add slides for the tutorial

amanzi · Nov 11, 2024 · f62004d · f62004d
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diff --git a/.gitignore b/.gitignore
@@ -9,4 +9,10 @@ observations.csv
 
 1-hydrology/results/
 2-transport/results/
-3-submesh/results/
+3-submesh/results/
+
+slides/slides*bk*.Rmd
+slides/imgs/R/
+package*
+notebooks/.ipynb_checkpoints/
+node_modules/
diff --git a/2-transport/solution_transport.xml → 2-transport/.solution_transport.xml b/2-transport/solution_transport.xml → 2-transport/.solution_transport.xml
diff --git a/3-submesh/solution_submesh_transport.xml → 3-submesh/.solution_submesh_transport.xml b/3-submesh/solution_submesh_transport.xml → 3-submesh/.solution_submesh_transport.xml
diff --git a/README.md b/README.md
@@ -1,15 +1,15 @@
 # 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](https://ideas-watersheds.github.io/) all-hands meeting 2024 in Denver, CO.
+This 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.
 
 **Instructors:** Phong Le, Ethan Coon, Daniil Svyatsky
 
 ---
 
 ### 1. Learning Objectives :dart:
 By the end of this workshop, participants will be able to:
-* 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.
+* Understand key concepts of the [transport process kernel (PK)](https://github.com/amanzi/ats/tree/master/src/pk_transport) in Amanzi-ATS;
+* Develop workflows that couple transport PK with [hydrology PK](https://amanzi.github.io/ats/stable/input_spec/process_kernels/physical/flow.html).
 
 ---
 
@@ -20,8 +20,10 @@ To get the most out of this tutorial, participants should have:
 
 ---
 ### 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:**
+The slides for the tutorial can be found [here](./slides/slides.html).
+
+The tutorial will be conducted in a `docker` container. The container 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
 docker pull --platform linux/amd64 metsi/ideas-watersheds-all-hands-2024:v0
@@ -48,11 +50,11 @@ git clone https://github.com/amanzi/ats-hands-on-transport.git
 ---
 
 ### 4. Workshop Outline :memo:
-1. **Introduction to ATS Hydrology and Transport:**
-   *Overview of fundamental equations in hydrology and transport in Amanzi-ATS*
-
-2. **Hands-On Session: Building Transport Simulations:**
-   *Step-by-step guidance on developing transport simulations in ATS based on the integrated hydrology model*
-
-3. **Discussion and Feedback:**
-   *Open session for questions, insights, and feedback*
+* **Introduction to Hydrology and Transport PKs in ATS:**
+   - Overview of governing equations
+   
+* **Hands-On Session: Building Transport Simulations:**
+   - Step-by-step guidance on developing transport simulations in ATS based on the integrated hydrology model*
+
+* **Discussion and Feedback:**
+   - Open session for questions, insights, and feedback*
diff --git a/notebooks/1-hydrology.ipynb b/notebooks/1-hydrology.ipynb
@@ -3,7 +3,10 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import sys\n",
@@ -25,25 +28,34 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": "slide"
+    },
+    "tags": []
+   },
    "source": [
     "## Visualize exodus2 mesh"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "efb5afc79b7e44268273f426db3a0c07",
+       "model_id": "aae8240f242243cd92194c64c13a17b5",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Widget(value='<iframe src=\"http://localhost:59416/index.html?ui=P_0x300398c20_0&reconnect=auto\" class=\"pyvista…"
+       "Widget(value='<iframe src=\"http://localhost:59178/index.html?ui=P_0x16524d6a0_0&reconnect=auto\" class=\"pyvista…"
       ]
      },
      "metadata": {},
@@ -52,8 +64,8 @@
    ],
    "source": [
     "domain_mesh = atsvis.load_mesh_exodus('../data/synthetic_catchment.exo', z_scale=20)\n",
-    "atsvis.plot_mesh(domain_mesh, show_scalar_bar=True, set_background=False,\n",
-    "                 show_toplayer=True, window_size=[800, 600])"
+    "pl = atsvis.plot_mesh(domain_mesh, show_scalar_bar=True, set_background=False, \n",
+    "                      clim=[8, 11], show_toplayer=True, window_size=[960, 420])"
    ]
   },
   {
@@ -66,7 +78,10 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Load mesh polygons and data\n",
@@ -80,7 +95,10 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "tags": []
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -122,12 +140,15 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "dcc9daaa4ba442c5acc3d98946ae0866",
+       "model_id": "066e6b69832a42c0a8384cbad1a402be",
        "version_major": 2,
        "version_minor": 0
       },
@@ -178,7 +199,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "3551c51a43bc4ca188fbd9421a913047",
+       "model_id": "9fffdaa5a41f469ab7b457f4cda21638",
        "version_major": 2,
        "version_minor": 0
       },
@@ -269,7 +290,13 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
@@ -307,7 +334,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pyvista",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -325,5 +352,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }