v0.6.0

What's new in v0.6.0

New features

Förster theory (#78)

• absorption_spectrum and emission_spectrum — vibronic lineshapes from Franck-Condon factors with Gaussian broadening, temperature-weighted
• spectral_overlap — overlap integral between donor emission and acceptor absorption
• forster_rate(J, donor, acceptor) — Förster EET rate scaling as J²
• forster_rate_matrix(aggCore) — pairwise rate matrix for all molecules in an aggregate

Modified Redfield theory (#79)

• exciton_basis — transform site-basis Hamiltonian to exciton basis
• modified_redfield_rates — population transfer rates using full non-perturbative lineshape treatment
• modified_redfield_dynamics — time evolution of populations under modified Redfield

Spectral density (#79)

• SpectralDensity, spectral_density — bath spectral density from discrete LHO modes
• reorganization_energy — λ from J(ω)
• lineshape_function, lineshape_derivative, lineshape_second_derivative — g(t) and derivatives

Transition dipole moments (#80)

• TransitionDipole — store 3D position (Å) and dipole vector (Debye)
• dipole_dipole_coupling — point-dipole J from geometry and orientation
• coupling_from_dipoles — full coupling matrix for an aggregate
• AggregateCore(molecules, dipoles) constructor convenience overload

Corrected memory kernel (#88, #89, #90)

• analytic_correlation_nn, analytic_correlation_nn_high_T — closed-form bath correlation functions
• zeroth_order_memory_kernel_cf, zeroth_order_memory_kernel_high_T — M⁰ from correlation functions
• first_order_memory_kernel_cf, first_order_memory_kernel_high_T — M¹ with non-equilibrium bath correction
• corrected_rates_cf, corrected_qme_rdm — iterative RDM solver with corrected kernel
• site_to_exciton_kernel — transform memory kernel to exciton basis

Bug fixes

• #86 — Fix missing ρ factor in default iterative QME bath correction (W_abcd_1_bath_core). The ad(rho_t2, W_bath_t2, ...) result was erroneously overwritten with bare W_bath_t2, dropping the ρ_{cd}(t₂) weighting.
• #87 — Fix docstring labels M_2, M_3, M_4 in memory_kernel.jl (all previously said M_1); remove unused type parameters U, V from QME_sS_exact.

Internal

• src/ reorganized into subdirectories: base/, aggregate/, evolution/, spectroscopy/, utils/
• 5 new test files covering all new features (443 new tests)
• Tutorials: simulation method comparison notebook added

Resolved issues

#78, #79, #80, #86, #87, #88, #89, #90

v0.5.0

What's Changed

New Features

• #68 Add SimulationResult type with populations accessor — consistent return value across all solvers
• #71 Add unified solve() entry point dispatching to all solvers
• #75 Add convenience constructors for common systems: setup_dimer, setup_trimer, setup_linear_chain
• #69 Add molecule-only coupling matrix constructor for AggregateCore — no more +1 ground state offset confusion
• #72 Add physical validation functions for density matrix states

Refactoring

• #76 Replace symbol if/elseif dispatch chains with type dispatch for vib_basis
• #66 Standardize all exported function names to snake_case with backward-compatible deprecated aliases

Documentation

• #67 Rewrite dimer tutorial to use current API
• #70 Add naming conventions glossary
• #74 Add solver selection guide
• #73 Fix unit conversion: use Julia pi, consolidate tspan_cm_to_fs

Developer Experience

• Add commit-msg hook to block Co-Authored-By AI attribution (.githooks/)
• Add setup instructions to CONTRIBUTING.md

Full Changelog: v0.4.0...v0.5.0

v0.4.0

What's Changed

Bug Fixes

• #52 Fix risky divisions in master_iterative.jl — replace exact ==0 checks with tolerance-based guards using _safe_div/_safe_inv helpers
• #60 Fix unsafe divisions in trace.jl and rate_constant.jl — same safe division pattern applied throughout
• #65 Remove hardcoded OpenQuantumSystems. module self-references in aggregateTools.jl and trace.jl

Refactoring

• #61 Extract shared integration setup boilerplate into _setup_integration helper — eliminates ~150 duplicated lines across 4 solver files
• #62 Refactor deeply nested getAggHamInteraction in aggregateOperators.jl — reduced from 5 levels of nesting
• #63 Remove Union{T, Nothing} fields from Aggregate struct — fields are now non-nullable
• #64 Replace hardcoded 2-level system magic numbers with named constants in molecules.jl and aggregateOperators.jl

Other

• Added ISSUES.md with full code quality audit, UX analysis, and Julia pattern recommendations
• Added project-level Claude Code settings (disables co-author attribution)

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's changed

Code quality & Julia 1.12 compatibility (#50–#58)

• #50 — Refactored master_ansatz.jl: eliminated 8-way duplication in QME_sI_ansatz_* functions; unified into a single QME_sI_ansatz with ansatz::Symbol dispatch and backward-compatible wrappers
• #51 — Refactored master_iterative.jl: consolidated duplicated solvers into QME_sI_iterative with method::Symbol dispatch; removed all _old versions
• #52 — Fixed risky division in master_iterative.jl that could silently produce Inf; replaced with safe element-wise inverse
• #53 — Replaced typeof(rho) <: Operator type-checking anti-pattern with proper Julia dispatch via _to_matrix helper
• #54 — Replaced bare positional parameter tuples in ODE callbacks with NamedTuple for clarity and safety
• #55 — Added input validation for magic symbol strings (vib_basis, picture, mode flags) with descriptive ArgumentError
• #56 — Fixed potential nothing return in trace.jl when vib_basis doesn't match any branch
• #57 — Improved type annotations throughout: replaced bare ::Array with ::AbstractMatrix / ::AbstractVector
• #58 — Cleaned up technical debt: removed dead make.bat, resolved duplicate _to_matrix definition

GitHub Actions modernization

• Updated all CI workflows to Julia 1.12
• Updated all action versions (checkout@v4, setup-julia@v2, julia-actions/cache@v2, codecov@v4)
• Fixed compat-helper.yml which was written in GitLab CI syntax and never ran
• Fixed docs.yml: added missing setup-julia and cache steps, updated Documenter compat to v1

Full changelog: v0.2.0...v0.3.0

v0.2.0

OpenQuantumSystems v0.2.0

Diff since v0.1.7

v0.1.7

OpenQuantumSystems v0.1.7

Diff since v0.1.6

v0.1.6

OpenQuantumSystems v0.1.6

Diff since v0.1.5

Merged pull requests:

• Devel (#41) (@detrin)
• Updating Readme (#43) (@detrin)
• Devel (#45) (@detrin)
• CompatHelper: add new compat entry for "Interpolations" at version "0.13" (#46) (@github-actions[bot])
• Devel (#47) (@detrin)

v0.1.5

OpenQuantumSystems v0.1.5

Diff since v0.1.4

Merged pull requests:

• Devel (#32) (@detrin)
• CompatHelper: add new compat entry for "StableRNGs" at version "1" (#34) (@github-actions[bot])
• Devel (#35) (@detrin)
• Devel (#39) (@detrin)

v0.1.4

OpenQuantumSystems v0.1.4

Diff since v0.1.3

Merged pull requests:

• CompatHelper: bump compat for "QuantumOpticsBase" to "0.3" (#29) (@github-actions[bot])
• Devel (#30) (@detrin)

v0.1.3

OpenQuantumSystems v0.1.3

Diff since v0.1.2