wiki:PaperTutorials/EMBC2018

Model of Vascular Remodelling

This section contains pages generated automatically from the source code accompanying Osborne and Bernabeu (2018) "A fully discrete open source framework for the simulation of vascular remodelling". in TODO doi:TODO

Email jmosborne@… or miguel.bernabeu@… with any questions.

The code to run the multiple cylinder comparison simulations, which were used to produce Figure 2, can be found here TestAnalyticComparisonLiteratePaper.hpp

The code to run single coupled simulations, which was used to produce Figure 3, can be found in the python and src folders.

Before looking at this, you may wish to look at some of the basic user tutorials for Chaste.

Getting the code and installing dependencies

Before running these examples you will need to install Chaste's dependencies and the source code for version 3.3. The easiest way to do this is using an Ubuntu machine (or an Ubuntu virtual machine) as discussed on InstallGuides/UbuntuPackage. Note that Chaste is only fully supported on Linux/Unix systems, so users of Windows or Mac OS X may need to follow the virtual machine route. For manual installation of each dependency, on any version of Linux, see DeveloperInstallGuide.

YOU WILL ALSO NEED TO INSTALL HEMELB. INSTRUCTIONS TO FOLLOW.

Finally you will need the source for the EMBC2018 project. This can be done by checking out the version from the repository by using the command

svn checkout https://chaste.cs.ox.ac.uk/svn/chaste/projects/EMBC2018

in the projects folder of the Chaste directory. You can register for a username and password or use username: anonymous password: [your email].

Now the project should be installed, and everything should compile and run correctly. You can now run the tests or simulations, or create your own test suites.

Documentation

There are four folders - matlab,python',src and test`.

  1. The matlab folder contains scripts to plot Figure 2 from the paper.
  2. The python folder contains python scrips to couple our Chaste executables from src to HemeLB.
  3. The src folder contains the classes necesary to run the simulation. These define the aditional forces and boundary conditions not in the core Chaste code.
  4. The test folder contains:

Running tests

You can then run tests and simulations with,

cd <Chaste path>
scons b=GccOpt ts=projects/EMBC2018/test/TestAnalyticComparisonLiteratePaper.hpp

NB: the paper was developed with release version 3.4. It will not work with with release version 3.3 or under.

For further information on using Chaste, see the extensive guide material. You may also wish to look at some of the basic user tutorials.


Section contents

  • AnalyticComparison 50.0; //50 class RadialForce : public AbstractForce<2,3> { private: double mStrength; friend class boost::serialization::access; template void serialize(Archive & archive, const unsigned int version) { archive & boost::serialization::base_object >(*this); archive & mStrength; } public: RadialForce(double strength

    Last modified 6 years ago Last modified on Jun 20, 2018, 8:19:53 AM