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Refactor Python Concatenation Scripts + Add Dask Templates #347

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merged 16 commits into from
Nov 27, 2023
Merged

Refactor Python Concatenation Scripts + Add Dask Templates #347

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c373116
Refactor cat_dset_3d.py for easier parallelization
bcaddy Oct 1, 2023
47f9430
Refactor cat_slice.py to be more flexible + a CLI
bcaddy Oct 1, 2023
ecc13ae
Add python templates for using Dask
bcaddy Oct 1, 2023
6120ad3
Refactor slice & dset_3d scripts with common structure
bcaddy Oct 30, 2023
ebd9ef0
Add chunking option to concatenation scripts
bcaddy Oct 31, 2023
bb8c39a
Update cat_slice to work with projection data
bcaddy Nov 11, 2023
47df926
Rename concat scripts for clarity
bcaddy Nov 11, 2023
ee587e9
Add rotated projection support to concat_2d_data.py
bcaddy Nov 12, 2023
3a89830
Add safer method of opening destination HDF5 file
bcaddy Nov 12, 2023
da1c672
Convert to Numpy docstrings
bcaddy Nov 13, 2023
3fbd108
Move all concat common tools into their own file
bcaddy Nov 13, 2023
572ac72
Remove deprecated cat.py
bcaddy Nov 13, 2023
8152145
Rename concat_3d_output to concat_3d_dataset for consistency with 2d …
bcaddy Nov 13, 2023
611eb16
Update particles concatenation file to new method
bcaddy Nov 13, 2023
9b751a5
Update python_scripts/README.md for new concat scripts
bcaddy Nov 13, 2023
c1f6d9e
Fix placeholder comment
bcaddy Nov 16, 2023
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9 changes: 1 addition & 8 deletions python_scripts/README.md
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Expand Up @@ -5,15 +5,8 @@ You will likely develop more customized, robust, and flexible scripts for your o
These simple scripts here are intended to help you understand the basics of the generated data from Cholla.

## Merging HDF5 files
Multi-processor runs generate HDF5 files per-timestep per-processor.
To treat each timestep together we want to merge those per-processor HDF5 files.

| Script | Concatenate |
| ------ | ----------- |
`cat_dset_3d.py` | 3D HDF5 datasets
`cat_projection.py` | The on-axis projection data created when the -DPROJECTION flag is turned on
`cat_rotated_projection.py` | The rotated projection data created when the -DROTATED_PROJECTION flag is turned on
`cat_slice.py` | The on-axis slice data created when the -DSLICES flag is turned on
Multi-processor runs generate HDF5 files per-timestep per-processor. Merging these per process output into a single file can be done with the concatenation scripts detailed in the "Outputs" section of the wiki.

## Plotting data
We here present simple Python matplotlib-based scripts to plot density, velocity, energy, and pressure.
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