forked from lijiext/lammps
small edits for reformatting
This commit is contained in:
Steve Plimpton
parent
51efee43be
commit
aa70f8cc6b
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@ -19,40 +19,40 @@
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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 "force.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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#include "error.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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FixWallReflectStochastic::
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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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if (domain->triclinic != 0)
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error->all(FLERR, "Fix wall/reflect/stochastic cannot be used with "
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"triclinic simulation box");
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dynamic_group_allow = 1;
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// parse args
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int arginc;
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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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@ -67,14 +67,14 @@ FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char *
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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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if (iarg+2 > narg)
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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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@ -86,7 +86,8 @@ FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char *
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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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error->all(FLERR,
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"Fix wall/reflect/stochastic command wall defined twice");
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wallwhich[nwall] = newwall;
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if (strcmp(arg[iarg+1],"EDGE") == 0) {
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@ -100,18 +101,19 @@ FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char *
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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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for (int 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 ((wallvel[nwall][dir] !=0) & (dir == dim))
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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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// one accommodation coefficient for all directions
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wallaccom[nwall][dir]= force->numeric(FLERR,arg[iarg+6]);
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}
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}
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@ -119,7 +121,8 @@ FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char *
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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 (iarg+2 > narg)
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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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@ -133,17 +136,21 @@ FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char *
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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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error->all(FLERR,"Cannot use fix wall/reflect/stochastic "
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"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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error->all(FLERR,"Cannot use fix wall/reflect/stochastic "
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"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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error->all(FLERR,"Cannot use fix wall/reflect/stochastic "
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"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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"Cannot use fix wall/reflect/stochastic zlo/zhi "
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"for a 2d simulation");
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// scale factors for CONSTANT walls, VARIABLE wall is not allowed
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@ -167,14 +174,16 @@ FixWallReflectStochastic::FixWallReflectStochastic(LAMMPS *lmp, int narg, char *
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}
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}
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// random number generator
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random = new RanMars(lmp,seedfix + comm->me);
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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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@ -188,7 +197,6 @@ void FixWallReflectStochastic::wall_particle(int m, int which, double coord)
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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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@ -200,67 +208,67 @@ void FixWallReflectStochastic::wall_particle(int m, int which, double coord)
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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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if (!(mask[i] & groupbit)) continue;
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sign = 0;
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if ((side == 0) & (x[i][dim] < coord)) sign = 1;
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else if ((side == 1) & (x[i][dim] > coord)) sign = -1;
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if (sign == 0) continue;
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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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// theta = kT/m
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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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if (rmass) theta = force->boltz*walltemp[m]/(rmass[i]*force->mvv2e);
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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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// time travelling after collision
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if (reflectionstyle == MAXWELL) {difftest = random->uniform(); }// for Maxwell model only
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timecol = (x[i][dim]-coord) / v[i][dim];
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// only needed for Maxwell model
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if (reflectionstyle == MAXWELL) difftest = random->uniform();
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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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// pushing back atoms to wall position, assign new reflected velocity
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x[i][dir] -= v[i][dir]*timecol;
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// diffusive reflection
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// Diffusive reflection
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if (reflectionstyle == DIFFUSIVE) {
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if (dir != dim) {
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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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else v[i][dir] = sign*random->rayleigh(factor);
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// Maxwell reflection
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if (reflectionstyle == MAXWELL){
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} else if (reflectionstyle == MAXWELL) {
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if (difftest < wallaccom[m][dir]) {
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if (dir != dim) {
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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 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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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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} else if (reflectionstyle == CERCIGNANILAMPIS) {
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if (dir != dim)
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v[i][dir] = wallvel[m][dir] +
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random->gaussian((1-wallaccom[m][dir]) *
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(v[i][dir] - wallvel[m][dir]),
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sqrt((2-wallaccom[m][dir]) *
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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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if (dir != dim) x[i][dir] += v[i][dir]*timecol;
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else x[i][dir] = coord + v[i][dir]*timecol;
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}
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}
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}
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@ -20,7 +20,6 @@ FixStyle(wall/reflect/stochastic,FixWallReflectStochastic)
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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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@ -29,20 +28,16 @@ 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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private:
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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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class RanMars *random;
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void wall_particle(int m,int which, double coord);
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};
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}
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@ -18,30 +18,26 @@
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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 "force.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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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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nwall(0)
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{
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if (narg < 4) error->all(FLERR,"Illegal fix wall/reflect command");
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if (strcmp(arg[2],"wall/reflect/stochastic") == 0) return;// child class can be stochastic
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// let child class process all args
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if (strcmp(arg[2],"wall/reflect/stochastic") == 0) return;
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dynamic_group_allow = 1;
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@ -89,13 +85,13 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
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nwall++;
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iarg += 2;
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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 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 command");
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iarg += 2;
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} else error->all(FLERR,"Illegal fix wall/reflect command");
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}
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@ -146,8 +142,6 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
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if (wallstyle[m] == VARIABLE) varflag = 1;
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}
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/* ---------------------------------------------------------------------- */
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FixWallReflect::~FixWallReflect()
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@ -194,14 +188,11 @@ void FixWallReflect::init()
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void FixWallReflect::post_integrate()
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{
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//int m;
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double coord;
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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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if (varflag) modify->clearstep_compute();
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for (int m = 0; m < nwall; m++) {
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@ -212,17 +203,19 @@ void FixWallReflect::post_integrate()
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else coord *= zscale;
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} else coord = coord0[m];
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wall_particle(m,wallwhich[m],coord);
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}
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if (varflag) modify->addstep_compute(update->ntimestep + 1);
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}
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}
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/* ----------------------------------------------------------------------
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this method may be overwritten by a child class
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------------------------------------------------------------------------- */
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void FixWallReflect::wall_particle(int m, int which, double coord)
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{
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int i, dim, side,sign;
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int i,dim,side;
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double **x = atom->x;
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double **v = atom->v;
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@ -232,9 +225,8 @@ void FixWallReflect::wall_particle(int m, int which, double coord)
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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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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (side == 0) {
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if (x[i][dim] < coord) {
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x[i][dim] = coord + (coord - x[i][dim]);
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@ -248,3 +240,4 @@ void FixWallReflect::wall_particle(int m, int which, double coord)
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}
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}
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}
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}
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@ -26,14 +26,14 @@ namespace LAMMPS_NS {
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class FixWallReflect : public Fix {
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public:
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enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5};
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enum{NONE=0,EDGE,CONSTANT,VARIABLE};
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FixWallReflect(class LAMMPS *, int, char **);
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virtual ~FixWallReflect();
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virtual void wall_particle(int m, int which, double coord);
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int setmask();
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void init();
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void post_integrate();
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enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5};
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enum{NONE=0,EDGE,CONSTANT,VARIABLE};
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protected:
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int nwall;
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@ -43,6 +43,8 @@ class FixWallReflect : public Fix {
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int varindex[6];
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int varflag;
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double xscale,yscale,zscale;
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virtual void wall_particle(int m, int which, double coord);
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||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -90,7 +90,6 @@ double RanMars::uniform()
|
|||
return uni;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
gaussian RN
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
@ -127,7 +126,6 @@ double RanMars::gaussian(double mu, double sigma)
|
|||
return v1;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Rayleigh RN
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
@ -136,15 +134,12 @@ double RanMars::rayleigh(double sigma)
|
|||
{
|
||||
double first,v1;
|
||||
|
||||
if (sigma <= 0) {
|
||||
error->all(FLERR,"Invalid Rayleigh parameter");
|
||||
} else {
|
||||
if (sigma <= 0) error->all(FLERR,"Invalid Rayleigh parameter");
|
||||
|
||||
v1 = uniform();
|
||||
first = sigma*sqrt(-2.0*log(v1));
|
||||
return first;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Bessel exponential RN
|
||||
|
|
@ -153,20 +148,21 @@ double RanMars::rayleigh(double sigma)
|
|||
double RanMars::besselexp(double theta, double alpha, double cp)
|
||||
{
|
||||
double first,v1,v2;
|
||||
if ((theta < 0) || (alpha < 0) || (alpha >1)) {
|
||||
|
||||
if (theta < 0.0 || alpha < 0.0 || alpha < 1.0)
|
||||
error->all(FLERR,"Invalid Bessel exponential distribution parameters");
|
||||
} else {
|
||||
|
||||
v1 = uniform();
|
||||
v2 = uniform();
|
||||
if (cp < 0) {
|
||||
first = sqrt((1.0-alpha)*cp*cp - 2.0*alpha*theta*log(v1)
|
||||
+ 2.0*sqrt(-2.0*theta*(1.0-alpha)*alpha*log(v1))
|
||||
* cos(2.0*MathConst::MY_PI*v2)*cp);
|
||||
} else {
|
||||
first = -sqrt((1.0-alpha)*cp*cp - 2.0*alpha*theta*log(v1)
|
||||
- 2.0*sqrt(-2.0*theta*(1.0-alpha)*alpha*log(v1))
|
||||
* cos(2.0*MathConst::MY_PI*v2)*cp);
|
||||
}
|
||||
|
||||
if (cp < 0.0)
|
||||
first = sqrt((1.0-alpha)*cp*cp - 2.0*alpha*theta*log(v1) +
|
||||
2.0*sqrt(-2.0*theta*(1.0-alpha)*alpha*log(v1)) *
|
||||
cos(2.0*MathConst::MY_PI*v2)*cp);
|
||||
else
|
||||
first = -sqrt((1.0-alpha)*cp*cp - 2.0*alpha*theta*log(v1) -
|
||||
2.0*sqrt(-2.0*theta*(1.0-alpha)*alpha*log(v1)) *
|
||||
cos(2.0*MathConst::MY_PI*v2)*cp);
|
||||
|
||||
return first;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue