MicrovesselChaste - Multi-Scale Agent-Based Modelling with Microvessels

This is an add-on for agent-based modelling of microvessels with Chaste. See the project website for more details.

Release Notes:

3.4.3

geometry

• Added labelling for edges and polygons. Labels can now be written to VTK files.
• Dropped voronoi generator based on tetgen. May replace with VTK version in future.

mesh

• Major refactor to present homogeneous interface to both regular grids and unstructured meshes.
• Initial support for parallel solution storage on grids.
• Added a grid calculator for generating and storing maps of discrete entities to grid locations.
• Significant performance improvements in the generation of disrete entity maps.

pde

• Major refactor of finite element and finite difference solvers. Now includes parabolic PDE solvers.
• The density map now plays a fundamental role in relating discrete entity densitities to sink and source strengths in PDEs.
• Easier application of boundary conditions through geometry labelling.

vessel

• Significant performance improvements in merging coincident nodes.

python

• Simplify automatic wrapper generation

infra

• Add travis CI
• Keep up with Chaste modifications

3.4.2

• First public release

Install from Source (Linux Only)

The project can be used directly as a typical C++ Chaste project. First, Chaste dependencies need to be built following the Chaste Install Guide.

The project tracks the Chaste master release, this can be obtained by doing:

git clone https://chaste.cs.ox.ac.uk/git/chaste.git $CHASTE_SOURCE_DIR

The project code itself can be obtained by doing:

git clone https://github.com/jmsgrogan/MicrovesselChaste.git $MICROVESSEL_PROJECT_SOURCE_DIR

The Microvessel project code needs to be included in the main Chaste source. This can be done with a symbolic link:

cd $CHASTE_SOURCE_DIR/projects
ln -s $MICROVESSEL_PROJECT_SOURCE_DIR

The C++ libraries can be built using the Chaste CMake build system. First, create a build directory outside the source tree and proceed as:

cd $CHASTE_BUILD_DIR
cmake $CHASTE_SOURCE_DIR
make project_MicrovesselChaste -j $NUM_AVAILABLE_CPUS

This will build the C++ library and all tests. To avoid building tests do:

make chaste_project_MicrovesselChaste -j $NUM_AVAILABLE_CPUS

as the final command. The Chaste CMake build system guide should be consulted for options related to generating optimized builds, running other types of test and installation as a system library.

To build the Python package it is necessary to first build PyChaste following the instructions here. The MicrovesselChaste package can then be built in a similar way.

cd $BUILD_DIR
make project_MicrovesselChaste_Python

The Python package microvessel-chaste will be in $BUILD_DIR under projects/MicrovesselChaste/python. You can either add $BUILD_DIR/projects/MicrovesselChaste/python to your PYTHONPATH or do:

cd $BUILD_DIR/projects/MicrovesselChaste/python
python setup.py install