ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'master' into comm_tiled_sendself_fix

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-07-29 18:23:51 -04:00
parent 59ff6b7abc 2923dcbbd6
commit b402b00882
8870 changed files with 1724000 additions and 456647 deletions
Download Patch File Download Diff File Expand all files Collapse all files

69
src/comm_tiled.cpp
View File

@ -11,19 +11,17 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <cstring>
#include "comm_tiled.h"
#include "comm_brick.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "output.h"
#include "dump.h"
#include "memory.h"
#include "error.h"
@ -32,8 +30,7 @@ using namespace LAMMPS_NS;
#define BUFFACTOR 1.5
#define BUFFACTOR 1.5
#define BUFMIN 1000
#define BUFEXTRA 1000
#define BUFMIN 1024
#define EPSILON 1.0e-6
#define DELTA_PROCS 16
@ -80,17 +77,9 @@ CommTiled::~CommTiled()
void CommTiled::init_buffers()
{
// bufextra = max size of one exchanged atom
// = allowed overflow of sendbuf in exchange()
// atomvec, fix reset these 2 maxexchange values if needed
// only necessary if their size > BUFEXTRA
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
maxsend = BUFMIN;
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
maxrecv = BUFMIN;
buf_send = buf_recv = NULL;
maxsend = maxrecv = BUFMIN;
grow_send(maxsend,2);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
maxoverlap = 0;
@ -108,6 +97,10 @@ void CommTiled::init()
{
Comm::init();
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
// temporary restrictions
if (triclinic)
@ -157,7 +150,11 @@ void CommTiled::setup()
// set cutoff for comm forward and comm reverse
// check that cutoff < any periodic box length
double cut = MAX(neighbor->cutneighmax,cutghostuser);
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.");
cutghost[0] = cutghost[1] = cutghost[2] = cut;
if ((periodicity[0] && cut > prd[0]) ||
@ -621,7 +618,7 @@ void CommTiled::reverse_comm()
atoms exchanged with procs that touch sub-box in each of 3 dims
send out atoms that have left my box, receive ones entering my box
atoms will be lost if not inside a touching proc's box
can happen if atom moves outside of non-periodic bounary
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
@ -644,15 +641,14 @@ void CommTiled::exchange()
atom->nghost = 0;
atom->avec->clear_bonus();
// insure send buf is large enough for single atom
// bufextra = max size of one atom = allowed overflow of sendbuf
// fixes can change per-atom size requirement on-the-fly
// insure send buf has extra space for a single atom
// only need to reset if a fix can dynamically add to size of single atom
int bufextra_old = bufextra;
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
if (bufextra > bufextra_old)
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
if (maxexchange_fix_dynamic) {
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
}
// domain properties used in exchange method and methods it calls
// subbox bounds for orthogonal or triclinic
@ -1811,18 +1807,23 @@ int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR and bufextra
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
flag = 1, realloc with BUFFACTOR
flag = 2, free/malloc w/out BUFFACTOR
------------------------------------------------------------------------- */
void CommTiled::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
if (flag)
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
else {
if (flag == 0) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->destroy(buf_send);
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
} else if (flag == 1) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
} else {
memory->destroy(buf_send);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
}
}