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