lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, 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: Jeremy Lechman (SNL)
------------------------------------------------------------------------- */

#include "fix_wall_colloid.h"
#include <mpi.h>
#include <cmath>
#include "atom.h"
#include "atom_vec.h"
#include "error.h"

using namespace LAMMPS_NS;
using namespace FixConst;

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

FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
  FixWall(lmp, narg, arg) {}

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

void FixWallColloid::init()
{
  if (!atom->sphere_flag)
    error->all(FLERR,"Fix wall/colloid requires atom style sphere");

  // insure all particles in group are extended particles

  double *radius = atom->radius;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;

  int flag = 0;
  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit)
      if (radius[i] == 0.0) flag = 1;

  int flagall;
  MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
  if (flagall) error->all(FLERR,"Fix wall/colloid requires extended particles");

  FixWall::init();
}

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

void FixWallColloid::precompute(int m)
{
  coeff1[m] = 4.0/315.0 * epsilon[m] * pow(sigma[m],6.0);
  coeff2[m] = 2.0/3.0 * epsilon[m];
  coeff3[m] = epsilon[m] * pow(sigma[m],6.0)/7560.0;
  coeff4[m] = epsilon[m]/6.0;
}

/* ----------------------------------------------------------------------
   interaction of all particles in group with a wall
   m = index of wall coeffs
   which = xlo,xhi,ylo,yhi,zlo,zhi
   error if any finite-size particle is touching or penetrating wall
------------------------------------------------------------------------- */

void FixWallColloid::wall_particle(int m, int which, double coord)
{
  double delta,delta2,rinv,r2inv,r4inv,r8inv,fwall;
  double r2,rinv2,r2inv2,r4inv2;
  double r3,rinv3,r2inv3,r4inv3;
  double rad,rad2,rad4,rad8,diam,new_coeff2;
  double eoffset;
  double vn;

  double **x = atom->x;
  double **f = atom->f;
  double *radius = atom->radius;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;

  int dim = which  / 2;
  int side = which % 2;
  if (side == 0) side = -1;

  int onflag = 0;

  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit) {
      if (side < 0) delta = x[i][dim] - coord;
      else delta = coord - x[i][dim];
      if (delta >= cutoff[m]) continue;
      rad = radius[i];
      if (rad >= delta) {
        onflag = 1;
        continue;
      }

      new_coeff2 = coeff2[m]*rad*rad*rad;
      diam = 2.0*rad;
      rad2 = rad*rad;
      rad4 = rad2*rad2;
      rad8 = rad4*rad4;
      delta2 = rad2 - delta*delta;
      rinv = 1.0/delta2;
      r2inv = rinv*rinv;
      r4inv = r2inv*r2inv;
      r8inv = r4inv*r4inv;
      fwall = side * (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
                                 + 63.0*rad4*rad*pow(delta,4.0)
                                 + 21.0*rad2*rad*pow(delta,6.0))*r8inv -
                      new_coeff2*r2inv);
      f[i][dim] -= fwall;

      r2 = rad - delta;
      rinv2 = 1.0/r2;
      r2inv2 = rinv2*rinv2;
      r4inv2 = r2inv2*r2inv2;
      r3 = delta + rad;
      rinv3 = 1.0/r3;
      r2inv3 = rinv3*rinv3;
      r4inv3 = r2inv3*r2inv3;
      ewall[0] += coeff3[m]*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
                             + (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
        coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
                   (-rinv2)*rinv3);

      // offset depends on particle size

      r2 = rad - cutoff[m];
      rinv2 = 1.0/r2;
      r2inv2 = rinv2*rinv2;
      r4inv2 = r2inv2*r2inv2;
      r3 = cutoff[m] + rad;
      rinv3 = 1.0/r3;
      r2inv3 = rinv3*rinv3;
      r4inv3 = r2inv3*r2inv3;
      eoffset = coeff3[m]*((-3.5*diam+cutoff[m])*r4inv2*r2inv2*rinv2
                           + (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
        coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*
                   (-rinv2)*rinv3);
      ewall[0] -= eoffset;

      ewall[m+1] += fwall;

      if (evflag) {
        if (side < 0) vn = -fwall*delta;
        else vn = fwall*delta;
        v_tally(dim, i, vn);
      }
    }

  if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
}