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comm_brick.cpp
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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: [email protected]
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author (triclinic) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "comm_brick.h"
#include "atom.h"
#include "atom_vec.h"
#include "bond.h"
#include "compute.h"
#include "domain.h"
#include "dump.h"
#include "error.h"
#include "fix.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include <cmath>
#include <cstring>
#include "pair_e3gnn_parallel.h"
using namespace LAMMPS_NS;
#define BUFFACTOR 1.5
#define BUFMIN 1024
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
CommBrick::CommBrick(LAMMPS *lmp) :
Comm(lmp),
sendnum(nullptr), recvnum(nullptr), sendproc(nullptr), recvproc(nullptr),
size_forward_recv(nullptr), size_reverse_send(nullptr), size_reverse_recv(nullptr),
slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr),
multioldlo(nullptr), multioldhi(nullptr), cutghostmulti(nullptr), cutghostmultiold(nullptr),
pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), sendlist(nullptr),
localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr)
{
style = Comm::BRICK;
layout = Comm::LAYOUT_UNIFORM;
pbc_flag = nullptr;
init_buffers();
}
/* ---------------------------------------------------------------------- */
CommBrick::~CommBrick()
{
CommBrick::free_swap();
if (mode == Comm::MULTI) {
CommBrick::free_multi();
memory->destroy(cutghostmulti);
}
if (mode == Comm::MULTIOLD) {
CommBrick::free_multiold();
memory->destroy(cutghostmultiold);
}
if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
if (localsendlist) memory->destroy(localsendlist);
memory->sfree(sendlist);
memory->destroy(maxsendlist);
memory->destroy(buf_send);
memory->destroy(buf_recv);
}
/* ---------------------------------------------------------------------- */
//IMPORTANT: we *MUST* pass "*oldcomm" to the Comm initializer here, as
// the code below *requires* that the (implicit) copy constructor
// for Comm is run and thus creating a shallow copy of "oldcomm".
// The call to Comm::copy_arrays() then converts the shallow copy
// into a deep copy of the class with the new layout.
CommBrick::CommBrick(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm)
{
if (oldcomm->layout == Comm::LAYOUT_TILED)
error->all(FLERR,"Cannot change to comm_style brick from tiled layout");
style = Comm::BRICK;
layout = oldcomm->layout;
Comm::copy_arrays(oldcomm);
init_buffers();
}
/* ----------------------------------------------------------------------
initialize comm buffers and other data structs local to CommBrick
------------------------------------------------------------------------- */
void CommBrick::init_buffers()
{
multilo = multihi = nullptr;
cutghostmulti = nullptr;
multioldlo = multioldhi = nullptr;
cutghostmultiold = nullptr;
buf_send = buf_recv = nullptr;
maxsend = maxrecv = BUFMIN;
CommBrick::grow_send(maxsend,2);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
nswap = 0;
maxswap = 6;
CommBrick::allocate_swap(maxswap);
sendlist = (int **) memory->smalloc(maxswap*sizeof(int *),"comm:sendlist");
memory->create(maxsendlist,maxswap,"comm:maxsendlist");
for (int i = 0; i < maxswap; i++) {
maxsendlist[i] = BUFMIN;
memory->create(sendlist[i],BUFMIN,"comm:sendlist[i]");
}
}
/* ---------------------------------------------------------------------- */
void CommBrick::init()
{
Comm::init();
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
// memory for multi style communication
// allocate in setup
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);
}
}
// 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 || mode == Comm::MULTIOLD) && multilo) {
free_multi();
memory->destroy(cutghostmulti);
}
// memory for multi/old-style communication
if (mode == Comm::MULTIOLD && multioldlo == nullptr) {
allocate_multiold(maxswap);
memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold");
}
if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) {
free_multiold();
memory->destroy(cutghostmultiold);
}
}
/* ----------------------------------------------------------------------
setup spatial-decomposition communication patterns
function of neighbor cutoff(s) & cutghostuser & current box size
single mode sets slab boundaries (slablo,slabhi) based on max cutoff
multi mode sets collection-dependent slab boundaries (multilo,multihi)
multi/old mode sets type-dependent slab boundaries (multioldlo,multioldhi)
------------------------------------------------------------------------- */
void CommBrick::setup()
{
// cutghost[] = max distance at which ghost atoms need to be acquired
// for orthogonal:
// cutghost is in box coords = neigh->cutghost in all 3 dims
// for triclinic:
// neigh->cutghost = distance between tilted planes in box coords
// cutghost is in lamda coords = distance between those planes
// for multi:
// cutghostmulti = same as cutghost, only for each atom collection
// for multi/old:
// cutghostmultiold = same as cutghost, only for each atom type
int i,j;
int ntypes = atom->ntypes;
double *prd,*sublo,*subhi;
double cut = get_comm_cutoff();
if ((cut == 0.0) && (me == 0))
error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
"will be generated. Atoms may get lost.");
if (mode == Comm::MULTI) {
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];
cutghostmulti[i][1] = cutusermulti[i];
cutghostmulti[i][2] = cutusermulti[i];
} else {
cutghostmulti[i][0] = 0.0;
cutghostmulti[i][1] = 0.0;
cutghostmulti[i][2] = 0.0;
}
for (j = 0; j < ncollections; j++){
if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue;
cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j]));
cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j]));
cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j]));
}
}
}
if (mode == Comm::MULTIOLD) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
double tmp = 0.0;
if (cutusermultiold) tmp = cutusermultiold[i];
cutghostmultiold[i][0] = MAX(tmp,cuttype[i]);
cutghostmultiold[i][1] = MAX(tmp,cuttype[i]);
cutghostmultiold[i][2] = MAX(tmp,cuttype[i]);
}
}
if (triclinic == 0) {
prd = domain->prd;
sublo = domain->sublo;
subhi = domain->subhi;
cutghost[0] = cutghost[1] = cutghost[2] = cut;
} else {
prd = domain->prd_lamda;
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
double *h_inv = domain->h_inv;
double length0,length1,length2;
length0 = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]);
cutghost[0] = cut * length0;
length1 = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]);
cutghost[1] = cut * length1;
length2 = h_inv[2];
cutghost[2] = cut * length2;
if (mode == Comm::MULTI) {
for (i = 0; i < ncollections; i++) {
cutghostmulti[i][0] *= length0;
cutghostmulti[i][1] *= length1;
cutghostmulti[i][2] *= length2;
}
}
if (mode == Comm::MULTIOLD) {
for (i = 1; i <= ntypes; i++) {
cutghostmultiold[i][0] *= length0;
cutghostmultiold[i][1] *= length1;
cutghostmultiold[i][2] *= length2;
}
}
}
// recvneed[idim][0/1] = # of procs away I recv atoms from, within cutghost
// 0 = from left, 1 = from right
// do not cross non-periodic boundaries, need[2] = 0 for 2d
// sendneed[idim][0/1] = # of procs away I send atoms to
// 0 = to left, 1 = to right
// set equal to recvneed[idim][1/0] of neighbor proc
// maxneed[idim] = max procs away any proc recvs atoms in either direction
// layout = UNIFORM = uniform sized sub-domains:
// maxneed is directly computable from sub-domain size
// limit to procgrid-1 for non-PBC
// recvneed = maxneed except for procs near non-PBC
// sendneed = recvneed of neighbor on each side
// layout = NONUNIFORM = non-uniform sized sub-domains:
// compute recvneed via updown() which accounts for non-PBC
// sendneed = recvneed of neighbor on each side
// maxneed via Allreduce() of recvneed
int *periodicity = domain->periodicity;
int left,right;
if (layout == Comm::LAYOUT_UNIFORM) {
maxneed[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd[0]) + 1;
maxneed[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd[1]) + 1;
maxneed[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd[2]) + 1;
if (domain->dimension == 2) maxneed[2] = 0;
if (!periodicity[0]) maxneed[0] = MIN(maxneed[0],procgrid[0]-1);
if (!periodicity[1]) maxneed[1] = MIN(maxneed[1],procgrid[1]-1);
if (!periodicity[2]) maxneed[2] = MIN(maxneed[2],procgrid[2]-1);
if (!periodicity[0]) {
recvneed[0][0] = MIN(maxneed[0],myloc[0]);
recvneed[0][1] = MIN(maxneed[0],procgrid[0]-myloc[0]-1);
left = myloc[0] - 1;
if (left < 0) left = procgrid[0] - 1;
sendneed[0][0] = MIN(maxneed[0],procgrid[0]-left-1);
right = myloc[0] + 1;
if (right == procgrid[0]) right = 0;
sendneed[0][1] = MIN(maxneed[0],right);
} else recvneed[0][0] = recvneed[0][1] =
sendneed[0][0] = sendneed[0][1] = maxneed[0];
if (!periodicity[1]) {
recvneed[1][0] = MIN(maxneed[1],myloc[1]);
recvneed[1][1] = MIN(maxneed[1],procgrid[1]-myloc[1]-1);
left = myloc[1] - 1;
if (left < 0) left = procgrid[1] - 1;
sendneed[1][0] = MIN(maxneed[1],procgrid[1]-left-1);
right = myloc[1] + 1;
if (right == procgrid[1]) right = 0;
sendneed[1][1] = MIN(maxneed[1],right);
} else recvneed[1][0] = recvneed[1][1] =
sendneed[1][0] = sendneed[1][1] = maxneed[1];
if (!periodicity[2]) {
recvneed[2][0] = MIN(maxneed[2],myloc[2]);
recvneed[2][1] = MIN(maxneed[2],procgrid[2]-myloc[2]-1);
left = myloc[2] - 1;
if (left < 0) left = procgrid[2] - 1;
sendneed[2][0] = MIN(maxneed[2],procgrid[2]-left-1);
right = myloc[2] + 1;
if (right == procgrid[2]) right = 0;
sendneed[2][1] = MIN(maxneed[2],right);
} else recvneed[2][0] = recvneed[2][1] =
sendneed[2][0] = sendneed[2][1] = maxneed[2];
} else {
recvneed[0][0] = updown(0,0,myloc[0],prd[0],periodicity[0],xsplit);
recvneed[0][1] = updown(0,1,myloc[0],prd[0],periodicity[0],xsplit);
left = myloc[0] - 1;
if (left < 0) left = procgrid[0] - 1;
sendneed[0][0] = updown(0,1,left,prd[0],periodicity[0],xsplit);
right = myloc[0] + 1;
if (right == procgrid[0]) right = 0;
sendneed[0][1] = updown(0,0,right,prd[0],periodicity[0],xsplit);
recvneed[1][0] = updown(1,0,myloc[1],prd[1],periodicity[1],ysplit);
recvneed[1][1] = updown(1,1,myloc[1],prd[1],periodicity[1],ysplit);
left = myloc[1] - 1;
if (left < 0) left = procgrid[1] - 1;
sendneed[1][0] = updown(1,1,left,prd[1],periodicity[1],ysplit);
right = myloc[1] + 1;
if (right == procgrid[1]) right = 0;
sendneed[1][1] = updown(1,0,right,prd[1],periodicity[1],ysplit);
if (domain->dimension == 3) {
recvneed[2][0] = updown(2,0,myloc[2],prd[2],periodicity[2],zsplit);
recvneed[2][1] = updown(2,1,myloc[2],prd[2],periodicity[2],zsplit);
left = myloc[2] - 1;
if (left < 0) left = procgrid[2] - 1;
sendneed[2][0] = updown(2,1,left,prd[2],periodicity[2],zsplit);
right = myloc[2] + 1;
if (right == procgrid[2]) right = 0;
sendneed[2][1] = updown(2,0,right,prd[2],periodicity[2],zsplit);
} else recvneed[2][0] = recvneed[2][1] =
sendneed[2][0] = sendneed[2][1] = 0;
int all[6];
MPI_Allreduce(&recvneed[0][0],all,6,MPI_INT,MPI_MAX,world);
maxneed[0] = MAX(all[0],all[1]);
maxneed[1] = MAX(all[2],all[3]);
maxneed[2] = MAX(all[4],all[5]);
}
// allocate comm memory
nswap = 2 * (maxneed[0]+maxneed[1]+maxneed[2]);
if (nswap > maxswap) grow_swap(nswap);
// setup parameters for each exchange:
// sendproc = proc to send to at each swap
// recvproc = proc to recv from at each swap
// for mode SINGLE:
// slablo/slabhi = boundaries for slab of atoms to send at each swap
// use -BIG/midpt/BIG to ensure all atoms included even if round-off occurs
// if round-off, atoms recvd across PBC can be < or > than subbox boundary
// note that borders() only loops over subset of atoms during each swap
// treat all as PBC here, non-PBC is handled in borders() via r/s need[][]
// for mode MULTI:
// multilo/multihi is same, with slablo/slabhi for each atom type
// pbc_flag: 0 = nothing across a boundary, 1 = something across a boundary
// pbc = -1/0/1 for PBC factor in each of 3/6 orthogonal/triclinic dirs
// for triclinic, slablo/hi and pbc_border will be used in lamda (0-1) coords
// 1st part of if statement is sending to the west/south/down
// 2nd part of if statement is sending to the east/north/up
int dim,ineed;
int iswap = 0;
for (dim = 0; dim < 3; dim++) {
for (ineed = 0; ineed < 2*maxneed[dim]; ineed++) {
pbc_flag[iswap] = 0;
pbc[iswap][0] = pbc[iswap][1] = pbc[iswap][2] =
pbc[iswap][3] = pbc[iswap][4] = pbc[iswap][5] = 0;
if (ineed % 2 == 0) {
sendproc[iswap] = procneigh[dim][0];
recvproc[iswap] = procneigh[dim][1];
if (mode == Comm::SINGLE) {
if (ineed < 2) slablo[iswap] = -BIG;
else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
slabhi[iswap] = sublo[dim] + cutghost[dim];
} else if (mode == Comm::MULTI) {
for (i = 0; i < ncollections; i++) {
if (ineed < 2) multilo[iswap][i] = -BIG;
else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim];
}
} else {
for (i = 1; i <= ntypes; i++) {
if (ineed < 2) multioldlo[iswap][i] = -BIG;
else multioldlo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
multioldhi[iswap][i] = sublo[dim] + cutghostmultiold[i][dim];
}
}
if (myloc[dim] == 0) {
pbc_flag[iswap] = 1;
pbc[iswap][dim] = 1;
if (triclinic) {
if (dim == 1) pbc[iswap][5] = 1;
else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = 1;
}
}
} else {
sendproc[iswap] = procneigh[dim][1];
recvproc[iswap] = procneigh[dim][0];
if (mode == Comm::SINGLE) {
slablo[iswap] = subhi[dim] - cutghost[dim];
if (ineed < 2) slabhi[iswap] = BIG;
else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
} else if (mode == Comm::MULTI) {
for (i = 0; i < ncollections; i++) {
multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim];
if (ineed < 2) multihi[iswap][i] = BIG;
else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
}
} else {
for (i = 1; i <= ntypes; i++) {
multioldlo[iswap][i] = subhi[dim] - cutghostmultiold[i][dim];
if (ineed < 2) multioldhi[iswap][i] = BIG;
else multioldhi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
}
}
if (myloc[dim] == procgrid[dim]-1) {
pbc_flag[iswap] = 1;
pbc[iswap][dim] = -1;
if (triclinic) {
if (dim == 1) pbc[iswap][5] = -1;
else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = -1;
}
}
}
iswap++;
}
}
}
/* ----------------------------------------------------------------------
walk up/down the extent of nearby processors in dim and dir
loc = myloc of proc to start at
dir = 0/1 = walk to left/right
do not cross non-periodic boundaries
is not called for z dim in 2d
return how many procs away are needed to encompass cutghost away from loc
------------------------------------------------------------------------- */
int CommBrick::updown(int dim, int dir, int loc, double prd, int periodicity, double *split)
{
int index,count;
double frac,delta;
if (dir == 0) {
frac = cutghost[dim]/prd;
index = loc - 1;
delta = 0.0;
count = 0;
while (delta < frac) {
if (index < 0) {
if (!periodicity) break;
index = procgrid[dim] - 1;
}
count++;
delta += split[index+1] - split[index];
index--;
}
} else {
frac = cutghost[dim]/prd;
index = loc + 1;
delta = 0.0;
count = 0;
while (delta < frac) {
if (index >= procgrid[dim]) {
if (!periodicity) break;
index = 0;
}
count++;
delta += split[index+1] - split[index];
index++;
}
}
return count;
}
/* ----------------------------------------------------------------------
forward communication of atom coords every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
void CommBrick::forward_comm(int /*dummy*/)
{
int n;
MPI_Request request;
AtomVec *avec = atom->avec;
double **x = atom->x;
double *buf;
// exchange data with another proc
// if other proc is self, just copy
// if comm_x_only set, exchange or copy directly to x, don't unpack
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap] != me) {
if (comm_x_only) {
if (size_forward_recv[iswap]) {
buf = x[firstrecv[iswap]];
MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request);
}
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE);
} else if (ghost_velocity) {
if (size_forward_recv[iswap])
MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,recvproc[iswap],0,world,&request);
n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE);
avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
} else {
if (size_forward_recv[iswap])
MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE);
avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
} else {
if (comm_x_only) {
if (sendnum[iswap])
avec->pack_comm(sendnum[iswap],sendlist[iswap],
x[firstrecv[iswap]],pbc_flag[iswap],pbc[iswap]);
} else if (ghost_velocity) {
avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send);
} else {
avec->pack_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
}
}
}
}
/* ----------------------------------------------------------------------
reverse communication of forces on atoms every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
void CommBrick::reverse_comm()
{
int n;
MPI_Request request;
AtomVec *avec = atom->avec;
double **f = atom->f;
double *buf;
// exchange data with another proc
// if other proc is self, just copy
// if comm_f_only set, exchange or copy directly from f, don't pack
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap] != me) {
if (comm_f_only) {
if (size_reverse_recv[iswap])
MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request);
if (size_reverse_send[iswap]) {
buf = f[firstrecv[iswap]];
MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
}
if (size_reverse_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE);
} else {
if (size_reverse_recv[iswap])
MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,sendproc[iswap],0,world,&request);
n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
if (size_reverse_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE);
}
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv);
} else {
if (comm_f_only) {
if (sendnum[iswap])
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],f[firstrecv[iswap]]);
} else {
avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
}
}
}
}
/* ----------------------------------------------------------------------
exchange: move atoms to correct processors
atoms exchanged with all 6 stencil neighbors
send out atoms that have left my box, receive ones entering my box
atoms will be lost if not inside a stencil proc's box
can happen if atom moves outside of non-periodic boundary
or if atom moves more than one proc away
this routine called before every reneighboring
for triclinic, atoms must be in lamda coords (0-1) before exchange is called
------------------------------------------------------------------------- */
void CommBrick::exchange()
{
int i,m,nsend,nrecv,nrecv1,nrecv2,nlocal;
double lo,hi,value;
double **x;
double *sublo,*subhi;
MPI_Request request;
AtomVec *avec = atom->avec;
// clear global->local map for owned and ghost atoms
// b/c atoms migrate to new procs in exchange() and
// new ghosts are created in borders()
// map_set() is done at end of borders()
// clear ghost count and any ghost bonus data internal to AtomVec
if (map_style != Atom::MAP_NONE) atom->map_clear();
atom->nghost = 0;
atom->avec->clear_bonus();
// ensure send buf has extra space for a single atom
// only need to reset if a fix can dynamically add to size of single atom
if (maxexchange_fix_dynamic) {
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
}
// subbox bounds for orthogonal or triclinic
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
// loop over dimensions
int dimension = domain->dimension;
for (int dim = 0; dim < dimension; dim++) {
// fill buffer with atoms leaving my box, using < and >=
// when atom is deleted, fill it in with last atom
x = atom->x;
lo = sublo[dim];
hi = subhi[dim];
nlocal = atom->nlocal;
i = nsend = 0;
while (i < nlocal) {
if (x[i][dim] < lo || x[i][dim] >= hi) {
if (nsend > maxsend) grow_send(nsend,1);
nsend += avec->pack_exchange(i,&buf_send[nsend]);
avec->copy(nlocal-1,i,1);
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
// send/recv atoms in both directions
// send size of message first so receiver can realloc buf_recv if needed
// if 1 proc in dimension, no send/recv
// set nrecv = 0 so buf_send atoms will be lost
// if 2 procs in dimension, single send/recv
// if more than 2 procs in dimension, send/recv to both neighbors
if (procgrid[dim] == 1) nrecv = 0;
else {
MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][0],0,
&nrecv1,1,MPI_INT,procneigh[dim][1],0,world,MPI_STATUS_IGNORE);
nrecv = nrecv1;
if (procgrid[dim] > 2) {
MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0,
&nrecv2,1,MPI_INT,procneigh[dim][0],0,world,MPI_STATUS_IGNORE);
nrecv += nrecv2;
}
if (nrecv > maxrecv) grow_recv(nrecv);
MPI_Irecv(buf_recv,nrecv1,MPI_DOUBLE,procneigh[dim][1],0,world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][0],0,world);
MPI_Wait(&request,MPI_STATUS_IGNORE);
if (procgrid[dim] > 2) {
MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world);
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
}
// check incoming atoms to see if they are in my box
// if so, add to my list
// box check is only for this dimension,
// atom may be passed to another proc in later dims
m = 0;
while (m < nrecv) {
value = buf_recv[m+dim+1];
if (value >= lo && value < hi) m += avec->unpack_exchange(&buf_recv[m]);
else m += static_cast<int> (buf_recv[m]);
}
}
if (atom->firstgroupname) atom->first_reorder();
}
/* ----------------------------------------------------------------------
borders: list nearby atoms to send to neighboring procs at every timestep
one list is created for every swap that will be made
as list is made, actually do swaps
this does equivalent of a forward_comm(), so don't need to explicitly
call forward_comm() on reneighboring timestep
this routine is called before every reneighboring
for triclinic, atoms must be in lamda coords (0-1) before borders is called
------------------------------------------------------------------------- */
void CommBrick::borders()
{
int i,n,itype,icollection,iswap,dim,ineed,twoneed;
int nsend,nrecv,sendflag,nfirst,nlast,ngroup,nprior;
double lo,hi;
int *type;
int *collection;
double **x;
double *buf,*mlo,*mhi;
MPI_Request request;
AtomVec *avec = atom->avec;
// After exchanging/sorting, need to reconstruct collection array for border communication
if (mode == Comm::MULTI) neighbor->build_collection(0);
// do swaps over all 3 dimensions
iswap = 0;
smax = rmax = 0;
for (dim = 0; dim < 3; dim++) {
nlast = 0;
twoneed = 2*maxneed[dim];
for (ineed = 0; ineed < twoneed; ineed++) {
// find atoms within slab boundaries lo/hi using <= and >=
// check atoms between nfirst and nlast
// for first swaps in a dim, check owned and ghost
// for later swaps in a dim, only check newly arrived ghosts
// store sent atom indices in sendlist for use in future timesteps
x = atom->x;
if (mode == Comm::SINGLE) {
lo = slablo[iswap];
hi = slabhi[iswap];
} else if (mode == Comm::MULTI) {
collection = neighbor->collection;
mlo = multilo[iswap];
mhi = multihi[iswap];
} else {
type = atom->type;
mlo = multioldlo[iswap];
mhi = multioldhi[iswap];
}
if (ineed % 2 == 0) {
nfirst = nlast;
nlast = atom->nlocal + atom->nghost;
}
nsend = 0;
// sendflag = 0 if I do not send on this swap
// sendneed test indicates receiver no longer requires data
// e.g. due to non-PBC or non-uniform sub-domains
if (ineed/2 >= sendneed[dim][ineed % 2]) sendflag = 0;
else sendflag = 1;
// find send atoms according to SINGLE vs MULTI
// all atoms eligible versus only atoms in bordergroup
// can only limit loop to bordergroup for first sends (ineed < 2)
// on these sends, break loop in two: owned (in group) and ghost
if (sendflag) {
if (!bordergroup || ineed >= 2) {
if (mode == Comm::SINGLE) {
for (i = nfirst; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
} else if (mode == Comm::MULTI) {
for (i = nfirst; i < nlast; i++) {
icollection = collection[i];
if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
} else {
for (i = nfirst; i < nlast; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
}
} else {
if (mode == Comm::SINGLE) {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
for (i = atom->nlocal; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
} else if (mode == Comm::MULTI) {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
icollection = collection[i];
if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
for (i = atom->nlocal; i < nlast; i++) {
icollection = collection[i];
if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
} else {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
for (i = atom->nlocal; i < nlast; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
}
}
}
// pack up list of border atoms
if (nsend*size_border > maxsend) grow_send(nsend*size_border,0);
if (ghost_velocity)
n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
else
n = avec->pack_border(nsend,sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);
// swap atoms with other proc
// no MPI calls except SendRecv if nsend/nrecv = 0
// put incoming ghosts at end of my atom arrays
// if swapping with self, simply copy, no messages
if (sendproc[iswap] != me) {
MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
&nrecv,1,MPI_INT,recvproc[iswap],0,world,MPI_STATUS_IGNORE);
if (nrecv*size_border > maxrecv) grow_recv(nrecv*size_border);
if (nrecv) MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
recvproc[iswap],0,world,&request);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
if (nrecv) MPI_Wait(&request,MPI_STATUS_IGNORE);
buf = buf_recv;
} else {
nrecv = nsend;
buf = buf_send;
}
// unpack buffer
if (ghost_velocity)
avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
else
avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
// set all pointers & counters
smax = MAX(smax,nsend);
rmax = MAX(rmax,nrecv);
sendnum[iswap] = nsend;
recvnum[iswap] = nrecv;
size_forward_recv[iswap] = nrecv*size_forward;
size_reverse_send[iswap] = nrecv*size_reverse;
size_reverse_recv[iswap] = nsend*size_reverse;
firstrecv[iswap] = atom->nlocal + atom->nghost;
nprior = atom->nlocal + atom->nghost;
atom->nghost += nrecv;
if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior);
iswap++;
}
}
// For molecular systems we lose some bits for local atom indices due
// to encoding of special pairs in neighbor lists. Check for overflows.
if ((atom->molecular != Atom::ATOMIC)
&& ((atom->nlocal + atom->nghost) > NEIGHMASK))
error->one(FLERR,"Per-processor number of atoms is too large for "
"molecular neighbor lists");
// ensure send/recv buffers are long enough for all forward & reverse comm
int max = MAX(maxforward*smax,maxreverse*rmax);
if (max > maxsend) grow_send(max,0);
max = MAX(maxforward*rmax,maxreverse*smax);
if (max > maxrecv) grow_recv(max);
// reset global->local map
if (map_style != Atom::MAP_NONE) atom->map_set();
}
/* ----------------------------------------------------------------------
forward communication invoked by a Pair
nsize used only to set recv buffer limit
------------------------------------------------------------------------- */
void CommBrick::forward_comm(Pair *pair)
{
int iswap,n;
double *buf;
MPI_Request request;
int nsize = pair->comm_forward;
for (iswap = 0; iswap < nswap; iswap++) {
// pack buffer
n = pair->pack_forward_comm(sendnum[iswap],sendlist[iswap],buf_send,pbc_flag[iswap],pbc[iswap]);