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src/USER-MISC/fix_wall_reflect_stochastic.cpp
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266
src/USER-MISC/fix_wall_reflect_stochastic.cpp
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/* ----------------------------------------------------------------------
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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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#include "fix_wall_reflect_stochastic.h"
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#include <cstring>
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#include <cstdlib>
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#include "atom.h"
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#include "comm.h"
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#include "update.h"
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#include "modify.h"
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#include "domain.h"
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#include "lattice.h"
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#include "input.h"
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#include "variable.h"
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#include "error.h"
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#include "force.h"
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#include "random_mars.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{NONE=0,DIFFUSIVE=1,MAXWELL=2,CERCIGNANILAMPIS=3};
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/* ---------------------------------------------------------------------- */
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FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) :
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FixWallReflect(lmp, narg, arg), random(NULL)
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{
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int arginc,dir;
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if (narg < 8) error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
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if (domain->triclinic != 0) error->all(FLERR, "This fix wall/reflect/stochastic is not incompatible with triclinic simulation box");
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dynamic_group_allow = 1;
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// parse args
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nwall = 0;
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int scaleflag = 1;
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reflectionstyle = NONE;
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if (strcmp(arg[3],"diffusive") == 0) {
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reflectionstyle = DIFFUSIVE;
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arginc = 6;
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} else if (strcmp(arg[3],"maxwell") == 0) {
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reflectionstyle = MAXWELL;
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arginc = 7;
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} else if (strcmp(arg[3],"cercignanilampis") == 0) {
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reflectionstyle = CERCIGNANILAMPIS;
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arginc = 9;
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} else error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
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seedfix = force->inumeric(FLERR,arg[4]);
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if (seedfix <=0) error->all(FLERR,"Random seed must be a postive number");
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random = new RanMars(lmp,seedfix + comm->me);
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int iarg = 5;
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while (iarg < narg) {
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if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
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(strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
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(strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
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int newwall;
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if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO;
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else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI;
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else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO;
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else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI;
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else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO;
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else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
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for (int m = 0; (m < nwall) && (m < 6); m++)
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if (newwall == wallwhich[m])
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error->all(FLERR,"Wall defined twice in fix wall/reflect/stochastic command");
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wallwhich[nwall] = newwall;
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if (strcmp(arg[iarg+1],"EDGE") == 0) {
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wallstyle[nwall] = EDGE;
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int dim = wallwhich[nwall] / 2;
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int side = wallwhich[nwall] % 2;
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if (side == 0) coord0[nwall] = domain->boxlo[dim];
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else coord0[nwall] = domain->boxhi[dim];
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} else {
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wallstyle[nwall] = CONSTANT;
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coord0[nwall] = force->numeric(FLERR,arg[iarg+1]);
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}
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walltemp[nwall]= force->numeric(FLERR,arg[iarg+2]);
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for (dir = 0; dir < 3; dir++) {
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wallvel[nwall][dir]= force->numeric(FLERR,arg[iarg+dir+3]);
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int dim = wallwhich[nwall] / 2;
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if ((wallvel[nwall][dir] !=0) & (dir == dim)) error->all(FLERR,"The wall velocity must be tangential");
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if (reflectionstyle == CERCIGNANILAMPIS) {
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wallaccom[nwall][dir]= force->numeric(FLERR,arg[iarg+dir+6]);
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} else if (reflectionstyle == MAXWELL) {
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wallaccom[nwall][dir]= force->numeric(FLERR,arg[iarg+6]);// One accommodation coefficient for all directions
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}
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}
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nwall++;
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iarg += arginc;
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} else if (strcmp(arg[iarg],"units") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal wall/reflect/stochastic command");
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if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
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else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
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else error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
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iarg += 2;
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} else error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
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}
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// error check
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if (nwall == 0) error->all(FLERR,"Illegal fix wall command");
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for (int m = 0; m < nwall; m++) {
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if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic)
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error->all(FLERR,"Cannot use fix wall/reflect/stochastic in periodic dimension");
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if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic)
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error->all(FLERR,"Cannot use fix wall/reflect/stochastic in periodic dimension");
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if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic)
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error->all(FLERR,"Cannot use fix wall/reflect/stochastic in periodic dimension");
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}
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for (int m = 0; m < nwall; m++)
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if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
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error->all(FLERR,
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"Cannot use fix wall/reflect/stochastic zlo/zhi for a 2d simulation");
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// scale factors for CONSTANT walls, VARIABLE wall is not allowed
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int flag = 0;
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for (int m = 0; m < nwall; m++)
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if (wallstyle[m] != EDGE) flag = 1;
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if (flag) {
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if (scaleflag) {
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xscale = domain->lattice->xlattice;
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yscale = domain->lattice->ylattice;
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zscale = domain->lattice->zlattice;
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}
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else xscale = yscale = zscale = 1.0;
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for (int m = 0; m < nwall; m++) {
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if (wallstyle[m] != CONSTANT) continue;
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if (wallwhich[m] < YLO) coord0[m] *= xscale;
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else if (wallwhich[m] < ZLO) coord0[m] *= yscale;
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else coord0[m] *= zscale;
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}
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}
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}
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FixWallReflectStochastic::~FixWallReflectStochastic()
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{
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delete random ;
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}
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/* ---------------------------------------------------------------------- */
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void FixWallReflectStochastic::wall_particle(int m, int which, double coord)
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{
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int i, dir, dim, side, sign;
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double vsave,factor,timecol,difftest,theta;
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double *rmass;
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double *mass = atom->mass;
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// coord = current position of wall
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// evaluate variable if necessary, wrap with clear/add
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double **x = atom->x;
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double **v = atom->v;
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int *mask = atom->mask;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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dim = which / 2;
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side = which % 2;
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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sign = 0;
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if ((side == 0) & (x[i][dim] < coord)){
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sign = 1;
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} else if ((side == 1) & (x[i][dim] > coord)){
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sign = -1;
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}
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if (sign != 0) {
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if (rmass) theta = force->boltz*walltemp[m]/(rmass[i]*force->mvv2e);// theta = kT/m
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else theta = force->boltz*walltemp[m]/(mass[type[i]]*force->mvv2e);
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factor = sqrt(theta);
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timecol= (x[i][dim] - coord)/v[i][dim]; // time travelling after collision
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if (reflectionstyle == MAXWELL) {difftest = random->uniform(); }// for Maxwell model only
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for (dir = 0; dir < 3; dir++) {
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x[i][dir] -= v[i][dir]*timecol; // pushing back atoms to the wall position and assign new reflected velocity
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// Diffusive reflection
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if (reflectionstyle == DIFFUSIVE){
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if (dir != dim) {
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v[i][dir] = wallvel[m][dir] + random->gaussian(0,factor);
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} else { v[i][dir] = sign*random->rayleigh(factor) ; }
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}
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// Maxwell reflection
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if (reflectionstyle == MAXWELL){
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if (difftest < wallaccom[m][dir]) {
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if (dir != dim) {
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v[i][dir] = wallvel[m][dir] + random->gaussian(0,factor);
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} else { v[i][dir] = sign*random->rayleigh(factor) ; }
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} else {
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if (dir == dim) {v[i][dir] = -v[i][dir];
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}
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}
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}
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// Cercignani Lampis reflection
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if (reflectionstyle == CERCIGNANILAMPIS){
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if (dir != dim) {
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v[i][dir] = wallvel[m][dir] + random->gaussian((1-wallaccom[m][dir])*(v[i][dir]-wallvel[m][dir]),sqrt((2-wallaccom[m][dir])*wallaccom[m][dir]*theta)) ;
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} else { v[i][dir] = random->besselexp(theta, wallaccom[m][dir], v[i][dir]) ; }
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}
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// update new position due to the new velocity
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if (dir != dim) {
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x[i][dir] += v[i][dir]*timecol; }
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else {x[i][dir] = coord + v[i][dir]*timecol;}
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}// for loop
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}// if sign
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}// if mask
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}
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}
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85
src/USER-MISC/fix_wall_reflect_stochastic.h
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85
src/USER-MISC/fix_wall_reflect_stochastic.h
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@ -0,0 +1,85 @@
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/* -*- 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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#ifdef FIX_CLASS
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FixStyle(wall/reflect/stochastic,FixWallReflectStochastic)
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#else
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#ifndef LMP_FIX_WALL_REFLECT_STOCHASTIC_H
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#define LMP_FIX_WALL_REFLECT_STOCHASTIC_H
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#include "random_mars.h"
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#include "fix_wall_reflect.h"
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namespace LAMMPS_NS {
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class FixWallReflectStochastic : public FixWallReflect {
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public:
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FixWallReflectStochastic(class LAMMPS *, int, char **);
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void wall_particle(int m,int which, double coord);
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virtual ~FixWallReflectStochastic();
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protected:
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class RanMars *random;
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int seedfix;
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double walltemp[6],wallvel[6][3],wallaccom[6][3];
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int reflectionstyle;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Wall defined twice in fix wall/stochastic command
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Self-explanatory.
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E: Cannot use fix wall/stochastic in periodic dimension
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Self-explanatory.
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E: Cannot use fix wall/stochastic zlo/zhi for a 2d simulation
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Self-explanatory.
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E: Variable name for fix wall/stochastic does not exist
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Self-explanatory.
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E: Variable for fix wall/stochastic is invalid style
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Only equal-style variables can be used.
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W: Should not allow rigid bodies to bounce off relecting walls
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LAMMPS allows this, but their dynamics are not computed correctly.
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*/
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