diff --git a/.gitignore b/.gitignore index aa03390..869924c 100644 --- a/.gitignore +++ b/.gitignore @@ -11,8 +11,8 @@ observations.csv 2-transport/results/ 3-submesh/results/ -slides/slides*bk*.Rmd -slides/imgs/R/ +docs/slides*bk*.Rmd +docs/imgs/R/ package* notebooks/.ipynb_checkpoints/ node_modules/ diff --git a/README.md b/README.md index 4e0adc5..d406cfb 100644 --- a/README.md +++ b/README.md @@ -8,8 +8,9 @@ This tutorial offers a hands-on experience in setting up and running transport s ### 1. Learning Objectives :dart: By the end of this workshop, participants will be able to: -* 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). +* Understand the basics 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); +* Visualize and analyze Amanzi-ATS model outputs. --- @@ -20,9 +21,9 @@ To get the most out of this tutorial, participants should have: --- ### 3. Setup Instructions :wrench: -The slides for the tutorial can be found [here](./slides/slides.html). +The slides for the tutorial can be found [here](https://amanzi.github.io/ats-hands-on-transport/slides.html){:target="_blank"}. -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. +The tutorial will be run 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 diff --git a/slides/assets/IDEASLogo.png b/docs/assets/IDEASLogo.png similarity index 100% rename from slides/assets/IDEASLogo.png rename to docs/assets/IDEASLogo.png diff --git a/slides/assets/custom.css b/docs/assets/custom.css similarity index 100% rename from slides/assets/custom.css rename to docs/assets/custom.css diff --git a/slides/assets/mathjax-equation-numbers.html b/docs/assets/mathjax-equation-numbers.html similarity index 100% rename from slides/assets/mathjax-equation-numbers.html rename to docs/assets/mathjax-equation-numbers.html diff --git a/slides/assets/remark-zoom.js b/docs/assets/remark-zoom.js similarity index 100% rename from slides/assets/remark-zoom.js rename to docs/assets/remark-zoom.js diff --git a/slides/assets/sydney-fonts.css b/docs/assets/sydney-fonts.css similarity index 100% rename from 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b/docs/libs/remark-css/default-fonts.css similarity index 100% rename from slides/libs/remark-css/default-fonts.css rename to docs/libs/remark-css/default-fonts.css diff --git a/slides/libs/remark-css/default.css b/docs/libs/remark-css/default.css similarity index 100% rename from slides/libs/remark-css/default.css rename to docs/libs/remark-css/default.css diff --git a/slides/slides.Rmd b/docs/slides.Rmd similarity index 59% rename from slides/slides.Rmd rename to docs/slides.Rmd index 19ade69..9a1c1db 100644 --- a/slides/slides.Rmd +++ b/docs/slides.Rmd @@ -24,16 +24,38 @@ output:
--- -- Understand the basics of .content-box-purple[`transport PK`] - --- +- Understand the basics of the .content-box-purple[`transport PK`] - Build simple to advanced transport models with .content-box-yellow[`Amanzi-ATS`] +- .content-box-red[Visualize and analyze] `Amanzi-ATS` model outputs --- -- .content-box-red[Visualize and analyze] ATS model outputs +--- + +# Website + +
+ +**Github `r fontawesome::fa("github")`:** + +[`https://github.com/amanzi/ats-hands-on-transport`](https://github.com/amanzi/ats-hands-on-transport) + +
+ +**Slides for tutorial:** + +[`https://amanzi.github.io/ats-hands-on-transport/slides.html`](https://amanzi.github.io/ats-hands-on-transport/slides.html) + +
+ +.font70[ +**Other `Amanzi-ATS` resources:** +- Documentation: [`https://amanzi.github.io/ats/stable/`](https://amanzi.github.io/ats/stable/) +- Short course: [`https://github.com/amanzi/ats-short-course`](https://github.com/amanzi/ats-short-course) +- Regression tests: [`https://github.com/amanzi/ats-regression-tests`](https://github.com/amanzi/ats-regression-tests) +- Demos: [`https://github.com/amanzi/ats-demos`](https://github.com/amanzi/ats-demos) +] --- + # Setting up environment
@@ -49,9 +71,22 @@ docker pull --platform linux/amd64 metsi/ideas-watersheds-all-hands-2024:v0 - Run the `docker` container to start the `JupyterLab` server ```{bash, eval=FALSE} -docker run --rm -it -p 8888:8888 metsi/ideas-watersheds-all-hands-2024:v0 +docker run -p 8888:8888 metsi/ideas-watersheds-all-hands-2024:v0 ``` +--- +# VSCode and Dev Containers + +
+ +### If you prefer VSCode/Cursor editors, use the extensions: +- .content-box-green[`Dev Containers`] to connect to the container and edit files (e.g., `XML`). + - .font90[Convenient for data transfer between `host` and `container`] + +
+ +- .content-box-purple[`jupyter`] to edit/run notebooks inside the container with VSCode. + --- class: phong-dark # .brand-orange[Integrated hydrology model] @@ -91,6 +126,87 @@ $$ \frac{\partial \Theta_g}{\partial t} + \nabla \cdot \vec{\mathbf{q}_g} = Q_g$ ] .footnote[```Molins et al. (2022)```] + +--- +# Steps to Construct a Model +.pull-left-21[ +.font90[ +- **.brand-blue[Simulation domains]** `r fontawesome::fa("map")` + - Where the processes happen + +- **.brand-blue[Dependency graph]** `r fontawesome::fa("network-wired")` + - Which `PKs` to use and how they are coupled + + +- **.brand-blue[Model parameters]** `r fontawesome::fa("cog")` + - Physical and numerical properties + +- **.brand-blue[Initial and boundary conditions]** `r fontawesome::fa("object-ungroup")` `r fontawesome::fa("clock")` + - State of the system at $t=0$ + - How system behaves at the boundaries at $t>0$ + +- **.brand-blue[Forcing, sources and sinks]** `r fontawesome::fa("cloud-sun-rain")` + - External forces that drive changes in the system + - Material or energy added/removed to/from the system +]] + +-- + +
+ +.pull-right-12[ +.small[ +```xml + + + + + + + + + + + + + + + + + + +``` +]] + +--- + +# Dependency Graph - Integrated Hydrology + +.pull-left-21[ + +] + +-- + +.pull-right-12[ +

+ +.font70[ +```xml + + + + + + + + + + + +``` +]] + --- # Domain of simulation @@ -132,33 +248,15 @@ $\Delta$z = [0.1, 0.1, 0.1, 0.2, 0.2, 0.4, 0.4] .font60[.footnote[```domain of simulation```]] --- - -# Dependency Graph - Integrated Hydrology - +# Simulation Time .pull-left-21[ - +- 24 hours ] --- - -.pull-right-12[ -

+--- +class: phong-dark +# .brand-orange[Transport hands-on] -.font70[ -```xml - - - - - - - - - - - -``` -]] --- # Transport diff --git a/docs/slides.html b/docs/slides.html new file mode 100644 index 0000000..bff41c3 --- /dev/null +++ b/docs/slides.html @@ -0,0 +1,465 @@ + + + + Amanzi-ATS Transport + + + + + + + + + + + + + + + + + + + + + diff --git a/slides/slides_files/DiagrammeR-binding/DiagrammeR.js b/docs/slides_files/DiagrammeR-binding/DiagrammeR.js similarity index 100% rename from slides/slides_files/DiagrammeR-binding/DiagrammeR.js rename to docs/slides_files/DiagrammeR-binding/DiagrammeR.js diff --git a/slides/slides_files/DiagrammeR-styles/styles.css b/docs/slides_files/DiagrammeR-styles/styles.css similarity index 100% rename from slides/slides_files/DiagrammeR-styles/styles.css rename to docs/slides_files/DiagrammeR-styles/styles.css diff --git a/slides/slides_files/chromatography/LICENSE b/docs/slides_files/chromatography/LICENSE similarity index 100% rename from slides/slides_files/chromatography/LICENSE rename to docs/slides_files/chromatography/LICENSE diff --git a/slides/slides_files/chromatography/chromatography.js b/docs/slides_files/chromatography/chromatography.js similarity index 100% rename from slides/slides_files/chromatography/chromatography.js rename to docs/slides_files/chromatography/chromatography.js diff --git a/slides/slides_files/d3/LICENSE b/docs/slides_files/d3/LICENSE similarity index 100% rename from slides/slides_files/d3/LICENSE rename to docs/slides_files/d3/LICENSE diff --git a/slides/slides_files/d3/d3.min.js b/docs/slides_files/d3/d3.min.js similarity index 100% rename from slides/slides_files/d3/d3.min.js rename to docs/slides_files/d3/d3.min.js diff --git a/slides/slides_files/dagre/LICENSE b/docs/slides_files/dagre/LICENSE similarity index 100% rename from slides/slides_files/dagre/LICENSE rename to docs/slides_files/dagre/LICENSE diff --git a/slides/slides_files/dagre/dagre-d3.min.js b/docs/slides_files/dagre/dagre-d3.min.js similarity index 100% rename from slides/slides_files/dagre/dagre-d3.min.js rename to docs/slides_files/dagre/dagre-d3.min.js diff --git a/slides/slides_files/grViz-binding/grViz.js b/docs/slides_files/grViz-binding/grViz.js similarity index 100% rename from slides/slides_files/grViz-binding/grViz.js rename to docs/slides_files/grViz-binding/grViz.js diff --git a/slides/slides_files/header-attrs-2.29/header-attrs.js b/docs/slides_files/header-attrs-2.29/header-attrs.js similarity index 100% rename from slides/slides_files/header-attrs-2.29/header-attrs.js rename to docs/slides_files/header-attrs-2.29/header-attrs.js diff --git a/slides/slides_files/header-attrs/header-attrs.js b/docs/slides_files/header-attrs/header-attrs.js similarity index 100% rename from slides/slides_files/header-attrs/header-attrs.js rename to docs/slides_files/header-attrs/header-attrs.js diff --git a/slides/slides_files/htmltools-fill/fill.css b/docs/slides_files/htmltools-fill/fill.css similarity index 100% rename from slides/slides_files/htmltools-fill/fill.css rename to docs/slides_files/htmltools-fill/fill.css diff --git a/slides/slides_files/htmlwidgets/htmlwidgets.js b/docs/slides_files/htmlwidgets/htmlwidgets.js similarity index 100% rename from slides/slides_files/htmlwidgets/htmlwidgets.js rename to docs/slides_files/htmlwidgets/htmlwidgets.js diff --git a/slides/slides_files/mermaid/LICENSE b/docs/slides_files/mermaid/LICENSE similarity index 100% rename from slides/slides_files/mermaid/LICENSE rename to docs/slides_files/mermaid/LICENSE diff --git a/slides/slides_files/mermaid/dist/mermaid.css b/docs/slides_files/mermaid/dist/mermaid.css similarity index 100% rename from slides/slides_files/mermaid/dist/mermaid.css rename to docs/slides_files/mermaid/dist/mermaid.css diff --git a/slides/slides_files/mermaid/dist/mermaid.slim.min.js b/docs/slides_files/mermaid/dist/mermaid.slim.min.js similarity index 100% rename from slides/slides_files/mermaid/dist/mermaid.slim.min.js rename to docs/slides_files/mermaid/dist/mermaid.slim.min.js diff --git a/slides/slides_files/remark-css-0.0.1/default.css b/docs/slides_files/remark-css-0.0.1/default.css similarity index 100% rename from slides/slides_files/remark-css-0.0.1/default.css rename to docs/slides_files/remark-css-0.0.1/default.css diff --git a/slides/slides_files/remark-css/default.css b/docs/slides_files/remark-css/default.css similarity index 100% rename from slides/slides_files/remark-css/default.css rename to docs/slides_files/remark-css/default.css diff --git a/slides/slides_files/viz/viz.js b/docs/slides_files/viz/viz.js similarity index 100% rename from slides/slides_files/viz/viz.js rename to docs/slides_files/viz/viz.js diff --git a/slides/slides.html b/slides/slides.html deleted file mode 100644 index 5e7bca7..0000000 --- a/slides/slides.html +++ /dev/null @@ -1,367 +0,0 @@ - - - - Amanzi-ATS Transport - - - - - - - - - - - - - - - - - - - - -