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.