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neigh_gran_omp.cpp
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Sat, Nov 9, 17:49

neigh_gran_omp.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 "neighbor_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
#include "fix_shear_history.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
granular particles
N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
shear history must be accounted for when a neighbor pair is added
pair added to list if atoms i and j are both owned and i < j
pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
FixShearHistory * const fix_history = list->fix_history;
NeighList * listgranhistory = list->listgranhistory;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,m,n,nn,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
double **x = atom->x;
double *radius = atom->radius;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage+tid;
dpage_shear = listgranhistory->dpage+tid;
dnum = listgranhistory->dnum;
dnumbytes = dnum * sizeof(double);
ipage_touch->reset();
dpage_shear->reset();
}
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
if (fix_history) {
nn = 0;
touchptr = ipage_touch->vget();
shearptr = dpage_shear->vget();
}
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
neighptr[n] = j;
if (fix_history) {
if (rsq < radsum*radsum) {
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == tag[j]) 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;
}
} else {
touchptr[n] = 0;
memcpy(&shearptr[nn],zeroes,dnumbytes);
nn += dnum;
}
}
n++;
}
}
ilist[i] = 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);
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
granular particles
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
no shear history is allowed for this option
pair added to list if atoms i and j are both owned and i < j
if j is ghost only me or other proc adds pair
decision based on itag,jtag tests
------------------------------------------------------------------------- */
void Neighbor::granular_nsq_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,n,itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
itag = tag[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) 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;
}
}
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) neighptr[n++] = j;
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with partial Newton's 3rd law
shear history must be accounted for when a neighbor pair is added
each owned atom i checks own bin and surrounding bins in non-Newton stencil
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)
------------------------------------------------------------------------- */
void Neighbor::granular_bin_no_newton_omp(NeighList *list)
{
// bin local & ghost atoms
if (binatomflag) bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
FixShearHistory * const fix_history = list->fix_history;
NeighList * listgranhistory = list->listgranhistory;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
// loop over each atom, storing neighbors
double **x = atom->x;
double *radius = atom->radius;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage+tid;
dpage_shear = listgranhistory->dpage+tid;
dnum = listgranhistory->dnum;
dnumbytes = dnum * sizeof(double);
ipage_touch->reset();
dpage_shear->reset();
}
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
if (fix_history) {
nn = 0;
touchptr = ipage_touch->vget();
shearptr = dpage_shear->vget();
}
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
ibin = coord2bin(x[i]);
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs on both procs
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[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) {
neighptr[n] = j;
if (fix_history) {
if (rsq < radsum*radsum) {
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == tag[j]) 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;
}
} else {
touchptr[n] = 0;
memcpy(&shearptr[nn],zeroes,dnumbytes);
nn += dnum;
}
}
n++;
}
}
}
ilist[i] = 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);
}
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with full Newton's 3rd law
no shear history is allowed for this option
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::granular_bin_newton_omp(NeighList *list)
{
// bin local & ghost atoms
if (binatomflag) bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
// loop over each atom, storing neighbors
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the right" of i
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
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;
}
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) neighptr[n++] = j;
}
// loop over all atoms in other bins in stencil, store every pair
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[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) neighptr[n++] = j;
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with Newton's 3rd law for triclinic
no shear history is allowed for this option
each owned atom i checks its own bin and other bins in triclinic stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
{
// bin local & ghost atoms
if (binatomflag) bin_atoms();
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nlocal);
int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
// loop over each atom, storing neighbors
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
// each thread has its own page allocator
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
for (i = ifrom; i < ito; i++) {
n = 0;
neighptr = ipage.vget();
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
}
}
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) neighptr[n++] = j;
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage.vgot(n);
if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
}

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