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Fix order of bins for neighbor list construction #3195

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Fix order of bins for neighbor list construction #3195

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32c12e5
fix order of bins for neighbor list construction
atmyers Mar 10, 2023
bb3e1d4
a couple that I missed
atmyers Mar 10, 2023
0c5f182
change order of for loops too
atmyers Mar 11, 2023
adf95f1
Fix loops correctly
atmyers Mar 13, 2023
7b40abf
merging
atmyers Jul 22, 2024
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6 changes: 3 additions & 3 deletions Src/Particle/AMReX_DenseBins.H
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Original file line number Diff line number Diff line change
Expand Up @@ -185,7 +185,7 @@ public:
index_type uix = amrex::min(nx-1,amrex::max(0,iv3.x));
index_type uiy = amrex::min(ny-1,amrex::max(0,iv3.y));
index_type uiz = amrex::min(nz-1,amrex::max(0,iv3.z));
return (uix * ny + uiy) * nz + uiz;
return (uiz * ny + uiy) * nx + uix;
});
}

Expand Down Expand Up @@ -289,7 +289,7 @@ public:
index_type uix = amrex::min(nx-1,amrex::max(0,iv3.x));
index_type uiy = amrex::min(ny-1,amrex::max(0,iv3.y));
index_type uiz = amrex::min(nz-1,amrex::max(0,iv3.z));
return (uix * ny + uiy) * nz + uiz;
return (uiz * ny + uiy) * nx + uix;
});
}

Expand Down Expand Up @@ -428,7 +428,7 @@ public:
index_type uix = amrex::min(nx-1,amrex::max(0,iv3.x));
index_type uiy = amrex::min(ny-1,amrex::max(0,iv3.y));
index_type uiz = amrex::min(nz-1,amrex::max(0,iv3.z));
return (uix * ny + uiy) * nz + uiz;
return (uiz * ny + uiy) * nx + uix;
});
}

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12 changes: 6 additions & 6 deletions Src/Particle/AMReX_NeighborList.H
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Original file line number Diff line number Diff line change
Expand Up @@ -368,10 +368,10 @@ public:
int ny = hi_p[type].y-lo_p[type].y+1;
int nz = hi_p[type].z-lo_p[type].z+1;

for (int ii = amrex::max(ix-num_cells, 0); ii <= amrex::min(ix+num_cells, nx-1); ++ii) {
for (int kk = amrex::max(iz-num_cells, 0); kk <= amrex::min(iz+num_cells, nz-1); ++kk) {
for (int jj = amrex::max(iy-num_cells, 0); jj <= amrex::min(iy+num_cells, ny-1); ++jj) {
for (int kk = amrex::max(iz-num_cells, 0); kk <= amrex::min(iz+num_cells, nz-1); ++kk) {
int index = (ii * ny + jj) * nz + kk + off_bins;
for (int ii = amrex::max(ix-num_cells, 0); ii <= amrex::min(ix+num_cells, nx-1); ++ii) {
int index = (kk * ny + jj) * nx + ii + off_bins;
for (auto p = poffset[index]; p < poffset[index+1]; ++p) {
const auto& pid = pperm[p];
bool ghost_pid = (pid >= np_real);
Expand Down Expand Up @@ -428,10 +428,10 @@ public:
int ny = hi_p[type].y-lo_p[type].y+1;
int nz = hi_p[type].z-lo_p[type].z+1;

for (int ii = amrex::max(ix-num_cells, 0); ii <= amrex::min(ix+num_cells, nx-1); ++ii) {
for (int kk = amrex::max(iz-num_cells, 0); kk <= amrex::min(iz+num_cells, nz-1); ++kk) {
for (int jj = amrex::max(iy-num_cells, 0); jj <= amrex::min(iy+num_cells, ny-1); ++jj) {
for (int kk = amrex::max(iz-num_cells, 0); kk <= amrex::min(iz+num_cells, nz-1); ++kk) {
int index = (ii * ny + jj) * nz + kk + off_bins;
for (int ii = amrex::max(ix-num_cells, 0); ii <= amrex::min(ix+num_cells, nx-1); ++ii) {
int index = (kk * ny + jj) * nx + ii + off_bins;
for (auto p = poffset[index]; p < poffset[index+1]; ++p) {
const auto& pid = pperm[p];
bool ghost_pid = (pid >= np_real);
Expand Down
6 changes: 3 additions & 3 deletions Src/Particle/AMReX_NeighborParticlesI.H
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Expand Up @@ -1054,11 +1054,11 @@ selectActualNeighbors (CheckPair&& check_pair, int num_cells)
int nz = hi.z-lo.z+1;

bool isActualNeighbor = false;
for (int ii = amrex::max(ix-num_cells, 0); ii <= amrex::min(ix+num_cells, nx); ++ii) {
for (int kk = amrex::max(iz-num_cells, 0); kk <= amrex::min(iz+num_cells, nz); ++kk) {
for (int jj = amrex::max(iy-num_cells, 0); jj <= amrex::min(iy+num_cells, ny); ++jj) {
for (int kk = amrex::max(iz-num_cells, 0); kk <= amrex::min(iz+num_cells, nz); ++kk) {
for (int ii = amrex::max(ix-num_cells, 0); ii <= amrex::min(ix+num_cells, nx); ++ii) {
if (isActualNeighbor) break;
int nbr_cell_id = (ii * ny + jj) * nz + kk;
int nbr_cell_id = (kk * ny + jj) * nx + ii;
for (auto p = poffset[nbr_cell_id]; p < poffset[nbr_cell_id+1]; ++p) {
if (pperm[p] == i) continue;
if (call_check_pair(check_pair, ptile_data, ptile_data, i, pperm[p])) {
Expand Down
6 changes: 3 additions & 3 deletions Src/Particle/AMReX_ParticleLocator.H
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Expand Up @@ -64,10 +64,10 @@ struct AssignGrid
int iy_hi = amrex::min((lo.y + nGrow - m_lo.y) / m_bin_size.y, m_num_bins.y-1);
int iz_hi = amrex::min((lo.z + nGrow - m_lo.z) / m_bin_size.z, m_num_bins.z-1);
int loc = -1;
for (int ii = ix_lo; ii <= ix_hi; ++ii) {
for (int kk = iz_lo; kk <= iz_hi; ++kk) {
for (int jj = iy_lo; jj <= iy_hi; ++jj) {
for (int kk = iz_lo; kk <= iz_hi; ++kk) {
int index = (ii * m_num_bins.y + jj) * m_num_bins.z + kk;
for (int ii = ix_lo; ii <= ix_hi; ++ii) {
int index = (kk * m_num_bins.y + jj) * m_num_bins.x + ii;
for (const auto& nbor : m_bif.getBinIterator(index)) {
Box bx = nbor.second;
if (bx.contains(iv)) {
Expand Down
2 changes: 1 addition & 1 deletion Src/Particle/AMReX_ParticleUtil.H
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Original file line number Diff line number Diff line change
Expand Up @@ -498,7 +498,7 @@ struct BinMapper
int uix = amrex::min(nx-1,amrex::max(0,iv3.x));
int uiy = amrex::min(ny-1,amrex::max(0,iv3.y));
int uiz = amrex::min(nz-1,amrex::max(0,iv3.z));
return static_cast<unsigned int>( (uix * ny + uiy) * nz + uiz + offset );
return static_cast<unsigned int>( (uiz * ny + uiy) * nx + uix + offset );
}

private:
Expand Down