History for Creating Dot Com Files

changed:
-
For Bidomain/Monodomain with Collocation or Structured FEM

  * **Parameters**:  a 'dot-ippara' file is needed for anything but 
    a toy problem. 

  * **Mesh**: define the finite element mesh in one of two ways

    * If you want a structured mesh, then you must set a 'dot-ipbase' 
      file and a 'dot-ipmesh' file.
    
    * If you need a less structured mesh, then you must set
      set a 'dot-ipnode' file, a 'dot-ipbase' file, 
      and a 'dot-ipelem' file in that order.

  * **Fibre** : unless you want default fibre orientation, then you must
    define a 'dot-ipfibr' file for describing the fibre orientation.
    You will probably need to also define a 'dot-ipelfb' file for 
    defining the basis functions to represent the fibre orientation.

  * **Grid points**: define the gridpoints that will be hosted by the
    previously defined elements through a 'dot-ipgrid' file.  

    * 'fem update grid geometry' is a command that must be issued
      in order to get the correct coordinates for the grid points 
      in the mapped space.  (Grid points are originally defined in 
      local xi space.)

    * 'fem update grid metric' is a command that you must issue if
      you are using collocation, in order to update the metric
      information. (NOTE: Only needed with collocation.)

    * 'fem group grid external as boundary' is used to define one 
      group called 'boundary' that can be used later for boundary
      conditions.

    * 'fem group xi1=low as stimulus' is used in a similar way to
      group a set of points together.

  * **Problem Type**: define the problem through a 'dot-ipequa' file. 
    A few options that you can change inside of this file are
    *discretization*, *electrical model*, or *cellular type model*.

  * **Material Parameters**: define the intracellular and extracellular
    parameter values (for fibre direction, sheet direction, and cross
    direction) with a 'dot-ipmat' file.