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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@937 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-10-03 16:22:30 +00:00
parent 92ff097469
commit 9be7620ace
96 changed files with 3347 additions and 3735 deletions
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172
src/neigh_gran.cpp
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@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "modify.h"
#include "fix_shear_history.h"
#include "error.h"
@ -27,22 +27,21 @@ using namespace LAMMPS_NS;
pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void Neighbor::granular_nsq_no_newton()
void Neighbor::granular_nsq_no_newton(NeighList *list)
{
int i,j,m,n,nn;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
int *npartner;
int **partner;
double ***shearpartner;
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
}
NeighList *listgranhistory;
int *npartner,**partner;
double ***shearpartner;
int **firsttouch;
double **firstshear;
int **pages_touch;
double **pages_shear;
double **x = atom->x;
double *radius = atom->radius;
@ -53,6 +52,26 @@ void Neighbor::granular_nsq_no_newton()
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
pages_touch = listgranhistory->pages;
pages_shear = listgranhistory->dpages;
}
int inum = 0;
int npage = 0;
int npnt = 0;
@ -61,9 +80,12 @@ void Neighbor::granular_nsq_no_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) {
add_pages(npage);
if (fix_history) add_pages_history(npage);
if (npage == list->maxpage) {
pages = list->add_pages();
if (fix_history) {
pages_touch = listgranhistory->add_pages();
pages_shear = listgranhistory->dpages;
}
}
}
@ -83,7 +105,7 @@ void Neighbor::granular_nsq_no_newton()
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -122,16 +144,21 @@ void Neighbor::granular_nsq_no_newton()
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
}
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
@ -143,7 +170,7 @@ void Neighbor::granular_nsq_no_newton()
decision based on itag,jtag tests
------------------------------------------------------------------------- */
void Neighbor::granular_nsq_newton()
void Neighbor::granular_nsq_newton(NeighList *list)
{
int i,j,n,itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@ -159,6 +186,14 @@ void Neighbor::granular_nsq_newton()
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int inum = 0;
int npage = 0;
int npnt = 0;
@ -167,7 +202,7 @@ void Neighbor::granular_nsq_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
if (npage == list->maxpage) pages = list->add_pages();
}
n = 0;
@ -196,7 +231,7 @@ void Neighbor::granular_nsq_newton()
}
}
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -208,12 +243,16 @@ void Neighbor::granular_nsq_newton()
if (rsq <= cutsq) neighptr[n++] = j;
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
@ -225,22 +264,21 @@ void Neighbor::granular_nsq_newton()
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void Neighbor::granular_bin_no_newton()
void Neighbor::granular_bin_no_newton(NeighList *list)
{
int i,j,k,m,n,nn,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
int *npartner;
int **partner;
double ***shearpartner;
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
}
NeighList *listgranhistory;
int *npartner,**partner;
double ***shearpartner;
int **firsttouch;
double **firstshear;
int **pages_touch;
double **pages_shear;
// bin local & ghost atoms
@ -256,6 +294,26 @@ void Neighbor::granular_bin_no_newton()
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
pages_touch = listgranhistory->pages;
pages_shear = listgranhistory->dpages;
}
int inum = 0;
int npage = 0;
int npnt = 0;
@ -264,9 +322,12 @@ void Neighbor::granular_bin_no_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) {
add_pages(npage);
if (fix_history) add_pages_history(npage);
if (npage == list->maxpage) {
pages = list->add_pages();
if (fix_history) {
pages_touch = listgranhistory->add_pages();
pages_shear = listgranhistory->dpages;
}
}
}
@ -292,7 +353,7 @@ void Neighbor::granular_bin_no_newton()
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -332,16 +393,21 @@ void Neighbor::granular_bin_no_newton()
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
}
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
@ -352,7 +418,7 @@ void Neighbor::granular_bin_no_newton()
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::granular_bin_newton()
void Neighbor::granular_bin_newton(NeighList *list)
{
int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@ -372,6 +438,14 @@ void Neighbor::granular_bin_newton()
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int inum = 0;
int npage = 0;
int npnt = 0;
@ -380,7 +454,7 @@ void Neighbor::granular_bin_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
if (npage == list->maxpage) pages = list->add_pages();
}
n = 0;
@ -400,7 +474,7 @@ void Neighbor::granular_bin_newton()
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
}
delx = xtmp - x[j][0];
@ -418,7 +492,7 @@ void Neighbor::granular_bin_newton()
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -431,12 +505,16 @@ void Neighbor::granular_bin_newton()
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
@ -447,7 +525,7 @@ void Neighbor::granular_bin_newton()
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::granular_bin_newton_tri()
void Neighbor::granular_bin_newton_tri(NeighList *list)
{
int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@ -467,6 +545,14 @@ void Neighbor::granular_bin_newton_tri()
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int inum = 0;
int npage = 0;
int npnt = 0;
@ -475,7 +561,7 @@ void Neighbor::granular_bin_newton_tri()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
if (npage == list->maxpage) pages = list->add_pages();
}
n = 0;
@ -497,7 +583,7 @@ void Neighbor::granular_bin_newton_tri()
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
if (exclude && exclusion(i,j,type,mask,molecule)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -510,10 +596,14 @@ void Neighbor::granular_bin_newton_tri()
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = inum;
}