Tutorial Wiki Template

Use this page to help you build Continuity tutorial pages on this Wiki

Contents

  1. Tutorial Wiki Template
    1. Description
    2. Start Continuity
    3. File Menu
      1. Send
      2. Load Modules
      3. Load Model
    4. View Menu
      1. Show Open Mesh
    5. Mesh Menu
      1. Edit Coordinates
      2. Edit Material Coordinates
      3. Edit Basis
      4. Edit Nodes
      5. Edit Elements
      6. Calculate Mesh
      7. Refine
      8. List Lines
      9. List Elements
      10. List Grid Points
      11. List Element Points
      12. List Nodes
      13. List Volume
      14. List Nodal Field
      15. Render Elements
      16. Render Boundaries
      17. Render Nodes
      18. Render Fibers
    6. Biomechanics Menu
      1. Edit Constitutive Model
      2. Edit Boundary Conditions
      3. Update Initial conditions with undeformed nodes
      4. Solve Nonlinear
      5. List Stress and Strain
      6. Render Surface
Use this page to help you build Continuity tutorial pages on this Wiki
[[TableOfContents(4)]]

Description

  • These step-by-step instructions will guide you through <<describe problem here>>.

=== Description ===
 * These step-by-step instructions will guide you through <<describe problem here>>.

Start Continuity

  • Launch the Continuity 6.4 Client

  • On the About Continuity 6.4 startup screen

    • leave the mesh checkbox checked under Use Modules:

    • check the biomechanics/electrophysiology/fitting checkbox under Use Modules:

  • Click OK to bring up the main window

=== Start Continuity ===
 * Launch the Continuity 6.4 Client
 * On the [:Continuity/Documentation/Help/HelpAboutContinuity:About Continuity 6.4 startup screen]
  * leave the '''mesh''' checkbox checked under `Use Modules:`
  * check the '''biomechanics'''/'''electrophysiology'''/'''fitting'''/'''bioheat''' checkbox under `Use Modules:`
 * Click '''OK''' to bring up the main window

File Menu

Send

 * [:Continuity/Documentation/Help/FileSend:File→Send] or click attachment:sendIcon.png

Load Modules

  • File→Load Modules… or click 

    • Select the check boxes next to Continuity modules you wish to add

    • Click OK. Menus for the checked modules will be added to the menu bar.

 * [:Continuity/Documentation/Help/FileLoadModule:File→Load Modules...] or click attachment:loadModuleIcon.png
  * Select the check boxes next to Continuity modules you wish to add
  * Click '''OK'''. Menus for the checked modules will be added to the menu bar.

Load Model

 * [:Continuity/Documentation/Help/FileLoadModel:File→Load Model...] or click attachment:LoadModel.png
  * Choose the .cont6 file from the file browser
  * Click '''Open'''.

View Menu

Show Open Mesh

  • View→Show→OpenMesh… or click on 

    • Click on 2. element lines2 in the list on the left, and enter 1,0,0 in the R,G,B entry field to change the mesh lines from blue to red.

    • Press [return] and close the window
 * [:Continuity/Documentation/Help/ViewShowOpenMesh:View→Show→OpenMesh...] or click on attachment:OpenMeshButton.png
  * Click on '''2. element lines2''' in the list on the left, and enter '''1,0,0''' in the `R,G,B` entry field to change the mesh lines from blue to red.
  * Press [return] and close the window

Mesh Menu

Edit Coordinates

  • Mesh→Edit→Coordinates…

    • Select rectangular Cartesian/cylindrical polar/spherical polar/prolate spheroidal in the Global Coordinates: pop-up menu

    • For prolate spheroidal coordinates, enter a focal length in the focal position input field

    • Click OK to submit Coordinate Form

 * [:Continuity/Documentation/Help/MeshEditCoordinates:Mesh→Edit→Coordinates...]
  * Select '''rectangular Cartesian/cylindrical polar/spherical polar/prolate spheroidal''' in the `Global Coordinates:` pop-up menu
  * For prolate spheroidal coordinates, eneter a focal length in the `focus` input field
  * Click '''OK''' to submit `Coordinate Form`

Edit Material Coordinates

  • Mesh→Edit→Material Coordinates…

    • In the Select Model tab confirm that the default model MatCoordStandard:Standard Material Coordinates [compiled] is highlighted

    • Click the Edit equations tab to view the mathematical expressions defining the material coordinate transformation, which is defined by the dependent variable dYdMatl that rotates global rectangular Cartesian coordinates to locally orthonormal material coordinates.

    • Click the Set parameters tab to assign fiber_angle, transverse_angle, and sheet_angle parameters of the standard model.

      • Select fiber_angle in the Parameters List on the left.

        • Choose Fiber Angle from the pop-up menu next to For default values use

      • Select transverse_angle in the Parameters List on the left.

        • Choose Transverse Angle from the pop-up menu next to For default values use

      • Select sheet_angle in the Parameters List on the left.

        • Choose Sheet Angle from the pop-up menu next to For default values use

      • Select fiber_angle in the Parameters List on the left.

        • If a Fiber Angle field variables has not been defined in the Node Form, select value in the pop-up menu next to For default values use

        • Enter a fiber angle value (in radians) in the value entry field

      • Select transverse_angle in the Parameters List on the left.

        • If a Transverse Angle field variables has not been defined in the Node Form, select value in the pop-up menu next to For default values use

        • Enter a transverse angle value (in radians) in the value entry field

      • Select sheet_angle in the Parameters List on the left.

        • If a Sheet Angle field variables has not been defined in the Node Form, select value in the pop-up menu next to For default values use

        • Enter a sheet angle value (in radians) in the value entry field

      • Click Submit tab

        • Click Submit to submit Material Coordinate Transformation model

 * [:Continuity/Documentation/Help/MeshEditMaterialCoordinates:Mesh→Edit→Material Coordinates...]
  * In the `Select Model` tab confirm that the default model '''MatCoordStandard:Standard Material Coordinates [compiled]''' is highlighted
  * Click the '''Edit equations''' tab to view the mathematical expressions defining the material coordinate transformation, which is defined by the dependent variable `dYdMatl` that rotates global `rectangular Cartesian coordinates` to locally orthonormal `material coordinates`.
  * Click the '''Set parameters''' tab to assign `fiber_angle`, `transverse_angle`, and `sheet_angle` parameters of the standard model.
   * Select '''fiber_angle''' in the `Parameters List` on the left.
    * Choose '''Fiber Angle''' from the pop-up menu next to `For default values use`
   * Select '''transverse_angle''' in the `Parameters List` on the left.
    * Choose '''Transverse Angle''' from the pop-up menu next to `For default values use`
   * Select '''sheet_angle''' in the `Parameters List` on the left.
    * Choose '''Sheet Angle''' from the pop-up menu next to `For default values use`
   * Select '''fiber_angle''' in the `Parameters List` on the left.
    * If a `Fiber Angle` field variables has not been defined in the `Node Form`, select '''value''' in the pop-up menu next to `For default values use`
    * Enter a '''fiber angle value''' (in radians) in the value entry field
   * Select '''transverse_angle''' in the `Parameters List` on the left.
    * If a `Transverse Angle` field variables has not been defined in the `Node Form`, select '''value''' in the pop-up menu next to `For default values use`
    * Enter a '''transverse angle value''' (in radians) in the value entry field
   * Select '''sheet_angle''' in the `Parameters List` on the left.
    * If a `Sheet Angle` field variables has not been defined in the `Node Form`, select '''value''' in the pop-up menu next to `For default values use`
    * Enter a '''sheet angle value''' (in radians) in the value entry field
   * Click '''Submit''' tab
    * Click '''Submit''' to submit `Material Coordinate Transformation` model

Edit Basis

  • Mesh→Edit→Basis…

    • Select 2/3 integration/collocation points for Xi 1

    • Select 2/3 integration/collocation points for Xi 2

    • Select 2/3 integration/collocation points for Xi 3

 * [:Continuity/Documentation/Help/MeshEditBasis:Mesh→Edit→Basis...]
  * Select '''2/3''' `integration/collocation points` for Xi 1
  * Select '''2/3''' `integration/collocation points` for Xi 2
  * Select '''2/3''' `integration/collocation points` for Xi 3

  • Choose Lagrange Basis Function→1D→Linear

    • Click Add Linear

  • Choose Lagrange Basis Function→1D→Quadratic

    • Click Add Quadratic

  • Choose Lagrange Basis Function→1D→Cubic

    • Click Add Cubic

  • Choose Hermite Basis Function→1D→Cubic

    • Click Add Cubic

  • Choose Lagrange Basis Function→2D→Linear-Linear

    • Click Add Linear-Linear

  • Choose Lagrange Basis Function→2D→Linear-Quadratic

    • Click Add Linear-Quadratic

  • Choose Lagrange Basis Function→2D→Linear-Cubic

    • Click Add Linear-Cubic

  • Choose Lagrange Basis Function→2D→Quadratic-Quadratic

    • Click Add Quadratic-Quadratic

  • Choose Lagrange Basis Function→2D→Quadratic-Linear

    • Click Add Quadratic-Linear

  • Choose Lagrange Basis Function→2D→Cubic-Cubic

    • Click Add Cubic-Cubic

  • Choose Lagrange Basis Function→2D→Cubic-Linear

    • Click Add Cubic-Linear

  • Choose Hermite Basis Function→2D→Linear-Cubic

    • Click Add Linear-Cubic

  • Choose Hermite Basis Function→2D→Cubic-Cubic

    • Click Add Cubic-Cubic

  • Choose Hermite Basis Function→2D→Cubic-Linear

    • Click Add Cubic-Linear

  • Choose Lagrange Basis Function→3D→Linear-Linear-Linear

    • Click Add Linear-Linear-Linear

  • Choose Lagrange Basis Function→3D→Linear-Linear-Quadratic

    • Click Add Linear-Linear-Quadratic

  • Choose Hermite Basis Function→3D→Linear-Linear-Cubic

    • Click Add Linear-Linear-Cubic

  • Choose Hermite Basis Function→3D→Linear-Cubic-Linear

    • Click Add Linear-Cubic-Linear

  • Choose Hermite Basis Function→3D→Linear-Cubic-Cubic

    • Click Add Linear-Cubic-Cubic

  • Choose Hermite Basis Function→3D→Cubic-Cubic-Linear

    • Click Add Cubic-Cubic-Linear

  • Choose Hermite Basis Function→3D→Cubic-Linear-Linear

    • Click Add Cubic-Linear-Linear

  • Choose Hermite Basis Function→3D→Cubic-Cubic-Cubic

    • Click Add Cubic-Cubic-Cubic

  • Note that when 3D Basis Functions are created, the 2D basis functions corresponding to the element faces are also added automatically
  * Choose '''Lagrange Basis Function→1D→Linear'''
   * Click '''Add Linear'''
  * Choose '''Lagrange Basis Function→1D→Quadratic'''
   * Click '''Add Quadratic'''
  * Choose '''Lagrange Basis Function→1D→Cubic'''
   * Click '''Add Cubic'''
  * Choose '''Hermite Basis Function→1D→Cubic'''
   * Click '''Add Cubic'''
  * Choose '''Lagrange Basis Function→2D→Linear-Linear'''
   * Click '''Add Linear-Linear'''
  * Choose '''Lagrange Basis Function→2D→Linear-Quadratic'''
   * Click '''Add Linear-Quadratic'''
  * Choose '''Lagrange Basis Function→2D→Linear-Cubic'''
   * Click '''Add Linear-Cubic'''
  * Choose '''Lagrange Basis Function→2D→Quadratic-Quadratic'''
   * Click '''Add Quadratic-Quadratic'''
  * Choose '''Lagrange Basis Function→2D→Quadratic-Linear'''
   * Click '''Add Quadratic-Linear'''
  * Choose '''Lagrange Basis Function→2D→Cubic-Cubic'''
   * Click '''Add Cubic-Cubic'''
  * Choose '''Lagrange Basis Function→2D→Cubic-Linear'''
   * Click '''Add Cubic-Linear'''
  * Choose '''Hermite Basis Function→2D→Linear-Cubic'''
   * Click '''Add Linear-Cubic'''
  * Choose '''Hermite Basis Function→2D→Cubic-Cubic'''
   * Click '''Add Cubic-Cubic'''
  * Choose '''Hermite Basis Function→2D→Cubic-Linear'''
   * Click '''Add Cubic-Linear'''
  * Choose '''Lagrange Basis Function→3D→Linear-Linear-Linear'''
   * Click '''Add Linear-Linear-Linear'''
  * Choose '''Lagrange Basis Function→3D→Linear-Linear-Quadratic'''
   * Click '''Add Linear-Linear-Quadratic'''
  * Choose '''Hermite Basis Function→3D→Linear-Linear-Cubic'''
   * Click '''Add Linear-Linear-Cubic'''
  * Choose '''Hermite Basis Function→3D→Linear-Cubic-Linear'''
   * Click '''Add Linear-Cubic-Linear'''
  * Choose '''Hermite Basis Function→3D→Linear-Cubic-Cubic'''
   * Click '''Add Linear-Cubic-Cubic'''
  * Choose '''Hermite Basis Function→3D→Cubic-Cubic-Linear'''
   * Click '''Add Cubic-Cubic-Linear'''
  * Choose '''Hermite Basis Function→3D→Cubic-Linear-Linear'''
   * Click '''Add Cubic-Linear-Linear'''
  * Choose '''Hermite Basis Function→3D→Cubic-Cubic-Cubic'''
   * Click '''Add Cubic-Cubic-Cubic'''
  * Note that when 3D Basis Functions are created, the 2D basis functions corresponding to the element faces are also added automatically
  • Verify that the list of basis functions now contains:
    • Linear Lagrange 2/3
    • Quadratic Lagrange 2/3
    • Cubic Lagrange 2/3
    • Cubic Hermite 2/3
    • Linear-Linear Lagrange 2*2/3*3
    • Linear-Quadratic Lagrange 2*2/3*3
    • Linear-Cubic Lagrange 2*2/3*3
    • Quadratic-Quadratic 2*2/3*3
    • Quadratic-Linear Lagrange 2*2/3*3
    • Cubic-Cubic Lagrange 2*2/3*3
    • Cubic-Linear Lagrange 2*2/3*3
    • Linear-Cubic Hermite 2*2/3*3
    • Cubic-Cubic Hermite 2*2/3*3
    • Cubic-Linear Hermite 2*2/3*3
    • Linear-Linear-Linear Lagrange 2*2*2/3*3*3
    • Linear-Linear-Quadratic Lagrange 2*2*2/3*3*3
    • Linear-Linear-Cubic Hermite 2*2*2/3*3*3
    • Linear-Cubic-Linear Hermite 2*2*2/3*3*3
    • Linear-Cubic-Cubic Hermite 2*2*2/3*3*3
    • Cubic-Cubic-Linear Hermite 2*2*2/3*3*3
    • Cubic-Linear-Linear Hermite 2*2*2/3*3*3
    • Cubic-Cubic-Cubic Hermite 2*2*2/3*3*3

  • Click OK to submit Basis Form

  * Verify that the list of basis functions now contains:
   * Linear Lagrange 2/3
   * Quadratic Lagrange 2/3
   * Cubic Lagrange 2/3
   * Cubic Hermite 2/3
   * Linear-Linear Lagrange 2*2/3*3
   * Linear-Quadratic Lagrange 2*2/3*3
   * Linear-Cubic Lagrange 2*2/3*3
   * Quadratic-Quadratic 2*2/3*3
   * Quadratic-Linear Lagrange 2*2/3*3
   * Cubic-Cubic Lagrange 2*2/3*3
   * Cubic-Linear Lagrange 2*2/3*3
   * Linear-Cubic Hermite 2*2/3*3
   * Cubic-Cubic Hermite 2*2/3*3
   * Cubic-Linear Hermite 2*2/3*3
   * Linear-Linear-Linear Lagrange 2*2*2/3*3*3
   * Linear-Linear-Quadratic Lagrange 2*2*2/3*3*3
   * Linear-Linear-Cubic Hermite 2*2*2/3*3*3
   * Linear-Cubic-Linear Hermite 2*2*2/3*3*3
   * Linear-Cubic-Cubic Hermite 2*2*2/3*3*3
   * Cubic-Cubic-Linear Hermite 2*2*2/3*3*3
   * Cubic-Linear-Linear Hermite 2*2*2/3*3*3
   * Cubic-Cubic-Cubic Hermite 2*2*2/3*3*3
  * Click '''OK''' to submit `Basis Form`

Edit Nodes

  • Mesh→Edit→Nodes…

    • Click Insert Node in the left panel <N> times to create a total of <N+1> nodes

    • Note that the first basis function you created (Linear-Linear Lagrange 3*3) with the Edit Basis Functioncommand is already selected in the menus below Coordinate 1, Coordinate 2, and Coordinate 3

    • Enable Fiber Angles or Field Vector by selecting their tabs and choosing a basis function from the Select Basis Number menus.

    • Use the Insert Node button in the left panel to create 5 additional nodes for a total of 6

    • In the Value fields under Coordinate 1, Coordinate 2, and Coordinate 3 enter the following (X,Y,Z) nodal coordinates:

      • Node 1: (0., 0., 0.)
      • Node 2: (0., 1., 0.)

    • When you choose an Hermite basis function, the fields wrt s(1), wrt s(2), …wrt s(1)s(2)s(3), fields under Value represent nodal derivative parameters. All basis functions require a value. A Cubic-Cubic-Cubic Hermitebasis function is the only one that also requires all 7 derivatives.

    • The menus and entry fields immediately below the derivative inputs are for metadata describing the geometric/fields variable and it units.

    • If you chosen world Coordinate System is curvilinear and has angular coordinates, click the Radians radio button if your input angles are in radians. The defaults is degrees, but the internal representation is in radians.

    • The default input units for Fiber Angle, Transverse Angle and Sheet Angle are degrees, The defaults is degrees, but the internal representation is in radians. Click the Radians radio button if your input angles are in radians.

    • Click Import/Export/Graph in the left panel

    • Click OK to submit Node Form

 * [:Continuity/Documentation/Help/MeshEditNodes:Mesh→Edit→Nodes...]
  * Click '''Insert Node''' in the left panel <N> times to create a total of <N+1> nodes
  * Note that the first basis function you created ('''Linear-Linear Lagrange 3*3''') with the `Edit Basis Function` command is already selected in the menus below `Coordinate 1`, `Coordinate 2`, and `Coordinate 3`
  * Enable '''Fiber Angles''' or '''Field Vector''' by selecting their tabs and choosing a basis function from the '''Select Basis Number''' menus.
  * Use the '''Insert Node''' button in the left panel to create 5 additional nodes for a total of 6
  * In the '''Value''' fields under `Coordinate 1`, `Coordinate 2`, and `Coordinate 3` enter the following (X,Y,Z) nodal coordinates:
   * Node 1: (0., 0., 0.)
   * Node 2: (0., 1., 0.)
  * When you choose an Hermite basis function, the fields '''wrt s(1)''', '''wrt s(2)''', ...'''wrt s(1)s(2)s(3)''',  fields under '''Value''' represent nodal derivative parameters. All basis functions require a value. A `Cubic-Cubic-Cubic Hermite` basis function is the only one that also requires all 7 derivatives.
  * The menus and entry fields immediately below the derivative inputs are for metadata describing the geometric/fields variable and it units.
  * If you chosen world Coordinate System is curvilinear and has angular coordinates, click the '''Radians''' radio button if your input angles are in radians. The defaults is degrees, but the internal representation is in radians.
  * The default input units for `Fiber Angle`, `Transverse Angle` and `Sheet Angle` are degrees, The defaults is degrees, but the internal representation is in radians. Click the '''Radians''' radio button if your input angles are in radians.
  * Click '''Import/Export/Graph''' in the left panel
   * This will open the [:Continuity/Documentation/Help/TableManager:Continuity Table Manager] window
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited nodes file (attachment:nodes.xls)
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
   * The `Node Form` should now display nodes numbered 1 to <N>
   * Click on the '''Fiber Angles''' and '''Field Vector''' tabs to see additional nodal variables
  * Click '''OK''' to submit `Node Form`

Edit Elements

 * [:Continuity/Documentation/Help/MeshEditElements:Mesh→Edit→Elements...]
  * Element 1 consists of global nodes '''1, 2, 4, 5''', so enter these numbers in the `Global Node Numbers` boxes. Use the `tab` key to change the input focus to the next box. Note that the order that global node numbers are entered determines the local `Xi` coordinate directions in the element, as illustrated by the graphic in the input form.
  * Use the '''Insert Element''' button in the left panel to create another element
  * For Element 2, enter '''2, 3, 5, 6''' in the `Global Node Numbers` boxes
  * 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:elems.xls)
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
    * You should now have elements numbered 1-<N>
  * Click '''OK''' to submit `Element Form`

Calculate Mesh

  • Mesh→Calculate Mesh… or click 

    • Click OK to close the Calculate Mesh Form and execute mesh calculations on the server

 * [:Continuity/Documentation/Help/MeshCalculateMesh:Mesh→Calculate Mesh...] or click attachment:calcmeshbut.png
  * Click '''OK''' to close the `Calculate Mesh Form` and execute mesh calculations on the server

Refine

  • Mesh→Refine…

    • Under New Element per old element in, select N in xi1, M in xi2, and P in xi3

    • Click OK

    • This will calculate new nodes and elements creating N new elements per each original element in the xi1direction, M new elements per each original element in the xi2 direction, and P new elements per each original element in the xi3 direction

  • Mesh→Edit→Nodes…

    • You should now have nodes numbered 1-XX

  • Mesh→Edit→Elements…

    • You should now have elements numbered 1-YY

  • Mesh→Calculate Mesh… or click  to calculate the new mesh before you re-render it.

 * [:Continuity/Documentation/Help/MeshRefine:Mesh→Refine...]
  * Under `New Element per old element in`, select '''N''' in `xi1`, '''M''' in `xi2`, and '''P''' in `xi3` 
  * Click '''OK'''
  * This will calculate new nodes and elements creating '''N''' new elements per each original element in the Xi1 direction, '''M''' new elements per each original element in the Xi2 direction, and '''P''' new elements per each original element in the Xi3 direction
 * [:Continuity/Documentation/Help/MeshEditNodes:Mesh→Edit→Nodes...]
  * You should now have nodes numbered 1-XX
 * [:Continuity/Documentation/Help/MeshEditElements:Mesh→Edit→Elements...]
  * You should now have elements numbered 1-YY
 * [:Continuity/Documentation/Help/MeshCalculateMesh:Mesh→Calculate Mesh...] or click attachment:calcmeshbut.png to calculate the new mesh before you re-rerender it.

List Lines

 * [:Continuity/Documentation/Help/MeshListLines:Mesh→List→Lines (Tabled)...]

List Elements

 * [:Continuity/Documentation/Help/MeshListElements:Mesh→List→Elements...]

List Grid Points

  • Mesh→List→Grid points (Tabled)…

    • Enter the Min and Max values for X, Y and Z and the number of divisions in each direction within those ranges

    • Click OK to display a table of element coordinates and interpolated nodal variables at the prescribed regular Cartesian grid

 * [:Continuity/Documentation/Help/MeshListGridPoints:Mesh→List→Grid points (Tabled)...]
  * Enter the `Min` and `Max` values for X, Y and Z and the number of divisions in each direction within those ranges
  * Click '''OK''' to display a listing of element coordinates and interpolated nodal variables at the prescribed regular Cartesian grid

List Element Points

  • Mesh→List→Element Points…

    • Specify Element list or choose All Elements

    • Select from Gauss Points, Prescribed Point, Regular Grid or From File to specify the xi local element coordinates where World coordinates, Fiber Angles and Field variables will be interpolated and listed

    • Click OK to submit Show Element Points

 * [:Continuity/Documentation/Help/MeshListElementPoints:Mesh→List→Element Points...]
  * Specify '''Element list''' or choose '''All Elements'''
  * Select from '''Gauss Points''', '''Prescribed Point''', '''Regular Grid''' or '''From File''' to specify the `xi` local element coordinates where `World coordinates`, `Fiber Angles` and `Field variables` will be interpolated and listed
  * Click '''OK''' to submit `Show Element Points`

List Nodes

 * [:Continuity/Documentation/Help/MeshListNodes:Mesh→List→Nodes...]

List Volume

  • Mesh→List→Volume…

    • Specify X, Y and Z coordinates of the origin to be used for the volume integration

    • Specify or more more Element Lists whose surfaces will be used to define volumes to be integrated.

    • Select undeformed or deformed under Select a Mesh

    • Click OK to submit List Volume Form

 * [:Continuity/Documentation/Help/MeshListVolume:Mesh→List→Volume...]
  * Specify '''X''', '''Y''' and '''Z''' coordinates of the origin to be used for the volume integration
  * Specify or more more '''Element Lists''' whose surfaces will be used to define volumes to be integrated.
  * Select '''undeformed''' or '''deformed''' under `Select a Mesh`
  * Click '''OK''' to submit `List Volume Form`

List Nodal Field

  • Mesh→List→Nodal Field…

    • Browse your directories to locate a file with Gauss Point values of the variable to be used to create a nodal field.
 * [:Continuity/Documentation/Help/MeshListNodalField:Mesh→List→Nodal Field...]
  * Browse your directories to locate a file with Gauss Point values of the variable to be used to create a nodal field.

Render Elements

  • Mesh→Render→Elements… or click 

    • Click the lines radio button

    • Click Render to display mesh lines

    • Click the surfaces or texture radio button

    • For 3D elements, chose an Xi plane (1, 2 or 3) to render

    • Enter an Xi Location between 0.0 and 1.0 for rendering the surface

    • Click Render to display mesh surfaces or texture maps

 * [:Continuity/Documentation/Help/MeshRenderElements:Mesh→Render→Elements...] or click attachment:RenderElementsButton.png
  * Click the '''lines''' radio button
  * Click '''Render''' to display mesh lines
  * Click the '''surfaces''' or '''texture''' radio button
  * For 3D elements, chose an `Xi` plane ('''1''', '''2''' or '''3''') to render
  * Enter an `Xi Location` between '''0.0''' and '''1.0''' for rendering the surface
  * Click '''Render''' to display mesh surfaces or texture maps

Render Boundaries

 * [:Continuity/Documentation/Help/MeshRenderBoundaries:Mesh→Render→Boundaries...]
  * This shortcut for rendering boundary surfaces requires labels to be defined using `Mesh→Labels Wizard...`

Render Nodes

  • Mesh→Render→Nodes… or click 

    • Specify a Node List to render or leave the default all

    • Select the undeformed or deformed radio button

    • Click the Render button to display the nodes

 * [:Continuity/Documentation/Help/MeshRenderNodes:Mesh→Render→Nodes...] or click attachment:RenderNodesButton.png
  * Specify a '''Node List''' to render or leave the default `all`
  * Select the '''undeformed''' or '''deformed''' radio button
  * Click the '''Render''' button to display the nodes

Render Fibers

  • Mesh→Render→Fibers… or click 

    • Specify a list of Elements to render or leave the default all

    • Specify a list of Xi3 Locations

    • Specify a vector Length normalized by the element dimension or click Auto

    • Specify the number of material vectors to render per element in each direction

    • Click OK to render material axes

 * [:Continuity/Documentation/Help/MeshRenderFibers:Mesh→Render→Fibers...] or click attachment:RenderFibersButton.png
  * Specify a list of '''Elements''' to render or leave the default `all`
  * Specify a list of '''Xi3 Locations'''
  * Specify a vector '''Length''' normalized by the element dimension or click '''Auto'''
  * Specify the number of material vectors to render per element in each direction
  * Click '''OK''' to render material axes

Biomechanics Menu

Edit Constitutive Model

  • Biomechanics→Edit→Constitutive Model…

  • Use the Select model tab to select a Constitutive Model or to <<add new model>>

    • If the model includes the label [compiled] after the model name, a compiled binary for this model was found on the server.

    • If the model does not have the label [compiled] after the model name, a compiled binary for this model was not found on the server. The model will first have to be compiled on the Compile tab to be used. This requires that the compilation environment has been set up on your server. For installation and setup instructions, see CompilingModels.

  • Use the Edit properties tab to view or edit the model filename, author and description

    • You can only change properties for models that you authored

  • Use the Edit equations tab to create and name intermediate symbolic or evaluated variables and write the equations that define the Dependent variable for this model, which is Stress in terms of the Independent variableswhich include hydrostatic pressure, the material coordinate transformation dY_dMatl, the deformation gradient of deformed curvilinear coordinate with respect to undeformed material coordinates dX_dMatl, and the curvilinear world coordinate transformation dy_dx.

    • Stress is a square matrix containing the components of the Lagrangian Second Piola-Kirchhoff Stress tensor with respect to material coordinates.

    • Equations are entered using Sympy

  • The View equations displays a complete listing of the Sympy equations defining the model.

  • The Compile tab is where C code is generated from the Sympy model and compiled

    • If compilation is possible on the chosen server, there will be a message underneath the server name that the server is Build Enabled.

    • If the model is already compiled, there will be a message under the server name saying compiled

    • Click the Compile button to compile the model on the default server

    • Click Save file to save the model and metadata on the server

    • Click View code to generate and view a C code listing of the model

  • Use the Set parameters tab to set adjustable material parameters

    • The model Parameters list is generated from the equations. Quantities delimited by <anglebrackets> in the equations are parameters

    • Select a parameter in the list

      • You can edit its Description, specify its default value to be defined by a constant value or a field variable or a field variable derivative.

      • You can also add exceptions using the Add exception in… popup menu that allows alternative parameter values or fields to be specified according to a prescribed element list or a prescribed field range for a specified field variable.

  • Click the Submit button in the Submit tab to submit the Constitutive Model.

 * [:Continuity/Documentation/Help/ModelsEditor:Biomechanics→Edit→Constitutive Model...]
 * Use the '''Select model''' tab to select a `Constitutive Model` or  to '''<<add new model>>'''
  * If the model includes the label `[compiled]` after the model name, a compiled binary for this model was found on the server.
  * If the model does not have the label `[compiled]` after the model name, a compiled binary for this model was not found on the server. The model will first have to be compiled on the '''Compile''' tab to be used. This requires that the compilation environment has been set up on your server. For installation and setup instructions, see CompilingModels.
 * Use the '''Edit properties''' tab to view or edit the model filename, author and description
  * You can only change properties for models that you authored
 * Use the '''Edit equations''' tab to create and name intermediate symbolic or evaluated variables and write the equations that define the `Dependent variable` for this model, which is '''Stress''' in terms of the `Independent variables` which include hydrostatic '''pressure''', the `material coordinate transformation` '''dY_dMatl''', the deformation gradient of deformed curvilinear coordinate with respect to undeformed material coordinates '''dX_dMatl''',  and the curvilinear world coordinate transformation '''dy_dx'''.
  * '''Stress''' is a square matrix containing the components of the `Lagrangian Second Piola-Kirchhoff Stress tensor` with respect to `material coordinates`.
  * Equations are entered using [http://docs.sympy.org/dev/index.html Sympy]
 * The '''View equations''' displays a complete listing of the Sympy equations defining the model.
 * The '''Compile''' tab is where C code is generated from the Sympy model and compiled
  * If compilation is possible on the chosen server, there will be a message underneath the server name that the server is `Build Enabled`.
  * If the model is already compiled, there will be a message under the server name saying `compiled`
  * Click the '''Compile''' button to compile the model on the default server
  * Click '''Save file''' to save the model and metadata on the server
  * Click '''View code''' to generate and view a C code listing of the model
 * Use the '''Set parameters''' tab to set adjustable material parameters
  * The model `Parameters list` is generated from the equations. Quantities delimited by <anglebrackets> in the equations are parameters
  * Select a `parameter` in the list
   * You can edit its `Description`, specify its default value to be defined by a constant `value` or a `field variable` or a `field variable derivative`.
   * You can also add exceptions using the '''Add exception in...''' popup menu that allows alternative parameter values or fields to be specified according to a prescribed `element list` or a prescribed `field range` for a specified field variable.
 * Click the '''Submit''' button in the '''Submit''' tab to submit the `Constitutive Model`.

Edit Boundary Conditions

  • Biomechanics→Edit→Boundary Conditions…

    • The Initial Conditions tab looks like the Coordinates tab of the Mesh→Edit→Nodes… form.

    • You can use the Biomechanics→Update→Initial conditions with undeformed nodes command to initialize the Deformed Coordinates with the undeformed nodal coordinates.

    • Use the tabs Deformed Coordinate 1, Deformed Coordinate 2, Deformed Coordinate 3, Hydrostatic Pressure (if an incompressible constitutive law is submitted) to specify nodal boundary conditions

      • Click Insert Nodes to create a boundary condition for one or more nodes.

      • Insert a node number, list of node numbers or node number label in the Node(s) field

      • Use the pop-up menu to choose a nodal Derivative parameter to constrain or apply force to

      • Use the pop-up menu to select displacement, force, coupled or spring Boundary Condition Type

      • Enter a value where 0.0 would mean no displacement or force

      • If coupled Boundary Condition Type is selected, the second row of options is enabled

        • You can couple the specified constrained nodal degrees of freedom to a selected Derivative of one or more Coupled Node(s) of a selected Dependent variable via a coupling Coefficient. Enter one or more Coupled Node(s), select Derivative and Dependent Variable from the appropriate pop-pu menus and enter the coupling Coefficient

    • Click the OK button to submit Boundary Conditions Form

 * [:Continuity/Documentation/Help/BiomechanicsEditBoundaryConditions:Biomechanics→Edit→Boundary Conditions...]
  * The '''Initial Conditions''' tab looks like the '''Coordinates''' tab of the  [:Continuity/Documentation/Help/MeshEditNodes:Mesh→Edit→Nodes...] form.
  * You can use the [:Continuity/Documentation/Help/BiomechanicsUpdateInitialConditionsUndeformedNodes:Biomechanics→Update→Initial conditions with undeformed nodes] command to initialize the `Deformed Coordinates` with the undeformed nodal coordinates.
  * Use the tabs '''Deformed Coordinate 1''', '''Deformed Coordinate 2''', '''Deformed Coordinate 3''', '''Hydrostatic Pressure''' (if an incompressible constitutive law is submitted) to specify nodal boundary conditions
   * Click '''Insert Nodes''' to create a boundary condition for one or more nodes.
   * Insert a '''node number''', list of '''node numbers''' or '''node number''' label in the `Node(s)` field
   * Use the pop-up menu to choose a nodal '''Derivative''' parameter to constrain or apply force to
   * Use the pop-up menu to select '''displacement''', '''force''', '''coupled''' or '''spring''' `Boundary Condition Type`
   * Enter a '''value''' where 0.0 would mean no displacement or force
   * If '''coupled''' `Boundary Condition Type` is selected, the second row of options is enabled
    * You can couple the specified constrained nodal degrees of freedom to a selected `Derivative` of one or more `Coupled Node(s)` of a selected `Dependent variable` via a coupling `Coefficient`. Enter one or more '''Coupled Node(s)''', select '''Derivative''' and '''Dependent Variable''' from the appropriate pop-pu menus and enter the coupling '''Coefficient'''
  * Click the '''OK''' button to submit `Boundary Conditions Form`

Update Initial conditions with undeformed nodes

 *[:Continuity/Documentation/Help/BiomechanicsUpdateInitialConditionsUndeformedNodes:Biomechanics→Update→Initial conditions with undeformed nodes]
  * This command copies the nodal geometric coordinates and derivatives from the `Node Form` to the `Initial Conditions` tab of the `Boundary Conditions Form`

Solve Nonlinear

  • Biomechanics→Solve Nonlinear…

    • Specify the Time Step

    • Click the Solve button, and wait for the solver to finish. While the solution is being computed the window will remain open. There will also be output listed to the console window and the Python shell.

 * [:Continuity/Documentation/Help/BiomechanicsSolveNonlinear:Biomechanics→Solve Nonlinear...]
  * Specify the '''Time Step''' 
  * Click the '''Solve''' button, and wait for the solver to finish. While the solution is being computed the window will remain open. There will also be output listed to the console window and the Python shell.

List Stress and Strain

  • Biomechanics→List Stress and Strain…

    • In the Variables tab, use checkboxes to deselect any variables you do not wish to list

    • Note that the Output Variables are calculated using the equations entered in the Output Variable folder of the submitted Constitutive model

    • In the Locations tab, you can selected the element list and points which which solutions will be listed

    • Click OK to display a listing of the selected Output Variables in the Table Manager

 * [:Continuity/Documentation/Help/BiomechanicsListStressAndStrain:Biomechanics→List Stress and Strain...]
  * In the `Variables` tab, use checkboxes to deselect any variables you do not wish to list
  * Note that the `Output Variables` are calculated using the equations entered in the `Output Variable` folder of the submitted `Constitutive model`
  * In the `Locations` tab, you can selected the element list and points which which solutions will be listed
  * Click '''OK''' to display a listing of the selected `Output Variables` in the [:Continuity/Documentation/Help/TableManager:Table Manager]

Render Surface

  • Biomechanics→Render Surface…

    • Enter Element List or leave default value or all

    • Select an unused Field Variable that will hold nodal values of the solution to be interpolated and rendered

    • Check the undeformed or deformed radio button to indicate whether you want to the solution rendered on the undeformed or deformed geometry

    • Select the output variable form the menu. For vector and tensor variables, a choice of components will be presented. Output will be referred to coordinate frames as determined by equations in the Output Variablesfolder of the Constitutive Model Editor

    • Click OK to create a color-coded surface rendering of the chosen output variable

 * [:Continuity/Documentation/Help/BiomechanicsRenderSurface:Biomechanics→Render Surface...]
  * Enter '''Element List''' or leave default value or '''all'''
  * Select an unused '''Field Variable''' that will hold nodal values of the solution to be interpolated and rendered
  * Check the '''undeformed''' or '''deformed''' radio button to indicate whether you want to the solution rendered on the undeformed or deformed geometry
  * Select the output variable form the menu. For vector and tensor variables, a choice of components will be presented. Output will be referred to coordinate frames as determined by equations in the `Output Variables` folder of the `Constitutive Model Editor`
  * Click '''OK''' to create a color-coded surface rendering of the chosen output variable