Acherus

Acherus v0.8.0 🚀 New Features 🧩 Configuration Replaced the options configuration module with a new config class that unifies all user-related options. Input options are now provided through a dictionary at the __main__ entry. Added a new gpu boolean variable as an entry in the config dictionary, in preparation for future GPU-acceleration. Removed the method_raman string variable from the config dictionary, since only a single trapezoidal integration method is now used. Added a package-oriented CLI/config flow with TOML loading in __main__, optional --output override, and standardized output-path handling through configuration and path helpers. 🧩 Plotting Simplified and renamed some variables and classes for simplicity. Plot1D now plots beam radius using a new compute_radius() function and beam fluence loaded fluence_rz data. Plot2D now supports log-scale plotting for radial vs time images using the contourf function. Plot2D now supports new colormap options via the third party library cmasher, which provides better color gradients and considers color vision deficiencies. The monitoring module now imports input and output data paths from the paths submodule in data. The monitoring and plotting modules now have clearer defaults/options, stricter validation, and cleaner plotting controls. 🧩 Mesh Modified the radial grid index to go from 0 to N (instead of from 0 to N + 1) to matching boundary conditions. 🧩 Solvers Refactored core propagation internals: unified FCN and SSCN variants, improved linear-step performance with tridiagonal LAPACK workflows, and added optional radial PML support. Renamed the base submodule to shared to match the solver structure. Added a new Adams-Bashforth two-step (AB2) integrator for nonlinear terms. All solvers now use AB2 to preserve Crank-Nicolson accuracy; the first propagation step is computed using the Forward Euler method. shared module now initializes all arrays to zero to prevent use of uninitialized memory or empty values. Refactored Crank-Nicolson matrix creation into a single compute_matrices() routine. FCN solver now precomputes and stores the matrices in parallel using ThreadPoolExecutor() for faster execution. FCN solver now uses ThreadPoolExecutor() for parallel computation across frequency slides in compute_envelope(). Every single z-independent coefficient which depends on frequency, such as constants optical shock operators, is now precomputed and stored as a 1D array and passed to compute_nonlinear() functions for faster computation and reduced floating-point errors. 🧩 Physics Added a new keldysh module replacing previous ionization approaches. It computes ionization rates over a desired intensity interval and provides an interpolating object to convert intensity arrays into ionization rates. Supports gaseous and condensed media, including the multiphoton limit and the full generalized Keldysh theory. Added a new medium module storing medium properties from config and dispersive properties from sellmeier. Refactored laser and grid modules to use input options from the config class. Added molecular correction and electron momentum dependence for ionization rates of gases based on Mishima et al. in the keldysh module. 🧩 Constants Added a new constants.py module to centralize physical and mathematical constants across the package. 🧩 Functions Removed the mathematics folder; replaced with a functions folder containing all previous modules. Moved compute_radius() to plotting module to increase execution speed by avoiding unnecessary computation inside the propagation loop and storage in diagnostics files. Refactored fourier imports to use the gpu boolean from computing_backend option in config. CuPy's backend cufft is now used only when gpu=true and the library is available; otherwise SciPy fft() and ifft() is used. compute_raman() now uses a second-order trapezoidal integration method for the Raman integral. Removed unused SciPy solve_ivp() routines. compute_nonlinear() now uses z-independent frequency tables for faster broadcasting computations. Optimized compute_density() and compute_nonlinear() with in-place operations using temporary buffer arrays _nlin_tmp_t, _nlin_tmp_w, and dens_tmp_buf to improve speed. Replaced RegularGridInterpolator for intensity/ionization 2D arrays with SciPy's linear make_interp_spline interpolation along the time axis only. Replaced interp1d in keldysh with SciPy's cubic PchipInterpolator for monotonic, shape-preserving interpolation. Added keldysh_rates and keldysh_sum functions for truncated series computation of Keldysh ionization rates. Added sellmeier functions providing complete Sellmeier formulas for air, water, and silica. 🧩 Data validate_step in diagnostics now saves propagation results in case of failure. Output_manager is initialized in __main__ and accessible from shared to save results when density or envelope values overflow. Removed profiling capabilities from diagnostics, as they are no longer needed. 🏷️ Other Features 🔁 Tests Added a tests folder for development and quality control through GitHub Actions workflows. 📚 Documentation and Examples Added a docs folder for Read The Docs powered by Sphinx, hosting the official up-to-date documentation. Acherus is now an official PyPI package. Install it from PyPI. Added an examples folder with four configuration examples: 001_air_IR_ps.toml, 002_air_IR_fs.toml, 003_water_IR_fs.toml, and 004_water_UV_fs.toml. Moved README.md to the repository root and updated badges. 🐍 Build and Compatibility Added repository automation under the .github folder for nightly tests, Codecov, and manual badge generation. Added release-notes guidance in .github/agent/release_notes_agent.md. Renamed main entry as __main__ to comply with Python CLI standards. Removed old directory in favor of Git version control. Updated release-readiness metadata (PyPI URL normalization and README badge/link cleanup, including Codecov, LoC, and LoD). 🎨 Code Style Improved various helper module descriptions. Configuration options now accept uppercase and lowercase strings. Applied consistency/readability cleanups across touched plotting/function modules. 🛡️ Security Added SECURITY.md file to the repository root. 🐛 Bug-fixes Fixed compute_envelope() in fcn module: mats_right was incorrectly used in solve_banded() instead of mats_left. Fixed fourier import error when CuPy was unavailable; previously, global backend cufft was used alongside SciPy workers option. Fixed axis node conversion from float to integer in init_grid_nodes within the plotting module. Fixed --radial-limit parser argument value not being converted to float. Fixed duplicated axis data in init_sliced_arrays and flip_radial_data when plotting radially symmetric figures. Fixed overflow in snapshot_z_index; data type changed from int16 to uint16. Fixed elementwise unit conversion, small-z snapshot formatting, flat-ended rt log colorbars, and corrected beam-radius extraction. Fixed plotting CLI argument parsing consistency: --radial-symmetry True/False boolean conversion, and numeric range parsing/validation. Fixed SSCN propagation duplicate ion-rate handling and boundary alignment issues. 📝 Full changelog | N commits | 📚 Docs | 🔁 Tests | 🐛 Fixes | 🎨 Style | 🚀 Features | Other ||----------------|----------|----------|----------|----------|-------------|--------|| % of Commits | 11% | 4% | 25% | 10% | 44% | 6% | Full changelog: https://github.com/ismatorresgarcia/acherus/compare/v0.7.0...v0.8.0