Deleted A Study of Studies - moved its content

A_Getting_started/index.md

@@ -1,10 +1,12 @@
 # Getting Started - First steps
 
-The objective of this tutorial is to demonstrate some of the features of
-the AnyBody Modeling System using an existing model.
+The objective of this tutorial is to demonstrate some of the features of the
+AnyBody Modeling System using an existing model. The reader will get an
+impression of the system’s capabilities and see a complex musculoskeletal model
+in action.
 
-The reader will get an impression of the system’s capabilities and see a
-complex musculoskeletal model in action.
+Finally, the last lesson will explain some general concepts about simulations 
+in AnyBody Modeling System.
 
 ::::{if-builder:: html
 ```{rubric} Tutorial content
@@ -18,4 +20,5 @@ Introduction <intro>
 lesson1
 lesson2
 lesson3
+lesson4
 ```

A_Getting_started/intro.md

@@ -21,7 +21,7 @@ the model view window
 This tutorial relies heavily on using the AnyBody Managed Model Repository (AMMR). 
 Follow the steps below to unpack a local version of the AMMR.
 
-# Setup the AMMR
+## Setup the AMMR
 
 Before you continue, you must unpack the entire repository and save it on your
 hard disk. To get a copy of the AMMR, press the Demo tab in the AnyBody
@@ -34,7 +34,7 @@ your documents folder by default. It is good practice to create a second local
 copy of the AMMR so that you do not overwrite the original AMMR folder by
 accident.
 
-# AMMR structure
+## AMMR structure
 
 Open a file manager and navigate to the directory where you unpacked the
 repository. You should see a folder structure that includes the following

A_Getting_started/lesson4.md

@@ -0,0 +1,203 @@
+::: {rst-class} break
+:::
+
+# Lesson 4: Understanding Simulations
+
+Now that you have a basic understanding of the AnyBody Modeling System and have
+had some hands-on experience, this lesson will give you a deeper understanding
+of what studies and operations are - the core components of all simulations in
+AnyBody. 
+
+In the AnyBody Modeling System, all types of simulations, whether they are pure
+mechanical system analysis, musculoskeletal analysis or design analysis, are
+carried out by objects that are referred to as “studies”. Studies have
+operations that can be executed to perform the analysis. 
+
+Meaning, studies and operations are the mechanisms used to specify tasks to
+be performed on the model. Think of a study as a collector that brings together
+a model definition, the operations that execute the model, and the results to be
+analyzed afterwards. Meaning, operations are the tasks performed on the model.
+They can be executed from the AnyBody interface, generating and storing output
+in the study based on the function of the specific operation.
+
+## Why Do We Need Studies?
+
+You might wonder why we need studies. After all, couldn’t you just load a model
+and have operations readily available in the AnyBody interface? The answer lies
+in the flexibility that studies offer.
+
+Studies are defined as special classes, allowing you to have multiple studies in
+the same model. As objects in the model, you can have as many studies as you
+need (or as many as your computer can handle), and they don’t necessarily have
+to operate on the same model definition, even if they share elements.
+
+For instance, you might want to perform different operations on the same model,
+or perform the same operation on nearly identical models, and then compare the
+results. With two studies, you can do this within a single AnyBody model.
+
+## The Hierarchy of Study Classes
+
+Studies are derived from a base class called `AnyStudy`, and the operations found
+within studies are also defined as classes, all derived from the base class
+`AnyOperation`.
+
+Here's a look at the hierarchy of study classes in AnyBody:
+
+
+- `AnyStudy` (Base class for all studies)
+
+  - `AnyTimeStudy` (Base class for time variation studies)
+
+    - `AnyKinStudy`
+
+      - `AnyMechStudy`
+      - `AnyBodyStudy`
+      - `AnyBodyCalibrationStudy`
+
+  - `AnyDesStudy` (design variable studies, see *a separate tutorial*)
+
+
+## Mechanical Studies
+
+Mechanical studies, derived from `AnyMechStudyBase`, are quite similar, but they
+contain different sets of available operations. The base class is empty, with
+`AnyKinStudy` extending it with functionality for kinematic analysis.
+`AnyMechStudy` further extends this with kinetic (dynamic) analysis of basic
+mechanical systems.
+
+`AnyBodyStudy` is the most frequently used study by AnyBody users, as it extends
+the kinematic analysis functions with operations for kinetic (dynamic) analysis
+of musculoskeletal systems, which is the core functionality of the AnyBody
+Modeling System. It also contains almost all of the operations found in other
+mechanical studies. `AnyBodyCalibrationStudy` provides additional functionality
+to adjust/calibrate the musculoskeletal models systematically.
+
+## Understanding the Structure of a Study
+
+A study in AnyBody is essentially a folder that contains specifications. These
+specifications are placed between a pair of braces and become part of the study.
+A study has predefined properties that you can set, must set, or cannot modify.
+
+When you create a new model using `File` -> `New from Template...`, the system
+automatically inserts an AnyBodyStudy in the main file. It looks like this:
+
+```AnyScriptDoc
+// The study: Operations to be performed on the model
+AnyBodyStudy MyStudy = {
+  AnyFolder &Model = .MyModel;
+  Gravity = {0.0, -9.81, 0.0};
+};
+```
+
+This study contains all the necessary elements. The first word after
+`AnyBodyStudy` defines the name of the study, which in this case is "MyStudy". The
+last line `Gravity = {0.0, -9.81, 0.0};` assigns a value to the Gravity
+variable, which specifies the gravitational acceleration vector affecting the
+model.
+
+An `AnyBodyStudy` has many more predefined properties that you can modify. You
+can view these properties using the Model Tree View, which is attached to the
+left of the Main Frame. Double-clicking any object in the Model Tree will show
+you properties of the objects in the Object Description dialog box.
+
+Most of the properties deal with solution methods, tolerances, and other
+advanced user features. However, some properties are essential for all users:
+
+* `tStart`: The time at which the study begins. Usually, this is zero.
+* `tEnd`: The time at which the study ends. This often needs to be set by the user.
+* `nStep`: Specifies how many steps the system should use to go from tStart to tEnd.
+
+Let's take a closer look at the first line of the study:
+
+```AnyScriptDoc
+AnyFolder &Model = .MyModel;
+```
+
+:::{note}
+:class: margin
+You can choose to point to some subfolders of `MyModel` instead of the entire
+model. This means the study would work on just a subset of the model. For
+example, you might want to compare two nearly identical models. In this case,
+you can put all common parts in one folder and the distinctive parts in separate
+folders. Then, you can create two studies that reference the common part and
+their respective distinctive parts.
+:::
+
+Here, "AnyFolder" is a type definition. Unlike the predefined properties
+discussed above, this line introduces a new property to the study. This is a
+key aspect of studies: you can add almost anything to a study, and the study
+doesn't need to know its type in advance.
+
+This line defines a variable called "Model" and assigns it to `.MyModel`. In 
+this case, `MyModel` is the folder that contains the entire model. The prefix `.`
+before `MyModel` indicates that it's one level up from where it's referenced.
+
+By assigning `MyModel` to the Model variable, the entire model comes under the
+influence of the study. The `&` before "Model" means that Model doesn't get
+replicated inside the study. Instead, it's a pointer to `MyModel`. If you're
+familiar with C, C++, or Java programming, you'll recognize this as the concept
+of pointers. If not, think of a pointer as a reference to something defined
+elsewhere. When you access it, you're actually interacting with what it points
+to.
+
+## The Standard Operations in a Study 
+
+When you create an `AnyBodyStudy`, it automatically includes three standard
+operations in the study tree. These operations represent different actions you
+can perform on the model elements that the study points to:
+
+* `InitialConditions`: This operation reads the values of all drivers
+  included in the study, and sets the model to match these drivers at the
+  start time (tStart). Meaning it puts the model in the position it has at
+  `time=tStart`. The model is first initialized into the positions from
+  load time, and the kinematics is then solved in a few steps. This is
+  especially helpful for inspecting the specified initial positions if you're
+  having issues with the initial configuration of the mechanism. The
+  `InitialConditions` can only run successfully if all joints and drivers are
+  fully defined.
+
+  Note, that the the model's positions after running `InitialConditions`
+  is different from the position after just loading the model, called
+  the load-time position.
+
+* `Kinematics`: This operation performs a kinematic analysis, which is a
+  simulation of the model's movement without calculating any forces. This means
+  you can run a Kinematics operation as soon as you've uniquely defined the
+  movement and the model is kinematically determinate. You don't need any
+  muscles in the model for this operation.
+
+  The data you can extract from the Kinematics study includes positions,
+  velocities, and accelerations.
+
+* `InverseDynamics`: This operation simulates the forces involved in the given
+  movement or posture, along with anything that can be derived from them. The
+  InverseDynamics operation uses the Kinematics operation as a subroutine, so it
+  requires a correctly defined movement or posture, as well as the necessary
+  muscles or motors to drive the model.
+  This is also known as kinetic or dynamic analysis.
+
+:::{admonition} Note on InverseDynamics
+:class: note
+You might think that calculating forces in a rigid body mechanical system is
+straightforward. After all, isn’t it just about setting up equilibrium equations
+and solving them? Well, it’s a bit more complex than that, especially when it
+comes to biomechanics.
+
+In biomechanics, we often deal with statically indeterminate systems. This means
+we don’t have enough equilibrium equations to resolve the forces in the system.
+Plus, we have to consider that muscles can only pull, not push. This adds
+another layer of complexity to the problem.
+
+The `AnyBodyStudy` class is designed to handle these complexities. It uses
+algorithms that are tailored for musculoskeletal systems.
+
+There’s also the `AnyMechStudy` class, which contains a simpler InverseDynamics
+operation. This operation doesn’t deal with the complexities of musculoskeletal
+systems. Instead, it solves the basic inverse dynamics problem for a simple
+mechanical system, finding the reaction forces that balance the system.
+:::
+
+When you execute each of these operations, they compile their output in the
+Output section under the study tree. This allows you to easily access and
+analyze the results of each operation.
+

A_Getting_started_anyscript/Downloads/demo.lesson5.any

@@ -109,19 +109,18 @@ Main = {
 
     AnyFolder Drivers = {
       //---------------------------------
-      AnyKinEqSimpleDriver ShoulderMotion = {
+      AnyKinDriver ShoulderMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
-        DriverPos = {-100*pi/180};
-        DriverVel = {30*pi/180};
+        DriverPos0 = {-100*pi/180};
+        DriverVel0 = {30*pi/180};
       }; // Shoulder driver
       //---------------------------------
-      AnyKinEqSimpleDriver ElbowMotion = {
+      AnyKinDriver ElbowMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
-        DriverPos = {90*pi/180};
-        DriverVel = {45*pi/180};
+        DriverPos0 = {90*pi/180};
+        DriverVel0 = {45*pi/180};
       }; // Elbow driver
     }; // Driver folder
-
   }; // MyModel
 
   // The study: Operations to be performed on the model

A_Getting_started_anyscript/Downloads/demo.lesson6.any

@@ -112,22 +112,20 @@ Main = {
 
     AnyFolder Drivers = {
       //---------------------------------
-
-      AnyKinEqSimpleDriver ShoulderMotion = {
+      AnyKinDriver ShoulderMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
-        DriverPos = {-100*pi/180};
-        DriverVel = {30*pi/180};
+        DriverPos0 = {-100*pi/180};
+        DriverVel0 = {30*pi/180};
         Reaction.Type = {Off};
       }; // Shoulder driver
-
       //---------------------------------
-      AnyKinEqSimpleDriver ElbowMotion = {
+      AnyKinDriver ElbowMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
-        DriverPos = {90*pi/180};
-        DriverVel = {45*pi/180};
+        DriverPos0 = {90*pi/180};
+        DriverVel0 = {45*pi/180};
         Reaction.Type = {Off};
       }; // Elbow driver
-    }; // Driver folder
+    }; // Driver folder   
 
     AnyFolder Muscles = {
     // Simple muscle model with constant strength = 400 Newton

A_Getting_started_anyscript/Snippets/lesson4/snip.NewModel.main-1.any

@@ -110,16 +110,16 @@ Main = {
 
 §AnyFolder Drivers = {
   //---------------------------------
-  AnyKinEqSimpleDriver ShoulderMotion = {
+  AnyKinDriver ShoulderMotion = {
     AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
-    DriverPos = {-100*pi/180};
-    DriverVel = {30*pi/180};
+    DriverPos0 = {-100*pi/180};
+    DriverVel0 = {30*pi/180};
   }; // Shoulder driver
   //---------------------------------
-  AnyKinEqSimpleDriver ElbowMotion = {
+  AnyKinDriver ElbowMotion = {
     AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
-    DriverPos = {90*pi/180};
-    DriverVel = {45*pi/180};
+    DriverPos0 = {90*pi/180};
+    DriverVel0 = {45*pi/180};
   }; // Elbow driver
 }; // Driver folder§
 //# END SNIPPET 1

A_Getting_started_anyscript/Snippets/lesson4/snip.NewModel.main-2.any

@@ -109,20 +109,20 @@ Main = {
 
     AnyFolder Drivers = {
       //---------------------------------
-      AnyKinEqSimpleDriver ShoulderMotion = {
+      AnyKinDriver ShoulderMotion = {
 //# BEGIN SNIPPET 1
 AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
 //# END SNIPPET 1
-        DriverPos = {-100*pi/180};
-        DriverVel = {30*pi/180};
+        DriverPos0 = {-100*pi/180};
+        DriverVel0 = {30*pi/180};
       }; // Shoulder driver
       //---------------------------------
-      AnyKinEqSimpleDriver ElbowMotion = {
+      AnyKinDriver ElbowMotion = {
 //# BEGIN SNIPPET 2
 AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
 //# END SNIPPET 2
-        DriverPos = {90*pi/180};
-        DriverVel = {45*pi/180};
+        DriverPos0 = {90*pi/180};
+        DriverVel0 = {45*pi/180};
       }; // Elbow driver
     }; // Driver folder
 

A_Getting_started_anyscript/Snippets/lesson5/snip.NewModel.main-1.any

@@ -109,16 +109,16 @@ Main = {
 
     AnyFolder Drivers = {
       //---------------------------------
-      AnyKinEqSimpleDriver ShoulderMotion = {
+      AnyKinDriver ShoulderMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
-        DriverPos = {-100*pi/180};
-        DriverVel = {30*pi/180};
+        DriverPos0 = {-100*pi/180};
+        DriverVel0 = {30*pi/180};
       }; // Shoulder driver
       //---------------------------------
-      AnyKinEqSimpleDriver ElbowMotion = {
+      AnyKinDriver ElbowMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
-        DriverPos = {90*pi/180};
-        DriverVel = {45*pi/180};
+        DriverPos0 = {90*pi/180};
+        DriverVel0 = {45*pi/180};
       }; // Elbow driver
 //# BEGIN SNIPPET 1
 }; // Driver folder

A_Getting_started_anyscript/Snippets/lesson5/snip.NewModel.main-2.any

@@ -109,16 +109,16 @@ Main = {
 
     AnyFolder Drivers = {
       //---------------------------------
-      AnyKinEqSimpleDriver ShoulderMotion = {
+      AnyKinDriver ShoulderMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Shoulder;
-        DriverPos = {-100*pi/180};
-        DriverVel = {30*pi/180};
+        DriverPos0 = {-100*pi/180};
+        DriverVel0 = {30*pi/180};
       }; // Shoulder driver
       //---------------------------------
-      AnyKinEqSimpleDriver ElbowMotion = {
+      AnyKinDriver ElbowMotion = {
         AnyRevoluteJoint &Jnt = ..Jnts.Elbow;
-        DriverPos = {90*pi/180};
-        DriverVel = {45*pi/180};
+        DriverPos0 = {90*pi/180};
+        DriverVel0 = {45*pi/180};
       }; // Elbow driver
     }; // Driver folder
 //# BEGIN SNIPPET 1