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pair_gran_hertz_history.cpp
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Tue, Jun 4, 18:05

pair_gran_hertz_history.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)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "pair_gran_hertz_history.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "fix.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairGranHertzHistory::PairGranHertzHistory(LAMMPS *lmp) :
PairGranHookeHistory(lmp) {}
/* ---------------------------------------------------------------------- */
void PairGranHertzHistory::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
double radi,radj,radsum,rsq,r,rinv,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3;
double vtr1,vtr2,vtr3,vrel;
double mi,mj,meff,damp,ccel,tor1,tor2,tor3;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht,polyhertz;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *shear,*allshear,**firstshear;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int shearupdate = 1;
if (update->setupflag) shearupdate = 0;
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if (fix_rigid && neighbor->ago == 0) {
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,"pair: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;
comm->forward_comm_pair(this);
}
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;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
firsttouch = list->listhistory->firstneigh;
firstshear = list->listhistory->firstdouble;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
touch = firsttouch[i];
allshear = firstshear[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radj = radius[j];
radsum = radi + radj;
if (rsq >= radsum*radsum) {
// unset non-touching neighbors
touch[jj] = 0;
shear = &allshear[3*jj];
shear[0] = 0.0;
shear[1] = 0.0;
shear[2] = 0.0;
} else {
r = sqrt(rsq);
rinv = 1.0/r;
rsqinv = 1.0/rsq;
// relative translational velocity
vr1 = v[i][0] - v[j][0];
vr2 = v[i][1] - v[j][1];
vr3 = v[i][2] - v[j][2];
// normal component
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
mi = rmass[i];
mj = rmass[j];
if (fix_rigid) {
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);
if (mask[i] & freeze_group_bit) meff = mj;
if (mask[j] & freeze_group_bit) meff = mi;
// normal force = Hertzian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
ccel *= polyhertz;
// relative velocities
vtr1 = vt1 - (delz*wr2-dely*wr3);
vtr2 = vt2 - (delx*wr3-delz*wr1);
vtr3 = vt3 - (dely*wr1-delx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
// shear history effects
touch[jj] = 1;
shear = &allshear[3*jj];
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]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
if (shearupdate) {
shear[0] -= rsht*delx;
shear[1] -= rsht*dely;
shear[2] -= rsht*delz;
}
// 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 = delx*ccel + fs1;
fy = dely*ccel + fs2;
fz = delz*ccel + fs3;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
tor1 = rinv * (dely*fs3 - delz*fs2);
tor2 = rinv * (delz*fs1 - delx*fs3);
tor3 = rinv * (delx*fs2 - dely*fs1);
torque[i][0] -= radi*tor1;
torque[i][1] -= radi*tor2;
torque[i][2] -= radi*tor3;
if (newton_pair || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
torque[j][0] -= radj*tor1;
torque[j][1] -= radj*tor2;
torque[j][2] -= radj*tor3;
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,fx,fy,fz,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairGranHertzHistory::settings(int narg, char **arg)
{
if (narg != 6) error->all(FLERR,"Illegal pair_style command");
kn = force->numeric(FLERR,arg[0]);
if (strcmp(arg[1],"NULL") == 0) kt = kn * 2.0/7.0;
else kt = force->numeric(FLERR,arg[1]);
gamman = force->numeric(FLERR,arg[2]);
if (strcmp(arg[3],"NULL") == 0) gammat = 0.5 * gamman;
else gammat = force->numeric(FLERR,arg[3]);
xmu = force->numeric(FLERR,arg[4]);
dampflag = force->inumeric(FLERR,arg[5]);
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 pair_style command");
// convert Kn and Kt from pressure units to force/distance^2
kn /= force->nktv2p;
kt /= force->nktv2p;
}
/* ---------------------------------------------------------------------- */
double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double radi,radj,radsum;
double r,rinv,rsqinv,delx,dely,delz;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3,wr1,wr2,wr3;
double mi,mj,meff,damp,ccel,polyhertz;
double vtr1,vtr2,vtr3,vrel,shrmag,rsht;
double fs1,fs2,fs3,fs,fn;
double *radius = atom->radius;
radi = radius[i];
radj = radius[j];
radsum = radi + radj;
if (rsq >= radsum*radsum) {
fforce = 0.0;
for (int m = 0; m < single_extra; m++) svector[m] = 0.0;
return 0.0;
}
r = sqrt(rsq);
rinv = 1.0/r;
rsqinv = 1.0/rsq;
// relative translational velocity
double **v = atom->v;
vr1 = v[i][0] - v[j][0];
vr2 = v[i][1] - v[j][1];
vr3 = v[i][2] - v[j][2];
// normal component
double **x = atom->x;
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
double **omega = atom->omega;
wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
double *rmass = atom->rmass;
int *mask = atom->mask;
mi = rmass[i];
mj = rmass[j];
if (fix_rigid) {
// NOTE: insure mass_rigid is current for owned+ghost atoms?
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);
if (mask[i] & freeze_group_bit) meff = mj;
if (mask[j] & freeze_group_bit) meff = mi;
// normal force = Hertzian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;
polyhertz = sqrt((radsum-r)*radi*radj / radsum);
ccel *= polyhertz;
// relative velocities
vtr1 = vt1 - (delz*wr2-dely*wr3);
vtr2 = vt2 - (delx*wr3-delz*wr1);
vtr3 = vt3 - (dely*wr1-delx*wr2);
vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
vrel = sqrt(vrel);
// shear history effects
// neighprev = index of found neigh on previous call
// search entire jnum list of neighbors of I for neighbor J
// start from neighprev, since will typically be next neighbor
// reset neighprev to 0 as necessary
int jnum = list->numneigh[i];
int *jlist = list->firstneigh[i];
double *allshear = list->listhistory->firstdouble[i];
for (int jj = 0; jj < jnum; jj++) {
neighprev++;
if (neighprev >= jnum) neighprev = 0;
if (jlist[neighprev] == j) break;
}
double *shear = &allshear[3*neighprev];
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
shear[2]*shear[2]);
// rotate shear displacements
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht *= rsqinv;
// 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) {
fs1 *= fn/fs;
fs2 *= fn/fs;
fs3 *= fn/fs;
fs *= fn/fs;
} else fs1 = fs2 = fs3 = fs = 0.0;
}
// set force and return no energy
fforce = ccel;
// set single_extra quantities
svector[0] = fs1;
svector[1] = fs2;
svector[2] = fs3;
svector[3] = fs;
svector[4] = vn1;
svector[5] = vn2;
svector[6] = vn3;
svector[7] = vt1;
svector[8] = vt2;
svector[9] = vt3;
return 0.0;
}

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