[Draft] AMR support for particles with terrain-following coordinates#3082
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debog wants to merge 22 commits intoerf-model:developmentfrom
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[Draft] AMR support for particles with terrain-following coordinates#3082debog wants to merge 22 commits intoerf-model:developmentfrom
debog wants to merge 22 commits intoerf-model:developmentfrom
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Instead of aborting when user-specified refinement box indices are not divisible by ref_ratio, automatically snap lo indices down and hi indices up to the nearest aligned value, with a diagnostic print.
ERF_InitCustomPertVels_ParticleTests.H accessed z_nd at the full domain khi+1, which is out of bounds for partial-z L1 boxes. Use geomdata.ProbHi()[2] for the domain top height instead. ERF_InitCustomPert_ParticleTests.H had an assertion requiring the box to span the full z-domain, which fails with partial-z AMR. Removed the assertion and unused khi variable.
Add terrain-aware k-index fixing (FixKIndexAMR) and per-level Redistribute for particles on refined levels. Add ExtractAndRouteOORParticles to handle particles escaping the fine level z-extent in partial-z refinement by recomputing k-indices for the target level. Add compute_k_from_z for uniform and stretched vertical grids. Add k-clamping in ERFParticlesAssignor and bounds checks in AdvectWithFlow and ComputeTemperature. Use terrain-aware Redistribute(z_phys_nd) in post_timestep and after regrid. Remove premature Redistribute calls from MakeNewLevel functions.
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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…l-by-level Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
asalmgren
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Apr 8, 2026
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Enables tracer particles (and any
ERFPC-based species) to work correctly with AMR, including partial-z refinement and terrain-following coordinates.Tagging: Auto-snap refinement box indices to
ref_ratioalignment instead of aborting when user-specified box coordinates don't produce aligned indices.Particle advection with AMR: On level 0,
Redistribute(0,0)keeps particles local. On fine levels,ExtractAndRouteOORParticleshandles particles escaping the fine level's z-extent by recomputing k-indices for the target level before per-level redistribute.FixKIndexAMRrecomputes terrain-aware k-indices after regrid.compute_k_from_zsupports both uniform and stretched vertical grids.Cell assignor:
ERFParticlesAssignornow clamps k to domain bounds so that out-of-range particles survive untilExtractAndRouteOORParticlescan route them. AddedGetParticleBinERFbinner struct forDenseBins.Bounds checks:
AdvectWithFlowguards against out-of-bounds terrain stencil access (k+2 >= z_nd extent) and NaN velocities.ComputeTemperatureskips interpolation for particles whose k-index is outside the local z_nd range.Redistribute plumbing:
ParticleData::Redistribute(z_phys_nd)callsFixKIndexAMRper species.post_timestepand post-regrid paths use the terrain-aware overload. PrematureRedistribute()calls removed fromMakeNewLevelFromScratchandRemakeLevel.InitCustomPert fixes: Removed
AMREX_ALWAYS_ASSERT(bx.length()[2] == khi+1)inERF_InitCustomPert_ParticleTests.H(fails for partial-z boxes). FixedERF_InitCustomPertVels_ParticleTests.Hto useProbHi[2]for domain top instead ofz_nd(i,j,khi+1)which is out of bounds for partial-z L1.Diagnostics: Per-level particle counts printed in
EvolveParticles. Verbose level read from<species_name>.verbosein inputs.Example input files: Added 4 tracer particle advection test cases in
Exec/RegTests/ParticleTests/— flat terrain and Witch-of-Agnesi hill, each with full-z and partial-z AMR1 refinement (ref_ratio 2 1 2, box-tagged L1 covering x=[4,6]).