diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index fa01ac15ac95c2340503f452a324c8de3b4a5c5e..f6555063dc42ca3b261cd257e111842214a92c97 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -31,6 +31,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
+#include "my_page.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
@@ -55,8 +56,9 @@ PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp)
maxlocal = 0;
REBO_numneigh = NULL;
REBO_firstneigh = NULL;
- maxpage = 0;
- pages = NULL;
+ ipage = NULL;
+ pgsize = oneatom = 0;
+
nC = nH = NULL;
manybody_flag = 1;
}
@@ -69,8 +71,7 @@ PairAIREBO::~PairAIREBO()
{
memory->destroy(REBO_numneigh);
memory->sfree(REBO_firstneigh);
- for (int i = 0; i < maxpage; i++) memory->destroy(pages[i]);
- memory->sfree(pages);
+ delete [] ipage;
memory->destroy(nC);
memory->destroy(nH);
@@ -221,11 +222,24 @@ void PairAIREBO::init_style()
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
- // local REBO neighbor list memory
+ // local REBO neighbor list
+ // create pages if first time or if neighbor pgsize/oneatom has changed
+
+ int create = 0;
+ if (ipage == NULL) create = 1;
+ if (pgsize != neighbor->pgsize) create = 1;
+ if (oneatom != neighbor->oneatom) create = 1;
- pgsize = neighbor->pgsize;
- oneatom = neighbor->oneatom;
- if (maxpage == 0) add_pages();
+ if (create) {
+ delete [] ipage;
+ pgsize = neighbor->pgsize;
+ oneatom = neighbor->oneatom;
+
+ int nmypage= comm->nthreads;
+ ipage = new MyPage<int>[nmypage];
+ for (int i = 0; i < nmypage; i++)
+ ipage[i].init(oneatom,pgsize,PGDELTA);
+ }
}
/* ----------------------------------------------------------------------
@@ -329,19 +343,13 @@ void PairAIREBO::REBO_neigh()
// store all REBO neighs of owned and ghost atoms
// scan full neighbor list of I
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (ii = 0; ii < allnum; ii++) {
i = ilist[ii];
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages();
- }
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -371,10 +379,9 @@ void PairAIREBO::REBO_neigh()
REBO_firstneigh[i] = neighptr;
REBO_numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one(FLERR,
- "Neighbor list overflow, boost neigh_modify one or page");
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
@@ -3285,21 +3292,6 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
return Tijf;
}
-/* ----------------------------------------------------------------------
- add pages to REBO neighbor list
-------------------------------------------------------------------------- */
-
-void PairAIREBO::add_pages(int howmany)
-{
- int toppage = maxpage;
- maxpage += howmany*PGDELTA;
-
- pages = (int **)
- memory->srealloc(pages,maxpage*sizeof(int *),"AIREBO:pages");
- for (int i = toppage; i < maxpage; i++)
- memory->create(pages[i],pgsize,"AIREBO:pages[i]");
-}
-
/* ----------------------------------------------------------------------
read AIREBO potential file
------------------------------------------------------------------------- */
@@ -4199,7 +4191,10 @@ double PairAIREBO::memory_usage()
double bytes = 0.0;
bytes += maxlocal * sizeof(int);
bytes += maxlocal * sizeof(int *);
- bytes += maxpage * neighbor->pgsize * sizeof(int);
- bytes += 3 * maxlocal * sizeof(double);
+
+ for (int i = 0; i < comm->nthreads; i++)
+ bytes += ipage[i].size();
+
+ bytes += 2*maxlocal * sizeof(double);
return bytes;
}
diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h
index fc8378b98be312fc2b9279714ec0b0cb897b747a..8536d6ab012e03772e569f5010bc47b140c712bf 100644
--- a/src/MANYBODY/pair_airebo.h
+++ b/src/MANYBODY/pair_airebo.h
@@ -21,6 +21,7 @@ PairStyle(airebo,PairAIREBO)
#define LMP_PAIR_AIREBO_H
#include "pair.h"
+#include "my_page.h"
#include "math.h"
#include "math_const.h"
@@ -38,15 +39,10 @@ class PairAIREBO : public Pair {
double memory_usage();
protected:
- int **pages; // neighbor list pages
int *map; // 0 (C), 1 (H), or -1 (NULL) for each type
int me;
int ljflag,torflag; // 0/1 if LJ,torsion terms included
- int maxlocal; // size of numneigh, firstneigh arrays
- int maxpage; // # of pages currently allocated
- int pgsize; // size of neighbor page
- int oneatom; // max # of neighbors for one atom
double cutlj; // user-specified LJ cutoff
double cutljrebosq; // cut for when to compute
@@ -56,8 +52,13 @@ class PairAIREBO : public Pair {
double **lj1,**lj2,**lj3,**lj4; // pre-computed LJ coeffs for C,H types
double cut3rebo; // maximum distance for 3rd REBO neigh
+ int maxlocal; // size of numneigh, firstneigh arrays
+ int pgsize; // size of neighbor page
+ int oneatom; // max # of neighbors for one atom
+ MyPage<int> *ipage; // neighbor list pages
int *REBO_numneigh; // # of pair neighbors for each atom
int **REBO_firstneigh; // ptr to 1st neighbor of each atom
+
double *closestdistsq; // closest owned atom dist to each ghost
double *nC,*nH; // sum of weighting fns with REBO neighs
@@ -101,7 +102,6 @@ class PairAIREBO : public Pair {
double piRCSpline(double, double, double, int, int, double *);
double TijSpline(double, double, double, double *);
- void add_pages(int howmany = 1);
void read_file(char *);
double Sp5th(double, double *, double *);
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index d5982caf0eb068dd5ce8497fececf77802ba58f7..2da2fc93d96f3144e52e5ccacd71e71db70736c0 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -31,6 +31,7 @@
#include "neigh_request.h"
#include "group.h"
#include "update.h"
+#include "my_page.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@@ -73,8 +74,9 @@ PairComb::PairComb(LAMMPS *lmp) : Pair(lmp)
sht_num = NULL;
sht_first = NULL;
- maxpage = 0;
- pages = NULL;
+
+ ipage = NULL;
+ pgsize = oneatom = 0;
// set comm size needed by this Pair
@@ -108,6 +110,8 @@ PairComb::~PairComb()
memory->destroy(sht_num);
memory->destroy(sht_first);
+ delete [] ipage;
+
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
@@ -541,9 +545,24 @@ void PairComb::init_style()
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
- pgsize = neighbor->pgsize;
- oneatom = neighbor->oneatom;
- if (maxpage == 0) add_pages();
+ // local Comb neighbor list
+ // create pages if first time or if neighbor pgsize/oneatom has changed
+
+ int create = 0;
+ if (ipage == NULL) create = 1;
+ if (pgsize != neighbor->pgsize) create = 1;
+ if (oneatom != neighbor->oneatom) create = 1;
+
+ if (create) {
+ delete [] ipage;
+ pgsize = neighbor->pgsize;
+ oneatom = neighbor->oneatom;
+
+ int nmypage = comm->nthreads;
+ ipage = new MyPage<int>[nmypage];
+ for (int i = 0; i < nmypage; i++)
+ ipage[i].init(oneatom,pgsize);
+ }
}
/* ----------------------------------------------------------------------
@@ -1364,8 +1383,7 @@ void PairComb::sm_table()
memory->create(NCo,nmax,"pair:NCo");
memory->create(bbij,nmax,MAXNEIGH,"pair:bbij");
memory->create(sht_num,nmax,"pair:sht_num");
- sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
- "pair:sht_first");
+ sht_first = (int **) memory->smalloc(nmax*sizeof(int *),"pair:sht_first");
// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
@@ -2023,18 +2041,6 @@ void PairComb::unpack_reverse_comm(int n, int *list, double *buf)
}
}
-/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
-------------------------------------------------------------------------- */
-
-double PairComb::memory_usage()
-{
- double bytes = maxeatom * sizeof(double);
- bytes += maxvatom*6 * sizeof(double);
- bytes += nmax * sizeof(int);
- bytes += MAXNEIGH * nmax * sizeof(int);
- return bytes;
-}
/* ---------------------------------------------------------------------- */
void PairComb::Short_neigh()
@@ -2064,21 +2070,17 @@ void PairComb::Short_neigh()
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- int npntj = 0;
- int npage = 0;
+
+ // create Comb neighbor list
+
+ ipage->reset();
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
- if (pgsize - npntj < oneatom) {
- npntj = 0;
- npage++;
- if (npage == maxpage) add_pages();
- }
-
nj = 0;
- neighptrj = &pages[npage][npntj];
+ neighptrj = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -2103,19 +2105,27 @@ void PairComb::Short_neigh()
sht_first[i] = neighptrj;
sht_num[i] = nj;
- npntj += nj;
+ ipage->vgot(nj);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
-void PairComb::add_pages(int howmany)
+double PairComb::memory_usage()
{
- int toppage = maxpage;
- maxpage += howmany*PGDELTA;
+ double bytes = maxeatom * sizeof(double);
+ bytes += maxvatom*6 * sizeof(double);
+ bytes += nmax * sizeof(int);
+ bytes += nmax * sizeof(int *);
+
+ for (int i = 0; i < comm->nthreads; i++)
+ bytes += ipage[i].size();
- pages = (int **)
- memory->srealloc(pages,maxpage*sizeof(int *),"pair:pages");
- for (int i = toppage; i < maxpage; i++)
- memory->create(pages[i],pgsize,"pair:pages[i]");
+ bytes += nmax * sizeof(int);
+ bytes += MAXNEIGH*nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h
index 3131c95b1b82dd9081e443a2c194efc6ae25a9f6..cd3947a3d7e1d07944af75e0182570b933ea5d89 100644
--- a/src/MANYBODY/pair_comb.h
+++ b/src/MANYBODY/pair_comb.h
@@ -21,6 +21,7 @@ PairStyle(comb,PairComb)
#define LMP_PAIR_COMB_H
#include "pair.h"
+#include "my_page.h"
namespace LAMMPS_NS {
@@ -77,6 +78,12 @@ class PairComb : public Pair {
int *NCo, cor_flag, cuo_flag, cuo_flag1, cuo_flag2;
double **bbij;
+ int pgsize; // size of neighbor page
+ int oneatom; // max # of neighbors for one atom
+ int *sht_num,**sht_first; // short-range neighbor list
+ MyPage<int> *ipage; // neighbor list pages
+ double cutmin;
+
void allocate();
virtual void read_file(char *);
void setup();
@@ -145,13 +152,7 @@ class PairComb : public Pair {
int pack_comm(int , int *, double *, int, int *);
void unpack_comm(int , int , double *);
- // short range neighbor list
-
- void add_pages(int howmany = 1);
void Short_neigh();
- int maxpage, pgsize, oneatom, **pages;
- int *sht_num, **sht_first; // short-range neighbor list
- double cutmin;
// vector functions, inline for efficiency
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 5e7c6974c20cf66e06c60064107d8e2e235671cf..cc511d59a40064ee8fe1a164534b2a94717c4816 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -30,6 +30,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
+#include "my_page.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@@ -52,8 +53,9 @@ PairLCBOP::PairLCBOP(LAMMPS *lmp) : Pair(lmp) {
maxlocal = 0;
SR_numneigh = NULL;
SR_firstneigh = NULL;
- maxpage = 0;
- pages = NULL;
+ ipage = NULL;
+ pgsize = oneatom = 0;
+
N = NULL;
M = NULL;
}
@@ -62,11 +64,11 @@ PairLCBOP::PairLCBOP(LAMMPS *lmp) : Pair(lmp) {
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
-PairLCBOP::~PairLCBOP() {
+PairLCBOP::~PairLCBOP()
+{
memory->destroy(SR_numneigh);
memory->sfree(SR_firstneigh);
- for (int i = 0; i < maxpage; i++) memory->destroy(pages[i]);
- memory->sfree(pages);
+ delete [] ipage;
memory->destroy(N);
memory->destroy(M);
@@ -191,11 +193,24 @@ void PairLCBOP::init_style()
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
- // local SR neighbor list memory
+ // local SR neighbor list
+ // create pages if first time or if neighbor pgsize/oneatom has changed
+
+ int create = 0;
+ if (ipage == NULL) create = 1;
+ if (pgsize != neighbor->pgsize) create = 1;
+ if (oneatom != neighbor->oneatom) create = 1;
- pgsize = neighbor->pgsize;
- oneatom = neighbor->oneatom;
- if (maxpage == 0) add_pages();
+ if (create) {
+ delete [] ipage;
+ pgsize = neighbor->pgsize;
+ oneatom = neighbor->oneatom;
+
+ int nmypage = comm->nthreads;
+ ipage = new MyPage<int>[nmypage];
+ for (int i = 0; i < nmypage; i++)
+ ipage[i].init(oneatom,pgsize,PGDELTA);
+ }
}
/* ----------------------------------------------------------------------
@@ -238,9 +253,7 @@ double PairLCBOP::init_one(int i, int j)
void PairLCBOP::SR_neigh()
{
- int i,j,ii,jj,n,
- allnum, // number of atoms(both local and ghost) neighbors are stored for
- jnum;
+ int i,j,ii,jj,n,allnum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;
int *ilist,*jlist,*numneigh,**firstneigh;
int *neighptr;
@@ -270,19 +283,13 @@ void PairLCBOP::SR_neigh()
// store all SR neighs of owned and ghost atoms
// scan full neighbor list of I
- int npage = 0;
- int npnt = 0; // position in current page
+ ipage->reset();
for (ii = 0; ii < allnum; ii++) {
i = ilist[ii];
- if (pgsize - npnt < oneatom) { // ensure at least oneatom space free at current page
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages();
- }
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -307,14 +314,13 @@ void PairLCBOP::SR_neigh()
SR_firstneigh[i] = neighptr;
SR_numneigh[i] = n;
- npnt += n;
- if( npnt >= pgsize )
- error->one(FLERR,
- "Neighbor list overflow, boost neigh_modify one or page");
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
-
// calculate M_i
+
for (ii = 0; ii < allnum; ii++) {
i = ilist[ii];
@@ -861,21 +867,6 @@ double PairLCBOP::b(int i, int j, double rij[3],
return bij;
}
-/* ----------------------------------------------------------------------
- add pages to SR neighbor list
-------------------------------------------------------------------------- */
-
-void PairLCBOP::add_pages(int howmany)
-{
- int toppage = maxpage;
- maxpage += howmany*PGDELTA;
-
- pages = (int **)
- memory->srealloc(pages,maxpage*sizeof(int *),"LCBOP:pages");
- for (int i = toppage; i < maxpage; i++)
- memory->create(pages[i],pgsize,"LCBOP:pages[i]");
-}
-
/* ----------------------------------------------------------------------
spline interpolation for G
------------------------------------------------------------------------- */
@@ -1287,11 +1278,15 @@ void PairLCBOP::spline_init() {
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
-double PairLCBOP::memory_usage() {
+double PairLCBOP::memory_usage()
+{
double bytes = 0.0;
bytes += maxlocal * sizeof(int);
bytes += maxlocal * sizeof(int *);
- bytes += maxpage * neighbor->pgsize * sizeof(int);
- bytes += 3 * maxlocal * sizeof(double);
+
+ for (int i = 0; i < comm->nthreads; i++)
+ bytes += ipage[i].size();
+
+ bytes += 3*maxlocal * sizeof(double);
return bytes;
}
diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h
index 71567cec95da7fa668391ac1e4e865706d408587..dc0ad61c7c99a5f485b99252eb508e6a5449256e 100644
--- a/src/MANYBODY/pair_lcbop.h
+++ b/src/MANYBODY/pair_lcbop.h
@@ -21,6 +21,7 @@ PairStyle(lcbop,PairLCBOP)
#define LMP_PAIR_LCBOP_H
#include "pair.h"
+#include "my_page.h"
#include "math.h"
#include "math_const.h"
@@ -42,18 +43,20 @@ class PairLCBOP : public Pair {
int *map; // 0 (C) or -1 (NULL) for each type
int me;
- int maxlocal; // size of numneigh, firstneigh arrays
- int maxpage; // # of pages currently allocated
- int pgsize; // size of neighbor page
- int oneatom; // max # of neighbors for one atom
double cutLR; // LR cutoff
double cutLRsq; // LR cutoff squared
double cut3rebo; // maximum distance for 3rd SR neigh
+ int maxlocal; // size of numneigh, firstneigh arrays
+ int maxpage; // # of pages currently allocated
+ int pgsize; // size of neighbor page
+ int oneatom; // max # of neighbors for one atom
+ MyPage<int> *ipage; // neighbor list pages
int *SR_numneigh; // # of pair neighbors for each atom
int **SR_firstneigh; // ptr to 1st neighbor of each atom
+
double *N; // sum of cutoff fns ( f_C ) with SR neighs
double *M; // sum_j f_C_ij*F(N_j - f_C_ij)
@@ -80,6 +83,7 @@ class PairLCBOP : public Pair {
f_y_10,
f_y_11;
} F_conj_field[3][3][2];
+
double F_conj_data[4][4][2][3]; // temporary data from file
double gX[6]; // x coordinates for described points[# of points];
double gC[5+1][6-1]; // coefficients for each period between described points [degree of polynomial+1][# of points-1]
@@ -98,7 +102,6 @@ class PairLCBOP : public Pair {
void g_decompose_x( double, size_t*, double* );
double F_conj( double, double, double, double*, double*, double* );
- void add_pages(int howmany = 1);
void read_file( char * );
void spline_init();
diff --git a/src/USER-OMP/fix_shear_history_omp.cpp b/src/USER-OMP/fix_shear_history_omp.cpp
index d410f6363c57b36da87224ae28baa411aab27b0f..1fe89de3e4268505120d56a71f5b386b7720b751 100644
--- a/src/USER-OMP/fix_shear_history_omp.cpp
+++ b/src/USER-OMP/fix_shear_history_omp.cpp
@@ -31,8 +31,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-#define MAXTOUCH 15
-
/* ----------------------------------------------------------------------
copy shear partner info from neighbor lists to atom arrays
so can be exchanged with atoms
@@ -45,10 +43,10 @@ void FixShearHistoryOMP::pre_exchange()
const int nghost = atom->nghost;
const int nall = nlocal + nghost;
const int nthreads = comm->nthreads;
-
- int flag = 0;
+ maxtouch = 0;
+
#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(flag)
+#pragma omp parallel default(none)
#endif
{
@@ -64,22 +62,23 @@ void FixShearHistoryOMP::pre_exchange()
const int lmax = lfrom +ldelta;
const int lto = (lmax > nlocal) ? nlocal : lmax;
- const int gdelta = 1 + nghost/nthreads;
- const int gfrom = nlocal + tid*gdelta;
- const int gmax = gfrom + gdelta;
- const int gto = (gmax > nall) ? nall : gmax;
-
-
- int i,j,ii,jj,m,inum,jnum;
+ int i,j,ii,jj,m,n,inum,jnum;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *shear,*allshear,**firstshear;
- // zero npartners for all current atoms
+ // zero npartners for all current atoms and
+ // clear page data structures for this thread
for (i = lfrom; i < lto; i++) npartner[i] = 0;
- // copy shear info from neighbor list atoms to atom arrays
+ MyPage <int> &ipg = ipage[tid];
+ MyPage <double[3]> &dpg = dpage[tid];
+ ipg.reset();
+ dpg.reset();
+
+ // 1st loop over neighbor list
+ // calculate nparter for each owned atom
int *tag = atom->tag;
@@ -94,59 +93,81 @@ void FixShearHistoryOMP::pre_exchange()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
- allshear = firstshear[i];
jnum = numneigh[i];
touch = firsttouch[i];
for (jj = 0; jj < jnum; jj++) {
if (touch[jj]) {
+ if ((i >= lfrom) && (i < lto))
+ npartner[i]++;
+
j = jlist[jj];
j &= NEIGHMASK;
+ if ((j >= lfrom) && (j < lto))
+ npartner[j]++;
+ }
+ }
+ }
+
+ // get page chunks to store atom IDs and shear history for my atoms
+
+ for (ii = lfrom; ii < lto; ii++) {
+ i = ilist[ii];
+ n = npartner[i];
+ partner[i] = ipg.get(n);
+ shearpartner[i] = dpg.get(n);
+ if (partner[i] == NULL || shearpartner[i] == NULL)
+ error->one(FLERR,"Shear history overflow, boost neigh_modify one");
+ }
+
+ // 2nd loop over neighbor list
+ // store atom IDs and shear history for my atoms
+ // re-zero npartner to use as counter for all my atoms
+
+ for (i = lfrom; i < lto; i++) npartner[i] = 0;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ jlist = firstneigh[i];
+ allshear = firstshear[i];
+ jnum = numneigh[i];
+ touch = firsttouch[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ if (touch[jj]) {
shear = &allshear[3*jj];
+ j = jlist[jj];
+ j &= NEIGHMASK;
if ((i >= lfrom) && (i < lto)) {
- if (npartner[i] < MAXTOUCH) {
- m = npartner[i];
- partner[i][m] = tag[j];
- shearpartner[i][m][0] = shear[0];
- shearpartner[i][m][1] = shear[1];
- shearpartner[i][m][2] = shear[2];
- }
+ m = npartner[i];
+ partner[i][m] = tag[j];
+ shearpartner[i][m][0] = shear[0];
+ shearpartner[i][m][1] = shear[1];
+ shearpartner[i][m][2] = shear[2];
npartner[i]++;
}
if ((j >= lfrom) && (j < lto)) {
- if (npartner[j] < MAXTOUCH) {
- m = npartner[j];
- partner[j][m] = tag[i];
- shearpartner[j][m][0] = -shear[0];
- shearpartner[j][m][1] = -shear[1];
- shearpartner[j][m][2] = -shear[2];
- }
- npartner[j]++;
- }
-
- if ((j >= gfrom) && (j < gto)) {
+ m = npartner[j];
+ partner[j][m] = tag[i];
+ shearpartner[j][m][0] = -shear[0];
+ shearpartner[j][m][1] = -shear[1];
+ shearpartner[j][m][2] = -shear[2];
npartner[j]++;
}
}
}
}
- // test for too many touching neighbors
- int myflag = 0;
+ // set maxtouch = max # of partners of any owned atom
+ m = 0;
for (i = lfrom; i < lto; i++)
- if (npartner[i] >= MAXTOUCH) myflag = 1;
+ m = MAX(m,npartner[i]);
- if (myflag)
#if defined(_OPENMP)
-#pragma omp atomic
+#pragma omp critical
#endif
- ++flag;
+ maxtouch = MAX(m,maxtouch);
}
-
- int flag_all;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all)
- error->all(FLERR,"Too many touching neighbors - boost MAXTOUCH");
}
diff --git a/src/USER-OMP/neigh_derive_omp.cpp b/src/USER-OMP/neigh_derive_omp.cpp
index 4356f17b62388ae1bc60500e957ea4e6c4803491..8f5fa05e81457cd78fe4c7a5c17744479f161df6 100644
--- a/src/USER-OMP/neigh_derive_omp.cpp
+++ b/src/USER-OMP/neigh_derive_omp.cpp
@@ -16,6 +16,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -48,27 +49,16 @@ void Neighbor::half_from_full_no_newton_omp(NeighList *list)
int *numneigh_full = list->listfull->numneigh;
int **firstneigh_full = list->listfull->firstneigh;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over atoms in full list
for (ii = ifrom; ii < ito; ii++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- // only one thread at a time may check whether we
- // need new neighbor list pages and then add to them.
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
// loop over parent full list
@@ -85,8 +75,8 @@ void Neighbor::half_from_full_no_newton_omp(NeighList *list)
ilist[ii] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -124,27 +114,16 @@ void Neighbor::half_from_full_newton_omp(NeighList *list)
int *numneigh_full = list->listfull->numneigh;
int **firstneigh_full = list->listfull->firstneigh;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over parent full list
for (ii = ifrom; ii < ito; ii++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- // only one thread at a time may check whether we
- // need new neighbor list pages and then add to them.
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
i = ilist_full[ii];
xtmp = x[i][0];
@@ -174,8 +153,8 @@ void Neighbor::half_from_full_newton_omp(NeighList *list)
ilist[ii] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neigh_full_omp.cpp b/src/USER-OMP/neigh_full_omp.cpp
index 8ba2ffaf2b5533abb6d95007c4f849b902186159..e609627897c6f993643e6c6703614521b42997e6 100644
--- a/src/USER-OMP/neigh_full_omp.cpp
+++ b/src/USER-OMP/neigh_full_omp.cpp
@@ -18,6 +18,7 @@
#include "comm.h"
#include "domain.h"
#include "group.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -57,24 +58,16 @@ void Neighbor::full_nsq_omp(NeighList *list)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over owned atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -108,8 +101,8 @@ void Neighbor::full_nsq_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -152,24 +145,16 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over owned & ghost atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -218,8 +203,8 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -266,24 +251,16 @@ void Neighbor::full_bin_omp(NeighList *list)
int nstencil = list->nstencil;
int *stencil = list->stencil;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over owned atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -322,8 +299,8 @@ void Neighbor::full_bin_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -374,24 +351,16 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over owned & ghost atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -457,8 +426,8 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -510,22 +479,14 @@ void Neighbor::full_multi_omp(NeighList *list)
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -569,8 +530,8 @@ void Neighbor::full_multi_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neigh_gran_omp.cpp b/src/USER-OMP/neigh_gran_omp.cpp
index e8634dcf3acd49f89732d299fdcac5c1ae3e4088..5f0402f36397e230670e84b409b9a6b71c1492a5 100644
--- a/src/USER-OMP/neigh_gran_omp.cpp
+++ b/src/USER-OMP/neigh_gran_omp.cpp
@@ -40,10 +40,6 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
NEIGH_OMP_INIT;
- if (fix_history)
- if (nthreads > listgranhistory->maxpage)
- listgranhistory->add_pages(nthreads - listgranhistory->maxpage);
-
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
@@ -59,6 +55,8 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
double (**shearpartner)[3];
int **firsttouch;
double **firstshear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
double **x = atom->x;
double *radius = atom->radius;
@@ -72,41 +70,32 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
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;
+ ipage_touch->reset();
+ dpage_shear->reset();
}
- int npage = tid;
- int npnt = 0;
-
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) {
- list->add_pages(nthreads);
- if (fix_history)
- listgranhistory->add_pages(nthreads);
- }
- }
-
- n = nn = 0;
- neighptr = &(list->pages[npage][npnt]);
- if (fix_history) {
- touchptr = &(listgranhistory->pages[npage][npnt]);
- shearptr = &(listgranhistory->dpages[npage][3*npnt]);
- }
+ 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];
@@ -158,13 +147,16 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
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);
}
- npnt += n;
- if (n > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
@@ -207,22 +199,14 @@ void Neighbor::granular_nsq_newton_omp(NeighList *list)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itag = tag[i];
xtmp = x[i][0];
@@ -265,8 +249,8 @@ void Neighbor::granular_nsq_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -295,10 +279,6 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
NEIGH_OMP_INIT;
- if (fix_history)
- if (nthreads > listgranhistory->maxpage)
- listgranhistory->add_pages(nthreads - listgranhistory->maxpage);
-
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listgranhistory)
#endif
@@ -309,6 +289,8 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
int *npartner,**partner;
double (**shearpartner)[3];
@@ -330,39 +312,30 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
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;
+ ipage_touch->reset();
+ dpage_shear->reset();
}
- int npage = tid;
- int npnt = 0;
-
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) {
- list->add_pages(nthreads);
- if (fix_history)
- listgranhistory->add_pages(nthreads);
- }
- }
-
- n = nn = 0;
- neighptr = &(list->pages[npage][npnt]);
- if (fix_history) {
- touchptr = &(listgranhistory->pages[npage][npnt]);
- shearptr = &(listgranhistory->dpages[npage][3*npnt]);
- }
+ n = 0;
+ neighptr = ipage.vget();
+ if (fix_history) {
+ nn = 0;
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
}
xtmp = x[i][0];
@@ -422,13 +395,16 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
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);
}
- npnt += n;
- if (n > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
@@ -475,22 +451,14 @@ void Neighbor::granular_bin_newton_omp(NeighList *list)
int nstencil = list->nstencil;
int *stencil = list->stencil;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
n = 0;
- neighptr = &(list->pages[npage][npnt]);
+ neighptr = ipage.vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -543,8 +511,8 @@ void Neighbor::granular_bin_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -592,22 +560,14 @@ void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
int nstencil = list->nstencil;
int *stencil = list->stencil;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
n = 0;
- neighptr = &(list->pages[npage][npnt]);
+ neighptr = ipage.vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -648,8 +608,8 @@ void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neigh_half_bin_omp.cpp b/src/USER-OMP/neigh_half_bin_omp.cpp
index ba0a180410361f820ad5892cbe8057002464f3e1..f501684a19642d7a79782c644da6426f02f0e2a0 100644
--- a/src/USER-OMP/neigh_half_bin_omp.cpp
+++ b/src/USER-OMP/neigh_half_bin_omp.cpp
@@ -17,6 +17,7 @@
#include "atom.h"
#include "comm.h"
#include "domain.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -64,23 +65,14 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
int nstencil = list->nstencil;
int *stencil = list->stencil;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -121,8 +113,8 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -177,23 +169,14 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -263,8 +246,8 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -314,23 +297,14 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
int nstencil = list->nstencil;
int *stencil = list->stencil;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -399,8 +373,8 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -449,23 +423,14 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
int nstencil = list->nstencil;
int *stencil = list->stencil;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -513,8 +478,8 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neigh_half_multi_omp.cpp b/src/USER-OMP/neigh_half_multi_omp.cpp
index 5cc6ba140128ea8266afdabbeaf1fa1ef8027a11..b46594870fa38100b833d3d457ee4e605e030abe 100644
--- a/src/USER-OMP/neigh_half_multi_omp.cpp
+++ b/src/USER-OMP/neigh_half_multi_omp.cpp
@@ -17,6 +17,7 @@
#include "atom.h"
#include "comm.h"
#include "domain.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -67,23 +68,14 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -129,8 +121,8 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -182,23 +174,14 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -272,8 +255,8 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -325,23 +308,14 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -396,8 +370,8 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neigh_half_nsq_omp.cpp b/src/USER-OMP/neigh_half_nsq_omp.cpp
index 6a8bee491a2b85859fbc40daca03fbb133280153..a98c4721f3d5dfe2a91be852874e191a618d5ac2 100644
--- a/src/USER-OMP/neigh_half_nsq_omp.cpp
+++ b/src/USER-OMP/neigh_half_nsq_omp.cpp
@@ -18,6 +18,7 @@
#include "comm.h"
#include "domain.h"
#include "group.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -58,25 +59,16 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over owned atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -110,8 +102,8 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -156,25 +148,16 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- // each thread works on its own page
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
// loop over owned & ghost atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itype = type[i];
xtmp = x[i][0];
@@ -228,8 +211,8 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
@@ -275,22 +258,14 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ ipage.reset();
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
-
- neighptr = &(list->pages[npage][npnt]);
n = 0;
+ neighptr = ipage.vget();
itag = tag[i];
itype = type[i];
@@ -341,8 +316,8 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
diff --git a/src/USER-OMP/neigh_respa_omp.cpp b/src/USER-OMP/neigh_respa_omp.cpp
index 28afc81f1154cd15cc55e8c41a4b7edc4a8e4e19..11c7fd9ae307a5c00ccd853461fdfbf8ec349213 100644
--- a/src/USER-OMP/neigh_respa_omp.cpp
+++ b/src/USER-OMP/neigh_respa_omp.cpp
@@ -18,6 +18,7 @@
#include "comm.h"
#include "domain.h"
#include "group.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -37,16 +38,8 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
- if (nthreads > listinner->maxpage)
- listinner->add_pages(nthreads - listinner->maxpage);
-
- NeighList *listmiddle;
+ NeighList *listmiddle = list->listmiddle;
const int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- if (nthreads > listmiddle->maxpage)
- listmiddle->add_pages(nthreads - listmiddle->maxpage);
- }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
@@ -85,48 +78,30 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
firstneigh_middle = listmiddle->firstneigh;
}
- int npage = tid;
- int npnt = 0;
- int npage_inner = tid;
- int npnt_inner = 0;
- int npage_middle = tid;
- int npnt_middle = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
- neighptr = &(list->pages[npage][npnt]);
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner += nthreads;
- if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
- }
- neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
- }
- neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
- }
itype = type[i];
xtmp = x[i][0];
@@ -172,23 +147,23 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
@@ -214,16 +189,8 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
- if (nthreads > listinner->maxpage)
- listinner->add_pages(nthreads - listinner->maxpage);
-
- NeighList *listmiddle;
+ NeighList *listmiddle = list->listmiddle;
const int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- if (nthreads > listmiddle->maxpage)
- listmiddle->add_pages(nthreads - listmiddle->maxpage);
- }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
@@ -262,48 +229,30 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
firstneigh_middle = listmiddle->firstneigh;
}
- int npage = tid;
- int npnt = 0;
- int npage_inner = tid;
- int npnt_inner = 0;
- int npage_middle = tid;
- int npnt_middle = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
- neighptr = &(list->pages[npage][npnt]);
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner += nthreads;
- if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
- }
- neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
- }
- neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
- }
itag = tag[i];
itype = type[i];
@@ -367,23 +316,23 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
@@ -412,16 +361,8 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
- if (nthreads > listinner->maxpage)
- listinner->add_pages(nthreads - listinner->maxpage);
-
- NeighList *listmiddle;
+ NeighList *listmiddle = list->listmiddle;
const int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- if (nthreads > listmiddle->maxpage)
- listmiddle->add_pages(nthreads - listmiddle->maxpage);
- }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
@@ -461,48 +402,30 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
firstneigh_middle = listmiddle->firstneigh;
}
- int npage = tid;
- int npnt = 0;
- int npage_inner = tid;
- int npnt_inner = 0;
- int npage_middle = tid;
- int npnt_middle = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
- neighptr = &(list->pages[npage][npnt]);
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner += nthreads;
- if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
- }
- neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
- }
- neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
- }
itype = type[i];
xtmp = x[i][0];
@@ -557,23 +480,23 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
@@ -601,16 +524,8 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
- if (nthreads > listinner->maxpage)
- listinner->add_pages(nthreads - listinner->maxpage);
-
- NeighList *listmiddle;
+ NeighList *listmiddle = list->listmiddle;
const int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- if (nthreads > listmiddle->maxpage)
- listmiddle->add_pages(nthreads - listmiddle->maxpage);
- }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
@@ -650,48 +565,30 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
firstneigh_middle = listmiddle->firstneigh;
}
- int npage = tid;
- int npnt = 0;
- int npage_inner = tid;
- int npnt_inner = 0;
- int npage_middle = tid;
- int npnt_middle = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
- neighptr = &(list->pages[npage][npnt]);
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner += nthreads;
- if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
- }
- neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
- }
- neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
- }
itype = type[i];
xtmp = x[i][0];
@@ -787,23 +684,23 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
@@ -831,16 +728,8 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
NEIGH_OMP_INIT;
NeighList *listinner = list->listinner;
- if (nthreads > listinner->maxpage)
- listinner->add_pages(nthreads - listinner->maxpage);
-
- NeighList *listmiddle;
+ NeighList *listmiddle = list->listmiddle;
const int respamiddle = list->respamiddle;
- if (respamiddle) {
- listmiddle = list->listmiddle;
- if (nthreads > listmiddle->maxpage)
- listmiddle->add_pages(nthreads - listmiddle->maxpage);
- }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list,listinner,listmiddle)
@@ -880,48 +769,30 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
firstneigh_middle = listmiddle->firstneigh;
}
- int npage = tid;
- int npnt = 0;
- int npage_inner = tid;
- int npnt_inner = 0;
- int npage_middle = tid;
- int npnt_middle = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipage = list->ipage[tid];
+ MyPage<int> &ipage_inner = listinner->ipage[tid];
+ ipage.reset();
+ ipage_inner.reset();
+
+ MyPage<int> *ipage_middle;
+ if (respamiddle) {
+ ipage_middle = listmiddle->ipage + tid;
+ ipage_middle->reset();
+ }
int which = 0;
int minchange = 0;
for (i = ifrom; i < ito; i++) {
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- {
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= list->maxpage) list->add_pages(nthreads);
- }
- neighptr = &(list->pages[npage][npnt]);
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner += nthreads;
- if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
- }
- neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage.vget();
+ neighptr_inner = ipage_inner.vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle += nthreads;
- if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
- }
- neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
- }
itype = type[i];
xtmp = x[i][0];
@@ -984,23 +855,23 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage.vgot(n);
+ if (ipage.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage.vgot(n_inner);
+ if (ipage_inner.status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
diff --git a/src/USER-OMP/neighbor_omp.h b/src/USER-OMP/neighbor_omp.h
index 8db58c7e20be9ede45ca12b83d0ce4364eb9bd0b..2b2ad24fe5312806e78bef1ac0487a0fa49be76d 100644
--- a/src/USER-OMP/neighbor_omp.h
+++ b/src/USER-OMP/neighbor_omp.h
@@ -25,9 +25,7 @@ namespace LAMMPS_NS {
// make sure we have at least one page for each thread
#define NEIGH_OMP_INIT \
- const int nthreads = comm->nthreads; \
- if (nthreads > list->maxpage) \
- list->add_pages(nthreads - list->maxpage)
+ const int nthreads = comm->nthreads;
// get thread id and then assign each thread a fixed chunk of atoms
#define NEIGH_OMP_SETUP(num) \
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index 8ab26e9bf7edf82c4b86bb9f8cb45882cd0fbda9..ec788fd6ce8e0c7c993c767aeb3b5971f14708e2 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -19,6 +19,7 @@
#include "error.h"
#include "force.h"
#include "memory.h"
+#include "my_page.h"
#include "math_special.h"
#include "neighbor.h"
#include "neigh_list.h"
@@ -2671,9 +2672,6 @@ void PairAIREBOOMP::REBO_neigh_thr()
memory->create(nH,maxlocal,"AIREBO:nH");
}
- if (nthreads > maxpage)
- add_pages(nthreads - maxpage);
-
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
@@ -2704,22 +2702,15 @@ void PairAIREBOOMP::REBO_neigh_thr()
// store all REBO neighs of owned and ghost atoms
// scan full neighbor list of I
- int npage = tid;
- int npnt = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipg = ipage[tid];
+ ipg.reset();
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage += nthreads;
- if (npage >= maxpage) add_pages(nthreads);
- }
- neighptr = &(pages[npage][npnt]);
n = 0;
+ neighptr = ipg.vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -2749,10 +2740,9 @@ void PairAIREBOOMP::REBO_neigh_thr()
REBO_firstneigh[i] = neighptr;
REBO_numneigh[i] = n;
- npnt += n;
-
- if (npnt >= pgsize)
- error->one(FLERR,"REBO list overflow, boost neigh_modify one or page");
+ ipg.vgot(n);
+ if (ipg.status())
+ error->one(FLERR,"REBO list overflow, boost neigh_modify one");
}
}
}
diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp
index eea2c6b61027d3a55aeccf3c75b2a31c3350ec07..1a8c32f4a79c70abbc0078170674dd00d5a7c57c 100644
--- a/src/USER-OMP/pair_comb_omp.cpp
+++ b/src/USER-OMP/pair_comb_omp.cpp
@@ -19,6 +19,7 @@
#include "group.h"
#include "force.h"
#include "memory.h"
+#include "my_page.h"
#include "neighbor.h"
#include "neigh_list.h"
@@ -553,15 +554,13 @@ void PairCombOMP::Short_neigh_thr()
nmax = atom->nmax;
memory->sfree(sht_first);
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
- "pair:sht_first");
+ "pair:sht_first");
memory->grow(sht_num,nmax,"pair:sht_num");
memory->grow(NCo,nmax,"pair:NCo");
- memory->grow(bbij,nmax,nmax,"pair:bbij");
+ memory->grow(bbij,nmax,MAXNEIGH,"pair:bbij");
}
const int nthreads = comm->nthreads;
- if (nthreads > maxpage)
- add_pages(nthreads - maxpage);
#if defined(_OPENMP)
#pragma omp parallel default(none)
@@ -588,51 +587,44 @@ void PairCombOMP::Short_neigh_thr()
const int iidelta = 1 + inum/nthreads;
const int iifrom = tid*iidelta;
- int iito = iifrom + iidelta;
- if (iito > inum) iito = inum;
+ const int iito = ((iifrom + iidelta) > inum) ? inum : (iifrom+iidelta);
- int npage = tid;
- npntj = 0;
+ // each thread has its own page allocator
+ MyPage<int> &ipg = ipage[tid];
+ ipg.reset();
- if (iifrom < inum) {
- for (ii = iifrom; ii < iito; ii++) {
- i = ilist[ii];
+ // create Comb neighbor list
-#if defined(_OPENMP)
-#pragma omp critical
-#endif
- if(pgsize - npntj < oneatom) {
- npntj = 0;
- npage += nthreads;
- if (npage >= maxpage) add_pages(nthreads);
- }
+ for (ii = iifrom; ii < iito; ii++) {
+ i = ilist[ii];
- neighptrj = &pages[npage][npntj];
- nj = 0;
+ nj = 0;
+ neighptrj = ipg.vget();
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
- jlist = firstneigh[i];
- jnum = numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
- delrj[0] = xtmp - x[j][0];
- delrj[1] = ytmp - x[j][1];
- delrj[2] = ztmp - x[j][2];
- rsq = vec3_dot(delrj,delrj);
+ delrj[0] = xtmp - x[j][0];
+ delrj[1] = ytmp - x[j][1];
+ delrj[2] = ztmp - x[j][2];
+ rsq = vec3_dot(delrj,delrj);
- if (rsq > cutmin) continue;
- neighptrj[nj++] = j;
- }
- sht_first[i] = neighptrj;
- sht_num[i] = nj;
- npntj += nj;
+ if (rsq > cutmin) continue;
+ neighptrj[nj++] = j;
}
+ sht_first[i] = neighptrj;
+ sht_num[i] = nj;
+ ipg.vgot(nj);
+ if (ipg.status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
}
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index da0def908b4b8067b0c653241db8dab8c23fa713..5da158339f711f51c30a0154ef14f3b84a9ce6c1 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -16,6 +16,7 @@
#include "stdio.h"
#include "fix_shear_history.h"
#include "atom.h"
+#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
@@ -71,8 +72,8 @@ FixShearHistory::~FixShearHistory()
memory->destroy(npartner);
memory->sfree(partner);
memory->sfree(shearpartner);
- delete ipage;
- delete dpage;
+ delete [] ipage;
+ delete [] dpage;
}
/* ---------------------------------------------------------------------- */
@@ -105,10 +106,18 @@ void FixShearHistory::init()
if (oneatom != neighbor->oneatom) create = 1;
if (create) {
+ delete [] ipage;
+ delete [] dpage;
+
pgsize = neighbor->pgsize;
oneatom = neighbor->oneatom;
- ipage = new MyPage<int>(oneatom,pgsize);
- dpage = new MyPage<double[3]>(oneatom,pgsize);
+ int nmypage = comm->nthreads;
+ ipage = new MyPage<int>[nmypage];
+ dpage = new MyPage<double[3]>[nmypage];
+ for (int i = 0; i < nmypage; i++) {
+ ipage[i].init(oneatom,pgsize);
+ dpage[i].init(oneatom,pgsize);
+ }
}
}
@@ -260,8 +269,13 @@ double FixShearHistory::memory_usage()
double bytes = nmax * sizeof(int);
bytes = nmax * sizeof(int *);
bytes = nmax * sizeof(double *);
- bytes += ipage->ndatum * sizeof(int);
- bytes += dpage->ndatum * sizeof(double[3]);
+
+ int nmypage = comm->nthreads;
+ for (int i = 0; i < nmypage; i++) {
+ bytes += ipage[i].size();
+ bytes += dpage[i].size();
+ }
+
return bytes;
}
diff --git a/src/my_page.h b/src/my_page.h
index 1628a4bab6c1804a8f607b83b2d4ef9db908c890..5fdf1e13516ab3ade4f761c99c08a331b1dc4054 100644
--- a/src/my_page.h
+++ b/src/my_page.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@@ -24,22 +24,25 @@ usage:
inputs:
template T = one datum, e.g. int, double, struct, int[3]
for int[3], access datum as ivec[i][2]
- maxchunk = max # of datums in one chunk, default = 1
- pagesize = # of datums in one page, default = 1024
- should be insure big enough to store multiple chunks
- pagedelta = # of pages to allocate at a time, default = 1
methods:
T *get() = return ptr to one datum
T *get(N) = return ptr to N datums, N < maxchunk required
T *vget() = return ptr to maxchunk datums, use as needed, then call vgot()
all gets return NULL if error encountered
vgot(N) = used N datums of previous vget(), N < maxchunk required
+ void init(maxchunk, pagesize, pagedelta)
+ define allocation params and allocate first page(s)
+ call right after constructor
+ can call again to reset allocation params and free previous pages
+ maxchunk = max # of datums in one chunk, default = 1
+ pagesize = # of datums in one page, default = 1024
+ should be big enough to store multiple chunks
+ pagedelta = # of pages to allocate at a time, default = 1
+ return 1 if bad params
void reset() = clear pages w/out freeing
int size() = return total size of allocated pages in bytes
-public variables:
- ndatum = total # of stored datums
- nchunk = total # of stored chunks
- errorflag = flag for various error conditions
+ int status() = return error status
+ 0 = ok, 1 = chunksize > maxchunk, 2 = allocation error
------------------------------------------------------------------------- */
#ifndef LAMMPS_MY_PAGE_H
@@ -50,24 +53,33 @@ namespace LAMMPS_NS {
template<class T>
class MyPage {
- public:
int ndatum; // total # of stored datums
int nchunk; // total # of stored chunks
- int errorflag; // flag > 1 if error has occurred
- // 1 = invalid inputs
- // 2 = memory allocation error
- // 3 = chunk size exceeded maxchunk
- MyPage(int user_maxchunk = 1, int user_pagesize = 1024,
- int user_pagedelta = 1) {
+ public:
+ MyPage() {
+ ndatum = nchunk = 0;
+ pages = NULL;
+ npage = 0;
+ errorflag = 0;
+ }
+
+ // (re)initialize allocation params
+ // also allocate first page(s)
+
+ int init(int user_maxchunk = 1, int user_pagesize = 1024,
+ int user_pagedelta = 1) {
maxchunk = user_maxchunk;
pagesize = user_pagesize;
pagedelta = user_pagedelta;
- errorflag = 0;
- if (maxchunk <= 0 || pagesize <= 0 || pagedelta <= 0) errorflag = 1;
- if (maxchunk > pagesize) errorflag = 1;
- if (errorflag) return;
+ if (maxchunk <= 0 || pagesize <= 0 || pagedelta <= 0) return 1;
+ if (maxchunk > pagesize) return 1;
+
+ // free any previously allocated pages
+
+ for (int i = 0; i < npage; i++) free(pages[i]);
+ free(pages);
// initial page allocation
@@ -75,12 +87,13 @@ class MyPage {
pages = NULL;
npage = 0;
allocate();
- if (errorflag) return;
+ if (errorflag) return 2;
ipage = index = 0;
page = pages[ipage];
+ return 0;
}
- // free all pages of allocated memory
+ // free all allocated pages
~MyPage() {
for (int i = 0; i < npage; i++) free(pages[i]);
@@ -110,7 +123,7 @@ class MyPage {
T *get(int n) {
if (n > maxchunk) {
- errorflag = 3;
+ errorflag = 1;
return NULL;
}
ndatum += n;
@@ -151,14 +164,13 @@ class MyPage {
// error if N > maxchunk
void vgot(int n) {
- if (n > maxchunk) errorflag = 3;
+ if (n > maxchunk) errorflag = 1;
ndatum += n;
nchunk++;
index += n;
}
- // reset index to beginning of first page
- // effectively clears all pages, without freeing any memory
+ // clear all pages, without freeing any memory
void reset() {
ndatum = nchunk = 0;
@@ -166,23 +178,33 @@ class MyPage {
page = pages[ipage];
}
- // return total size of all allocated pages
+ // return total size of allocated pages
- int size() {
+ int size() const {
return npage*pagesize*sizeof(T);
}
- private:
- int maxchunk; // max # of datums in one requested chunk
- int pagesize; // # of datums in one page, default = 1024
- int pagedelta; // # of pages to allocate at once, default = 1
+ // return error status
+ int status() const {
+ return errorflag;
+ }
+
+ private:
T **pages; // list of allocated pages
T *page; // ptr to current page
int npage; // # of allocated pages
int ipage; // index of current page
int index; // current index on current page
+ int maxchunk; // max # of datums in one requested chunk
+ int pagesize; // # of datums in one page, default = 1024
+ int pagedelta; // # of pages to allocate at once, default = 1
+
+ int errorflag; // flag > 0 if error has occurred
+ // 1 = chunk size exceeded maxchunk
+ // 2 = memory allocation error
+
void allocate() {
npage += pagedelta;
pages = (T **) realloc(pages,npage*sizeof(T *));
@@ -190,9 +212,17 @@ class MyPage {
errorflag = 2;
return;
}
+
+ void *ptr;
for (int i = npage-pagedelta; i < npage; i++) {
+#if defined(LAMMPS_MEMALIGN)
+ if (posix_memalign(&ptr, LAMMPS_MEMALIGN, pagesize*sizeof(T)))
+ errorflag = 2;
+ pages[i] = (T *) ptr;
+#else
pages[i] = (T *) malloc(pagesize*sizeof(T));
if (!pages[i]) errorflag = 2;
+#endif
}
}
};
diff --git a/src/neigh_derive.cpp b/src/neigh_derive.cpp
index 4bda3d71d08b49080e079c5944c128979a9aa05d..343dc1dc6e494874790ec6714f07b8b742717cfd 100644
--- a/src/neigh_derive.cpp
+++ b/src/neigh_derive.cpp
@@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -33,28 +34,21 @@ void Neighbor::half_from_full_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ 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;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over atoms in full list
for (ii = 0; ii < inum_full; ii++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
// loop over parent full list
@@ -71,8 +65,8 @@ void Neighbor::half_from_full_no_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -98,28 +92,21 @@ void Neighbor::half_from_full_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ 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;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over parent full list
for (ii = 0; ii < inum_full; ii++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
i = ilist_full[ii];
xtmp = x[i][0];
@@ -149,8 +136,8 @@ void Neighbor::half_from_full_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -175,7 +162,8 @@ void Neighbor::skip_from(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
+
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
@@ -186,8 +174,7 @@ void Neighbor::skip_from(NeighList *list)
int **ijskip = list->ijskip;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
@@ -198,14 +185,8 @@ void Neighbor::skip_from(NeighList *list)
itype = type[i];
if (iskip[itype]) continue;
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
// loop over parent non-skip list
@@ -222,8 +203,8 @@ void Neighbor::skip_from(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -255,7 +236,8 @@ void Neighbor::skip_from_granular(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
+
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
@@ -269,12 +251,13 @@ void Neighbor::skip_from_granular(NeighList *list)
NeighList *listgranhistory = list->listgranhistory;
int **firsttouch = listgranhistory->firstneigh;
double **firstshear = listgranhistory->firstdouble;
- int **pages_touch = listgranhistory->pages;
- double **pages_shear = listgranhistory->dpages;
+ MyPage<int> *ipage_touch = listgranhistory->ipage;
+ MyPage<double> *dpage_shear = listgranhistory->dpage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
+ ipage_touch->reset();
+ dpage_shear->reset();
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
@@ -285,21 +268,10 @@ void Neighbor::skip_from_granular(NeighList *list)
itype = type[i];
if (iskip[itype]) continue;
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) {
- pages = list->add_pages();
- pages_touch = listgranhistory->add_pages();
- pages_shear = listgranhistory->dpages;
- }
- }
-
- n = 0;
- neighptr = &pages[npage][npnt];
- nn = 0;
- touchptr = &pages_touch[npage][npnt];
- shearptr = &pages_shear[npage][3*npnt];
+ n = nn = 0;
+ neighptr = ipage->vget();
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
// loop over parent non-skip granular list and its history info
@@ -322,11 +294,14 @@ void Neighbor::skip_from_granular(NeighList *list)
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");
+
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
- npnt += n;
- if (n > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ ipage_touch->vgot(n);
+ dpage_shear->vgot(nn);
}
list->inum = inum;
@@ -348,7 +323,8 @@ void Neighbor::skip_from_respa(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
+
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
@@ -360,30 +336,29 @@ void Neighbor::skip_from_respa(NeighList *list)
NeighList *listinner = list->listinner;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
- int **pages_inner = listinner->pages;
+ 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 *numneigh_middle,**firstneigh_middle,**pages_middle;
+ 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;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
- pages_middle = listmiddle->pages;
+ ipage_middle = listmiddle->ipage;
numneigh_middle_skip = list->listskip->listmiddle->numneigh;
firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
- int npage_inner = 0;
- int npnt_inner = 0;
- int npage_middle = 0;
- int npnt_middle = 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]
@@ -394,32 +369,12 @@ void Neighbor::skip_from_respa(NeighList *list)
itype = type[i];
if (iskip[itype]) continue;
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
- neighptr = &pages[npage][npnt];
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner++;
- if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
- }
- neighptr_inner = &pages_inner[npage_inner][npnt_inner];
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
- }
- neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
// loop over parent outer rRESPA list
@@ -460,24 +415,24 @@ void Neighbor::skip_from_respa(NeighList *list)
}
}
- ilist[inum++] = i;
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage_inner->vgot(n);
+ if (ipage_inner->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
@@ -499,6 +454,6 @@ void Neighbor::copy_from(NeighList *list)
list->numneigh = listcopy->numneigh;
list->firstneigh = listcopy->firstneigh;
list->firstdouble = listcopy->firstdouble;
- list->pages = listcopy->pages;
- list->dpages = listcopy->dpages;
+ list->ipage = listcopy->ipage;
+ list->dpage = listcopy->dpage;
}
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index 970e3c5725c3de6cd091c22ee1bec0804dc4bd82..0c830b372026cef0f86d8793bb225806967bd393 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -15,6 +15,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
+#include "my_page.h"
#include "group.h"
#include "error.h"
@@ -50,24 +51,16 @@ void Neighbor::full_nsq(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over owned atoms, storing neighbors
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -101,8 +94,8 @@ void Neighbor::full_nsq(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -137,24 +130,16 @@ void Neighbor::full_nsq_ghost(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over owned & ghost atoms, storing neighbors
for (i = 0; i < nall; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -203,8 +188,8 @@ void Neighbor::full_nsq_ghost(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -242,26 +227,18 @@ void Neighbor::full_bin(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over owned atoms, storing neighbors
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -300,8 +277,8 @@ void Neighbor::full_bin(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -341,27 +318,19 @@ void Neighbor::full_bin_ghost(NeighList *list)
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 **stencilxyz = list->stencilxyz;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over owned & ghost atoms, storing neighbors
for (i = 0; i < nall; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -427,8 +396,8 @@ void Neighbor::full_bin_ghost(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -470,25 +439,17 @@ void Neighbor::full_multi(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -532,8 +493,8 @@ void Neighbor::full_multi(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index b9fd604f619b28336572ef5322cab015cc260b7d..204988e23049d31aec75fa2ed91eb269688d74f0 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -41,8 +41,8 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
double (**shearpartner)[3];
int **firsttouch;
double **firstshear;
- int **pages_touch;
- double **pages_shear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
double **x = atom->x;
double *radius = atom->radius;
@@ -60,7 +60,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
@@ -70,34 +70,24 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
- pages_touch = listgranhistory->pages;
- pages_shear = listgranhistory->dpages;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) {
- pages = list->add_pages();
- if (fix_history) {
- pages_touch = listgranhistory->add_pages();
- pages_shear = listgranhistory->dpages;
- }
- }
- }
-
n = 0;
- neighptr = &pages[npage][npnt];
+ neighptr = ipage->vget();
if (fix_history) {
nn = 0;
- touchptr = &pages_touch[npage][npnt];
- shearptr = &pages_shear[npage][3*npnt];
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
}
xtmp = x[i][0];
@@ -151,13 +141,16 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
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);
}
- npnt += n;
- if (n > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
@@ -195,22 +188,14 @@ void Neighbor::granular_nsq_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
n = 0;
- neighptr = &pages[npage][npnt];
+ neighptr = ipage->vget();
itag = tag[i];
xtmp = x[i][0];
@@ -253,8 +238,8 @@ void Neighbor::granular_nsq_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -283,8 +268,8 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
double (**shearpartner)[3];
int **firsttouch;
double **firstshear;
- int **pages_touch;
- double **pages_shear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
// bin local & ghost atoms
@@ -304,9 +289,9 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
FixShearHistory *fix_history = list->fix_history;
if (fix_history) {
@@ -316,34 +301,24 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
- pages_touch = listgranhistory->pages;
- pages_shear = listgranhistory->dpages;
+ ipage_touch = listgranhistory->ipage;
+ dpage_shear = listgranhistory->dpage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
+ if (fix_history) {
+ ipage_touch->reset();
+ dpage_shear->reset();
+ }
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) {
- pages = list->add_pages();
- if (fix_history) {
- pages_touch = listgranhistory->add_pages();
- pages_shear = listgranhistory->dpages;
- }
- }
- }
-
n = 0;
- neighptr = &pages[npage][npnt];
+ neighptr = ipage->vget();
if (fix_history) {
nn = 0;
- touchptr = &pages_touch[npage][npnt];
- shearptr = &pages_shear[npage][3*npnt];
+ touchptr = ipage_touch->vget();
+ shearptr = dpage_shear->vget();
}
xtmp = x[i][0];
@@ -403,13 +378,16 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
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);
}
- npnt += n;
- if (n > oneatom)
- error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
@@ -447,24 +425,16 @@ void Neighbor::granular_bin_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
n = 0;
- neighptr = &pages[npage][npnt];
+ neighptr = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -517,8 +487,8 @@ void Neighbor::granular_bin_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -557,24 +527,16 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
n = 0;
- neighptr = &pages[npage][npnt];
+ neighptr = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
@@ -615,8 +577,8 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
index 9d89274abccb9b8813a089f221dfbac5613b1575..ef55cb5ba145de4461e40f873919bee496946077 100644
--- a/src/neigh_half_bin.cpp
+++ b/src/neigh_half_bin.cpp
@@ -15,6 +15,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -53,24 +54,16 @@ void Neighbor::half_bin_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -111,8 +104,8 @@ void Neighbor::half_bin_no_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -156,25 +149,17 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
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 **stencilxyz = list->stencilxyz;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nall; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -244,8 +229,8 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -286,24 +271,16 @@ void Neighbor::half_bin_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -372,8 +349,8 @@ void Neighbor::half_bin_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -413,24 +390,16 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -478,8 +447,8 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
index bee0bfffcd023aa40b3552fd3360fa870bb36046..46a76be6dbd45fa2d58b47feaa3856912b3df0d0 100644
--- a/src/neigh_half_multi.cpp
+++ b/src/neigh_half_multi.cpp
@@ -15,6 +15,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "domain.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -55,25 +56,17 @@ void Neighbor::half_multi_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -119,8 +112,8 @@ void Neighbor::half_multi_no_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -162,25 +155,17 @@ void Neighbor::half_multi_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -254,8 +239,8 @@ void Neighbor::half_multi_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -297,25 +282,17 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int *nstencil_multi = list->nstencil_multi;
int **stencil_multi = list->stencil_multi;
double **distsq_multi = list->distsq_multi;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -370,8 +347,8 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
index 7266df0ebd93de710e762aa24266e83e197b70e2..8446c9d982ff1f1f2065e25d33bb18ac85064a57 100644
--- a/src/neigh_half_nsq.cpp
+++ b/src/neigh_half_nsq.cpp
@@ -51,24 +51,16 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over owned atoms, storing neighbors
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -102,8 +94,8 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -143,24 +135,16 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
// loop over owned & ghost atoms, storing neighbors
for (i = 0; i < nall; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
@@ -214,8 +198,8 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -256,22 +240,14 @@ void Neighbor::half_nsq_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
int inum = 0;
- int npage = 0;
- int npnt = 0;
+ ipage->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
-
- neighptr = &pages[npage][npnt];
n = 0;
+ neighptr = ipage->vget();
itag = tag[i];
itype = type[i];
@@ -322,8 +298,8 @@ void Neighbor::half_nsq_newton(NeighList *list)
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ ipage->vgot(n);
+ if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 316b39ed7746fe3f6159a9894e7100948d36cfa3..aac201b012fe5f539b671f0777d94428a69d0098 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -17,6 +17,7 @@
#include "update.h"
#include "neighbor.h"
#include "neigh_request.h"
+#include "my_page.h"
#include "memory.h"
#include "error.h"
@@ -28,11 +29,10 @@ enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
/* ---------------------------------------------------------------------- */
-NeighList::NeighList(LAMMPS *lmp, int size, int onesize) : Pointers(lmp)
+NeighList::NeighList(LAMMPS *lmp) :
+ Pointers(lmp)
{
maxatoms = 0;
- pgsize = size;
- oneatom = onesize;
inum = gnum = 0;
ilist = NULL;
@@ -40,11 +40,6 @@ NeighList::NeighList(LAMMPS *lmp, int size, int onesize) : Pointers(lmp)
firstneigh = NULL;
firstdouble = NULL;
- maxpage = 0;
- pages = NULL;
- dpages = NULL;
- dnum = 0;
-
iskip = NULL;
ijskip = NULL;
@@ -66,6 +61,9 @@ NeighList::NeighList(LAMMPS *lmp, int size, int onesize) : Pointers(lmp)
nstencil_multi = NULL;
stencil_multi = NULL;
distsq_multi = NULL;
+
+ ipage = NULL;
+ dpage = NULL;
}
/* ---------------------------------------------------------------------- */
@@ -78,12 +76,8 @@ NeighList::~NeighList()
memory->sfree(firstneigh);
memory->sfree(firstdouble);
- for (int i = 0; i < maxpage; i++) memory->destroy(pages[i]);
- memory->sfree(pages);
- if (dnum) {
- for (int i = 0; i < maxpage; i++) memory->destroy(dpages[i]);
- memory->sfree(dpages);
- }
+ delete [] ipage;
+ if (dnum) delete [] dpage;
}
delete [] iskip;
@@ -103,6 +97,28 @@ NeighList::~NeighList()
}
}
+/* ---------------------------------------------------------------------- */
+
+void NeighList::setup_pages(int pgsize_caller, int oneatom_caller,
+ int dnum_caller)
+{
+ pgsize = pgsize_caller;
+ oneatom = oneatom_caller;
+ dnum = dnum_caller;
+
+ int nmypage = comm->nthreads;
+ ipage = new MyPage<int>[nmypage];
+ for (int i = 0; i < nmypage; i++)
+ ipage[i].init(oneatom,pgsize,PGDELTA);
+
+ if (dnum) {
+ dpage = new MyPage<double>[nmypage];
+ for (int i = 0; i < nmypage; i++)
+ dpage[i].init(dnum*oneatom,dnum*pgsize,PGDELTA);
+ }
+ else dpage = NULL;
+}
+
/* ----------------------------------------------------------------------
grow atom arrays to allow for nmax atoms
triggered by more atoms on a processor
@@ -177,30 +193,6 @@ void NeighList::stencil_allocate(int smax, int style)
}
}
-/* ----------------------------------------------------------------------
- add PGDELTA pages to neighbor list
-------------------------------------------------------------------------- */
-
-int **NeighList::add_pages(int howmany)
-{
- int toppage = maxpage;
- maxpage += howmany*PGDELTA;
-
- pages = (int **)
- memory->srealloc(pages,maxpage*sizeof(int *),"neighlist:pages");
- for (int i = toppage; i < maxpage; i++)
- memory->create(pages[i],pgsize,"neighlist:pages[i]");
-
- if (dnum) {
- dpages = (double **)
- memory->srealloc(dpages,maxpage*sizeof(double *),"neighlist:dpages");
- for (int i = toppage; i < maxpage; i++)
- memory->create(dpages[i],dnum*pgsize,"neighlist:dpages[i]");
- }
-
- return pages;
-}
-
/* ----------------------------------------------------------------------
copy skip info from request rq into list's iskip,ijskip
------------------------------------------------------------------------- */
@@ -272,11 +264,16 @@ bigint NeighList::memory_usage()
bytes += memory->usage(ilist,maxatoms);
bytes += memory->usage(numneigh,maxatoms);
bytes += maxatoms * sizeof(int *);
- bytes += memory->usage(pages,maxpage,pgsize);
+ int nmypage = comm->nthreads;
+ for (int i = 0; i < nmypage; i++)
+ bytes += ipage[i].size();
+
if (dnum) {
- bytes += maxatoms * sizeof(double *);
- bytes += memory->usage(dpages,maxpage,dnum*pgsize);
+ for (int i = 0; i < nmypage; i++) {
+ bytes += maxatoms * sizeof(double *);
+ bytes += dpage[i].size();
+ }
}
if (maxstencil) bytes += memory->usage(stencil,maxstencil);
diff --git a/src/neigh_list.h b/src/neigh_list.h
index d29f3a7db63ae41fea2b33963b5296decc9d0ebf..b5b277c218697842a73f860c54b275f07a71b6fc 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -41,12 +41,9 @@ class NeighList : protected Pointers {
int pgsize; // size of each page
int oneatom; // max size for one atom
- int maxpage; // # of pages currently allocated
- int **pages; // neighbor list pages for ints
- double **dpages; // neighbor list pages for doubles
- int dnum; // # of doubles for each pair (0 if none)
-
- MyPage<int> *page;
+ int dnum; // # of doubles per neighbor, 0 if none
+ MyPage<int> *ipage; // pages of neighbor indices
+ MyPage<double> *dpage; // pages of neighbor doubles, if dnum > 0
// atom types to skip when building list
// iskip,ijskip are just ptrs to corresponding request
@@ -80,11 +77,11 @@ class NeighList : protected Pointers {
class CudaNeighList *cuda_list; // CUDA neighbor list
- NeighList(class LAMMPS *, int, int);
+ NeighList(class LAMMPS *);
~NeighList();
+ void setup_pages(int, int, int); // setup page data structures
void grow(int); // grow maxlocal
void stencil_allocate(int, int); // allocate stencil arrays
- int **add_pages(int howmany=1); // add pages to neigh list
void copy_skip_info(int *, int **); // copy skip info from a neigh request
void print_attributes(); // debug routine
int get_maxlocal() {return maxatoms;}
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index c152eba2b8d8cd52ec0642457a5915f27e4e3241..8d1ea14ae5e5d88d2f374082ee3a762659ea4969 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -16,6 +16,7 @@
#include "atom.h"
#include "domain.h"
#include "group.h"
+#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -54,64 +55,40 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
- int **pages_inner = listinner->pages;
+ MyPage<int> *ipage_inner = listinner->ipage;
NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
- pages_middle = listmiddle->pages;
+ ipage_middle = listmiddle->ipage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
- int npage_inner = 0;
- int npnt_inner = 0;
- int npage_middle = 0;
- int npnt_middle = 0;
-
int which = 0;
int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
- neighptr = &pages[npage][npnt];
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner++;
- if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
- }
- neighptr_inner = &pages_inner[npage_inner][npnt_inner];
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
- }
- neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
itype = type[i];
@@ -158,23 +135,23 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ 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;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage_inner->vgot(n_inner);
+ 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;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -221,64 +198,40 @@ void Neighbor::respa_nsq_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
- int **pages_inner = listinner->pages;
+ MyPage<int> *ipage_inner = listinner->ipage;
NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
- pages_middle = listmiddle->pages;
+ ipage_middle = listmiddle->ipage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
- int npage_inner = 0;
- int npnt_inner = 0;
- int npage_middle = 0;
- int npnt_middle = 0;
-
int which = 0;
int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
- neighptr = &pages[npage][npnt];
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner++;
- if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
- }
- neighptr_inner = &pages_inner[npage_inner][npnt_inner];
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
- }
- neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
itag = tag[i];
@@ -343,23 +296,23 @@ void Neighbor::respa_nsq_newton(NeighList *list)
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ 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;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage_inner->vgot(n_inner);
+ 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;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -406,66 +359,42 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
- int **pages_inner = listinner->pages;
+ MyPage<int> *ipage_inner = listinner->ipage;
NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
- pages_middle = listmiddle->pages;
+ ipage_middle = listmiddle->ipage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
- int npage_inner = 0;
- int npnt_inner = 0;
- int npage_middle = 0;
- int npnt_middle = 0;
-
int which = 0;
int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
- neighptr = &pages[npage][npnt];
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner++;
- if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
- }
- neighptr_inner = &pages_inner[npage_inner][npnt_inner];
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
- }
- neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
itype = type[i];
@@ -521,23 +450,23 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ 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;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage_inner->vgot(n_inner);
+ 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;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -583,66 +512,42 @@ void Neighbor::respa_bin_newton(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
- int **pages_inner = listinner->pages;
+ MyPage<int> *ipage_inner = listinner->ipage;
NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
- pages_middle = listmiddle->pages;
+ ipage_middle = listmiddle->ipage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
- int npage_inner = 0;
- int npnt_inner = 0;
- int npage_middle = 0;
- int npnt_middle = 0;
-
int which = 0;
int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
- neighptr = &pages[npage][npnt];
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner++;
- if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
- }
- neighptr_inner = &pages_inner[npage_inner][npnt_inner];
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
- }
- neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
itype = type[i];
@@ -739,23 +644,23 @@ void Neighbor::respa_bin_newton(NeighList *list)
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ 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;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage_inner->vgot(n_inner);
+ 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;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
@@ -801,66 +706,42 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
+ MyPage<int> *ipage = list->ipage;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
- int **pages_inner = listinner->pages;
+ MyPage<int> *ipage_inner = listinner->ipage;
NeighList *listmiddle;
- int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
+ int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+ MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
- pages_middle = listmiddle->pages;
+ ipage_middle = listmiddle->ipage;
}
int inum = 0;
- int npage = 0;
- int npnt = 0;
- int npage_inner = 0;
- int npnt_inner = 0;
- int npage_middle = 0;
- int npnt_middle = 0;
-
int which = 0;
int minchange = 0;
+ ipage->reset();
+ ipage_inner->reset();
+ if (respamiddle) ipage_middle->reset();
for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == list->maxpage) pages = list->add_pages();
- }
- neighptr = &pages[npage][npnt];
- n = 0;
-
- if (pgsize - npnt_inner < oneatom) {
- npnt_inner = 0;
- npage_inner++;
- if (npage_inner == listinner->maxpage)
- pages_inner = listinner->add_pages();
- }
- neighptr_inner = &pages_inner[npage_inner][npnt_inner];
- n_inner = 0;
-
+ n = n_inner = 0;
+ neighptr = ipage->vget();
+ neighptr_inner = ipage_inner->vget();
if (respamiddle) {
- if (pgsize - npnt_middle < oneatom) {
- npnt_middle = 0;
- npage_middle++;
- if (npage_middle == listmiddle->maxpage)
- pages_middle = listmiddle->add_pages();
- }
- neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
+ neighptr_middle = ipage_middle->vget();
}
itype = type[i];
@@ -924,23 +805,23 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
- npnt += n;
- if (n > oneatom)
+ 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;
- npnt_inner += n_inner;
- if (n_inner > oneatom)
+ ipage_inner->vgot(n_inner);
+ 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;
- npnt_middle += n_middle;
- if (n_middle > oneatom)
+ ipage_middle->vgot(n_middle);
+ if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 0f597b64d773d1b6d02f5ada9ba71b1eebaa69cf..b9ecb4c47136318fbeb9902a40f5548d69268161 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -456,9 +456,9 @@ void Neighbor::init()
// pass list ptr back to requestor (except for Command class)
for (i = 0; i < nlist; i++) {
- lists[i] = new NeighList(lmp,pgsize,oneatom);
+ lists[i] = new NeighList(lmp);
+ lists[i]->setup_pages(pgsize,oneatom,requests[i]->dnum);
lists[i]->index = i;
- lists[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
Pair *pair = (Pair *) requests[i]->requestor;
@@ -620,14 +620,11 @@ void Neighbor::init()
for (i = 0; i < nlist; i++) lists[i]->print_attributes();
#endif
- // allocate atom arrays and 1st pages of lists that store them
+ // allocate atom arrays for neighbor lists that store them
maxatom = atom->nmax;
for (i = 0; i < nlist; i++)
- if (lists[i]->growflag) {
- lists[i]->grow(maxatom);
- lists[i]->add_pages();
- }
+ if (lists[i]->growflag) lists[i]->grow(maxatom);
// setup 3 vectors of pairwise neighbor lists
// blist = lists whose pair_build() is invoked every reneighbor