1535 particle bed modificaiton and alternative packing algorithms

[danieljvickers]

Description

As requested by @sbryngelson, the particle "bed" code has been renamed to an appropriate particle "cloud". In addition I separated out the particle cloud generation into two separate subroutines. One iterates through all clouds and sorts them by packing method. The other contains all of the generation for a specific packing method.

This will enhance the ability to build upon the code, as users can now add their specific packing algorithm of choice as a case-file-selectable parameter. This architecture should make it easier for others to edit the code and maintain cleanliness moving forward.

Closes #1535

Type of change (delete unused ones)

• Refactor

Testing

Ran CPU tests locally (all modifications are CPU-only)

[github-actions]

Claude Code Review

Head SHA: 4fbeacd

Files changed:

• 14
• docs/documentation/case.md
• src/common/m_constants.fpp
• src/common/m_derived_types.fpp
• src/simulation/m_checker.fpp
• src/simulation/m_global_parameters.fpp
• src/simulation/m_mpi_proxy.fpp
• src/simulation/m_particle_cloud.fpp
• src/simulation/m_start_up.fpp
• toolchain/mfc/case_validator.py
• toolchain/mfc/params/definitions.py

Findings

Missing Python-side validation for packing_method in case_validator.py

definitions.py adds packing_method as a new particle_cloud attribute with a hard constraint (only value 1 is valid). The Fortran-side check is correctly added in m_checker.fpp:

@:PROHIBIT(particle_cloud(i)%packing_method == dflt_int, ...)
@:PROHIBIT(particle_cloud(i)%packing_method /= 1, ...)

However, case_validator.py (which is changed in this PR) has no corresponding check for packing_method. Per the project's parameter system rules (.claude/rules/parameter-system.md): "Add validation rules if the parameter has physics constraints." This means ./mfc.sh validate case.py will silently accept a case with an invalid or omitted packing_method, and the error is only caught at simulation startup. Given that packing_method is currently a required enum field with a single valid value, the Python validator is the right place to surface this early.

[danieljvickers]

AI is correct, and comment has been addressed

[codecov]

Codecov Report

❌ Patch coverage is 80.40541% with 29 lines in your changes missing coverage. Please review.
✅ Project coverage is 60.80%. Comparing base (68dbb6b) to head (865a737).

Files with missing lines	Patch %	Lines
src/simulation/m_particle_cloud.fpp	82.24%	12 Missing and 7 partials ⚠️
src/simulation/m_start_up.fpp	46.15%	6 Missing and 1 partial ⚠️
src/simulation/m_checker.fpp	57.14%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1539   +/-   ##
=======================================
  Coverage   60.80%   60.80%           
=======================================
  Files          73       73           
  Lines       20199    20209   +10     
  Branches     2932     2933    +1     
=======================================
+ Hits        12281    12289    +8     
- Misses       5932     5933    +1     
- Partials     1986     1987    +1     

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