forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12219 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
24f79216b1
commit
e4915201df
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@ -176,6 +176,8 @@ void CommTiled::init()
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/* ----------------------------------------------------------------------
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setup spatial-decomposition communication patterns
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function of neighbor cutoff(s) & cutghostuser & current box size and tiling
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sets nsendproc, nrecvproc, sendproc, recvproc
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sets sendother, sendself, pbc_flag, pbc, sendbox
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------------------------------------------------------------------------- */
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void CommTiled::setup()
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@ -203,7 +205,12 @@ void CommTiled::setup()
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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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// allocate overlap
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// NOTE: allocate overlap (to Nprocs?)
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// NOTE: allocate 2nd dim of sendproc, recvproc, sendbox
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// NOTE: func pointers for box_drop and box_other
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// NOTE: write box_drop and box_other methods
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// NOTE: for tiled, must do one-time gather of RCB cuts and proc boxes
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int *overlap;
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int noverlap,noverlap1,indexme;
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double lo1[3],hi1[3],lo2[3],hi2[3];
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@ -211,134 +218,155 @@ void CommTiled::setup()
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nswap = 0;
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for (int idim = 0; idim < dimension; idim++) {
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for (int iswap = 0; iswap < 2; iswap++) {
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// ghost box in lower direction
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// ghost box in lower direction
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one = 1;
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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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lo1[idim] = sublo[idim] - cut;
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hi1[idim] = sublo[idim];
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two = 0;
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if (periodicity[idim] && lo1[idim] < boxlo[idim]) {
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two = 1;
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lo2[0] = sublo[0]; lo2[1] = sublo[1]; lo2[2] = sublo[2];
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hi2[0] = subhi[0]; hi2[1] = subhi[1]; hi2[2] = subhi[2];
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lo2[idim] = lo1[idim] + prd[idim];
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hi2[idim] = hi1[idim] + prd[idim];
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if (sublo[idim] == boxlo[idim]) {
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one = 0;
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hi2[idim] = boxhi[idim];
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}
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}
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indexme = -1;
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noverlap = 0;
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if (one) {
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if (layout == LAYOUT_UNIFORM)
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box_drop_uniform(idim,lo1,hi1,noverlap,overlap,indexme);
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else if (layout == LAYOUT_NONUNIFORM)
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box_drop_nonuniform(idim,lo1,hi1,noverlap,overlap,indexme);
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else
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box_drop_tiled(lo1,hi1,0,nprocs-1,noverlap,overlap,indexme);
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}
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noverlap1 = noverlap;
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if (two) {
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if (layout == LAYOUT_UNIFORM)
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box_drop_uniform(idim,lo2,hi2,noverlap,overlap,indexme);
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else if (layout == LAYOUT_NONUNIFORM)
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box_drop_nonuniform(idim,lo2,hi2,noverlap,overlap,indexme);
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else
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box_drop_tiled(lo2,hi2,0,nprocs-1,noverlap,overlap,indexme);
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}
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// if this (self) proc is in overlap list, move it to end of list
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if (indexme >= 0) {
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int tmp = overlap[noverlap-1];
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overlap[noverlap-1] = overlap[indexme];
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overlap[indexme] = tmp;
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}
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// overlap how has list of noverlap procs
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// includes PBC effects
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if (overlap[noverlap-1] == me) sendself[nswap] = 1;
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else sendself[nswap] = 0;
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if (noverlap-sendself[nswap]) sendother[nswap] = 1;
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else sendother[nswap] = 0;
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nsendproc[nswap] = noverlap;
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for (i = 0; i < noverlap; i++) sendproc[nswap][i] = overlap[i];
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nrecvproc[nswap+1] = noverlap;
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for (i = 0; i < noverlap; i++) recvproc[nswap+1][i] = overlap[i];
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// compute sendbox for each of my sends
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// ibox = intersection of ghostbox with other proc's sub-domain
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// sendbox = ibox displaced by cutoff in dim
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// NOTE: need to extend send box in lower dims by cutoff
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// NOTE: this logic for overlapping boxes is not correct for sending
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double oboxlo[3],oboxhi[3],sbox[6];
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for (i = 0; i < noverlap; i++) {
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pbc_flag[nswap][i] = 0;
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pbc[nswap][i][0] = pbc[nswap][i][1] = pbc[nswap][i][2] =
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pbc[nswap][i][3] = pbc[nswap][i][4] = pbc[nswap][i][5] = 0;
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if (layout == LAYOUT_UNIFORM)
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box_other_uniform(overlap[i],oboxlo,oboxhi);
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else if (layout == LAYOUT_NONUNIFORM)
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box_other_nonuniform(overlap[i],oboxlo,oboxhi);
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else
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box_other_tiled(overlap[i],oboxlo,oboxhi);
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if (i < noverlap1) {
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sbox[0] = MAX(oboxlo[0],lo1[0]);
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sbox[1] = MAX(oboxlo[1],lo1[1]);
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sbox[2] = MAX(oboxlo[2],lo1[2]);
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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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sbox[idim] += cut;
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sbox[3+idim] += cut;
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if (sbox[idim] == lo1[idim]) sbox[idim] = sublo[idim];
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one = 1;
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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 (iswap == 0) {
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lo1[idim] = sublo[idim] - cut;
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hi1[idim] = sublo[idim];
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} else {
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pbc_flag[nswap][i] = 1;
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pbc[nswap][i][idim] = 1;
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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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sbox[3] = MIN(oboxhi[0],hi2[0]);
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sbox[4] = MIN(oboxhi[1],hi2[1]);
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sbox[5] = MIN(oboxhi[2],hi2[2]);
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sbox[idim] -= prd[idim] - cut;
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sbox[3+idim] -= prd[idim] + cut;
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if (sbox[idim] == lo1[idim]) sbox[idim] = sublo[idim];
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lo1[idim] = subhi[idim];
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hi1[idim] = subhi[idim] + cut;
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}
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if (idim >= 1) {
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if (sbox[0] == sublo[0]) sbox[0] -= cut;
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if (sbox[4] == subhi[0]) sbox[4] += cut;
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}
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if (idim == 2) {
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if (sbox[1] == sublo[1]) sbox[1] -= cut;
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if (sbox[5] == subhi[1]) sbox[5] += cut;
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two = 0;
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if (iswap == 0 && periodicity[idim] && lo1[idim] < boxlo[idim]) two = 1;
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if (iswap == 1 && periodicity[idim] && hi1[idim] > boxhi[idim]) two = 1;
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if (two) {
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lo2[0] = sublo[0]; lo2[1] = sublo[1]; lo2[2] = sublo[2];
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hi2[0] = subhi[0]; hi2[1] = subhi[1]; hi2[2] = subhi[2];
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if (iswap == 0) {
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lo2[idim] = lo1[idim] + prd[idim];
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hi2[idim] = hi1[idim] + prd[idim];
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if (sublo[idim] == boxlo[idim]) {
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one = 0;
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hi2[idim] = boxhi[idim];
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}
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} else {
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lo2[idim] = lo1[idim] - prd[idim];
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hi2[idim] = hi1[idim] - prd[idim];
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if (subhi[idim] == boxhi[idim]) {
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one = 0;
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lo2[idim] = boxlo[idim];
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}
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}
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}
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memcpy(sendbox[nswap][i],sbox,6*sizeof(double));
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indexme = -1;
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noverlap = 0;
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if (one) {
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if (layout == LAYOUT_UNIFORM)
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box_drop_uniform(idim,lo1,hi1,noverlap,overlap,indexme);
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else if (layout == LAYOUT_NONUNIFORM)
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box_drop_nonuniform(idim,lo1,hi1,noverlap,overlap,indexme);
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else
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box_drop_tiled(lo1,hi1,0,nprocs-1,noverlap,overlap,indexme);
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}
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noverlap1 = noverlap;
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if (two) {
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if (layout == LAYOUT_UNIFORM)
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box_drop_uniform(idim,lo2,hi2,noverlap,overlap,indexme);
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else if (layout == LAYOUT_NONUNIFORM)
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box_drop_nonuniform(idim,lo2,hi2,noverlap,overlap,indexme);
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else
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box_drop_tiled(lo2,hi2,0,nprocs-1,noverlap,overlap,indexme);
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}
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// if this (self) proc is in overlap list, move it to end of list
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if (indexme >= 0) {
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int tmp = overlap[noverlap-1];
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overlap[noverlap-1] = overlap[indexme];
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overlap[indexme] = tmp;
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}
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// overlap how has list of noverlap procs
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// includes PBC effects
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if (overlap[noverlap-1] == me) sendself[nswap] = 1;
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else sendself[nswap] = 0;
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if (noverlap-sendself[nswap]) sendother[nswap] = 1;
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else sendother[nswap] = 0;
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nsendproc[nswap] = noverlap;
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for (i = 0; i < noverlap; i++) sendproc[nswap][i] = overlap[i];
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if (iswap == 0) {
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nrecvproc[nswap+1] = noverlap;
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for (i = 0; i < noverlap; i++) recvproc[nswap+1][i] = overlap[i];
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} else {
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nrecvproc[nswap-1] = noverlap;
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for (i = 0; i < noverlap; i++) recvproc[nswap-1][i] = overlap[i];
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}
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// compute sendbox for each of my sends
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// obox = intersection of ghostbox with other proc's sub-domain
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// sbox = what I need to send to other proc
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// = sublo to MIN(sublo+cut,subhi) in idim, for iswap = 0
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// = MIN(subhi-cut,sublo) to subhi in idim, for iswap = 1
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// = obox in other 2 dims
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// if sbox touches sub-box boundaries in lower dims,
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// extend sbox in those lower dims to include ghost atoms
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double oboxlo[3],oboxhi[3],sbox[6];
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for (i = 0; i < noverlap; i++) {
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pbc_flag[nswap][i] = 0;
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pbc[nswap][i][0] = pbc[nswap][i][1] = pbc[nswap][i][2] =
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pbc[nswap][i][3] = pbc[nswap][i][4] = pbc[nswap][i][5] = 0;
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if (layout == LAYOUT_UNIFORM)
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box_other_uniform(overlap[i],oboxlo,oboxhi);
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else if (layout == LAYOUT_NONUNIFORM)
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box_other_nonuniform(overlap[i],oboxlo,oboxhi);
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else
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box_other_tiled(overlap[i],oboxlo,oboxhi);
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if (i < noverlap1) {
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sbox[0] = MAX(oboxlo[0],lo1[0]);
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sbox[1] = MAX(oboxlo[1],lo1[1]);
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sbox[2] = MAX(oboxlo[2],lo1[2]);
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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[nswap][i] = 1;
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pbc[nswap][i][idim] = 1;
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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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sbox[3] = MIN(oboxhi[0],hi2[0]);
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sbox[4] = MIN(oboxhi[1],hi2[1]);
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sbox[5] = MIN(oboxhi[2],hi2[2]);
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}
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if (iswap == 0) {
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sbox[idim] = sublo[idim];
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sbox[3+idim] = MIN(sublo[idim]+cut,subhi[idim]);
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} else {
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sbox[idim] = MAX(subhi[idim]-cut,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] == sublo[0]) sbox[0] -= cut;
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if (sbox[4] == subhi[0]) sbox[4] += cut;
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}
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if (idim == 2) {
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if (sbox[1] == sublo[1]) sbox[1] -= cut;
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if (sbox[5] == subhi[1]) sbox[5] += cut;
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}
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memcpy(sendbox[nswap][i],sbox,6*sizeof(double));
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}
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nswap++;
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}
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// ghost box in upper direction
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nswap += 2;
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}
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@ -1064,7 +1092,7 @@ int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf)
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/* ----------------------------------------------------------------------
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determine overlap list of Noverlap procs the lo/hi box overlaps
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overlap = non-zero area in common between box and proc sub-domain
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box is onwed by me and extends in dim
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box is owned by me and extends in dim
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------------------------------------------------------------------------- */
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void CommTiled::box_drop_uniform(int dim, double *lo, double *hi,
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@ -1086,7 +1114,8 @@ void CommTiled::box_drop_nonuniform(int dim, double *lo, double *hi,
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/* ----------------------------------------------------------------------
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determine overlap list of Noverlap procs the lo/hi box overlaps
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overlap = non-zero area in common between box and proc sub-domain
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recursive routine for traversing an RCB tree of cuts
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recursive method for traversing an RCB tree of cuts
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no need to split lo/hi box as recurse b/c OK if box extends outside RCB box
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------------------------------------------------------------------------- */
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void CommTiled::box_drop_tiled(double *lo, double *hi,
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@ -1103,7 +1132,7 @@ void CommTiled::box_drop_tiled(double *lo, double *hi,
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}
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// drop box on each side of cut it extends beyond
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// use > and < criteria to not include procs it only touches
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// use > and < criteria so does not include a box it only touches
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// procmid = 1st processor in upper half of partition
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// = location in tree that stores this cut
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// dim = 0,1,2 dimension of cut
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