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fix_wall_gran.cpp
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Tue, Feb 18, 23:00

fix_wall_gran.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL),
Dan Bolintineanu (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_wall_gran.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "modify.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
// XYZ PLANE need to be 0,1,2
enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION};
enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,BONDED_HISTORY};
enum{NONE,CONSTANT,EQUAL};
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), idregion(NULL), shearone(NULL), fix_rigid(NULL), mass_rigid(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix wall/gran command");
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/gran requires atom style sphere");
create_attribute = 1;
// set interaction style
// disable bonded/history option for now
if (strcmp(arg[3],"hooke") == 0) pairstyle = HOOKE;
else if (strcmp(arg[3],"hooke/history") == 0) pairstyle = HOOKE_HISTORY;
else if (strcmp(arg[3],"hertz/history") == 0) pairstyle = HERTZ_HISTORY;
//else if (strcmp(arg[3],"bonded/history") == 0) pairstyle = BONDED_HISTORY;
else error->all(FLERR,"Invalid fix wall/gran interaction style");
history = restart_peratom = 1;
if (pairstyle == HOOKE) history = restart_peratom = 0;
// wall/particle coefficients
int iarg;
if (pairstyle != BONDED_HISTORY) {
if (narg < 11) error->all(FLERR,"Illegal fix wall/gran command");
kn = force->numeric(FLERR,arg[4]);
if (strcmp(arg[5],"NULL") == 0) kt = kn * 2.0/7.0;
else kt = force->numeric(FLERR,arg[5]);
gamman = force->numeric(FLERR,arg[6]);
if (strcmp(arg[7],"NULL") == 0) gammat = 0.5 * gamman;
else gammat = force->numeric(FLERR,arg[7]);
xmu = force->numeric(FLERR,arg[8]);
int dampflag = force->inumeric(FLERR,arg[9]);
if (dampflag == 0) gammat = 0.0;
if (kn < 0.0 || kt < 0.0 || gamman < 0.0 || gammat < 0.0 ||
xmu < 0.0 || xmu > 10000.0 || dampflag < 0 || dampflag > 1)
error->all(FLERR,"Illegal fix wall/gran command");
// convert Kn and Kt from pressure units to force/distance^2 if Hertzian
if (pairstyle == HERTZ_HISTORY) {
kn /= force->nktv2p;
kt /= force->nktv2p;
}
iarg = 10;
}
else {
if (narg < 10) error->all(FLERR,"Illegal fix wall/gran command");
E = force->numeric(FLERR,arg[4]);
G = force->numeric(FLERR,arg[5]);
SurfEnergy = force->numeric(FLERR,arg[6]);
// Note: this doesn't get used, check w/ Jeremy?
gamman = force->numeric(FLERR,arg[7]);
xmu = force->numeric(FLERR,arg[8]);
// pois = E/(2.0*G) - 1.0;
// kn = 2.0*E/(3.0*(1.0+pois)*(1.0-pois));
// gammat=0.5*gamman;
iarg = 9;
}
// wallstyle args
idregion = NULL;
if (strcmp(arg[iarg],"xplane") == 0) {
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/gran command");
wallstyle = XPLANE;
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
else lo = force->numeric(FLERR,arg[iarg+1]);
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
else hi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"yplane") == 0) {
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/gran command");
wallstyle = YPLANE;
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
else lo = force->numeric(FLERR,arg[iarg+1]);
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
else hi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"zplane") == 0) {
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/gran command");
wallstyle = ZPLANE;
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
else lo = force->numeric(FLERR,arg[iarg+1]);
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
else hi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"zcylinder") == 0) {
if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command");
wallstyle = ZCYLINDER;
lo = hi = 0.0;
cylradius = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command");
wallstyle = REGION;
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
}
// optional args
wiggle = 0;
wshear = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"wiggle") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/gran command");
if (strcmp(arg[iarg+1],"x") == 0) axis = 0;
else if (strcmp(arg[iarg+1],"y") == 0) axis = 1;
else if (strcmp(arg[iarg+1],"z") == 0) axis = 2;
else error->all(FLERR,"Illegal fix wall/gran command");
amplitude = force->numeric(FLERR,arg[iarg+2]);
period = force->numeric(FLERR,arg[iarg+3]);
wiggle = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"shear") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix wall/gran command");
if (strcmp(arg[iarg+1],"x") == 0) axis = 0;
else if (strcmp(arg[iarg+1],"y") == 0) axis = 1;
else if (strcmp(arg[iarg+1],"z") == 0) axis = 2;
else error->all(FLERR,"Illegal fix wall/gran command");
vshear = force->numeric(FLERR,arg[iarg+2]);
wshear = 1;
iarg += 3;
} else error->all(FLERR,"Illegal fix wall/gran command");
}
if (wallstyle == XPLANE && domain->xperiodic)
error->all(FLERR,"Cannot use wall in periodic dimension");
if (wallstyle == YPLANE && domain->yperiodic)
error->all(FLERR,"Cannot use wall in periodic dimension");
if (wallstyle == ZPLANE && domain->zperiodic)
error->all(FLERR,"Cannot use wall in periodic dimension");
if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic))
error->all(FLERR,"Cannot use wall in periodic dimension");
if (wiggle && wshear)
error->all(FLERR,"Cannot wiggle and shear fix wall/gran");
if (wiggle && wallstyle == ZCYLINDER && axis != 2)
error->all(FLERR,"Invalid wiggle direction for fix wall/gran");
if (wshear && wallstyle == XPLANE && axis == 0)
error->all(FLERR,"Invalid shear direction for fix wall/gran");
if (wshear && wallstyle == YPLANE && axis == 1)
error->all(FLERR,"Invalid shear direction for fix wall/gran");
if (wshear && wallstyle == ZPLANE && axis == 2)
error->all(FLERR,"Invalid shear direction for fix wall/gran");
if ((wiggle || wshear) && wallstyle == REGION)
error->all(FLERR,"Cannot wiggle or shear with fix wall/gran/region");
// setup oscillations
if (wiggle) omega = 2.0*MY_PI / period;
// perform initial allocation of atom-based arrays
// register with Atom class
if (pairstyle == BONDED_HISTORY) sheardim = 7;
else sheardim = 3;
shearone = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
nmax = 0;
mass_rigid = NULL;
// initialize shear history as if particle is not touching region
// shearone will be NULL for wallstyle = REGION
if (history && shearone) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < sheardim; j++)
shearone[i][j] = 0.0;
}
time_origin = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
FixWallGran::~FixWallGran()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete local storage
delete [] idregion;
memory->destroy(shearone);
memory->destroy(mass_rigid);
}
/* ---------------------------------------------------------------------- */
int FixWallGran::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWallGran::init()
{
int i;
dt = update->dt;
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// check for FixRigid so can extract rigid body masses
fix_rigid = NULL;
for (i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) break;
if (i < modify->nfix) fix_rigid = modify->fix[i];
}
/* ---------------------------------------------------------------------- */
void FixWallGran::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixWallGran::post_force(int vflag)
{
int i,j;
double dx,dy,dz,del1,del2,delxy,delr,rsq,rwall,meff;
double vwall[3];
// do not update shear history during setup
shearupdate = 1;
if (update->setupflag) shearupdate = 0;
// if just reneighbored:
// update rigid body masses for owned atoms if using FixRigid
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if (neighbor->ago == 0 && fix_rigid) {
int tmp;
int *body = (int *) fix_rigid->extract("body",tmp);
double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
if (atom->nmax > nmax) {
memory->destroy(mass_rigid);
nmax = atom->nmax;
memory->create(mass_rigid,nmax,"wall/gran:mass_rigid");
}
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
else mass_rigid[i] = 0.0;
}
}
// set position of wall to initial settings and velocity to 0.0
// if wiggle or shear, set wall position and velocity accordingly
double wlo = lo;
double whi = hi;
vwall[0] = vwall[1] = vwall[2] = 0.0;
if (wiggle) {
double arg = omega * (update->ntimestep - time_origin) * dt;
if (wallstyle == axis) {
wlo = lo + amplitude - amplitude*cos(arg);
whi = hi + amplitude - amplitude*cos(arg);
}
vwall[axis] = amplitude*omega*sin(arg);
} else if (wshear) vwall[axis] = vshear;
// loop over all my atoms
// rsq = distance from wall
// dx,dy,dz = signed distance from wall
// for rotating cylinder, reset vwall based on particle position
// skip atom if not close enough to wall
// if wall was set to NULL, it's skipped since lo/hi are infinity
// compute force and torque on atom if close enough to wall
// via wall potential matched to pair potential
// set shear if pair potential stores history
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
rwall = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dx = dy = dz = 0.0;
if (wallstyle == XPLANE) {
del1 = x[i][0] - wlo;
del2 = whi - x[i][0];
if (del1 < del2) dx = del1;
else dx = -del2;
} else if (wallstyle == YPLANE) {
del1 = x[i][1] - wlo;
del2 = whi - x[i][1];
if (del1 < del2) dy = del1;
else dy = -del2;
} else if (wallstyle == ZPLANE) {
del1 = x[i][2] - wlo;
del2 = whi - x[i][2];
if (del1 < del2) dz = del1;
else dz = -del2;
} else if (wallstyle == ZCYLINDER) {
delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]);
delr = cylradius - delxy;
if (delr > radius[i]) {
dz = cylradius;
rwall = 0.0;
} else {
dx = -delr/delxy * x[i][0];
dy = -delr/delxy * x[i][1];
// rwall = -2r_c if inside cylinder, 2r_c outside
rwall = (delxy < cylradius) ? -2*cylradius : 2*cylradius;
if (wshear && axis != 2) {
vwall[0] += vshear * x[i][1]/delxy;
vwall[1] += -vshear * x[i][0]/delxy;
vwall[2] = 0.0;
}
}
}
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) {
if (history)
for (j = 0; j < sheardim; j++)
shearone[i][j] = 0.0;
} else {
// meff = effective mass of sphere
// if I is part of rigid body, use body mass
meff = rmass[i];
if (fix_rigid && mass_rigid[i] > 0.0) meff = mass_rigid[i];
// invoke sphere/wall interaction
if (pairstyle == HOOKE)
hooke(rsq,dx,dy,dz,vwall,v[i],f[i],
omega[i],torque[i],radius[i],meff);
else if (pairstyle == HOOKE_HISTORY)
hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],
omega[i],torque[i],radius[i],meff,shearone[i]);
else if (pairstyle == HERTZ_HISTORY)
hertz_history(rsq,dx,dy,dz,vwall,rwall,v[i],f[i],
omega[i],torque[i],radius[i],meff,shearone[i]);
else if (pairstyle == BONDED_HISTORY)
bonded_history(rsq,dx,dy,dz,vwall,rwall,v[i],f[i],
omega[i],torque[i],radius[i],meff,shearone[i]);
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixWallGran::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallGran::hooke(double rsq, double dx, double dy, double dz,
double *vwall, double *v,
double *f, double *omega, double *torque,
double radius, double meff)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,damp,ccel,vtr1,vtr2,vtr3,vrel;
double fn,fs,ft,fs1,fs2,fs3,fx,fy,fz,tor1,tor2,tor3,rinv,rsqinv;
r = sqrt(rsq);
rinv = 1.0/r;
rsqinv = 1.0/rsq;
// relative translational velocity
vr1 = v[0] - vwall[0];
vr2 = v[1] - vwall[1];
vr3 = v[2] - vwall[2];
// normal component
vnnr = vr1*dx + vr2*dy + vr3*dz;
vn1 = dx*vnnr * rsqinv;
vn2 = dy*vnnr * rsqinv;
vn3 = dz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
wr1 = radius*omega[0] * rinv;
wr2 = radius*omega[1] * rinv;
wr3 = radius*omega[2] * rinv;
// normal forces = Hookian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radius-r)*rinv - damp;
// relative velocities
vtr1 = vt1 - (dz*wr2-dy*wr3);
vtr2 = vt2 - (dx*wr3-dz*wr1);
vtr3 = vt3 - (dy*wr1-dx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
// force normalization
fn = xmu * fabs(ccel*r);
fs = meff*gammat*vrel;
if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
else ft = 0.0;
// tangential force due to tangential velocity damping
fs1 = -ft*vtr1;
fs2 = -ft*vtr2;
fs3 = -ft*vtr3;
// forces & torques
fx = dx*ccel + fs1;
fy = dy*ccel + fs2;
fz = dz*ccel + fs3;
f[0] += fx;
f[1] += fy;
f[2] += fz;
tor1 = rinv * (dy*fs3 - dz*fs2);
tor2 = rinv * (dz*fs1 - dx*fs3);
tor3 = rinv * (dx*fs2 - dy*fs1);
torque[0] -= radius*tor1;
torque[1] -= radius*tor2;
torque[2] -= radius*tor3;
}
/* ---------------------------------------------------------------------- */
void FixWallGran::hooke_history(double rsq, double dx, double dy, double dz,
double *vwall, double *v,
double *f, double *omega, double *torque,
double radius, double meff, double *shear)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,damp,ccel,vtr1,vtr2,vtr3,vrel;
double fn,fs,fs1,fs2,fs3,fx,fy,fz,tor1,tor2,tor3;
double shrmag,rsht,rinv,rsqinv;
r = sqrt(rsq);
rinv = 1.0/r;
rsqinv = 1.0/rsq;
// relative translational velocity
vr1 = v[0] - vwall[0];
vr2 = v[1] - vwall[1];
vr3 = v[2] - vwall[2];
// normal component
vnnr = vr1*dx + vr2*dy + vr3*dz;
vn1 = dx*vnnr * rsqinv;
vn2 = dy*vnnr * rsqinv;
vn3 = dz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
wr1 = radius*omega[0] * rinv;
wr2 = radius*omega[1] * rinv;
wr3 = radius*omega[2] * rinv;
// normal forces = Hookian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radius-r)*rinv - damp;
// relative velocities
vtr1 = vt1 - (dz*wr2-dy*wr3);
vtr2 = vt2 - (dx*wr3-dz*wr1);
vtr3 = vt3 - (dy*wr1-dx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
// shear history effects
if (shearupdate) {
shear[0] += vtr1*dt;
shear[1] += vtr2*dt;
shear[2] += vtr3*dt;
}
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] + shear[2]*shear[2]);
// rotate shear displacements
rsht = shear[0]*dx + shear[1]*dy + shear[2]*dz;
rsht = rsht*rsqinv;
if (shearupdate) {
shear[0] -= rsht*dx;
shear[1] -= rsht*dy;
shear[2] -= rsht*dz;
}
// tangential forces = shear + tangential velocity damping
fs1 = - (kt*shear[0] + meff*gammat*vtr1);
fs2 = - (kt*shear[1] + meff*gammat*vtr2);
fs3 = - (kt*shear[2] + meff*gammat*vtr3);
// rescale frictional displacements and forces if needed
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
fn = xmu * fabs(ccel*r);
if (fs > fn) {
if (shrmag != 0.0) {
shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
meff*gammat*vtr1/kt;
shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
meff*gammat*vtr2/kt;
shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
meff*gammat*vtr3/kt;
fs1 *= fn/fs ;
fs2 *= fn/fs;
fs3 *= fn/fs;
} else fs1 = fs2 = fs3 = 0.0;
}
// forces & torques
fx = dx*ccel + fs1;
fy = dy*ccel + fs2;
fz = dz*ccel + fs3;
f[0] += fx;
f[1] += fy;
f[2] += fz;
tor1 = rinv * (dy*fs3 - dz*fs2);
tor2 = rinv * (dz*fs1 - dx*fs3);
tor3 = rinv * (dx*fs2 - dy*fs1);
torque[0] -= radius*tor1;
torque[1] -= radius*tor2;
torque[2] -= radius*tor3;
}
/* ---------------------------------------------------------------------- */
void FixWallGran::hertz_history(double rsq, double dx, double dy, double dz,
double *vwall, double rwall, double *v,
double *f, double *omega, double *torque,
double radius, double meff, double *shear)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,damp,ccel,vtr1,vtr2,vtr3,vrel;
double fn,fs,fs1,fs2,fs3,fx,fy,fz,tor1,tor2,tor3;
double shrmag,rsht,polyhertz,rinv,rsqinv;
r = sqrt(rsq);
rinv = 1.0/r;
rsqinv = 1.0/rsq;
// relative translational velocity
vr1 = v[0] - vwall[0];
vr2 = v[1] - vwall[1];
vr3 = v[2] - vwall[2];
// normal component
vnnr = vr1*dx + vr2*dy + vr3*dz;
vn1 = dx*vnnr / rsq;
vn2 = dy*vnnr / rsq;
vn3 = dz*vnnr / rsq;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
wr1 = radius*omega[0] * rinv;
wr2 = radius*omega[1] * rinv;
wr3 = radius*omega[2] * rinv;
// normal forces = Hertzian contact + normal velocity damping
// rwall = 0 is flat wall case
// rwall positive or negative is curved wall
// will break (as it should) if rwall is negative and
// its absolute value < radius of particle
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radius-r)*rinv - damp;
if (rwall == 0.0) polyhertz = sqrt((radius-r)*radius);
else polyhertz = sqrt((radius-r)*radius*rwall/(rwall+radius));
ccel *= polyhertz;
// relative velocities
vtr1 = vt1 - (dz*wr2-dy*wr3);
vtr2 = vt2 - (dx*wr3-dz*wr1);
vtr3 = vt3 - (dy*wr1-dx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
// shear history effects
if (shearupdate) {
shear[0] += vtr1*dt;
shear[1] += vtr2*dt;
shear[2] += vtr3*dt;
}
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] + shear[2]*shear[2]);
// rotate shear displacements
rsht = shear[0]*dx + shear[1]*dy + shear[2]*dz;
rsht = rsht*rsqinv;
if (shearupdate) {
shear[0] -= rsht*dx;
shear[1] -= rsht*dy;
shear[2] -= rsht*dz;
}
// tangential forces = shear + tangential velocity damping
fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);
fs2 = -polyhertz * (kt*shear[1] + meff*gammat*vtr2);
fs3 = -polyhertz * (kt*shear[2] + meff*gammat*vtr3);
// rescale frictional displacements and forces if needed
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
fn = xmu * fabs(ccel*r);
if (fs > fn) {
if (shrmag != 0.0) {
shear[0] = (fn/fs) * (shear[0] + meff*gammat*vtr1/kt) -
meff*gammat*vtr1/kt;
shear[1] = (fn/fs) * (shear[1] + meff*gammat*vtr2/kt) -
meff*gammat*vtr2/kt;
shear[2] = (fn/fs) * (shear[2] + meff*gammat*vtr3/kt) -
meff*gammat*vtr3/kt;
fs1 *= fn/fs ;
fs2 *= fn/fs;
fs3 *= fn/fs;
} else fs1 = fs2 = fs3 = 0.0;
}
// forces & torques
fx = dx*ccel + fs1;
fy = dy*ccel + fs2;
fz = dz*ccel + fs3;
f[0] += fx;
f[1] += fy;
f[2] += fz;
tor1 = rinv * (dy*fs3 - dz*fs2);
tor2 = rinv * (dz*fs1 - dx*fs3);
tor3 = rinv * (dx*fs2 - dy*fs1);
torque[0] -= radius*tor1;
torque[1] -= radius*tor2;
torque[2] -= radius*tor3;
}
/* ---------------------------------------------------------------------- */
void FixWallGran::bonded_history(double rsq, double dx, double dy, double dz,
double *vwall, double rwall, double *v,
double *f, double *omega, double *torque,
double radius, double meff, double *shear)
{
double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3,damp,ccel,vtr1,vtr2,vtr3,vrel;
double fn,fs,fs1,fs2,fs3,fx,fy,fz,tor1,tor2,tor3;
double shrmag,rsht,polyhertz,rinv,rsqinv;
double pois,E_eff,G_eff,rad_eff;
double a0,Fcrit,delcrit,delcritinv;
double overlap,olapsq,olapcubed,sqrtterm,tmp,keyterm,keyterm2,keyterm3;
double aovera0,foverFc;
double gammatsuji;
double ktwist,kroll,twistcrit,rollcrit;
double relrot1,relrot2,relrot3,vrl1,vrl2,vrl3,vrlmag,vrlmaginv;
double magtwist,magtortwist;
double magrollsq,magroll,magrollinv,magtorroll;
r = sqrt(rsq);
rinv = 1.0/r;
rsqinv = 1.0/rsq;
// relative translational velocity
vr1 = v[0] - vwall[0];
vr2 = v[1] - vwall[1];
vr3 = v[2] - vwall[2];
// normal component
vnnr = vr1*dx + vr2*dy + vr3*dz;
vn1 = dx*vnnr / rsq;
vn2 = dy*vnnr / rsq;
vn3 = dz*vnnr / rsq;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
wr1 = radius*omega[0] * rinv;
wr2 = radius*omega[1] * rinv;
wr3 = radius*omega[2] * rinv;
// normal forces = Hertzian contact + normal velocity damping
// material properties: currently assumes identical materials
pois = E/(2.0*G) - 1.0;
E_eff=0.5*E/(1.0-pois*pois);
G_eff=G/(4.0-2.0*pois);
// rwall = 0 is infinite wall radius of curvature (flat wall)
if (rwall == 0) rad_eff = radius;
else rad_eff = radius*rwall/(radius+rwall);
Fcrit = rad_eff * (3.0 * M_PI * SurfEnergy);
a0=pow(9.0*M_PI*SurfEnergy*rad_eff*rad_eff/E_eff,1.0/3.0);
delcrit = 1.0/rad_eff*(0.5 * a0*a0/pow(6.0,1.0/3.0));
delcritinv = 1.0/delcrit;
overlap = (radius-r) * delcritinv;
olapsq = overlap*overlap;
olapcubed = olapsq*overlap;
sqrtterm = sqrt(1.0 + olapcubed);
tmp = 2.0 + olapcubed + 2.0*sqrtterm;
keyterm = pow(tmp,THIRD);
keyterm2 = olapsq/keyterm;
keyterm3 = sqrt(overlap + keyterm2 + keyterm);
aovera0 = pow(6.0,-TWOTHIRDS) * (keyterm3 +
sqrt(2.0*overlap - keyterm2 - keyterm + 4.0/keyterm3));
foverFc = 4.0*((aovera0*aovera0*aovera0) - pow(aovera0,1.5));
ccel = Fcrit*foverFc*rinv;
// damp = meff*gamman*vnnr*rsqinv;
// ccel = kn*(radius-r)*rinv - damp;
// polyhertz = sqrt((radius-r)*radius);
// ccel *= polyhertz;
// use Tsuji et al form
polyhertz = 1.2728- 4.2783*0.9 + 11.087*0.9*0.9 - 22.348*0.9*0.9*0.9 +
27.467*0.9*0.9*0.9*0.9 - 18.022*0.9*0.9*0.9*0.9*0.9 +
4.8218*0.9*0.9*0.9*0.9*0.9*0.9;
gammatsuji = 0.2*sqrt(meff*kn);
damp = gammatsuji*vnnr/rsq;
ccel = ccel - polyhertz * damp;
// relative velocities
vtr1 = vt1 - (dz*wr2-dy*wr3);
vtr2 = vt2 - (dx*wr3-dz*wr1);
vtr3 = vt3 - (dy*wr1-dx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
// shear history effects
if (shearupdate) {
shear[0] += vtr1*dt;
shear[1] += vtr2*dt;
shear[2] += vtr3*dt;
}
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] + shear[2]*shear[2]);
// rotate shear displacements
rsht = shear[0]*dx + shear[1]*dy + shear[2]*dz;
rsht = rsht*rsqinv;
if (shearupdate) {
shear[0] -= rsht*dx;
shear[1] -= rsht*dy;
shear[2] -= rsht*dz;
}
// tangential forces = shear + tangential velocity damping
fs1 = -polyhertz * (kt*shear[0] + meff*gammat*vtr1);
fs2 = -polyhertz * (kt*shear[1] + meff*gammat*vtr2);
fs3 = -polyhertz * (kt*shear[2] + meff*gammat*vtr3);
kt=8.0*G_eff*a0*aovera0;
// shear damping uses Tsuji et al form also
fs1 = -kt*shear[0] - polyhertz*gammatsuji*vtr1;
fs2 = -kt*shear[1] - polyhertz*gammatsuji*vtr2;
fs3 = -kt*shear[2] - polyhertz*gammatsuji*vtr3;
// rescale frictional displacements and forces if needed
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
fn = xmu * fabs(ccel*r + 2.0*Fcrit);
if (fs > fn) {
if (shrmag != 0.0) {
shear[0] = (fn/fs) * (shear[0] + polyhertz*gammatsuji*vtr1/kt) -
polyhertz*gammatsuji*vtr1/kt;
shear[1] = (fn/fs) * (shear[1] + polyhertz*gammatsuji*vtr2/kt) -
polyhertz*gammatsuji*vtr2/kt;
shear[2] = (fn/fs) * (shear[2] + polyhertz*gammatsuji*vtr3/kt) -
polyhertz*gammatsuji*vtr3/kt;
fs1 *= fn/fs ;
fs2 *= fn/fs;
fs3 *= fn/fs;
} else fs1 = fs2 = fs3 = 0.0;
}
// calculate twisting and rolling components of torque
// NOTE: this assumes spheres!
relrot1 = omega[0];
relrot2 = omega[1];
relrot3 = omega[2];
// rolling velocity
// NOTE: this assumes mondisperse spheres!
vrl1 = -rad_eff*rinv * (relrot2*dz - relrot3*dy);
vrl2 = -rad_eff*rinv * (relrot3*dx - relrot1*dz);
vrl3 = -rad_eff*rinv * (relrot1*dy - relrot2*dx);
vrlmag = sqrt(vrl1*vrl1+vrl2*vrl2+vrl3*vrl3);
if (vrlmag != 0.0) vrlmaginv = 1.0/vrlmag;
else vrlmaginv = 0.0;
// bond history effects
shear[3] += vrl1*dt;
shear[4] += vrl2*dt;
shear[5] += vrl3*dt;
// rotate bonded displacements correctly
double rlt = shear[3]*dx + shear[4]*dy + shear[5]*dz;
rlt /= rsq;
shear[3] -= rlt*dx;
shear[4] -= rlt*dy;
shear[5] -= rlt*dz;
// twisting torque
magtwist = rinv*(relrot1*dx + relrot2*dy + relrot3*dz);
shear[6] += magtwist*dt;
ktwist = 0.5*kt*(a0*aovera0)*(a0*aovera0);
magtortwist = -ktwist*shear[6] -
0.5*polyhertz*gammatsuji*(a0*aovera0)*(a0*aovera0)*magtwist;
twistcrit=TWOTHIRDS*a0*aovera0*Fcrit;
if (fabs(magtortwist) > twistcrit)
magtortwist = -twistcrit * magtwist/fabs(magtwist);
// rolling torque
magrollsq = shear[3]*shear[3] + shear[4]*shear[4] + shear[5]*shear[5];
magroll = sqrt(magrollsq);
if (magroll != 0.0) magrollinv = 1.0/magroll;
else magrollinv = 0.0;
kroll = 1.0*4.0*Fcrit*pow(aovera0,1.5);
magtorroll = -kroll*magroll - 0.1*gammat*vrlmag;
rollcrit = 0.01;
if (magroll > rollcrit) magtorroll = -kroll*rollcrit;
// forces & torques
fx = dx*ccel + fs1;
fy = dy*ccel + fs2;
fz = dz*ccel + fs3;
f[0] += fx;
f[1] += fy;
f[2] += fz;
tor1 = rinv * (dy*fs3 - dz*fs2);
tor2 = rinv * (dz*fs1 - dx*fs3);
tor3 = rinv * (dx*fs2 - dy*fs1);
torque[0] -= radius*tor1;
torque[1] -= radius*tor2;
torque[2] -= radius*tor3;
torque[0] += magtortwist * dx*rinv;
torque[1] += magtortwist * dy*rinv;
torque[2] += magtortwist * dz*rinv;
torque[0] += magtorroll * (shear[4]*dz - shear[5]*dy)*rinv*magrollinv;
torque[1] += magtorroll * (shear[5]*dx - shear[3]*dz)*rinv*magrollinv;
torque[2] += magtorroll * (shear[3]*dy - shear[4]*dx)*rinv*magrollinv;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixWallGran::memory_usage()
{
int nmax = atom->nmax;
double bytes = 0.0;
if (history) bytes += nmax*sheardim * sizeof(double); // shear history
if (fix_rigid) bytes += nmax * sizeof(int); // mass_rigid
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixWallGran::grow_arrays(int nmax)
{
if (history) memory->grow(shearone,nmax,sheardim,"fix_wall_gran:shearone");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixWallGran::copy_arrays(int i, int j, int delflag)
{
if (history)
for (int m = 0; m < sheardim; m++)
shearone[j][m] = shearone[i][m];
}
/* ----------------------------------------------------------------------
initialize one atom's array values, called when atom is created
------------------------------------------------------------------------- */
void FixWallGran::set_arrays(int i)
{
if (history)
for (int m = 0; m < sheardim; m++)
shearone[i][m] = 0;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixWallGran::pack_exchange(int i, double *buf)
{
if (!history) return 0;
int n = 0;
for (int m = 0; m < sheardim; m++)
buf[n++] = shearone[i][m];
return n;
}
/* ----------------------------------------------------------------------
unpack values into local atom-based arrays after exchange
------------------------------------------------------------------------- */
int FixWallGran::unpack_exchange(int nlocal, double *buf)
{
if (!history) return 0;
int n = 0;
for (int m = 0; m < sheardim; m++)
shearone[nlocal][m] = buf[n++];
return n;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixWallGran::pack_restart(int i, double *buf)
{
if (!history) return 0;
int n = 0;
buf[n++] = sheardim + 1;
for (int m = 0; m < sheardim; m++)
buf[n++] = shearone[i][m];
return n;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixWallGran::unpack_restart(int nlocal, int nth)
{
if (!history) return;
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
for (int i = 0; i < sheardim; i++)
shearone[nlocal][i] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixWallGran::maxsize_restart()
{
if (!history) return 0;
return 1 + sheardim;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixWallGran::size_restart(int nlocal)
{
if (!history) return 0;
return 1 + sheardim;
}
/* ---------------------------------------------------------------------- */
void FixWallGran::reset_dt()
{
dt = update->dt;
}

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