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OutputParticles work #339

Merged
merged 49 commits into from
Aug 30, 2024
Merged

OutputParticles work #339

merged 49 commits into from
Aug 30, 2024

Commits on Aug 29, 2024

  1. build: add .venv to .gitignore

    @germasch
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  2. build: fix various warnings

    @germasch
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  3. outp: psc_flatfoil_small: output particles every 4 steps; for half of… 

    … the domain only
    @germasch
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  4. outp: put particles at x=1 and x=40 

    So that they are in different cells.
    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  5. outp/hdf5: use MPI_UNSIGNED_LONG to avoid warning

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  6. outp/hdf5: compute wdims in impl class

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  7. outp/hdf5: use std::vector for off, map, idx

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  8. outp/hdf5: pass off, map, idx as std::vector

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  9. outp/hdf5: std::vector for off2

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  10. outp/hdf5: fix swapped off, map args 

    Fortunately they were swapped throughout, so very confusing but not an
actual bug...
    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  11. outp/hdf5: use std::vector<std::vector<int>> for off, map

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  12. outp/hdf5: use std::vector for gidx_{begin,end}

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  13. outp/hdf5: much easier to init to -1 now

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  14. outp/hdf5: use std::vector for idx

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  15. outp/hdf5: consolidate sort_index()

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  16. outp/hdf5: pass just the data to write_idx()

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  17. outp/hdf5: use 4-d xtensor arrays for gidx_{begin,end}

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  18. outp/hdf5: access idx as 5-d through gtensor

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  19. outp/hdf5: idx directly gtensor-based

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  20. outp/hdf5: use std::vector some more

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  21. outp/hdf5: more std::vector

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  22. outp/hdf5: remote_sz as std::vector

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  23. outp/hdf5: std::vector for lidx

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  24. outp/hdf5: use loop over dims in get_sort_index()

    @germasch
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  25. outp/hdf5: std::vector for temp array of particles

    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  26. outp: use 2 patches in test, one particle each 

    should work on 2 MPI procs now, too.
    @germasch
    Kai Germaschewski authored and germasch committed Aug 29, 2024
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  27. outp: pass gidx_{begin,end} as gtensor's to write_idx()

    @germasch
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  28. outp: start a separate write_hdf5() function 

    The goal being to have the hdf5 specific stuff in one place
    @germasch
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  29. outp: all of the writing is now in write_hdf5()

    @germasch
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  30. outp/hdf5: start OutputParticlesWriterHDF5 class 

    That will eventually do all HDF5 specific writing
    @germasch
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  31. outp/hdf5: all writing -> OutputParticlesWriterHDF5 class

    @germasch
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  32. outp/hdf5: move Hdf5ParticleType class

    @germasch
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  33. outp/hdf5: keep writer around through life of class

    @germasch
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  34. outp/hdf5: don't keep prt_type_ in intermediate class

    @germasch
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  35. outp/hdf5: keep writer in top-level class 

    so that it's persistent and can, next, take care of creating the
hdf5 particle type
    @germasch
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  36. outp/hdf5: particle type now within WriterHDF5

    @germasch
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  37. outp/hdf5: prettify H5Type helper

    @germasch
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  38. outp/hdf5: avoid using hdf5_prt directly

    @germasch
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  39. outp/hdf5: do conversion to hdf5_prt in constructor

    @germasch
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  40. outp/hdf5: use std::{min,max}

    @germasch
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  41. outp/hdf5: pass/keep Params around

    @germasch
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  42. outp/hdf5: make filename inside of Writer

    @germasch
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  43. outp/hdf5: adjust hi initially in Params 

    So we don't need to keep passing this otherwise redundant info around.
    @germasch
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  44. outp/hdf5: Consistently use params instead of prm

    @germasch
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  45. outp/hdf5: rename {rank,size} -> mpi_{rank,size}

    @germasch
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  46. outp/hdf5: don't need to count all particles 

    Since we already know how many particles we have on a proc.
    @germasch
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  47. outp/hdf5: don't pass redundant n_write 

    The number of particles is arr.size()
    @germasch
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  48. outp/hdf5: loop over particle by index

    @germasch
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  49. outp/hdf5: add template argument for particle selector 

    This particle selector decides whether to include a given particle in the
output. Other than the trivial ParticleSelectorAll,
ParticleSelectorEveryNth<N> is provided ot select every nth particle.
    @germasch
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