Creating Dot Com Files

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.