add integrated and extract transport runs, including changes in noteb…

…ooks

.gitignore

@@ -2,6 +2,11 @@
 .vscode/
 __pycache__/
 
-*.h5
+ats*.h5
+checkpoint*.h5
+ats*.xmf
+observations.csv
+
 1-hydrology/results/
-2-transport/results/
+2-transport/results/
+3-submesh/results/

README.md

@@ -1,25 +1,26 @@
 # Amanzi-ATS Transport Tutorial
 
-This hands-on tutorial offers a hands-on experience in setting up and running transport simulations based on hydrology models in [Amanzi-ATS](https://github.com/amanzi/ats). This is part of the IDEAS-Watershed All-hands Meeting 2024 in Denver, CO.
+This hands-on tutorial offers a hands-on experience in setting up and running transport simulations based on hydrology models in [Amanzi-ATS](https://github.com/amanzi/ats). This is part of the [IDEAS-Watershed](https://ideas-watersheds.github.io/) all-hands meeting 2024 in Denver, CO.
 
-**Facilitators:** Phong Le, Ethan Coon, Daniil Svyatsky
+**Instructors:** Phong Le, Ethan Coon, Daniil Svyatsky
 
 ---
 
-### 1. Learning Objectives
+### 1. Learning Objectives :dart:
 By the end of this workshop, participants will be able to:
-* Understand core concepts of the [transport process kernel (PK)](https://github.com/amanzi/ats/tree/master/src/pk_transport) in Amanzi-ATS
-* Develop workflows that integrate transport processes into [hydrology](https://amanzi.github.io/ats/stable/input_spec/process_kernels/physical/flow.html) models
+* Understand key concepts of the [transport](https://github.com/amanzi/ats/tree/master/src/pk_transport) process kernel (PK) in Amanzi-ATS;
+* Develop workflows that integrate transport PK into [hydrology](https://amanzi.github.io/ats/stable/input_spec/process_kernels/physical/flow.html) PK.
 
 ---
 
-### 2. Prerequisites
+### 2. Prerequisites :bulb:
 To get the most out of this tutorial, participants should have:
-* Basic skills in Python and familiarity with [Jupyter Notebook](https://jupyter.org/). We will use [PyVista](https://pyvista.org/) for visualization.
+* Basic skills in [python](https://www.python.org/) and [jupyter notebook](https://jupyter.org/). We will use [pyvista](https://pyvista.org/) and [ipywidgets](https://ipywidgets.readthedocs.io/) for interactive visualization.
 * A fundamental understanding of watershed hydrology is encouraged.
 
 ---
-### 3. Setup Instructions
+### 3. Setup Instructions :wrench:
+The tutorial will be conducted in a Docker container. The docker includes the `terminal`, `text editor`, `ats`, `python`, `jupyter notebook`, and other dependencies. The `text editor` is customized to better work with the `ats` input files in `xml` format. Follow the steps below to set up the environment.
 1. **Pull the Docker Image:**
 Make sure to pull the Docker container for this tutorial:
 ```bash
@@ -32,17 +33,26 @@ Start the container and open the Jupyter Notebook interface:
 docker run --rm -it -p 8888:8888 metsi/ideas-watersheds-all-hands-2024:v0
 ```
 
-3. **Access Jupyter Notebooks:**
-Open the link displayed in your terminal to access Jupyter Notebook in your browser.
+3. **Access Jupyter notebooks:**
+Open the link displayed in your terminal to access `jupyter notebook` in your browser. 
+
+4. **Clone the tutorial repository:**
+Open a terminal in the Jupyter notebook interface and run:
+```bash
+git clone https://github.com/amanzi/ats-hands-on-transport.git
+```
+
+> [!IMPORTANT]
+> If you're familiar with the `VSCode` editor, you can use the [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) extension to connect to the container and edit XML files. You can also use the [jupyter](https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter) extension in `VSCode` to run notebooks directly within the Docker container.
 
 ---
 
-### 4. Workshop Outline
-* **Introduction to ATS Hydrology and Transport:**  
-Overview of fundamental equations in hydrology and transport in Amanzi-ATS
+### 4. Workshop Outline :memo:
+1. **Introduction to ATS Hydrology and Transport:**
+   *Overview of fundamental equations in hydrology and transport in Amanzi-ATS*
 
-* **Hands-On Session: Building transport simulations:**
-Step-by-step guidance on developing transport simulations in ATS based on the integrated hydrology model.
+2. **Hands-On Session: Building Transport Simulations:**
+   *Step-by-step guidance on developing transport simulations in ATS based on the integrated hydrology model*
 
-* **Discussion and Feedbacks** 
-Open session for questions, insights, and feedback on the tutorial content.
+3. **Discussion and Feedback:**
+   *Open session for questions, insights, and feedback*