Major cleanup of initial and evolve modules

[danieljprice]

Description:
This is a refactoring effort to break up two of the major vomit-on-the-page modules (initial.F90 and evolve.F90) into manageable, smaller and modular chunks. There is no change in functionality.

The p-r also fixes a small bug in computing velocity derivatives when APR is employed, where there was a pmassi instead of a pmassj in the density routine

Components modified:

• Setup (src/setup)
• Main code (src/main)
• Moddump utilities (src/utils/moddump)
• Analysis utilities (src/utils/analysis)
• Documentation (docs/)

Type of change:

• Bug fix
• Physics improvements
• Better initial conditions
• Performance improvements
• Documentation update
• Cleanup
• Other (please describe)

Testing:
Code compiles and appears to work as previously

Did you run the bots? no

Did you update relevant documentation in the docs directory? no

Did you add comments such that the purpose of the code is understandable? yes

Is there a unit test that could be added for this feature/bug? yes

If so, please describe what a unit test might check:

• the major functionality that is not tested anywhere (and for which the logic is spread through several routines) concerns the procedures for changing dtmax on-the-fly. This could do with a unit test.

Related issues: #55

[gemini-code-assist]

Summary of Changes

Hello @danieljprice, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on enhancing the modularity and maintainability of the codebase through a substantial refactoring effort, particularly within the core initial and evolve modules. By decomposing complex routines into more focused subroutines, the code becomes easier to understand and manage. Alongside this structural improvement, a critical bug affecting velocity derivative calculations under specific conditions has been resolved, and new utilities for analyzing the spatial distribution of particles have been introduced. The changes aim to improve the overall robustness and clarity of the simulation framework.

Highlights

• Major Refactoring: The initial.F90 and evolve.F90 modules have undergone significant refactoring, breaking down large, monolithic subroutines into smaller, more modular and manageable routines. This improves code organization and maintainability without altering functionality.
• Bug Fix: A bug in dens.F90 was fixed where pmassi was incorrectly used instead of pmassj in the calculation of velocity derivatives when using the APR (Adaptive Particle Refinement) scheme.
• Particle Extent Calculation: New functionality has been added to centreofmass.f90 to compute and print the spatial extent (min/max coordinates and dimensions) of the particle distribution, excluding dead or accreted particles.
• Streamlined Conservation Checks and Dump Writing: The logic for conservation checks and dump file writing has been streamlined by consolidating related operations into new, dedicated wrapper subroutines, improving clarity and reducing redundancy.

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[gemini-code-assist]

Code Review

This pull request is a significant and well-executed refactoring of the initial.F90 and evolve.F90 modules. By breaking down these large modules into smaller, more manageable subroutines, you've greatly improved the code's readability, modularity, and maintainability. This is a fantastic cleanup effort.

The pull request also includes a critical bug fix in src/main/dens.F90, correcting the use of pmassi to pmassj in the velocity derivative calculation, which is an important correction.

My review focuses on ensuring the refactoring is clean and doesn't introduce new issues. I have one minor suggestion in src/main/initial.F90 to rename a subroutine to avoid potential confusion with another one of the same name, further enhancing clarity.