deleteing USER-EES

This package implements the EES potential between ellipsoidal particles and a semi finite LJ wall introduced by Babadi and Ejtehadi. 

This potential has fixes in both "fix wall" style and "fix wall/region" style so can be used as a boundary of simulation box or on the sides of a region inside the simulation box. 

The ASPHERE package is required for using this fixes.

For more details please refer to documentation of LAMMPS under "fix wall/ees" entry. 

There are also some example of using this code in /examples/usr/EES.

This implementation is done by Abdoreza Ershadinia at Sharif University of Technology--Tehran (a.ershdinia@physics.sahrif.edu). 

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

   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");

}

/* -*- 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.

*/

/* -*- 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];