on-the-fly rotation tracker following ParticlesMC architecture

[cyfraysse]

Two new algorithms

1- ComputeRotation —> [[simulation.observable]]

• Updates system.phi at every compute step
• Handles three methods via theta_T convention:
  • 0.0 → Integral (relay every step)
  • π → Euler (compare to initial frame)
  • any other value → Threshold (relay when rotation exceeds theta_T)
• Internal state (R0, R_ref, phi_acc) kept in RotationState, one per chain

2- StorePhiTrajectories —> [[simulation.output]]

• Reads system.phi and writes to disk on its scheduler
• One file per theta_T per chain: chains/1/phitrajectories_k.dat

Key design decisions

• system.phi added to Molecules struct right after position — rotation vectors live on the system like positions
• New [[simulation.observable]] TOML section for non-output algorithms
• Parallelizes across chains using Transducers.Map, following the same pattern as Arianna's Metropolis algorithm

TOML usage

[[simulation.observable]]
algorithm = "ComputeRotation"
scheduler_params = {linear_interval = 1}
parameters = {theta_T = [0.0, 0.7854, 3.1416]}

[[simulation.output]]
algorithm = "StorePhiTrajectories"
scheduler_params = {linear_interval = 1, log_base = 2.0}

Note: depends on TheDisorderedOrganization/Arianna.jl#87

[codecov]

Codecov Report

❌ Patch coverage is 89.53488% with 18 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/ParticlesMC.jl	0.00%	17 Missing ⚠️
src/rotation.jl	99.34%	1 Missing ⚠️

Files with missing lines	Coverage Δ
src/molecules.jl	69.89% <100.00%> (+0.32%)	⬆️
src/rotation.jl	99.34% <99.34%> (ø)
src/ParticlesMC.jl	7.31% <0.00%> (-1.18%)	⬇️

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[romainljsimon]

I like this version a lot, thanks @cyfraysse for the nice PR!
Let's wait for the StoreLastPhiFrame method before merging the PR :)

[romainljsimon]

I was also thinking we could change the phi variable to Φ !

[V-Francois]

Great stuff, I just have a few minor comments.

Could you maybe add a test in the test folder that runs this? Just to have an end-to-end working case.

[cyfraysse]

I've added the StoreLastPhiFrame, corrected the few remarks you both did and added a little test on the different rotation algorithms