220 lines
6.5 KiB
C++
220 lines
6.5 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
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------------------------------------------------------------------------- */
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#include <cmath>
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#include "math_extra.h"
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#include "fix_wall_ees.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_ellipsoid.h"
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#include "domain.h"
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#include "region.h"
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#include "force.h"
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#include "lattice.h"
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#include "update.h"
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#include "output.h"
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#include "respa.h"
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#include "error.h"
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#include "math_extra.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixWallEES::FixWallEES(LAMMPS *lmp, int narg, char **arg) :
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FixWall(lmp, narg, arg) {}
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/* ---------------------------------------------------------------------- */
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void FixWallEES::precompute(int m)
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{
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coeff1[m] = ( 2. / 4725. ) * epsilon[m] * pow(sigma[m],12.0);
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coeff2[m] = ( 1. / 24. ) * epsilon[m] * pow(sigma[m],6.0);
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coeff3[m] = ( 2. / 315. ) * epsilon[m] * pow(sigma[m],12.0);
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coeff4[m] = ( 1. / 3. ) * epsilon[m] * pow(sigma[m],6.0);
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coeff5[m] = ( 4. / 315. ) * epsilon[m] * pow(sigma[m],12.0);
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coeff6[m] = ( 1. / 12. ) * epsilon[m] * pow(sigma[m],6.0);
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}
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/* ---------------------------------------------------------------------- */
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void FixWallEES::init()
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{
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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if (!avec)
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error->all(FLERR,"Fix wall/ees requires atom style ellipsoid");
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// check that all particles are finite-size ellipsoids
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// no point particles allowed, spherical is OK
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (ellipsoid[i] < 0)
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error->one(FLERR,"Fix wall/ees requires extended particles");
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FixWall::init();
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}
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/* ----------------------------------------------------------------------
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interaction of all particles in group with a wall
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m = index of wall coeffs
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which = xlo,xhi,ylo,yhi,zlo,zhi
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error if any particle is on or behind wall
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------------------------------------------------------------------------- */
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void FixWallEES::wall_particle(int m, int which, double coord)
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{
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double delta;
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double **x = atom->x;
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double **f = atom->f;
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double **tor = atom->torque;
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int dim = which / 2;
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int side = which % 2;
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if (side == 0) side = -1;
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int onflag = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (side < 0)
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delta = x[i][dim] - coord;
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else
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delta = coord - x[i][dim];
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if (delta >= cutoff[m])
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continue;
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double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
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double tempvec[3]= {0,0,0};
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double sigman = 0.0, sigman2 = 0.0;
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double nhat[3] = {0,0,0};
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nhat[dim]=-1*side;
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nhat[(dim+1)%3] = 0 ;
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nhat[(dim+2)%3] = 0 ;
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double* shape = bonus[ellipsoid[i]].shape;;
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MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
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MathExtra::transpose_matvec(A,nhat,tempvec);
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for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
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for(int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k];
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sigman = sqrt(sigman2);
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if (delta <= sigman) {
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onflag = 1;
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continue;
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}
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double fwall = 0.0, twall = 0.0;
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double delta2 = 0.0, delta3 = 0.0, delta4 = 0.0, delta5 = 0.0, delta6 = 0.0;
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double sigman3 = 0.0, sigman4 = 0.0, sigman5 = 0.0, sigman6 = 0.0;
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double hhss = 0.0, hhss2 = 0.0, hhss4 = 0.0, hhss7 = 0.0, hhss8 = 0.0;
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double hps = 0.0;
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double hms = 0.0;
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double tempvec2[3]= {0,0,0};
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double SAn[3] = {0,0,0};
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double that[3] = {0,0,0};
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double Lx[3][3] = {{0,0,0},{0,0,-1},{0,1,0}};
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double Ly[3][3] = {{0,0,1},{0,0,0},{-1,0,0}};
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double Lz[3][3] = {{0,-1,0},{1,0,0},{0,0,0}};
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for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
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sigman3 = sigman2 * sigman;
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sigman4 = sigman2 * sigman2;
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sigman5 = sigman4 * sigman;
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sigman6 = sigman3 * sigman3;
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delta2 = delta * delta;
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delta3 = delta2 * delta;
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delta4 = delta2 * delta2;
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delta5 = delta3 * delta2;
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delta6 = delta3 * delta3;
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hhss = delta2 - sigman2;
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hhss2 = hhss * hhss;
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hhss4 = hhss2 * hhss2;
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hhss8 = hhss4 * hhss4;
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hhss7 = hhss4 * hhss2 * hhss;
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hps = delta + sigman;
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hms = delta - sigman;
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fwall = side*(
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-1*coeff4[m]/hhss2 +
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coeff3[m] * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8
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);
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f[i][dim] -= fwall;
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ewall[0] += -1*coeff2[m] * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) +
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coeff1[m] * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7;
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ewall[m+1] += fwall;
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twall = coeff6[m] * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
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coeff5[m] * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ;
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MathExtra::matvec(Lx,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
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that[0] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Ly,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
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that[1] = MathExtra::dot3(SAn,tempvec2);
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MathExtra::matvec(Lz,nhat,tempvec);
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MathExtra::transpose_matvec(A,tempvec,tempvec2);
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for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
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that[2] = MathExtra::dot3(SAn,tempvec2);
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for(int j = 0; j<3 ; j++)
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tor[i][j] += twall * that[j];
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}
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if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
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}
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