lesson4.md

::: {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:

// 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:

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.