== Tutorial Title ==

[[TableOfContents(3)]]

=== Description ===
 * This example ...
 * The steps below are saved in a script that can be found in the examples directory on your Continuity client `.../continuity/pcty/examples/directory/filename` and can be executed automatically with [:Continuity/Documentation/Help/ReadPythonScript:File→Read→Python script]

=== 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 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 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