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