User tutorials

The basics#

These tutorials assume prior knowledge or understanding of various C++ language features and some libraries, including (at least): std::vectors, c_vectors, and object-oriented inheritance including abstract classes and virtual methods.

If you don’t know anything about these we recommend a first course in C++, there are plenty online (here is one from cplusplus.com). There is also a Scientific Computing in C++ book by some of our team available too.

To run any of these tutorials, it is assumed you have first configured Chaste using CMake:

cmake /path/to/chaste/src

Then, run

make <NAME_OF_TUTORIAL_FILE>

(without the .hpp on the end) to compile the tutorial source code, and

ctest -V -R <NAME_OF_TUTORIAL_FILE>

to run it. The -V is a flag to give verbose output, i.e. show the full output from the test on screen. The -R allows you to run all tests matching a ‘regular expression’, if you don’t know what that means don’t worry, if you just write the full tutorial class name it tells ctest to run that one in particular.

For instance:

make TestSolvingOdesTutorial
ctest -V -R TestSolvingOdesTutorial

Before you do anything else#

• Start with UserTutorials/WritingTests
• Then choose from the headings below Core, Cardiac, Cell-based, or Lung.

Core functionality#

Solving ODEs#

• UserTutorials/SolvingOdes

Solving PDEs#

• UserTutorials/SolvingLinearPdes
• UserTutorials/SolvingNonlinearPdes
• UserTutorials/SolvingLinearParabolicPdeSystemsWithCoupledOdeSystems

Writing new PDE solvers (advanced)#

• UserTutorials/WritingPdeSolvers
• UserTutorials/WritingPdeSolversTwo

Solid Mechanics#

• UserTutorials/SolvingElasticityProblems - computing the deformation of a nonlinearly elastic body
• UserTutorials/SolvingMoreElasticityProblems

Cardiac#

Executable users#

The cardiac executable is a compiled CardiacSimulation object that uses an XML file to specify the settings that C++ users would do via HeartConfig. It is therefore a bit easier to use but less flexible than using Chaste classes via C++.

• UserTutorials/CardiacExecutable - a submenu with links to various tutorials for users of the cardiac executable binary where settings are specified via an XML file (not the source code).

Single Cardiac Cell Simulations#

• UserTutorials/SingleCellSimulation - how to run ODE simulations for action potential models, handy methods for getting to steady pacing response.

Mono/Biodomain Simulations#

• 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/Monodomain3dExampleWithCvode - illustrates how to adapt the previous tutorial to create cells with CVODE solvers, which can provide increased speed and accuracy.
• UserTutorials/Monodomain3dRabbitHeart - illustrates loading meshes from file, and specifying fibre and cross-fibre conductivities, on a realistic (but low res) rabbit whole ventricles mesh.
• UserTutorials/BidomainWithBath - illustrates the use of Backward Euler ODE solvers (very stable), and solving a bidomain problem in tissue surrounded by (extra-cellular domain) bath.
• UserTutorials/BidomainWithBathAndFibres
• UserTutorials/BidomainWithConductivityModifier - shows how to use conductivity modifiers in a bidomain simulation.

Checkpointing (saving/loading)#

• UserTutorials/CardiacCheckpointingAndRestarting

Electro-mechanics#

• UserTutorials/CardiacElectroMechanics
• UserTutorials/AnotherCardiacElectroMechanics

Cell-based#

Where to start with cell-based simulations:

• UserTutorials/CellBasedDemo - a quick introduction to the basics of cell-based simulations in Chaste.
• UserTutorials/VisualizingWithParaview

Running basic simulation types:#

• UserTutorials/RunningMeshBasedSimulations - the first type of cell-based simulation included in Chaste, 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/RunningImmersedBoundarySimulations - immersed boundary simulations

Running crypt-specific simulations:#

• UserTutorials/RunningMeshBasedCryptSimulations
• UserTutorials/RunningVertexBasedCryptSimulations
• UserTutorials/RunningCryptSimulationsWithMutations

More advanced examples:#

• UserTutorials/RunningContactInhibitionSimulations
• UserTutorials/RunningDeltaNotchSimulations
• UserTutorials/RunningDifferentialAdhesionSimulations
• UserTutorials/RunningTumourSpheroidSimulations

Adding new functionality:#

To do new things in Chaste that haven’t been coded before you’ll often have to add your own new C++ classes. Here are a set of examples to use as a basis for that.

• UserTutorials/CreatingAndUsingANewCellCycleModel
• UserTutorials/CreatingAndUsingANewCellKiller
• UserTutorials/CreatingAndUsingANewCellPopulationBoundaryCondition
• UserTutorials/CreatingAndUsingANewForce
• UserTutorials/CreatingAndUsingANewCellMutationState
• UserTutorials/CreatingAndUsingANewCellProperty
• UserTutorials/CreatingAndUsingNewCellBasedWriters
• UserTutorials/CreatingAndUsingANewCellBasedSimulationModifier

Lung#

Generation and manipulation of airway geometries

• UserTutorials/AirwayGeneration

Simulating ventilation and impedance

• UserTutorials/StaticVentilation
• UserTutorials/DynamicVentilation
• UserTutorials/SimpleImpedanceProblem