3385 Update the plasma composition docs to include all new models

[chris-ashe]

Description

This PR was originally meant to cover the radiation section of the code as well but will be put into a separate issue to prevent conflicts.

• zeffai now added to output.

---

Namespace changes

Functions

• radpwr() -> calculate_radiation_powers()

---

Variables

Plasma Composition

• afuel -> m_fuel_amu: This has now been added to output
• abeam -> m_beam_amu: This has now been added to output
• dnalp -> nd_alphas
• dnprot -> nd_protons
• protium -> f_nd_protium_electrons
• dnbeam -> nd_beam_ions
• dnitot -> nd_ions_total
• dnz -> nd_impurities
• aion -> m_ions_total_amu
• ralpne -> f_nd_alpha_electron
• rnbeam -> f_nd_beam_electron
• deni -> nd_fuel_ions

⚡ Radiation

• pradpv -> pden_plasma_rad_mw
• pradmw -> p_plasma_rad_mw
• peakfactrad -> f_fw_rad_max
• pouterzoneradmw -> p_plasma_outer_rad_mw
• pinnerzoneradmw -> p_plasma_inner_rad_mw
• photon_wall -> pflux_fw_rad_mw
• peakradwallload -> pflux_fw_rad_max_mw
• psyncpv -> pden_plasma_sync_mw
• ssync -> f_sync_reflect

---

✨ New additions

The new constants have been added to constants.f90 for the different fuel species atomic masses from NIST. These updated mass values caused the plasma composition and first wall heating unit tests to fail.

• m_deuteron_amu: 2.0 -> 2.013553212544
• m_helion_amu: 3.0 -> 3.014932246932
• m_triton_amu: 3.0 -> 3.01550071597
• m_alpha_amu: 4.0 -> 4.001506179129
• m_proton_amu:1.0 -> 1.0072764665789

The ATOMIC_MASS_DEUTERIUM and ATOMIC_MASS_TRITIUM local variables in physics_functions.py has been replaced with the values above.

The same has been done for the impurity species taking in impurity_radiation.py:

• m_protium_amu: 1.01 -> 1.00782503223
• m_helium_amu: 4.003 -> 4.002602
• m_beryllium_amu: 9.01 -> 9.0121831
• m_carbon_amu: 12.01 -> 12.0096
• m_nitrogen_amu: 14.01 -> 14.00643
• m_oxygen_amu: 15.999 -> 15.99903
• m_neon_amu: 20.18 -> 20.1797
• m_silicon_amu: 28.09 -> 28.084
• m_argon_amu: 39.95 -> 39.948
• m_iron_amu: 55.85 -> 55.845
• m_nickel_amu: 58.70 -> 58.6934
• m_krypton_amu: 83.80 -> 83.798
• m_xenon_amu: 131.30 -> 131.293
• m_tungsten_amu: 183.85 -> 183.84

🐛 Bugs

• In psync_albajar_fidone() the temperature profile parameter tbeta was not used as intended by the model authors but was just fixed to a value of 2.0.
• In psync_albajar_fidone() the plasma elongation kappa is not given to the function as intded, instead it was calculated internally as follows:

kap = physics_variables.plasma_volume / (
        2.0e0 * np.pi**2 * physics_variables.rmajor * physics_variables.rminor**2
    )

• In the calculation of the density weighted mass of all ions in plasma_composition() the proton density was not multiplied by its true mass value and was just set to 1.0.
• Calculation the mass-weighted effective charge (zeffai) did not use the true masses of the particles in atomic mass units. Impleneting the true masses causes a change in unit tests as such:

Obtained: 0.43056686748101997
Expected: 0.4325898512799211 ± 4.3e-07

Checklist

I confirm that I have completed the following checks:

• My changes follow the PROCESS style guide
• I have justified any large differences in the regression tests caused by this pull request in the comments.
• I have added new tests where appropriate for the changes I have made.
• If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
• If I have made documentation changes, I have checked they render correctly.
• I have added documentation for my change, if appropriate.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 34.09091% with 87 lines in your changes missing coverage. Please review.

Project coverage is 30.41%. Comparing base (04b487e) to head (c5c962b).

Files with missing lines	Patch %	Lines
process/physics.py	47.27%	29 Missing ⚠️
process/stellarator.py	0.00%	18 Missing ⚠️
process/io/sankey_funcs.py	0.00%	10 Missing ⚠️
process/physics_functions.py	52.38%	10 Missing ⚠️
process/current_drive.py	11.11%	8 Missing ⚠️
process/io/plot_proc.py	0.00%	5 Missing ⚠️
process/power.py	0.00%	2 Missing ⚠️
process/dcll.py	66.66%	1 Missing ⚠️
process/divertor.py	0.00%	1 Missing ⚠️
process/init.py	66.66%	1 Missing ⚠️
... and 2 more

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3386   +/-   ##
=======================================
  Coverage   30.41%   30.41%           
=======================================
  Files          80       80           
  Lines       19389    19373   -16     
=======================================
- Hits         5897     5893    -4     
+ Misses      13492    13480   -12     

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