Documentation for ACCESS-RAM3 beta release

.github/workflows/automatic_merge.yml

@@ -13,7 +13,7 @@ jobs:
 
   auto-merge:
     runs-on: ubuntu-latest
-    # needs: check-links
+    needs: check-links
     steps:
     - name: Checkout repo
       uses: actions/checkout@master

.lycheecache

@@ -73,7 +73,7 @@ https://github.com/ACCESS-NRI/access-hive.org.au/pull/new/spongebob/fix-hive-tit
 https://docs.esmvaltool.org/en/latest/,200,1736735565
 https://github.com/ACCESS-NRI/workshop-training-2023,200,1736735564
 https://creativecommons.org/licenses/by/4.0/legalcode,200,1736735563
-https://access-hive.org.au/assets/model-config-logos/globe_visualisation/build_a_model.png,200,1736735566
+https://access-hive.org.au/assets/model-config-logos/model_visualisation/build_a_model.png,200,1736735566
 https://github.com/COSIMA/cosima-recipes/tree/main/ACCESS-OM2-GMD-Paper-Figs,200,1736735565
 https://creativecommons.org/licenses/by/4.0/?ref=chooser-v1%22,200,1736735567
 https://github.com/jbusecke/xMIP,200,1736735564
@@ -239,7 +239,7 @@ https://opus.nci.org.au/display/Help/0.+Welcome+to+Gadi,200,1736735565
 https://unidata.github.io/MetPy/latest/examples/index.html,200,1736735564
 https://my.nci.org.au/mancini/project/access/join,200,1736735566
 https://forum.access-hive.org.au/t/access-om2-payu-tutorial/1750,200,1736735567
-https://access-hive.org.au/assets/model-config-logos/globe_visualisation/access_om_globe_visualisation.png,200,1736735566
+https://access-hive.org.au/assets/model-config-logos/model_visualisation/access_om_model_visualisation.png,200,1736735566
 https://opus.nci.org.au/display/Help/FAQ+1%3A+Why+My+Jobs+are+NOT+Running,200,1736735567
 https://my.nci.org.au/mancini/project/xp65/join,200,1736735564
 https://github.com/mom-ocean/MOM5,200,1736735566
@@ -258,7 +258,7 @@ https://my.nci.org.au/mancini/project/zv30,200,1736735563
 https://access-hive.org.au/assets/component-logos/component-maps/land-component-map.png,200,1736735566
 https://github.com/skills/introduction-to-github,200,1736735564
 https://access-hive.org.au/models/model_components/sea-ice,200,1736735566
-https://access-hive.org.au/assets/model-config-logos/globe_visualisation/access_esm_globe_visualisation.png,200,1736735566
+https://access-hive.org.au/assets/model-config-logos/model_visualisation/access_esm_model_visualisation.png,200,1736735566
 https://access-nri.github.io/CMIP7_MED_Hackathon/02-runarecipe/index.html,200,1736735567
 https://monet-arl.readthedocs.io/en/stable/,200,1736735564
 https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation#ERA5:datadocumentation-Parameterlistings,200,1736735567
@@ -490,7 +490,7 @@ https://access-hive.org.au/#code-exists,200,1736735566
 https://www.ilamb.org/doc/index.html,200,1736735565
 https://access-hive.org.au/assets/github-how-to-contribute.jpg,200,1736735563
 https://github.com/dtcenter/METcalcpy,200,1736735564
-https://access-hive.org.au/assets/model-config-logos/globe_visualisation/access_cm_globe_visualisation.png,200,1736735566
+https://access-hive.org.au/assets/model-config-logos/model_visualisation/access_cm_model_visualisation.png,200,1736735566
 https://linuxize.com/post/using-the-ssh-config-file,200,1736735564
 https://www.unidata.ucar.edu/software/netcdf/,200,1736735566
 https://livvkit.github.io/Docs/,200,1736735564

docs/css/access-nri.css

@@ -301,6 +301,7 @@
   padding: 0.5rem;
   width: max-content;
   height: 2.5rem;
+  margin: 0.5em;
 }
 .text-card:hover {
   border-color: var(--md-accent-fg-color);
@@ -1320,6 +1321,8 @@ img.intro-img {
 /* Style for icons before text (used for example in User Support and Contribute pages) */
 .icon-before-text {
   margin-right: 0.5em;
+  font-size: 1.5rem;
+  width: 1.5rem;
 }
 /* =============================================================== 
   Media queries for website responsiveness

docs/model_evaluation/evaluation_on_gadi/cosima.md

@@ -1,14 +1,14 @@
 # COSIMA Cookbook on Gadi
 
 
-COSIMA is the Consortium for Ocean-Sea Ice Modelling in Australia, which brings together Australian researchers involved in global ocean and sea ice modelling. The <i>COSIMA Cookbook</i> is a collection of computational notebooks (called <i>cosima-recipes</i>) in the form of tutorials and documented examples that are curated on <i>Gadi</i> for analysing output from ocean-sea ice models.
+<a href="http://cosima.org.au/" target="_blank">COSIMA</a> stands for the Consortium for Ocean-Sea Ice Modelling in Australia, which brings together Australian-based researchers involved in global ocean and sea ice modelling. The <i>COSIMA Cookbook</i> is a collection of "recipes", i.e., computational notebooks in the form of tutorials and documented examples that are curated for analysing output from ocean-sea ice models.
 
 ???+ warning "Support Level: Supported on <i>Gadi</i>, but not owned by ACCESS-NRI"
     <!-- Who develped the tool? -->
-    The <i>COSIMA Cookbook</i> is developed and maintained by COSIMA. While ACCESS-NRI does not own the code, it actively supports the use of the <i>COSIMA Cookbook</i> and its collection of <i>cosima-recipes</i> on <i>Gadi</i>. 
+    The <i>COSIMA Cookbook</i> is developed and maintained by COSIMA. While ACCESS-NRI does not own the code, it actively supports the use of the recipes within the <i>COSIMA Cookbook</i> on <i>Gadi</i>. 
     ACCESS-NRI provides access to the latest version of <i>COSIMA Cookbook</i> via the `hh5` `access-med` conda environment for Model Evaluation on Gadi.
 
- The <i>COSIMA Cookbook</i> framework focuses on the <a href="/models/configurations/access-om">ACCESS-OM2</a> suite of models being developed and run by members of <a href="http://cosima.org.au/" target="_blank">COSIMA</a>. Nevertheless, this framework is suited to analysing any MOM5/ MOM6 output as well as output from other models.
+The <i>COSIMA Cookbook</i> framework focuses on the <a href="/models/configurations/access-om">ACCESS-OM2</a> suite of models being developed and run by members of <a href="http://cosima.org.au/" target="_blank">COSIMA</a>. Nevertheless, this framework is suited to analysing any MOM5/MOM6 output as well as output from other models.
 
 ## Getting Started
 
@@ -32,9 +32,10 @@ To use the <i>COSIMA Cookbook</i> that is pre-installed in the `conda/analysis3`
 
 ## COSIMA Cookbook information
 
-For more information on the <i>COSIMA Cookbook</i>, refer to the <a href="https://github.com/COSIMA/cosima-cookbook" target="_blank">cosima-cookbook</a> GitHub repository, as well as the following lists of recipes:
+For more information on the <i>COSIMA Cookbook</i>, refer to the <a href="https://github.com/COSIMA/cosima-recipes" target="_blank">GitHub repository</a>, as well as the following lists of recipes:
 
-- <a href="https://github.com/COSIMA/cosima-recipes/tree/main/Tutorials" target="_blank">Tutorials</a>
+- <a href="https://cosima-recipes.readthedocs.io/en/latest/tutorials.html" target="_blank">Tutorials</a>
+- <a href="https://cosima-recipes.readthedocs.io/en/latest/recipes.html" target="_blank">Recipes</a>
 - <a href="https://github.com/COSIMA/cosima-recipes/tree/main/ACCESS-OM2-GMD-Paper-Figs" target="_blank">Notebooks</a> to reproduce figures of the <a href="https://gmd.copernicus.org/articles/13/401/2020/" target="_blank">ACCESS-OM2 announcement paper</a>
-- <a href="https://github.com/COSIMA/cosima-recipes/tree/main/Recipes" target="_blank">Recipes</a>
+
 

docs/models/configurations/access-ram.md

@@ -0,0 +1,5 @@
+# ACCESS-RAM
+
+TODO
+{: style="color:red"}
+<!-- Create the model overview page for ACCESS-RAM. Refer to the ACCESS-ESM1.5 one for an example. -->

docs/models/configurations/index.md

@@ -1,6 +1,6 @@
-# Supported ACCESS Model Configurations
-
+<!-- This entire file is used as a snippet in other pages -->
 <div class="card-container">
+    <!-- ACCESS-CM -->
     <a href="/models/configurations/access-cm/" class="horizontal-card">
         <div class="card-image-container">
             <img src="/assets/model-config-logos/configurations-without-titles/access-cm.png" class="white-background img-contain"></img> 
@@ -12,6 +12,7 @@
             </span>
         </div>
     </a>
+    <!-- ACCESS-ESM -->
     <a href="/models/configurations/access-esm/" class="horizontal-card">
         <div class="card-image-container">
             <img src="/assets/model-config-logos/configurations-without-titles/access-esm.png" class="white-background img-contain"></img> 
@@ -23,6 +24,7 @@
             </span>
         </div>
     </a>
+    <!-- ACCESS-OM -->
     <a href="/models/configurations/access-om/" class="horizontal-card">
         <div class="card-image-container">
             <img src="/assets/model-config-logos/configurations-without-titles/access-om.png" class="white-background img-contain"></img> 
@@ -34,4 +36,16 @@
             </span>
         </div>
     </a>
+    <!-- ACCESS-RAM -->
+    <a href="/models/configurations/access-ram/" class="horizontal-card">
+        <div class="card-image-container">
+            <img src="/assets/model-config-logos/configurations-without-titles/access-om.png" class="white-background img-contain"></img> 
+        </div>
+        <div class="card-text-container">
+            <span class="bold" >ACCESS-RAM</span>
+            <span>
+                ACCESS-RAM -- add text here. Also add correct image.
+            </span>
+        </div>
+    </a>
 </div>

docs/models/index.md

@@ -5,41 +5,8 @@
 ACCESS models are computer codes comprising complex mathematical representations of major Earth system components (atmosphere, land surface, ocean and sea ice) based on physical, biological and chemical principles or laws. Different ACCESS model components can be linked together via a coupler to form ACCESS model configurations (e.g. ACCESS-ESM), which are then used to simulate realistic past or future conditions and idealised experiments.
 
 ## Supported ACCESS Model Configurations
-<div class="card-container">
-    <a href="/models/configurations/access-cm/" class="horizontal-card">
-        <div class="card-image-container">
-            <img src="/assets/model-config-logos/configurations-without-titles/access-cm.png" class="white-background img-contain"></img> 
-        </div>
-        <div class="card-text-container">
-            <span class="bold" >ACCESS-CM</span>
-            <span>
-                ACCESS-CM is a global climate model that includes the atmosphere, land, ocean and sea-ice components, and produces physical climate simulations.
-            </span>
-        </div>
-    </a>
-    <a href="/models/configurations/access-esm/" class="horizontal-card">
-        <div class="card-image-container">
-            <img src="/assets/model-config-logos/configurations-without-titles/access-esm.png" class="white-background img-contain"></img> 
-        </div>
-        <div class="card-text-container">
-            <span class="bold" >ACCESS-ESM</span>
-            <span>
-                ACCESS-ESM is a global climate model with additional land and ocean biogeochemical components to simulate both the physical climate and global biogeochemical cycles.
-            </span>
-        </div>
-    </a>
-    <a href="/models/configurations/access-om/" class="horizontal-card">
-        <div class="card-image-container">
-            <img src="/assets/model-config-logos/configurations-without-titles/access-om.png" class="white-background img-contain"></img> 
-        </div>
-        <div class="card-text-container">
-            <span class="bold" >ACCESS-OM</span>
-            <span>
-                ACCESS-OM is a global coupled ocean and sea ice model used to understand both physical and biogeochemical processes in the ocean.
-            </span>
-        </div>
-    </a>
-</div>
+<!-- Using pymdown.snippets extension; https://facelessuser.github.io/pymdown-extensions/extensions/snippets/ -->
+--8<-- "docs/models/configurations/index.md"
 
 ## ACCESS Model Components
 <div class="card-container">

docs/models/run-a-model/index.md

@@ -4,33 +4,46 @@ If you are a new user of ACCESS climate models, please refer to how to [Set Up y
 If you are unsure which ACCESS model is the right choice for your experiment, take a look at the overview of [ACCESS Models](/models).
 
 <div class="card-container">
+    <!-- Run ACCESS-CM -->
     <a href="/models/run-a-model/run-access-cm" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
-            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/globe_visualisation/access_cm_globe_visualisation.png" alt="ACCESS-CM">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_cm_model_visualisation.png" alt="ACCESS-CM">
         </div>
         <div class="card-text-container bold">   
             Run ACCESS-CM
         </div>
     </a>
+    <!-- Run ACCESS-ESM -->
     <a href="/models/run-a-model/run-access-esm" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
-            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/globe_visualisation/access_esm_globe_visualisation.png" alt="ACCESS-ESM">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_esm_model_visualisation.png" alt="ACCESS-ESM">
         </div>
         <div class="card-text-container bold">   
             Run ACCESS-ESM
         </div>
     </a>
+    <!-- Run ACCESS-OM -->
     <a href="/models/run-a-model/run-access-om" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
-            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/globe_visualisation/access_om_globe_visualisation.png" alt="ACCESS-OM">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_om_model_visualisation.png" alt="ACCESS-OM">
         </div>
         <div class="card-text-container bold">   
             Run ACCESS-OM
         </div>
     </a>
+    <!-- Run ACCESS-RAM -->
+    <a href="/models/run-a-model/run-access-ram" class="vertical-card aspect-ratio1to1">
+        <div class="card-image-container">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_ram_model_visualisation.png" alt="ACCESS-RAM">
+        </div>
+        <div class="card-text-container bold">   
+            Run ACCESS-RAM
+        </div>
+    </a>
+    <!-- Modify ACCESS model's source code -->
     <a href="/models/run-a-model/build_a_model" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
-            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/globe_visualisation/build_a_model.png" alt="Modify a model's source code">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/build_a_model.png" alt="Modify a model's source code">
         </div>
         <div class="card-text-container bold">   
             Modify an ACCESS model's source code

docs/models/run-a-model/run-access-cm.md

@@ -383,7 +383,7 @@ To access a specific task, click on the arrow next to the task to extend the dro
 #### Through the suite directory
 The suite's log directories are stored in `~/cylc-run/<suite-ID>` as `log.<TIMESTAMP>`, and the latest set of logs are also symlinked in the `~/cylc-run/<suite-ID>/log` directory.<br>
 The logs for the main job can be found in the `~/cylc-run/<suite-ID>/log/job` directory.<br>
-Logs are separated into simulation cycles according to their starting dates, and then differentiated by task. They are then further separated into "attempts" (consecutive failed/successful tasks), where `NN` is a symlink to the most recent attempt.
+Logs are separated into simulation cycles according to their starting dates, then divided into subdirectories according to the task name. They are then further separated into "attempts" (consecutive failed/successful tasks), where `NN` is a symlink to the most recent attempt.
 
 In the example above, a failure occurred for the _09500101_ simulation cycle (i.e. starting date: 1st January 950) in the _coupled_ task. Hence, the `job.err` and `job.out` files can be found in the `~/cylc-run/<suite-ID>/log/job/09500101/coupled/NN` directory.
 <terminal-window>