User Guides

Users can download the latest stable release of the source code from our GitHub releases page, or checkout the develop branch to get the latest features.

Installation#

• Install Guides: How to install Chaste and its dependencies.
• CMake First Run Guide: How to configure, build, and run tests to check the installation.

Running Chaste Simulations#

• Tutorials: Detailed lessons on using Chaste’s capabilities.
• Visualisation Guides: Information on how to visualise simulation results.
• How-to Index: Links to code snippets illustrating how various things can be done in Chaste.
• User Projects: Creating/using a project which can utilize the core Chaste code and build/testing framework.

Code Documentation#

• Changes Since Last Release
• Release Notes
• API Documentation

Miscellaneous Information#

• Chaste Units: Units of parameters used in Chaste.
• Default Cardiac parameter values: These are read off from heart/src/problem/HeartConfigDefaults.hpp (ignore the Simulation block, which only applies to the old cardiac executable).
• File Formats: This information is given in the version of docs/FileFormats.html supplied with the release.

Advanced#

• Boost Serialization: Notes on using the the Serialization library from Boost to checkpoint and save/resume simulations.
• Cardiac Mechanics Solvers: A bit of information on how the cardiac mechanics solvers are connected to the main mechanics solvers.
• Cell-based Chaste Code Structure: An overview of the structure of the cell-based Chaste codebase.
• Code Generation from CellML: Notes on generating Chaste code for cardiac cell models from CellML files, using chaste_codegen.
• Finding Chaste Dependencies: Notes on manually setting hints for Chaste dependency locations if they are not found automatically.
• Finite Element Assemblers and Solvers: Notes on how PDE assemblers and solvers work internally.
• Finite Element Implementations: A lists of the equations and finite element implementations used in various solvers in the Chaste codebase.
• Installing chaste_codegen: Guidance on manually installing chaste_codegen.
• Running Binaries From Command Line: How to run binaries directly rather than via ctest.
• Solving Cardiac Problems: A high-level overview of the code execution flow when solving a cardiac problem.
• State Variable Interpolation: How and when to use state-variable interpolation to compute the ionic current in tissue simulations.
• Structure of Cell-based Simulations: An overview of the steps involved in setting up and running a cell-based simulation.