Moved a lot of content from the AMMR Page to Tutorials.

A_Getting_started/intro.md

@@ -3,7 +3,8 @@
 
 # Getting Started Tutorial
 
-:::{note} The AnyBody software comes with an inbuilt model repository - The
+:::{note} 
+The AnyBody software comes with an inbuilt model repository - The
 AnyBody Managed Model Repository (AMMR). This tutorial starts with unpacking a
 local version of the AMMR. You can skip to {doc}`lesson 1 <lesson1>` if you have
 already done this. 
@@ -21,24 +22,48 @@ 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.
+# Seting 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. 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

@@ -59,21 +59,21 @@ location of the file is shown in the title bar:
 :align: center
 ```
 
-:::{warning}
-If you saved your model in an other location be
-sure to modify the {file}`../libdef.any` file so it points
-to AMMR repository you want to use.
+:::{warning} 
+If you saved your model in an other location be sure to modify the file
+{file}`../libdef.any` so it points to AnyBody Managed Model Repository you
+want to use. 
 :::
 
 (loading-a-model)=
 
 ## Loading a model
 
-To see the 3D graphical representation of the model you need to load.
+To see the 3D graphical representation of the model you need to load it.
 
-**Load/reload is a frequent operation and has been assigned to function key F7.
-You may also load your model by clicking** ![Load](_static/lesson1/image_6.png)
-**in the toolbar.**
+Load/reload is a frequent operation and has been assigned the function key F7.
+You may also load your model by clicking ![Load](_static/lesson1/image_6.png)
+in the toolbar.
 
 This action will load whatever file is chosen in the text editor. If a file is
 already loaded, the above action will simply reload the file until you give
@@ -88,12 +88,13 @@ 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
 :class: bg-primary
 :align: center
+:width: 70%
 ```
 
 The icons in the toolbar at the top of the Model View window allow you to modify
@@ -110,5 +111,149 @@ 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 
+Your 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 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 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
 
@@ -20,12 +19,12 @@ 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
-following structure. (In the interest of legibility we have removed many
+following structure (in the interest of legibility we have removed many
 of the lines):
 
 ```{literalinclude} Snippets/lesson2/MyStandingHuman-2/Model/Mannequin.any

A_Getting_started_AMMR/index.md

@@ -18,19 +18,21 @@ The AnyBody Managed Model Repository (AMMR), is an open library of musculoskelet
 models and examples ready to be used with the AnyBody Modeling System.
 
 The [AMMR documentation](https://anyscript.org/ammr/) is hosted
-separately, and contains a few tutorials and other usefull information. The
-[Creating a Human Model from scratch](https://anyscript.org/ammr/creating_model_from_scratch.html) tutorial is
-recommended for new users.
-
+separately and contains usefull information. See the below links for more information.
 
 
 ```{rubric} AMMR documentation
 ```
 
 - [Main AMMR documentation](https://anyscript.org/ammr/)
-- [Getting started with the AMMR](https://anyscript.org/ammr/getting_started.html)
 - [Configuring the Body Model](https://anyscript.org/ammr/bm_config/index.html)
+- [Application Examples](https://anyscript.org/ammr/Applications/index.html)
+<!-- - [Getting started with the AMMR](https://anyscript.org/ammr/getting_started.html) -->
+
 
+
+<!--
+References to previous AMMR chapters
 ```{rubric} AMMR Tutorials
 ```
 
@@ -42,3 +44,4 @@ Scaling: Joint to joint scaling <https://anyscript.org/ammr/Scaling/lesson1.html
 Scaling: External Body Measurements <https://anyscript.org/ammr/Scaling/lesson2.html>
 Scaling: Segmental scaling factors <https://anyscript.org/ammr/Scaling/lesson3.html>
 ```
+-->

A_Getting_started_anyscript/index.md

@@ -1,6 +1,7 @@
 ::: {rst-class} break
 :::
 
+(How_to_write_AnyScript)=
 # How to write AnyScript
 
 This tutorial introduces the AnyScript modeling language, which is used

A_Getting_started_anyscript/intro.md

@@ -8,12 +8,19 @@ System (AMS). It has been specially designed for describing the workings
 of the human body and its interactions with environmental objects such as
 exoskeletons, sports equipment, workplaces, etc.
 
-**In this tutorial, you will create your first AnyScript model, a
-simplified model of an arm.**
+In this tutorial, you will create your first AnyScript model, a
+simplified model of an arm.
 
 Each lesson (after lesson 1) begins with a link to a file containing the
-AnyScript code introduced up to that point. If you have a problem getting your code to work, simply
-download the demo files and start from there.
+AnyScript code introduced up to that point. If you have a problem getting your
+code to work, simply download the demo files and start from there.
+
+:::{seealso}
+*The AnyScript Reference Manual* provides comprehensive details on all the
+classes, functions, etc. available in AnyScript. You can access The AnyScript
+Reference Manual by opening an AnyBody window and selecting 'Help' -> 'AnyScript
+Reference' from the top menu.
+:::
 
 Let's get started with {doc}`Lesson 1: Basic concepts <lesson1>`
 

A_Getting_started_anyscript/lesson1.md

@@ -5,7 +5,7 @@
 
 :::{note}
 **To follow this tutorial, it is recommended to first watch the
-introductory video found at this link:** "{doc}`Tutorial Overview <../index>`".
+introductory video found at this link:** "{doc}`Getting Started <../GettingStarted>`".
 :::
 
 To create an AnyScript model from scratch, go to "File menu -> New from

A_Getting_started_modeling/intro.md

@@ -5,18 +5,23 @@
 # Introduction: Getting Started with Modeling
 
 Developing accurate models of the human body from scratch is an enormous task.
-It is thus practical to use the models in the [The AnyBody Managed Model
-Repository](https://anyscript.org/ammr/)
+It is thus practical to use the models in the 
+[The AnyBody Managed Model Repository](https://anyscript.org/ammr/)
 as a starting template for a new application.
 
 The following elements of the AnyScript language make such templating easier:
 
 - Include files - Which aid templating and sharing model components across different applications
 - Body model parameters - For customizing the default AMMR body models
 
-The AMMR installation folder also contains a library of [demo applications](https://anyscript.org/ammr/Applications/index.html)
-such as MoCap gait, cycling, leg-press exercises etc. If any of these applications are similar to your end goal, you can copy the
-application's model files and then modify them as required.
+The AMMR installation folder also contains a library of 
+[demo applications](https://anyscript.org/ammr/Applications/index.html) 
+such as MoCap gait, cycling, leg-press exercises etc. If any of these
+applications are similar to your end goal you can use the models. To do this,
+navigate to the ‘AMMR’ folder in your file explorer and open the ‘Application’
+folder. Here, you will find all the available models and examples. Navigate to
+the model you want to work on and copy its containing folder and paste it into
+your working director. Now, you can safely modify them as required. 
 
 **But in this tutorial, you will build a model from the bottom-up using the AMMR model templates.**