Add Ability to Write Boozmn.nc style output files #680

dpanici · 2023-09-19T16:43:07Z

Add make_boozmn_output utility function to vmec_utils, which allows DESC to write boozmn.nc style output files containing Boozer harmonics. I/O based heavily off of the hidden symmetries version of booz_xform

add documentation (in form of notebook or a page) on our Boozer transform setup and how to use and the meaning of our "|B|_mn_B" and how to get into the familiar double angle form - make issue
deprecate |B|_mn
make issue for asym boozmn and kick can down the road - only issue is the numnc from the DESC-saved boozmn is the opposite sign to the C++ saved boozmn. Not sure what the issue is... the DESC-saved nu agrees better with the DESC nu, and the other quantities are all in agreement from both C++ and DESC, so it is something subtle

…t the non-sym modes

dpanici · 2023-09-21T10:11:00Z

make a norm name in data index

…l sym

… on the grids (calcuated with cos sym transforms)

…, add test for the quantities saved in boozmn.nc file

…ELIOTRON from scratch

dpanici · 2023-09-27T21:48:59Z

notes to self on Booz_xform

modenumbers are defined here:

if m=0, they only include n from 0 -> nboz
else if m is not 0, they include all n modes from -nboz -> nboz
this means that they include the (0,0) mode even for their sin terms, but they skip the (0,-nboz -_ nboz) modes. This may explain the discrepancy in modes I see

github-actions · 2023-11-08T22:48:24Z

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     +0.64 +/- 2.10     | +9.97e-05 +/- 3.25e-04 |  1.56e-02 +/- 2.9e-04  |  1.55e-02 +/- 1.5e-04  |
 test_build_transform_fft_midres         |     +0.16 +/- 1.35     | +1.55e-04 +/- 1.29e-03 |  9.51e-02 +/- 1.2e-03  |  9.50e-02 +/- 4.9e-04  |
 test_build_transform_fft_highres        |     +1.14 +/- 0.84     | +5.29e-03 +/- 3.88e-03 |  4.69e-01 +/- 3.3e-03  |  4.63e-01 +/- 2.1e-03  |
 test_equilibrium_init_lowres            |     +0.48 +/- 1.46     | +3.14e-03 +/- 9.60e-03 |  6.61e-01 +/- 7.5e-03  |  6.58e-01 +/- 6.0e-03  |
 test_equilibrium_init_medres            |     -0.17 +/- 0.92     | -1.74e-03 +/- 9.23e-03 |  1.00e+00 +/- 5.7e-03  |  1.01e+00 +/- 7.2e-03  |
 test_equilibrium_init_highres           |     +0.41 +/- 1.07     | +1.04e-02 +/- 2.74e-02 |  2.57e+00 +/- 1.6e-02  |  2.56e+00 +/- 2.2e-02  |
 test_objective_compile_dshape_current   |     -1.97 +/- 6.87     | -8.34e-02 +/- 2.91e-01 |  4.16e+00 +/- 2.1e-01  |  4.24e+00 +/- 2.0e-01  |
 test_objective_compile_atf              |     -3.31 +/- 4.88     | -3.18e-01 +/- 4.69e-01 |  9.29e+00 +/- 3.4e-01  |  9.61e+00 +/- 3.2e-01  |
 test_objective_compute_dshape_current   |     +0.07 +/- 2.30     | +1.56e-06 +/- 5.03e-05 |  2.19e-03 +/- 3.3e-05  |  2.19e-03 +/- 3.8e-05  |
 test_objective_compute_atf              |     -1.34 +/- 2.16     | -1.04e-04 +/- 1.67e-04 |  7.63e-03 +/- 1.0e-04  |  7.73e-03 +/- 1.3e-04  |
 test_objective_jac_dshape_current       |     -6.37 +/- 7.16     | -3.01e-03 +/- 3.38e-03 |  4.42e-02 +/- 1.5e-03  |  4.72e-02 +/- 3.0e-03  |
 test_objective_jac_atf                  |     -7.77 +/- 4.22     | -1.86e-01 +/- 1.01e-01 |  2.21e+00 +/- 5.0e-02  |  2.39e+00 +/- 8.8e-02  |
 test_perturb_1                          |     -1.10 +/- 11.89    | -9.66e-02 +/- 1.04e+00 |  8.67e+00 +/- 7.6e-01  |  8.77e+00 +/- 7.2e-01  |
 test_perturb_2                          |     -2.40 +/- 5.40     | -3.52e-01 +/- 7.91e-01 |  1.43e+01 +/- 6.2e-01  |  1.47e+01 +/- 4.9e-01  |

…script

github-actions · 2023-11-09T02:23:01Z

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     +0.74 +/- 1.72     | +1.13e-04 +/- 2.63e-04 |  1.54e-02 +/- 2.1e-04  |  1.53e-02 +/- 1.5e-04  |
 test_build_transform_fft_midres         |     +0.54 +/- 1.12     | +5.06e-04 +/- 1.06e-03 |  9.44e-02 +/- 8.6e-04  |  9.39e-02 +/- 6.1e-04  |
 test_build_transform_fft_highres        |     +0.73 +/- 0.94     | +3.36e-03 +/- 4.34e-03 |  4.65e-01 +/- 3.9e-03  |  4.62e-01 +/- 2.0e-03  |
 test_equilibrium_init_lowres            |     +2.80 +/- 2.13     | +1.84e-02 +/- 1.40e-02 |  6.75e-01 +/- 1.3e-02  |  6.57e-01 +/- 5.4e-03  |
 test_equilibrium_init_medres            |     +0.00 +/- 2.85     | +3.23e-05 +/- 2.83e-02 |  9.94e-01 +/- 2.6e-02  |  9.94e-01 +/- 1.2e-02  |
 test_equilibrium_init_highres           |     +0.07 +/- 0.69     | +1.89e-03 +/- 1.78e-02 |  2.56e+00 +/- 1.1e-02  |  2.56e+00 +/- 1.4e-02  |
 test_objective_compile_dshape_current   |     -1.40 +/- 6.95     | -5.85e-02 +/- 2.91e-01 |  4.14e+00 +/- 2.5e-01  |  4.19e+00 +/- 1.6e-01  |
 test_objective_compile_atf              |     -0.55 +/- 8.21     | -5.14e-02 +/- 7.62e-01 |  9.22e+00 +/- 5.6e-01  |  9.27e+00 +/- 5.2e-01  |
 test_objective_compute_dshape_current   |     +0.83 +/- 2.06     | +1.80e-05 +/- 4.48e-05 |  2.19e-03 +/- 2.5e-05  |  2.17e-03 +/- 3.7e-05  |
 test_objective_compute_atf              |     -1.90 +/- 1.03     | -1.45e-04 +/- 7.82e-05 |  7.48e-03 +/- 4.9e-05  |  7.62e-03 +/- 6.1e-05  |
 test_objective_jac_dshape_current       |     +5.20 +/- 10.14    | +2.31e-03 +/- 4.51e-03 |  4.68e-02 +/- 3.6e-03  |  4.45e-02 +/- 2.8e-03  |
 test_objective_jac_atf                  |     -0.24 +/- 6.29     | -5.71e-03 +/- 1.47e-01 |  2.34e+00 +/- 5.8e-02  |  2.34e+00 +/- 1.4e-01  |
 test_perturb_1                          |     -1.35 +/- 12.01    | -1.16e-01 +/- 1.03e+00 |  8.45e+00 +/- 7.3e-01  |  8.57e+00 +/- 7.3e-01  |
 test_perturb_2                          |     -1.29 +/- 3.45     | -1.85e-01 +/- 4.95e-01 |  1.42e+01 +/- 4.1e-01  |  1.44e+01 +/- 2.8e-01  |

github-actions · 2023-11-09T20:28:11Z

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     +2.27 +/- 9.81     | +3.48e-04 +/- 1.50e-03 |  1.56e-02 +/- 1.5e-03  |  1.53e-02 +/- 2.7e-04  |
 test_build_transform_fft_midres         |     +2.74 +/- 1.39     | +2.54e-03 +/- 1.29e-03 |  9.53e-02 +/- 1.2e-03  |  9.28e-02 +/- 3.1e-04  |
 test_build_transform_fft_highres        |     +0.95 +/- 1.08     | +4.36e-03 +/- 4.96e-03 |  4.62e-01 +/- 3.9e-03  |  4.58e-01 +/- 3.0e-03  |
 test_equilibrium_init_lowres            |     -0.12 +/- 1.35     | -7.75e-04 +/- 8.80e-03 |  6.49e-01 +/- 6.6e-03  |  6.50e-01 +/- 5.8e-03  |
 test_equilibrium_init_medres            |     -0.04 +/- 0.92     | -3.69e-04 +/- 9.11e-03 |  9.88e-01 +/- 5.7e-03  |  9.89e-01 +/- 7.1e-03  |
 test_equilibrium_init_highres           |     +1.01 +/- 1.18     | +2.56e-02 +/- 2.98e-02 |  2.56e+00 +/- 2.6e-02  |  2.53e+00 +/- 1.5e-02  |
 test_objective_compile_dshape_current   |     +4.79 +/- 7.87     | +1.96e-01 +/- 3.22e-01 |  4.29e+00 +/- 2.2e-01  |  4.10e+00 +/- 2.3e-01  |
 test_objective_compile_atf              |     +2.39 +/- 5.66     | +2.23e-01 +/- 5.27e-01 |  9.54e+00 +/- 4.4e-01  |  9.31e+00 +/- 2.9e-01  |
 test_objective_compute_dshape_current   |     +1.45 +/- 2.72     | +3.17e-05 +/- 5.94e-05 |  2.22e-03 +/- 3.3e-05  |  2.19e-03 +/- 5.0e-05  |
 test_objective_compute_atf              |     +0.33 +/- 1.33     | +2.55e-05 +/- 1.02e-04 |  7.71e-03 +/- 9.5e-05  |  7.69e-03 +/- 3.7e-05  |
 test_objective_jac_dshape_current       |     +1.53 +/- 12.32    | +7.10e-04 +/- 5.72e-03 |  4.71e-02 +/- 2.4e-03  |  4.64e-02 +/- 5.2e-03  |
 test_objective_jac_atf                  |     -0.09 +/- 7.71     | -2.06e-03 +/- 1.80e-01 |  2.33e+00 +/- 1.5e-01  |  2.33e+00 +/- 9.3e-02  |
 test_perturb_1                          |     -1.74 +/- 11.99    | -1.53e-01 +/- 1.05e+00 |  8.63e+00 +/- 7.9e-01  |  8.78e+00 +/- 7.0e-01  |
 test_perturb_2                          |     -1.60 +/- 5.50     | -2.31e-01 +/- 7.93e-01 |  1.42e+01 +/- 5.6e-01  |  1.44e+01 +/- 5.6e-01  |

github-actions · 2023-11-09T22:50:34Z

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     -0.13 +/- 1.07     | -1.98e-05 +/- 1.65e-04 |  1.54e-02 +/- 1.2e-04  |  1.54e-02 +/- 1.1e-04  |
 test_build_transform_fft_midres         |     -0.83 +/- 1.27     | -7.86e-04 +/- 1.20e-03 |  9.39e-02 +/- 9.1e-04  |  9.47e-02 +/- 7.9e-04  |
 test_build_transform_fft_highres        |     +0.10 +/- 0.70     | +4.55e-04 +/- 3.24e-03 |  4.66e-01 +/- 2.1e-03  |  4.66e-01 +/- 2.5e-03  |
 test_equilibrium_init_lowres            |     +0.50 +/- 1.37     | +3.26e-03 +/- 8.88e-03 |  6.53e-01 +/- 5.3e-03  |  6.50e-01 +/- 7.2e-03  |
 test_equilibrium_init_medres            |     -0.57 +/- 1.52     | -5.75e-03 +/- 1.52e-02 |  9.96e-01 +/- 1.2e-02  |  1.00e+00 +/- 9.5e-03  |
 test_equilibrium_init_highres           |     -0.26 +/- 0.75     | -6.71e-03 +/- 1.92e-02 |  2.55e+00 +/- 1.5e-02  |  2.56e+00 +/- 1.2e-02  |
 test_objective_compile_dshape_current   |     +0.15 +/- 8.35     | +6.09e-03 +/- 3.46e-01 |  4.15e+00 +/- 2.2e-01  |  4.14e+00 +/- 2.6e-01  |
 test_objective_compile_atf              |     +0.66 +/- 5.56     | +6.07e-02 +/- 5.10e-01 |  9.24e+00 +/- 4.2e-01  |  9.18e+00 +/- 2.9e-01  |
 test_objective_compute_dshape_current   |     +0.01 +/- 2.04     | +3.11e-07 +/- 4.44e-05 |  2.18e-03 +/- 3.1e-05  |  2.18e-03 +/- 3.2e-05  |
 test_objective_compute_atf              |     -1.51 +/- 0.90     | -1.16e-04 +/- 6.93e-05 |  7.55e-03 +/- 4.1e-05  |  7.67e-03 +/- 5.6e-05  |
 test_objective_jac_dshape_current       |     -5.38 +/- 11.78    | -2.56e-03 +/- 5.60e-03 |  4.50e-02 +/- 4.3e-03  |  4.75e-02 +/- 3.6e-03  |
 test_objective_jac_atf                  |     -3.50 +/- 5.85     | -8.40e-02 +/- 1.40e-01 |  2.32e+00 +/- 6.8e-02  |  2.40e+00 +/- 1.2e-01  |
 test_perturb_1                          |     +0.24 +/- 13.29    | +2.04e-02 +/- 1.14e+00 |  8.58e+00 +/- 8.3e-01  |  8.56e+00 +/- 7.8e-01  |
 test_perturb_2                          |     -0.62 +/- 5.57     | -8.88e-02 +/- 8.03e-01 |  1.43e+01 +/- 7.0e-01  |  1.44e+01 +/- 4.0e-01  |

… boozmn output function

…to zernike_to_fourier to use input basis sym

github-actions · 2023-11-10T00:14:11Z

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     -1.60 +/- 1.92     | -3.65e-04 +/- 4.37e-04 |  2.24e-02 +/- 3.2e-04  |  2.28e-02 +/- 2.9e-04  |
 test_build_transform_fft_midres         |     +1.25 +/- 0.85     | +1.65e-03 +/- 1.13e-03 |  1.34e-01 +/- 8.3e-04  |  1.32e-01 +/- 7.7e-04  |
 test_build_transform_fft_highres        |     +0.55 +/- 0.86     | +3.35e-03 +/- 5.19e-03 |  6.10e-01 +/- 3.7e-03  |  6.06e-01 +/- 3.7e-03  |
 test_equilibrium_init_lowres            |     -1.47 +/- 1.22     | -1.48e-02 +/- 1.22e-02 |  9.89e-01 +/- 6.6e-03  |  1.00e+00 +/- 1.0e-02  |
 test_equilibrium_init_medres            |     -1.76 +/- 1.06     | -2.64e-02 +/- 1.59e-02 |  1.48e+00 +/- 1.3e-02  |  1.50e+00 +/- 8.6e-03  |
 test_equilibrium_init_highres           |     -0.41 +/- 0.74     | -1.47e-02 +/- 2.65e-02 |  3.56e+00 +/- 1.9e-02  |  3.57e+00 +/- 1.8e-02  |
 test_objective_compile_dshape_current   |     -1.90 +/- 6.58     | -1.22e-01 +/- 4.22e-01 |  6.29e+00 +/- 2.8e-01  |  6.42e+00 +/- 3.2e-01  |
 test_objective_compile_atf              |     -0.55 +/- 3.67     | -1.04e-01 +/- 6.89e-01 |  1.87e+01 +/- 4.4e-01  |  1.88e+01 +/- 5.3e-01  |
 test_objective_compute_dshape_current   |     -2.77 +/- 3.84     | -1.13e-04 +/- 1.56e-04 |  3.96e-03 +/- 1.3e-04  |  4.07e-03 +/- 9.2e-05  |
 test_objective_compute_atf              |     -0.89 +/- 2.60     | -1.21e-04 +/- 3.52e-04 |  1.34e-02 +/- 2.7e-04  |  1.35e-02 +/- 2.2e-04  |
 test_objective_jac_dshape_current       |     +2.84 +/- 11.42    | +4.67e-03 +/- 1.87e-02 |  1.69e-01 +/- 9.0e-03  |  1.64e-01 +/- 1.6e-02  |
 test_objective_jac_atf                  |     -3.27 +/- 2.77     | -2.79e-01 +/- 2.37e-01 |  8.26e+00 +/- 1.9e-01  |  8.54e+00 +/- 1.5e-01  |
 test_perturb_1                          |     -0.88 +/- 10.48    | -1.15e-01 +/- 1.36e+00 |  1.29e+01 +/- 8.9e-01  |  1.30e+01 +/- 1.0e+00  |
 test_perturb_2                          |     -1.54 +/- 6.16     | -3.49e-01 +/- 1.40e+00 |  2.23e+01 +/- 1.0e+00  |  2.27e+01 +/- 9.7e-01  |

CHANGELOG.md

Co-authored-by: Yigit Gunsur Elmacioglu <[email protected]>

ddudt

A few minor comments

tests/test_plotting.py

tests/test_compute_funs.py

ddudt · 2025-02-07T20:24:41Z

desc/compute/_omnigenity.py

+    label="",
+    units="~",
+    units_long="None",
+    description="Inner product norm for boozer modes basis.",


I know what this is, but it's not obvious from the name/description. Is this something that has to be its own compute quantity? It's really just a weighting used for other calculations, and it's a constant determined by the basis modes. I think it would make more sense to have it passed in with the transforms (or even add it as an attribute to the Basis class?).

It is a constant which has to be re-calculated for a few other things, so to me makes sense to ahve it computed once and stored. Whether that is here or elsewhere does not really matter, but to pass it in transforms I would need to compute it in like get_transforms or something, and that will require other special logic as well. If possible I'd like to keep it as is here, if people are curious they can check the source code like the other stuff in our list of variables.

This also could be used to transform other quantities to Boozer as well, so it is useful to have as a compute quantiity I think.

dpanici · 2025-02-10T20:30:55Z

For future reference, the norm thing comes from (from my quick check here)

If you consider the m=0 n=0 case and plug in $\Omega$ into eq 20 (the cosine eqn specifically), you find that

$$ \begin{align} \bar{\Omega}^C_{00} &= norm\frac{1}{4\pi^2} \bar{\Omega}^C_{00}\int_0^{2\pi}\int_0^{2\pi} d\theta_B d\zeta_B\\ &= \bar{\Omega}^C_{00} norm \end{align} $$

So for the m=0 n=0 mode, norm=1 is required to recover the Boozer Fourier coefficient.

For n=0 m!=0 (in first line here, all other modes are killed by the inner product and mutual orthogonality of the trig functions)

$$ \begin{align} \bar{\Omega}^C_{m0} &= norm\frac{1}{4\pi^2} \bar{\Omega}^C_{m0}\int_0^{2\pi} d\zeta_B \int_0^{2\pi} d\theta_B cos^2(m\theta_B)\\ &= \bar{\Omega}^C_{m0} norm \frac{1}{4\pi^2} (2\pi) (\pi)\\ &= \bar{\Omega}^C_{m0} norm / 2 \end{align} $$

So for the m!=0 n=0 mode, norm=2 is required to recover the Boozer Fourier coefficient. Same thing for the m=0 n!=0 mode, and for the m!=0 n!=0 mode, you find you need norm=4

first commit, machinery working but need to figure out good way to fi…

72da051

…t the non-sym modes

dpanici changed the title ~~first commit, machinery working but need to figure out good way to fi…~~ Add Ability to Write Boozmn.nc style output files Sep 21, 2023

dpanici added 2 commits September 25, 2023 16:18

properly save nu_mn and zmns using sin bases when equilibrium is stel…

efb9245

…l sym

fix Z_mn and nu_mn calculations by having them use the correct values…

a15b3f3

… on the grids (calcuated with cos sym transforms)

dpanici mentioned this pull request Sep 25, 2023

Error when computing Poloidal flux and Boozer toroidal stream function #664

Closed

dpanici added 4 commits September 25, 2023 18:57

rename sqrt(g)_B to jac_Boozer_DESC for clarity, add proper sqrt(g)_B…

64b9b29

…, add test for the quantities saved in boozmn.nc file

Merge branch 'master' into dp/boozmn_style_output

d20de7a

fix extra/lacking dependencies

a11e1ab

add missing file.close(), change test to use get instead of solving H…

279535b

…ELIOTRON from scratch

dpanici marked this pull request as draft October 11, 2023 19:33

Merge branch 'master' into dp/boozmn_style_output

7aa6318

dpanici added 3 commits November 8, 2023 20:07

correct signs of sin(theta) modes before conversion in boozmn output …

1600f49

…script

add test against c++ version of booz_xform

36749f6

fix test half grid

84fd8f7

Merge branch 'master' into dp/boozmn_style_output

2aed44e

dpanici added 2 commits November 9, 2023 16:55

fix boozmn test

8a1f5b8

reduce grid resolution for boozmn

4a0014f

dpanici added 4 commits November 9, 2023 17:56

precompute quantities that don't need to use a single surface grid in…

31614d8

… boozmn output function

add more precomputed quantities

46f1eda

Merge branch 'master' into dp/boozmn_style_output

5e69f19

precompute fitted quanttities (B_theta_mn and B_zeta_mn), add option …

40e24c8

…to zernike_to_fourier to use input basis sym

dpanici added 2 commits November 9, 2023 22:11

fix error in logic in zernike to fourier util

b2d9ca4

update master data pkl bc sqrt(g)_B changed definition

b3b8e04

dpanici requested a review from f0uriest February 6, 2025 01:24

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Co-authored-by: Yigit Gunsur Elmacioglu <[email protected]>

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move deprecated name in tests

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Merge branch 'master' into dp/boozmn_style_output

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update description, change some cosmetic things

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Add Ability to Write Boozmn.nc style output files #680

Add Ability to Write Boozmn.nc style output files #680

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Add Ability to Write Boozmn.nc style output files #680

Add Ability to Write Boozmn.nc style output files #680

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dpanici commented Sep 19, 2023 •

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