Introduction for new users

• Getting Started How to install AGILE and run your first test problem.
• Acknowledgments Information on collaboration and financial support.
• FAQ Frequently asked questions.
• Examples An overview of documented example simulations.
• Contributing to AGILE and its documentation
• Documentation How the documentation works.

General

• Equations The equations and parameters in physics modules.
• Coordinate systems Cartesian, spherical, cylindrical and logarithmic-radius geometries, the geometric source terms each one adds, and the polar axis.
• Parameters Description of all parameters in "amrvac.par" parameter file.
• Auxiliary variables Description of the intended use for nw, nwflux, nwaux, nwextra, nwauxio parameters.
• Command line Help on command-line parameters.

Discretization methods and AMR strategy

• Discretization The equation and its discretization, the basic variables, the structure of the grid, boundaries, ghost cells.
• AMR aspects Some essential info on global parameters and the data structures for the block-tree AMR.

Additional Physics

• Radiative cooling Description of adding radiative cooling.

IO and data analysis

• File format Description of the format of AGILE data file (.dat).
• Visualisation and analysis in Python with yt without data conversion.
• Converting data files for visualization Brief notes on how to convert to Tecplot (.plt), and VTK (.vtu) data files.
• Slices How to output hypersurfaces (slices) for restart or visualization.
• Line of sight views How to output collapsed views for visualisation and analysis (e.g. column densities).
• Analysis routine Using the run-time analysis routine.
• 3D Printing A note on how to generate 3D printed results.