== Tutorial Title ==

[[TableOfContents(3)]]

=== Description ===
 * This example makes use of the Electrophysiology Module's Equation Editor to create a 2D action potential propagation model on a mesh with heterogeneous properties. In essence, we will be making part of the mesh 'dead' electrically and note its influence on the shape of the propagating wave.

=== Start Continuity ===
 * Launch the Continuity 6.3 Client
 * On the [:Continuity/Documentation/Help/HelpAboutContinuity:About Continuity 6.3 startup screen]
  * check the '''specify module''' box under `Use Modules:`

=== Create Mesh ===
 * [:Continuity/Documentation/Help/MeshEditCoordinates:Mesh→Edit→Coordinates...]
  * Select '''rectangular cartesian''' in the `Global Coordinates:` pop-up menu
  * Click '''OK''' to submit `Coordinate Form`
 * [:Continuity/Documentation/Help/MeshEditBasis:Mesh→Edit→Basis...]
  * Choose '''Lagrange Basis Function→2D→Linear-Linear''' with '''2''' `integration/collocation points` for Xi 1 and Xi 2
  * Click '''Add'''
  * Choose '''Hermite Basis Function→2D→Cubic-Cubic''' with '''2''' `integration/collocation points` for Xi 1 and Xi 2
  * Click '''Add'''
  * Click '''OK''' to submit `Basis Form`
 * [:Continuity/Documentation/Help/MeshEditNodes:Mesh→Edit→Nodes...]
  * Click '''Import/Export/Graph''' button to open [:Continuity/Documentation/Help/TableManager:Continuity Table Manager]
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited nodes file [attachment:filename.xls]
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
  * Select '''Linear-Linear Lagrange 2*2''' under `Coordinate 1`, `Coordinate 2`, and `Coordinate 3`
  * In the `Field Vector 1` tab, select '''Linear-Linear Lagrange 2*2''' under `Field Variable 1`, `Field Variable 2`, and `Field Variable 3`
  * In the `Field Vector 2` tab, select '''Cubic-Cubic Hermite 2*2''' under `Field Variable 4`
  * Click '''OK''' to submit `Node Form`
 * [:Continuity/Documentation/Help/MeshEditElements:Mesh→Edit→Elements...]
  * Click '''Import/Export/Graph''' button to open [:Continuity/Documentation/Help/TableManager:Continuity Table Manager]
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited nodes file [attachment:filename.xls]
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form] 
  * Click '''OK''' to submit `Element Form`

=== Formulate XXXXX Problem ===
 * If the `XXXX` menu is not loaded, [:Continuity/Documentation/Help/FileLoadModule:File→Load Module]
  * Select '''xxxxxxxxCommands''' and click '''Load Module'''
 * [:Continuity/Documentation/Help/BiotransportEditSource:Biotransport→Edit Source...]
  * In `General Parameters` tab
   * Enter '''output''' in the field next to `Write output at nodes:`
  * In the `Fields definitions` tab
   * Change the default `Field Numbers` from 1,2,3,4,5 to '''1,2,2,3,4'''
   * Set `Initial Intracellular Calcium Conc.` to '''0.1'''
   * Set `Total Intracellular TnC Conc.` to '''70.0'''
  * Click '''OK''' to submit `Edit Source Form`
 * [:Continuity/Documentation/Help/BiotransportSelectSolvers:Biotransport→Select Solvers...]
  * Select '''Radau in serial mode''' from `ODE Integration` pop-up menu
  * Select '''SuperLU in serial mode''' from `Linear System Solver` pop-up menu
 * [:Continuity/Documentation/Help/FileSend:File→Send]
 * [:Continuity/Documentation/Help/MeshCalculateMesh:Mesh→Calculate Mesh...]
 * [:Continuity/Documentation/Help/MeshRenderElements:Mesh→Render Elements...]
  * Click '''surfaces''' radio button next to `Normal to Xi`
  * Click '''Render''' to display mesh surface

=== Compute and Render Solutions ===
 * [:Continuity/Documentation/Help/BiotransportSolveInitialize:Biotransport→Solve→Initialize]
 * [:Continuity/Documentation/Help/BiotransportSolveIntegrate:Biotransport→Solve→Integrate]
  * Set `Duration` to '''80''' (ms)
  * Set `Step Size` to '''0.5''' (ms)
  * Under `Solutions` tab, select `Display solution every` '''5''' `steps`
  * click '''OK''' to start solving
 * When solution is complete, [:Continuity/Documentation/Help/ViewChangeRenderer:View→Change Renderer...]
  * Click '''!OpenMesh''' radio button
  * Click '''OK''' to change renderer
 * [:Continuity/Documentation/Help/ViewSetDivisions:View→Set Divisions...]
 * Set `Number of Divisions:` to '''4'''
 * [:Continuity/Documentation/Help/BiotransportRenderSolution:Biotransport→Render→Solution]
  * Set `End Frame` to '''80'''
  * Set `Max value:` to '''50'''
  * Click '''OK''' to view an animated color map of intracellular Calcium concentrations