enable CommStyle tiled and load-balancing to work for triclinic
This commit is contained in:
Steve Plimpton
@ -67,7 +67,7 @@ CommTiled::~CommTiled()
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memory->destroy(buf_send);
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memory->destroy(buf_recv);
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memory->destroy(overlap);
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deallocate_swap(nswap);
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deallocate_swap(maxswap);
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memory->sfree(rcbinfo);
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}
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@ -85,8 +85,8 @@ void CommTiled::init_buffers()
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maxoverlap = 0;
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overlap = NULL;
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nswap = 2 * domain->dimension;
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allocate_swap(nswap);
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maxswap = 6;
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allocate_swap(maxswap);
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rcbinfo = NULL;
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}
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@ -97,14 +97,14 @@ void CommTiled::init()
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{
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Comm::init();
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nswap = 2 * domain->dimension;
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int bufextra_old = bufextra;
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init_exchange();
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if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
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// temporary restrictions
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if (triclinic)
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error->all(FLERR,"Cannot yet use comm_style tiled with triclinic box");
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if (mode == Comm::MULTI)
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error->all(FLERR,"Cannot yet use comm_style tiled with multi-mode comm");
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}
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@ -121,14 +121,22 @@ void CommTiled::setup()
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// domain properties used in setup method and methods it calls
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dimension = domain->dimension;
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prd = domain->prd;
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boxlo = domain->boxlo;
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boxhi = domain->boxhi;
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sublo = domain->sublo;
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subhi = domain->subhi;
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int *periodicity = domain->periodicity;
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if (triclinic == 0) {
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prd = domain->prd;
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boxlo = domain->boxlo;
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boxhi = domain->boxhi;
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sublo = domain->sublo;
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subhi = domain->subhi;
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} else {
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prd = domain->prd_lamda;
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boxlo = domain->boxlo_lamda;
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boxhi = domain->boxhi_lamda;
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sublo = domain->sublo_lamda;
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subhi = domain->subhi_lamda;
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}
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// set function pointers
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if (layout != Comm::LAYOUT_TILED) {
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@ -155,11 +163,21 @@ void CommTiled::setup()
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error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
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"will be generated. Atoms may get lost.");
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cutghost[0] = cutghost[1] = cutghost[2] = cut;
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if (triclinic == 0) cutghost[0] = cutghost[1] = cutghost[2] = cut;
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else {
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double *h_inv = domain->h_inv;
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double length0,length1,length2;
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length0 = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]);
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cutghost[0] = cut * length0;
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length1 = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]);
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cutghost[1] = cut * length1;
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length2 = h_inv[2];
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cutghost[2] = cut * length2;
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}
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if ((periodicity[0] && cut > prd[0]) ||
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(periodicity[1] && cut > prd[1]) ||
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(dimension == 3 && periodicity[2] && cut > prd[2]))
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if ((periodicity[0] && cutghost[0] > prd[0]) ||
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(periodicity[1] && cutghost[1] > prd[1]) ||
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(dimension == 3 && periodicity[2] && cutghost[2] > prd[2]))
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error->all(FLERR,"Communication cutoff for comm_style tiled "
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"cannot exceed periodic box length");
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@ -174,6 +192,7 @@ void CommTiled::setup()
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cut = MIN(prd[0],prd[1]);
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if (dimension == 3) cut = MIN(cut,prd[2]);
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cut *= EPSILON*EPSILON;
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cutghost[0] = cutghost[1] = cutghost[2] = cut;
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}
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// setup forward/reverse communication
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@ -200,11 +219,11 @@ void CommTiled::setup()
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lo1[0] = sublo[0]; lo1[1] = sublo[1]; lo1[2] = sublo[2];
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hi1[0] = subhi[0]; hi1[1] = subhi[1]; hi1[2] = subhi[2];
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if (idir == 0) {
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lo1[idim] = sublo[idim] - cut;
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lo1[idim] = sublo[idim] - cutghost[idim];
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hi1[idim] = sublo[idim];
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} else {
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lo1[idim] = subhi[idim];
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hi1[idim] = subhi[idim] + cut;
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hi1[idim] = subhi[idim] + cutghost[idim];
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}
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two = 0;
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@ -306,10 +325,16 @@ void CommTiled::setup()
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sbox[3] = MIN(oboxhi[0],hi1[0]);
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sbox[4] = MIN(oboxhi[1],hi1[1]);
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sbox[5] = MIN(oboxhi[2],hi1[2]);
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} else {
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pbc_flag[iswap][i] = 1;
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if (idir == 0) pbc[iswap][i][idim] = 1;
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else pbc[iswap][i][idim] = -1;
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if (triclinic) {
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if (idim == 1) pbc[iswap][i][5] = pbc[iswap][i][idim];
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if (idim == 2) pbc[iswap][i][4] = pbc[iswap][i][3] = pbc[iswap][i][idim];
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}
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sbox[0] = MAX(oboxlo[0],lo2[0]);
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sbox[1] = MAX(oboxlo[1],lo2[1]);
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sbox[2] = MAX(oboxlo[2],lo2[2]);
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@ -320,21 +345,22 @@ void CommTiled::setup()
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if (idir == 0) {
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sbox[idim] = sublo[idim];
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if (i < noverlap1) sbox[3+idim] = MIN(sbox[3+idim]+cut,subhi[idim]);
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else sbox[3+idim] = MIN(sbox[3+idim]-prd[idim]+cut,subhi[idim]);
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if (i < noverlap1)
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sbox[3+idim] = MIN(sbox[3+idim]+cutghost[idim],subhi[idim]);
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else sbox[3+idim] = MIN(sbox[3+idim]-prd[idim]+cutghost[idim],subhi[idim]);
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} else {
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if (i < noverlap1) sbox[idim] = MAX(sbox[idim]-cut,sublo[idim]);
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else sbox[idim] = MAX(sbox[idim]+prd[idim]-cut,sublo[idim]);
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if (i < noverlap1) sbox[idim] = MAX(sbox[idim]-cutghost[idim],sublo[idim]);
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else sbox[idim] = MAX(sbox[idim]+prd[idim]-cutghost[idim],sublo[idim]);
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sbox[3+idim] = subhi[idim];
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}
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if (idim >= 1) {
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if (sbox[0] == oboxlo[0]) sbox[0] -= cut;
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if (sbox[3] == oboxhi[0]) sbox[3] += cut;
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if (sbox[0] == oboxlo[0]) sbox[0] -= cutghost[0];
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if (sbox[3] == oboxhi[0]) sbox[3] += cutghost[0];
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}
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if (idim == 2) {
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if (sbox[1] == oboxlo[1]) sbox[1] -= cut;
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if (sbox[4] == oboxhi[1]) sbox[4] += cut;
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if (sbox[1] == oboxlo[1]) sbox[1] -= cutghost[1];
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if (sbox[4] == oboxhi[1]) sbox[4] += cutghost[1];
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}
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memcpy(sendbox[iswap][i],sbox,6*sizeof(double));
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@ -344,6 +370,7 @@ void CommTiled::setup()
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}
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}
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// setup exchange communication = subset of forward/reverse comm procs
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// loop over dimensions
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// determine which procs I will exchange with in each dimension
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@ -653,14 +680,16 @@ void CommTiled::exchange()
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// domain properties used in exchange method and methods it calls
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// subbox bounds for orthogonal or triclinic
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prd = domain->prd;
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boxlo = domain->boxlo;
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boxhi = domain->boxhi;
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if (triclinic == 0) {
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prd = domain->prd;
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boxlo = domain->boxlo;
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boxhi = domain->boxhi;
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sublo = domain->sublo;
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subhi = domain->subhi;
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} else {
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prd = domain->prd_lamda;
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boxlo = domain->boxlo_lamda;
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boxhi = domain->boxhi_lamda;
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sublo = domain->sublo_lamda;
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subhi = domain->subhi_lamda;
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}
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@ -687,7 +716,11 @@ void CommTiled::exchange()
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if (proc != me) {
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buf_send[nsend++] = proc;
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nsend += avec->pack_exchange(i,&buf_send[nsend]);
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}
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} else {
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// DEBUG statment
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// error->warning(FLERR,"Losing atom in CommTiled::exchange() send, "
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// "likely bad dynamics");
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}
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avec->copy(nlocal-1,i,1);
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nlocal--;
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} else i++;
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@ -736,7 +769,10 @@ void CommTiled::exchange()
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if (value >= lo && value < hi) {
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m += avec->unpack_exchange(&buf_recv[m]);
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continue;
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}
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} else {
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// DEBUG statment
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// error->warning(FLERR,"Losing atom in CommTiled::exchange() recv");
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}
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}
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m += static_cast<int> (buf_recv[m]);
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}
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@ -785,6 +821,7 @@ void CommTiled::borders()
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if (iswap % 2 == 0) nlast = atom->nlocal + atom->nghost;
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ncountall = 0;
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for (m = 0; m < nsendproc[iswap]; m++) {
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bbox = sendbox[iswap][m];
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xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
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