lammps/src/RHEO/pair_rheo_solid.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 authors:
   Joel Clemmer (SNL)
----------------------------------------------------------------------- */

#include "pair_rheo_solid.h"

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

#include <cmath>

using namespace LAMMPS_NS;
using namespace RHEO_NS;

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

PairRHEOSolid::PairRHEOSolid(LAMMPS *_lmp) : Pair(_lmp)
{
  writedata = 1;
}

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

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

    memory->destroy(k);
    memory->destroy(cut);
    memory->destroy(gamma);
  }
}

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

void PairRHEOSolid::compute(int eflag, int vflag)
{
  int i, j, ii, jj, inum, jnum, itype, jtype;
  double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
  double r, rsq, rinv, factor_lj;
  int *ilist, *jlist, *numneigh, **firstneigh;
  double vxtmp, vytmp, vztmp, delvx, delvy, delvz, dot, smooth;

  evdwl = 0.0;
  if (eflag || vflag)
    ev_setup(eflag, vflag);
  else
    evflag = vflag_fdotr = 0;

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

  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];
    if (!(status[i] & STATUS_SOLID)) continue;

    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    vxtmp = v[i][0];
    vytmp = v[i][1];
    vztmp = v[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)];
      if (factor_lj == 0) continue;
      j &= NEIGHMASK;

      if (!(status[j] & STATUS_SOLID)) continue;

      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]) {
        r = sqrt(rsq);

        rinv = 1.0 / r;
        fpair = k[itype][jtype] * (cut[itype][jtype] - r);

        smooth = rsq / cutsq[itype][jtype];
        smooth *= smooth;
        smooth *= smooth;
        smooth = 1.0 - smooth;
        delvx = vxtmp - v[j][0];
        delvy = vytmp - v[j][1];
        delvz = vztmp - v[j][2];
        dot = delx * delvx + dely * delvy + delz * delvz;
        fpair -= gamma[itype][jtype] * dot * smooth * rinv;

        fpair *= factor_lj * rinv;
        if (eflag) evdwl = 0.0;

        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 (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 PairRHEOSolid::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(k, np1, np1, "pair:k");
  memory->create(cut, np1, np1, "pair:cut");
  memory->create(gamma, np1, np1, "pair:gamma");
}

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

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

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

void PairRHEOSolid::coeff(int narg, char **arg)
{
  if (narg != 5) error->all(FLERR, "Incorrect args for pair coefficients");
  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 k_one = utils::numeric(FLERR, arg[2], false, lmp);
  double cut_one = utils::numeric(FLERR, arg[3], false, lmp);
  double gamma_one = utils::numeric(FLERR, arg[4], false, lmp);

  if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients");

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo, i); j <= jhi; j++) {
      k[i][j] = k_one;
      cut[i][j] = cut_one;
      gamma[i][j] = gamma_one;

      setflag[i][j] = 1;
      count++;
    }
  }

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

/* ----------------------------------------------------------------------
   init specific to this pair style
------------------------------------------------------------------------- */

void PairRHEOSolid::init_style()
{
  if (comm->ghost_velocity == 0)
    error->all(FLERR,"Pair rheo/solid requires ghost atoms store velocity");

  if (!atom->status_flag)
    error->all(FLERR,"Pair rheo/solid requires atom_style rheo");

  neighbor->add_request(this);
}


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

double PairRHEOSolid::init_one(int i, int j)
{
  if (setflag[i][j] == 0) {
    cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
    k[i][j] = mix_energy(k[i][i], k[j][j], cut[i][i], cut[j][j]);
    gamma[i][j] = mix_energy(gamma[i][i], gamma[j][j], cut[i][i], cut[j][j]);
  }

  cut[j][i] = cut[i][j];
  k[j][i] = k[i][j];
  gamma[j][i] = gamma[i][j];

  return cut[i][j];
}

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

void PairRHEOSolid::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(&k[i][j], sizeof(double), 1, fp);
        fwrite(&cut[i][j], sizeof(double), 1, fp);
        fwrite(&gamma[i][j], sizeof(double), 1, fp);
      }
    }
}

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

void PairRHEOSolid::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, &k[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &gamma[i][j], sizeof(double), 1, fp, nullptr, error);
        }
        MPI_Bcast(&k[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&gamma[i][j], 1, MPI_DOUBLE, 0, world);
      }
    }
}

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

void PairRHEOSolid::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    fprintf(fp, "%d %g %g %g\n", i, k[i][i], cut[i][i], gamma[i][i]);
}

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

void PairRHEOSolid::write_data_all(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    for (int j = i; j <= atom->ntypes; j++)
      fprintf(fp, "%d %d %g %g %g\n", i, j, k[i][j], cut[i][j], gamma[i][j]);
}

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

double PairRHEOSolid::single(int i, int j, int itype, int jtype, double rsq, double /*factor_coul*/,
                             double factor_lj, double &fforce)
{
  double fpair, r, rinv;
  double delx, dely, delz, delvx, delvy, delvz, dot, smooth;

  if (rsq > cutsq[itype][jtype]) return 0.0;

  double **x = atom->x;
  double **v = atom->v;

  r = sqrt(rsq);
  rinv = 1.0 / r;

  fpair = k[itype][jtype] * (cut[itype][jtype] - r);

  smooth = rsq / cutsq[itype][jtype];
  smooth *= smooth;
  smooth = 1.0 - smooth;
  delx = x[i][0] - x[j][0];
  dely = x[i][1] - x[j][1];
  delz = x[i][2] - x[j][2];
  delvx = v[i][0] - v[j][0];
  delvy = v[i][1] - v[j][1];
  delvz = v[i][2] - v[j][2];
  dot = delx * delvx + dely * delvy + delz * delvz;
  fpair -= gamma[itype][jtype] * dot * rinv * smooth;

  fpair *= factor_lj;
  fforce = fpair;

  return 0.0;
}