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Changing how multi/cutoff works, changing collection indexing in user args

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This commit is contained in:
Joel Clemmer
2021-05-04 17:12:17 -06:00
parent bd6dd658d6
commit fa386c0e96
12 changed files with 100 additions and 103 deletions
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2
src/GRANULAR/pair_gran_hooke_history.cpp
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@ -824,4 +824,4 @@ double PairGranHookeHistory::radii2cut(double r1, double r2)
{
double cut = r1+r2;
return cut;
}
}

22
src/comm.cpp
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@ -35,7 +35,6 @@
#include "update.h"
#include <cstring>
#include <vector>
#ifdef _OPENMP
#include <omp.h>
#endif
@ -58,9 +57,8 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
bordergroup = 0;
cutghostuser = 0.0;
cutusermulti = nullptr;
cutusermultiflag = 0;
cutusermultiold = nullptr;
ncollections_prior = 0;
ncollections = 0;
ghost_velocity = 0;
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
@ -149,6 +147,7 @@ void Comm::copy_arrays(Comm *oldcomm)
memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double));
}
ncollections = oldcomm->ncollections;
if (oldcomm->cutusermulti) {
memory->create(cutusermulti,ncollections,"comm:cutusermulti");
memcpy(cutusermulti,oldcomm->cutusermulti,ncollections);
@ -354,14 +353,23 @@ void Comm::modify_params(int narg, char **arg)
error->all(FLERR,
"Cannot set cutoff/multi before simulation box is defined");
// save arguments so they can be parsed in comm->setup()
// ncollections can be changed by neigh_modify commands
// Check if # of collections has changed, if so erase any previously defined cutoffs
// Neighbor will reset ncollections if collections are redefined
if (ncollections_cutoff != neighbor->ncollections) {
ncollections_cutoff = neighbor->ncollections;
if (cutusermulti) memory->destroy(cutusermulti);
memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti");
for (i=0; i < ncollections_cutoff; ++i)
cutusermulti[i] = -1.0;
}
utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff+1,nlo,nhi,error);
cut = utils::numeric(FLERR,arg[iarg+2],false,lmp);
cutghostuser = MAX(cutghostuser,cut);
cutusermultiflag = 1;
if (cut < 0.0)
error->all(FLERR,"Invalid cutoff in comm_modify command");
usermultiargs.emplace_back(arg[iarg+1], cut);
// collections use 1-based indexing externally and 0-based indexing internally
for (i=nlo; i<=nhi; ++i)
cutusermulti[i-1] = cut;
iarg += 3;
} else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) {
int i,nlo,nhi;

7
src/comm.h
View File

@ -33,10 +33,9 @@ class Comm : protected Pointers {
double cutghost[3]; // cutoffs used for acquiring ghost atoms
double cutghostuser; // user-specified ghost cutoff (mode == 0)
double *cutusermulti; // per collection user ghost cutoff (mode == 1)
int cutusermultiflag;
std::vector<std::pair<std::string, double>> usermultiargs;
// collection args for custom ghost cutoffs
double *cutusermultiold; // per type user ghost cutoff (mode == 2)
int ncollections; // # of collections known by comm, used to test if # has changed
int ncollections_cutoff; // # of collections stored b cutoff/multi
int recv_from_partition; // recv proc layout from this partition
int send_to_partition; // send my proc layout to this partition
// -1 if no recv or send
@ -157,8 +156,6 @@ class Comm : protected Pointers {
int coregrid[3]; // 3d grid of cores within a node
int user_coregrid[3]; // user request for cores in each dim
int multi_reduce; // 1 if multi cutoff is intra-collection cutoff
int ncollections; // number of collection cutoffs defined for multi
int ncollections_prior; // value of ncollections at last setup
void init_exchange();
int rendezvous_irregular(int, char *, int, int, int *,

71
src/comm_brick.cpp
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@ -141,19 +141,30 @@ void CommBrick::init()
// memory for multi style communication
// allocate in setup
if (mode == Comm::MULTI && multilo == nullptr) {
ncollections = neighbor->ncollections;
allocate_multi(maxswap);
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
if (cutusermultiflag) {
memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
for (int i = ncollections_prior; i < ncollections; i++)
cutusermulti[i] = -1.0;
}
if (mode == Comm::MULTI) {
// If inconsitent # of collections, destroy any preexisting arrays (may be missized)
if (ncollections != neighbor->ncollections) {
ncollections = neighbor->ncollections;
if (multilo != nullptr) {
free_multi();
memory->destroy(cutghostmulti);
}
}
ncollections_prior = ncollections;
// delete any old user cutoffs if # of collections chanaged
if (cutusermulti && ncollections != ncollections_cutoff) {
if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined"
" after customizing collections in neigh_modify");
memory->destroy(cutusermulti);
cutusermulti = nullptr;
}
if (multilo == nullptr) {
allocate_multi(maxswap);
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
}
}
if ((mode == Comm::SINGLE or mode == Comm::MULTIOLD) && multilo) {
if ((mode == Comm::SINGLE || mode == Comm::MULTIOLD) && multilo) {
free_multi();
memory->destroy(cutghostmulti);
}
@ -164,7 +175,7 @@ void CommBrick::init()
allocate_multiold(maxswap);
memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold");
}
if ((mode == Comm::SINGLE or mode == Comm::MULTI) && multioldlo) {
if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) {
free_multiold();
memory->destroy(cutghostmultiold);
}
@ -201,39 +212,11 @@ void CommBrick::setup()
"will be generated. Atoms may get lost.");
if (mode == Comm::MULTI) {
// build initial collection array
neighbor->build_collection(0);
ncollections = neighbor->ncollections;
// reallocate memory for multi-style communication at setup if ncollections change
if (ncollections_prior != ncollections) {
if (multilo) free_multi();
if (cutghostmulti) memory->destroy(cutghostmulti);
allocate_multi(maxswap);
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
if (cutusermultiflag) {
memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
for (i = ncollections_prior; i < ncollections; i++)
cutusermulti[i] = -1.0;
}
ncollections_prior = ncollections;
}
// parse any cutoff/multi commands
int nhi, nlo;
for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) {
utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error);
if (nhi >= ncollections)
error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command");
for (j = nlo; j<=nhi; ++j)
cutusermulti[j] = it->second;
}
usermultiargs.clear();
double **cutcollectionsq = neighbor->cutcollectionsq;
// build collection array for atom exchange
neighbor->build_collection(0);
// If using multi/reduce, communicate particles a distance equal
// to the max cutoff with equally sized or smaller collections
// If not, communicate the maximum cutoff of the entire collection

67
src/comm_tiled.cpp
View File

@ -104,12 +104,8 @@ void CommTiled::init_buffers()
cutghostmultiold = nullptr;
sendbox_multi = nullptr;
sendbox_multiold = nullptr;
// initialize ncollections so grow_swap_send_multi() will not
// construct arrays in init() but will wait for setup()
ncollections = 0;
ncollections_prior = 0;
// Note this may skip growing multi arrays, will call again in init()
maxswap = 6;
allocate_swap(maxswap);
}
@ -125,11 +121,32 @@ void CommTiled::init()
nswap = 2*domain->dimension;
memory->destroy(cutghostmulti);
if (mode == Comm::MULTI) {
// If inconsitent # of collections, destroy any preexisting arrays (may be missized)
if (ncollections != neighbor->ncollections) {
ncollections = neighbor->ncollections;
}
// delete any old user cutoffs if # of collections chanaged
if (cutusermulti && ncollections != ncollections_cutoff) {
if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined"
" after customizing collections in neigh_modify");
memory->destroy(cutusermulti);
cutusermulti = nullptr;
}
// grow sendbox_multi now that ncollections is known
for (int i = 0; i < maxswap; i ++)
grow_swap_send_multi(i,DELTA_PROCS);
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
}
memory->destroy(cutghostmultiold);
if (mode == Comm::MULTIOLD)
memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold");
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
@ -186,44 +203,14 @@ void CommTiled::setup()
// check that cutoff < any periodic box length
if (mode == Comm::MULTI) {
// build collection from scratch as it is needed for atom exchange
neighbor->build_collection(0);
ncollections = neighbor->ncollections;
// allocate memory for multi-style communication at setup as ncollections can change
if (ncollections_prior != ncollections) {
memory->destroy(cutghostmulti);
if (mode == Comm::MULTI)
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
for (i = 0; i < maxswap; i ++)
grow_swap_send_multi(i,DELTA_PROCS);
if (cutusermultiflag) {
memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
for (i = ncollections_prior; i < ncollections; i++)
cutusermulti[i] = -1.0;
}
ncollections_prior = ncollections;
}
// parse any cutoff/multi commands
int nhi, nlo;
for (auto it = usermultiargs.begin(); it != usermultiargs.end(); it ++) {
utils::bounds(FLERR,it->first,0,ncollections,nlo,nhi,error);
if (nhi >= ncollections)
error->all(FLERR, "Unused collection id in comm_modify cutoff/multi command");
for (j = nlo; j <= nhi; ++j)
cutusermulti[j] = it->second;
}
usermultiargs.clear();
double **cutcollectionsq = neighbor->cutcollectionsq;
// build collection array for atom exchange
neighbor->build_collection(0);
// If using multi/reduce, communicate particles a distance equal
// to the max cutoff with equally sized or smaller collections
// If not, communicate the maximum cutoff of the entire collection
for (i = 0; i < ncollections; i++) {
if (cutusermulti) {
cutghostmulti[i][0] = cutusermulti[i];

4
src/neighbor.cpp
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@ -2514,6 +2514,8 @@ void Neighbor::modify_params(int narg, char **arg)
int ntypes = atom->ntypes;
int n, nlo, nhi, i, j;
// Invalidate old user cutoffs
comm->ncollections_cutoff = 0;
interval_collection_flag = 1;
custom_collection_flag = 1;
memory->grow(collection2cut,ncollections,"neigh:collection2cut");
@ -2546,6 +2548,8 @@ void Neighbor::modify_params(int narg, char **arg)
int ntypes = atom->ntypes;
int n, nlo, nhi, i, j, k;
// Invalidate old user cutoffs
comm->ncollections_cutoff = 0;
interval_collection_flag = 0;
custom_collection_flag = 1;
if (not type2collection)

5
src/nstencil_full_multi_2d.cpp
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@ -56,7 +56,10 @@ void NStencilFullMulti2d::create()
for (icollection = 0; icollection < n; icollection++) {
for (jcollection = 0; jcollection < n; jcollection++) {
if (flag_skip_multi[icollection][jcollection]) continue;
if (flag_skip_multi[icollection][jcollection]) {
nstencil_multi[icollection][jcollection] = 0;
continue;
}
ns = 0;

5
src/nstencil_full_multi_3d.cpp
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@ -57,7 +57,10 @@ void NStencilFullMulti3d::create()
for (icollection = 0; icollection < n; icollection++) {
for (jcollection = 0; jcollection < n; jcollection++) {
if (flag_skip_multi[icollection][jcollection]) continue;
if (flag_skip_multi[icollection][jcollection]) {
nstencil_multi[icollection][jcollection] = 0;
continue;
}
ns = 0;

5
src/nstencil_half_multi_2d.cpp
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@ -68,7 +68,10 @@ void NStencilHalfMulti2d::create()
for (icollection = 0; icollection < n; icollection++) {
for (jcollection = 0; jcollection < n; jcollection++) {
if (flag_skip_multi[icollection][jcollection]) continue;
if (flag_skip_multi[icollection][jcollection]) {
nstencil_multi[icollection][jcollection] = 0;
continue;
}
ns = 0;

5
src/nstencil_half_multi_2d_tri.cpp
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@ -68,7 +68,10 @@ void NStencilHalfMulti2dTri::create()
for (icollection = 0; icollection < n; icollection++) {
for (jcollection = 0; jcollection < n; jcollection++) {
if (flag_skip_multi[icollection][jcollection]) continue;
if (flag_skip_multi[icollection][jcollection]) {
nstencil_multi[icollection][jcollection] = 0;
continue;
}
ns = 0;

5
src/nstencil_half_multi_3d.cpp
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@ -68,7 +68,10 @@ void NStencilHalfMulti3d::create()
for (icollection = 0; icollection < n; icollection++) {
for (jcollection = 0; jcollection < n; jcollection++) {
if (flag_skip_multi[icollection][jcollection]) continue;
if (flag_skip_multi[icollection][jcollection]) {
nstencil_multi[icollection][jcollection] = 0;
continue;
}
ns = 0;

5
src/nstencil_half_multi_3d_tri.cpp
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@ -68,7 +68,10 @@ void NStencilHalfMulti3dTri::create()
for (icollection = 0; icollection < n; icollection++) {
for (jcollection = 0; jcollection < n; jcollection++) {
if (flag_skip_multi[icollection][jcollection]) continue;
if (flag_skip_multi[icollection][jcollection]) {
nstencil_multi[icollection][jcollection] = 0;
continue;
}
ns = 0;