[WIP] Add TGLFInputs and TGLFNN

[theo-brown]

Add TGLFInputs class and TGLFNN model.
Note: completion depends on other work in progress in #476.

Remaining tasks:

• Inherit from QuasilinearTransportModelInputs
• Inherit from QuasilinearTransportModel
• Move calculation of Coulomb logarithm, nu, etc to physics.py
• Check normalisation, reference lengths, chiGB, etc

[theo-brown]

@lorenzozanisi could you lend a hand with checking the normalisations?

[theo-brown]

Is this definition (chiGB) correct / consistent with TGLF?

[jcitrin]

Use quasilinear_transport_model.calculate_chiGB , where you can set a b_unit and reference length as input.

For TGLF probably b_unit=Bunit which you need to define (it's not the same as geo.B0), and aminor for the reference length. Should double check

As always, be careful with sqrt(2) in rho_s_unit and compare to TORAX calculate_chiGB to make sure we didn't miss another input argument (to include sqrt(2) or not)

[theo-brown]

Cool, I think this might've been a function added in that I hadn't noticed. I'll recheck the tglf docs for the reference field etc.

[theo-brown]

@lorenzozanisi ready for your bits to be integrated as and when!

[jcitrin]

Note that you can use the new quasilinear_transport_model.NormalizedLogarithmicGradients.from_profiles for these. See

torax/torax/transport_model/qualikiz_based_transport_model.py

Line 138 in 4812e48

normalized_logarithmic_gradients = quasilinear_transport_model.NormalizedLogarithmicGradients.from_profiles(

1. I don't recommend on using the names Ate, Ati, etc., which are QuaLiKiz jargon. In any case Normalized logarithmic gradients contains general names
2. Note that Ati, Ate, (in QuaLiKiz jargon) should already include the normalization length, which is aminor for TGLF. NormalizedLogarithmicGradients takes the reference length as input

[jcitrin]

probably need alphaMHD as well? See quasilinear_transport_model.calculate_alpha

[fusionby2030]

Nice WIP. It is a pain to get these normalizations & miller geometry. I wonder if using the pyrokinetics would be of interest?

Is there a plan to push this through in any of the next few weeks? I've got a TGLF surrogate as well, was thinking to test it in TORAX alongside ASTRA (current approach) to possibly cover model validation/comparison.

I think there are also a few tglf inputs missing, namely q_prime: q^2 a^2 / r^2 * shat, drmindx= r * dr/dx, where r = Rmin_local = (x_surface.max() - x_surface.min()) / 2.0, and x = sin^-1 (triangularity).

I would be happy to contribute these.

[theo-brown]

@fusionby2030 welcome to this PR! Glad that it might be useful to you!

I wonder if using the pyrokinetics would be of interest?

Good shout - @jcitrin are you aware of pyrokinetics? I've basically been using its documentation (+Bhavin Patel, one of the developers) as my reference for trying to hook these TGLF bits in to TORAX. I feel like if there is interest in TORAX become a one-stop-shop for gyrokinetics surrogates taking advantage of the work done in pyrokinetics would be a bit of a no-brainer.

I've got a TGLF surrogate as well, was thinking to test it in TORAX alongside ASTRA (current approach) to possibly cover model validation/comparison.

Super interested in this, keep me posted!

I think there are also a few tglf inputs missing

Yep, our surrogate doesn't use the full set of TGLF inputs (for reasons that @lorenzozanisi would be able to explain - I wasn't involved in its development!). Makes sense to extend it to the full load and make some optional or something. Please go ahead with adding whatever you need! Admin-wise, can you add to this PR given it's from a fork? Or would it need to be a branch?

Is there a plan to push this through in any of the next few weeks?

@lorenzozanisi and I were tag-teaming a bit on this PR - I think Lorenzo wanted to connect full TGLF to TORAX, and has made big strides in the week before Christmas on it. Not sure where those commits are - I keep poking him to push them! Along the way, we also found a few bits that were needed to be changed more widely, such as #628 that Jonathan handled. Definitely on the agenda on UKAEA's side for January!

[fusionby2030]

To add to the pyrokinetics discussion, there are ways (albeit hacky) of passing core_profiles from TORAX (or arbitrary kinetic sources) to construct Pyro objects. The transformations between different code input parameters is then trivial. Tested with GENE and TGLF given kinetic profiles from example TORAX sim class and some experimental data. Generally follows most of the pyrokinetics.kinetics file readers, just without the file. Can set via

from pyrokinetics import Pyro 
from pyrokinetics.kinetics import Kinetics
from pyrokinetics.units import UnitSpline
from pyrokinetics.species import Species
from pyrokinetics.constants import electron_mass

pyro_obj = Pyro(eq_file=eqfilepath, eq_type="GEQDSK", gk_code="TGLF")

# self constructed from your kinetic profiles, see IMAS file reader for example in pyrokinetics.kinetics.imas.py -> read_from_file()
kinetic_species_data = {'electron': Species(
        species_type="electron",
        charge=electron_charge_func, # UnitSpline
        mass=electron_mass,      
        dens=electron_dens_func,       # UnitSpline
        temp=electron_temp_func,     # Unit Spline
        omega0=omega_func,            # Unit Spline
        rho=rho_func,                          # Unit Spline
    ), 
   # same for ions...
}
kinetic_struct = Kinetics(kinetics_type="IMAS", # dummy since there are supported type checks...
                                       **kinetic_species_data)

pyro_obj.kinetics: Kinetics = kinetic_struct 

# One could then loop through PSI_N or rho_tor values

local_psi_n = 0.5 
pyro_c.load_local_geometry(local_psi_n)
pyro_c.load_local_species(local_psi_n)
pyro_c.write_gk_file("input.tglf", "TGLF")

I have no idea how @lorenzozanisi is planning on running TGLF from TORAX without lots of IO. Would be nice if there was a python interface to TGLF...

Might be best to wait until January then, am trying to coordinate a visit to Culham in February.