Parameter studies updates

A_Getting_started/lesson2.md

@@ -3,10 +3,14 @@
 
 # Lesson 2: Controlling the Posture
 
-The Standing Model's posture is defined by the angles at the anatomical joints.
+The script editor currently shows the main file of the model, which includes the
+line of code `Main = {}`. Any basic AnyScript contains a main file that defines
+the model's structure and the operations to be performed on the model.
 
-These specifications have been collected in one of the model files, "Mannequin.any". Scroll
-down to the line which says `#include "Model\Mannequin.any"`.
+The `Mannequin.any` file, included in the main file, determines the posture of
+the Standing Model by specifying the angles at the anatomical joints.
+
+Scroll down to the line that says `#include "Model\Mannequin.any"`.
 
 ## Mannequin file structure
 
@@ -16,7 +20,7 @@ down to the line which says `#include "Model\Mannequin.any"`.
 :end-before: //# END SNIPPET 1
 ```
 
-**This line means that your model will include the "Mannequin.any" file located in the Model folder,
+**This line means that your model will include the content of the "Mannequin.any" file located in the Model folder,
 within the main file.**
 
 Double-clicking the file name in the editor window after loading
@@ -76,7 +80,11 @@ Simulation based analyses in AnyBody are termed "Studies".
 
 - **Kinematics**: Runs Kinematic analysis
 - **InverseDynamics**: Runs Inverse dynamic analysis
-- **InitialConditions**: Runs only the first time step of Kinematics. Useful for testing and debugging.
+
+To view all available operations in the model, click the "Open Operation Tree"
+button and navigate to "Main" > "Study". For example, the "InitialConditions"
+operation runs only the first time step of the kinematic analysis, which is
+useful for testing and debugging.
 
 ```{image} _static/lesson2/image2.png
 :alt: Operations drop down menu

A_Getting_started/lesson3.md

@@ -56,8 +56,8 @@ values. You will find the folder in the tree here:
 :align: center
 ```
 
-**Navigate to the "Right.Leg.JointReactionForce" folder
-by expanding the tree view like this**:
+**👉 Now** navigate to the "Right.Leg.JointReactionForce" folder
+by expanding the tree view like this:
 
 ```{image} _static/lesson3/image6.png
 :alt: Model tree forces

A_Getting_started_anyscript/intro.md

@@ -13,6 +13,6 @@ simplified model of an arm.**
 
 Each lesson (after lesson 1) begins with a link to a file containing the
 AnyScript code that has been introduced until that point. If you have a problem getting your to code work, simply
-download the file and start from there.
+download the demo files and start from there.
 
 Let's get started with {doc}`Lesson 1: Basic concepts <lesson1>`

A_Getting_started_anyscript/lesson1.md

@@ -12,16 +12,16 @@ To create an AnyScript model from scratch, go to "File menu -> New from template
 which you choose "Basic Main" and provide a "Target Name" (e.g.,
 *NewModel*) and click OK. This is similar to {ref}`this step <model-templates>` from the previous tutorial.
 
+The new file that opens up in the text editor contains a basic skeleton
+for your model, based on a built-in template.
+
 ```{image} _static/lesson1/image2.png
 :alt: Script editor 
 :class: bg-primary
 :width: 100%
 :align: center
 ```
 
-The new file that opens up in the text editor contains a basic skeleton
-for your model, based on a built-in template.
-
 ## What are Classes?
 
 Let's have a look at what the system has generated for you. If you ignore most of the text and comments (green lines beginning with {literal}`//`),
@@ -51,8 +51,8 @@ Main = {
 ```
 
 
-What you see is a hierarchy of braces - the outermost pair of braces is named `Main = {`.
-Everything else in the model goes between these braces.
+What you see is a hierarchy of braces - the outermost pair of braces is named `Main = {}`.
+Everything else in the model goes between these braces, and any basic AnyScript must contain this Main folder.
 
 "MyModel" (of class type `AnyFolder`) is simply an
 organizational folder for containing the entire model you are going to
@@ -69,6 +69,10 @@ All changes you need to do in your model will be highlighted in <span style="col
 
 **👉 Now** reename `MyStudy` to `ArmModelStudy`, and replace all occurences of `MyModel` with `ArmModel`.
 
+:::{note}
+Generally, when declaring an object in AnyScript, you typically start with the class type, followed by a chosen object name, and then assign it a value. The value can be a number, a string, or another object. 
+`<ClassName> <objectname> = <value>;`
+:::
 
 
 ## What does this file contain so far?

A_Getting_started_anyscript/lesson2.md

@@ -136,8 +136,8 @@ because it's defined to look exactly the same and is loaded exactly on top of th
 To solve this problem, you can change the initial/load time position of the two segments by adjusting
 r0 (translation w.r.t global frame at load-time) and Axes0 (rotation matrix w.r.t global frame at load-time).
 
-**Remember that your simulation, will only use these load-time positions as an initial guess, on the way to
-enforcing specified motions and constraints (such as joints between segments). More on this in the next lesson.**
+Remember that your simulation, will only use these load-time positions as an initial guess, on the way to
+enforcing specified motions and constraints (such as joints between segments). More on this in the next lesson.
 
 For now, let us first change `r0` - the global position of the segment at load-time.
 

A_Getting_started_anyscript/lesson3.md

@@ -86,16 +86,23 @@ purpose, we have the lines:
 :end-before: //# END SNIPPET 1
 ```
 
-**They refer to two nodes that we created earlier, located on the `GlobalRef` and `UpperArm`
-segments. Notice the two dots in front of the names. They signify that
+They refer to two previously created nodes located on the `GlobalRef` and `UpperArm` segments, using their 
+**relative folder paths**. Notice the two dots in front of the names. They signify that
 the `GlobalRef` and `Segs` folders are defined two levels outside the folder
-we are writing into, in the model tree.**
+we are writing into, in the model tree.
 
 If you neglected the two dots, then AnyBody would search for the two objects in the "Shoulder" folder and fail
 to find them. This "dot" system is quite similar to the system you may
 know from directory structures in Dos, Windows, Unix, or just about any
 other computer operating system.
 
+:::{seealso}
+:class: dropdown
+**Absolute folder path** is another way to refer to objects in AnyScript and wil be used later in this tutorial. Absolute references are made by the complete name of an object. The complete name specifies all folders from the root, 
+i.e. from Main, and to the object like for instance:
+`Main.<foldername>.<subfoldername>.<objectname>`
+:::
+
 (reference-objects)=
 
 ## Reference objects and the ‘&’ symbol

A_Getting_started_anyscript/lesson5.md

@@ -234,7 +234,7 @@ should see this:
 :::{note}
 :class: margin
 Applied forces do not have to be constant. They can change with time
-and other properties in the model.  Please refer to the {doc}`tutorial onforces <../The_mechanical_elements/intro>` for more
+and other properties in the model.  Please refer to the {doc}`tutorial on forces <../The_mechanical_elements/intro>` for more
 details.
 :::
 

A_Getting_started_anyscript/lesson6.md

@@ -103,9 +103,12 @@ An STL (or other geometrical) object's axes are always oriented parallel to the
 By visualizing the palm node's local reference system, you will realize that the dumbbell needs to be rotated 90 degrees
 about the local Y-axis.
 
-**Therefore to rotate the dumbbell by 90 degrees about the Y axis, you must rotate the "PalmNode" by 90 degrees w.r.t its parent
-frame, i.e. the "ForeArm". While the vector sRel denotes the "PalmNode's" relative location,you can add a rotation matrix
-ARel (optinal property) which will orient "PalmNode" w.r.t "ForeArm".**
+To rotate the dumbbell by 90 degrees around the Y-axis, adjust the orientation
+of the `PalmNode`, where the dumbbell is attached. The `sRel` vector specifies
+the position of the `PalmNode` relative to its parent frame, `ForeArm`. By
+adding the optional `ARel` property, you can set the orientation of the
+`PalmNode`. Set `ARel` to a rotation matrix that rotates 90 degrees around the
+Y-axis to correctly orient the dumbbell.
 
 You can use the `RotMat` function to generate the 3x3 rotation matrix:
 
@@ -132,4 +135,4 @@ The RGB property specifies the blend of colors Red, Green, and Blue on a normali
 ```
 
 This completes the Getting Started with AnyScript tutorial. The final
-result of your efforts is in {download}`demo.arm2d.any <Downloads/demo.arm2d.any>`.
+result of your efforts is in {download}`demo.arm2d.zip <Downloads/demo.arm2d.zip>`.

A_Getting_started_modeling/Downloads/MyPedal/MyPedal/Model/BodyModelConfiguration.any

@@ -0,0 +1,26 @@
+#path __BM_PLUGIN_FILE__ "BodyModelConfiguration.any"
+#define BM_CONFIG_PLUGIN __BM_PLUGIN_FILE__
+
+// -----------------------------------------------------------------------------------
+// The BodyModel configuration can be modified using BodyModel GUI plugin
+// or by manually editing this file.
+//
+// Please see this this file for more information on the options:
+// #path HTML_DOC "<AMMR_PATH_DOC>/bm_config/index.html"
+// -----------------------------------------------------------------------------------
+
+// Enable the TLEM2 lower extremity model
+#define BM_LEG_MODEL _LEG_MODEL_TLEM2_
+
+// Excluding the muscles in the trunk segments
+#define BM_TRUNK_MUSCLES OFF
+// Excluding the left arm segments
+#define BM_ARM_LEFT OFF
+// Excluding the right arm segments
+#define BM_ARM_RIGHT OFF
+// Excluding the left leg segments
+#define BM_LEG_LEFT OFF
+// Excluding the muscles in the right leg segments
+#define BM_LEG_MUSCLES_RIGHT _MUSCLES_SIMPLE_
+// Excluding the default drivers for the human model
+#define BM_MANNEQUIN_DRIVER_DEFAULT OFF

A_Getting_started_modeling/Downloads/MyPedal/MyPedal/Model/DrawSettings.any

@@ -0,0 +1,147 @@
+
+DrawSettings = {
+
+
+  //This is the color definitions of the nodes and segments
+  Colors = {
+    AnyBodyRed = {149/256,51/256,55/256};    //AnyBody standard red
+    AnyBodyGreen = {47/256,131/256,80/256};  //AnyBody standard green
+    AnyBodyBlue = {82/256,85/256,111/256};   //AnyBody standard blue
+    AnyBodyYellow= {235/256,197/256,17/256}; //AnyBody standard yellow
+    AnyBodyPaleYellow = {248/256,204/256,115/256}; //AnyBody standard pale yellow
+    AnyBodyGrey = {153/256,153/256,153/256};    //AnyBody standard grey
+
+    Nodes = AnyBodyPaleYellow; 
+    Segments =  AnyBodyPaleYellow; 
+  };
+
+  Muscle = { 
+    RGB = .Colors.AnyBodyRed;
+    Visible =On;
+    DrawScaleOnOff =Off;
+    Bulging =0.0;
+    ColorScale =1.0;
+    RGBColorScale = {0.957031, 0.785156, 0.785156};
+    MaxStress = 2500000.000000; //N/m^2 //This number is for graphics only!
+    Opacity =1.0;
+    DrawScale = {
+      EnableCreasing = Off;
+      CreasingAngle = 0.524;
+      EnableWireframe = Off;
+      EnableSmoothing = On;
+      Param = 0.0;
+      ParamArray = {0.0, 0.167, 0.333, 0.5, 0.667, 0.833, 1.0};
+      RGBArray = {{0.0, 0.0, 0.6}, {0.0, 0.0, 1.0}, {0.0, 1.0, 1.0}, {0.0, 1.0, 0.0}, {1.0, 1.0, 0.0}, {1.0, 0.0, 0.0}, {0.6, 0.0, 0.0}};
+      OpacityArray = {1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0};
+    };
+  }; 
+
+
+  BonesOpacity = {
+
+    GlobalCoef = 1;
+
+    Skull = 1*GlobalCoef;
+    Thorax = 1*GlobalCoef;
+    Pelvis = 1*GlobalCoef;
+    Sacrum = 1*GlobalCoef;
+    L5 = 1*GlobalCoef;
+    L4 = 1*GlobalCoef;
+    L3 = 1*GlobalCoef;
+    L2 = 1*GlobalCoef;
+    L1 = 1*GlobalCoef;
+
+    RightFoot = 1*GlobalCoef;
+    RightShank = 1*GlobalCoef;
+    RightThigh = 1*GlobalCoef;
+
+    LeftFoot = 1*GlobalCoef;
+    LeftShank = 1*GlobalCoef;
+    LeftThigh = 1*GlobalCoef;
+
+
+    RightClavicula = 1*GlobalCoef;
+    RightScapula = 1*GlobalCoef;
+    RightHumerus = 1*GlobalCoef;
+    RightUlna = 1*GlobalCoef;
+    RightRadius = 1*GlobalCoef;
+    RightHand = 1*GlobalCoef;
+
+    LeftClavicula = 1*GlobalCoef;
+    LeftScapula = 1*GlobalCoef;
+    LeftHumerus = 1*GlobalCoef;
+    LeftUlna = 1*GlobalCoef;
+    LeftRadius = 1*GlobalCoef;
+    LeftHand = 1*GlobalCoef;
+
+
+    // For leg TD only.
+    RightTalus = 1*GlobalCoef;
+    RightPatella = 1*GlobalCoef;
+
+    LeftTalus = 1*GlobalCoef;
+    LeftPatella = 1*GlobalCoef;
+
+
+    // For detailed cervical model only.
+    C1 = 1*GlobalCoef;
+    C2 = 1*GlobalCoef;
+    C3 = 1*GlobalCoef;
+    C4 = 1*GlobalCoef;
+    C5 = 1*GlobalCoef;
+    C6 = 1*GlobalCoef;
+    C7 = 1*GlobalCoef;
+  };
+
+
+
+  SegmentAxes ={
+    RGB ={0,0,1};
+    ScaleXYZ ={0.0001,0.00001,0.00001};
+  };
+  BML ={
+    ScaleXYZ ={0.0006,0.0006,0.0006};
+    RGB = .Colors.AnyBodyBlue;
+  };
+  JointAxesProximal = {
+    RGB = .Colors.AnyBodyRed;
+    ScaleXYZ = {0.015,0.015,0.015};
+  };
+  JointAxesDistal = {
+    RGB = .Colors.AnyBodyGreen;
+    ScaleXYZ = {0.01,0.01,0.01};
+  };
+
+
+  SegmentNodes ={
+    ScaleXYZ ={0.0005,0.0005,0.0005};
+    RGB = .Colors.AnyBodyRed;
+  };
+  WrapGeometry = {
+    RGB ={1,1,1};
+  };
+
+  DrawSettingsSupport= {
+    Lin = { 
+      ScaleFactor=0.004; 
+      RGB = {0,0,1};
+      Thickness = 0.004;
+      HeadThickness = 2*Thickness;
+      HeadLength = 3*Thickness;
+    };
+    Rot = { 
+      ScaleFactor=0.08; 
+      RGB = {1,0,0};
+      Thickness = 0.075;
+      HeadThickness = 2*Thickness;
+      HeadLength = 5*Thickness;
+    };
+  };
+
+
+  Marker = {
+    Color={0,0,1};
+    Radius=0.00;
+  };
+
+}; //DrawSettings

A_Getting_started_modeling/Downloads/MyPedal/MyPedal/Model/Environment.any

@@ -0,0 +1,34 @@
+//This is a place holder for the modeling of the environment.
+AnyFolder Environment = {
+  AnyFixedRefFrame GlobalRef = {
+    viewRefFrame.Visible=On;
+    viewRefFrame.ScaleXYZ = 0.5*{1,1,1};
+
+    AnyRefNode Hpoint = {
+      sRel = {-0.75, 0.5, 0};
+    }; 
+  };
+
+  AnySeg Pedal = {
+    viewInertia.Visible = On;
+    Mass = 2;
+    Jii = {0.05, 0.001, 0.05};
+    AnyRefNode Hinge = {
+      sRel = {0, -0.15, 0};
+    };
+    AnyRefNode FootNode = {
+      sRel = {0, 0.15, 0};
+    };
+  };
+
+  AnyRevoluteJoint HingeJoint = {
+    Axis = z;
+    AnyFixedRefFrame &Ground = .GlobalRef;
+    AnyRefNode &Pedal = .Pedal.Hinge;
+  };
+
+  AnyForce Spring = {
+    AnyRevoluteJoint &Hinge = .HingeJoint;
+    F = -0.0*.HingeJoint.Pos;
+  };
+};