Content added from the AMMR page

Author: Jacob Hilmar Adamsen

A_Getting_started/intro.md

@@ -21,24 +21,50 @@ 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
-
-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
-assistant dialog box.
-
-![...](_static/intro/image1.png)
-
-Following the instructions in the Demo tab will install a copy of the AMMR in
-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.
+(SettingUpAMMR)=
+## Setting Up the AMMR
+
+The *AnyBody Managed Model Repository* (AMMR) is a comprehensive open library of
+musculoskeletal models and examples designed to use with the AnyBody Modeling
+System. It allows users to configure and combine different body models, which
+can be easily integrated into their own simulations and analyses.
+
+The AnyBody Managed Model Repository (AMMR) is included with the AnyBody
+Modeling System, but it needs to be manually installed or unpacked after
+installing AnyBody. You can install the AMMR from the AnyBody Assistant dialog
+that appears when AnyBody starts.
+
+To get a copy of the latest AMMR files, press the Demo tab in the AnyBody
+assistant dialog box. Then select the *“Install the demo repository by clicking*
+*this link”*
+
+```{figure} _static/intro/image1.png
+:alt: AMMR setup
+:class: bg-primary
+:align: center
+```
+
+This installs a copy of the AMMR locally in your documents folder by default (e.g.
+{{AMMR_DEMO_INST_DIR}}). If
+there are multiple users using your computer, each of them will have to follow
+this guide. 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. There you can
+initialise a git repository in which you can version you models, keep a backup,
+or share them easily with the community.
+
+:::{important} 
+AnyBody Modelling System comes with a version of AMMR (not necessarily the
+latest) placed in the installation folder of the software. Do not directly use
+these files for your actual work as updates or reinstallation of AnyBody can
+overwrite your changes. So always **copy the files from the AMMR folder to your** 
+**working folder** before using them. 
+:::
 
 ## 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
-subfolders:
+repository (default is your documents folder). You should see a folder structure
+that includes the following subfolders:
 
 - **Application**: Includes demo simulations of activities such as cycling,
   lifting a box, or propelling a wheelchair.

A_Getting_started/lesson1.md

@@ -60,9 +60,16 @@ location of the file is shown in the title bar:
 ```
 
 :::{warning}
-If you saved your model in an other location be
+If you saved your model in another location be
 sure to modify the {file}`../libdef.any` file so it points
 to AMMR repository you want to use.
+
+The following line should always refer correctly to the libdef file
+regardless of where you save your model.
+
+```AnyScriptDoc
+#include "<ANYBODY_PATH_INSTALLDIR>/AMMR/libdef.any"
+```
 :::
 
 (loading-a-model)=
@@ -88,7 +95,7 @@ another file loading priority by right-clicking its tab and select “Load Model
 ## The model view
 
 When loading is completed, the Model View window opens and shows the standing
-model: (You can open it manually from View -> Model Views).
+model. You can open it manually from View -> Model Views.
 
 ```{image} _static/lesson1/image_5.png
 :alt: Model view
@@ -110,5 +117,149 @@ functions, so keyboard shortcuts have been provided:
 - If you have a scrolling wheel on your mouse, this will zoom the model
   in and out.
 
+## Understanding the AnyScript Model Structure
+
+This Human Standing Model is a model from the AnyBody Managed Model Repository
+(AMMR). It uses the [Human Model](https://anyscript.org/ammr/beta/body/models.html#the-body-model)
+from the AMMR, which is used by most models you will encounter when using the AMMR.
+Regardless of complexity, all models share a common structure used to set them
+up.
+
+The models will typically have the following overall structure (*notice*, the
+AnyScript below is not excatly the same as the Standing Model used in this
+tutorial, but contains the same overall structure):
+
+```AnyScriptDoc
+// Include the libdef file from the AMMR
+#include "libdef.any"
+
+Main =
+{
+  // Define the BodyModel configuration
+  #include "Model/BodyModelConfiguration.any"
+
+  // Include the Human model from AMMR
+  #include "<ANYBODY_PATH_BODY>/HumanModel.any"
+
+  // Define desired posture or movement of the model
+  #include "Model\Mannequin.any"
+
+  // Compose the model
+  AnyFolder Model =
+  {
+    AnyFolder &BodyModel = .HumanModel.BodyModel;
+    AnyFolder Drivers = {...};
+    AnyFolder Environment = {...};
+  };
+
+  // Configuring the Study
+  AnyBodyStudy Study =
+  {
+    AnyFolder &Model= .Model;
+    Gravity = {0.0, -9.81,0.0}; // Gravity Vector
+    nStep = 10; // Number of steps
+    tStart = 0; // Start time
+    tEnd = 10.0; // End time
+  };
+};
+```
+
+Let us go through the different components of this structure to understand how they work.
+
+### Path to AMMR:
+
+:::{note} 
+:class: margin 
+You can open a file by double-clicking on its name in the AnyScript.
+:::
+
+```AnyScriptDoc
+#include "libdef.any"
+```
+
+This means your model will include the content of the file called `libdef.any`.
+This file references to another `libdef.any` file located at the top-level
+folder of the AMMR, which specifies the AMMR directories to use in your model.
+You can have multiple versions of AMMR available on your computer, and this
+points to the version you wish to use. This line should be at the very beginning
+of your `main.any` file.
+
+### Configuring the Human Model:
+
+```AnyScriptDoc
+Main =
+{
+  // Define the BodyModel configuration
+  #include "Model/BodyModelConfiguration.any"
+```
+
+Here, the main declaration of the model, `Main = {}`, is initiated, and this file now
+becomes the main model file. All basic AnyScript contains a main file that
+defines the model’s structure, contents and the operations to be performed. 
+
+The file `BodyModelConfiguration.any` is included, which defines what parts of the
+human body model are included, through a number of switches called Body Model 
+(BM) parameters. BM parameters are always prefixed with `BM_` inside AnyScript.
+The values of these parameters are defined by `#define` and `#path` statements.
+
+### Including the Human Model
+
+```AnyScriptDoc
+#include "<ANYBODY_PATH_BODY>/HumanModel.any"
+```
+
+The AMMR contains multiple musculoskeletal models. The above line includes the
+Human Model from the AMMR. The file path `<ANYBODY_PATH_BODY>` is defined in
+`libdef.any`. 
+
+It is important that the above configuration statements are placed
+before this line.
+
+### Defining the Posture and Movement
+
+```AnyScriptDoc
+#include "Model\Mannequin.any"
+```
+
+This includes the file `Mannequin.any` which defines the posture and movement of
+the human body model.
+
+### Composing the Model
+
+```AnyScriptDoc
+AnyFolder Model =
+{
+  AnyFolder &BodyModel = .HumanModel.BodyModel;
+  AnyFolder Drivers = {...};
+  AnyFolder Environment = {...};
+};
+```
+
+This is where we combine the `Body` from the Human Model with extra things like
+drivers, external loads, and constraints. It could also be any models of the
+environment which the body interacts with or many other things.
+
+### The Study section
+
+```AnyScriptDoc
+AnyBodyStudy Study =
+{
+  AnyFolder &Model= .Model;
+  Gravity = {0.0, -9.81,0.0}; // Gravity Vector
+  nStep = 10; // Number of steps
+  tStart = 0; // Start time
+  tEnd = 10.0; // End time
+};
+```
+
+The `AnyBodyStudy` is where you configure and define your simulation. It
+specifies start and end times of the simulation, and the number of steps. It also
+configures which solvers are used.
+
+Only the model elements which are referenced to within the Study will be
+included in the simulation. In this case, the line `AnyFolder &Model= .Model;`
+references to the Model folder, meaning everything in the Model folder is part of the
+simulation.
+
 You can now proceed to {doc}`lesson2`.
 

A_Getting_started/lesson2.md

@@ -7,10 +7,9 @@ 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.
 
-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"`.
+Scroll down to the line that says `#include "Model\Mannequin.any"`. This line
+means that your model will include the content of the file called
+`Mannequin.any` located in the Model folder, within the main file. 
 
 ## Mannequin file structure
 
@@ -20,8 +19,8 @@ Scroll down to the line that says `#include "Model\Mannequin.any"`.
 :end-before: //# END SNIPPET 1
 ```
 
-**This line means that your model will include the content of the
-"Mannequin.any" file located in the Model folder, within the main file.**
+The `Mannequin.any` file determines the posture of the Standing Model by
+specifying the angles at the anatomical joints.
 
 Double-clicking the file name in the editor window after loading
 your model opens the mannequin file in a new tab. Then you see the