update slide and dependency graphs

amanzi · Nov 12, 2024 · 644a112 · 644a112
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diff --git a/README.md b/README.md
@@ -53,6 +53,7 @@ git clone https://github.com/amanzi/ats-hands-on-transport.git
 ### 4. Workshop Outline :memo:
 * **Introduction to Hydrology and Transport PKs in ATS:**
    - Overview of governing equations
+   - Review of ATS input files
 
 * **Hands-On Session: Building Transport Simulations:**
    - Step-by-step guidance on developing transport simulations in ATS based on the integrated hydrology model*

diff --git a/docs/assets/sydney.css b/docs/assets/sydney.css
@@ -70,6 +70,14 @@ To specify the margin of the first title h1
   width: 72%;
 }
 
+.pull-left-64 {
+  float: left;
+  width: 58%;
+}
+.pull-right-46 {
+  float: right;
+  width: 38%;
+}
 
 /* use to position text at the bottom */
 .pull-down {

diff --git a/docs/imgs/dependency.html b/docs/imgs/dependency.html
@@ -12,9 +12,9 @@
 </head>
 <body>
 <div id="htmlwidget_container">
-  <div class="visNetwork html-widget html-fill-item" id="htmlwidget-1c8565adf91cb5a36f7a" style="width:960px;height:500px;"></div>
+  <div class="visNetwork html-widget html-fill-item" id="htmlwidget-1c8565adf91cb5a36f7a" style="width:500px;height:300px;"></div>
 </div>
 <script type="application/json" data-for="htmlwidget-1c8565adf91cb5a36f7a">{"x":{"nodes":{"id":[1,2,3],"label":["MPC::flow coupler","PK::flow","PK::overland flow"],"shape":["box","box","box"],"color":[{"background":"coral"},{"background":"lightblue"},{"background":"lightblue"}],"title":["Strong coupling (PK Type: coupled water)","Richards Equation (PK Type: richards flow)","Diffusive Wave Equation (PK Type: overland flow, pressure basis)"],"x":[0,-100,100],"y":[-100,0,0]},"edges":{"from":[1,1],"to":[2,3]},"nodesToDataframe":true,"edgesToDataframe":true,"options":{"width":"100%","height":"100%","nodes":{"shape":"box","font":{"size":20}},"manipulation":{"enabled":true},"physics":{"enabled":false},"layout":{"randomSeed":1234}},"groups":null,"width":null,"height":null,"idselection":{"enabled":false,"style":"width: 150px; height: 26px","useLabels":true,"main":"Select by id"},"byselection":{"enabled":false,"style":"width: 150px; height: 26px","multiple":false,"hideColor":"rgba(200,200,200,0.5)","highlight":false},"main":null,"submain":null,"footer":null,"background":"rgba(0, 0, 0, 0)","opts_manipulation":{"datacss":"table.legend_table {\n  font-size: 11px;\n  border-width:1px;\n  border-color:#d3d3d3;\n  border-style:solid;\n}\ntable.legend_table td {\n  border-width:1px;\n  border-color:#d3d3d3;\n  border-style:solid;\n  padding: 2px;\n}\ndiv.table_content {\n  width:80px;\n  text-align:center;\n}\ndiv.table_description {\n  width:100px;\n}\n\n.operation {\n  font-size:20px;\n}\n\n.network-popUp {\n  display:none;\n  z-index:299;\n  width:250px;\n  /*height:150px;*/\n  background-color: #f9f9f9;\n  border-style:solid;\n  border-width:1px;\n  border-color: #0d0d0d;\n  padding:10px;\n  text-align: center;\n  position:fixed;\n  top:50%;  \n  left:50%;  \n  margin:-100px 0 0 -100px;  \n\n}","addNodeCols":["id","label"],"editNodeCols":["id","label"],"tab_add_node":"<span id=\"addnode-operation\" class = \"operation\">node<\/span> <br><table style=\"margin:auto;\"><tr><td>id<\/td><td><input id=\"addnode-id\"  type= \"text\" value=\"new value\"><\/td><\/tr><tr><td>label<\/td><td><input id=\"addnode-label\"  type= \"text\" value=\"new value\"><\/td><\/tr><\/table><input type=\"button\" value=\"save\" id=\"addnode-saveButton\"><\/button><input type=\"button\" value=\"cancel\" id=\"addnode-cancelButton\"><\/button>","tab_edit_node":"<span id=\"editnode-operation\" class = \"operation\">node<\/span> <br><table style=\"margin:auto;\"><tr><td>id<\/td><td><input id=\"editnode-id\"  type= \"text\" value=\"new value\"><\/td><\/tr><tr><td>label<\/td><td><input id=\"editnode-label\"  type= \"text\" value=\"new value\"><\/td><\/tr><\/table><input type=\"button\" value=\"save\" id=\"editnode-saveButton\"><\/button><input type=\"button\" value=\"cancel\" id=\"editnode-cancelButton\"><\/button>"},"highlight":{"enabled":false,"hoverNearest":false,"degree":1,"algorithm":"all","hideColor":"rgba(200,200,200,0.5)","labelOnly":true},"collapse":{"enabled":false,"fit":false,"resetHighlight":true,"clusterOptions":null,"keepCoord":true,"labelSuffix":"(cluster)"},"events":{"doubleClick":"function(nodes) {\n    // When a node is double-clicked, prompt the user for a color\n    var nodeId = nodes.nodes[0];\n    var newColor = prompt('Enter a color (e.g., lightblue, red, etc.):', 'lightblue');\n    if (newColor) {\n      var network = this;\n      // Update the selected node's background color\n      network.body.data.nodes.update({id: nodeId, color: {background: newColor}});\n    }\n  }"}},"evals":["events.doubleClick"],"jsHooks":[]}</script>
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 </body>
 </html>
diff --git a/docs/slides.Rmd b/docs/slides.Rmd
@@ -89,13 +89,19 @@ docker run -p 8888:8888 metsi/ideas-watersheds-all-hands-2024:latest
 
 ---
 # Outlines
+
 <br>
 
-.large[
-- Integrated hydrology model (2D & 3D)
-- Transport model over the entire domain (2D & 3D) 
-- Transport model over the river network (1D)
-]
+#### .blockquote[Integrated hydrology:]
+- Understand and run the model (2-D & 3-D)
+- Visualize and interpret the outputs
+
+#### .blockquote[Transport Modeling:]
+- **Catchment scale:** 2-D & 3-D transport across the entire domain
+- **River network scale:** 1-D transport within the river corridor
+  - .content-box-green[Develop and couple] transport models with integrated hydrology
+  - Visualize and interpret results
+
 
 ---
 class: phong-dark
@@ -139,21 +145,21 @@ $$ \frac{\partial \Theta_g}{\partial t} + \nabla \cdot \vec{\mathbf{q}_g} = Q_g$
 
 ---
 # Steps to Construct a Model
-.pull-left-21[
+.pull-left-64[
 .font90[
 - **.brand-blue[Simulation domains]** `r fontawesome::fa("map")`
   - Where the processes happen
 
-- **.brand-blue[Dependency graph]** `r fontawesome::fa("network-wired")`
+- .content-box-green[**.brand-blue[Dependency graph]** `r fontawesome::fa("sitemap")`]
   - Which `PKs` to use and how they are coupled
 
 
-- **.brand-blue[Model parameters]** `r fontawesome::fa("cog")`
+- **.brand-blue[Model parameters]** `r fontawesome::fa("sliders")`
   - 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 $t>0$
+  - State of the system at $t=t_0$
+  - How system behaves at the boundaries at $t \ge t_0$
 
 - **.brand-blue[Forcing, sources and sinks]** `r fontawesome::fa("cloud-sun-rain")`
   - External forces that drive changes in the system
@@ -164,36 +170,32 @@ $$ \frac{\partial \Theta_g}{\partial t} + \nabla \cdot \vec{\mathbf{q}_g} = Q_g$
 
 <br>
 
-.pull-right-12[
+.pull-right-46[
+
 .small[
-```xml
-<ParameterList name="cycle driver">
-  <Parameter name="end cycle" type="int" value="10000" />
-  <Parameter name="start time" type="double" value=" 0" />
-  <Parameter name="start time units" type="string" value="s" />
-  <Parameter name="end time" type="double" value="86400" />
-  <Parameter name="end time units" type="string" value="s" />
-  <ParameterList name="PK tree">
-    <ParameterList name="flow coupler">
-      <Parameter name="PK type" type="string" value="coupled water" />
-      <ParameterList name="flow">
-        <Parameter name="PK type" type="string" value="richards flow" />
-      </ParameterList>
-      <ParameterList name="overland flow">
-        <Parameter name="PK type" type="string" value="overland flow, pressure basis" />
-      </ParameterList>
-    </ParameterList>
-  </ParameterList>
-</ParameterList>
+**ATS `xml` top level list includes:**
+```r
+Main
+- mesh: ["mesh-typed-spec-list"]
+- regions: ["region-typedinline-spec-list"]
+- cycle driver: ["coordinator-spec"]
+- PKs: ["pk-typedinline-spec-list"]
+- state: ["state-spec"]
+*- visualization: ["visualization-spec-list"]
+*- checkpoint: ["checkpoint-spec"]
+*- observations: ["observation-spec-list"]
 ```
-]]
+]
+]
+
+.footnote[[ATS Documentation](https://amanzi.github.io/ats/stable/input_spec/main.html)]
 
 ---
 
 # Dependency Graph - Integrated Hydrology
 
-.pull-left-21[
-<iframe src="imgs/dependency.html" width="700" height="600" frameborder="0"></iframe>
+.pull-left-64[
+<iframe src="imgs/dependency.html" width="600" height="500" frameborder="1"></iframe>
 ]
 
 .font70[
@@ -203,30 +205,33 @@ $$ \frac{\partial \Theta_g}{\partial t} + \nabla \cdot \vec{\mathbf{q}_g} = Q_g$
 
 --
 
-.pull-right-12[
+.pull-right-46[
 .font70[
 ```xml
-<ParameterList name="PK tree">
-  <ParameterList name="flow coupler">
-    <Parameter name="PK type" type="string" value="coupled water" />
-    <ParameterList name="flow">
-      <Parameter name="PK type" type="string" value="richards flow" />
-    </ParameterList>
-    <ParameterList name="overland flow">
-      <Parameter name="PK type" type="string" value="overland flow, pressure basis" />
+<ParameterList name="Main">
+* OTHER LISTS...
+  <ParameterList name="PK tree">
+    <ParameterList name="flow coupler">
+      <Parameter name="PK type" type="string" value="coupled water" />
+      <ParameterList name="flow">
+        <Parameter name="PK type" type="string" value="richards flow" />
+      </ParameterList>
+      <ParameterList name="overland flow">
+        <Parameter name="PK type" type="string" value="overland flow, pressure basis" />
+      </ParameterList>
     </ParameterList>
   </ParameterList>
-</ParameterList>
 
-OTHER CODES...
+* OTHER LISTS...
 
-<ParameterList name="PKs">
-  <ParameterList name="flow coupler">
-    <Parameter name="PK type" type="string" value="coupled water" />
-    <Parameter name="PKs order" type="Array(string)" value="{flow, overland flow}" />
+  <ParameterList name="PKs">
+    <ParameterList name="flow coupler">
+      <Parameter name="PK type" type="string" value="coupled water" />
+      <Parameter name="PKs order" type="Array(string)" value="{flow, overland flow}" />
+    </ParameterList>
+*   OTHER SUB-LISTS...    
   </ParameterList>
-  OTHER CODES...    
-</ParameterList>
+</ParameterList>  
 ```
 ]]
 
@@ -271,11 +276,57 @@ $\Delta$z = [0.1, 0.1, 0.1, 0.2, 0.2, 0.4, 0.4]
 .font60[.footnote[<a href="imgs/domain.html" target="_blank">```domain of simulation```</a>]]
 
 ---
-# Simulation Time
-.pull-left-21[
-- 24 hours
+# Model Parameters
+.small[
+.pull-left-64[
+- Surface
+$$ \frac{\partial \Theta_s}{\partial t} + \nabla \cdot \mathbf{q}_s = Q_s + Q_e$$
+- Subsurface
+$$ \frac{\partial \Theta_g}{\partial t} + \nabla \cdot \mathbf{q}_g = Q_g$$
+]]
+
+--
+.footnotesize[.pull-right-46[
+<br>
+$$\mathbf{q}_s = -\eta h \frac{h^{4/3}} {n_{mann} \sqrt{|\nabla z|} } \nabla (\eta + z)$$
+
+<br>
+
+$$\mathbf{q}_g = -\frac{\eta}{\mu} k_r K (\nabla p +  \rho g\mathbf{z})$$
+
+.content-box-yellow[
+- $n_{mann}$: Manning's roughness coefficient
+- $k_r$: relative permeability
+- $K$: absolute permeability
+]]
 ]
 
+--
+
+.pull-left[
+.font60[
+```xml
+<ParameterList name="state">
+  <ParameterList name="evaluators">
+*   OTHER EVALUATORS ...
+    <ParameterList name="surface-manning_coefficient">
+      <Parameter name="evaluator type" type="string" value="independent variable constant" />
+      <Parameter name="value" type="double" value="0.15" />
+    </ParameterList>
+    <ParameterList name="permeability">
+      <Parameter name="evaluator type" type="string" value="independent variable constant" />
+      <Parameter name="value" type="double" value="5e-13" />
+    </ParameterList>
+    <ParameterList name="relative_permeability">
+      <Parameter name="evaluator type" type="string" value="relative permeability, water retention model" />
+      <Parameter name="model parameters" type="string" value="WRM parameters" />
+    </ParameterList>        
+  </ParameterList>
+*   OTHER EVALUATORS ...  
+</ParameterList>  
+```
+]]
+
 ---
 class: phong-dark
 # .brand-orange[Transport hands-on]