Particle balance constraint updated

[chris-ashe]

This pull request introduces a comprehensive plasma fuelling model to the codebase, including new physical variables, input parameters, constraints, and documentation. The main focus is to enable detailed particle balance and burnup fraction calculations for deuterium, tritium, and helium-3 in the plasma, and to ensure consistency through new constraint equations. Several new variables and iteration parameters are added to support these models, and the documentation is expanded to explain the physical basis and equations.

Key changes:

1. Plasma fuelling and particle balance model:

• Added a detailed plasma fuelling model and particle balance equations for deuterium, tritium, helium-3, and alpha particles to the documentation (plasma_fuelling.md). This includes explanations of fuelling efficiency, recycling, and burnup fractions.
• Added new physics variables in PhysicsData for burnup fractions and detailed fusion reaction rates, enabling more granular tracking of fuel species and reactions.

2. New input and iteration variables:

• Introduced new input parameters in input.py for fuelling efficiency, injected fuel rates, and fuelling fractions for each species.
• Added corresponding iteration variables for these new inputs, allowing them to be varied during optimization and scans.

3. Particle balance and consistency constraints:

• Implemented new constraint equations (93–97) in constraints.py to enforce particle balance for tritium, deuterium, helium-3, alpha particles, and to ensure fuelling fractions sum to unity. These constraints help maintain physical consistency in the plasma model.
• Updated numerics to include these new constraints, increasing the total number of constraints and variables.

4. Documentation and navigation updates:

• Added the new plasma fuelling documentation page to the navigation in mkdocs.yml, making the new model easily accessible in the documentation site.

5. Miscellaneous improvements:

• Added Avogadro's number to the constants module for use in physical calculations.
• Improved output reporting for constraint errors in scan.py.

These changes collectively provide a robust framework for modeling plasma fuelling, tracking individual fuel species, and ensuring physical consistency in fusion plasma simulations.

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.

[j-a-foster]

Just a couple of notes, otherwise happy with the changes.

[j-a-foster]

Why are these /sec and not /s?

[j-a-foster]

Is it worth adding a note or legend that explains what the star means in the PDF?