381 lines
11 KiB
C++
381 lines
11 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 "fix_wall_region_ees.h"
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#include <mpi.h>
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#include <cmath>
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#include <cstring>
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#include "atom.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 "update.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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FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 3;
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global_freq = 1;
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extscalar = 1;
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extvector = 1;
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// parse args
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iregion = domain->find_region(arg[3]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
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int n = strlen(arg[3]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[3]);
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epsilon = force->numeric(FLERR,arg[4]);
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sigma = force->numeric(FLERR,arg[5]);
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cutoff = force->numeric(FLERR,arg[6]);
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if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");
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eflag = 0;
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ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixWallRegionEES::~FixWallRegionEES()
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{
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delete [] idregion;
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}
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/* ---------------------------------------------------------------------- */
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int FixWallRegionEES::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= THERMO_ENERGY;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::init()
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{
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// set index and check validity of region
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
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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/region/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/region/ees requires extended particles");
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// setup coefficients
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coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
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coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
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coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
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coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
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coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
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coeff6 = ( 1. / 12. ) * epsilon * pow(sigma,6.0);
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offset = 0;
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::setup(int vflag)
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{
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if (strstr(update->integrate_style,"verlet"))
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::min_setup(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::post_force(int /*vflag*/)
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{
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//sth is needed here, but I dont know what
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//that is calculation of sn
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int i,m,n;
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double rinv,fx,fy,fz,sn,tooclose[3];
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eflag = 0;
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ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
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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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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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Region *region = domain->regions[iregion];
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region->prematch();
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int onflag = 0;
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// region->match() insures particle is in region or on surface, else error
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// if returned contact dist r = 0, is on surface, also an error
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// in COLLOID case, r <= radius is an error
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (!region->match(x[i][0],x[i][1],x[i][2])) {
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onflag = 1;
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continue;
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}
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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 sn2 = 0.0;
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double nhat[3] = {0,0,0};
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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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for(int which = 0 ; which < 3; which ++){//me
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nhat[which]=1;
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nhat[(which+1)%3] = 0 ;
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nhat[(which+2)%3] = 0 ;
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sn2 = 0 ;
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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++) sn2 += tempvec[k]*tempvec[k];
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sn = sqrt(sn2);
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tooclose[which] = sn;
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}
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n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
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for (m = 0; m < n; m++) {
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if (region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0]){
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onflag = 1;
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continue;
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} else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){
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onflag = 1;
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continue;
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} else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){
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onflag = 1;
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continue;
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} else rinv = 1.0/region->contact[m].r;
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ees(m,i);
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ewall[0] += eng;
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fx = fwall * region->contact[m].delx * rinv;
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fy = fwall * region->contact[m].dely * rinv;
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fz = fwall * region->contact[m].delz * rinv;
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f[i][0] += fx;
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f[i][1] += fy;
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f[i][2] += fz;
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ewall[1] -= fx;
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ewall[2] -= fy;
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ewall[3] -= fz;
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tor[i][0] += torque[0];
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tor[i][1] += torque[1];
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tor[i][2] += torque[2];
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}
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}
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if (onflag) error->one(FLERR,"Particle on or inside surface of region "
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"used in fix wall/region/ees");
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int /*iloop*/)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixWallRegionEES::min_post_force(int vflag)
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{
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post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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energy of wall interaction
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------------------------------------------------------------------------- */
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double FixWallRegionEES::compute_scalar()
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{
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// only sum across procs one time
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if (eflag == 0) {
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MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
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eflag = 1;
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}
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return ewall_all[0];
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}
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/* ----------------------------------------------------------------------
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components of force on wall
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------------------------------------------------------------------------- */
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double FixWallRegionEES::compute_vector(int n)
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{
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// only sum across procs one time
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if (eflag == 0) {
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MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
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eflag = 1;
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}
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return ewall_all[n+1];
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}
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/* ----------------------------------------------------------------------
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EES interaction for ellipsoid particle with wall
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compute eng and fwall and twall = magnitude of wall force and torque
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------------------------------------------------------------------------- */
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void FixWallRegionEES::ees(int m, int i)
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{
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Region *region = domain->regions[iregion];
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region->prematch();
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double delta, delta2, delta3, delta4, delta5, delta6;
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double sigman, sigman2 , sigman3, sigman4, sigman5, sigman6;
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double hhss, hhss2, hhss4, hhss7, hhss8; //h^2 - s_n^2
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double hps; //h+s_n
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double hms; //h-s_n
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double twall;
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double A[3][3], nhat[3], SAn[3], that[3];
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double tempvec[3]= {0,0,0};
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double tempvec2[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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nhat[0] = region->contact[m].delx / region->contact[m].r;
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nhat[1] = region->contact[m].dely / region->contact[m].r;
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nhat[2] = region->contact[m].delz / region->contact[m].r;
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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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int *ellipsoid = atom->ellipsoid;
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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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sigman2 = 0.0;
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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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for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
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sigman = sqrt(sigman2);
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delta = fabs(region->contact[m].r);
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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 = -1*coeff4/hhss2 + coeff3
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* (21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6) / hhss8;
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eng = -1*coeff2 * (4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3) +
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coeff1 * (35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4) / hhss7;
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twall = coeff6 * (6*delta3/sigman4/hhss2 - 10*delta/sigman2/hhss2
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+ 3*log(hms/hps)/sigman5)
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+ coeff5 * (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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torque[j] = twall * that[j];
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}
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