {
        r2inv = 1.0 / rsq;
        if (rsq <= cut_inner_sq[itype][jtype]) {
          r6inv = r2inv * r2inv * r2inv;
          forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
        } else {
          r = sqrt(rsq);
          rmin = sigma[itype][jtype] * RT6TWO;
          t = (r - cut_inner[itype][jtype]) / rmin;
          forcelj = epsilon[itype][jtype] * (-DPHIDS + A3 * t * t / 2.0) * r / rmin;
        }
        fpair = factor_lj * forcelj * r2inv;

        f[i][0] += delx * fpair;
        f[i][1] += dely * fpair;
        f[i][2] += delz * fpair;
        if (newton_pair || j < nlocal) {
          f[j][0] -= delx * fpair;
          f[j][1] -= dely * fpair;
          f[j][2] -= delz * fpair;
        }

        if (eflag) {
          if (rsq <= cut_inner_sq[itype][jtype])
            evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]);
          else
            evdwl = epsilon[itype][jtype] * (PHIS + DPHIDS * t - A3 * t * t * t / 6.0);
          evdwl *= factor_lj;

          if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
        }
      }
    }
  }

  if (vflag_fdotr) virial_fdotr_compute();
}

/* ----------------------------------------------------------------------
   allocate all arrays
------------------------------------------------------------------------- */

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

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

  memory->create(cutsq, np1, np1, "pair:cutsq");

  memory->create(cut, np1, np1, "pair:cut");
  memory->create(cut_inner, np1, np1, "pair:cut_inner");
  memory->create(cut_inner_sq, np1, np1, "pair:cut_inner_sq");
  memory->create(epsilon, np1, np1, "pair:epsilon");
  memory->create(sigma, np1, np1, "pair:sigma");
  memory->create(lj1, np1, np1, "pair:lj1");
  memory->create(lj2, np1, np1, "pair:lj2");
  memory->create(lj3, np1, np1, "pair:lj3");
  memory->create(lj4, np1, np1, "pair:lj4");
}

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

void PairLJCubic::settings(int narg, char ** /*arg*/)
{
  if (narg != 0) error->all(FLERR, "Illegal pair_style command");

  // NOTE: lj/cubic has no global cutoff. instead the cutoff is
  // inferred from the lj parameters. so we must not reset cutoffs here.
}

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

void PairLJCubic::coeff(int narg, char **arg)
{
  if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients" + utils::errorurl(21));
  if (!allocated) allocate();

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

  double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
  double sigma_one = utils::numeric(FLERR, arg[3], false, lmp);
  double rmin = sigma_one * RT6TWO;

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo, i); j <= jhi; j++) {
      epsilon[i][j] = epsilon_one;
      sigma[i][j] = sigma_one;
      cut_inner[i][j] = rmin * SS;
      cut[i][j] = rmin * SM;
      setflag[i][j] = 1;
      count++;
    }
  }

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

/* ----------------------------------------------------------------------
   init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

double PairLJCubic::init_one(int i, int j)
{
  if (setflag[i][j] == 0) {
    epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]);
    sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]);
    cut_inner[i][j] = mix_distance(cut_inner[i][i], cut_inner[j][j]);
    cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
  }

  cut_inner_sq[i][j] = cut_inner[i][j] * cut_inner[i][j];
  lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
  lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
  lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
  lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);

  cut_inner[j][i] = cut_inner[i][j];
  cut_inner_sq[j][i] = cut_inner_sq[i][j];
  epsilon[j][i] = epsilon[i][j];
  sigma[j][i] = sigma[i][j];
  lj1[j][i] = lj1[i][j];
  lj2[j][i] = lj2[i][j];
  lj3[j][i] = lj3[i][j];
  lj4[j][i] = lj4[i][j];

  return cut[i][j];
}

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

void PairLJCubic::write_restart(FILE *fp)
{
  write_restart_settings(fp);

  int i, j;
  for (i = 1; i <= atom->ntypes; i++)
    for (j = i; j <= atom->ntypes; j++) {
      fwrite(&setflag[i][j], sizeof(int), 1, fp);
      if (setflag[i][j]) {
        fwrite(&epsilon[i][j], sizeof(double), 1, fp);
        fwrite(&sigma[i][j], sizeof(double), 1, fp);
        fwrite(&cut_inner[i][j], sizeof(double), 1, fp);
        fwrite(&cut[i][j], sizeof(double), 1, fp);
      }
    }
}

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

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

  int i, j;
  int me = comm->me;
  for (i = 1; i <= atom->ntypes; i++)
    for (j = i; j <= atom->ntypes; j++) {
      if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
      MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
      if (setflag[i][j]) {
        if (me == 0) {
          utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &cut_inner[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
        }
        MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&cut_inner[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
      }
    }
}

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

void PairLJCubic::write_restart_settings(FILE *fp)
{
  fwrite(&mix_flag, sizeof(int), 1, fp);
}

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

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

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

double PairLJCubic::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
                           double /*factor_coul*/, double factor_lj, double &fforce)
{
  double r2inv, r6inv, forcelj, philj;
  double r, t;
  double rmin;

  // this is a truncated potential with an implicit cutoff

  if (rsq >= cutsq[itype][jtype]) {
    fforce = 0.0;
    return 0.0;
  }

  r2inv = 1.0 / rsq;
  if (rsq <= cut_inner_sq[itype][jtype]) {
    r6inv = r2inv * r2inv * r2inv;
    forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
  } else {
    r = sqrt(rsq);
    rmin = sigma[itype][jtype] * RT6TWO;
    t = (r - cut_inner[itype][jtype]) / rmin;
    forcelj = epsilon[itype][jtype] * (-DPHIDS + A3 * t * t / 2.0) * r / rmin;
  }
  fforce = factor_lj * forcelj * r2inv;

  if (rsq <= cut_inner_sq[itype][jtype])
    philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]);
  else
    philj = epsilon[itype][jtype] * (PHIS + DPHIDS * t - A3 * t * t * t / 6.0);

  return factor_lj * philj;
}

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

void *PairLJCubic::extract(const char *str, int &dim)
{
  dim = 2;
  if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
  if (strcmp(str, "sigma") == 0) return (void *) sigma;
  return nullptr;
}