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pair_gran_history.cpp
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Wed, Oct 16, 07:03

pair_gran_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 "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_gran_history.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_pour.h"
#include "fix_shear_history.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairGranHistory::PairGranHistory(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
for (int i = 0; i < 6; i++) virial[i] = 0.0;
history = 1;
fix_history = NULL;
}
/* ---------------------------------------------------------------------- */
PairGranHistory::~PairGranHistory()
{
if (fix_history) modify->delete_fix("SHEAR_HISTORY");
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
}
}
/* ---------------------------------------------------------------------- */
void PairGranHistory::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz;
double radi,radj,radsum,rsq,r,rinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3;
double vtr1,vtr2,vtr3,vrel;
double xmeff,damp,ccel,ccelx,ccely,ccelz,tor1,tor2,tor3;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *shear,*allshear,**firstshear;
double **f = atom->f;
double **x = atom->x;
double **v = atom->v;
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 = listgranhistory->firstneigh;
firstshear = listgranhistory->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];
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 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);
// relative translational velocity
vr1 = v[i][0] - v[j][0];
vr2 = v[i][1] - v[j][1];
vr3 = v[i][2] - v[j][2];
vr1 *= dt;
vr2 *= dt;
vr3 *= dt;
// normal component
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr / rsq;
vn2 = dely*vnnr / rsq;
vn3 = delz*vnnr / rsq;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// relative rotational velocity
wr1 = radi*omega[i][0] + radj*omega[j][0];
wr2 = radi*omega[i][1] + radj*omega[j][1];
wr3 = radi*omega[i][2] + radj*omega[j][2];
wr1 *= dt/r;
wr2 *= dt/r;
wr3 *= dt/r;
// normal damping term
// this definition of DAMP includes the extra 1/r term
xmeff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
if (mask[i] & freeze_group_bit) xmeff = rmass[j];
if (mask[j] & freeze_group_bit) xmeff = rmass[i];
damp = xmeff*gamman_dl*vnnr/rsq;
ccel = xkk*(radsum-r)/r - damp;
// 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
// shrmag = magnitude of shear
touch[jj] = 1;
shear = &allshear[3*jj];
shear[0] += vtr1;
shear[1] += vtr2;
shear[2] += vtr3;
shrmag = sqrt(shear[0]*shear[0] + shear[1]*shear[1] +
shear[2]*shear[2]);
// rotate shear displacements correctly
rsht = shear[0]*delx + shear[1]*dely + shear[2]*delz;
rsht /= rsq;
shear[0] -= rsht*delx;
shear[1] -= rsht*dely;
shear[2] -= rsht*delz;
// tangential forces
fs1 = - (xkkt*shear[0] + xmeff*gammas_dl*vtr1);
fs2 = - (xkkt*shear[1] + xmeff*gammas_dl*vtr2);
fs3 = - (xkkt*shear[2] + xmeff*gammas_dl*vtr3);
// force normalization
// 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] + xmeff*gammas_dl*vtr1/xkkt) -
xmeff*gammas_dl*vtr1/xkkt;
shear[1] = (fn/fs) * (shear[1] + xmeff*gammas_dl*vtr2/xkkt) -
xmeff*gammas_dl*vtr2/xkkt;
shear[2] = (fn/fs) * (shear[2] + xmeff*gammas_dl*vtr3/xkkt) -
xmeff*gammas_dl*vtr3/xkkt;
fs1 *= fn/fs;
fs2 *= fn/fs;
fs3 *= fn/fs;
} else {
fs1 = 0.0;
fs2 = 0.0;
fs3 = 0.0;
}
}
// forces & torques
ccelx = delx*ccel + fs1;
ccely = dely*ccel + fs2;
ccelz = delz*ccel + fs3;
f[i][0] += ccelx;
f[i][1] += ccely;
f[i][2] += ccelz;
rinv = 1/r;
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] -= ccelx;
f[j][1] -= ccely;
f[j][2] -= ccelz;
torque[j][0] -= radj*tor1;
torque[j][1] -= radj*tor2;
torque[j][2] -= radj*tor3;
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairGranHistory::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairGranHistory::settings(int narg, char **arg)
{
if (narg != 4) error->all("Illegal pair_style command");
xkk = atof(arg[0]);
gamman = atof(arg[1]);
xmu = atof(arg[2]);
dampflag = atoi(arg[3]);
// granular styles do not use pair_coeff, so set setflag for everything now
if (!allocated) allocate();
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
setflag[i][j] = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairGranHistory::coeff(int narg, char **arg)
{
error->all("Granular pair styles do not use pair_coeff settings");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairGranHistory::init_style()
{
int i;
if (!atom->radius_flag || !atom->omega_flag || !atom->torque_flag)
error->all("Pair granular requires atom attributes radius, omega, torque");
// need a half neigh list and optionally a granular history neigh list
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->gran = 1;
if (history) {
irequest = neighbor->request(this);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->granhistory = 1;
neighbor->requests[irequest]->dnum = 3;
}
xkkt = xkk * 2.0/7.0;
dt = update->dt;
double gammas = 0.5*gamman;
if (dampflag == 0) gammas = 0.0;
gamman_dl = gamman/dt;
gammas_dl = gammas/dt;
// if shear history is stored:
// check if newton flag is valid
// if first init, create Fix needed for storing shear history
if (history && force->newton_pair == 1)
error->all("Potential with shear history requires newton pair off");
if (history && fix_history == NULL) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "SHEAR_HISTORY";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "SHEAR_HISTORY";
modify->add_fix(3,fixarg);
delete [] fixarg;
fix_history = (FixShearHistory *) modify->fix[modify->nfix-1];
fix_history->pair = this;
}
// check for freeze Fix and set freeze_group_bit
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"freeze") == 0) break;
if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit;
else freeze_group_bit = 0;
// set cutoff by largest particles
// maxrad_dynamic = radius of largest dynamic particle, including inserted
// maxrad_frozen = radius of largest dynamic particle
// include frozen-dynamic interactions
// do not include frozen-frozen interactions
// include future inserted particles as dynamic
// cutforce was already set in pair::init(), but this sets it correctly
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double maxrad_dynamic = 0.0;
for (i = 0; i < nlocal; i++)
if (!(mask[i] & freeze_group_bit))
maxrad_dynamic = MAX(maxrad_dynamic,radius[i]);
double mine = maxrad_dynamic;
MPI_Allreduce(&mine,&maxrad_dynamic,1,MPI_DOUBLE,MPI_MAX,world);
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"pour") == 0)
maxrad_dynamic =
MAX(maxrad_dynamic,((FixPour *) modify->fix[i])->radius_hi);
double maxrad_frozen = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & freeze_group_bit)
maxrad_frozen = MAX(maxrad_frozen,radius[i]);
mine = maxrad_frozen;
MPI_Allreduce(&mine,&maxrad_frozen,1,MPI_DOUBLE,MPI_MAX,world);
cutforce = maxrad_dynamic + MAX(maxrad_dynamic,maxrad_frozen);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
optional granular history list
------------------------------------------------------------------------- */
void PairGranHistory::init_list(int id, NeighList *ptr)
{
if (id == 0) list = ptr;
else if (id == 1) listgranhistory = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairGranHistory::init_one(int i, int j)
{
if (!allocated) allocate();
// return dummy value used in neighbor setup,
// but not in actual neighbor calculation
// since particles have variable radius
return 1.0;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairGranHistory::write_restart(FILE *fp)
{
write_restart_settings(fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairGranHistory::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairGranHistory::write_restart_settings(FILE *fp)
{
fwrite(&xkk,sizeof(double),1,fp);
fwrite(&gamman,sizeof(double),1,fp);
fwrite(&xmu,sizeof(double),1,fp);
fwrite(&dampflag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairGranHistory::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&xkk,sizeof(double),1,fp);
fread(&gamman,sizeof(double),1,fp);
fread(&xmu,sizeof(double),1,fp);
fread(&dampflag,sizeof(int),1,fp);
}
MPI_Bcast(&xkk,1,MPI_DOUBLE,0,world);
MPI_Bcast(&gamman,1,MPI_DOUBLE,0,world);
MPI_Bcast(&xmu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&dampflag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
void PairGranHistory::extract_gran(double *p_xkk, double *p_gamman,
double *p_xmu, int *p_dampflag)
{
*p_xkk = xkk;
*p_gamman = gamman;
*p_xmu = xmu;
*p_dampflag = dampflag;
}

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