Experimental: indexed/flat particle backends

[rogeriojorge]

Summary

This PR adds physics-preserving, opt-in experimental particle backends that reduce CPU overhead via data layout changes:

• fast_backend = "indexed": stores per-particle cell indices + fractional offsets to avoid repeated position->index conversions.
• fast_backend = "flat": flattens all species into one container (uniform shape & periodic BCs) to reduce per-species overhead.

Core physics-kernel changes are limited to:

• PyPIC3D/boris.py (indexed interpolation/push)
• PyPIC3D/J.py (indexed current deposition + 1D/2D multi-species accumulation fix)
• PyPIC3D/evolve.py (indexed time loop)

All other touched files are routing/metadata only:

• PyPIC3D/indexed_particles.py (new container + periodic index normalization)
• PyPIC3D/flat_particles.py (new container)
• PyPIC3D/initialization.py (fast_backend routing + compatibility checks)
• PyPIC3D/utils.py (dump metadata for flat backend)

Usage

[simulation_parameters]
fast_backend = "indexed"  # or "flat"

Restrictions:

• Electrodynamic solver only (no electrostatic / vector potential)
• Periodic particle BCs required
• flat backend requires uniform particle shape + update flags across species

Benchmarks (CPU)

Configs: demos/two_stream/two_stream.toml, demos/weibel/weibel.toml, plotting disabled.

Variant	two_stream (s/step)	Speedup	weibel (s/step)	Speedup
baseline (origin/main)	5.55e-3	1.00x	2.15e-3	1.00x
default	2.29e-3	2.42x	1.16e-3	1.85x
fast_backend=indexed	2.66e-3	2.09x	1.22e-3	1.76x
fast_backend=flat	2.09e-3	2.66x	9.16e-4	2.35x
fast_mode=aggressive	1.94e-3	2.86x	9.68e-4	2.22x
fast_mode=extreme	1.83e-3	3.04x	9.04e-4	2.38x

Plots (artifacts branch)

Artifacts (plots + raw numbers) live in codex/cpu-5x-indexed-artifacts and are not intended to merge into main.

Runtime & speedup

Two-stream

Weibel

Raw numbers (artifacts branch)

• runtime_s_per_step.json
• two_stream_energy.json
• weibel_energy.json

[rogeriojorge]

As of now, it seems to be completely wrong, but the tests still pass. Perhaps we should harden the tests.