Merge commit '58136b60df981e8794331ed519acc16adaac0bd9'

doc/config.yml

@@ -25,6 +25,7 @@ Extensions:
                 Installation: getting_started/installation.md
                 Using Zapdos: getting_started/using_zapdos.md
                 Generating Meshes: getting_started/zapdos_meshing.md
+                Tutorial Slides: tutorial/index.md
             Documentation:
                 Zapdos Input Syntax: syntax/zapdos_only.md
                 Complete Code Syntax: syntax/index.md

doc/content/bib/documentation.bib

@@ -22,3 +22,35 @@ @article{Gogolides1992
   issn = {0009-2509},
   doi = {10.1016/0009-2509(92)85133-V}
 }
+
+@article{lieberman1994principles,
+  title={Principles of plasma discharges and materials processing},
+  author={Lieberman, Michael A and Lichtenberg, Allan J},
+  journal={MRS Bulletin},
+  volume={30},
+  number={12},
+  pages={899--901},
+  year={1994}
+}
+
+@article{mcmillin1995two,
+  title={Two-dimensional argon metastable density measurements in a radio frequency plasma reactor by planar laser-induced fluorescence imaging},
+  author={McMillin, Brian K and Zachariah, Michael R},
+  journal={Journal of applied physics},
+  volume={77},
+  number={11},
+  pages={5538--5544},
+  year={1995},
+  publisher={American Institute of Physics}
+}
+
+@article{greenberg1993electron,
+  title={Electron and metastable densities in parallel-plate radio-frequency discharges},
+  author={Greenberg, KE and Hebner, GA},
+  journal={Journal of applied physics},
+  volume={73},
+  number={12},
+  pages={8126--8133},
+  year={1993},
+  publisher={American Institute of Physics}
+}

doc/tutorial_config.yml

@@ -0,0 +1,44 @@
+Content:
+    tutorial:
+        root_dir: ${ROOT_DIR}/doc/workshops
+    moose:
+        root_dir: ${MOOSE_DIR}/framework/doc/content
+        content:
+            - ../../../tutorials/darcy_thermo_mech/doc/content/workshop/intro/moose_introduction.md
+
+Executioner:
+    type: MooseDocs.base.Serial
+
+Renderer:
+    type: MooseDocs.base.RevealRenderer
+    theme: simple
+
+Extensions:
+    disable_defaults: True
+    MooseDocs.extensions.reveal:
+        translate: tutorial/index.md
+        background_image: ncsu_slide_background.png
+    MooseDocs.extensions.comment: default
+    MooseDocs.extensions.command: default
+    MooseDocs.extensions.bibtex: default
+    MooseDocs.extensions.alert: default
+    MooseDocs.extensions.core: default
+    MooseDocs.extensions.config: default
+    MooseDocs.extensions.media: default
+    MooseDocs.extensions.floats: default
+    MooseDocs.extensions.include: default
+    MooseDocs.extensions.style: default
+    MooseDocs.extensions.autolink: default
+    MooseDocs.extensions.materialicon: default
+    MooseDocs.extensions.heading: default
+    MooseDocs.extensions.shortcut: default
+    MooseDocs.extensions.table: default
+    MooseDocs.extensions.layout: default
+    MooseDocs.extensions.content: default
+    MooseDocs.extensions.modal: default
+    MooseDocs.extensions.listing: default
+    MooseDocs.extensions.datetime: default
+    MooseDocs.extensions.katex:
+        macros:
+          included: !include ${MOOSE_DIR}/modules/doc/katex_macros.yml
+          \pf: "\\frac{\\partial #1}{\\partial #2}"

doc/workshops/tutorial/content/examples/global_model_visualization.md

@@ -0,0 +1,36 @@
+# Visualizing results from a 0D model
+
+# style=margin-top:3em;
+
+The results shown here are from Tutorial 2
+
+!---
+
+!media media/tutorial2_visualization/step1.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=After applying the results from your simulation, select the "Select Points On" icon.
+
+!---
+
+!media media/tutorial2_visualization/step2.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=Then, you will need to draw a box that contains at least a part of the singular element in order to select it.
+
+!---
+
+!media media/tutorial2_visualization/step3.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=After your box selection, you should see at least one of the ends of the element highlighted.
+
+
+!---
+
+!media media/tutorial2_visualization/step4.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=To see the time evolution of the system, select the "Plot Selection Over Time" button.
+
+!---
+
+!media media/tutorial2_visualization/step5.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=As you advance in time, you should see something that looks like this.

doc/workshops/tutorial/content/examples/helpful_resources.md

@@ -0,0 +1,14 @@
+# Zapdos Resources style=margin-bottom:2em;
+
+As a user of Zapdos, you have access to some support from developers and other users via the community discussions forum on GitHub:
+
+[https://github.com/shannon-lab/zapdos/discussions](https://github.com/shannon-lab/zapdos/discussions)
+
+
+If you are struggling with an issue, search to see if someone else has run into the same problem. If they haven't, start a new discussion! You're also welcome to start a discussion about how to contribute any functionality you have developed so others can use it, to share new ideas, or even show off new results! 
+
+Finally, if you encounter a replicable bug in Zapdos code or would like to request a new feature be developed, you can visit our issues page:
+
+[https://github.com/shannon-lab/zapdos/issues](https://github.com/shannon-lab/zapdos/issues)
+
+We do not have time to develop all requested features, but we are happy to help others get started in developing and contributing the features they need for their work. Reach out! :)

doc/workshops/tutorial/content/examples/lineplot_visualization.md

@@ -0,0 +1,36 @@
+# Visualizing 1D results
+
+# style=margin-top:3em;
+
+The results shown here are from Tutorial 1
+
+!---
+
+!media media/lineplot_visualization/step1.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=After opening an exodus file, the first step is always to click "Apply" or the eye icon.
+
+!---
+
+!media media/lineplot_visualization/step2.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=Once the results are loaded, select the "Plot Over Line" option to visualize a 1D result.
+
+!---
+
+!media media/lineplot_visualization/step3.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=The line plot also needs to be applied, so you can also use "Apply" or the eye icon here.
+
+
+!---
+
+!media media/lineplot_visualization/step4.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=Finally, you can navigate through time with the green triangle icons on the top of the page.
+
+!---
+
+!media media/lineplot_visualization/step5.png
+       style=width:100%;display:block;margin-top:1.5em;margin-left:auto;margin-right:auto;
+       caption=As you advance, you should see something that looks like this.

doc/workshops/tutorial/content/examples/tutorial1.md

@@ -0,0 +1,69 @@
+# Tutorial 1 - Diffusion + Constant Source
+
+!---
+
+# Problem Statement
+
+Consider a one dimensional single species, $i$, plasma on the domain $x\in\left[-\frac{l}{2}, \frac{l}{2}\right]$. Additionally, consider that this is a purely diffusive system with a constant source term due to a constant background gas density $n_g$. This system takes the following form
+
+\begin{equation}
+  -
+  \nabla
+  \cdot
+  \left(
+    D \nabla n_i
+  \right)
+  =
+  k
+  n_g
+\end{equation}
+
+
+Where $D$ is a constant diffusion coefficient, $n_i$ is the species density, and $k$ is a constant first order reaction rate. Additionally, a zero-density boundary condition will be imposed
+
+\begin{equation}
+  n_i
+  \left(
+    \pm \frac{l}{2}
+  \right)
+  =
+  0
+\end{equation}
+
+!---
+
+# style=margin-top:1em;
+
+### Explore what happens as the diffusion coefficient is varied.
+
+!listing tutorial/tutorial01-Diffusion/diffusion-only.i block=Materials/gas_species_0
+
+### Explore what happens as the reaction rate is varied.
+
+!listing tutorial/tutorial01-Diffusion/diffusion-only.i block=Materials/FirstOrder_Reaction
+
+!---
+
+# Analytic Solution
+
+!media media/tutorial1.png
+       style=width:300px;padding-left:20px;float:right;clear:right;
+       caption=Diffusive Species Solution.
+
+# style=margin-top:3em;
+
+\begin{equation}
+  n_i(x)
+  =
+  \frac{
+    k n_g l^2
+   }{
+    8 D
+   }
+   \left[
+    1  -
+    \left(
+    \frac{2x}{l}
+    \right)^2
+   \right]
+\end{equation}

doc/workshops/tutorial/content/examples/tutorial2.md

@@ -0,0 +1,105 @@
+# Tutorial 2 - Reaction Network
+
+!---
+
+# Problem Statement
+
+Consider a system of 3 species, $A, B, C$.
+
+- $A$ decays at a rate of $k_a$ into species $B$
+- $B$ decays at a rate of $k_b$ into species $C$
+- Species $C$ is a stable species
+
+The initial condition for this system is given by
+
+\begin{equation}
+  n_A(0) = n_{A_0}
+\end{equation}
+
+\begin{equation}
+  n_B(0) = n_C(0) = 0
+\end{equation}
+
+!---
+
+# System of Equations
+
+\begin{equation}
+  \pf{n_A}{t}
+  =
+  - k_A
+  n_A
+\end{equation}
+
+\begin{equation}
+  \pf{n_B}{t}
+  =
+  k_A n_A
+  -
+  k_B n_B
+\end{equation}
+
+\begin{equation}
+  \pf{n_C}{t}
+  =
+  k_B n_B
+\end{equation}
+
+!---
+
+### How would the reaction rates need to change to decrease the decay of $A$ and increase the growth of $B$?
+
+!listing tutorial/tutorial02-ReactionNetwork/transient-kinetics.i block=Reactions/Gas
+
+
+!---
+
+# Analytic Solution
+
+!media media/tutorial2.png
+       style=width:300px;padding-left:20px;float:right;clear:right;
+       caption=Species evolution over time.
+
+
+# style=margin-top:2.5em;
+
+\begin{equation}
+  n_A(t) =
+  n_{A_0}
+  e^{-k_A t}
+\end{equation}
+
+\begin{equation}
+  n_B(t) =
+  n_{A_0}
+  \frac{
+    k_A
+  }{
+    k_B - k_A
+  }
+  \left(
+    e^{-k_A t}
+    -
+    e^{-k_B t}
+  \right)
+\end{equation}
+
+
+\begin{equation}
+  n_C(t)
+  =
+  n_{A_0}
+  \left[
+    1 +
+    \frac{1}{
+      k_A - k_B
+    }
+    \left(
+      k_B
+      e^{-k_A t}
+      -
+      k_A e^{-k_B t}
+    \right)
+  \right]
+\end{equation}
+