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updated comm tiled to have multi

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This commit is contained in:
Diaz
2019-01-21 11:50:10 -05:00
parent bd3b712902
commit 9a3f90294c
1 changed files with 179 additions and 10 deletions
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189
src/comm_tiled.cpp
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@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author (multi) : Adrian Diaz (University of Florida)
------------------------------------------------------------------------- */
#include <cstring>
#include "comm_tiled.h"
#include "comm_brick.h"
@ -72,6 +76,9 @@ CommTiled::~CommTiled()
memory->destroy(overlap);
deallocate_swap(nswap);
memory->sfree(rcbinfo);
if (mode == Comm::MULTI) {
memory->destroy(cutghostmulti);
}
}
/* ----------------------------------------------------------------------
@ -80,6 +87,8 @@ CommTiled::~CommTiled()
void CommTiled::init_buffers()
{
sendbox_multi = NULL;
cutghostmulti = NULL;
// bufextra = max size of one exchanged atom
// = allowed overflow of sendbuf in exchange()
// atomvec, fix reset these 2 maxexchange values if needed
@ -108,12 +117,20 @@ void CommTiled::init()
{
Comm::init();
// memory for multi-style communication
int maxswap = 6;
if (mode == Comm::MULTI) {
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
}
if (mode == Comm::SINGLE && cutghostmulti) {
memory->destroy(cutghostmulti);
}
// temporary restrictions
if (triclinic)
error->all(FLERR,"Cannot yet use comm_style tiled with triclinic box");
if (mode == Comm::MULTI)
error->all(FLERR,"Cannot yet use comm_style tiled with multi-mode comm");
}
/* ----------------------------------------------------------------------
@ -124,7 +141,7 @@ void CommTiled::init()
void CommTiled::setup()
{
int i,j,n;
int ntypes = atom->ntypes;
// domain properties used in setup method and methods it calls
dimension = domain->dimension;
@ -157,9 +174,22 @@ 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;
if (mode == Comm::MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
cut = 0.0;
if (cutusermulti) cut = cutusermulti[i];
cutghostmulti[i][0] = MAX(cut,cuttype[i]);
cutghostmulti[i][1] = MAX(cut,cuttype[i]);
cutghostmulti[i][2] = MAX(cut,cuttype[i]);
}
}
cut = MAX(neighbor->cutneighmax,cutghostuser);
cutghost[0] = cutghost[1] = cutghost[2] = cut;
if ((periodicity[0] && cut > prd[0]) ||
(periodicity[1] && cut > prd[1]) ||
(dimension == 3 && periodicity[2] && cut > prd[2]))
@ -261,6 +291,7 @@ void CommTiled::setup()
grow_swap_send(iswap,nprocmax[iswap],oldmax);
if (idir == 0) grow_swap_recv(iswap+1,nprocmax[iswap]);
else grow_swap_recv(iswap-1,nprocmax[iswap]);
}
// overlap how has list of noverlap procs
@ -293,8 +324,8 @@ void CommTiled::setup()
// if sbox touches other proc's sub-box boundaries in lower dims,
// extend sbox in those lower dims to include ghost atoms
double oboxlo[3],oboxhi[3],sbox[6];
double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6];
if (mode == Comm::SINGLE) {
for (i = 0; i < noverlap; i++) {
pbc_flag[iswap][i] = 0;
pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
@ -342,7 +373,65 @@ void CommTiled::setup()
memcpy(sendbox[iswap][i],sbox,6*sizeof(double));
}
}
else{
for (i = 0; i < noverlap; i++) {
pbc_flag[iswap][i] = 0;
pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0;
(this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi);
if (i < noverlap1) {
sbox[0] = MAX(oboxlo[0],lo1[0]);
sbox[1] = MAX(oboxlo[1],lo1[1]);
sbox[2] = MAX(oboxlo[2],lo1[2]);
sbox[3] = MIN(oboxhi[0],hi1[0]);
sbox[4] = MIN(oboxhi[1],hi1[1]);
sbox[5] = MIN(oboxhi[2],hi1[2]);
} else {
pbc_flag[iswap][i] = 1;
if (idir == 0) pbc[iswap][i][idim] = 1;
else pbc[iswap][i][idim] = -1;
sbox[0] = MAX(oboxlo[0],lo2[0]);
sbox[1] = MAX(oboxlo[1],lo2[1]);
sbox[2] = MAX(oboxlo[2],lo2[2]);
sbox[3] = MIN(oboxhi[0],hi2[0]);
sbox[4] = MIN(oboxhi[1],hi2[1]);
sbox[5] = MIN(oboxhi[2],hi2[2]);
}
for (int itype = 1; itype <= atom->ntypes; itype++) {
sbox_multi[0] = sbox[0];
sbox_multi[1] = sbox[1];
sbox_multi[2] = sbox[2];
sbox_multi[3] = sbox[3];
sbox_multi[4] = sbox[4];
sbox_multi[5] = sbox[5];
if (idir == 0) {
sbox_multi[idim] = sublo[idim];
if (i < noverlap1) sbox_multi[3+idim] = MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]);
else sbox_multi[3+idim] = MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim],subhi[idim]);
} else {
if (i < noverlap1) sbox_multi[idim] = MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]);
else sbox_multi[idim] = MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim],sublo[idim]);
sbox_multi[3+idim] = subhi[idim];
}
if (idim >= 1) {
if (sbox_multi[0] == oboxlo[0]) sbox_multi[0] -= cutghostmulti[itype][idim];
if (sbox_multi[3] == oboxhi[0]) sbox_multi[3] += cutghostmulti[itype][idim];
}
if (idim == 2) {
if (sbox_multi[1] == oboxlo[1]) sbox_multi[1] -= cutghostmulti[itype][idim];
if (sbox_multi[4] == oboxhi[1]) sbox_multi[4] += cutghostmulti[itype][idim];
}
memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double));
}
}
}
iswap++;
}
}
@ -765,6 +854,7 @@ void CommTiled::borders()
double xlo,xhi,ylo,yhi,zlo,zhi;
double *bbox;
double **x;
AtomVec *avec = atom->avec;
// send/recv max one = max # of atoms in single send/recv for any swap
@ -790,6 +880,7 @@ void CommTiled::borders()
ncountall = 0;
for (m = 0; m < nsendproc[iswap]; m++) {
if (mode == Comm::SINGLE) {
bbox = sendbox[iswap][m];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
@ -829,6 +920,58 @@ void CommTiled::borders()
smaxone = MAX(smaxone,ncount);
ncountall += ncount;
}
else{
int* type=atom->type;
int itype;
ncount = 0;
if (!bordergroup) {
for (i = 0; i < nlast; i++) {
itype=type[i];
bbox = sendbox_multi[iswap][m][itype];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
} else {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
itype=type[i];
bbox = sendbox_multi[iswap][m][itype];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
for (i = atom->nlocal; i < nlast; i++) {
itype=type[i];
bbox = sendbox_multi[iswap][m][itype];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
}
sendnum[iswap][m] = ncount;
smaxone = MAX(smaxone,ncount);
ncountall += ncount;
}
}
smaxall = MAX(smaxall,ncountall);
// send sendnum counts to procs who recv from me except self
@ -1873,7 +2016,12 @@ void CommTiled::allocate_swap(int n)
pbc_flag = new int*[n];
pbc = new int**[n];
sendbox = new double**[n];
//if(mode == SINGLE){
sendbox = new double**[n];
//}
//else{
sendbox_multi = new double***[n];
//}
maxsendlist = new int*[n];
sendlist = new int**[n];
@ -1886,7 +2034,12 @@ void CommTiled::allocate_swap(int n)
pbc_flag[i] = NULL;
pbc[i] = NULL;
sendbox[i] = NULL;
//if(mode == SINGLE){
sendbox[i] = NULL;
// }
//else{
sendbox_multi[i] = NULL;
//}
maxsendlist[i] = NULL;
sendlist[i] = NULL;
}
@ -1933,8 +2086,14 @@ void CommTiled::grow_swap_send(int i, int n, int nold)
pbc_flag[i] = new int[n];
memory->destroy(pbc[i]);
memory->create(pbc[i],n,6,"comm:pbc_flag");
//if(mode == SINGLE){
memory->destroy(sendbox[i]);
memory->create(sendbox[i],n,6,"comm:sendbox");
//}
//else {
memory->destroy(sendbox_multi[i]);
memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi");
//}
delete [] maxsendlist[i];
maxsendlist[i] = new int[n];
@ -1992,7 +2151,12 @@ void CommTiled::deallocate_swap(int n)
delete [] pbc_flag[i];
memory->destroy(pbc[i]);
memory->destroy(sendbox[i]);
//if(mode == Comm::SINGLE){
memory->destroy(sendbox[i]);
// }
//else{
memory->destroy(sendbox_multi[i]);
// }
delete [] maxsendlist[i];
for (int j = 0; j < nprocmax[i]; j++) memory->destroy(sendlist[i][j]);
@ -2012,7 +2176,12 @@ void CommTiled::deallocate_swap(int n)
delete [] pbc_flag;
delete [] pbc;
delete [] sendbox;
//if(mode == SINGLE){
delete [] sendbox;
// }
//else{
delete [] sendbox_multi;
//}
delete [] maxsendlist;
delete [] sendlist;