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neigh_derive.cpp
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Thu, Nov 14, 19:23

neigh_derive.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.
------------------------------------------------------------------------- */
#include <string.h>
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
build half list from full list
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
works if full list is a skip list
------------------------------------------------------------------------- */
void Neighbor::half_from_full_no_newton(NeighList *list)
{
int i,j,ii,jj,n,jnum,joriginal;
int *neighptr,*jlist;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_full = list->listfull->ilist;
int *numneigh_full = list->listfull->numneigh;
int **firstneigh_full = list->listfull->firstneigh;
int inum_full = list->listfull->inum;
int inum = 0;
ipage->reset();
// loop over atoms in full list
for (ii = 0; ii < inum_full; ii++) {
n = 0;
neighptr = ipage->vget();
// loop over parent full list
i = ilist_full[ii];
jlist = firstneigh_full[i];
jnum = numneigh_full[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j > i) neighptr[n++] = joriginal;
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
build half list from full list
pair stored once if i,j are both owned and i < j
if j is ghost, only store if j coords are "above and to the right" of i
works if full list is a skip list
------------------------------------------------------------------------- */
void Neighbor::half_from_full_newton(NeighList *list)
{
int i,j,ii,jj,n,jnum,joriginal;
int *neighptr,*jlist;
double xtmp,ytmp,ztmp;
double **x = atom->x;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_full = list->listfull->ilist;
int *numneigh_full = list->listfull->numneigh;
int **firstneigh_full = list->listfull->firstneigh;
int inum_full = list->listfull->inum;
int inum = 0;
ipage->reset();
// loop over parent full list
for (ii = 0; ii < inum_full; ii++) {
n = 0;
neighptr = ipage->vget();
i = ilist_full[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over full neighbor list
jlist = firstneigh_full[i];
jnum = numneigh_full[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j < nlocal) {
if (i > j) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
neighptr[n++] = joriginal;
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
this is for half and full lists
if ghostflag, also store neighbors of ghost atoms & set inum,gnum correctly
------------------------------------------------------------------------- */
void Neighbor::skip_from(NeighList *list)
{
int i,j,ii,jj,n,itype,jnum,joriginal;
int *neighptr,*jlist;
int *type = atom->type;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int num_skip = list->listskip->inum;
if (list->ghostflag) num_skip += list->listskip->gnum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
int inum = 0;
ipage->reset();
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < num_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
n = 0;
neighptr = ipage->vget();
// loop over parent non-skip list
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n++] = joriginal;
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
if (list->ghostflag) {
int num = 0;
for (i = 0; i < inum; i++)
if (ilist[i] < nlocal) num++;
else break;
list->inum = num;
list->gnum = inum - num;
}
}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void Neighbor::skip_from_granular(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
tagint jtag;
int *neighptr,*jlist,*touchptr,*touchptr_skip;
double *shearptr,*shearptr_skip;
NeighList *listgranhistory;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal + atom->nghost;
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
dnum = listgranhistory->dnum;
dnumbytes = dnum * sizeof(double);
}
int inum = 0;
ipage->reset();
if (fix_history) {
ipage_touch->reset();
dpage_shear->reset();
}
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
n = 0;
neighptr = ipage->vget();
if (fix_history) {
nn = 0;
touchptr = ipage_touch->vget();
shearptr = dpage_shear->vget();
}
// loop over parent non-skip granular list and optionally its history info
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n] = joriginal;
// no numeric test for current touch
// just use FSH partner list to infer it
// would require distance calculation for spheres
// more complex calculation for surfs
if (fix_history) {
jtag = tag[j];
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == jtag) break;
if (m < npartner[i]) {
touchptr[n] = 1;
memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
nn += dnum;
} else {
touchptr[n] = 0;
memcpy(&shearptr[nn],zeroes,dnumbytes);
nn += dnum;
}
}
n++;
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
ipage_touch->vgot(n);
dpage_shear->vgot(nn);
}
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
parent non-skip list used newton off, this skip list is newton on
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void Neighbor::skip_from_granular_off2on(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
tagint itag,jtag;
int *neighptr,*jlist,*touchptr,*touchptr_skip;
double *shearptr,*shearptr_skip;
NeighList *listgranhistory;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal + atom->nghost;
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
dnum = listgranhistory->dnum;
dnumbytes = dnum * sizeof(double);
}
int inum = 0;
ipage->reset();
if (fix_history) {
ipage_touch->reset();
dpage_shear->reset();
}
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
itag = tag[i];
n = 0;
neighptr = ipage->vget();
if (fix_history) {
nn = 0;
touchptr = ipage_touch->vget();
shearptr = dpage_shear->vget();
}
// loop over parent non-skip granular list and optionally its history info
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
// only keep I,J when J = ghost if Itag < Jtag
jtag = tag[j];
if (j >= nlocal && jtag < itag) continue;
neighptr[n] = joriginal;
// no numeric test for current touch
// just use FSH partner list to infer it
// would require distance calculation for spheres
// more complex calculation for surfs
if (fix_history) {
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == jtag) break;
if (m < npartner[i]) {
touchptr[n] = 1;
memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
nn += dnum;
} else {
touchptr[n] = 0;
memcpy(&shearptr[nn],zeroes,dnumbytes);
nn += dnum;
}
}
n++;
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
ipage_touch->vgot(n);
dpage_shear->vgot(nn);
}
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
parent non-skip list used newton off and was not onesided,
this skip list is newton on and onesided
if list requests it, preserve shear history via fix shear/history
------------------------------------------------------------------------- */
void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
tagint itag,jtag;
int *surf,*neighptr,*jlist;
NeighList *listgranhistory;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
if (domain->dimension == 2) surf = atom->line;
else surf = atom->tri;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal + atom->nghost;
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
dnum = listgranhistory->dnum;
dnumbytes = dnum * sizeof(double);
}
int inum = 0;
ipage->reset();
if (fix_history) {
ipage_touch->reset();
dpage_shear->reset();
}
// two loops over parent list required, one to count, one to store
// because onesided constraint means pair I,J may be stored with I or J
// so don't know in advance how much space to alloc for each atom's neighs
// first loop over atoms in other list to count neighbors
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (i = 0; i < nlocal; i++) numneigh[i] = 0;
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
itag = tag[i];
n = 0;
// loop over parent non-skip granular list
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
// flip I,J if necessary to satisfy onesided constraint
// do not keep if I is now ghost
if (surf[i] >= 0) {
if (j >= nlocal) continue;
tmp = i;
i = j;
j = tmp;
flip = 1;
} else flip = 0;
numneigh[i]++;
if (flip) i = j;
}
}
// allocate all per-atom neigh list chunks, including history
for (i = 0; i < nlocal; i++) {
if (numneigh[i] == 0) continue;
n = numneigh[i];
firstneigh[i] = ipage->get(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (fix_history) {
firsttouch[i] = ipage_touch->get(n);
firstshear[i] = dpage_shear->get(dnum*n);
}
}
// second loop over atoms in other list to store neighbors
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (i = 0; i < nlocal; i++) numneigh[i] = 0;
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
itag = tag[i];
// loop over parent non-skip granular list and optionally its history info
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
// flip I,J if necessary to satisfy onesided constraint
// do not keep if I is now ghost
if (surf[i] >= 0) {
if (j >= nlocal) continue;
tmp = i;
i = j;
j = tmp;
flip = 1;
} else flip = 0;
// store j in neigh list, not joriginal, like other neigh methods
// OK, b/c there is no special list flagging for surfs
firstneigh[i][numneigh[i]] = j;
// no numeric test for current touch
// just use FSH partner list to infer it
// would require complex calculation for surfs
if (fix_history) {
jtag = tag[j];
n = numneigh[i];
nn = dnum*n;
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == jtag) break;
if (m < npartner[i]) {
firsttouch[i][n] = 1;
memcpy(&firstshear[i][nn],&shearpartner[i][dnum*m],dnumbytes);
} else {
firsttouch[i][n] = 0;
memcpy(&firstshear[i][nn],zeroes,dnumbytes);
}
}
numneigh[i]++;
if (flip) i = j;
}
// only add atom I to ilist if it has neighbors
// fix shear/history allows for this in pre_exchange_onesided()
if (numneigh[i]) ilist[inum++] = i;
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
this is for respa lists, copy the inner/middle values from parent
------------------------------------------------------------------------- */
void Neighbor::skip_from_respa(NeighList *list)
{
int i,j,ii,jj,n,itype,jnum,joriginal,n_inner,n_middle;
int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
int *type = atom->type;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
MyPage<int> *ipage_inner = listinner->ipage;
int *numneigh_inner_skip = list->listskip->listinner->numneigh;
int **firstneigh_inner_skip = list->listskip->listinner->firstneigh;
NeighList *listmiddle;
int *ilist_middle,*numneigh_middle,**firstneigh_middle;
MyPage<int> *ipage_middle;
int *numneigh_middle_skip,**firstneigh_middle_skip;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
ipage_middle = listmiddle->ipage;
numneigh_middle_skip = list->listskip->listmiddle->numneigh;
firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
}
int inum = 0;
ipage->reset();
ipage_inner->reset();
if (respamiddle) ipage_middle->reset();
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
n = n_inner = 0;
neighptr = ipage->vget();
neighptr_inner = ipage_inner->vget();
if (respamiddle) {
n_middle = 0;
neighptr_middle = ipage_middle->vget();
}
// loop over parent outer rRESPA list
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n++] = joriginal;
}
// loop over parent inner rRESPA list
jlist = firstneigh_inner_skip[i];
jnum = numneigh_inner_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_inner[n_inner++] = joriginal;
}
// loop over parent middle rRESPA list
if (respamiddle) {
jlist = firstneigh_middle_skip[i];
jnum = numneigh_middle_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_middle[n_middle++] = joriginal;
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
ipage_inner->vgot(n);
if (ipage_inner->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
ipage_middle->vgot(n);
if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
}
list->inum = inum;
listinner->inum = inum;
if (respamiddle) listmiddle->inum = inum;
}
/* ----------------------------------------------------------------------
create list which is simply a copy of parent list
------------------------------------------------------------------------- */
void Neighbor::copy_from(NeighList *list)
{
NeighList *listcopy = list->listcopy;
list->inum = listcopy->inum;
list->gnum = listcopy->gnum;
list->ilist = listcopy->ilist;
list->numneigh = listcopy->numneigh;
list->firstneigh = listcopy->firstneigh;
list->firstdouble = listcopy->firstdouble;
list->ipage = listcopy->ipage;
list->dpage = listcopy->dpage;
}

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