Proxies for neoclassical transport of energetic ions

[gretahibbard]

Adding proxies for neoclassical transport from Velasco's "A model for the fast evaluation of prompt losses of
energetic ions in stellarators" https://doi.org/10.1088/1741-4326/ac2994

• Gamma_c [ eq. 16 ]
• Gamma_delta [ eq. 19 ]
• and Gamma_alpha [ eq. 25 ]

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[YigitElma]

I know this is still a draft and you will probably make many changes but I want to make some kind suggestions,

• You can install pre-commit for automatic checks when you commit such that you don't get comments from github-actions https://github.com/PlasmaControl/DESC/blob/master/CONTRIBUTING.rst#python-styleguide
• On VS Code, there is black formatter plugin which will automatically format a file when you save it, I find this very usefull
• to exclude the files (you use for testing and debugging purposes) from git version control, you can update your .git/info/exclude file which is a local .gitignore file (because we don't want to add a bunch of files to the main .gitignore)
• if you run a jupyter notebook on tutorials folder, even if you don't make actual code changes, some device info part of the file will change which cause git to track those changes. I recommend don't commit those changes (in VS Code you can revert those files to the original format 'before committing') because in future it may cause merge conflicts which is very cumbersome to resolve for notebooks. If you already committed the changes, you can copy/paste the files from master branch

These are general suggestions for devs

[dpanici]

add thresh (or I'd prefer the full name threshold actually) as a keyword arg here, that way when this is computed it can be specified by the user. see for example helicity kwarg in the QS quantities (

DESC/desc/compute/_omnigenity.py

Line 414 in d2e9a2c

helicity="tuple: Type of quasisymmetry, (M,N). Default (1,0)",

)

[dpanici]

benchmark with KNOSOS

[github-actions]

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     +0.05 +/- 5.77     | +2.70e-04 +/- 3.04e-02 |  5.27e-01 +/- 3.0e-02  |  5.27e-01 +/- 6.4e-03  |
 test_equilibrium_init_medres            |     -0.64 +/- 0.99     | -2.64e-02 +/- 4.10e-02 |  4.10e+00 +/- 3.8e-02  |  4.13e+00 +/- 1.5e-02  |
 test_equilibrium_init_highres           |     +0.10 +/- 0.52     | +5.40e-03 +/- 2.83e-02 |  5.47e+00 +/- 2.3e-02  |  5.47e+00 +/- 1.7e-02  |
 test_objective_compile_dshape_current   |     +0.29 +/- 1.09     | +1.13e-02 +/- 4.24e-02 |  3.88e+00 +/- 3.9e-02  |  3.87e+00 +/- 1.6e-02  |
 test_objective_compute_dshape_current   |     +0.95 +/- 1.35     | +3.43e-05 +/- 4.88e-05 |  3.64e-03 +/- 3.3e-05  |  3.60e-03 +/- 3.6e-05  |
 test_objective_jac_dshape_current       |     +0.62 +/- 7.68     | +2.52e-04 +/- 3.10e-03 |  4.06e-02 +/- 2.3e-03  |  4.04e-02 +/- 2.1e-03  |
 test_perturb_2                          |     -0.01 +/- 1.43     | -1.85e-03 +/- 2.49e-01 |  1.74e+01 +/- 1.8e-01  |  1.74e+01 +/- 1.7e-01  |
 test_proximal_freeb_jac                 |     +0.19 +/- 1.49     | +1.39e-02 +/- 1.11e-01 |  7.48e+00 +/- 7.8e-02  |  7.46e+00 +/- 7.9e-02  |
 test_solve_fixed_iter                   |     -0.51 +/- 59.41    | -2.53e-02 +/- 2.97e+00 |  4.98e+00 +/- 2.1e+00  |  5.01e+00 +/- 2.1e+00  |
 test_build_transform_fft_midres         |     +0.30 +/- 6.99     | +1.82e-03 +/- 4.26e-02 |  6.11e-01 +/- 2.9e-02  |  6.09e-01 +/- 3.1e-02  |
 test_build_transform_fft_highres        |     +1.07 +/- 2.71     | +1.07e-02 +/- 2.69e-02 |  1.00e+00 +/- 2.2e-02  |  9.94e-01 +/- 1.6e-02  |
 test_equilibrium_init_lowres            |     +0.73 +/- 2.19     | +2.75e-02 +/- 8.25e-02 |  3.80e+00 +/- 7.9e-02  |  3.77e+00 +/- 2.4e-02  |
 test_objective_compile_atf              |     +0.64 +/- 1.84     | +5.07e-02 +/- 1.45e-01 |  7.93e+00 +/- 6.0e-02  |  7.88e+00 +/- 1.3e-01  |
 test_objective_compute_atf              |     +1.46 +/- 1.80     | +1.53e-04 +/- 1.88e-04 |  1.06e-02 +/- 1.5e-04  |  1.05e-02 +/- 1.2e-04  |
 test_objective_jac_atf                  |     -0.12 +/- 2.20     | -2.41e-03 +/- 4.28e-02 |  1.95e+00 +/- 3.9e-02  |  1.95e+00 +/- 1.7e-02  |
 test_perturb_1                          |     +2.83 +/- 3.66     | +3.44e-01 +/- 4.45e-01 |  1.25e+01 +/- 4.0e-01  |  1.22e+01 +/- 2.0e-01  |
 test_proximal_jac_atf                   |     -0.10 +/- 0.85     | -7.86e-03 +/- 6.88e-02 |  8.10e+00 +/- 4.7e-02  |  8.11e+00 +/- 5.0e-02  |
 test_proximal_freeb_compute             |     +0.48 +/- 0.72     | +8.68e-04 +/- 1.31e-03 |  1.83e-01 +/- 7.3e-04  |  1.82e-01 +/- 1.1e-03  |

[codecov]

Codecov Report

Attention: Patch coverage is 88.33333% with 35 lines in your changes missing coverage. Please review.

Project coverage is 95.39%. Comparing base (86376c4) to head (310157a).

Files with missing lines	Patch %	Lines
desc/compute/_neoclassical.py	80.98%	27 Missing ⚠️
desc/objectives/_neoclassical.py	92.13%	7 Missing ⚠️
desc/plotting.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1229      +/-   ##
==========================================
- Coverage   95.46%   95.39%   -0.08%     
==========================================
  Files          96       98       +2     
  Lines       23733    23983     +250     
==========================================
+ Hits        22657    22878     +221     
- Misses       1076     1105      +29     

Files with missing lines	Coverage Δ
desc/compute/__init__.py	100.00% <ø> (ø)
desc/compute/_basis_vectors.py	100.00% <100.00%> (ø)
desc/compute/_core.py	100.00% <100.00%> (ø)
desc/compute/_equil.py	100.00% <ø> (ø)
desc/compute/_field.py	100.00% <100.00%> (ø)
desc/compute/_metric.py	100.00% <ø> (ø)
desc/compute/_omnigenity.py	99.37% <ø> (-0.63%)	⬇️
desc/compute/_profiles.py	99.19% <100.00%> (ø)
desc/compute/_stability.py	100.00% <ø> (ø)
desc/equilibrium/coords.py	88.38% <ø> (ø)
... and 18 more

... and 1 file with indirect coverage changes

[dpanici]

update math label