[WIP] add utility to convert plotfiles to openPMD w/ compression#1507
[WIP] add utility to convert plotfiles to openPMD w/ compression#1507BenWibking wants to merge 2 commits intodevelopmentfrom
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| void SetupMesh(openPMD::Mesh &mesh, const amrex::Geometry &geom, | ||
| const amrex::IntVect &nodal) { | ||
| amrex::Box const &global_box = geom.Domain(); | ||
| auto const global_size = ToReversedVector(global_box.size()); | ||
| auto const grid_spacing = ToReversedVector(geom.CellSize()); | ||
| auto const global_offset = ToReversedVector(geom.ProbLo()); |
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In SetupMesh the dataset extent is derived from geom.Domain().size() irrespective of whether the MultiFab is nodal (nodal_flags argument). For nodal/face/edge-centered variables the boxes returned by PlotFileData::get are one cell larger than the cell-centered domain, so global_size underestimates the dataset dimensions while storeChunkRaw later uses the larger nodal local_box.size(). When converting any nodal variable, the chunk offset/size will fall outside the declared dataset and the openPMD write will error or truncate data. Compute the dataset size from a nodal version of the domain (e.g., amrex::convert(geom.Domain(), nodal).size()) before creating the dataset.
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Description
This allows us to use convert AMReX plotfiles to openPMD/ADIOS2 with highly efficient lossy compression.
NOTE: Particles are IGNORED completely in the conversion process.
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