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Completed Steps

  1. Research possible FE codes. (See Scientific Modelling Software.)
  2. Determine a test problem. (Model Bidomain on Full Ventricles.)
  3. Evaluate Sundance. (See Using Sundance.)
  4. Evaluate libMesh and compare with cm. (Karl? Shane?)
  5. Select a framework. (Using libMesh/PETSc.)
  6. Adapt libMesh transient diffusion example to only assemble the constant system matrices once. (Done)
  7. Adapt the CMISS examples framework to include examples of using libMesh.
  8. Translation of meshes from cm/cmgui to a libMesh format.
    • Currently Travis has code to export (most of) exelem and exnode files which in turn are converted to UNV mesh format and read into libmesh.
  9. Cell Model
    • A simple Cubic Model has been created that provides implementation of a cubic model.
    • An Aliev cell model (modified FHN model for GI work) has been created to recreate models of the stomach, intestines, etc.
    • A simple integrator has been created for use with these models.
    • Waiting for a CellML implementation that will replace these simple implementations.
  10. Compare solutions for simple reaction-diffusion using libmesh to cmiss.
  1. Can transfer data from CM to libMesh and recreate some of the GI examples. (See "this page":
  2. Have compiled versions of libMesh/PETSc/HYPRE combination on bioeng22 and hpc platforms.
  3. Interpretation of CMISS-style fibre angles as angles for Cardan rotations from element reference coordinates to material coordinates.