Commit d3b8e688 authored by Abdo's avatar Abdo
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Files Added to MISC

parent 67d474df
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/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

#include "math.h"
#include "math_extra.h"
#include "fix_wall_ees.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "error.h"

using namespace LAMMPS_NS;
using namespace FixConst;

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

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

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

void FixWallEES::precompute(int m)
{
  coeff1[m] = ( 2. / 4725. ) * epsilon[m] * pow(sigma[m],12.0);
  coeff2[m] = ( 1. / 24. ) * epsilon[m] * pow(sigma[m],6.0);

  coeff3[m] = ( 2. / 315. ) * epsilon[m] * pow(sigma[m],12.0);
  coeff4[m] = ( 1. / 3. ) * epsilon[m] * pow(sigma[m],6.0);

  coeff5[m] = ( 4. / 315. ) * epsilon[m] * pow(sigma[m],12.0);
  coeff6[m] = ( 1. / 12. )  * epsilon[m] * pow(sigma[m],6.0);
}

/* ---------------------------------------------------------------------- */
void FixWallEES::init()
{
  avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
  if (!avec)
    error->all(FLERR,"Fix wall/ees requires atom style ellipsoid");

  // check that all particles are finite-size ellipsoids
  // no point particles allowed, spherical is OK

  int *ellipsoid = atom->ellipsoid;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;

  for (int i = 0; i < nlocal; i++)
    if (mask[i] & groupbit)
      if (ellipsoid[i] < 0)
        error->one(FLERR,"Fix wall/ees requires extended particles");

  FixWall::init();
}


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

void FixWallEES::wall_particle(int m, int which, double coord)
{
  double delta;

  double **x = atom->x;
  double **f = atom->f;
  double **tor = atom->torque;


  avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
  int *ellipsoid = atom->ellipsoid;
  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;

      double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
      double tempvec[3]= {0,0,0};
      double sigman = 0.0, sigman2 = 0.0;
      double nhat[3] = {0,0,0};

      nhat[dim]=-1*side;
      nhat[(dim+1)%3] = 0 ;
      nhat[(dim+2)%3] = 0 ;


      double* shape = bonus[ellipsoid[i]].shape;;
      MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
      MathExtra::transpose_matvec(A,nhat,tempvec);
      for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
      for(int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k];
      sigman = sqrt(sigman2);

      if (delta <= sigman) {
        onflag = 1;
        continue;
      }


      double fwall = 0.0, twall = 0.0;
      double delta2 = 0.0, delta3 = 0.0, delta4 = 0.0, delta5 = 0.0, delta6 = 0.0;
      double sigman3 = 0.0, sigman4 = 0.0, sigman5 = 0.0, sigman6 = 0.0;
      double hhss = 0.0, hhss2 = 0.0, hhss4 = 0.0, hhss7 = 0.0, hhss8 = 0.0;
      double hps = 0.0;
      double hms = 0.0;

      double tempvec2[3]= {0,0,0};

      double SAn[3] = {0,0,0};
      double that[3] = {0,0,0};

      double Lx[3][3] =  {{0,0,0},{0,0,-1},{0,1,0}};
      double Ly[3][3] =  {{0,0,1},{0,0,0},{-1,0,0}};
      double Lz[3][3] =  {{0,-1,0},{1,0,0},{0,0,0}};


      for(int k = 0; k<3; k++) SAn[k] = tempvec[k];

      sigman3 = sigman2 * sigman;
      sigman4 = sigman2 * sigman2;
      sigman5 = sigman4 * sigman;
      sigman6 = sigman3 * sigman3;


      delta2 = delta  * delta;
      delta3 = delta2 * delta;
      delta4 = delta2 * delta2;
      delta5 = delta3 * delta2;
      delta6 = delta3 * delta3;

      hhss = delta2 - sigman2;
      hhss2 = hhss  * hhss;
      hhss4 = hhss2 * hhss2;
      hhss8 = hhss4 * hhss4;
      hhss7 = hhss4 * hhss2 * hhss;

      hps = delta + sigman;
      hms = delta - sigman;

      fwall = side*(
                  -1*coeff4[m]/hhss2 +
                  coeff3[m] * (  21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6  ) / hhss8
                  );
    f[i][dim] -= fwall;

    ewall[0] += -1*coeff2[m] * (  4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3  ) +
            coeff1[m] * (  35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4  ) / hhss7;

    ewall[m+1] += fwall;

    twall = coeff6[m] * (  6.*delta3/sigman4/hhss2  - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5  )  +
            coeff5[m] * (  21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4  ) / hhss8    ;


    MathExtra::matvec(Lx,nhat,tempvec);
    MathExtra::transpose_matvec(A,tempvec,tempvec2);
    for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
    that[0] = MathExtra::dot3(SAn,tempvec2);

    MathExtra::matvec(Ly,nhat,tempvec);
    MathExtra::transpose_matvec(A,tempvec,tempvec2);
    for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
    that[1] = MathExtra::dot3(SAn,tempvec2);

    MathExtra::matvec(Lz,nhat,tempvec);
    MathExtra::transpose_matvec(A,tempvec,tempvec2);
    for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
    that[2] = MathExtra::dot3(SAn,tempvec2);


    for(int j = 0; j<3 ; j++)
        tor[i][j] += twall * that[j];

    }

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

#ifdef FIX_CLASS

FixStyle(wall/ees,FixWallEES)

#else

#ifndef LMP_FIX_WALL_EES_H
#define LMP_FIX_WALL_EES_H

#include "fix_wall.h"

namespace LAMMPS_NS {

class FixWallEES : public FixWall {
 public:
  FixWallEES(class LAMMPS *, int, char **);
  void precompute(int);
  void init();
  void wall_particle(int, int, double);

 private:
  double coeff1[6],coeff2[6],coeff3[6],coeff4[6],coeff5[6],coeff6[6];
  class AtomVecEllipsoid *avec;
};

}

#endif
#endif

/* ERROR/WARNING messages:

E: Particle on or inside fix wall surface

Particles must be "exterior" to the wall in order for energy/force to
be calculated.

*/
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/* -*- c++ -*- ----------------------------------------------------------
   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.
------------------------------------------------------------------------- */
#include <iostream>
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_wall_region_ees.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "region.h"
#include "force.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
#include "math_extra.h"

using namespace LAMMPS_NS;
using namespace FixConst;

enum{LJ93,LJ126,COLLOID,HARMONIC,EES};//me

/* ---------------------------------------------------------------------- */
/// USAGE:
/// fix ID group-ID wall/region/ees region-ID epsilon sigma cutoff
///
FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
    Fix(lmp, narg, arg)
{
    if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
    scalar_flag = 1;
    vector_flag = 1;
    size_vector = 3;
    global_freq = 1;
    extscalar = 1;
    extvector = 1;

    // parse args

    iregion = domain->find_region(arg[3]);
    if (iregion == -1)
        error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
    int n = strlen(arg[3]) + 1;
    idregion = new char[n];
    strcpy(idregion,arg[3]);



    epsilon = force->numeric(FLERR,arg[4]);
    sigma = force->numeric(FLERR,arg[5]);
    cutoff = force->numeric(FLERR,arg[6]);

    if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");

    eflag = 0;
    ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
}

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

FixWallRegionEES::~FixWallRegionEES()
{
    delete [] idregion;
}

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

int FixWallRegionEES::setmask()
{
    int mask = 0;
    mask |= POST_FORCE;
    mask |= THERMO_ENERGY;
    mask |= POST_FORCE_RESPA;
    mask |= MIN_POST_FORCE;
    return mask;
}

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

void FixWallRegionEES::init()
{
    // set index and check validity of region

    iregion = domain->find_region(idregion);
    if (iregion == -1)
        error->all(FLERR,"Region ID for fix wall/region/ees does not exist");


    avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
    if (!avec)
        error->all(FLERR,"Fix wall/region/ees requires atom style ellipsoid");

    // check that all particles are finite-size ellipsoids
    // no point particles allowed, spherical is OK

    int *ellipsoid = atom->ellipsoid;
    int *mask = atom->mask;
    int nlocal = atom->nlocal;

    for (int i = 0; i < nlocal; i++)
        if (mask[i] & groupbit)
            if (ellipsoid[i] < 0)
                error->one(FLERR,"Fix wall/region/ees requires extended particles");


    // setup coefficients for each style

    coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
    coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
    coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
    coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
    coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
    coeff6 = ( 1. / 12. )  * epsilon * pow(sigma,6.0);
    offset = 0;


    if (strstr(update->integrate_style,"respa"))
        nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

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

void FixWallRegionEES::setup(int vflag)
{
    if (strstr(update->integrate_style,"verlet"))
        post_force(vflag);
    else {
        ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
        post_force_respa(vflag,nlevels_respa-1,0);
        ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
    }
}

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

void FixWallRegionEES::min_setup(int vflag)
{
    post_force(vflag);
}

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

void FixWallRegionEES::post_force(int vflag)
{
    //me
    //sth is needed here, but I dont know what
    //that is calculation of sn

    int i,m,n;
    double rinv,fx,fy,fz,tooclose[3];//me
    double sn;//me

    eflag = 0;
    ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;

    double **x = atom->x;
    double **f = atom->f;
    double *radius = atom->radius;

    double **tor = atom->torque; //me

    //avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");//me
    AtomVecEllipsoid::Bonus *bonus = avec->bonus;//me
    int *ellipsoid = atom->ellipsoid;//me

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

    Region *region = domain->regions[iregion];
    region->prematch();

    int onflag = 0;

    // region->match() insures particle is in region or on surface, else error
    // if returned contact dist r = 0, is on surface, also an error
    // in COLLOID case, r <= radius is an error

    for (i = 0; i < nlocal; i++)
        if (mask[i] & groupbit) {
            if (!region->match(x[i][0],x[i][1],x[i][2])) {
                onflag = 1;
                continue;
            }

            double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
            double tempvec[3]= {0,0,0};
            double sn2 = 0.0;
            double nhat[3] = {0,0,0};
            double* shape = bonus[ellipsoid[i]].shape;;
            MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);

            for(int which = 0 ; which < 3; which ++){//me
                nhat[which]=1;
                nhat[(which+1)%3] = 0 ;
                nhat[(which+2)%3] = 0 ;
                sn2 = 0 ;
                MathExtra::transpose_matvec(A,nhat,tempvec);
                for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
                for(int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
                sn = sqrt(sn2);
                tooclose[which] = sn;
            }



            n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);

            for (m = 0; m < n; m++) {

                if(region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0] ){
                    onflag = 1;
                    continue;

                }else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){
                    onflag = 1;
                    continue;
                }else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){
                    onflag = 1;
                    continue;
                }
                else rinv = 1.0/region->contact[m].r;

                ees(m,i);//me

                ewall[0] += eng;
                fx = fwall * region->contact[m].delx * rinv;
                fy = fwall * region->contact[m].dely * rinv;
                fz = fwall * region->contact[m].delz * rinv;
                f[i][0] += fx;
                f[i][1] += fy;
                f[i][2] += fz;

                ewall[1] -= fx;
                ewall[2] -= fy;
                ewall[3] -= fz;

                tor[i][0] += torque[0];
                tor[i][1] += torque[1];
                tor[i][2] += torque[2];

            }
        }

    if (onflag) error->one(FLERR,"Particle on or inside surface of region "
                           "used in fix wall/region/ees");
}

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

void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop)
{
    if (ilevel == nlevels_respa-1) post_force(vflag);
}

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

void FixWallRegionEES::min_post_force(int vflag)
{
    post_force(vflag);
}

/* ----------------------------------------------------------------------
   energy of wall interaction
------------------------------------------------------------------------- */

double FixWallRegionEES::compute_scalar()
{
    // only sum across procs one time

    if (eflag == 0) {
        MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
        eflag = 1;
    }
    return ewall_all[0];
}

/* ----------------------------------------------------------------------
   components of force on wall
------------------------------------------------------------------------- */

double FixWallRegionEES::compute_vector(int n)
{
    // only sum across procs one time

    if (eflag == 0) {
        MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
        eflag = 1;
    }
    return ewall_all[n+1];
}



//me
/* ----------------------------------------------------------------------
   EES interaction for ellipsoid particle with wall
   compute eng and fwall and twall = magnitude of wall force and torque
------------------------------------------------------------------------- */

void FixWallRegionEES::ees(int m, int i)
{
    Region *region = domain->regions[iregion];
    region->prematch();

    double delta = 0.0, delta2 = 0.0, delta3 = 0.0, delta4 = 0.0, delta5 = 0.0, delta6 = 0.0;
    double sigman = 0.0, sigman2 = 0.0 , sigman3 = 0.0, sigman4 = 0.0, sigman5 = 0.0, sigman6 = 0.0;
    double hhss = 0.0, hhss2 = 0.0, hhss4 = 0.0, hhss7 = 0.0, hhss8 = 0.0; //h^2 - s_n^2
    double hps = 0.0; //h+s_n
    double hms = 0.0; //h-s_n
    double twall = 0.0;
    double tempvec[3]={0,0,0};
    double tempvec2[3]= {0,0,0};

    double SAn[3] = {0,0,0};
    double that[3] = {0,0,0};

    double Lx[3][3] =  {{0,0,0},{0,0,-1},{0,1,0}};
    double Ly[3][3] =  {{0,0,1},{0,0,0},{-1,0,0}};
    double Lz[3][3] =  {{0,-1,0},{1,0,0},{0,0,0}};

    double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
    double nhat[3] = {0,0,0};

    nhat[0] = region->contact[m].delx / region->contact[m].r;
    nhat[1] = region->contact[m].dely / region->contact[m].r;
    nhat[2] = region->contact[m].delz / region->contact[m].r;

    //avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
    AtomVecEllipsoid::Bonus *bonus = avec->bonus;
    int *ellipsoid = atom->ellipsoid;//me

    double* shape = bonus[ellipsoid[i]].shape;;
    MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);

    MathExtra::transpose_matvec(A,nhat,tempvec);
    for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
    for(int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k];
    for(int k = 0; k<3; k++) SAn[k] = tempvec[k];


    sigman = sqrt(sigman2);
    delta = fabs(region->contact[m].r);

    sigman3 = sigman2 * sigman;
    sigman4 = sigman2 * sigman2;
    sigman5 = sigman4 * sigman;
    sigman6 = sigman3 * sigman3;

    delta2 = delta  * delta;
    delta3 = delta2 * delta;
    delta4 = delta2 * delta2;
    delta5 = delta3 * delta2;
    delta6 = delta3 * delta3;

    hhss = delta2 - sigman2;
    hhss2 = hhss  * hhss;
    hhss4 = hhss2 * hhss2;
    hhss8 = hhss4 * hhss4;
    hhss7 = hhss4 * hhss2 * hhss;

    hps = delta + sigman;
    hms = delta - sigman;

    fwall =  -1*coeff4/hhss2 +
            coeff3 * (  21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6  ) / hhss8
            ;

    eng = -1*coeff2 * (  4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3  ) +
            coeff1 * (  35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4  ) / hhss7;

    twall = coeff6 * (  6.*delta3/sigman4/hhss2  - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5  )  +
            coeff5 * (  21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4  ) / hhss8    ;

    MathExtra::matvec(Lx,nhat,tempvec);
    MathExtra::transpose_matvec(A,tempvec,tempvec2);
    for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
    that[0] = MathExtra::dot3(SAn,tempvec2);

    MathExtra::matvec(Ly,nhat,tempvec);
    MathExtra::transpose_matvec(A,tempvec,tempvec2);
    for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
    that[1] = MathExtra::dot3(SAn,tempvec2);

    MathExtra::matvec(Lz,nhat,tempvec);
    MathExtra::transpose_matvec(A,tempvec,tempvec2);
    for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
    that[2] = MathExtra::dot3(SAn,tempvec2);

    for(int j = 0; j<3 ; j++)
        torque[j] = twall * that[j];

}
+94 −0
Original line number Diff line number Diff line
/* -*- c++ -*- ----------------------------------------------------------
   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.
------------------------------------------------------------------------- */

#ifdef FIX_CLASS

FixStyle(wall/region/ees,FixWallRegionEES)

#else

#ifndef LMP_FIX_WALL_REGION_EES_H
#define LMP_FIX_WALL_REGION_EES_H

#include "fix.h"


namespace LAMMPS_NS {

class FixWallRegionEES : public Fix {
 public:
  FixWallRegionEES(class LAMMPS *, int, char **);
  ~FixWallRegionEES();
  int setmask();
  void init();
  void setup(int);
  void min_setup(int);
  void post_force(int);
  void post_force_respa(int, int, int);
  void min_post_force(int);
  double compute_scalar();
  double compute_vector(int);

 private:
  class AtomVecEllipsoid *avec;//me

  int iregion;
  double epsilon,sigma,cutoff;
  int eflag;
  double ewall[4],ewall_all[4];
  int nlevels_respa;
  char *idregion;

  double coeff1,coeff2,coeff3,coeff4,offset;
  double coeff5, coeff6;//me
  double eng,fwall;
  double torque[3];//me

  void ees(int, int);//me
};

}

#endif
#endif

/* ERROR/WARNING messages:

E: Illegal ... command

Self-explanatory.  Check the input script syntax and compare to the
documentation for the command.  You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.

E: Region ID for fix wall/region/ees does not exist

Self-explanatory.

E: Fix wall/region/ees cutoff <= 0.0

Self-explanatory.

E: Fix wall/region/ees colloid requires atom style sphere

Self-explanatory.

E: Fix wall/region/ees colloid requires extended particles

One of the particles has radius 0.0.

E: Particle on or inside surface of region used in fix wall/region

Particles must be "exterior" to the region surface in order for
energy/force to be calculated.

*/