From 778ae37e6e53fbe1b41499c1d0159f8911370a67 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 16 Jul 2016 22:27:01 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15338
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/Make.sh | 7 +-
src/USER-OMP/neigh_gran_omp.cpp | 43 ++-
src/neighbor.cpp | 542 +++++++++++++++++++++++++++++++-
src/neighbor.h | 24 +-
4 files changed, 584 insertions(+), 32 deletions(-)
diff --git a/src/Make.sh b/src/Make.sh
index 3332be92c4..9c115e1bdf 100644
--- a/src/Make.sh
+++ b/src/Make.sh
@@ -54,7 +54,8 @@ style () {
# col 1 = string to search for
# col 2 = search in *.h files starting with this name
# col 3 = prefix of style file
-# col 4
+# col 4 = file that includes the style file
+# col 5 = optional 2nd file that includes the style file
if (test $1 = "style") then
@@ -62,8 +63,9 @@ if (test $1 = "style") then
style ATOM_CLASS atom_vec_ atom atom atom_vec_hybrid
style BODY_CLASS body_ body atom_vec_body
style BOND_CLASS bond_ bond force
+ style BUILD_CLASS build_ build neighbor
style COMMAND_CLASS "" command input
- style COMPUTE_CLASS compute_ compute modify modify_cuda
+ style COMPUTE_CLASS compute_ compute modify
style DIHEDRAL_CLASS dihedral_ dihedral force
style DUMP_CLASS dump_ dump output write_dump
style FIX_CLASS fix_ fix modify
@@ -74,6 +76,7 @@ if (test $1 = "style") then
style PAIR_CLASS pair_ pair force
style READER_CLASS reader_ reader read_dump
style REGION_CLASS region_ region domain
+ style STENCIL_CLASS stencil_ stencil neighbor
# edit Makefile.lib, for creating non-shared lib
# called by "make makelib"
diff --git a/src/USER-OMP/neigh_gran_omp.cpp b/src/USER-OMP/neigh_gran_omp.cpp
index 55ab604b02..82794ff739 100644
--- a/src/USER-OMP/neigh_gran_omp.cpp
+++ b/src/USER-OMP/neigh_gran_omp.cpp
@@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include <string.h>
#include "neighbor.h"
#include "neighbor_omp.h"
#include "neigh_list.h"
@@ -45,7 +46,7 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
- int i,j,m,n,nn;
+ int i,j,m,n,nn,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -53,7 +54,7 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
int *npartner;
tagint **partner;
- double (**shearpartner)[3];
+ double **shearpartner;
int **firsttouch;
double **firstshear;
MyPage<int> *ipage_touch;
@@ -83,6 +84,8 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage+tid;
dpage_shear = listgranhistory->dpage+tid;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
ipage_touch->reset();
dpage_shear->reset();
}
@@ -124,20 +127,17 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
@@ -285,7 +285,7 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
#endif
NEIGH_OMP_SETUP(nlocal);
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -295,7 +295,7 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
int *npartner;
tagint **partner;
- double (**shearpartner)[3];
+ double **shearpartner;
int **firsttouch;
double **firstshear;
@@ -326,6 +326,8 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage+tid;
dpage_shear = listgranhistory->dpage+tid;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
ipage_touch->reset();
dpage_shear->reset();
}
@@ -372,20 +374,17 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 5aad5bfd6f..c4ce8b2eeb 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -22,6 +22,8 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
+#include "style_stencil.h"
+#include "style_build.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
@@ -35,10 +37,13 @@
#include "update.h"
#include "respa.h"
#include "output.h"
+#include "stencil.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
+#include <map>
+
using namespace LAMMPS_NS;
#define RQDELTA 1
@@ -51,6 +56,9 @@ using namespace LAMMPS_NS;
enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
+enum{STENCIL_HALF_BIN_3D_NEWTON};
+enum{BUILD_HALF_BIN_NEWTON};
+
static const char cite_neigh_multi[] =
"neighbor multi command:\n\n"
"@Article{Intveld08,\n"
@@ -125,7 +133,9 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
nlist = 0;
lists = NULL;
+ pair_build_new = NULL;
pair_build = NULL;
+ stencil_create_new = NULL;
stencil_create = NULL;
blist = glist = slist = NULL;
anyghostlist = 0;
@@ -159,6 +169,28 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
improperlist = NULL;
copymode = 0;
+
+ // fill map with stencil classes listed in style_stencil.h
+
+ stencil_map = new std::map<int,StencilCreator>();
+
+#define STENCIL_CLASS
+#define StencilStyle(key,Class) \
+ (*stencil_map)[key] = &stencil_creator<Class>;
+#include "style_stencil.h"
+#undef StencilStyle
+#undef STENCIL_CLASS
+
+ // fill map with build classes listed in style_build.h
+
+ build_map = new std::map<int,BuildCreator>();
+
+#define BUILD_CLASS
+#define BuildStyle(key,Class) \
+ (*build_map)[key] = &build_creator<Class>;
+#include "style_build.h"
+#undef BuildStyle
+#undef BUILD_CLASS
}
/* ---------------------------------------------------------------------- */
@@ -192,7 +224,11 @@ Neighbor::~Neighbor()
for (int i = 0; i < nlist; i++) delete lists[i];
delete [] lists;
+ for (int i = 0; i < nlist; i++) delete pair_build_new[i];
+ delete [] pair_build_new;
delete [] pair_build;
+ for (int i = 0; i < nlist; i++) delete stencil_create_new[i];
+ delete [] stencil_create_new;
delete [] stencil_create;
delete [] blist;
delete [] glist;
@@ -209,6 +245,9 @@ Neighbor::~Neighbor()
memory->destroy(anglelist);
memory->destroy(dihedrallist);
memory->destroy(improperlist);
+
+ delete stencil_map;
+ delete build_map;
}
/* ---------------------------------------------------------------------- */
@@ -492,21 +531,29 @@ void Neighbor::init()
for (i = 0; i < nlist; i++) delete lists[i];
delete [] lists;
+ for (i = 0; i < nlist; i++) delete pair_build_new[i];
+ delete [] pair_build_new;
delete [] pair_build;
+ for (i = 0; i < nlist; i++) delete stencil_create_new[i];
+ delete [] stencil_create_new;
delete [] stencil_create;
if (lmp->kokkos) nlist = init_lists_kokkos();
else nlist = nrequest;
lists = new NeighList*[nrequest];
+ pair_build_new = new Build*[nrequest];
pair_build = new PairPtr[nrequest];
+ stencil_create_new = new Stencil*[nrequest];
stencil_create = new StencilPtr[nrequest];
// initialize to NULL since some may be Kokkos lists
for (i = 0; i < nrequest; i++) {
lists[i] = NULL;
+ pair_build_new[i] = NULL;
pair_build[i] = NULL;
+ stencil_create_new[i] = NULL;
stencil_create[i] = NULL;
}
@@ -671,9 +718,15 @@ void Neighbor::init()
// ptrs set to NULL if not set explicitly
for (i = 0; i < nrequest; i++) {
+ choose_build_new(i,requests[i]);
choose_build(i,requests[i]);
- if (style != NSQ) choose_stencil(i,requests[i]);
- else stencil_create[i] = NULL;
+ if (style != NSQ) {
+ choose_stencil_new(i,requests[i]);
+ choose_stencil(i,requests[i]);
+ } else {
+ stencil_create_new[i] = NULL;
+ stencil_create[i] = NULL;
+ }
}
// set each list's build/grow/stencil/ghost flags based on neigh request
@@ -689,6 +742,8 @@ void Neighbor::init()
for (i = 0; i < nrequest; i++) {
if (lists[i]) {
lists[i]->buildflag = 1;
+ // NOTE: let old pair_build determine buildflag
+ //if (pair_build_new[i] == NULL) lists[i]->buildflag = 0;
if (pair_build[i] == NULL) lists[i]->buildflag = 0;
if (requests[i]->occasional) lists[i]->buildflag = 0;
if (lists[i]->buildflag) anybuild = 1;
@@ -698,6 +753,8 @@ void Neighbor::init()
lists[i]->stencilflag = 1;
if (style == NSQ) lists[i]->stencilflag = 0;
+ // NOTE: let old stencil_create determine stencilflag
+ //if (stencil_create_new[i] == NULL) lists[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
lists[i]->ghostflag = 0;
@@ -1018,6 +1075,331 @@ int Neighbor::request(void *requestor, int instance)
return nrequest-1;
}
+/* ----------------------------------------------------------------------
+ determine which Build class each neigh list needs
+ based on settings of neigh request
+ copy -> copy_from function
+ skip -> granular function if gran, several options
+ respa function if respaouter,
+ skip_from function for everything else
+ ssa -> special case for USER-DPD pair styles
+ half_from_full, half, full, gran, respaouter ->
+ choose by newton and rq->newton and triclinic settings
+ style NSQ options = newton off, newton on
+ style BIN options = newton off, newton on and not tri, newton on and tri
+ stlye MULTI options = same options as BIN
+ if none of these, ptr = NULL since pair_build is not invoked for this list
+ use "else if" logic b/c skip,copy can be set in addition to half,full,etc
+------------------------------------------------------------------------- */
+
+void Neighbor::choose_build_new(int index, NeighRequest *rq)
+{
+ int build = -1;
+
+ if (rq->omp == 0 && rq->intel == 0) {
+
+ if (rq->copy) build = -1; // BUILD_COPY_FROM;
+
+ else if (rq->skip) {
+ if (rq->gran) {
+ NeighRequest *otherrq = requests[rq->otherlist];
+ if (otherrq->newton == 0) {
+ build = -1; // BUILD_SKIP_FROM_GRANULAR;
+ } else if (otherrq->newton == 1) {
+ error->all(FLERR,"Neighbor build method not supported");
+ } else if (otherrq->newton == 2) {
+ if (rq->granonesided == 0)
+ build = -1; // BUILD_SKIP_FROM_GRANULAR_OFF2ON;
+ else if (rq->granonesided == 1)
+ build = -1; // BUILD_SKIP_FROM_GRANULAR_OFF2ON_ONESIDED;
+ }
+ }
+ else if (rq->respaouter) build = -1; // BUILD_SKIP_FROM_RESPA;
+ else build = -1; // BUILD_SKIP_FROM;
+
+ } else if (rq->ssa) {
+ if (rq->half_from_full) build = -1; // BUILD_HALF_FROM_FULL_NEWTON_SSA;
+ else build = -1; // BUILD_HALF_BIN_NEWTON_SSA;
+
+ } else if (rq->half_from_full) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) build = -1; // BUILD_HALF_FROM_FULL_NO_NEWTON;
+ else if (newton_pair == 1) build = -1; // BUILD_HALF_FROM_FULL_NEWTON;
+ } else if (rq->newton == 1) {
+ build = -1; // BUILD_HALF_FROM_FULL_NEWTON;
+ } else if (rq->newton == 2) {
+ build = -1; // BUILD_HALF_FROM_FULL_NO_NEWTON;
+ }
+
+ } else if (rq->half) {
+ if (style == NSQ) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) {
+ if (rq->ghost == 0) build = -1; // BUILD_HALF_NSQ_NO_NEWTON;
+ else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_NSQ_NO_NEWTON_GHOST;
+ } else if (newton_pair == 1) build = -1; // BUILD_HALF_NSQ_NEWTON;
+ } else if (rq->newton == 1) {
+ build = -1; // BUILD_HALF_NSQ_NEWTON;
+ } else if (rq->newton == 2) {
+ if (rq->ghost == 0) build = -1; // BUILD_HALF_NSQ_NO_NEWTON;
+ else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_NSQ_NO_NEWTON_GHOST;
+ }
+ } else if (style == BIN) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) {
+ if (rq->ghost == 0) build = -1; // BUILD_HALF_BIN_NO_NEWTON;
+ else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_BIN_NO_NEWTON_GHOST;
+ } else if (triclinic == 0) {
+ build = BUILD_HALF_BIN_NEWTON;
+ } else if (triclinic == 1)
+ build = -1; // BUILD_HALF_BIN_NEWTON_TRI;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) build = BUILD_HALF_BIN_NEWTON;
+ else if (triclinic == 1) build = -1; // BUILD_HALF_BIN_NEWTON_TRI;
+ } else if (rq->newton == 2) {
+ if (rq->ghost == 0) build = -1; // BUILD_HALF_BIN_NO_NEWTON;
+ else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_BIN_NO_NEWTON_GHOST;
+ }
+ } else if (style == MULTI) {
+ if (rq->ghost == 1)
+ error->all(FLERR,
+ "Neighbor multi not yet enabled for ghost neighbors");
+ if (rq->newton == 0) {
+ if (newton_pair == 0) build = -1; // BUILD_HALF_MULTI_NO_NEWTON;
+ else if (triclinic == 0) build = -1; // BUILD_HALF_MULTI_NEWTON;
+ else if (triclinic == 1) build = -1; // BUILD_HALF_MULTI_NEWTON_TRI;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) build = -1; // BUILD_HALF_MULTI_NEWTON;
+ else if (triclinic == 1) build = -1; // BUILD_HALF_MULTI_NEWTON_TRI;
+ } else if (rq->newton == 2) build = -1; // BUILD_HALF_MULTI_NO_NEWTON;
+ }
+
+ } else if (rq->full) {
+ if (style == NSQ) {
+ if (rq->ghost == 0) build = -1; // BUILD_FULL_NSQ;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else build = -1; // BUILD_FULL_NSQ_GHOST;
+ } else if (style == BIN) {
+ if (rq->ghost == 0) build = -1; // BUILD_FULL_BIN;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else build = -1; // BUILD_FULL_BIN_GHOST;
+ } else if (style == MULTI) {
+ if (rq->ghost == 1)
+ error->all(FLERR,
+ "Neighbor multi not yet enabled for ghost neighbors");
+ build = -1; // BUILD_FULL_MULTI;
+ }
+
+ } else if (rq->gran) {
+ if (rq->newton == 0) {
+ if (style == NSQ) {
+ if (newton_pair == 0) build = -1; // BUILD_GRANULAR_NSQ_NO_NEWTON;
+ else if (newton_pair == 1) {
+ if (rq->granonesided == 0) build = -1; // BUILD_GRANULAR_NSQ_NEWTON;
+ else build = -1; // BUILD_GRANULAR_NSQ_NEWTON_ONESIDED;
+ }
+ } else if (style == BIN) {
+ if (newton_pair == 0) build = -1; // BUILD_GRANULAR_BIN_NO_NEWTON;
+ else if (newton_pair == 1) {
+ if (triclinic == 0) {
+ if (rq->granonesided == 0) build = -1; // BUILD_GRANULAR_BIN_NEWTON;
+ else build = -1; // BUILD_GRANULAR_BIN_NEWTON_ONESIDED;
+ } else if (triclinic == 1) {
+ if (rq->granonesided == 0)
+ build = -1; // BUILD_GRANULAR_BIN_NEWTON_TRI;
+ else error->all(FLERR,"Neighbor build method not supported");
+ }
+ }
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
+ } else if (rq->newton == 1) {
+ error->all(FLERR,"Neighbor build method not yet supported");
+ } else if (rq->newton == 2) {
+ if (style == NSQ) build = -1; // BUILD_GRANULAR_NSQ_NO_NEWTON;
+ else if (style == BIN) {
+ if (triclinic == 0) build = -1; // BUILD_GRANULAR_BIN_NO_NEWTON;
+ else if (triclinic == 1)
+ error->all(FLERR,"Neighbor build method not yet supported");
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
+ }
+
+ } else if (rq->respaouter) {
+ if (style == NSQ) {
+ if (newton_pair == 0) build = -1; // BUILD_RESPA_NSQ_NO_NEWTON;
+ else if (newton_pair == 1) build = -1; // BUILD_RESPA_NSQ_NEWTON;
+ } else if (style == BIN) {
+ if (newton_pair == 0) build = -1; // BUILD_RESPA_BIN_NO_NEWTON;
+ else if (triclinic == 0) build = -1; // BUILD_RESPA_BIN_NEWTON;
+ else if (triclinic == 1) build = -1; // BUILD_RESPA_BIN_NEWTON_TRI;
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
+ }
+
+ // OMP versions of build methods
+
+ } else {
+
+ if (rq->copy) build = -1; // BUILD_COPY_FROM;
+
+ else if (rq->skip) {
+ if (rq->gran && lists[index]->listgranhistory)
+ build = -1; // BUILD_SKIP_FROM_GRANULAR;
+ else if (rq->respaouter) build = -1; // BUILD_SKIP_FROM_RESPA;
+ else build = -1; // BUILD_SKIP_FROM;
+
+ } else if (rq->half_from_full) {
+ if (newton_pair == 0) build = -1; // BUILD_HALF_FROM_FULL_NO_NEWTON_OMP;
+ else if (newton_pair == 1) build = -1; // BUILD_HALF_FROM_FULL_NEWTON_OMP;
+
+ } else if (rq->half) {
+ if (style == NSQ) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) {
+ if (rq->ghost == 0) build = -1; // BUILD_HALF_NSQ_NO_NEWTON_OMP;
+ else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_NSQ_NO_NEWTON_GHOST_OMP;
+ } else if (newton_pair == 1) build = -1; // BUILD_HALF_NSQ_NEWTON_OMP;
+ } else if (rq->newton == 1) {
+ build = -1; // BUILD_HALF_NSQ_NEWTON_OMP;
+ } else if (rq->newton == 2) {
+ if (rq->ghost == 0) build = -1; // BUILD_HALF_NSQ_NO_NEWTON_OMP;
+ else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_NSQ_NO_NEWTON_GHOST_OMP;
+ }
+ } else if (style == BIN) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) {
+ if (rq->ghost == 0) {
+ if (rq->intel) build = -1; // BUILD_HALF_BIN_NO_NEWTON_INTEL;
+ else build = -1; // BUILD_HALF_BIN_NO_NEWTON_OMP;
+ } else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_BIN_NO_NEWTON_GHOST_OMP;
+ } else if (triclinic == 0) {
+ if (rq->intel) build = -1; // BUILD_HALF_BIN_NEWTON_INTEL;
+ else build = -1; // BUILD_HALF_BIN_NEWTON_OMP;
+ } else if (triclinic == 1) {
+ if (rq->intel) build = -1; // BUILD_HALF_BIN_NEWTON_TRI_INTEL;
+ else build = -1; // BUILD_HALF_BIN_NEWTON_TRI_OMP;
+ }
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) {
+ if (rq->intel) build = -1; // BUILD_HALF_BIN_NEWTON_INTEL;
+ else build = -1; // BUILD_HALF_BIN_NEWTON_OMP;
+ } else if (triclinic == 1) {
+ if (rq->intel) build = -1; // BUILD_HALF_BIN_NEWTON_TRI_INTEL;
+ else build = -1; // BUILD_HALF_BIN_NEWTON_TRI_OMP;
+ }
+ } else if (rq->newton == 2) {
+ if (rq->ghost == 0) {
+ if (rq->intel) build = -1; // BUILD_HALF_BIN_NO_NEWTON_INTEL;
+ else build = -1; // BUILD_HALF_BIN_NO_NEWTON_OMP;
+ } else if (includegroup)
+ error->all(FLERR,"Neighbor include group not allowed "
+ "with ghost neighbors");
+ else build = -1; // BUILD_HALF_BIN_NO_NEWTON_GHOST_OMP;
+ }
+ } else if (style == MULTI) {
+ if (rq->ghost == 1)
+ error->all(FLERR,
+ "Neighbor multi not yet enabled for ghost neighbors");
+ if (rq->newton == 0) {
+ if (newton_pair == 0) build = -1; // BUILD_HALF_MULTI_NO_NEWTON_OMP;
+ else if (triclinic == 0) build = -1; // BUILD_HALF_MULTI_NEWTON_OMP;
+ else if (triclinic == 1) build = -1; // BUILD_HALF_MULTI_NEWTON_TRI_OMP;
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) build = -1; // BUILD_HALF_MULTI_NEWTON_OMP;
+ else if (triclinic == 1) build = -1; // BUILD_HALF_MULTI_NEWTON_TRI_OMP;
+ } else if (rq->newton == 2) build = -1; // BUILD_HALF_MULTI_NO_NEWTON_OMP;
+ }
+
+ } else if (rq->full) {
+ if (style == NSQ) {
+ if (rq->ghost == 0) build = -1; // BUILD_FULL_NSQ_OMP;
+ else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else build = -1; // BUILD_FULL_NSQ_GHOST_OMP;
+ } else if (style == BIN) {
+ if (rq->ghost == 0) {
+ if (rq->intel) build = -1; // BUILD_FULL_BIN_INTEL;
+ else build = -1; // BUILD_FULL_BIN_OMP;
+ } else if (includegroup)
+ error->all(FLERR,
+ "Neighbor include group not allowed with ghost neighbors");
+ else build = -1; // BUILD_FULL_BIN_GHOST_OMP;
+ } else if (style == MULTI) {
+ if (rq->ghost == 1)
+ error->all(FLERR,
+ "Neighbor multi not yet enabled for ghost neighbors");
+ build = -1; // BUILD_FULL_MULTI_OMP;
+ }
+
+ } else if (rq->gran) {
+ if (style == NSQ) {
+ if (newton_pair == 0) build = -1; // BUILD_GRANULAR_NSQ_NO_NEWTON_OMP;
+ else if (newton_pair == 1) build = -1; // BUILD_GRANULAR_NSQ_NEWTON_OMP;
+ } else if (style == BIN) {
+ if (newton_pair == 0) build = -1; // BUILD_GRANULAR_BIN_NO_NEWTON_OMP;
+ else if (triclinic == 0) build = -1; // BUILD_GRANULAR_BIN_NEWTON_OMP;
+ else if (triclinic == 1) build = -1; // BUILD_GRANULAR_BIN_NEWTON_TRI_OMP;
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
+
+ } else if (rq->respaouter) {
+ if (style == NSQ) {
+ if (newton_pair == 0) build = -1; // BUILD_RESPA_NSQ_NO_NEWTON_OMP;
+ else if (newton_pair == 1) build = -1; // BUILD_RESPA_NSQ_NEWTON_OMP;
+ } else if (style == BIN) {
+ if (newton_pair == 0) build = -1; // BUILD_RESPA_BIN_NO_NEWTON_OMP;
+ else if (triclinic == 0) build = -1; // BUILD_RESPA_BIN_NEWTON_OMP;
+ else if (triclinic == 1) build = -1; // BUILD_RESPA_BIN_NEWTON_TRI_OMP;
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
+ }
+ }
+
+ // instantiate selected Stencil class
+
+ if (build < 0) pair_build_new[index] = NULL;
+ else if (build_map->find(build) != build_map->end()) {
+ BuildCreator build_creator = (*build_map)[build];
+ pair_build_new[index] = build_creator(lmp);
+ } else error->all(FLERR,"Neighbor build class does not exit");
+}
+
+/* ----------------------------------------------------------------------
+ one instance per fix in style_build.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Build *Neighbor::build_creator(LAMMPS *lmp)
+{
+ return new T(lmp);
+}
+
/* ----------------------------------------------------------------------
determine which pair_build function each neigh list needs
based on settings of neigh request
@@ -1327,6 +1709,133 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
pair_build[index] = pb;
}
+/* ----------------------------------------------------------------------
+ determine which Stencil class each neigh list needs
+ based on settings of neigh request, only called if style != NSQ
+ skip or copy or half_from_full -> no stencil
+ ssa = special case for USER-DPD pair styles
+ half, gran, respaouter, full -> choose by newton and tri and dimension
+ if none of these, ptr = NULL since this list needs no stencils
+ use "else if" b/c skip,copy can be set in addition to half,full,etc
+------------------------------------------------------------------------- */
+
+void Neighbor::choose_stencil_new(int index, NeighRequest *rq)
+{
+ int stencil = -1;
+
+ if (rq->skip || rq->copy || rq->half_from_full) stencil = -1;
+
+ else if (rq->ssa) {
+ if (dimension == 2) stencil = -1; // STENCIL_HALF_BIN_2D_SSA;
+ else if (dimension == 3) stencil = -1; // STENCIL_HALF_BIN_3D_SSA;
+
+ } else if (rq->half || rq->gran || rq->respaouter) {
+ if (style == BIN) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) {
+ if (dimension == 2) {
+ if (rq->ghost) stencil = -1; // STENCIL_HALF_GHOST_BIN_2D_NO_NEWTON;
+ else stencil = -1; // STENCIL_HALF_BIN_2D_NO_NEWTON;
+ } else if (dimension == 3) {
+ if (rq->ghost) stencil = -1; // STENCIL_HALF_GHOST_BIN_3D_NO_NEWTON;
+ else stencil = -1; // STENCIL_HALF_BIN_3D_NO_NEWTON;
+ }
+ } else if (triclinic == 0) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_BIN_2D_NEWTON;
+ else if (dimension == 3)
+ stencil = STENCIL_HALF_BIN_3D_NEWTON;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_BIN_2D_NEWTON_TRI;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_BIN_3D_NEWTON_TRI;
+ }
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_BIN_2D_NEWTON;
+ else if (dimension == 3)
+ stencil = STENCIL_HALF_BIN_3D_NEWTON;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_BIN_2D_NEWTON_TRI;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_BIN_3D_NEWTON_TRI;
+ }
+ } else if (rq->newton == 2) {
+ if (dimension == 2)
+ if (rq->ghost) stencil = -1; // STENCIL_HALF_GHOST_BIN_2D_NO_NEWTON;
+ else stencil = -1; // STENCIL_HALF_BIN_2D_NO_NEWTON;
+ else if (dimension == 3) {
+ if (rq->ghost) stencil = -1; // STENCIL_HALF_GHOST_BIN_3D_NO_NEWTON;
+ else stencil = -1; // STENCIL_HALF_BIN_3D_NO_NEWTON;
+ }
+ }
+
+ } else if (style == MULTI) {
+ if (rq->newton == 0) {
+ if (newton_pair == 0) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_MULTI_2D_NO_NEWTON;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_MULTI_3D_NO_NEWTON;
+ } else if (triclinic == 0) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_MULTI_2D_NEWTON;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_MULTI_3D_NEWTON;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_MULTI_2D_NEWTON_TRI;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_MULTI_3D_NEWTON_TRI;
+ }
+ } else if (rq->newton == 1) {
+ if (triclinic == 0) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_MULTI_2D_NEWTON;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_MULTI_3D_NEWTON;
+ } else if (triclinic == 1) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_MULTI_2D_NEWTON_TRI;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_MULTI_3D_NEWTON_TRI;
+ }
+ } else if (rq->newton == 2) {
+ if (dimension == 2)
+ stencil = -1; // STENCIL_HALF_MULTI_2D_NO_NEWTON;
+ else if (dimension == 3)
+ stencil = -1; // STENCIL_HALF_MULTI_3D_NO_NEWTON;
+ }
+ }
+
+ } else if (rq->full) {
+ if (style == BIN) {
+ if (dimension == 2) {
+ if (rq->ghost) stencil = -1; // STENCIL_FULL_GHOST_BIN_2D;
+ else stencil = -1; // STENCIL_FULL_BIN_2D;
+ }
+ else if (dimension == 3) {
+ if (rq->ghost) stencil = -1; // STENCIL_FULL_GHOST_BIN_3D;
+ else stencil = -1; // STENCIL_FULL_BIN_3D;
+ }
+ } else if (style == MULTI) {
+ if (dimension == 2) stencil = -1; // STENCIL_FULL_MULTI_2D;
+ else if (dimension == 3) stencil = -1; // STENCIL_FULL_MULTI_3D;
+ }
+ }
+
+ // instantiate selected Stencil class
+
+ if (stencil < 0) stencil_create_new[index] = NULL;
+ else if (stencil_map->find(stencil) != stencil_map->end()) {
+ StencilCreator stencil_creator = (*stencil_map)[stencil];
+ stencil_create_new[index] = stencil_creator(lmp);
+ } else error->all(FLERR,"Neighbor stencil class does not exit");
+}
+
/* ----------------------------------------------------------------------
determine which stencil_create function each neigh list needs
based on settings of neigh request, only called if style != NSQ
@@ -1448,6 +1957,16 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
stencil_create[index] = sc;
}
+/* ----------------------------------------------------------------------
+ one instance per fix in style_stencil.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Stencil *Neighbor::stencil_creator(LAMMPS *lmp)
+{
+ return new T(lmp);
+}
+
/* ---------------------------------------------------------------------- */
void Neighbor::print_lists_of_lists()
@@ -1627,8 +2146,11 @@ void Neighbor::build(int topoflag)
// only for pairwise lists with buildflag set
// blist is for standard neigh lists, otherwise is a Kokkos list
- for (i = 0; i < nblist; i++)
- (this->*pair_build[blist[i]])(lists[blist[i]]);
+ for (i = 0; i < nblist; i++) {
+ if (pair_build_new[blist[i]])
+ pair_build_new[blist[i]]->compute(lists[blist[i]]);
+ else (this->*pair_build[blist[i]])(lists[blist[i]]);
+ }
if (atom->molecular && topoflag) build_topology();
}
@@ -1677,7 +2199,9 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
if (mylist->stencilflag) {
mylist->stencil_allocate(smax,style);
- (this->*stencil_create[mylist->index])(mylist,sx,sy,sz);
+ if (stencil_create_new[mylist->index])
+ stencil_create_new[mylist->index]->compute(mylist,sx,sy,sz);
+ else (this->*stencil_create[mylist->index])(mylist,sx,sy,sz);
}
if (mylist->growflag) mylist->grow(maxatom);
@@ -1688,7 +2212,9 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
// leading to errors or even a crash
binatomflag = 0;
- (this->*pair_build[mylist->index])(mylist);
+ if (pair_build_new[mylist->index])
+ pair_build_new[mylist->index]->compute(mylist);
+ else (this->*pair_build[mylist->index])(mylist);
binatomflag = 1;
}
@@ -1880,7 +2406,9 @@ void Neighbor::setup_bins()
for (int i = 0; i < nslist; i++) {
if (lists[slist[i]]) {
lists[slist[i]]->stencil_allocate(smax,style);
- (this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
+ if (stencil_create_new[slist[i]])
+ stencil_create_new[slist[i]]->compute(lists[slist[i]],sx,sy,sz);
+ else (this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
} else setup_bins_kokkos(i);
}
}
diff --git a/src/neighbor.h b/src/neighbor.h
index 7a098e9be2..c2c3cdde97 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -15,11 +15,13 @@
#define LMP_NEIGHBOR_H
#include "pointers.h"
+#include <map>
namespace LAMMPS_NS {
class Neighbor : protected Pointers {
- friend class Cuda;
+ friend class StencilHalfBin3dNewton;
+ friend class BuildHalfBinNewton;
public:
int style; // 0,1,2 = nsq, bin, multi
@@ -186,9 +188,29 @@ class Neighbor : protected Pointers {
int exclusion(int, int, int,
int, int *, tagint *) const; // test for pair exclusion
+ // choose stencil and build methods
+
virtual void choose_build(int, class NeighRequest *);
void choose_stencil(int, class NeighRequest *);
+ // new versions
+ // choose stencil and build classes
+
+ void choose_stencil_new(int, class NeighRequest *);
+ void choose_build_new(int, class NeighRequest *);
+
+ typedef class Stencil *(*StencilCreator)(class LAMMPS *);
+ std::map<int,StencilCreator> *stencil_map;
+
+ typedef class Build *(*BuildCreator)(class LAMMPS *);
+ std::map<int,BuildCreator> *build_map;
+
+ template <typename T> static Stencil *stencil_creator(class LAMMPS *);
+ template <typename T> static Build *build_creator(class LAMMPS *);
+
+ class Stencil **stencil_create_new;
+ class Build **pair_build_new;
+
// dummy functions provided by NeighborKokkos
virtual void init_cutneighsq_kokkos(int) {}
--
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