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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@930 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-10-03 16:15:11 +00:00
parent 54a88a9bc7
commit 201466f4f1
6 changed files with 168 additions and 88 deletions
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84
src/GRANULAR/fix_gran_diag.cpp
View File

@ -24,6 +24,7 @@
#include "pair.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "modify.h"
#include "comm.h"
#include "domain.h"
@ -116,13 +117,13 @@ void FixGranDiag::init()
// insure use of granular pair_style
// set local values from Pair values
Pair *pair = force->pair_match("gran");
pair = force->pair_match("gran");
if (pair == NULL)
error->all("Fix gran/diag is incompatible with Pair style");
int dampflag;
double gamman;
pair->extract_gran(&xkk,&gamman,&xmu,&dampflag);
// same initialization as in pair_gran_history::init_style()
xkkt = xkk * 2.0/7.0;
@ -151,6 +152,11 @@ void FixGranDiag::init()
void FixGranDiag::setup()
{
// get neighbor list from Pair class
// can't do this until setup since lists are setup by neighbor::init()
list = pair->list;
if (first) end_of_step();
first = 0;
}
@ -462,7 +468,7 @@ void FixGranDiag::deallocate()
void FixGranDiag::stress_no_history()
{
int i,j,k,m,numneigh;
int i,j,ii,jj,m,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz;
double radi,radj,radsum,rsq,r;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
@ -470,7 +476,7 @@ void FixGranDiag::stress_no_history()
double vtr1,vtr2,vtr3,vrel;
double xmeff,damp,ccel,ccelx,ccely,ccelz;
double fn,fs,ft,fs1,fs2,fs3;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **v = atom->v;
@ -481,19 +487,25 @@ void FixGranDiag::stress_no_history()
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over all neighbors of my atoms
// store stress for both atoms i and j
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
// skip if neither atom is in fix group
@ -613,7 +625,7 @@ void FixGranDiag::stress_no_history()
void FixGranDiag::stress_history()
{
int i,j,k,m,numneigh;
int i,j,ii,jj,m,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz;
double radi,radj,radsum,rsq,r;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
@ -622,8 +634,8 @@ void FixGranDiag::stress_history()
double xmeff,damp,ccel,ccelx,ccely,ccelz;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht;
int *neighs;
double *firstshear,*shear;
int *ilist,*jlist,*numneigh,**firstneigh;
double *shear,*allshear,**firstshear;
double **x = atom->x;
double **v = atom->v;
@ -634,20 +646,27 @@ void FixGranDiag::stress_history()
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->listgranhistory->firstneigh;
firstshear = list->listgranhistory->firstdouble;
// loop over all neighbors of my atoms
// store stress on both atoms i and j
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
neighs = neighbor->firstneigh[i];
firstshear = neighbor->firstshear[i];
numneigh = neighbor->numneigh[i];
allshear = firstshear[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
// skip if neither atom is in fix group
@ -718,7 +737,7 @@ void FixGranDiag::stress_history()
// shrmag = magnitude of shear
// do not update shear history since not timestepping
shear = &firstshear[3*k];
shear = &allshear[3*jj];
shrx = shear[0] + vtr1;
shry = shear[1] + vtr2;
shrz = shear[2] + vtr3;
@ -796,7 +815,7 @@ void FixGranDiag::stress_history()
void FixGranDiag::stress_hertzian()
{
int i,j,k,m,numneigh;
int i,j,ii,jj,m,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz;
double radi,radj,radsum,rsq,r;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
@ -805,8 +824,8 @@ void FixGranDiag::stress_hertzian()
double xmeff,damp,ccel,ccelx,ccely,ccelz;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht,rhertz;
int *neighs;
double *firstshear,*shear;
int *ilist,*jlist,*numneigh,**firstneigh;
double *shear,*allshear,**firstshear;
double **x = atom->x;
double **v = atom->v;
@ -817,20 +836,27 @@ void FixGranDiag::stress_hertzian()
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
firstshear = listgran->firstdouble;
// loop over all neighbors of my atoms
// store stress on both atoms i and j
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
neighs = neighbor->firstneigh[i];
firstshear = neighbor->firstshear[i];
numneigh = neighbor->numneigh[i];
allshear = firstshear[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
// skip if neither atom is in fix group
@ -903,7 +929,7 @@ void FixGranDiag::stress_hertzian()
// shrmag = magnitude of shear
// do not update shear history since not timestepping
shear = &firstshear[3*k];
shear = &allshear[3*jj];
shrx = shear[0] + vtr1;
shry = shear[1] + vtr2;
shrz = shear[2] + vtr3;

3
src/GRANULAR/fix_gran_diag.h
View File

@ -45,6 +45,9 @@ class FixGranDiag : public Fix {
double *velfxx,*velfyy,*velfzz,*velfxy,*velfxz,*velfyz;
double *sigx2,*sigy2,*sigz2,*sigxy2,*sigxz2,*sigyz2;
class Pair *pair;
class NeighList *list,*listgran;
void allocate();
void deallocate();
void stress_no_history();

39
src/GRANULAR/pair_gran_hertzian.cpp
View File

@ -21,7 +21,7 @@
#include "pair_gran_hertzian.h"
#include "atom.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
@ -39,7 +39,7 @@ PairGranHertzian::PairGranHertzian(LAMMPS *lmp) : PairGranHistory(lmp)
void PairGranHertzian::compute(int eflag, int vflag)
{
int i,j,k,numneigh;
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;
@ -48,8 +48,9 @@ void PairGranHertzian::compute(int eflag, int vflag)
double xmeff,damp,ccel,ccelx,ccely,ccelz,tor1,tor2,tor3;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht,rhertz;
int *neighs,*touch;
double *firstshear,*shear;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *shear,*allshear,**firstshear;
double **f = atom->f;
double **x = atom->x;
@ -62,20 +63,28 @@ void PairGranHertzian::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
firsttouch = list->listgranhistory->firstneigh;
firstshear = list->listgranhistory->firstdouble;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
neighs = neighbor->firstneigh[i];
touch = neighbor->firsttouch[i];
firstshear = neighbor->firstshear[i];
numneigh = neighbor->numneigh[i];
touch = firsttouch[i];
allshear = firstshear[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -88,8 +97,8 @@ void PairGranHertzian::compute(int eflag, int vflag)
// unset touching neighbors
touch[k] = 0;
shear = &firstshear[3*k];
touch[jj] = 0;
shear = &allshear[3*jj];
shear[0] = 0.0;
shear[1] = 0.0;
shear[2] = 0.0;
@ -152,8 +161,8 @@ void PairGranHertzian::compute(int eflag, int vflag)
// shear history effects
// shrmag = magnitude of shear
touch[k] = 1;
shear = &firstshear[3*k];
touch[jj] = 1;
shear = &allshear[3*jj];
shear[0] += vtr1;
shear[1] += vtr2;
shear[2] += vtr3;

105
src/GRANULAR/pair_gran_history.cpp
View File

@ -27,9 +27,12 @@
#include "modify.h"
#include "fix.h"
#include "fix_pour.h"
#include "fix_shear_history.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -64,7 +67,7 @@ PairGranHistory::~PairGranHistory()
void PairGranHistory::compute(int eflag, int vflag)
{
int i,j,k,numneigh;
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;
@ -73,8 +76,9 @@ void PairGranHistory::compute(int eflag, int vflag)
double xmeff,damp,ccel,ccelx,ccely,ccelz,tor1,tor2,tor3;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht;
int *neighs,*touch;
double *firstshear,*shear;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *shear,*allshear,**firstshear;
double **f = atom->f;
double **x = atom->x;
@ -87,20 +91,28 @@ void PairGranHistory::compute(int eflag, int vflag)
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 (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
neighs = neighbor->firstneigh[i];
touch = neighbor->firsttouch[i];
firstshear = neighbor->firstshear[i];
numneigh = neighbor->numneigh[i];
touch = firsttouch[i];
allshear = firstshear[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -113,8 +125,8 @@ void PairGranHistory::compute(int eflag, int vflag)
// unset touching neighbors
touch[k] = 0;
shear = &firstshear[3*k];
touch[jj] = 0;
shear = &allshear[3*jj];
shear[0] = 0.0;
shear[1] = 0.0;
shear[2] = 0.0;
@ -175,8 +187,8 @@ void PairGranHistory::compute(int eflag, int vflag)
// shear history effects
// shrmag = magnitude of shear
touch[k] = 1;
shear = &firstshear[3*k];
touch[jj] = 1;
shear = &allshear[3*jj];
shear[0] += vtr1;
shear[1] += vtr2;
shear[2] += vtr3;
@ -274,8 +286,6 @@ void PairGranHistory::allocate()
void PairGranHistory::settings(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Pair_style granular command before simulation box is defined");
if (narg != 4) error->all("Illegal pair_style command");
xkk = atof(arg[0]);
@ -302,21 +312,6 @@ void PairGranHistory::coeff(int narg, char **arg)
error->all("Granular pair styles do not use pair_coeff settings");
}
/* ----------------------------------------------------------------------
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;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
@ -328,6 +323,19 @@ void PairGranHistory::init_style()
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;
@ -344,12 +352,13 @@ void PairGranHistory::init_style()
if (history && fix_history == NULL) {
char **fixarg = new char*[3];
fixarg[0] = "SHEAR_HISTORY";
fixarg[1] = "all";
fixarg[2] = "SHEAR_HISTORY";
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
@ -393,6 +402,32 @@ void PairGranHistory::init_style()
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
------------------------------------------------------------------------- */

3
src/GRANULAR/pair_gran_history.h
View File

@ -25,8 +25,9 @@ class PairGranHistory : public Pair {
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);

22
src/GRANULAR/pair_gran_no_history.cpp
View File

@ -21,7 +21,7 @@
#include "pair_gran_no_history.h"
#include "atom.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
@ -39,7 +39,7 @@ PairGranNoHistory::PairGranNoHistory(LAMMPS *lmp) : PairGranHistory(lmp)
void PairGranNoHistory::compute(int eflag, int vflag)
{
int i,j,k,numneigh;
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;
@ -47,7 +47,7 @@ void PairGranNoHistory::compute(int eflag, int vflag)
double vtr1,vtr2,vtr3,vrel;
double xmeff,damp,ccel,ccelx,ccely,ccelz,tor1,tor2,tor3;
double fn,fs,ft,fs1,fs2,fs3;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **f = atom->f;
double **x = atom->x;
@ -60,18 +60,24 @@ void PairGranNoHistory::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];