These tutorials assume prior knowledge or understanding of various C++ language features and some libraries, including (at least): std::vectors, c_vectors, and abstract and concrete base classes.

To run any of these tutorials, call scons test_suite=<NAME_OF_TUTORIAL_FILE>, from the main chaste directory, e.g.

scons test_suite=ode/test/TestSolvingOdesTutorial.hpp

To do this, either call this from the command line, or create a new make target in eclipse, with the above command as the 'Build command'

See also a cancer Chaste practical and a cardiac Chaste practical.

Tutorials corresponding to released versions of Chaste can be found at https://chaste.github.io/releases/

Tutorials

The basics

• UserTutorials/WritingTests - start here, then choose any of the following three sections

Solving ODEs and PDEs

• UserTutorials/SolvingOdes
• UserTutorials/SolvingLinearPdes
• UserTutorials/SolvingNonlinearPdes

Cardiac Chaste

For executable users:

• UserTutorials/CardiacExecutable

Source code users:

• UserTutorials/RunningBidomainSimulations - basic bidomain simulation; note monodomain is virtually the same
• UserTutorials/AnotherBidomainSimulation - shows how to use varying fibre directions and different output formats in particular
• UserTutorials/Monodomain3dExample - illustrates the (trivial) changes required to go from 2d to 3d, or bidomain to monodomain
• UserTutorials/BidomainWithBath
• UserTutorials/BidomainWithBathAndFibres
• UserTutorials/CardiacCheckpointingAndRestarting

Cell-based Chaste

• UserTutorials/RunningCryptSimulations
• UserTutorials/RunningTumourSpheroidSimulations
• UserTutorials/CreatingAndUsingANewCellCycleModel
• UserTutorials/CreatingAndUsingANewCellKiller
• UserTutorials/CreatingAndUsingANewCellPopulationBoundaryCondition
• UserTutorials/CreatingAndUsingANewForce
• UserTutorials/CreatingAndUsingANewCellMutationState
• UserTutorials/CreatingAndUsingANewCellProperty
• UserTutorials/RunningVertexBasedSimulations
• UserTutorials/VisualizingWithParaview

Solid Mechanics (incl. cardiac electro-mechanics)

• UserTutorials/SolvingElasticityProblems - computing the deformation of a nonlinearly elasticity body
• UserTutorials/CardiacElectroMechanics

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Automatically generated alphabetical listing

• AnotherBidomainSimulation Another example showing how to run a bidomain simulation
• BidomainWithBath An example showing how to run a bidomain simulation for tissue contained in a perfusing bath
• BidomainWithBathAndFibres Running a bidomain simulation with a bath and fibres
• CardiacCheckpointingAndRestarting Checkpointing and restarting cardiac simulations
• CardiacElectroMechanics Cardiac Electro-mechanical Problems
• CardiacExecutable Using the cardiac executable
  • BidomainSimulationsWithPerfusingBath Running a bidomain simulation of cardiac tissue contained in a perfusing bath
  • CheckpointingAndRestarting Checkpointing
  • DrugAction Running a simulation with multiple-channel drug action
  • HardCodedCellModels Hardcoded cell model options
  • HeterogeneousExample Simulations with heterogeneities
  • MeshConvert Making the `MeshConvert` utility and using it the help produce scalable mesh loading
  • Propagation1d Running a simple example: propagation in a tissue fibre
  • Propagation3d 3D on a realistic cardiac geometry
  • S1S2Protocol Running a simulation of a spiral wave in 2d mesh
  • UsingCellmlFiles UserTutorials/CardiacExecutable/UsingCellmlFiles
  • UsingFibreDefinitions Using fibre directions and postprocessing
• CreatingAndUsingANewCellCycleModel An example showing how to create a new cell-cycle model and use it in a cell-based simulation
• CreatingAndUsingANewCellKiller An example showing how to create a new cell killer and use it in a cell-based simulation
• CreatingAndUsingANewCellMutationState An example showing how to create a new cell mutation state and use it in a cell-based simulation
• CreatingAndUsingANewCellPopulationBoundaryCondition An example showing how to create and use a new cell population boundary condition
• CreatingAndUsingANewCellProperty An example showing how to create a new cell property and use it in a cell-based simulation
• CreatingAndUsingANewForce An example showing how to create and use a new force
• Monodomain3dExample 3D monodomain example
• RunningBidomainSimulations An example showing how to run bidomain simulations
• RunningCryptSimulations Examples showing how to run crypt simulations on periodic meshes with different cell-cycle models
• RunningTumourSpheroidSimulations An example showing how to run tumour spheroid simulations
• RunningVertexBasedSimulations Examples showing how to create, run and visualize vertex-based simulations on periodic meshes with different cell-cycle models
• SolvingElasticityProblems Solving solid mechanics problems
• SolvingLinearPdes Examples showing how to solve linear elliptic and parabolic PDEs
• SolvingNonlinearPdes An example showing how to solve a nonlinear elliptic PDE. Also includes function-based boundary conditions
• SolvingOdes In this tutorial we show how Chaste can be used to solve an ODE system
• VisualizingWithParaview Examples showing how to visualize simulations in Paraview
• WritingTests Writing tests