From 5fb5f70ec6847f971bcf74d40022a4f6cd4396ac Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 16 Oct 2017 14:37:20 -0400
Subject: [PATCH] update USER-OMP code for shear history neighbor refactoring
---
.../npair_half_size_bin_newtoff_omp.cpp | 77 ++----------
.../npair_half_size_bin_newton_omp.cpp | 110 +++---------------
.../npair_half_size_bin_newton_tri_omp.cpp | 12 +-
.../npair_half_size_nsq_newtoff_omp.cpp | 80 ++-----------
.../npair_half_size_nsq_newton_omp.cpp | 79 ++-----------
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 1 +
src/USER-OMP/pair_gran_hooke_history_omp.cpp | 1 +
7 files changed, 50 insertions(+), 310 deletions(-)
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
index 120658b714..6a1cb46ea6 100644
--- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
index cf0c6d20fe..d8e1e6da44 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
index da04eebd1e..b02bfa345e 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
@@ -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;
+ }
}
}
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
index f898ec3828..3c7b6b118f 100644
--- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
index a7caac372a..37a4181af7 100644
--- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
index 0863559afb..046b71a73a 100644
--- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
@@ -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"
diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
index 73952a5141..2e7d55aff0 100644
--- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
@@ -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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