User guide

• Configuring a simulation
• Domain parameters
• Species
• Solver parameters
• Boundary conditions
• External fields and sources
• Running simulations
• Output and diagnostics
• Plotting and animation
• Differentiable simulations
• Performance
• Units and normalisations

The user guide is organised by what you do with the code: Configuring a simulation explains how the input tree is structured and validated, and the following four pages list every parameter of each section with its default and meaning. Running simulations covers the Simulation object, re-running with different inputs, and recompilation. Output and diagnostics documents every key of the result dictionary. Differentiable simulations shows how to take gradients through a run, and Performance what to expect from compilation and scaling.