v0.2.0

What's new

Features

• Added cluster snapshot capture during sweeps and a new cluster snapshot plotter for visualization from saved .npz results
• Persisted cluster snapshots in sweep --save-data outputs

Fixes

• Fixed autocorrelation wraparound behavior
• Fixed CMR bond decomposition and cluster flip logic in the cluster algorithms
• Fixed CLI simulate argument handling to avoid duplicate kwargs

Tooling

• Added a CI smoke test for README examples
• Added Ruff formatting and pre-commit cleanup to the repo

Docs

• Updated README badges and cleaned up the CSD image section

v0.1.8

What's new

Features

• Split overlap cluster modes: monolithic overlap_update → separate houdayer_step, jorg_step, cmr_step with clean dispatch
• CMR grey cluster phase: full two-phase CMR algorithm (grey randomization + blue flip)
• Alternating overlap modes: "cmr+houdayer" syntax round-robins each overlap update call, with per-mode cluster stats
• Per-sample conditional sums: proper [A_s(q)]_J disorder averaging for link overlap variance
• Link overlap statistics: conditional variance A(q) = Var(q_l | q) and per-temperature link overlap moments

Improvements

• Exact dot-product overlap histogram (replaces artificial binning)
• Houdayer-N isoenergetic balanced-site criterion (replaces CMR-N)
• Per-sample overlap histograms returned from Rust for I(q)/X(q) metrics
• Extracted OverlapStats + OverlapAccum into statistics/overlap.rs

Fixes

• Fixed duplicate --collect-cluster-stats argparse flag in CLI

v0.1.7

What's new

• Overlap distribution P(q): collect and plot the full overlap histogram per temperature
• CMR-N generalization (experimental): overlap cluster updates with arbitrary group size N ≥ 2 — groups of N replicas are shuffled per temperature and flipped together. N ≥ 3 likely does not satisfy detailed balance; under active revision.
• Simplified overlap update: removed OverlapUpdateMode enum (swap / free) — the update now always flips all replicas in the group, equivalent to swap on active sites

Cleanup

• CI test for P(q) symmetry in the paramagnetic phase
• Removed overlap_update_mode parameter from Python API, CLI, and sweep runner

v0.1.6

What's new

Features

• Equilibration diagnostic Δ(t): Link-overlap energy identity (Zhu et al. 2015) tracks running averages of energy and q_l at power-of-2 checkpoints for thermalization monitoring. Available via --equilibration-diagnostic CLI flag, TOML config, and Python API.
• 3-replica CMR (cmr3): Overlap cluster updates with triply-satisfied bonds for 3+ replicas.
• Streaming autocorrelation: Integrated autocorrelation time τ_int(m²) and τ_int(q²) computed per realization, averaged across disorder.
• --sequential flag: Disable inner-loop parallelism so each disorder realization gets its own L1 cache.
• TOML config files: peapods sweep --config sweep_config.toml for reproducible parameter sweeps.

Codebase

• Restructured SweepResult with ClusterStats + Diagnostics substructs.
• Extracted Realization into simulation/realization.rs, autocorrelation into statistics/autocorrelation.rs.
• Added compute_link_overlaps to spins/energy.rs.
• Moved rayon parallelism over realizations from PyO3 into spin-sim crate.
• Profiling infrastructure: bench profile, profile feature, inline(never) attrs.

Fixes

• Ctrl+C now actually stops long simulations.
• Skip redundant energy recomputation during warmup.

v0.1.5

What's New

Features

• CLI: peapods simulate command for running simulations from the terminal without writing Python scripts
• Mean cluster size: site-weighted mean FK cluster size computed from CSD (mean_cluster_size attribute)

Fixes

• Heat capacity: fixed missing factor of N in heat_capacity computation (was off by n_spins)

Docs

• CLI-first quickstart examples in README
• MkDocs API docs and docstrings
• README badges, license, and crates.io link

Maintenance

• Consolidated and refactored test suite

v0.1.4

What's new

General Bravais lattice geometry

• Lattice now supports arbitrary neighbor offsets via Lattice::with_offsets(shape, offsets), enabling triangular, FCC, and other Bravais lattices
• Precomputed neighbor table replaces on-the-fly div/mod — faster lookups even for hypercubic
• New geometry/ module with hypercubic() and triangular() offset factories
• Python Ising class accepts neighbor_offsets parameter
• Triangular Binder crossing test validates T_c = 4/ln(3)

Cluster algorithms

• CMR (Chayes-Machta-Redner) blue-bond overlap cluster mode
• Jörg stochastic overlap cluster move
• Configurable overlap_cluster_mode (Wolff / SW) for all overlap updates
• On-the-fly CSD histogramming (no raw cluster size storage)
• Generic bfs_cluster + uf_bonds helpers with closure-based bond activation

Architecture

• spin-sim split into geometry/, spins/, mcmc/, clusters/, statistics/ submodules
• Parallel overlap update across all (temp, pair) slots with per-pair RNGs
• Rayon parallelism over disorder realizations

v0.1.3

Changes

Algorithm

• Reorder MC steps: ICM before PT to match Houdayer/Zhu convention

Docs

• Add README to PyPI listing and spin-sim crate on crates.io
• Add doc comments to all public items in spin-sim for docs.rs
• Add project metadata (description, license, keywords) to pyproject.toml and spin-sim/Cargo.toml

v0.1.2

What's new

• Split into spin-sim core crate + PyO3 wrapper: Pure Rust spin-sim library (zero Python deps) is now publishable to crates.io independently. The root crate is a thin PyO3 wrapper.
• Progress callback API: run_sweep_loop takes a generic on_sweep callback instead of indicatif::ProgressBar, keeping the core crate UI-agnostic.
• Workspace layout: Cargo workspace with spin-sim as a member; release workflow publishes both spin-sim to crates.io and peapods wheels to PyPI.

Other changes

• Parallel tempering over disorder realizations with rayon (Vec<Realization> + n_disorder API)
• Houdayer isoenergetic cluster move (ICM) + overlap observables
• CI fix for maturin venv targeting

v0.1.1

What's New

• Replica support — run multiple independent copies of the PT ladder (n_replicas parameter, replaces old ensemble interface)
• Overlap statistics — spin overlap q, q², q⁴ between replica pairs; spin glass Binder ratio
• Houdayer isoenergetic cluster move (ICM) — replica cluster move for spin glasses, exchanges clusters on the negative-overlap subgraph between replicas at the same temperature