== Action potential propagation example ==
[[Gallery]]

[[TableOfContents(3)]]

=== Description ===
 * This example simulates action potential propagation across a 4 mm by 5 mm piece of tissue.
 * A 50 mA stimulus with user-defined start time and duration parameters is applied along the center of the tissue. The start time and duration may be altered by the user in the stimulus form. The stimulus strength can be altered in the node form. 
 * This simulation will make use of the MFHN Ionic model, so we need to load and compile that model.
  * Connect to the database from File→Library→Search
  * At the top of the search form search for a '''Title''' '''containing''' mfhn
  * Right-click on '''EP_MFHN_sympy''' and select '''Load'''
  * You will get a warning window, select ''Reset (without save) then proceed''
 * Edit the model Electrophysiology→Edit→Ionic Model
  * Set Parameters {{{stim_start}}} to '''1.0''' , {{{stim_dur}}} to '''10.0''' next to '''Value''' and {{{stim_mag}}} to '''Field1''' next to {{{For default values use}}}
  * Click on the '''Set initial values''' tab
  * Click on '''ug''' under {{{Variable List}}} and select '''Field2''' next to {{{For default values use}}} 
 * Compile the model from Electrophysiology→Edit→Ionic Model
  * Under the ''Compile'' button near the bottom, select ''Compile Code as: C Double Precision''.  That will compile the model and should display a message saying that compilation was successful.
 * We need to define a Conductivity model
   * Electrophysiology→Edit→Conductivity Model
   * Change the following: f11 to have ''Value'' of 24.0e-4 and '''f22''' and '''f33''' have  ''Value'' of 23.0e-4
   * Change the name of the model, by clicking on 'New_Model' and define the name to be '''Conductivity''' and hit '''return'''
   * Under the ''Compile'' button near the bottom, select ''Compile Code as: C Double Precision''.
 * It would be a good time to save the model: File→Save→Save model as... and save it as 2d_ep.cont6
 * [: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 '''Hermite Basis Function→2D→Cubic-Cubic''' with '''4''' {{{integration/collocation points}}} for Xi 1 and Xi 2
  * Click '''Add'''
  * Choose '''Lagrange Basis Function→2D→Linear-Linear''' with '''4''' {{{integration/collocation points}}} for Xi 1 and Xi 2
  * Click '''Add'''
  * Verify that the list of basis functions now contains:
   * Cubic-Cubic Hermite 4*4
   * Linear-Linear Lagrange 4*4
  * 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:2d_class_nodes.xls )
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
  * You should now have nodes numbered 1-484
  * Select '''Linear-Linear Lagrange''' under {{{Coordinate 1}}}, {{{Coordinate 2}}}, and {{{Coordinate 3}}}
  * Click on the {{{Fiber Angles}}} tab
  * Select '''Linear-Linear Lagrange''' under {{{Fiber Angle}}}, {{{Transverse Angle}}} and {{{Sheet Angle}}}
  * Click on the {{{Field Vector 1}}} tab
  * Select '''Linear-Linear Lagrange''' under {{{Field Variable 1}}} and '''Cubic-Cubic Hermite''' {{{Field Variable 2}}}
  * Click '''OK''' to submit {{{Node Form}}}
 * [:Continuity/Documentation/Help/MeshEditElements:Mesh→Edit→Elements...]
  * Click '''Import/Export''' button to open [:Continuity/Documentation/Help/TableManager:Continuity Table Manager]
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited elements file ( attachment:2d_class_elems.xls )
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
  * You should now have 441 elements in the list
  * Click '''OK''' to submit {{{Element Form}}}
 * Make sure to send data to the server: File->Send
 * [:Continuity/Documentation/Help/MeshEditMaterialCoordinates:Mesh→Edit→Material Coordinates...]
  * Click '''OK'''
 * [:Continuity/Documentation/Help/ViewChangeRenderer:View→Change Renderer...]
  * Select the '''Open{{{}}}Mesh''' radio button
  * Click '''OK'''
 * [:Continuity/Documentation/Help/FileSaveModel:File→Save→Model...]
  * Enter a file name and browse to a location to save your current problem as a cont6 file
  * Click '''Save'''
 * [:Continuity/Documentation/Help/FileSend:File→Send]
 * [:Continuity/Documentation/Help/MeshCalculateMesh:Mesh→Calculate Mesh...]
 * [:Continuity/Documentation/Help/MeshRenderElements:Mesh→Render→Elements...]
  * Click the '''surfaces''' radio button
  * Click '''Render''' to display mesh surface
=== Solve for action potential propagation ===
 * Electrophysiology→Solve→Initialize...
 * [:Continuity/Documentation/Help/ElectriophysiologySolveInitialize:Electrophysiology→Calculate→Constraints]
  * Make sure the '''Fix out-of-plane boundary node derivatives''' check-box is checked
  * Make sure the '''Automatically update constraints form from table''' check-box is checked
  * Click '''OK'''
 * Electriophysiology→Solve→Initialize...
 * [:Continuity/Documentation/Help/ElectriophysiologySolveInitialize:Electriophysiology→Solve→Integration...]
  * Verify that {{{Start Time}}} is '''0.0'''
  * Set {{{Duration}}} to '''30'''
  * Set {{{Step Size}}} to '''0.1'''
  * In the {{{Filename distinction}}} box type {{{2D_mfhn}}} or something similar.  The files that will have the action potentials and ECG will be saved in the user temp directory as {{{AP_out_}}}''{{{2D_mfhn.txt}}}'' and {{{ECG_}}}''{{{2D_mfhn.txt}}}''
  * Go to the {{{Output}}} tab
   * For {{{Display solution every}}}, choose '''20''' steps
  * Go to the {{{APs}}} tab
   * Make sure {{{Write APs to file}}} is checked and specify {{{At nodes:}}} to be '''all'''
  * Click '''OK''' and wait for the solver to complete its job (observe progress in the Python shell)
=== Rendering and output ===
 * [:Continuity/Documentation/Help/ElectriophysiologyRenderSolution:Electriophysiology→Render→Render Solution...]
  * Verify that {{{Min Value}}} is '''0.0''' and {{{Max Value}}} is '''1.0'''
  * Click '''OK'''
  * Wait for the rendering to complete all frames before proceeding (observe status in Python shell)
 * When the 300 animation frames have been computed, you should see an animation in Continuity of the action propagation.
  * See the screen shots above for sample snapshots of the animation
 * Exporting the individual frames as bmps (for single frame shots or for movie making)
  * Pause the movie after all frames are rendered (blue pause sign near right hand end on upper row of command icons)
  * View->Snapshot->Save Animation Frames...
  * Choose element surfaces0
  * Save As test.bmp
   * Make sure no window is covering the main window at this point
   * Note: The export process will take a couple of minutes to complete
  * [:Continuity/Documentation/Help/FileSaveVisualization:File→Save→Visualization...]
   * Enter a file name and browse to a location to save the solution
   * Click '''Save'''
  * [:Continuity/Documentation/Help/FileLoadVisualization:File→Load→Visualization...]
   * Select the file you saved in the previous step
  * Open your favorite plotting program (Excel or Matlab) and plot the action potentials
   * The first column is time, the second should all be zeros, and the subsequent columns the nodal output
  * Open your favorite plotting program (Excel or Matlab) and plot the ECG
   * The first column is time, the second is the ECG
=== Pre-built model ===
This cont6 file contains all data and parameters for this problem, before the Electrophysiology solve: attachment:elec1.cont6