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 ]

[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