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add new APIs for creating and manipulating neighbor list requests

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also add a few new (delegating) constructors to simplify code
This commit is contained in:
Axel Kohlmeyer
2022-03-02 19:12:00 -05:00
parent f7514ce358
commit d4272815a3
4 changed files with 168 additions and 37 deletions
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67
src/neigh_request.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,14 +12,17 @@
------------------------------------------------------------------------- */
#include "neigh_request.h"
#include "atom.h"
#include "memory.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
using namespace NeighConst;
/* ---------------------------------------------------------------------- */
NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp)
{
// default ID = 0
@ -96,6 +98,24 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
/* ---------------------------------------------------------------------- */
NeighRequest::NeighRequest(LAMMPS *_lmp, int idx, void *ptr, int num)
: NeighRequest(_lmp)
{
index = idx;
requestor = ptr;
requestor_instance = num;
}
/* ---------------------------------------------------------------------- */
NeighRequest::NeighRequest(NeighRequest *old)
: NeighRequest(old->lmp)
{
copy_request(old,1);
}
/* ---------------------------------------------------------------------- */
NeighRequest::~NeighRequest()
{
delete[] iskip;
@ -165,15 +185,13 @@ int NeighRequest::identical(NeighRequest *other)
int NeighRequest::same_skip(NeighRequest *other)
{
int i,j;
int ntypes = atom->ntypes;
const int ntypes = atom->ntypes;
int same = 1;
for (i = 1; i <= ntypes; i++)
for (int i = 1; i <= ntypes; i++)
if (iskip[i] != other->iskip[i]) same = 0;
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
for (int i = 1; i <= ntypes; i++)
for (int j = 1; j <= ntypes; j++)
if (ijskip[i][j] != other->ijskip[i][j]) same = 0;
return same;
@ -230,15 +248,40 @@ void NeighRequest::copy_request(NeighRequest *other, int skipflag)
if (other->iskip) {
iskip = new int[ntypes + 1];
for (i = 1; i <= ntypes; i++)
iskip[i] = other->iskip[i];
for (i = 1; i <= ntypes; i++) iskip[i] = other->iskip[i];
}
if (other->ijskip) {
memory->create(ijskip, ntypes + 1, ntypes + 1, "neigh_request:ijskip");
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
ijskip[i][j] = other->ijskip[i][j];
for (j = 1; j <= ntypes; j++) ijskip[i][j] = other->ijskip[i][j];
}
}
/* ---------------------------------------------------------------------- */
void NeighRequest::apply_flags(int flags)
{
if (flags & REQ_FULL) {
half = 0;
full = 1;
}
if (flags & REQ_GHOST) { ghost = 1; }
if (flags & REQ_SIZE) { size = 1; }
if (flags & REQ_HISTORY) { history = 1; }
if (flags & REQ_OCCASIONAL) { occasional = 1; }
if (flags & REQ_RESPA_INOUT) { respainner = respaouter = 1; }
if (flags & REQ_RESPA_ALL) { respainner = respamiddle = respaouter = 1; }
}
/* ---------------------------------------------------------------------- */
void NeighRequest::set_id(int _id) {
id = _id;
}
void NeighRequest::set_cutoff(double _cutoff)
{
cut = 1;
cutoff = _cutoff;
}

7
src/neigh_request.h
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@ -112,11 +112,18 @@ class NeighRequest : protected Pointers {
// methods
NeighRequest(class LAMMPS *);
NeighRequest(class LAMMPS *, int, void *, int);
NeighRequest(NeighRequest *);
~NeighRequest() override;
void archive();
int identical(NeighRequest *);
int same_skip(NeighRequest *);
void copy_request(NeighRequest *, int);
void apply_flags(int);
void set_id(int);
void set_cutoff(double);
};
} // namespace LAMMPS_NS

83
src/neighbor.cpp
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@ -1715,13 +1715,10 @@ void Neighbor::requests_new2old()
old_nrequest = nrequest;
old_requests = (NeighRequest **)
memory->smalloc(old_nrequest*sizeof(NeighRequest *),
"neighbor:old_requests");
memory->smalloc(old_nrequest*sizeof(NeighRequest *),"neighbor:old_requests");
for (int i = 0; i < old_nrequest; i++) {
old_requests[i] = new NeighRequest(lmp);
old_requests[i]->copy_request(requests[i],1);
}
for (int i = 0; i < old_nrequest; i++)
old_requests[i] = new NeighRequest(requests[i]);
old_style = style;
old_triclinic = triclinic;
@ -1731,7 +1728,8 @@ void Neighbor::requests_new2old()
/* ----------------------------------------------------------------------
find and return request made by classptr
if not found or classpt = nullptr, return nullptr
if not found or classptr = nullptr, return nullptr
TODO: should have optional argument "id" to match ID if multiple requests
------------------------------------------------------------------------- */
NeighRequest *Neighbor::find_request(void *classptr)
@ -1744,6 +1742,22 @@ NeighRequest *Neighbor::find_request(void *classptr)
return nullptr;
}
/* ----------------------------------------------------------------------
find and return list requested by classptr
if not found or classptr = nullptr, return nullptr
TODO: should have optional argument "id" to match ID if multiple requests
------------------------------------------------------------------------- */
NeighList *Neighbor::find_list(void *classptr)
{
if (classptr == nullptr) return nullptr;
for (int i = 0; i < nrequest; i++)
if (lists[i]->requestor == classptr) return lists[i];
return nullptr;
}
/* ----------------------------------------------------------------------
assign NBin class to a NeighList
use neigh request settings to build mask
@ -2028,14 +2042,55 @@ int Neighbor::request(void *requestor, int instance)
"neighbor:requests");
}
requests[nrequest] = new NeighRequest(lmp);
requests[nrequest]->index = nrequest;
requests[nrequest]->requestor = requestor;
requests[nrequest]->requestor_instance = instance;
requests[nrequest] = new NeighRequest(lmp, nrequest, requestor, instance);
nrequest++;
return nrequest-1;
}
/* ----------------------------------------------------------------------
called by other classes to request a pairwise neighbor list
------------------------------------------------------------------------- */
NeighRequest *Neighbor::add_request(Pair *requestor, int flags)
{
int irequest = request(requestor, requestor->instance_me);
auto req = requests[irequest];
req->apply_flags(flags);
return req;
}
NeighRequest *Neighbor::add_request(Fix *requestor, int flags)
{
int irequest = request(requestor, requestor->instance_me);
auto req = requests[irequest];
req->pair = 0;
req->fix = 1;
req->apply_flags(flags);
return req;
}
NeighRequest *Neighbor::add_request(Compute *requestor, int flags)
{
int irequest = request(requestor, requestor->instance_me);
auto req = requests[irequest];
req->pair = 0;
req->compute = 1;
req->apply_flags(flags);
return req;
}
NeighRequest *Neighbor::add_request(Command *requestor, const char *style, int flags)
{
int irequest = request(requestor, 0);
auto req = requests[irequest];
req->pair = 0;
req->command = 1;
req->occasional = 1;
req->command_style = style;
req->apply_flags(flags);
return req;
}
/* ----------------------------------------------------------------------
setup neighbor binning and neighbor stencils
called before run and every reneighbor if box size/shape changes
@ -2275,13 +2330,11 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
// check if list structure is initialized
if (mylist == nullptr)
error->all(FLERR,"Trying to build an occasional neighbor list "
"before initialization completed");
error->all(FLERR,"Trying to build an occasional neighbor list before initialization complete");
// build_one() should never be invoked on a perpetual list
if (!mylist->occasional)
error->all(FLERR,"Neighbor build one invoked on perpetual list");
if (!mylist->occasional) error->all(FLERR,"Neighbor::build_one() invoked on perpetual list");
// no need to build if already built since last re-neighbor
// preflag is set by fix bond/create and fix bond/swap

38
src/neighbor.h
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@ -18,6 +18,10 @@
namespace LAMMPS_NS {
// forward declarations
class NeighRequest;
class NeighList;
class Neighbor : protected Pointers {
public:
enum { NSQ, BIN, MULTI_OLD, MULTI };
@ -87,9 +91,9 @@ class Neighbor : protected Pointers {
int nrequest; // # of requests, same as nlist
int old_nrequest; // # of requests for previous run
class NeighList **lists;
class NeighRequest **requests; // from Pair,Fix,Compute,Command classes
class NeighRequest **old_requests; // copy of requests to compare to
NeighList **lists;
NeighRequest **requests; // from Pair,Fix,Compute,Command classes
NeighRequest **old_requests; // copy of requests to compare to
// data from topology neighbor lists
@ -119,7 +123,16 @@ class Neighbor : protected Pointers {
Neighbor(class LAMMPS *);
~Neighbor() override;
virtual void init();
int request(void *, int instance = 0);
// old API for creating neighbor list requests
int request(void *, int instance_me = 0);
// new API for creating neighbor list requests
NeighRequest *add_request(class Pair *, int);
NeighRequest *add_request(class Fix *, int);
NeighRequest *add_request(class Compute *, int);
NeighRequest *add_request(class Command *, const char *, int);
int decide(); // decide whether to build or not
virtual int check_distance(); // check max distance moved since last build
void setup_bins(); // setup bins based on box and cutoff
@ -134,7 +147,8 @@ class Neighbor : protected Pointers {
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
int exclude_setting(); // return exclude value to accelerator pkg
class NeighRequest *find_request(void *); // find a neighbor request
NeighList *find_list(void *); // find a neighbor request
NeighRequest *find_request(void *); // find a neighbor request
int any_full(); // Check if any old requests had full neighbor lists
void build_collection(int); // build peratom collection array starting at the given index
@ -246,6 +260,7 @@ class Neighbor : protected Pointers {
};
namespace NeighConst {
enum {
NB_INTEL = 1 << 0,
NB_KOKKOS_DEVICE = 1 << 1,
@ -297,6 +312,19 @@ namespace NeighConst {
NP_OFF2ON = 1 << 24,
NP_MULTI_OLD = 1 << 25
};
enum {
REQ_DEFAULT = 0,
REQ_FULL = 1 << 0,
REQ_GHOST = 1 << 1,
REQ_SIZE = 1 << 2,
REQ_HISTORY = 1 << 3,
REQ_OCCASIONAL = 1 << 4,
REQ_RESPA_INOUT = 1 << 5,
REQ_RESPA_ALL = 1 << 6,
REQ_NEWTON_ON = 1 << 8,
REQ_NEWTON_OFF = 1 << 9,
};
} // namespace NeighConst
} // namespace LAMMPS_NS