History for Completed Steps

changed:
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  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.

     * Provides regression tests.

     * Includes parallel testing.

     * See "parallel diffusion":http://cmiss.bioeng.auckland.ac.nz/development/examples/3/33/parallel-diffusion/

     * See "monodomain":http://cmiss.bioeng.auckland.ac.nz/development/examples/b/b2/b21/b211/parallel-monodomain/index.html

  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.

     * Memory Comparison. (See "slides":http://www.cmiss.org/openCMISS/wiki/libmeshvcm/view)

     * Timing comparisons. (See "slides":http://www.cmiss.org/openCMISS/wiki/libmeshvcm/view)

  11. Can transfer data from CM to libMesh and recreate some of the GI examples.  (See "this page":http://www.cmiss.org/openCMISS/wiki/ReadingInCMISSDataUsingMeshData.)

  12. Have compiled versions of libMesh/PETSc/HYPRE combination on bioeng22 and hpc platforms.

  13. Interpretation of CMISS-style fibre angles as angles for Cardan rotations
      from element reference coordinates to material coordinates.

     * See "anisotropic diffusion":http://cmiss.bioeng.auckland.ac.nz/development/examples/3/33/anisotropic-diffusion/ example.