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Hypertrophic cardiomyopathy project

The mathematical details, data, simulation protocols and results are explained in the manuscript. If you have access to the manuscript, please, follow it first.

Simulator of mechanics in the heart based on FEniCS library.

Installation and Running the code

A singularity "build" file is provided that will install all the libraries required to run the code.

  1. Install singularity by following the instruction in here

  2. Build a singularity container using the "build" file with

sudo singularity build <container_name>.img Singularity_fenics2017_msucompbiomechlab
  1. Once the container is built, you can launch the Singularity container by
 singularity run <container_name>.img
  1. The code can be run within the singularity container. For example, for the code createLV_refine
python createLV_refine.py

or in parallel

mpirun.mpich -np <# processors> python createLV_refine.py

Organization of the code

The code is organized as follows:

Demo python scripts are also provided to simulate

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