lammps/src/pair_buck_coul_cut.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: Eduardo Bringa (LLNL)
------------------------------------------------------------------------- */

#include "pair_buck_coul_cut.h"

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

#include <cmath>
#include <cstring>

using namespace LAMMPS_NS;
using namespace MathConst;

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

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

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

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

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

    memory->destroy(cut_lj);
    memory->destroy(cut_ljsq);
    memory->destroy(cut_coul);
    memory->destroy(cut_coulsq);
    memory->destroy(a);
    memory->destroy(rho);
    memory->destroy(c);
    memory->destroy(rhoinv);
    memory->destroy(buck1);
    memory->destroy(buck2);
    memory->destroy(offset);
  }
}

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

void PairBuckCoulCut::compute(int eflag, int vflag)
{
  int i, j, ii, jj, inum, jnum, itype, jtype;
  double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair;
  double rsq, r2inv, r6inv, r, rexp, forcecoul, forcebuck, factor_coul, factor_lj;
  int *ilist, *jlist, *numneigh, **firstneigh;

  evdwl = ecoul = 0.0;
  ev_init(eflag, vflag);

  double **x = atom->x;
  double **f = atom->f;
  double *q = atom->q;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  double *special_coul = force->special_coul;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;
  double qqrd2e = force->qqrd2e;

  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];
    qtmp = q[i];
    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)];
      factor_coul = special_coul[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;
        r = sqrt(rsq);

        if (rsq < cut_coulsq[itype][jtype])
          forcecoul = qqrd2e * qtmp * q[j] / r;
        else
          forcecoul = 0.0;

        if (rsq < cut_ljsq[itype][jtype]) {
          r6inv = r2inv * r2inv * r2inv;
          rexp = exp(-r * rhoinv[itype][jtype]);
          forcebuck = buck1[itype][jtype] * r * rexp - buck2[itype][jtype] * r6inv;
        } else
          forcebuck = 0.0;

        fpair = (factor_coul * forcecoul + factor_lj * forcebuck) * 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_coulsq[itype][jtype])
            ecoul = factor_coul * qqrd2e * qtmp * q[j] / r;
          else
            ecoul = 0.0;
          if (rsq < cut_ljsq[itype][jtype]) {
            evdwl = a[itype][jtype] * rexp - c[itype][jtype] * r6inv - offset[itype][jtype];
            evdwl *= factor_lj;
          } else
            evdwl = 0.0;
        }

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

  if (vflag_fdotr) virial_fdotr_compute();
}

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

void PairBuckCoulCut::allocate()
{
  allocated = 1;
  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_lj, np1, np1, "pair:cut_lj");
  memory->create(cut_ljsq, np1, np1, "pair:cut_ljsq");
  memory->create(cut_coul, np1, np1, "pair:cut_coul");
  memory->create(cut_coulsq, np1, np1, "pair:cut_coulsq");
  memory->create(a, np1, np1, "pair:a");
  memory->create(rho, np1, np1, "pair:rho");
  memory->create(c, np1, np1, "pair:c");
  memory->create(rhoinv, np1, np1, "pair:rhoinv");
  memory->create(buck1, np1, np1, "pair:buck1");
  memory->create(buck2, np1, np1, "pair:buck2");
  memory->create(offset, np1, np1, "pair:offset");
}

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

void PairBuckCoulCut::settings(int narg, char **arg)
{
  if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");

  cut_lj_global = utils::numeric(FLERR, arg[0], false, lmp);
  if (narg == 1)
    cut_coul_global = cut_lj_global;
  else
    cut_coul_global = utils::numeric(FLERR, arg[1], 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_lj[i][j] = cut_lj_global;
          cut_coul[i][j] = cut_coul_global;
        }
  }
}

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

void PairBuckCoulCut::coeff(int narg, char **arg)
{
  if (narg < 5 || narg > 7) 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 a_one = utils::numeric(FLERR, arg[2], false, lmp);
  double rho_one = utils::numeric(FLERR, arg[3], false, lmp);
  if (rho_one <= 0) error->all(FLERR, "Incorrect args for pair coefficients");
  double c_one = utils::numeric(FLERR, arg[4], false, lmp);

  double cut_lj_one = cut_lj_global;
  double cut_coul_one = cut_coul_global;
  if (narg >= 6) cut_coul_one = cut_lj_one = utils::numeric(FLERR, arg[5], false, lmp);
  if (narg == 7) cut_coul_one = utils::numeric(FLERR, arg[6], false, lmp);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo, i); j <= jhi; j++) {
      a[i][j] = a_one;
      rho[i][j] = rho_one;
      c[i][j] = c_one;
      cut_lj[i][j] = cut_lj_one;
      cut_coul[i][j] = cut_coul_one;
      setflag[i][j] = 1;
      count++;
    }
  }

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

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

void PairBuckCoulCut::init_style()
{
  if (!atom->q_flag) error->all(FLERR, "Pair style buck/coul/cut requires atom attribute q");

  neighbor->add_request(this);
}

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

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

  double cut = MAX(cut_lj[i][j], cut_coul[i][j]);
  cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
  cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];

  rhoinv[i][j] = 1.0 / rho[i][j];
  buck1[i][j] = a[i][j] / rho[i][j];
  buck2[i][j] = 6.0 * c[i][j];

  if (offset_flag && (cut_lj[i][j] > 0.0)) {
    double rexp = exp(-cut_lj[i][j] / rho[i][j]);
    offset[i][j] = a[i][j] * rexp - c[i][j] / pow(cut_lj[i][j], 6.0);
  } else
    offset[i][j] = 0.0;

  cut_ljsq[j][i] = cut_ljsq[i][j];
  cut_coulsq[j][i] = cut_coulsq[i][j];
  a[j][i] = a[i][j];
  c[j][i] = c[i][j];
  rhoinv[j][i] = rhoinv[i][j];
  buck1[j][i] = buck1[i][j];
  buck2[j][i] = buck2[i][j];
  offset[j][i] = offset[i][j];

  // compute I,J contribution to long-range tail correction
  // count total # of atoms of type I and J via Allreduce

  if (tail_flag) {
    int *type = atom->type;
    int nlocal = atom->nlocal;

    double count[2], all[2];
    count[0] = count[1] = 0.0;
    for (int k = 0; k < nlocal; k++) {
      if (type[k] == i) count[0] += 1.0;
      if (type[k] == j) count[1] += 1.0;
    }
    MPI_Allreduce(count, all, 2, MPI_DOUBLE, MPI_SUM, world);

    double rho1 = rho[i][j];
    double rho2 = rho1 * rho1;
    double rho3 = rho2 * rho1;
    double rc = cut_lj[i][j];
    double rc2 = rc * rc;
    double rc3 = rc2 * rc;
    etail_ij = 2.0 * MY_PI * all[0] * all[1] *
        (a[i][j] * exp(-rc / rho1) * rho1 * (rc2 + 2.0 * rho1 * rc + 2.0 * rho2) -
         c[i][j] / (3.0 * rc3));
    ptail_ij = (-1 / 3.0) * 2.0 * MY_PI * all[0] * all[1] *
        (-a[i][j] * exp(-rc / rho1) * (rc3 + 3.0 * rho1 * rc2 + 6.0 * rho2 * rc + 6.0 * rho3) +
         2.0 * c[i][j] / rc3);
  }

  return cut;
}

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

void PairBuckCoulCut::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(&a[i][j], sizeof(double), 1, fp);
        fwrite(&rho[i][j], sizeof(double), 1, fp);
        fwrite(&c[i][j], sizeof(double), 1, fp);
        fwrite(&cut_lj[i][j], sizeof(double), 1, fp);
        fwrite(&cut_coul[i][j], sizeof(double), 1, fp);
      }
    }
}

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

void PairBuckCoulCut::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, &a[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &rho[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &c[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &cut_lj[i][j], sizeof(double), 1, fp, nullptr, error);
          utils::sfread(FLERR, &cut_coul[i][j], sizeof(double), 1, fp, nullptr, error);
        }
        MPI_Bcast(&a[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&rho[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&c[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&cut_lj[i][j], 1, MPI_DOUBLE, 0, world);
        MPI_Bcast(&cut_coul[i][j], 1, MPI_DOUBLE, 0, world);
      }
    }
}

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

void PairBuckCoulCut::write_restart_settings(FILE *fp)
{
  fwrite(&cut_lj_global, sizeof(double), 1, fp);
  fwrite(&cut_coul_global, 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 PairBuckCoulCut::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    utils::sfread(FLERR, &cut_lj_global, sizeof(double), 1, fp, nullptr, error);
    utils::sfread(FLERR, &cut_coul_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);
    utils::sfread(FLERR, &tail_flag, sizeof(int), 1, fp, nullptr, error);
  }
  MPI_Bcast(&cut_lj_global, 1, MPI_DOUBLE, 0, world);
  MPI_Bcast(&cut_coul_global, 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 PairBuckCoulCut::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->ntypes; i++)
    fprintf(fp, "%d %g %g %g\n", i, a[i][i], rho[i][i], c[i][i]);
}

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

void PairBuckCoulCut::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 %g\n", i, j, a[i][j], rho[i][j], c[i][j], cut_lj[i][j],
              cut_coul[i][j]);
}

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

double PairBuckCoulCut::single(int i, int j, int itype, int jtype, double rsq, double factor_coul,
                               double factor_lj, double &fforce)
{
  double r2inv, r6inv, r, rexp, forcecoul, forcebuck, phicoul, phibuck;

  r2inv = 1.0 / rsq;
  if (rsq < cut_coulsq[itype][jtype])
    forcecoul = force->qqrd2e * atom->q[i] * atom->q[j] * sqrt(r2inv);
  else
    forcecoul = 0.0;
  if (rsq < cut_ljsq[itype][jtype]) {
    r6inv = r2inv * r2inv * r2inv;
    r = sqrt(rsq);
    rexp = exp(-r * rhoinv[itype][jtype]);
    forcebuck = buck1[itype][jtype] * r * rexp - buck2[itype][jtype] * r6inv;
  } else
    forcebuck = 0.0;
  fforce = (factor_coul * forcecoul + factor_lj * forcebuck) * r2inv;

  double eng = 0.0;
  if (rsq < cut_coulsq[itype][jtype]) {
    phicoul = force->qqrd2e * atom->q[i] * atom->q[j] * sqrt(r2inv);
    eng += factor_coul * phicoul;
  }
  if (rsq < cut_ljsq[itype][jtype]) {
    phibuck = a[itype][jtype] * rexp - c[itype][jtype] * r6inv - offset[itype][jtype];
    eng += factor_lj * phibuck;
  }
  return eng;
}

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

void PairBuckCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq,
                                  double factor_coul, double factor_lj, double &dupair,
                                  double &du2pair)
{
  double rinv, r2inv, r3inv, r6inv, r7inv, r8inv, r, rexp;
  double du_lj, du2_lj, du_coul, du2_coul;

  double *q = atom->q;
  double qqrd2e = force->qqrd2e;

  r = sqrt(rsq);
  rexp = exp(-r * rhoinv[itype][jtype]);

  r2inv = 1.0 / rsq;
  rinv = sqrt(r2inv);
  r3inv = r2inv * rinv;
  r6inv = r2inv * r2inv * r2inv;
  r7inv = r6inv * rinv;
  r8inv = r6inv * r2inv;

  // Reminder: buck1[itype][jtype] = a[itype][jtype]/rho[itype][jtype];
  // Reminder: buck2[itype][jtype] = 6.0*c[itype][jtype];

  du_lj = buck2[itype][jtype] * r7inv - buck1[itype][jtype] * rexp;
  du2_lj = (buck1[itype][jtype] / rho[itype][jtype]) * rexp - 7 * buck2[itype][jtype] * r8inv;

  // Reminder: qqrd2e converts  q^2/r to energy w/ dielectric constant

  du_coul = -qqrd2e * q[i] * q[j] * r2inv;
  du2_coul = 2.0 * qqrd2e * q[i] * q[j] * r3inv;

  dupair = factor_lj * du_lj + factor_coul * du_coul;
  du2pair = factor_lj * du2_lj + factor_coul * du2_coul;
}

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

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