Particle balance constraint

[chris-ashe]

This pull request introduces significant improvements to the plasma fuelling model, including new documentation, expanded input variables, and updates to output data and plotting routines. The changes enhance the clarity, flexibility, and scientific accuracy of plasma fuelling calculations and reporting.

Key changes include:

1. Plasma Fuelling Model Documentation and Inputs

• Added a comprehensive new documentation page (plasma_fuelling.md) describing the plasma fuelling model, governing equations, constraints, and references. This improves transparency and usability for end users.
• Introduced several new input variables in process/core/input.py to support detailed plasma fuelling modeling, including recycling fractions, fuelling efficiency, injected rates, and fuel species fractions.

2. Output Data and Variable Naming

• Updated output files for several example tokamak cases to change the burn-up fraction variable name from burnup to f_plasma_fuel_burnupma_fuel_burnup for clarity and consistency.

3. Plotting and Reporting Enhancements

• Improved the main plasma information and fusion rate plots to use the new variable names and provide more precise outputs (e.g., more significant digits for power, updated units for densities, and inclusion of additional fusion rate details).
• Added the new plasma fuelling documentation page to the MkDocs navigation for easier access.

4. Constants and Codebase Maintenance

• Defined AVOGADRO_NUMBER in process/core/constants.py for scientific consistency and future use.
• Removed the unused or deprecated tauratio input variable to clean up the codebase.

5. Internal Model Integration

• Imported the new PlasmaFuelling model into the plotting module to enable future extensions and tighter integration of the fuelling model with data visualization.

These changes collectively improve the accuracy, documentation, and maintainability of the plasma fuelling model and its associated outputs.## Description

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.

[chris-ashe]

Opening this up now just to get the ball rolling with the review. @jonmaddock a discussion should be had about how we implement this into the regression tests, e.g is the 4 balance constraints always on as default

[jonmaddock]

As this is contingent on the wider "solution mode" work going in (which I am currently working on), I am converting this to a draft until that is merged.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 32.65993% with 200 lines in your changes missing coverage. Please review.
✅ Project coverage is 48.81%. Comparing base (d84e9dd) to head (3e5c5fd).

Files with missing lines	Patch %	Lines
process/core/io/plot/summary.py	4.13%	139 Missing ⚠️
process/models/physics/fuelling.py	43.54%	35 Missing ⚠️
process/models/physics/physics.py	5.55%	17 Missing ⚠️
process/core/solver/constraints.py	82.60%	4 Missing ⚠️
process/models/physics/fusion_reactions.py	0.00%	3 Missing ⚠️
process/core/scan.py	0.00%	1 Missing ⚠️
process/models/stellarator/stellarator.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4139      +/-   ##
==========================================
- Coverage   48.86%   48.81%   -0.06%     
==========================================
  Files         151      152       +1     
  Lines       29461    29671     +210     
==========================================
+ Hits        14397    14484      +87     
- Misses      15064    15187     +123     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.