Detailed plasma part 3

[chris-ashe]

This pull request introduces several new plasma physics variables and expands the visualization capabilities for plasma profile plots. The main improvements are the addition of new variables for deuteron and triton Larmor radii, alpha particle velocities, Coulomb logarithms, and plasma frequencies, as well as new and enhanced plotting functions to visualize these profiles. The changes also reorganize subplot assignments in the main plotting routine to accommodate the new plots.

Additions and enhancements to plasma physics variables:

• Added new variables in physics_variables.py for deuteron and triton toroidal Larmor radii, alpha particle thermal and birth velocities, deuteron-triton and electron-alpha Coulomb logarithms, deuteron plasma frequency, and upper hybrid frequency.
• Updated initialization logic in init_physics_variables() to include the new variables.

Plotting and visualization improvements:

• Added plot_larmor_radius_profile function to visualize deuteron and triton Larmor radius profiles, and integrated it into the main plot routine.
• Enhanced plot_velocity_profile to plot alpha particle thermal velocity and birth velocity, including a new legend and line style for clarity.
• Improved plot_electron_frequency_profile to show harmonics of the electron Larmor frequency and upper hybrid frequency, and added a secondary x-axis for physical radius.
• Expanded plot_plasma_coloumb_logarithms to include deuteron-triton and electron-alpha Coulomb logarithm profiles, with new color coding for each interaction.

Plot layout and figure management:

• Modified subplot assignments in main_plot and increased the number of figure pages to accommodate the new plots, ensuring each profile is displayed on its own subplot and maintaining clarity in the overall visualization.

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.

[timothy-nunn]

Unit test failure needs to be fixed before a proper review is conducted.

Could you also include the plots that have been added/changed

[codecov-commenter]

Codecov Report

❌ Patch coverage is 31.93277% with 81 lines in your changes missing coverage. Please review.
✅ Project coverage is 46.85%. Comparing base (bb358d5) to head (02682d1).

Files with missing lines	Patch %	Lines
process/io/plot_proc.py	1.47%	67 Missing ⚠️
process/models/physics/physics.py	48.14%	14 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4099      +/-   ##
==========================================
- Coverage   46.86%   46.85%   -0.02%     
==========================================
  Files         136      136              
  Lines       29228    29318      +90     
==========================================
+ Hits        13698    13736      +38     
- Misses      15530    15582      +52     

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