⚡ Profiler: Fused Diffusion-Reaction Loop

[fderuiter]

📉 The Bottleneck: The TuringSystem::step method was performing two passes over the state vectors: one for diffusion (reading u, v, writing next_u, next_v) and one for reaction/integration (reading all four, writing next_u, next_v). This double memory traversal was limiting throughput.
🚀 The Boost: Before: ~537ms -> After: ~257ms (52% improvement / 2.08x speedup).
💻 Technical Detail: Added apply_step to SpatialDiffusion trait and implemented it for FiniteDifference1D using a fused loop that computes the Laplacian and immediately applies the reaction and Euler step, keeping data in registers/L1 cache.
🧪 Verification: Logic preservation verified with test_turing_system_logic_preservation. Performance verified with bench_morphogenesis.

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PR created automatically by Jules for task 2088545017155205550 started by @fderuiter

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[Copilot]

Pull request overview

This PR optimizes the reaction–diffusion “TuringSystem” stepping routine by fusing diffusion, reaction, and Euler integration into a single pass to reduce memory bandwidth pressure and improve runtime throughput.

Changes:

• Added a new apply_step method to the SpatialDiffusion trait with a default (non-fused) implementation.
• Updated TuringSystem::step to use SpatialDiffusion::apply_step instead of separate diffusion + reaction/integration passes.
• Implemented a fused apply_step hot path for FiniteDifference1D using a sliding-window stencil and unsafe indexing.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.

File	Description
math_explorer/src/biology/morphogenesis.rs	Switches the main Turing step to the new fused diffusion+reaction+integration entry point.
math_explorer/src/biology/diffusion.rs	Extends the diffusion trait with apply_step and provides an optimized fused implementation for FiniteDifference1D.

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[Copilot]

These assert! length checks execute in release builds and add overhead on the step hot path. If the goal is maximum throughput, consider using debug_assert! (or feature-gating the checks) so they’re compiled out in optimized builds while still catching issues during development/testing.

Suggested change

	assert!(v.len() >= n, "v buffer too small");
	assert!(out_u.len() >= n, "out_u buffer too small");
	assert!(out_v.len() >= n, "out_v buffer too small");
	debug_assert!(v.len() >= n, "v buffer too small");
	debug_assert!(out_u.len() >= n, "out_u buffer too small");
	debug_assert!(out_v.len() >= n, "out_v buffer too small");

[Copilot]

The closure parameters |u, v| shadow the outer u/v slice bindings in this function, which makes the fused-step call harder to read. Renaming the closure parameters (e.g., u_curr, v_curr) or using a small helper function would avoid the shadowing.

Suggested change

	.apply_step(u, v, next_u, next_v, self.d_u, self.d_v, dt, |u, v| {
	self.kinetics.reaction(u, v)
	.apply_step(u, v, next_u, next_v, self.d_u, self.d_v, dt, |u_curr, v_curr| {
	self.kinetics.reaction(u_curr, v_curr)

[Copilot]

SpatialDiffusion is a public trait, and adding a generic method (apply_step<F>) makes the trait non-object-safe. Any downstream code that used dyn SpatialDiffusion (e.g., Box<dyn SpatialDiffusion>) will stop compiling. If object safety/backwards compatibility matters, consider moving apply_step to a separate extension trait, or changing the signature to take reaction: &mut dyn FnMut(f64, f64) -> (f64, f64) (non-generic) to preserve object safety.

[Copilot]

The reaction callback is constrained to Fn, which prevents callers from passing closures that need internal mutable state (those require FnMut). Since Fn closures also implement FnMut, changing the bound to FnMut(f64, f64) -> (f64, f64) would be strictly more flexible without impacting current call sites.

Suggested change

	reaction: F,
	) where
	F: Fn(f64, f64) -> (f64, f64),
	mut reaction: F,
	) where
	F: FnMut(f64, f64) -> (f64, f64),