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Commit 5fb5f70e authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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update USER-OMP code for shear history neighbor refactoring

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src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+ 9
− 68
View file @ 5fb5f70e
......@@ -18,9 +18,6 @@
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
......@@ -34,7 +31,6 @@ NPairHalfSizeBinNewtoffOmp::NPairHalfSizeBinNewtoffOmp(LAMMPS *lmp) :
/* ----------------------------------------------------------------------
size 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)
......@@ -43,30 +39,20 @@ NPairHalfSizeBinNewtoffOmp::NPairHalfSizeBinNewtoffOmp(LAMMPS *lmp) :
void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
FixShearHistory * const fix_history = (FixShearHistory *) list->fix_history;
NeighList * listhistory = list->listhistory;
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listhistory)
#pragma omp parallel default(none) shared(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
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;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
int *neighptr;
// loop over each atom, storing neighbors
......@@ -85,29 +71,10 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listhistory->firstneigh;
firstshear = listhistory->firstdouble;
ipage_touch = listhistory->ipage+tid;
dpage_shear = listhistory->dpage+tid;
dnum = listhistory->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];
......@@ -133,29 +100,10 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
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++;
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
......@@ -166,13 +114,6 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
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);
}
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
......
src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+ 13
− 97
View file @ 5fb5f70e
......@@ -18,9 +18,6 @@
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
......@@ -34,7 +31,6 @@ NPairHalfSizeBinNewtonOmp::NPairHalfSizeBinNewtonOmp(LAMMPS *lmp) :
/* ----------------------------------------------------------------------
size particles
binned neighbor list construction with full Newton's 3rd law
shear history must be accounted for when a neighbor pair is added
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
......@@ -42,36 +38,20 @@ NPairHalfSizeBinNewtonOmp::NPairHalfSizeBinNewtonOmp(LAMMPS *lmp) :
void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
FixShearHistory * const fix_history = (FixShearHistory *) list->fix_history;
NeighList * listhistory = list->listhistory;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal + atom->nghost;
}
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listhistory)
#pragma omp parallel default(none) shared(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
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;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
int *npartner;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
// loop over each atom, storing neighbors
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
......@@ -88,29 +68,10 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listhistory->firstneigh;
firstshear = listhistory->firstdouble;
ipage_touch = listhistory->ipage+tid;
dpage_shear = listhistory->dpage+tid;
dnum = listhistory->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];
......@@ -140,29 +101,10 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
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++;
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
......@@ -181,29 +123,10 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
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++;
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
......@@ -214,13 +137,6 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
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);
}
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
......
src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
+ 8
− 4
View file @ 5fb5f70e
......@@ -17,8 +17,6 @@
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
......@@ -32,7 +30,6 @@ NPairHalfSizeBinNewtonTriOmp::NPairHalfSizeBinNewtonTriOmp(LAMMPS *lmp) :
/* ----------------------------------------------------------------------
size 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
------------------------------------------------------------------------- */
......@@ -40,6 +37,8 @@ NPairHalfSizeBinNewtonTriOmp::NPairHalfSizeBinNewtonTriOmp(LAMMPS *lmp) :
void NPairHalfSizeBinNewtonTriOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
......@@ -105,7 +104,12 @@ void NPairHalfSizeBinNewtonTriOmp::build(NeighList *list)
radsum = radi + radius[j];
cutsq = (radsum+skin) * (radsum+skin);
if (rsq <= cutsq) neighptr[n++] = j;
if (rsq <= cutsq) {
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
}
......
src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
+ 9
− 71
View file @ 5fb5f70e
......@@ -19,9 +19,6 @@
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
......@@ -44,34 +41,20 @@ void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
FixShearHistory * const fix_history = (FixShearHistory *) list->fix_history;
NeighList * listhistory = list->listhistory;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal + atom->nghost;
}
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listhistory)
#pragma omp parallel default(none) shared(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,m,n,nn,dnum,dnumbytes;
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;
tagint **partner;
double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
MyPage<double> *dpage_shear;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
......@@ -89,29 +72,10 @@ void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listhistory->firstneigh;
firstshear = listhistory->firstdouble;
ipage_touch = listhistory->ipage+tid;
dpage_shear = listhistory->dpage+tid;
dnum = listhistory->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];
......@@ -132,29 +96,10 @@ void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
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++;
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
......@@ -164,13 +109,6 @@ void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
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);
}
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
......
src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
+ 9
− 70
View file @ 5fb5f70e
......@@ -19,9 +19,6 @@
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "molecule.h"
#include "domain.h"
#include "fix_shear_history.h"
#include "my_page.h"
#include "error.h"
......@@ -45,34 +42,20 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;;
FixShearHistory * const fix_history = (FixShearHistory *) list->fix_history;
NeighList * listhistory = list->listhistory;
if (fix_history) {
fix_history->nlocal_neigh = nlocal;
fix_history->nall_neigh = nlocal+atom->nghost;
}
const int history = list->history;
const int mask_history = 3 << SBBITS;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listhistory)
#pragma omp parallel default(none) shared(list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,m,n,nn,itag,jtag,dnum,dnumbytes;
int i,j,m,n,nn,itag,jtag;
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;
int *neighptr;
double **x = atom->x;
double *radius = atom->radius;
......@@ -90,29 +73,10 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
MyPage<int> &ipage = list->ipage[tid];
ipage.reset();
if (fix_history) {
npartner = fix_history->npartner;
partner = fix_history->partner;
shearpartner = fix_history->shearpartner;
firsttouch = listhistory->firstneigh;
firstshear = listhistory->firstdouble;
ipage_touch = listhistory->ipage+tid;
dpage_shear = listhistory->dpage+tid;
dnum = listhistory->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();
}
itag = tag[i];
xtmp = x[i][0];
......@@ -150,29 +114,10 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
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++;
if (history && rsq < radsum*radsum)
neighptr[n++] = j ^ mask_history;
else
neighptr[n++] = j;
}
}
......@@ -183,12 +128,6 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
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);
}
}
NPAIR_OMP_CLOSE;
list->inum = nlocal;
......
src/USER-OMP/pair_gran_hertz_history_omp.cpp
+ 1
− 0
View file @ 5fb5f70e
......@@ -14,6 +14,7 @@
#include <math.h>
#include "pair_gran_hertz_history_omp.h"
#include "fix_neigh_history.h"
#include "atom.h"
#include "comm.h"
#include "fix.h"
......
src/USER-OMP/pair_gran_hooke_history_omp.cpp
+ 1
− 0
View file @ 5fb5f70e
......@@ -14,6 +14,7 @@
#include <math.h>
#include "pair_gran_hooke_history_omp.h"
#include "fix_neigh_history.h"
#include "atom.h"
#include "comm.h"
#include "fix.h"
......
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