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'
Tutorials corresponding to released versions of Chaste can be found at https://chaste.github.io/releases/
The basics
- UserTutorials/WritingTests - start here, then choose core/cardiac/cell-based
Core functionality
Solving ODEs
Solving PDEs
- UserTutorials/SolvingLinearPdes
- UserTutorials/SolvingNonlinearPdes
- UserTutorials/SolvingLinearParabolicPdeSystemsWithCoupledOdeSystems
Writing new PDE solvers (advanced)
Solid Mechanics
- UserTutorials/SolvingElasticityProblems - computing the deformation of a nonlinearly elastic body
- UserTutorials/SolvingMoreElasticityProblems
Cardiac Chaste
For executable users:
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
- UserTutorials/CardiacElectroMechanics
See also cardiac Chaste practical for details of a practical we have used to teach cardiac Chaste.
Cell-based Chaste
Where to start with cell-based simulations:
Running basic simulations:
- UserTutorials/RunningMeshBasedSimulations - the simplest (and first to be implemented in Chaste) type of cell-based simulation, start here
- UserTutorials/RunningNodeBasedSimulations - includes details of how to simplify cell-based tests
- UserTutorials/RunningVertexBasedSimulations - includes adding boundary conditions and removing cells from simulations
- UserTutorials/RunningPottsBasedSimulations - lattice based simulations
- UserTutorials/VisualizingWithParaview
Running crypt-specific simulations:
- UserTutorials/RunningMeshBasedCryptSimulations
- UserTutorials/RunningVertexBasedCryptSimulations
- UserTutorials/RunningCryptSimulationsWithMutations
More advanced examples:
- UserTutorials/RunningContactInhibitionSimulations
- UserTutorials/RunningDeltaNotchSimulations
- UserTutorials/RunningTumourSpheroidSimulations
Adding new functionality:
- UserTutorials/CreatingAndUsingANewCellCycleModel
- UserTutorials/CreatingAndUsingANewCellKiller
- UserTutorials/CreatingAndUsingANewCellPopulationBoundaryCondition
- UserTutorials/CreatingAndUsingANewForce
- UserTutorials/CreatingAndUsingANewCellMutationState
- UserTutorials/CreatingAndUsingANewCellProperty
See also cell-based Chaste practical for details of a practical we have used to teach cell-based Chaste.
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
- CellBasedDemo Examples showing how to create, run and cell-based simulations in Chaste
- 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
- RunningContactInhibitionSimulations An example showing how to use the contact inhibition cell cycle model (with the contact inhibition simulator)
- RunningCryptSimulationsWithMutations Examples showing how to run crypt simulations with various mutations
- RunningDeltaNotchSimulations An example showing how to run Delta/Notch simulations
- RunningMeshBasedCryptSimulations Examples showing how to run crypt simulations on periodic meshes with different cell-cycle models
- RunningMeshBasedSimulations Examples showing how to create, run and visualize mesh-based simulations
- RunningNodeBasedSimulations Examples showing how to create, run and visualize node-based simulations
- RunningPottsBasedSimulations Examples showing how to create, run and visualize Potts-based simulations
- RunningTumourSpheroidSimulations An example showing how to run tumour spheroid simulations
- RunningVertexBasedCryptSimulations Examples showing how to create, run and visualize vertex-based simulations on periodic meshes with different cell-cycle models
- RunningVertexBasedSimulations Examples showing how to create, run and visualize vertex-based simulations
- SolvingElasticityProblems Solving solid mechanics problems
- SolvingLinearParabolicPdeSystemsWithCoupledOdeSystems Examples showing how to solve a system of coupled linear parabolic PDEs and ODEs
- SolvingLinearPdes Examples showing how to solve linear elliptic and parabolic PDEs
- SolvingMoreElasticityProblems Introduction
- 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
- WritingPdeSolvers Introduction
- WritingPdeSolversTwo Introduction
- WritingTests Writing tests