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Changed the section heading from 'Simulation Output' to 'Output' in docs/user/output.md for consistency and brevity.
Added new parameters to the Soulsby method configuration in population.schema.json, including flow_field_name, background_grain_size, soulsby_b_e, soulsby_theta_s, soulsby_gamma_e, soulsby_mu_d, and soulsby_freedom_factor. Updated descriptions for legacy parameters f and r to clarify their status. Will probably get rid of these later
Updated ParticlePopulation to determine particle exposure based on the selected transport_probability method. The update_position method now accepts a transport_probability_method argument, and Simulation passes the configured method when updating particle positions.
Introduces debug_sedtrails.py, a script to facilitate debugging of SedTRAILS simulations in VS Code, because Stuart was having a hard time doing it from the command line. The script allows step-through debugging, breakpoint setting, and targeted testing of configuration loading and simulation object creation.
Updated plot title and comments to specify that the average distance is calculated per output timestep, improving clarity in the simulation dashboard.
Refactored variable names in read_netcdf for clarity and improved plot_trajectories to better determine the output directory when saving plots. The CLI now only displays a message when the plot is shown, not when saved.
Removed the legacy 'f' and 'r' parameters from the Soulsby method configuration and introduced a new 'tracer_grain_size' property to specify the grain size of tracer sediment.
The _get_output_dir method now resolves default or relative output directories relative to the config file's location, ensuring outputs are placed consistently regardless of the working directory. This change improves usability when running simulations from different paths.
Updated PhysicsConverter and Soulsby physics plugin to use 'tracer_grain_size' instead of 'grain_diameter' when the Soulsby method is selected. Added validation for missing 'tracer_grain_size' in configuration and included comments to vectorize nested loops for performance improvements.
local testing and debugging
Renamed and updated particle populations to 'FineSand' and 'MediumSand' with revised grain sizes, tracer parameters, and seeding strategies. Adjusted transport probability to 'no_probability' and modified bounding boxes and number of locations for random seeding. Commented out the output directory path.
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Updated soulsby and related scripts such that soulsby now seems to run for concrete bed (no_probability). Has not yet been tested extensively.