lammps/src/pair_zbl.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.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing authors: Stephen Foiles, Aidan Thompson (SNL)
------------------------------------------------------------------------- */

#include "pair_zbl.h"

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

#include "pair_zbl_const.h"

#include <cmath>

// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.

using namespace LAMMPS_NS;
using namespace PairZBLConstants;

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

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

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

PairZBL::~PairZBL()
{
  if (copymode) return;

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

    memory->destroy(z);
    memory->destroy(d1a);
    memory->destroy(d2a);
    memory->destroy(d3a);
    memory->destroy(d4a);
    memory->destroy(zze);
    memory->destroy(sw1);
    memory->destroy(sw2);
    memory->destroy(sw3);
    memory->destroy(sw4);
    memory->destroy(sw5);
  }
}

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

void PairZBL::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, t, fswitch, eswitch;
  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;
  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];
      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 < cut_globalsq) {
        r = sqrt(rsq);
        fpair = dzbldr(r, itype, jtype);

        if (rsq > cut_innersq) {
          t = r - cut_inner;
          fswitch = t * t * (sw1[itype][jtype] + sw2[itype][jtype] * t);
          fpair += fswitch;
        }

        fpair *= -1.0 / 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 = e_zbl(r, itype, jtype);
          evdwl += sw5[itype][jtype];
          if (rsq > cut_innersq) {
            eswitch = t * t * t * (sw3[itype][jtype] + sw4[itype][jtype] * t);
            evdwl += eswitch;
          }
        }

        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 PairZBL::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(z, np1, "pair:z");
  memory->create(d1a, np1, np1, "pair:d1a");
  memory->create(d2a, np1, np1, "pair:d2a");
  memory->create(d3a, np1, np1, "pair:d3a");
  memory->create(d4a, np1, np1, "pair:d4a");
  memory->create(zze, np1, np1, "pair:zze");
  memory->create(sw1, np1, np1, "pair:sw1");
  memory->create(sw2, np1, np1, "pair:sw2");
  memory->create(sw3, np1, np1, "pair:sw3");
  memory->create(sw4, np1, np1, "pair:sw4");
  memory->create(sw5, np1, np1, "pair:sw5");
}

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

void PairZBL::settings(int narg, char **arg)
{
  if (narg != 2) error->all(FLERR, "Illegal pair_style command");

  cut_inner = utils::numeric(FLERR, arg[0], false, lmp);
  cut_global = utils::numeric(FLERR, arg[1], false, lmp);

  if (cut_inner <= 0.0) error->all(FLERR, "Illegal pair_style command");
  if (cut_inner > cut_global) error->all(FLERR, "Illegal pair_style command");
}

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

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

void PairZBL::coeff(int narg, char **arg)
{
  double z_one, z_two;

  if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients");
  if (!allocated) allocate();

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

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

  z_one = utils::numeric(FLERR, arg[2], false, lmp);
  z_two = utils::numeric(FLERR, arg[3], false, lmp);

  // set flag for each i-j pair
  // set z-parameter only for i-i pairs

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo, i); j <= jhi; j++) {
      if (i == j) {
        if (z_one != z_two) error->all(FLERR, "Incorrect args for pair coefficients");
        z[i] = z_one;
      }
      setflag[i][j] = 1;
      set_coeff(i, j, z_one, z_two);
      count++;
    }
  }

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

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

void PairZBL::init_style()
{
  neighbor->add_request(this);

  cut_innersq = cut_inner * cut_inner;
  cut_globalsq = cut_global * cut_global;
}

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

double PairZBL::init_one(int i, int j)
{
  if (setflag[i][j] == 0) set_coeff(i, j, z[i], z[j]);

  return cut_global;
}

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

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

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

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

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

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

  for (i = 1; i <= atom->ntypes; i++)
    for (j = 1; j <= atom->ntypes; j++) set_coeff(i, j, z[i], z[j]);
}

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

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

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

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

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

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

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

void PairZBL::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\n", i, j, z[i], z[j]);
}

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

double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double /*dummy1*/,
                       double /*dummy2*/, double &fforce)
{
  double phi, r, t, eswitch, fswitch;

  r = sqrt(rsq);
  fforce = dzbldr(r, itype, jtype);
  if (rsq > cut_innersq) {
    t = r - cut_inner;
    fswitch = t * t * (sw1[itype][jtype] + sw2[itype][jtype] * t);
    fforce += fswitch;
  }
  fforce *= -1.0 / r;

  phi = e_zbl(r, itype, jtype);
  phi += sw5[itype][jtype];
  if (rsq > cut_innersq) {
    eswitch = t * t * t * (sw3[itype][jtype] + sw4[itype][jtype] * t);
    phi += eswitch;
  }

  return phi;
}

/* ----------------------------------------------------------------------
   compute ZBL pair energy
------------------------------------------------------------------------- */

double PairZBL::e_zbl(double r, int i, int j)
{

  double d1aij = d1a[i][j];
  double d2aij = d2a[i][j];
  double d3aij = d3a[i][j];
  double d4aij = d4a[i][j];
  double zzeij = zze[i][j];
  double rinv = 1.0 / r;

  double sum = c1 * exp(-d1aij * r);
  sum += c2 * exp(-d2aij * r);
  sum += c3 * exp(-d3aij * r);
  sum += c4 * exp(-d4aij * r);

  double result = zzeij * sum * rinv;

  return result;
}

/* ----------------------------------------------------------------------
   compute ZBL first derivative
------------------------------------------------------------------------- */

double PairZBL::dzbldr(double r, int i, int j)
{

  double d1aij = d1a[i][j];
  double d2aij = d2a[i][j];
  double d3aij = d3a[i][j];
  double d4aij = d4a[i][j];
  double zzeij = zze[i][j];
  double rinv = 1.0 / r;

  double e1 = exp(-d1aij * r);
  double e2 = exp(-d2aij * r);
  double e3 = exp(-d3aij * r);
  double e4 = exp(-d4aij * r);

  double sum = c1 * e1;
  sum += c2 * e2;
  sum += c3 * e3;
  sum += c4 * e4;

  double sum_p = -c1 * d1aij * e1;
  sum_p -= c2 * d2aij * e2;
  sum_p -= c3 * d3aij * e3;
  sum_p -= c4 * d4aij * e4;

  double result = zzeij * (sum_p - sum * rinv) * rinv;

  return result;
}

/* ----------------------------------------------------------------------
   compute ZBL second derivative
------------------------------------------------------------------------- */

double PairZBL::d2zbldr2(double r, int i, int j)
{

  double d1aij = d1a[i][j];
  double d2aij = d2a[i][j];
  double d3aij = d3a[i][j];
  double d4aij = d4a[i][j];
  double zzeij = zze[i][j];
  double rinv = 1.0 / r;

  double e1 = exp(-d1aij * r);
  double e2 = exp(-d2aij * r);
  double e3 = exp(-d3aij * r);
  double e4 = exp(-d4aij * r);

  double sum = c1 * e1;
  sum += c2 * e2;
  sum += c3 * e3;
  sum += c4 * e4;

  double sum_p = c1 * e1 * d1aij;
  sum_p += c2 * e2 * d2aij;
  sum_p += c3 * e3 * d3aij;
  sum_p += c4 * e4 * d4aij;

  double sum_pp = c1 * e1 * d1aij * d1aij;
  sum_pp += c2 * e2 * d2aij * d2aij;
  sum_pp += c3 * e3 * d3aij * d3aij;
  sum_pp += c4 * e4 * d4aij * d4aij;

  double result = zzeij * (sum_pp + 2.0 * sum_p * rinv + 2.0 * sum * rinv * rinv) * rinv;

  return result;
}

/* ----------------------------------------------------------------------
   calculate the i,j entries in the various coeff arrays
------------------------------------------------------------------------- */

void PairZBL::set_coeff(int i, int j, double zi, double zj)
{
  double ainv = (pow(zi, pzbl) + pow(zj, pzbl)) / (a0 * force->angstrom);
  d1a[i][j] = d1 * ainv;
  d2a[i][j] = d2 * ainv;
  d3a[i][j] = d3 * ainv;
  d4a[i][j] = d4 * ainv;
  zze[i][j] = zi * zj * force->qqr2e * force->qelectron * force->qelectron;

  d1a[j][i] = d1a[i][j];
  d2a[j][i] = d2a[i][j];
  d3a[j][i] = d3a[i][j];
  d4a[j][i] = d4a[i][j];
  zze[j][i] = zze[i][j];

  // e =  t^3 (sw3 + sw4*t) + sw5
  //   = A/3*t^3 + B/4*t^4 + C
  // sw3 = A/3
  // sw4 = B/4
  // sw5 = C

  // dedr = t^2 (sw1 + sw2*t)
  //      = A*t^2 + B*t^3
  // sw1 = A
  // sw2 = B

  // de2dr2 = 2*A*t + 3*B*t^2

  // Require that at t = tc:
  // e = -Fc
  // dedr = -Fc'
  // d2edr2 = -Fc''

  // Hence:
  // A = (-3Fc' + tc*Fc'')/tc^2
  // B = ( 2Fc' - tc*Fc'')/tc^3
  // C = -Fc + tc/2*Fc' - tc^2/12*Fc''

  double tc = cut_global - cut_inner;
  double fc = e_zbl(cut_global, i, j);
  double fcp = dzbldr(cut_global, i, j);
  double fcpp = d2zbldr2(cut_global, i, j);

  double swa = (-3.0 * fcp + tc * fcpp) / (tc * tc);
  double swb = (2.0 * fcp - tc * fcpp) / (tc * tc * tc);
  double swc = -fc + (tc / 2.0) * fcp - (tc * tc / 12.0) * fcpp;

  sw1[i][j] = swa;
  sw2[i][j] = swb;
  sw3[i][j] = swa / 3.0;
  sw4[i][j] = swb / 4.0;
  sw5[i][j] = swc;

  sw1[j][i] = sw1[i][j];
  sw2[j][i] = sw2[i][j];
  sw3[j][i] = sw3[i][j];
  sw4[j][i] = sw4[i][j];
  sw5[j][i] = sw5[i][j];
}