Continuation _solve_axisym and Surface from_input_file hotfix

[dpanici]

• let surface from_input_file method find a VMEC file if INDATA is not first line, change input.DSHAPE to have a comment line
• fix bug in _solve_axisym method where if the resolution is low enough, the method does not run to the full resolution of the desired axisymmetric vacuum equilibrium

resolves #710
resolves #712

[github-actions]

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     -3.11 +/- 1.39     | -6.01e-04 +/- 2.68e-04 |  1.87e-02 +/- 2.0e-04  |  1.93e-02 +/- 1.8e-04  |
 test_build_transform_fft_midres         |     -2.12 +/- 0.78     | -2.42e-03 +/- 8.93e-04 |  1.12e-01 +/- 6.7e-04  |  1.14e-01 +/- 5.9e-04  |
 test_build_transform_fft_highres        |     -1.59 +/- 1.04     | -8.29e-03 +/- 5.40e-03 |  5.13e-01 +/- 3.7e-03  |  5.21e-01 +/- 4.0e-03  |
 test_equilibrium_init_lowres            |     -1.86 +/- 1.54     | -8.11e-03 +/- 6.72e-03 |  4.29e-01 +/- 5.1e-03  |  4.37e-01 +/- 4.4e-03  |
 test_equilibrium_init_medres            |     -2.08 +/- 1.29     | -1.16e-02 +/- 7.24e-03 |  5.48e-01 +/- 3.8e-03  |  5.60e-01 +/- 6.2e-03  |
 test_equilibrium_init_highres           |     -1.51 +/- 0.79     | -1.50e-02 +/- 7.89e-03 |  9.79e-01 +/- 3.8e-03  |  9.94e-01 +/- 6.9e-03  |
 test_objective_compile_dshape_current   |     -1.61 +/- 6.10     | -8.45e-02 +/- 3.19e-01 |  5.15e+00 +/- 2.3e-01  |  5.24e+00 +/- 2.2e-01  |
 test_objective_compile_atf              |     -0.77 +/- 4.58     | -1.16e-01 +/- 6.90e-01 |  1.49e+01 +/- 4.5e-01  |  1.51e+01 +/- 5.3e-01  |
 test_objective_compute_dshape_current   |     -1.87 +/- 1.14     | -6.28e-05 +/- 3.84e-05 |  3.29e-03 +/- 2.1e-05  |  3.36e-03 +/- 3.2e-05  |
 test_objective_compute_atf              |     -0.38 +/- 1.13     | -4.30e-05 +/- 1.27e-04 |  1.11e-02 +/- 1.1e-04  |  1.12e-02 +/- 5.8e-05  |
 test_objective_jac_dshape_current       |     +1.63 +/- 7.91     | +2.06e-03 +/- 9.99e-03 |  1.28e-01 +/- 5.5e-03  |  1.26e-01 +/- 8.3e-03  |
 test_objective_jac_atf                  |     +1.66 +/- 1.17     | +1.06e-01 +/- 7.46e-02 |  6.49e+00 +/- 5.8e-02  |  6.38e+00 +/- 4.6e-02  |
 test_perturb_1                          |     +0.29 +/- 13.97    | +2.50e-02 +/- 1.21e+00 |  8.66e+00 +/- 8.3e-01  |  8.64e+00 +/- 8.8e-01  |
 test_perturb_2                          |     -0.88 +/- 6.93     | -1.45e-01 +/- 1.14e+00 |  1.63e+01 +/- 6.8e-01  |  1.64e+01 +/- 9.1e-01  |

[codecov]

Codecov Report

Merging #711 (f45bac0) into master (be530ca) will increase coverage by 0.01%.
The diff coverage is 100.00%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #711      +/-   ##
==========================================
+ Coverage   94.96%   94.97%   +0.01%     
==========================================
  Files          79       79              
  Lines       19317    19322       +5     
==========================================
+ Hits        18345    18352       +7     
+ Misses        972      970       -2     

Files	Coverage Δ
desc/continuation.py	93.70% <100.00%> (+0.33%)	⬆️
desc/geometry/surface.py	96.15% <100.00%> (+0.07%)	⬆️

... and 1 file with indirect coverage changes

[github-actions]

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     +2.16 +/- 1.87     | +4.21e-04 +/- 3.64e-04 |  1.99e-02 +/- 3.2e-04  |  1.94e-02 +/- 1.8e-04  |
+test_build_transform_fft_midres         |     -2.80 +/- 0.73     | -3.27e-03 +/- 8.56e-04 |  1.13e-01 +/- 5.5e-04  |  1.17e-01 +/- 6.5e-04  |
 test_build_transform_fft_highres        |     -1.85 +/- 1.00     | -9.80e-03 +/- 5.30e-03 |  5.20e-01 +/- 4.5e-03  |  5.30e-01 +/- 2.8e-03  |
 test_equilibrium_init_lowres            |     +0.67 +/- 1.86     | +2.96e-03 +/- 8.25e-03 |  4.46e-01 +/- 6.7e-03  |  4.44e-01 +/- 4.9e-03  |
 test_equilibrium_init_medres            |     +0.74 +/- 1.42     | +4.20e-03 +/- 8.04e-03 |  5.69e-01 +/- 4.9e-03  |  5.64e-01 +/- 6.4e-03  |
 test_equilibrium_init_highres           |     +0.40 +/- 1.23     | +3.99e-03 +/- 1.23e-02 |  1.00e+00 +/- 7.7e-03  |  1.00e+00 +/- 9.6e-03  |
 test_objective_compile_dshape_current   |     +3.38 +/- 6.28     | +1.79e-01 +/- 3.32e-01 |  5.46e+00 +/- 2.4e-01  |  5.28e+00 +/- 2.3e-01  |
 test_objective_compile_atf              |     +4.46 +/- 4.70     | +6.74e-01 +/- 7.11e-01 |  1.58e+01 +/- 5.9e-01  |  1.51e+01 +/- 4.0e-01  |
-test_objective_compute_dshape_current   |    +10.20 +/- 3.00     | +3.45e-04 +/- 1.02e-04 |  3.72e-03 +/- 7.6e-05  |  3.38e-03 +/- 6.7e-05  |
-test_objective_compute_atf              |     +7.19 +/- 2.03     | +8.12e-04 +/- 2.30e-04 |  1.21e-02 +/- 1.5e-04  |  1.13e-02 +/- 1.8e-04  |
 test_objective_jac_dshape_current       |     +1.46 +/- 9.66     | +1.91e-03 +/- 1.26e-02 |  1.33e-01 +/- 8.4e-03  |  1.31e-01 +/- 9.5e-03  |
-test_objective_jac_atf                  |     +5.74 +/- 1.22     | +3.73e-01 +/- 7.96e-02 |  6.87e+00 +/- 6.1e-02  |  6.50e+00 +/- 5.1e-02  |
 test_perturb_1                          |     +2.23 +/- 14.53    | +1.95e-01 +/- 1.27e+00 |  8.93e+00 +/- 9.1e-01  |  8.73e+00 +/- 8.9e-01  |
 test_perturb_2                          |     +0.73 +/- 6.59     | +1.21e-01 +/- 1.09e+00 |  1.67e+01 +/- 6.1e-01  |  1.66e+01 +/- 9.1e-01  |

[dpanici]

@f0uriest do we want to make a similar change to the _add_pressure function, where if pres_step is zero it will just solve with the entire pressure? right now it will just run through the function and not run anything if pres_step is zero, effectively skipping that step, which is fine but it is now different than the behavior of _solve_axisym if mres_step is 0 (where that function will now run the equilibrium at the full poloidal resolutoin in one step if mres_step is 0)

we could revert that behavior to skipping the axisym solve if mres_step is 0 by reverting the <= to < in that function's while loop, I think

[github-actions]

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
+test_build_transform_fft_lowres         |    -10.94 +/- 2.35     | -2.31e-03 +/- 4.96e-04 |  1.88e-02 +/- 1.1e-04  |  2.12e-02 +/- 4.8e-04  |
+test_build_transform_fft_midres         |     -6.90 +/- 1.08     | -8.15e-03 +/- 1.28e-03 |  1.10e-01 +/- 1.0e-03  |  1.18e-01 +/- 7.7e-04  |
+test_build_transform_fft_highres        |     -4.74 +/- 1.01     | -2.55e-02 +/- 5.41e-03 |  5.13e-01 +/- 1.9e-03  |  5.38e-01 +/- 5.1e-03  |
 test_equilibrium_init_lowres            |     -7.71 +/- 2.96     | -3.65e-02 +/- 1.40e-02 |  4.37e-01 +/- 7.6e-03  |  4.73e-01 +/- 1.2e-02  |
+test_equilibrium_init_medres            |     -6.18 +/- 1.71     | -3.70e-02 +/- 1.02e-02 |  5.62e-01 +/- 6.0e-03  |  5.99e-01 +/- 8.3e-03  |
+test_equilibrium_init_highres           |     -3.87 +/- 1.06     | -4.00e-02 +/- 1.10e-02 |  9.93e-01 +/- 8.2e-03  |  1.03e+00 +/- 7.3e-03  |
 test_objective_compile_dshape_current   |    -11.06 +/- 5.52     | -6.50e-01 +/- 3.24e-01 |  5.22e+00 +/- 2.4e-01  |  5.87e+00 +/- 2.2e-01  |
 test_objective_compile_atf              |     -3.34 +/- 4.32     | -6.07e-01 +/- 7.86e-01 |  1.76e+01 +/- 7.2e-01  |  1.82e+01 +/- 3.1e-01  |
 test_objective_compute_dshape_current   |    -13.69 +/- 6.52     | -6.29e-04 +/- 3.00e-04 |  3.97e-03 +/- 2.5e-04  |  4.60e-03 +/- 1.7e-04  |
 test_objective_compute_atf              |     -2.69 +/- 2.65     | -3.41e-04 +/- 3.36e-04 |  1.23e-02 +/- 1.8e-04  |  1.27e-02 +/- 2.8e-04  |
 test_objective_jac_dshape_current       |     -2.28 +/- 7.67     | -3.27e-03 +/- 1.10e-02 |  1.40e-01 +/- 8.3e-03  |  1.43e-01 +/- 7.2e-03  |
 test_objective_jac_atf                  |     +8.51 +/- 6.81     | +6.91e-01 +/- 5.52e-01 |  8.81e+00 +/- 3.3e-01  |  8.11e+00 +/- 4.4e-01  |
 test_perturb_1                          |     +0.17 +/- 16.88    | +1.59e-02 +/- 1.58e+00 |  9.36e+00 +/- 1.1e+00  |  9.34e+00 +/- 1.1e+00  |
 test_perturb_2                          |     +3.80 +/- 6.44     | +6.67e-01 +/- 1.13e+00 |  1.82e+01 +/- 4.3e-01  |  1.75e+01 +/- 1.0e+00  |

[f0uriest]

@f0uriest do we want to make a similar change to the _add_pressure function, where if pres_step is zero it will just solve with the entire pressure? right now it will just run through the function and not run anything if pres_step is zero, effectively skipping that step, which is fine but it is now different than the behavior of _solve_axisym if mres_step is 0 (where that function will now run the equilibrium at the full poloidal resolutoin in one step if mres_step is 0)

we could revert that behavior to skipping the axisym solve if mres_step is 0 by reverting the <= to < in that function's while loop, I think

I don't think that's necessary. In general neither step should ever be zero.

[github-actions]

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     -3.93 +/- 8.08     | -1.10e-03 +/- 2.27e-03 |  2.69e-02 +/- 1.2e-03  |  2.80e-02 +/- 1.9e-03  |
 test_build_transform_fft_midres         |     -2.38 +/- 4.53     | -3.78e-03 +/- 7.21e-03 |  1.55e-01 +/- 3.7e-03  |  1.59e-01 +/- 6.2e-03  |
 test_build_transform_fft_highres        |     -1.52 +/- 5.37     | -1.10e-02 +/- 3.90e-02 |  7.14e-01 +/- 3.0e-02  |  7.25e-01 +/- 2.5e-02  |
 test_equilibrium_init_lowres            |     -4.23 +/- 5.31     | -2.61e-02 +/- 3.27e-02 |  5.90e-01 +/- 2.2e-02  |  6.16e-01 +/- 2.4e-02  |
 test_equilibrium_init_medres            |     -3.63 +/- 5.07     | -2.77e-02 +/- 3.88e-02 |  7.37e-01 +/- 2.4e-02  |  7.65e-01 +/- 3.0e-02  |
 test_equilibrium_init_highres           |     -3.06 +/- 3.05     | -3.89e-02 +/- 3.87e-02 |  1.23e+00 +/- 2.2e-02  |  1.27e+00 +/- 3.1e-02  |
 test_objective_compile_dshape_current   |     -3.84 +/- 3.37     | -2.77e-01 +/- 2.43e-01 |  6.93e+00 +/- 1.8e-01  |  7.21e+00 +/- 1.7e-01  |
 test_objective_compile_atf              |     -1.28 +/- 4.35     | -2.47e-01 +/- 8.41e-01 |  1.91e+01 +/- 6.6e-01  |  1.93e+01 +/- 5.2e-01  |
 test_objective_compute_dshape_current   |     +1.11 +/- 8.20     | +4.08e-05 +/- 3.00e-04 |  3.70e-03 +/- 2.5e-04  |  3.66e-03 +/- 1.6e-04  |
 test_objective_compute_atf              |     +0.68 +/- 11.72    | +8.55e-05 +/- 1.47e-03 |  1.26e-02 +/- 6.9e-04  |  1.25e-02 +/- 1.3e-03  |
 test_objective_jac_dshape_current       |     -7.79 +/- 10.69    | -9.18e-03 +/- 1.26e-02 |  1.09e-01 +/- 1.0e-02  |  1.18e-01 +/- 7.5e-03  |
 test_objective_jac_atf                  |     +0.35 +/- 1.93     | +2.50e-02 +/- 1.36e-01 |  7.07e+00 +/- 9.9e-02  |  7.05e+00 +/- 9.4e-02  |
 test_perturb_1                          |     -3.49 +/- 11.66    | -4.22e-01 +/- 1.41e+00 |  1.17e+01 +/- 9.9e-01  |  1.21e+01 +/- 1.0e+00  |
 test_perturb_2                          |     -0.85 +/- 7.19     | -1.96e-01 +/- 1.65e+00 |  2.27e+01 +/- 1.0e+00  |  2.29e+01 +/- 1.3e+00  |

[github-actions]

|             benchmark_name             |         dt(%)          |         dt(s)          |        t_new(s)        |        t_old(s)        | 
| -------------------------------------- | ---------------------- | ---------------------- | ---------------------- | ---------------------- |
 test_build_transform_fft_lowres         |     -3.90 +/- 2.95     | -7.84e-04 +/- 5.94e-04 |  1.93e-02 +/- 4.4e-04  |  2.01e-02 +/- 4.0e-04  |
+test_build_transform_fft_midres         |     -4.29 +/- 0.67     | -4.99e-03 +/- 7.79e-04 |  1.11e-01 +/- 5.4e-04  |  1.16e-01 +/- 5.6e-04  |
+test_build_transform_fft_highres        |     -3.76 +/- 0.88     | -2.01e-02 +/- 4.69e-03 |  5.13e-01 +/- 3.5e-03  |  5.33e-01 +/- 3.2e-03  |
 test_equilibrium_init_lowres            |     -1.29 +/- 1.53     | -5.71e-03 +/- 6.75e-03 |  4.36e-01 +/- 4.9e-03  |  4.42e-01 +/- 4.6e-03  |
 test_equilibrium_init_medres            |     -0.86 +/- 2.16     | -4.86e-03 +/- 1.22e-02 |  5.60e-01 +/- 1.1e-02  |  5.65e-01 +/- 6.1e-03  |
 test_equilibrium_init_highres           |     -0.56 +/- 0.93     | -5.59e-03 +/- 9.25e-03 |  9.90e-01 +/- 6.5e-03  |  9.95e-01 +/- 6.5e-03  |
 test_objective_compile_dshape_current   |     -1.12 +/- 7.00     | -5.97e-02 +/- 3.72e-01 |  5.26e+00 +/- 2.3e-01  |  5.32e+00 +/- 2.9e-01  |
 test_objective_compile_atf              |     +1.25 +/- 3.99     | +1.90e-01 +/- 6.04e-01 |  1.53e+01 +/- 4.4e-01  |  1.51e+01 +/- 4.1e-01  |
 test_objective_compute_dshape_current   |     -1.70 +/- 12.85    | -5.88e-05 +/- 4.43e-04 |  3.39e-03 +/- 9.1e-05  |  3.45e-03 +/- 4.3e-04  |
 test_objective_compute_atf              |     +0.52 +/- 2.75     | +5.89e-05 +/- 3.13e-04 |  1.14e-02 +/- 2.7e-04  |  1.14e-02 +/- 1.5e-04  |
 test_objective_jac_dshape_current       |     -2.07 +/- 14.49    | -2.78e-03 +/- 1.94e-02 |  1.31e-01 +/- 1.8e-02  |  1.34e-01 +/- 7.8e-03  |
 test_objective_jac_atf                  |     +1.20 +/- 1.29     | +7.77e-02 +/- 8.35e-02 |  6.54e+00 +/- 6.0e-02  |  6.46e+00 +/- 5.8e-02  |
 test_perturb_1                          |     -0.55 +/- 14.16    | -4.83e-02 +/- 1.23e+00 |  8.66e+00 +/- 8.6e-01  |  8.71e+00 +/- 8.8e-01  |
 test_perturb_2                          |     -1.63 +/- 6.42     | -2.73e-01 +/- 1.07e+00 |  1.64e+01 +/- 6.8e-01  |  1.67e+01 +/- 8.3e-01  |