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V0.1 #7

Merged
merged 37 commits into from
Oct 30, 2024
Merged

V0.1 #7

merged 37 commits into from
Oct 30, 2024

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Benncs
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@Benncs Benncs commented Oct 30, 2024

Summary

October 2024 working version

The Monod model and basic uptake system have been successfully implemented and are functional under batch and continuous reactor configurations, supporting 0D, 1D, and 3D simulations. Oxygen mass transfer processes are also operational.

Content

  • Scope:

    • Code: (if relevant, add affected target)
    • Build script: (if relevant, add affected target)
    • Documentation
    • CI
    • Repository
    • Other: ...

  • Type of Change:

    • New feature(s)
    • Fix: (if relevant, add issue #...)
    • Testing
    • Refactor
    • Revert
    • Chore

  • Other:

    • Breaking change
    • New dependency

  • Necessary Follow-up:

    • Needs documentation
    • Needs testing
    • Other: ...

Casale Benjamin and others added 30 commits September 4, 2024 08:38
separate core from cli + start doc
544de61
pass lib from .so to .a
f682af0
add custom initialiser feature
3f2bbd8
check rd perf + clean wrap cereal dep
03a1df0
start implementing cereal serialization
8c2c515
Improve post process package + check monod model
8dc31d2
improve way to get particle properties with kokkos_view in post_proce…
d75a6a6 
…ss and data_exporter
Refractor kernel into functor + reduce branching in move process + ch…
9ae456c 
…eck cstr simulation
Refractor and add autogenerated compile_time flag + start impl probes
479b37a 
Remove all compile time flag from core and lib to put them into Meson
Generated header + move model selection output dir ("autogenerated").
Working poc implementation of probes to export some events during
simulation using fixed size buffer.

Check RTD for 0D reactor : OK with same stochastic algo
Fix(simulation) RTD for batch and continuous reactor; Fix(init) gas s…
fa00757 
…calar initialiaser
Fix(model): mass_transfer + feed support, optimisation(MC), refractor…
985222d 
…(data_exporter_wip)

MC: use of Kokkos Scatter to limit use of atomic with host space +
change algortihm to remove dead particle
WIP(Data exporter): new data exporter architecture
fc6ad6f
@Benncs
feat: Implement DataExporter and MPI Feed
7706398 
- Added DataExporter feature to facilitate data export.
- Split DataExporter into two components: main file for host node and partial file for worker nodes.
- Workers now write particle data efficiently.
- Fixed Kokkos/MPI thread count settings for improved performance.
- Updated .dockerfile to ensure proper environment setup.
feat,fix: add mass calculation function and improve Monod uptake
d15407e 
fix: dataexporter OK
fix: correct weight calculation
feat: start updating postprocess package to handle new export format
chore, fix(dataexport): refractor, new files
f43e572 
chore: move simulation parameter to core
fix: datexporter file path + integration in to whole algorithm to
correclty export data
fix: post process data with multiple files
fix: matrix layout (row/column major) between Eigen and Kokkos
9307c1b
chore + fix rtd
675aedd
@Benncs
misc: test sanofi ok
5ba315c
@Benncs
fix(monod model): fix model to have correct final biomass concentration
3e963a3
feat: steady_state test
336243b
@Benncs
feat: test model parameters
207e966
Fix Monod and Uptake model, working in steady state
c3b6a6b
@Benncs
script steady
144ca33
perf: improve flowmap creation and transition performance
bc68353
chore
c7115d8
add external hdf5 compressor
964ea53
opti: bench and add profiling
3a22247
feat: add prng to division model function
529f346
opti,feat: bench try opti + start impl sunya's model
04355bf
refractor: model_uptake rename k_pts
de23d2f
@Benncs Benncs merged commit 653edfd into main Oct 30, 2024
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@Benncs