lammps/examples/plugins/pair_morse2.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 "pair_morse2.h"

#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;

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

PairMorse2::PairMorse2(LAMMPS *lmp) : Pair(lmp)
{
  writedata = 1;
}

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

PairMorse2::~PairMorse2()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);

    memory->destroy(cut);
    memory->destroy(d0);
    memory->destroy(alpha);
    memory->destroy(r0);
    memory->destroy(morse1);
    memory->destroy(offset);
  }
}

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

void PairMorse2::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, r, dr, dexp, factor_lj;
  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]) {
        r = sqrt(rsq);
        dr = r - r0[itype][jtype];
        dexp = exp(-alpha[itype][jtype] * dr);
        fpair = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r;

        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) {
          evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) - offset[itype][jtype];
          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 PairMorse2::allocate()
{
  allocated = 1;
  int n = atom->ntypes;

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

  memory->create(cutsq, n + 1, n + 1, "pair:cutsq");

  memory->create(cut, n + 1, n + 1, "pair:cut");
  memory->create(d0, n + 1, n + 1, "pair:d0");
  memory->create(alpha, n + 1, n + 1, "pair:alpha");
  memory->create(r0, n + 1, n + 1, "pair:r0");
  memory->create(morse1, n + 1, n + 1, "pair:morse1");
  memory->create(offset, n + 1, n + 1, "pair:offset");
}

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

void PairMorse2::settings(int narg, char **arg)
{
  if (narg != 1) error->all(FLERR, "Illegal pair_style command");

  cut_global = utils::numeric(FLERR, arg[0], false, lmp);

  // reset cutoffs that have been explicitly set

  if (allocated) {
    int i, j;
    for (i = 1; i <= atom->ntypes; i++)
      for (j = i; j <= atom->ntypes; j++)
        if (setflag[i][j]) cut[i][j] = cut_global;
  }
}

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

void PairMorse2::coeff(int narg, char **arg)
{
  if (narg < 5 || narg > 6) 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 d0_one = utils::numeric(FLERR, arg[2], false, lmp);
  double alpha_one = utils::numeric(FLERR, arg[3], false, lmp);
  double r0_one = utils::numeric(FLERR, arg[4], false, lmp);

  double cut_one = cut_global;
  if (narg == 6) cut_one = utils::numeric(FLERR, arg[5], false, lmp);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo, i); j <= jhi; j++) {
      d0[i][j] = d0_one;
      alpha[i][j] = alpha_one;
      r0[i][j] = r0_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
      count++;
    }
  }

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

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

double PairMorse2::init_one(int i, int j)
{
  if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");

  morse1[i][j] = 2.0 * d0[i][j] * alpha[i][j];

  if (offset_flag) {
    double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
    offset[i][j] = d0[i][j] * (exp(2.0 * alpha_dr) - 2.0 * exp(alpha_dr));
  } else
    offset[i][j] = 0.0;

  d0[j][i] = d0[i][j];
  alpha[j][i] = alpha[i][j];
  r0[j][i] = r0[i][j];
  morse1[j][i] = morse1[i][j];
  offset[j][i] = offset[i][j];

  return cut[i][j];
}

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

void PairMorse2::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(&d0[i][j], sizeof(double), 1, fp);
        fwrite(&alpha[i][j], sizeof(double), 1, fp);
        fwrite(&r0[i][j], sizeof(double), 1, fp);
        fwrite(&cut[i][j], sizeof(double), 1, fp);
      }
    }
}

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

void PairMorse2::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, &d0[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &alpha[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
        }
        MPI_Bcast(&d0[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&alpha[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
      }
    }
}

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

void PairMorse2::write_restart_settings(FILE *fp)
{
  fwrite(&cut_global, sizeof(double), 1, fp);
  fwrite(&offset_flag, sizeof(int), 1, fp);
  fwrite(&mix_flag, sizeof(int), 1, fp);
}

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

void PairMorse2::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
    utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
    utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
  }
  MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
  MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
  MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
}

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

void PairMorse2::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    fprintf(fp, "%d %g %g %g\n", i, d0[i][i], alpha[i][i], r0[i][i]);
}

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

void PairMorse2::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 %g\n", i, j, d0[i][j], alpha[i][j], r0[i][j], cut[i][j]);
}

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

double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
                          double /*factor_coul*/, double factor_lj, double &fforce)
{
  double r, dr, dexp, phi;

  r = sqrt(rsq);
  dr = r - r0[itype][jtype];
  dexp = exp(-alpha[itype][jtype] * dr);
  fforce = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r;

  phi = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) - offset[itype][jtype];
  return factor_lj * phi;
}

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

void *PairMorse2::extract(const char *str, int &dim)
{
  dim = 2;
  if (strcmp(str, "d0") == 0) return (void *) d0;
  if (strcmp(str, "r0") == 0) return (void *) r0;
  if (strcmp(str, "alpha") == 0) return (void *) alpha;
  return nullptr;
}