diff --git a/pr-preview/pr-396/404.html b/pr-preview/pr-396/404.html
index 32c6a536b..352b40dd9 100644
--- a/pr-preview/pr-396/404.html
+++ b/pr-preview/pr-396/404.html
@@ -38,8 +38,6 @@
       
     
     
-      <link rel="stylesheet" href="/css/termynal.css">
-    
       <link rel="stylesheet" href="/css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -344,7 +342,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="/models/running-a-model/" class="md-tabs__link">
+      <a href="/models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1206,7 +1204,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="/models/running-a-model/">Run a Model</a>
+          <a href="/models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1229,7 +1227,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="/models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="/models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="/models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="/models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="/models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2260,8 +2258,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2382,7 +2381,7 @@ <h1>404 - Not found</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="/js/termynal.js"></script>
+        <script src="/js/terminal_animation.js"></script>
       
         <script src="/js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/about/License/index.html b/pr-preview/pr-396/about/License/index.html
index 574ef6a9d..1c4fed519 100644
--- a/pr-preview/pr-396/about/License/index.html
+++ b/pr-preview/pr-396/about/License/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1232,7 +1230,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1255,7 +1253,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1269,7 +1267,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1283,7 +1281,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1297,7 +1295,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1311,7 +1309,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2286,8 +2284,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2366,11 +2365,11 @@ <h1 id="license"><div class="highlight-bg"> License </div></h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2484,7 +2483,7 @@ <h1 id="license"><div class="highlight-bg"> License </div></h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/about/code_of_conduct/index.html b/pr-preview/pr-396/about/code_of_conduct/index.html
index c15c8ccd1..d448652ec 100644
--- a/pr-preview/pr-396/about/code_of_conduct/index.html
+++ b/pr-preview/pr-396/about/code_of_conduct/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1232,7 +1230,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1255,7 +1253,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1269,7 +1267,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1283,7 +1281,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1297,7 +1295,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1311,7 +1309,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2286,8 +2284,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2335,11 +2334,11 @@ <h1 id="code-of-conduct"><div class="highlight-bg"> Code of Conduct </div></h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2453,7 +2452,7 @@ <h1 id="code-of-conduct"><div class="highlight-bg"> Code of Conduct </div></h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/about/contact/index.html b/pr-preview/pr-396/about/contact/index.html
index c3fff0b94..da7b78f1b 100644
--- a/pr-preview/pr-396/about/contact/index.html
+++ b/pr-preview/pr-396/about/contact/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -665,8 +663,9 @@
         Contact
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1265,7 +1264,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1288,7 +1287,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1302,7 +1301,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1316,7 +1315,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1330,7 +1329,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1344,7 +1343,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2319,8 +2318,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2394,11 +2394,11 @@ <h2 id="other-places-where-you-can-find-the-access-nri-team">Other places where
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2512,7 +2512,7 @@ <h2 id="other-places-where-you-can-find-the-access-nri-team">Other places where
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/about/policies/index.html b/pr-preview/pr-396/about/policies/index.html
index 1389ac77c..cc10be5d8 100644
--- a/pr-preview/pr-396/about/policies/index.html
+++ b/pr-preview/pr-396/about/policies/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -97,7 +95,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#policies" class="md-skip">
+        <a href="#policies-supported" class="md-skip">
           Skip to content
         </a>
       
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1232,7 +1230,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1255,7 +1253,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1269,7 +1267,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1283,7 +1281,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1297,7 +1295,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1311,7 +1309,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2286,8 +2284,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2326,7 +2325,7 @@
   
 
 
-<h1 id="policies"><div class="center-icons highlight-bg"> Policies <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h1>
+<h1 id="policies-supported"><div class="center-icons highlight-bg"> Policies {{ supported }} </div></h1>
 <ul>
 <li><a href="https://access-nri.github.io/procedures-and-practices/">Procedures and Practices</a>: Contains documents outlining how ACCESS-NRI will function. These documents describe what users can expect and justifications for the decisions against criteria that are based on the values of the organisation.</li>
 </ul>
@@ -2336,11 +2335,11 @@ <h1 id="policies"><div class="center-icons highlight-bg"> Policies <a href="http
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2454,7 +2453,7 @@ <h1 id="policies"><div class="center-icons highlight-bg"> Policies <a href="http
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/about/support/index.html b/pr-preview/pr-396/about/support/index.html
index 2d7283548..64069aa9a 100644
--- a/pr-preview/pr-396/about/support/index.html
+++ b/pr-preview/pr-396/about/support/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -679,8 +677,9 @@
         Support
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1272,7 +1271,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1295,7 +1294,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1309,7 +1308,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1323,7 +1322,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1337,7 +1336,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1351,7 +1350,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2326,8 +2325,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2392,33 +2392,33 @@ <h1 id="support"><div class="highlight-bg"> Support </div></h1>
 <h2 id="support-levels">Support levels</h2>
 <p>The site uses a system of tags to identify who supports the linked documentation or software, and the level of support you can expect:</p>
 <dl>
-<dt><code>Supported by ACCESS-NRI</code> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a></dt>
+<dt><code>Supported by ACCESS-NRI</code> {{ supported }}</dt>
 <dd>
 <p>Documentation that is actively maintained and supported by ACCESS-NRI. This is documentation that was either created by ACCESS-NRI, or it is existing documentation for which ACCESS-NRI has taken over responsibility.</p>
 </dd>
-<dt><code>Recommended by ACCESS-NRI</code> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a></dt>
+<dt><code>Recommended by ACCESS-NRI</code> {{ recommended }}</dt>
 <dd>
 <p>Documentation for third-party software that ACCESS-NRI recommends and facilitates the use of at <a href="https://www.nci.org.au">NCI</a> as a service to the community. This means ACCESS-NRI supports the infrastructure required to run the software, but not necessarily the software itself. </p>
 </dd>
-<dt><code>Community contributed</code> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></dt>
+<dt><code>Community contributed</code> {{ community }}</dt>
 <dd>
 <p>Documentation that is of use to the community, but is not explicitly endorsed or supported by ACCESS-NRI. </p>
 </dd>
 </dl>
 <h2 id="how-to-get-help">How to get help</h2>
 <p>Each entry on ACCESS-Hive links to another web site. There should be information on how to get help on the linked site. If there are no obvious channels for help, or the help is not adequate consider asking for assistance from fellow members of your community on the <a href="https://forum.access-hive.org.au">ACCESS-Hive forum</a>. </p>
-<p>In the case of ACCESS-NRI supported documentation and software, marked <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>, if there is no information on how to get help, or your query is not appropriate for the support channels provided, please either ask on the <a href="https://forum.access-hive.org.au">ACCESS-Hive forum</a> or <a href="../contact/">contact ACCESS-NRI directly</a>.</p>
+<p>In the case of ACCESS-NRI supported documentation and software, marked {{ supported }}, if there is no information on how to get help, or your query is not appropriate for the support channels provided, please either ask on the <a href="https://forum.access-hive.org.au">ACCESS-Hive forum</a> or <a href="../contact/">contact ACCESS-NRI directly</a>.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2532,7 +2532,7 @@ <h2 id="how-to-get-help">How to get help</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/call_contribute/index.html b/pr-preview/pr-396/call_contribute/index.html
index 90cdf66fd..44aca75dc 100644
--- a/pr-preview/pr-396/call_contribute/index.html
+++ b/pr-preview/pr-396/call_contribute/index.html
@@ -40,8 +40,6 @@
       
     
     
-      <link rel="stylesheet" href="../css/termynal.css">
-    
       <link rel="stylesheet" href="../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -346,7 +344,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../models/running-a-model/" class="md-tabs__link">
+      <a href="../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1208,7 +1206,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../models/running-a-model/">Run a Model</a>
+          <a href="../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1231,7 +1229,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1245,7 +1243,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1259,7 +1257,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1273,7 +1271,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1287,7 +1285,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2262,8 +2260,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2312,11 +2311,11 @@ <h1>Call contribute</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2430,7 +2429,7 @@ <h1>Call contribute</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../js/termynal.js"></script>
+        <script src="../js/terminal_animation.js"></script>
       
         <script src="../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/community_data_processing/index.html b/pr-preview/pr-396/community_resources/community_data_processing/index.html
index 63c012c7e..6aeb74b5c 100644
--- a/pr-preview/pr-396/community_resources/community_data_processing/index.html
+++ b/pr-preview/pr-396/community_resources/community_data_processing/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2026,8 +2024,9 @@
         Data Formatting
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2051,64 +2050,64 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#kerchunk" class="md-nav__link">
-    Kerchunk  
+  <a href="#kerchunk-community" class="md-nav__link">
+    Kerchunk  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#cmor3" class="md-nav__link">
-    CMOR3  
+  <a href="#cmor3-community" class="md-nav__link">
+    CMOR3  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#xmip" class="md-nav__link">
-    xMIP  
+  <a href="#xmip-community" class="md-nav__link">
+    xMIP  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#app4-the-access-post-processor" class="md-nav__link">
-    APP4 (The ACCESS Post Processor)  
+  <a href="#app4-the-access-post-processor-community" class="md-nav__link">
+    APP4 (The ACCESS Post Processor)  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#access-archiver" class="md-nav__link">
-    ACCESS-Archiver 
+  <a href="#access-archiver-community" class="md-nav__link">
+    ACCESS-Archiver {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#synda" class="md-nav__link">
-    Synda  
+  <a href="#synda-recommended" class="md-nav__link">
+    Synda  {{ recommended }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#fluxnetlsm" class="md-nav__link">
-    FluxnetLSM  
+  <a href="#fluxnetlsm-community" class="md-nav__link">
+    FluxnetLSM  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#metpy" class="md-nav__link">
-    Metpy  
+  <a href="#metpy-community" class="md-nav__link">
+    Metpy  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#xskillscore" class="md-nav__link">
-    xskillscore  
+  <a href="#xskillscore-community" class="md-nav__link">
+    xskillscore  {{ community }}
   </a>
   
 </li>
@@ -2119,8 +2118,8 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#analysis-blogposts-and-tutorials" class="md-nav__link">
-    Analysis blogposts and tutorials  
+  <a href="#analysis-blogposts-and-tutorials-community" class="md-nav__link">
+    Analysis blogposts and tutorials  {{ community }}
   </a>
   
 </li>
@@ -2397,8 +2396,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2422,64 +2422,64 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#kerchunk" class="md-nav__link">
-    Kerchunk  
+  <a href="#kerchunk-community" class="md-nav__link">
+    Kerchunk  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#cmor3" class="md-nav__link">
-    CMOR3  
+  <a href="#cmor3-community" class="md-nav__link">
+    CMOR3  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#xmip" class="md-nav__link">
-    xMIP  
+  <a href="#xmip-community" class="md-nav__link">
+    xMIP  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#app4-the-access-post-processor" class="md-nav__link">
-    APP4 (The ACCESS Post Processor)  
+  <a href="#app4-the-access-post-processor-community" class="md-nav__link">
+    APP4 (The ACCESS Post Processor)  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#access-archiver" class="md-nav__link">
-    ACCESS-Archiver 
+  <a href="#access-archiver-community" class="md-nav__link">
+    ACCESS-Archiver {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#synda" class="md-nav__link">
-    Synda  
+  <a href="#synda-recommended" class="md-nav__link">
+    Synda  {{ recommended }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#fluxnetlsm" class="md-nav__link">
-    FluxnetLSM  
+  <a href="#fluxnetlsm-community" class="md-nav__link">
+    FluxnetLSM  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#metpy" class="md-nav__link">
-    Metpy  
+  <a href="#metpy-community" class="md-nav__link">
+    Metpy  {{ community }}
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#xskillscore" class="md-nav__link">
-    xskillscore  
+  <a href="#xskillscore-community" class="md-nav__link">
+    xskillscore  {{ community }}
   </a>
   
 </li>
@@ -2490,8 +2490,8 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#analysis-blogposts-and-tutorials" class="md-nav__link">
-    Analysis blogposts and tutorials  
+  <a href="#analysis-blogposts-and-tutorials-community" class="md-nav__link">
+    Analysis blogposts and tutorials  {{ community }}
   </a>
   
 </li>
@@ -2533,46 +2533,46 @@ <h1 id="community-processing-data-processing-tools">Community Processing Data Pr
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
 <h2 id="tools">Tools</h2>
-<h3 id="kerchunk">Kerchunk  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="kerchunk-community">Kerchunk  {{ community }}</h3>
 <p><a href="https://fsspec.github.io/kerchunk/"><strong>Documentation</strong></a> | 
 <a href="https://github.com/fsspec/kerchunk"><strong>Sources</strong></a></p>
 <p>Kerchunk is a library that provides a unified way to represent a variety of chunked, compressed data formats (e.g. NetCDF/HDF5, GRIB2, TIFF, …), allowing efficient access to the data from traditional file systems or cloud object storage. It also provides a flexible way to create virtual datasets from multiple files.</p>
-<h3 id="cmor3">CMOR3  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="cmor3-community">CMOR3  {{ community }}</h3>
 <p><em>Climate Model Output Rewriter Version 3</em></p>
 <p><a href="https://cmor.llnl.gov/"><strong>Documentation</strong></a> | 
 <a href="https://github.com/PCMDI/cmor"><strong>Sources</strong></a></p>
 <p>CMOR is used to produce CF-compliant netCDF files. The structure of the files created by CMOR and the metadata they contain fulfill the requirements of many of the climate community’s standard model experiments (which are referred to here as “MIPs” and include, for example, AMIP, PMIP, APE, and IPCC scenario runs).</p>
-<h3 id="xmip">xMIP  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="xmip-community">xMIP  {{ community }}</h3>
 <p><a href="https://cmip6-preprocessing.readthedocs.io/en/latest/?badge=latest"><strong>Documentation</strong></a> |
 <a href="https://github.com/coecms/xmip_nci"><strong>Tutorial on NCI</strong></a> |
 <a href="https://github.com/jbusecke/xMIP"><strong>Sources</strong></a></p>
 <p>This package facilitates the cleaning, organization and interactive analysis of Model Intercomparison Projects (MIPs) within the Pangeo software stack.</p>
-<h3 id="app4-the-access-post-processor">APP4 (The ACCESS Post Processor)  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="app4-the-access-post-processor-community">APP4 (The ACCESS Post Processor)  {{ community }}</h3>
 <p><a href="https://github.com/ACCESS-Hive/APP4"><strong>Documentation</strong></a> | 
 <a href="https://github.com/ACCESS-Hive/APP4"><strong>Sources</strong></a></p>
 <p>The APP4 is a CMORisation tool designed to convert ACCESS model output to ESGF-compliant formats, primarily for publication to CMIP6. The code was originally built for CMIP5, and was further developed for CMIP6-era activities.
 Uses CMOR3 and files created with the CMIP6 data request to generate CF-compliant files according to the CMIP6 data standards.</p>
-<h3 id="access-archiver">ACCESS-Archiver <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="access-archiver-community">ACCESS-Archiver {{ community }}</h3>
 <p><a href="https://github.com/ACCESS-Hive/ACCESS-Archiver"><strong>Documentation</strong></a> | 
 <a href="https://github.com/ACCESS-Hive/ACCESS-Archiver"><strong>Sources</strong></a></p>
 <p>The ACCESS Archiver is designed to archive model output from ACCESS simulations. It's focus is to copy ACCESS model output from its initial location to a secondary location (typically from <code>/scratch</code> to <code>/g/data</code>), while converting UM files to netCDF, compressing MOM/CICE files, and culling restart files to 10-yearly. Saves 50-80% of storage space due to conversion and compression.</p>
-<h3 id="synda">Synda  <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a></h3>
+<h3 id="synda-recommended">Synda  {{ recommended }}</h3>
 <p>synda is a command line tool to search and download files from the Earth System Grid Federation (ESGF) archive.</p>
-<h3 id="fluxnetlsm">FluxnetLSM  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="fluxnetlsm-community">FluxnetLSM  {{ community }}</h3>
 <p><a href="https://gmd.copernicus.org/articles/10/3379/2017/"><strong>Citation</strong> <sup id="fnref:1"><a class="footnote-ref" href="#fn:1">1</a></sup></a> |
 <a href="https://github.com/aukkola/FluxnetLSM"><strong>Sources</strong></a></p>
 <p>R package for post-processing FLUXNET datasets for use in land surface modelling. Performs quality control and data conversion of FLUXNET data and collated site metadata. Supports FLUXNET2015, La Thuile, OzFlux and ICOS data releases.</p>
-<h3 id="metpy">Metpy  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="metpy-community">Metpy  {{ community }}</h3>
 <p>https://unidata.github.io/MetPy/latest/examples/formats/index.html</p>
 <p><a href="https://unidata.github.io/MetPy/latest/examples/formats/index.html"><strong>Documentation</strong></a> |
 <a href="https://github.com/Unidata/MetPy"><strong>Sources</strong></a></p>
 <p>MetPy is a collection of tools in Python for reading, visualizing, and performing calculations with weather data. MetPy supports Python &gt;= 3.8 and is freely available under a permissive open source license.</p>
 <p>Format types are: GINI Water Vapor Imagery, NEXRAD Level 3 File, and NEXRAD Level 2 File.</p>
-<h3 id="xskillscore">xskillscore  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h3>
+<h3 id="xskillscore-community">xskillscore  {{ community }}</h3>
 <p><a href="https://xskillscore.readthedocs.io/en/stable/"><strong>Documentation</strong></a> |
 <a href="https://github.com/xarray-contrib/xskillscore"><strong>Sources</strong></a></p>
 <p>xskillscore is a Python library for computing a wide variety of skill metrics. Its typical application is to verify deterministic and probabilistic forecasts relative to observations.</p>
-<h2 id="analysis-blogposts-and-tutorials">Analysis blogposts and tutorials  <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></h2>
+<h2 id="analysis-blogposts-and-tutorials-community">Analysis blogposts and tutorials  {{ community }}</h2>
 <p><a href="https://medium.com/pangeo/accessing-netcdf-and-grib-file-collections-as-cloud-native-virtual-datasets-using-kerchunk-625a2d0a9191">Accessing NetCDF and GRIB file collections as cloud-native virtual datasets using Kerchunk, Peter March, Sep 2022</a></p>
 <div class="footnote">
 <hr />
@@ -2588,11 +2588,11 @@ <h2 id="analysis-blogposts-and-tutorials">Analysis blogposts and tutorials  <a h
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2706,7 +2706,7 @@ <h2 id="analysis-blogposts-and-tutorials">Analysis blogposts and tutorials  <a h
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/community_med_recipes/index.html b/pr-preview/pr-396/community_resources/community_med_recipes/index.html
index 7b70ab091..a54696fec 100644
--- a/pr-preview/pr-396/community_resources/community_med_recipes/index.html
+++ b/pr-preview/pr-396/community_resources/community_med_recipes/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2332,7 +2331,7 @@ <h1 id="community-model-evaluation-and-diagnostics-med-recipe-gallery">Community
 <!-- ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
-<p>We are trying to ingest more and more model evaluation and diagnostics recipes in your currated <a href="../../model_evaluation/model_evaluation_recipe_gallery/">recipe gallery on this website</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>. While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>:</p>
+<p>We are trying to ingest more and more model evaluation and diagnostics recipes in your currated <a href="../../model_evaluation/model_evaluation_recipe_gallery/">recipe gallery on this website</a> {{ supported }}. While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community {{ community }}:</p>
 <table>
 <tr>
 <td width="25%">
@@ -2355,7 +2354,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://www.esmvaltool.org/">ESMValTool <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> <br>(Earth System Model EValuation Tool)</a>
+    <a href="https://www.esmvaltool.org/">ESMValTool {{ recommended }} <br>(Earth System Model EValuation Tool)</a>
     </div>
 </td>
 <td width="10%">
@@ -2378,7 +2377,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="http://cosima.org.au/">COSIMA Cookbook / Recipes <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a><br>(Consortium for Ocean-Sea Ice Modelling in Australia)</a>
+    <a href="http://cosima.org.au/">COSIMA Cookbook / Recipes {{ recommended }}<br>(Consortium for Ocean-Sea Ice Modelling in Australia)</a>
     </div>
 </td>
 <td width="10%">
@@ -2407,7 +2406,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://www.ilamb.org/">iLAMB <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a><br>(international Land Model Benchmarking)</a>
+    <a href="https://www.ilamb.org/">iLAMB {{ recommended }}<br>(international Land Model Benchmarking)</a>
     </div>
 </td>
 <td width="10%">
@@ -2428,7 +2427,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://cmec.llnl.gov/iomb.html">iOMB <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a><br>(international Ocean Model Benchmarking)</a>
+    <a href="https://cmec.llnl.gov/iomb.html">iOMB {{ recommended }}<br>(international Ocean Model Benchmarking)</a>
     </div>
 </td>
 <td width="10%">
@@ -2451,7 +2450,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://dtcenter.org/community-code/metplus">METPlus <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a><br>(Model Evaluation Tool Plus)</a>
+    <a href="https://dtcenter.org/community-code/metplus">METPlus {{ recommended }}<br>(Model Evaluation Tool Plus)</a>
     </div>
 </td>
 <td width="10%">
@@ -2465,7 +2464,7 @@ <h3>Description</h3>
         <a href="https://journals.ametsoc.org/view/journals/bams/102/4/BAMS-D-19-0093.1.xml">Paper</a>
         <!-- METplus is a verification framework that spans a wide range of temporal (warn-on-forecast to climate) and spatial (storm to global) scales.  It is intended to be extensible through additional capability developed by the community. The core components of the framework include MET, the associated database and display systems called METviewer and METexpress, and a suite of Python wrappers to provide low-level automation and examples, also called use-cases.  METplus will be a component of NOAA's Unified Forecast System (UFS) cross-cutting infrastructure as well as NCAR's System for Integrated Modeling of the Atmosphere (SIMA).
         METplus is being actively developed by NCAR/Research Applications Laboratory (RAL), NOAA/Earth Systems Research Laboratories (ESRL), NOAA/Environmental Modeling Center (EMC), and is open to community contributions.
-        ### METplus Components  <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+        ### METplus Components  {{ recommended }}
         Links to the code repository and documentation for each METplus component are provided below:
         - METplus Wrappers: [sources][METplusWrappers-source] | [docs][METplusWrappers-doc]
         - MET: [sources][MET-source] | [docs][MET-doc]
@@ -2495,7 +2494,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="http://pcmdi.github.io/pcmdi_metrics/index.html#">PMP <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a><br>(PCMDI Metrics Package)</a>
+    <a href="http://pcmdi.github.io/pcmdi_metrics/index.html#">PMP {{ recommended }}<br>(PCMDI Metrics Package)</a>
     </div>
 </td>
 <td width="10%">
@@ -2515,7 +2514,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://climpred.readthedocs.io/en/stable/index.html">climpred <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></a>
+    <a href="https://climpred.readthedocs.io/en/stable/index.html">climpred {{ community }}</a>
     </div>
 </td>
 <td width="10%">
@@ -2541,7 +2540,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://freva.gitlab-pages.dkrz.de/evaluation_system/sphinx_docs/index.html">FREVA <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a><br>(Free Evaluation System Framework)</a>
+    <a href="https://freva.gitlab-pages.dkrz.de/evaluation_system/sphinx_docs/index.html">FREVA {{ community }}<br>(Free Evaluation System Framework)</a>
     </div>
 </td>
 <td width="10%">
@@ -2564,7 +2563,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://cmec.llnl.gov/teca.html">TECA <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a><br>(Toolkit for Extremes Climate Analysis)</a>
+    <a href="https://cmec.llnl.gov/teca.html">TECA {{ community }}<br>(Toolkit for Extremes Climate Analysis)</a>
     </div>
 </td>
 <td width="10%">
@@ -2586,7 +2585,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://monet-arl.readthedocs.io/en/stable/#">MONET <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a><br>(Model and ObservatioN Evaluation Toolkit)</a>
+    <a href="https://monet-arl.readthedocs.io/en/stable/#">MONET {{ community }}<br>(Model and ObservatioN Evaluation Toolkit)</a>
     </div>
 </td>
 <td width="10%">
@@ -2609,7 +2608,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://livvkit.github.io/Docs/">LIVVkit <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a><br>(land ice verification & validation toolkit)</a>
+    <a href="https://livvkit.github.io/Docs/">LIVVkit {{ community }}<br>(land ice verification & validation toolkit)</a>
     </div>
 </td>
 <td width="10%">
@@ -2631,7 +2630,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://metoffice.github.io/CSET/index.html">CSET <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a><br>(Convective Scale Evaluation Tool )</a>
+    <a href="https://metoffice.github.io/CSET/index.html">CSET {{ community }}<br>(Convective Scale Evaluation Tool )</a>
     </div>
 </td>
 <td width="10%">
@@ -2653,7 +2652,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://unidata.github.io/MetPy/latest/index.html">MetPy <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a><br>(Model Evaluation Tool Plus)</a>
+    <a href="https://unidata.github.io/MetPy/latest/index.html">MetPy {{ community }}<br>(Model Evaluation Tool Plus)</a>
     </div>
 </td>
 <td width="10%">
@@ -2675,7 +2674,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://code.metoffice.gov.uk/doc/afterburner/current/html/index.html">Afterburner <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></a>
+    <a href="https://code.metoffice.gov.uk/doc/afterburner/current/html/index.html">Afterburner {{ community }}</a>
     </div>
 </td>
 <td width="10%">
@@ -2696,11 +2695,11 @@ <h3>Description</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2814,7 +2813,7 @@ <h3>Description</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/community_model_catalogs/index.html b/pr-preview/pr-396/community_resources/community_model_catalogs/index.html
index cdf428235..1493b9676 100644
--- a/pr-preview/pr-396/community_resources/community_model_catalogs/index.html
+++ b/pr-preview/pr-396/community_resources/community_model_catalogs/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2329,7 +2328,7 @@
 
 
 <h1 id="community-model-data-catalogs">Community Model Data Catalogs</h1>
-<p>We are trying to ingest more and more model data catalogs in your currated <a href="../../model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/">catalog on this website</a><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us (<a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>) or may be interesting for the community (<a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>):</p>
+<p>We are trying to ingest more and more model data catalogs in your currated <a _="{" href="../../model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/" supported="supported">catalog on this website</a>}. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us ({{ recommended }}) or may be interesting for the community ({{ community }}):</p>
 <table class="center">
 <tr>
 <td width="25%">
@@ -2353,7 +2352,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://geonetwork.nci.org.au/geonetwork/srv/eng/catalog.search#/home">NCI datasets</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://geonetwork.nci.org.au/geonetwork/srv/eng/catalog.search#/home">NCI datasets</a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2373,7 +2372,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://github.com/coecms/nci-intake-catalogue">CLEX NCI Data Collection Intake Catalogue</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://github.com/coecms/nci-intake-catalogue">CLEX NCI Data Collection Intake Catalogue</a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2396,7 +2395,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://oneclimate.dmponline.cloud.edu.au/">Australia Climate Data Guide Catalogue</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://oneclimate.dmponline.cloud.edu.au/">Australia Climate Data Guide Catalogue</a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2419,7 +2418,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://imos.org.au/facilities/aodn">Australian Ocean Data Network</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://imos.org.au/facilities/aodn">Australian Ocean Data Network</a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2440,7 +2439,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://github.com/nocollier/intake-ilamb">Intake-Ilamb Catalog</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>
+    <a href="https://github.com/nocollier/intake-ilamb">Intake-Ilamb Catalog</a> {{ supported }}
     </div>
 </td>
 <td width="10%">
@@ -2460,7 +2459,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://fluxnet.org/">FLUXNET</a> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>
+    <a href="https://fluxnet.org/">FLUXNET</a> {{ community }}
     </div>
 </td>
 <td width="10%">
@@ -2479,7 +2478,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://archive.ceda.ac.uk/">CEDA Archive</a> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>
+    <a href="https://archive.ceda.ac.uk/">CEDA Archive</a> {{ community }}
     </div>
 </td>
 <td width="10%">
@@ -2498,7 +2497,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://www.ozflux.org.au">OZFlux</a> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>
+    <a href="https://www.ozflux.org.au">OZFlux</a> {{ community }}
     </div>
 </td>
 <td width="10%">
@@ -2517,7 +2516,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://aus-ref-clim-data-nci.github.io/aus-ref-clim-data-nci/intro.html">Australian Community Reference Climate Data Collection</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://aus-ref-clim-data-nci.github.io/aus-ref-clim-data-nci/intro.html">Australian Community Reference Climate Data Collection</a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2543,11 +2542,11 @@ <h3>Description</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2661,7 +2660,7 @@ <h3>Description</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/community_observational_catalogs/index.html b/pr-preview/pr-396/community_resources/community_observational_catalogs/index.html
index 399ee251b..1dda94d51 100644
--- a/pr-preview/pr-396/community_resources/community_observational_catalogs/index.html
+++ b/pr-preview/pr-396/community_resources/community_observational_catalogs/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2329,7 +2328,7 @@
 
 
 <h1 id="community-observational-data-catalogs">Community Observational Data Catalogs</h1>
-<p>We are trying to ingest more and more model data catalogs in your currated <a href="../../model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/">catalog on this website</a><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us (<a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>) or may be interesting for the community (<a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>):</p>
+<p>We are trying to ingest more and more model data catalogs in your currated <a _="{" href="../../model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/" supported="supported">catalog on this website</a>}. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us ({{ recommended }}) or may be interesting for the community ({{ community }}):</p>
 <table class="center">
 <tr>
 <td width="25%">
@@ -2353,7 +2352,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://cds.climate.copernicus.eu/">Copernicus Climate Change Service (C3S) Data Store (CDS)</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://cds.climate.copernicus.eu/">Copernicus Climate Change Service (C3S) Data Store (CDS)</a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2375,7 +2374,7 @@ <h3>Description</h3>
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://catalogue.ceda.ac.uk">Catalogue Search at CEDA (Centre for Environmental Data Analysis) </a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+    <a href="https://catalogue.ceda.ac.uk">Catalogue Search at CEDA (Centre for Environmental Data Analysis) </a> {{ recommended }}
     </div>
 </td>
 <td width="10%">
@@ -2407,11 +2406,11 @@ <h3>Description</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2525,7 +2524,7 @@ <h3>Description</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/community_working_groups/index.html b/pr-preview/pr-396/community_resources/community_working_groups/index.html
index 73c7d135e..a0e9a50df 100644
--- a/pr-preview/pr-396/community_resources/community_working_groups/index.html
+++ b/pr-preview/pr-396/community_resources/community_working_groups/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2286,8 +2284,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2403,11 +2402,11 @@ <h1 id="community-working-groups">Community Working Groups</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2521,7 +2520,7 @@ <h1 id="community-working-groups">Community Working Groups</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/events/add_event/index.html b/pr-preview/pr-396/community_resources/events/add_event/index.html
index 246b9818f..4a5753ba2 100644
--- a/pr-preview/pr-396/community_resources/events/add_event/index.html
+++ b/pr-preview/pr-396/community_resources/events/add_event/index.html
@@ -42,8 +42,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -353,7 +351,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1218,7 +1216,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1241,7 +1239,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1255,7 +1253,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1269,7 +1267,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1283,7 +1281,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1297,7 +1295,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2230,8 +2228,9 @@
         Add Event
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2339,8 +2338,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2442,11 +2442,11 @@ <h3 id="create-a-pull-request-to-add-your-event">Create a pull-request to add yo
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2560,7 +2560,7 @@ <h3 id="create-a-pull-request-to-add-your-event">Create a pull-request to add yo
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/events/events/2022/ACCESSAmos2022/index.html b/pr-preview/pr-396/community_resources/events/events/2022/ACCESSAmos2022/index.html
index 00be37715..7c378d569 100644
--- a/pr-preview/pr-396/community_resources/events/events/2022/ACCESSAmos2022/index.html
+++ b/pr-preview/pr-396/community_resources/events/events/2022/ACCESSAmos2022/index.html
@@ -42,8 +42,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -348,7 +346,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1210,7 +1208,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1233,7 +1231,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1247,7 +1245,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../../../models/run-a-model/run-access-esm/" class="md-nav__link">
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               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2517,11 +2516,11 @@ <h3 class="events-post-title">World Climate Research Program (WCRP) Open Science
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2635,7 +2634,7 @@ <h3 class="events-post-title">World Climate Research Program (WCRP) Open Science
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/glossary_access_nri/index.html b/pr-preview/pr-396/community_resources/glossaries/glossary_access_nri/index.html
index c0c712a09..a4e0b03cc 100644
--- a/pr-preview/pr-396/community_resources/glossaries/glossary_access_nri/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/glossary_access_nri/index.html
@@ -40,8 +40,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -351,7 +349,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1213,7 +1211,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1236,7 +1234,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1250,7 +1248,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1264,7 +1262,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1278,7 +1276,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1292,7 +1290,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2267,8 +2265,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2309,20 +2308,20 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2436,7 +2435,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/glossary_cmip/index.html b/pr-preview/pr-396/community_resources/glossaries/glossary_cmip/index.html
index edec0e9ee..a14fa6888 100644
--- a/pr-preview/pr-396/community_resources/glossaries/glossary_cmip/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/glossary_cmip/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2330,20 +2329,20 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2457,7 +2456,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/glossary_cssr/index.html b/pr-preview/pr-396/community_resources/glossaries/glossary_cssr/index.html
index 14444f909..1da8d3fac 100644
--- a/pr-preview/pr-396/community_resources/glossaries/glossary_cssr/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/glossary_cssr/index.html
@@ -40,8 +40,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -351,7 +349,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1213,7 +1211,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1236,7 +1234,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1250,7 +1248,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1264,7 +1262,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1278,7 +1276,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1292,7 +1290,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2267,8 +2265,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2309,20 +2308,20 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2436,7 +2435,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/glossary_era/index.html b/pr-preview/pr-396/community_resources/glossaries/glossary_era/index.html
index cf4e6e93b..81d636e5a 100644
--- a/pr-preview/pr-396/community_resources/glossaries/glossary_era/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/glossary_era/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2330,20 +2329,20 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2457,7 +2456,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/glossary_ipcc/index.html b/pr-preview/pr-396/community_resources/glossaries/glossary_ipcc/index.html
index c92bf74e5..7313f1eea 100644
--- a/pr-preview/pr-396/community_resources/glossaries/glossary_ipcc/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/glossary_ipcc/index.html
@@ -40,8 +40,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -351,7 +349,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1213,7 +1211,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1236,7 +1234,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1250,7 +1248,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1264,7 +1262,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1278,7 +1276,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1292,7 +1290,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2267,8 +2265,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2309,20 +2308,20 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2436,7 +2435,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/glossary_um/index.html b/pr-preview/pr-396/community_resources/glossaries/glossary_um/index.html
index 2922ce510..428f5a06c 100644
--- a/pr-preview/pr-396/community_resources/glossaries/glossary_um/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/glossary_um/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2330,20 +2329,20 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2457,7 +2456,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/glossaries/index.html b/pr-preview/pr-396/community_resources/glossaries/index.html
index ad8520d00..6b2685ad3 100644
--- a/pr-preview/pr-396/community_resources/glossaries/index.html
+++ b/pr-preview/pr-396/community_resources/glossaries/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2286,8 +2284,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2328,23 +2327,23 @@
 
 <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Useful Terms </div></h1>
 <p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="#">CMIP(6)</a>:  </p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="#">ERA(5)</a>:  </p>
-<p><a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> <a href="#">UM</a>: </p>
+<p>{{ supported }} <a href="https://www.access-nri.org.au/community/access-glossary/">ACCESS-NRI Glossary</a>: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p>
+<p>{{ community }} <a href="https://www.ipcc.ch/site/assets/uploads/sites/2/2022/06/SR15_AnnexI.pdf">IPCC Acronyms</a>: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p>
+<p>{{ community }} <a href="https://science2017.globalchange.gov/chapter/appendix-d/">CSSR Acronyms and Units</a>: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>
+<p>{{ community }} <a href="#">CMIP(6)</a>:  </p>
+<p>{{ community }} <a href="#">ERA(5)</a>:  </p>
+<p>{{ community }} <a href="#">UM</a>: </p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2458,7 +2457,7 @@ <h1 id="glossary-and-useful-terms"><div class="highlight-bg"> Glossary and Usefu
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/index.html b/pr-preview/pr-396/community_resources/index.html
index 8dcae3527..13bfdc6c8 100644
--- a/pr-preview/pr-396/community_resources/index.html
+++ b/pr-preview/pr-396/community_resources/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../css/termynal.css">
-    
       <link rel="stylesheet" href="../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../models/running-a-model/" class="md-tabs__link">
+      <a href="../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../models/running-a-model/">Run a Model</a>
+          <a href="../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2276,8 +2274,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2334,11 +2333,11 @@ <h1 id="community-resources">Community Resources</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2452,7 +2451,7 @@ <h1 id="community-resources">Community Resources</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../js/termynal.js"></script>
+        <script src="../js/terminal_animation.js"></script>
       
         <script src="../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/training/ACCESS_training/index.html b/pr-preview/pr-396/community_resources/training/ACCESS_training/index.html
index 004eb08a6..49224f87a 100644
--- a/pr-preview/pr-396/community_resources/training/ACCESS_training/index.html
+++ b/pr-preview/pr-396/community_resources/training/ACCESS_training/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2140,8 +2138,9 @@
         ACCESS Training
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2157,8 +2156,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#jules-tutorials" class="md-nav__link">
-     JULES tutorials  
+  <a href="#jules-tutorials-recommended" class="md-nav__link">
+     JULES tutorials {{ recommended }} 
   </a>
   
 </li>
@@ -2321,8 +2320,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2338,8 +2338,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#jules-tutorials" class="md-nav__link">
-     JULES tutorials  
+  <a href="#jules-tutorials-recommended" class="md-nav__link">
+     JULES tutorials {{ recommended }} 
   </a>
   
 </li>
@@ -2383,7 +2383,7 @@ <h1 id="access-training-material">ACCESS Training Material</h1>
 <li>how to modify a model configuration</li>
 <li>how to test a model modification or validate a model run</li>
 </ul>
-<h2 id="jules-tutorials"><div class="center-icons"> <a href="https://jules-lsm.github.io/tutorial/bg_info/tutorial_julesrose/index.html">JULES tutorials</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="jules-tutorials-recommended"><div class="center-icons"> <a href="https://jules-lsm.github.io/tutorial/bg_info/tutorial_julesrose/index.html">JULES tutorials</a> {{ recommended }} </div></h2>
 <p>The JULES tutorials explain how to use FCM, Rose and Cylc both for using the model and for development work. They can be useful to ACCESS users as practical demonstrations of the Rose and Cylc infrastructure.</p>
 
   <hr>
@@ -2391,11 +2391,11 @@ <h2 id="jules-tutorials"><div class="center-icons"> <a href="https://jules-lsm.g
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2509,7 +2509,7 @@ <h2 id="jules-tutorials"><div class="center-icons"> <a href="https://jules-lsm.g
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/training/additional_training/index.html b/pr-preview/pr-396/community_resources/training/additional_training/index.html
index 8a4f0d5fb..90b6ec3cd 100644
--- a/pr-preview/pr-396/community_resources/training/additional_training/index.html
+++ b/pr-preview/pr-396/community_resources/training/additional_training/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2329,10 +2328,10 @@
 
 
 <h1 id="additional-training-material">Additional training material</h1>
-<!-- ## [Git and GitHub][GitAndGitHub] <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> -->
+<!-- ## [Git and GitHub][GitAndGitHub] {{ supported }} -->
 
 <p>To learn the basics of Git and GitHub. It also includes ACCESS-NRI's recommendations to setup GitHub. </p>
-<!-- ## [NCI training][nci-training] <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+<!-- ## [NCI training][nci-training] {{ recommended }}
 <div class="result" markdown> -->
 
 <p><img align="right" alt="NCI Logo" src="../../../assets/nci_logo_color.svg" width="40%" /></p>
@@ -2346,11 +2345,11 @@ <h1 id="additional-training-material">Additional training material</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2464,7 +2463,7 @@ <h1 id="additional-training-material">Additional training material</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/training/git-version-control/index.html b/pr-preview/pr-396/community_resources/training/git-version-control/index.html
index 37ef70b42..4d9c9643a 100644
--- a/pr-preview/pr-396/community_resources/training/git-version-control/index.html
+++ b/pr-preview/pr-396/community_resources/training/git-version-control/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -350,7 +348,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1215,7 +1213,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1238,7 +1236,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1252,7 +1250,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1266,7 +1264,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1280,7 +1278,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1294,7 +1292,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2281,8 +2279,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2328,11 +2327,11 @@ <h1>Git Version Control</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2446,7 +2445,7 @@ <h1>Git Version Control</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/training/hpc/index.html b/pr-preview/pr-396/community_resources/training/hpc/index.html
index 7494ac834..2e4e67c85 100644
--- a/pr-preview/pr-396/community_resources/training/hpc/index.html
+++ b/pr-preview/pr-396/community_resources/training/hpc/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -350,7 +348,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1215,7 +1213,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1238,7 +1236,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1252,7 +1250,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1266,7 +1264,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1280,7 +1278,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1294,7 +1292,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2281,8 +2279,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2328,11 +2327,11 @@ <h1>High Performance Computing (HPC)</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2446,7 +2445,7 @@ <h1>High Performance Computing (HPC)</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/training/index.html b/pr-preview/pr-396/community_resources/training/index.html
index 4c82d82c5..f4488fa99 100644
--- a/pr-preview/pr-396/community_resources/training/index.html
+++ b/pr-preview/pr-396/community_resources/training/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2278,8 +2276,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2342,11 +2341,11 @@ <h1 id="training-and-policies">Training and Policies</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2460,7 +2459,7 @@ <h1 id="training-and-policies">Training and Policies</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/community_resources/training/nci-training/index.html b/pr-preview/pr-396/community_resources/training/nci-training/index.html
index 3ce8e111b..aaaf89bd7 100644
--- a/pr-preview/pr-396/community_resources/training/nci-training/index.html
+++ b/pr-preview/pr-396/community_resources/training/nci-training/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -350,7 +348,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1215,7 +1213,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1238,7 +1236,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1252,7 +1250,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1266,7 +1264,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1280,7 +1278,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1294,7 +1292,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2281,8 +2279,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2328,11 +2327,11 @@ <h1>NCI Training</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2446,7 +2445,7 @@ <h1>NCI Training</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/contribute/change-the-navigation/index.html b/pr-preview/pr-396/contribute/change-the-navigation/index.html
index ea3db8b56..746879a83 100644
--- a/pr-preview/pr-396/contribute/change-the-navigation/index.html
+++ b/pr-preview/pr-396/contribute/change-the-navigation/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -788,8 +786,9 @@
         Change the Navigation
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1281,7 +1280,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1360,7 +1359,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2335,8 +2334,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2456,11 +2456,11 @@ <h2 id="add-sections-to-a-tab">Add sections to a tab</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2574,7 +2574,7 @@ <h2 id="add-sections-to-a-tab">Add sections to a tab</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/contribute/edit-locally/index.html b/pr-preview/pr-396/contribute/edit-locally/index.html
index 0024c12b3..1bbbbac6b 100644
--- a/pr-preview/pr-396/contribute/edit-locally/index.html
+++ b/pr-preview/pr-396/contribute/edit-locally/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -760,8 +758,9 @@
         Edit Locally
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1335,7 +1334,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1358,7 +1357,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1372,7 +1371,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1386,7 +1385,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1400,7 +1399,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1414,7 +1413,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2389,8 +2388,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2570,11 +2570,11 @@ <h4 id="start-the-server">Start the server</h4>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2688,7 +2688,7 @@ <h4 id="start-the-server">Start the server</h4>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/contribute/edit-on-github/index.html b/pr-preview/pr-396/contribute/edit-on-github/index.html
index 0b8efdd8c..751fc1baf 100644
--- a/pr-preview/pr-396/contribute/edit-on-github/index.html
+++ b/pr-preview/pr-396/contribute/edit-on-github/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -746,8 +744,9 @@
         Edit on Github
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1267,7 +1266,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1290,7 +1289,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2321,8 +2320,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2451,11 +2451,11 @@ <h2 id="further-edits">Further edits</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2569,7 +2569,7 @@ <h2 id="further-edits">Further edits</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/contribute/index.html b/pr-preview/pr-396/contribute/index.html
index 494b2736a..6c69da0e0 100644
--- a/pr-preview/pr-396/contribute/index.html
+++ b/pr-preview/pr-396/contribute/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../css/termynal.css">
-    
       <link rel="stylesheet" href="../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../models/running-a-model/" class="md-tabs__link">
+      <a href="../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1224,7 +1222,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../models/running-a-model/">Run a Model</a>
+          <a href="../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1247,7 +1245,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1261,7 +1259,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1275,7 +1273,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1289,7 +1287,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1303,7 +1301,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2278,8 +2276,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2379,11 +2378,11 @@ <h2 id="process-to-contribute">Process to contribute</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2497,7 +2496,7 @@ <h2 id="process-to-contribute">Process to contribute</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../js/termynal.js"></script>
+        <script src="../js/terminal_animation.js"></script>
       
         <script src="../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/contribute/reviewers/index.html b/pr-preview/pr-396/contribute/reviewers/index.html
index 26ea28d02..e5f9484c3 100644
--- a/pr-preview/pr-396/contribute/reviewers/index.html
+++ b/pr-preview/pr-396/contribute/reviewers/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -802,8 +800,9 @@
         Reviewers
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1274,7 +1273,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1297,7 +1296,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1311,7 +1310,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1325,7 +1324,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1339,7 +1338,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1353,7 +1352,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2328,8 +2327,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2416,11 +2416,11 @@ <h2 id="guiding-principles">Guiding principles</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2534,7 +2534,7 @@ <h2 id="guiding-principles">Guiding principles</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/contribute/standalone-documentation/index.html b/pr-preview/pr-396/contribute/standalone-documentation/index.html
index 46c1a987c..208c8afda 100644
--- a/pr-preview/pr-396/contribute/standalone-documentation/index.html
+++ b/pr-preview/pr-396/contribute/standalone-documentation/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1234,7 +1232,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1313,7 +1311,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2343,11 +2342,11 @@ <h1 id="standalone-documentation">Standalone documentation</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2461,7 +2460,7 @@ <h1 id="standalone-documentation">Standalone documentation</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/css/access-nri.css b/pr-preview/pr-396/css/access-nri.css
index 03ed67827..1d219b6bf 100644
--- a/pr-preview/pr-396/css/access-nri.css
+++ b/pr-preview/pr-396/css/access-nri.css
@@ -54,8 +54,9 @@
   --md-typeset-kbd-color: rgb(39, 39, 39); /* keyboard key background (<kbd> tag) */
   --md-typeset-kbd-accent-color: rgb(126, 126, 126, .16); /* keyboard key inner border (<kbd> tag) */
   --md-typeset-kbd-border-color: rgb(30, 30, 30); /* text as keyboard outer border (<kbd> tag) */
-  --navigation-borders: var(--md-default-fg-color--lighter); /* Left border on the toc and navigation, border of cards */
-  --md-typeset-table-color: var(--navigation-borders); /* table borders (<table> tag) */
+  --navigation-borders: #115D9750; /* Left border on the toc and navigation */
+  --card-borders: var(--md-primary-fg-color--dark); /* Borders of cards */
+  --md-typeset-table-color: var(--card-borders); /* table borders (<table> tag) */
   --md-admonition-fg-color: var(--md-typeset-color); /* Main text warnings */
   --md-admonition-bg-color: var(--md-default-bg-color); /* Background warnings */
   --md-footer-fg-color: var(--md-primary-bg-color); /* footer text (not much used) */
@@ -70,7 +71,11 @@
   --card-shadows: #00000075; /* Shadows on cards and other elements */
   --card-shadows-hover: #00000090; /* Shadows hover on cards and other elements */
   --img-background: #FFFFFF; /* Background for transparent images */
-  --shadow-hover-background: rgba(29, 28, 28, 0.185) /* Shadow Background on hover */
+  --shadow-hover-background: rgba(29, 28, 28, 0.185); /* Shadow Background on hover */
+  --terminal-animation-directory: var(--nri-green);
+  --terminal-animation-buttons: var(--nri-orange);
+  --terminal-animation-buttons-hover: var(--nri-dark-blue);
+  
 }
 
 [data-md-color-scheme="custom-light"] {
@@ -100,7 +105,7 @@
   --md-accent-bg-color: var(--nri-orange); /* back to top button text hover */
   --md-accent-bg-color--light: #115D97B0;
   --md-code-fg-color: rgb(33, 36, 44); /* code element text */
-  --md-code-bg-color: #c3c3c3; /* code element background */
+  --md-code-bg-color: #dedede; /* code element background */
   --md-code-hl-color: rgba(255,255,0,.5);
   --md-code-hl-number-color: #d52a2a;
   --md-code-hl-special-color: #db1457;
@@ -122,8 +127,9 @@
   --md-typeset-kbd-color: rgb(226, 226, 226); /* keyboard key background (<kbd> tag) */
   --md-typeset-kbd-accent-color: rgb(255, 255, 255, .78); /* keyboard key inner border (<kbd> tag) */
   --md-typeset-kbd-border-color: rgb(212, 212, 212); /* text as keyboard outer border (<kbd> tag) */
-  --navigation-borders: var(--md-default-fg-color--lighter); /* Left border on the toc and navigation, border of cards */
-  --md-typeset-table-color: var(--navigation-borders); /* table borders (<table> tag) */
+  --navigation-borders: #FAA61950; /* Left border on the toc and navigation */
+  --card-borders: var(--md-primary-fg-color--dark); /* Borders of cards */
+  --md-typeset-table-color: var(--card-borders); /* table borders (<table> tag) */
   --md-admonition-fg-color: var(--md-typeset-color); /* Main text warnings */
   --md-admonition-bg-color: var(--md-default-bg-color); /* Background warnings */
   --md-footer-fg-color: var(--md-primary-bg-color); /* footer text (not much used) */
@@ -138,7 +144,10 @@
   --card-shadows: #00000075; /* Shadows on cards and other elements */
   --card-shadows-hover: #00000090; /* Shadows hover on cards and other elements */
   --img-background: #FFFFFF; /* Background for transparent images */
-  --shadow-hover-background: rgba(29, 28, 28, 0.185) /* Shadow Background on hover */
+  --shadow-hover-background: rgba(29, 28, 28, 0.185); /* Shadow Background on hover */
+  --terminal-animation-directory: var(--nri-blue);
+  --terminal-animation-buttons: var(--nri-dark-blue);
+  --terminal-animation-buttons-hover: var(--nri-orange);
 }
 
 
@@ -150,6 +159,14 @@ h1 {
   font-weight: 600 !important;
 }
 
+h2 {
+  font-weight: 500 !important;
+}
+
+h3 {
+  margin: 1em 0 0.4em !important;
+}
+
 /* =============================================================== 
   Introductory paragraph
 */
@@ -381,7 +398,7 @@ h1 {
   display: flex;
   justify-content: center;
   align-items: center;
-  border: 2px solid var(--navigation-borders);
+  border: 1px solid var(--card-borders);
   border-radius: 15px;
   box-shadow: 6px 6px 10px var(--card-shadows);
 }
@@ -473,10 +490,131 @@ a.component-card {
   box-shadow: unset;
 }
 
+/* =============================================================== 
+  References
+*/
+.references {
+  font-size:0.8em;
+}
+
+/* =============================================================== 
+  Page summary ('on this page' section)
+*/
+div.page-summary {
+  max-width: 100%;
+  border: solid 0.5px var(--md-typeset-color);
+  border-radius: 3px;
+  padding: 0 15px 10px;
+  line-height: 1.2em;
+  margin: 20px 0;
+}
+
+.page-summary h4 {
+  margin: 0.7em 0;
+}
+
+.page-summary ol {
+  list-style-type: none !important;
+  counter-reset: item !important;
+  margin: 0 !important;
+  padding: 0 !important;
+}
+
+.page-summary li {
+  display: table !important;
+  counter-increment: item !important;
+  margin: 0 0 0.5em 0.5em !important;
+}
+
+.page-summary li:before {
+    content: counters(item, ".") ". " !important;
+    display: table-cell !important;
+    padding-right: 0.3em !important;    
+}
+
+.page-summary li li {
+    margin: 0.1em 0 0 0 !important;
+}
+
+.page-summary li li:before {
+    content: counters(item, ".") ". " !important;
+}
+
+
+/* =============================================================== 
+  Show different markers for different hierarchy of points (up to 3d hierarchy)
+*/
+ul:not([class^='md-']) li {
+  list-style-type: disc;
+}
+
+ul:not([class^='md-']) li ul li {
+  list-style-type: circle;
+} 
+
+ul:not([class^='md-']) li ul li ul li {
+  list-style-type: square;
+} 
+
+/* =============================================================== 
+  Code block
+*/
+pre:has(code) {
+  display: flow-root !important;
+  text-align: left !important;
+  padding: 0 0 !important;
+  margin-top: 0.5em !important; 
+  margin-bottom: 0.5em !important;
+}
+
+pre>code {
+  white-space: pre-line !important;
+  padding: 0.5em 0.8em !important;
+  word-break: break-all !important;
+}
+
+/* =============================================================== 
+  Terminal animations
+*/
+::part(terminal-container) {
+  background-color: var(--md-code-bg-color);
+  color: var(--md-code-fg-color);
+  font-family: var(--md-code-font-family);
+  font-weight: unset;
+}
+
+::part(input-character) {
+  color: var(--terminal-animation-buttons);
+}
+
+::part(directory) {
+  color: var(--terminal-animation-directory);
+}
+
+::part(fast-button), ::part(restart-button) {
+  color: var(--terminal-animation-buttons);
+  font-weight: 700;
+}
+
+::part(fast-button):hover, ::part(restart-button):hover {
+  color: var(--terminal-animation-buttons-hover);
+}
+
+/* Try to format like the output of `ls` command */
+.ls-output-format {
+  word-spacing: 2em;
+  word-break: normal;
+}
+
 /* =============================================================== 
   Miscellaneous
 */
 
+/* Justified text */
+.justified {
+  text-align: justify;  
+}
+
 /* Highlight the background */
 .highlight-bg {
   background-color: var(--highlight-bg);
@@ -500,7 +638,7 @@ a.component-card {
 /* With borders */
 .with-border {
   border-radius: 7px;
-  border: 2px solid var(--navigation-borders);
+  border: 1px solid var(--card-borders);
   box-sizing: border-box;
 }
 
diff --git a/pr-preview/pr-396/css/termynal.css b/pr-preview/pr-396/css/termynal.css
deleted file mode 100644
index a11274415..000000000
--- a/pr-preview/pr-396/css/termynal.css
+++ /dev/null
@@ -1,114 +0,0 @@
-/**
- * termynal.js
- *
- * @author Ines Montani <ines@ines.io>
- * @version 0.0.1
- * @license MIT
- */
-
-
-:root {
-    --color-bg: #252a33;
-    --color-text: #eee;
-    --color-text-subtle: #a2a2a2;
-    --color-text-directory: var(--nri-green); /* Colour taken from ACCESS-NRI website */
-    --color-text-symlink: var(--nri-blue);  /* Colour taken from ACCESS-NRI website */
-    --color-text-dollar-sign: var(--nri-orange);  /* Colour taken from ACCESS-NRI website */
-    --color-control-buttons: #115D97;
-}
-
-.termynal {
-    /* width: 750px; */
-    max-width: 100%;
-    background: var(--color-bg);
-    color: var(--color-text);
-    display: flex;
-    flex-direction: column;
-    justify-content: flex-start;
-    font-size: 13px;
-    font-family: 'Roboto Mono', 'Fira Mono', Consolas, Menlo, Monaco, 'Courier New', Courier, monospace;
-    font-weight: bold;
-    border-radius: 4px;
-    padding: 35px 25px 25px;
-    position: relative;
-    -webkit-box-sizing: border-box;
-            box-sizing: border-box;
-}
-
-.termynal::before {
-    content: '';
-    position: absolute;
-    top: 15px;
-    left: 15px;
-    display: inline-block;
-    width: 15px;
-    height: 15px;
-    border-radius: 50%;
-    /* A little hack to display the window buttons in one pseudo element. */
-    background: #d9515d;
-    -webkit-box-shadow: 25px 0 0 #f4c025, 50px 0 0 #3ec930;
-            box-shadow: 25px 0 0 #f4c025, 50px 0 0 #3ec930;
-}
-
-[data-ty] {
-    line-height: 2;
-    justify-self: center;
-}
-
-[data-ty]::before {
-    /* Set up defaults and ensure empty lines are displayed. */
-    content: '';
-    display: inline-block;
-}
-
-[data-ty][prompt]::before {
-    content: attr(prompt);
-    color: var(--color-text-subtle);
-}
-
-[data-ty="input"][directory]::before {
-    content: attr(directory);
-    color: var(--color-text-directory);
-}
-
-[cursor]::after {
-    content: attr(cursor);
-    font-family: monospace;
-    -webkit-animation: blink 1s infinite;
-            animation: blink 1s infinite;
-}
-
-a[termynal-control-buttons] {
-    align-self: flex-end;
-    color: var(--color-control-buttons);
-}
-
-.directory-text {
-    color: var(--color-text-directory);
-}
-
-.symlink-text {
-    color: var(--color-text-symlink);
-}
-
-.double-spaced {
-    word-spacing: 1em;
-}
-
-[charBeforeInput] {
-    color: var(--color-text-dollar-sign);
-}
-
-/* Cursor animation */
-
-@-webkit-keyframes blink {
-    50% {
-        opacity: 0;
-    }
-}
-
-@keyframes blink {
-    50% {
-        opacity: 0;
-    }
-}
diff --git a/pr-preview/pr-396/index.html b/pr-preview/pr-396/index.html
index f4994be59..ebf7bfa57 100644
--- a/pr-preview/pr-396/index.html
+++ b/pr-preview/pr-396/index.html
@@ -42,8 +42,6 @@
       
     
     
-      <link rel="stylesheet" href="css/termynal.css">
-    
       <link rel="stylesheet" href="css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -356,7 +354,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="models/running-a-model/" class="md-tabs__link">
+      <a href="models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="models/running-a-model/">Run a Model</a>
+          <a href="models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2274,8 +2272,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2402,13 +2401,13 @@ <h2 id="support">Support</h2>
 <p>There is a system of tags to identify who supports the linked documentation or software, and the level of support you can expect:</p>
 <ul>
 <li>
-<p><code>Supported by ACCESS-NRI</code> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a></p>
+<p><code>Supported by ACCESS-NRI</code> {{ supported }}</p>
 </li>
 <li>
-<p><code>Recommended by ACCESS-NRI</code> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a></p>
+<p><code>Recommended by ACCESS-NRI</code> {{ recommended }}</p>
 </li>
 <li>
-<p><code>Community contributed</code> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></p>
+<p><code>Community contributed</code> {{ community }}</p>
 </li>
 </ul>
 <p>See the <a href="about/support/">support page</a> for details about the support levels: what is supported, by who, and how to access help.</p>
@@ -2456,11 +2455,11 @@ <h2 id="acknowledgement-of-country">Acknowledgement of Country</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2574,7 +2573,7 @@ <h2 id="acknowledgement-of-country">Acknowledgement of Country</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="js/termynal.js"></script>
+        <script src="js/terminal_animation.js"></script>
       
         <script src="js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/js/terminal_animation.js b/pr-preview/pr-396/js/terminal_animation.js
new file mode 100644
index 000000000..e2d702c06
--- /dev/null
+++ b/pr-preview/pr-396/js/terminal_animation.js
@@ -0,0 +1,1032 @@
+/**
+ * terminal-animation components
+ * Components based on the animated terminal app 'termynal.js' by Ines Montani <ines@ines.io>.
+ *
+ * @author Davide Marchegiani <davide.marchegiani@gmail.com>
+ * @version 1.0.0
+ * 
+ * The usage is as follow:
+ * 
+ * <terminal-animation>
+ *      <terminal-line data="input">First input line</terminal-line>
+ *      <terminal-line data="input">Second input line</terminal-line>
+ *      <terminal-line data="input">Third input with <span style="color: red"> red span</span></terminal-line>
+ *      <terminal-line>First output line</terminal-line>
+ * </terminal-animation>
+ * 
+ * The <terminal-animation> tag allows only <terminal-line> and <img> tags inside it. All the other nodes will be removed.
+ * E.g.:
+ * <terminal-animation>
+ *      This line will be removed
+ *      <terminal-line>This line will be kept</terminal-line>
+ *      <div>Also this line will be removed</div>
+ * </terminal-animation>
+ *
+ * The <terminal-line> tag allows only text nodes or <span> tags inside it. All the other nodes will be removed.
+ * E.g.:
+ * <terminal-line>All this line will be <span>kept</span></terminal-line>
+ * <terminal-line>This will be kept but <div>this will be removed</div></terminal-line>
+ * 
+ * The animation starts only when the terminal becomes visible, unless the 'init'
+ * attribute is present (in that case the animation starts right after the page loads).
+ * To know all the other possible attributes and what they do please read the specific components.
+ * 
+ * 
+ * List of sub-components editable with the CSS ::part pseudo-element:
+ * - Terminal Container -> ::part(terminal-container)
+ * - Fast Button -> ::part(fast-button)
+ * - Restart Button -> ::part(restart-button)
+ * - Directory -> ::part(directory)
+ * - Input Character(s) -> ::part(input-character)
+ * - Prompt Character(s) -> ::part(prompt-character)
+*/
+'use strict';
+
+
+const terminalTemplate = document.createElement('template');
+terminalTemplate.innerHTML = `
+    <style>
+        /* Colors inkected by 'applyMode' method 
+        :host {
+            --color-bg: #252a33;
+            --color-text: #eee;
+            --color-control-buttons: #FAA619;
+            --color-control-buttons-hover: #115D97;
+            --color-scrollbar: rgba(255, 255, 255, .6);
+        }
+        */
+
+        .terminal-container::-webkit-scrollbar {
+            width: 14px;
+        }
+        
+        .terminal-container::-webkit-scrollbar-thumb {
+            border-radius: 20px;
+            border: 4px solid rgba(0,0,0,0);
+            background-clip: padding-box;
+            background-color: var(--color-scrollbar);
+        }
+
+        .terminal-container {
+            word-break: break-all;
+            scroll-behavior: smooth;
+            scrollbar-gutter: stable;
+            max-swidth: 100%;
+            max-height: 510px;
+            margin-top: 15px;
+            margin-bottom: 15px;
+            background-color: var(--color-bg);
+            color: var(--color-text);
+            display: flex;
+            flex-direction: column;
+            justify-content: flex-start;
+            font-size: 13px;
+            font-family: 'Roboto Mono', 'Fira Mono', Consolas, Menlo, Monaco, 'Courier New', Courier, monospace;
+            font-weight: bold;
+            border-radius: 4px;
+            padding: 30px 25px 10px;
+            position: relative;
+            overflow-y: auto;
+            overflow-x: hidden;
+            -webkit-box-sizing: border-box;
+                    box-sizing: border-box;
+        }
+
+        .terminal-container::before {
+            content: '';
+            position: absolute;
+            top: 12px;
+            left: 12px;
+            display: flex;
+            flex-direction: column;
+            width: 10px;
+            height: 10px;
+            border-radius: 50%;
+            /* A little hack to display the window buttons in one pseudo element. */
+            background-color: #d9515d;
+            -webkit-box-shadow: 0px 0 0 #d9515d, 25px 0 0 #f4c025, 50px 0 0 #3ec930;
+                    box-shadow: 0px 0 0 #d9515d, 25px 0 0 #f4c025, 50px 0 0 #3ec930;
+        }
+        
+        .fast-button {
+            text-decoration: none;
+            position: sticky;
+            align-self: flex-end;
+            justify-self: center;
+            top: 0;
+            margin-top: -5px;
+            margin-right: -20px;
+            color: var(--color-control-buttons);
+        }
+        
+        .fast-button:hover {
+            color: var(--color-control-buttons-hover);
+        }
+            
+        .restart-button {
+            text-decoration: none;
+            position: sticky;
+            align-self: flex-end;
+            justify-self: center;
+            bottom: 0;
+            margin-bottom: 0px;
+            margin-right: -20px;
+            color: var(--color-control-buttons);
+        }
+        
+        .restart-button:hover {
+            color: var(--color-control-buttons-hover);
+        
+        }
+
+        ::slotted(img) {
+            overflow: hidden;
+            border: solid 2px transparent;
+            border-radius: 2px;
+                    box-sizing: border-box;
+            -webkit-box-sizing: border-box;
+        }
+        
+        ::slotted(img:hover) {
+            border: solid 2px red;
+            cursor: move;
+        }
+        
+        /*  position: relative;
+            top: -108px;
+            height: 600px;
+            width: 700px;
+        */
+
+    </style>
+
+    <div class='terminal-container' part="terminal-container" tabindex=-1>
+        <slot></slot>
+    </div>
+`
+/* Terminal component */
+class TerminalAnimation extends HTMLElement {
+    /**
+    * Custom attributes for the <terminal-animation> component:
+    * 
+    * @param {string} mode - 'light' for light mode; 'dark' for dark mode (default).
+    * @param {string} data - Type of prompt for each line of the entire terminal. Choices can be:
+    *   - 'output': Output of the terminal. Written all at once; (default)
+    *   - 'input': Input to the terminal. Written with typing animation after 'directory' and 'inputChar' attributes;
+    *   - 'prompt': Same as input, but with written with typing animation after 'promptChar' attribute;
+    *   - 'progress' Line with progress bar animation.
+    * @param {number || string} startDelay - Delay before the start of terminal animation, in ms.
+    * @param {number || string} lineDelay - Delay before the start of each terminal line animation, in ms.
+    * @param {number || string} typingDelay - Delay between each typed character in the terminal, in ms.
+    * @param {string} progressChar – Character(s) to use for progress bar for the entire terminal, defaults to █.
+    * @param {number || string} progressPercent - Max percent of progress for the entire terminal, default 100%.
+    * @param {string} cursor – Character to use for cursor for the entire terminal, defaults to ▋.
+    * @param {string} inputChar – Character(s) to use before the 'input' prompt for the entire terminal, defaults to '$'.
+    * @param {string} directory – Directory to write in the 'input' prompt before the input character for the entire terminal.
+    * @param {string} promptChar – Character(s) to use before the 'prompt' prompt for the entire terminal, defaults to '>>>'.
+    * @param {string} PS1 – String to write in the 'input' prompt before the actual line for the entire terminal. 
+    *  If present, any 'directory' or 'input' attribute will be disregarded.
+    *  Accepts HTML format. E.g.: "This is a <span style='color: green;'>valid</span> PS1 attribute"
+    * @param {boolean} init - Initialise the terminal animation at page load.
+    * @param {boolean} static - Create a static terminal without animation.
+    */
+    constructor() {
+        super();
+        this.attachShadow({ mode: "open" });
+        this.shadowRoot.appendChild(terminalTemplate.content.cloneNode(true));
+        this.applyMode();
+        this.ALLOWED_TAGS = ['terminal-line','img'];
+        this.DATA_TYPES = ['input','prompt','progress','output'];
+        this.keepLines();
+        if (!this.static) {
+            this.setTerminal();
+            if (this.init) {
+                this.initialiseAnimation();
+            } else {
+                this.initialiseWhenVisible();
+            }
+        } else {
+            this.generateAllProgress();
+        }
+    }
+
+    get container() {
+        const container = this.shadowRoot.querySelector(".terminal-container");
+        if (this.hasAttribute('lineDelay')) {
+            container.setAttribute('lineDelay',parseFloat(this.getAttribute('lineDelay')))
+        }
+        if (this.hasAttribute('typingDelay')) {
+            container.setAttribute('typingDelay',parseFloat(this.getAttribute('typingDelay')))
+        }
+        return container
+    }
+
+    get mode() {
+        /**
+        * Getter for the mode property
+        */
+        if (this.getAttribute('mode')?.toString().toLowerCase() == 'light') {
+            return 'light';
+        } else {
+            return 'dark';
+        }
+    }
+
+    get data() {
+        /**
+        * Getter for the data property
+        */
+        let attr = this.getAttribute('data');
+        if (this.DATA_TYPES.includes(attr)) {
+            return attr;
+        } else {
+            return 'output'
+        }
+    }
+
+    get startDelay() {
+        /**
+        * Resets startDelay property.
+        */
+       return parseFloat(this.getAttribute('startDelay')) || 300;
+    }
+    
+    get progressChar() {
+        /**
+        * Getter for the progressChar property
+        */
+        return this.getAttribute('progressChar')?.toString() || '█';
+    }
+    
+    get progressPercent() {
+        /**
+        * Getter for the progressPercent property
+        */
+        return parseFloat(this.getAttribute('progressPercent')) || 100;
+    }
+    
+    get cursor() {
+        /**
+        * Getter for the cursor property
+        */
+        return this.getAttribute('cursor')?.toString() || '▋';
+    }
+    
+    get inputChar() {
+        /**
+        * Getter for the inputChar property
+        */
+        if (this.hasAttribute('PS1')) {
+            return '';
+        } else {
+            return this.getAttribute('inputChar')?.toString() || '$';
+        }
+    }
+    
+    get promptChar() {
+        /**
+        * Getter for the promptChar property
+        */
+        return this.getAttribute('promptChar')?.toString() || '>>>';
+    }
+    
+    get directory() {
+        /**
+        * Getter for the directory property
+        */
+        if (this.hasAttribute('PS1')) {
+            return '';
+        } else {
+            return this.getAttribute('directory')?.toString() || '';
+        }
+    }
+
+    get PS1() {
+        /**
+        * Getter for the PS1 property
+        */
+        if (this.hasAttribute('PS1')) {
+            return this.getAttribute('PS1');
+        } else {
+            return `<span class="directory" part='directory'>${this.directory}</span><span class="inputChar" part='input-character'>${this.inputChar}&nbsp;</span>`;
+        }
+    }
+
+    get static() {
+        /**
+        * Getter for the static property
+        */
+        let attr = this.getAttribute('static')
+        if (attr == 'false') {
+            return false
+        } else if (attr == "") {
+            return true
+        } else {
+            return !!attr
+        }
+    }
+    
+    get init() {
+        /**
+        * Getter for the init property
+        */
+        let attr = this.getAttribute('init')
+        if (attr == 'false') {
+            return false
+        } else if (attr == "") {
+            return true
+        } else {
+            return !!attr
+        }
+    }
+
+    applyMode() {
+        /**
+        * Sets the color scheme according to the mode selected.
+        */
+        const colors = document.createElement('style');
+        if (this.mode == 'dark') {
+            colors.innerHTML = `
+                    :host {
+                        --color-bg: #252a33;
+                        --color-text: #eee;
+                        --color-control-buttons: #FAA619;
+                        --color-control-buttons-hover: #115D97;
+                        --color-scrollbar: rgba(255, 255, 255, .6);
+            `
+        } else {
+            colors.innerHTML = `
+                :host {
+                    --color-text: #252a33;
+                    --color-bg: #eee;
+                    --color-control-buttons-hover: #FAA619;
+                    --color-control-buttons: #115D97;
+                    --color-scrollbar: rgba(0, 0, 0, .6);
+            `
+        }
+        this.shadowRoot.appendChild(colors);
+    }
+
+    keepLines() {
+        /*
+        * Delete all terminal lines without tags or whose tags are not within the elementList
+        * and create the lines property with the kept ones.
+        */
+        for (let i=0; i<this.childNodes.length; i++) {
+            let node = this.childNodes[i];
+            if (!this.ALLOWED_TAGS.includes(node.tagName?.toLowerCase())) {
+                node.remove();
+                i--;
+            }
+        }
+        this.lines = this.childNodes;
+    }
+
+    async generateAllProgress() {
+        await this.sleep(0.000000000001) // Wait for lines to load
+        this.lines.forEach(line => {
+            if (line.data == 'progress') {
+                line.generateProgress();
+            }
+        })
+    }
+
+    hide(element) {
+        /**
+        * Change element's style to 'hidden'
+        */
+        element.style.visibility = 'hidden';
+    }
+    
+    show(element) {
+        /**
+        * Change element's style to 'visible'
+        */
+        element.style.visibility = 'visible';
+    }
+    
+    sleep(time) {
+        /**
+        * Sleep for an amount of time
+        */
+        return new Promise(resolve => setTimeout(resolve, time));
+    }
+    
+    resetDelays() {
+        this.lines.forEach(line => {
+            line._lineDelay;
+            line._typingDelay;
+        })
+    }
+
+    hideLines() {
+        /**
+        * Hide lines inside the terminal
+        */
+        this.lines.forEach(line => this.hide(line));
+    }
+
+    generateRestartButton() {
+        /**
+        * Generate restart button and adds it hidden to 'this.container'
+        */
+        const restart = document.createElement('a')
+        restart.setAttribute('part','restart-button')
+        restart.onclick = e => {
+            e.preventDefault();
+            this.hideAll();
+            this.scrollToTop();
+            this.mutationObserver.disconnect();
+            this.initialiseAnimation();
+        }
+        restart.href = '';
+        restart.classList.add('restart-button');
+        restart.innerHTML = "restart ↻";
+        this.hide(restart);
+        restart.addEventListener('click', e => this.hide(restart));
+        this.restartButton = restart;
+        this.container.appendChild(restart);
+    }
+
+    generateFastButton() {
+        /**
+        * Generate fast button and adds it hidden to 'this.container'
+        */
+        function nullifyDelays(_this) {
+            _this.lines.forEach(line => {
+                line._lineDelay = 0;
+                line._typingDelay = 0;
+            })
+        }
+        const fast = document.createElement('a')
+        fast.setAttribute('part','fast-button')
+        fast.onclick = (e) => {
+            e.preventDefault();
+            nullifyDelays(this);
+        }
+        fast.href = '';
+        fast.classList.add('fast-button');
+        fast.innerHTML = "fast ❯❯❯";
+        this.hide(fast);
+        fast.addEventListener('click', e => this.hide(fast));
+        this.addFocusOnTerminalContainerOnClick(fast);
+        this.fastButton = fast;
+        this.container.prepend(fast);
+    }
+
+    setTerminal() {
+        /**
+        * Clear container and generate restart/fast buttons.
+        */
+        this.hideLines();
+        this.generateRestartButton();
+        this.generateFastButton();
+        this.generateObservers();
+    }
+    
+    hidePS1AndPromptChar() {
+        /**
+        * Hides PS1 and Prompt Char for terminal reset
+        */
+        this.lines.forEach(line => {
+            let elem = line.shadowRoot?.querySelector('.ps1, .promptChar');
+            if (elem) {
+                this.hide(elem);
+            }
+        })
+    }
+
+    hideAll() {
+        this.hideLines();
+        this.hidePS1AndPromptChar();
+    }
+
+    async initialiseAnimation() {
+         /**
+         * Start the animation and render the lines
+         */
+        // while (this.container.scrollTop != 0) {await this.sleep(50)} //Start when the container is scroll up to the top.
+        this.autoScroll();
+        await this.sleep(this.startDelay);
+        this.show(this.fastButton);
+        for (let line of this.lines) {
+            line.classList.add('isBeingTyped');
+            if (line.tagName.toLowerCase() == 'terminal-line') {
+                // Handle <terminal-line> lines
+                await line.type();
+            } else if (line.tagName.toLowerCase() == 'img') {
+                // Handle <img> lines
+                this.show(line);
+                // await this.sleep(2000);
+                // this.hide(line);
+            }
+            line.classList.remove('isBeingTyped');
+        }
+        this.hide(this.fastButton);
+        this.resetDelays();
+        this.show(this.restartButton);
+    }
+
+    initialiseWhenVisible() {
+        /**
+        * Initialise the terminal only when it becomes visible
+        */
+        let observer = new IntersectionObserver(entries => {
+            entries.forEach(entry => {
+                if (entry.isIntersecting) {
+                    this.initialiseAnimation();
+                    observer.unobserve(this);
+                }
+            })
+        },
+        {
+            rootMargin: "-50px",
+        })
+        observer.observe(this);
+    }
+
+    addFocusOnTerminalContainerOnClick(elem) {
+        elem.addEventListener('click',() => this.container.focus())
+    }
+
+    scrollToTop() {
+        // Scroll to the bottom of the container.
+        this.container.scrollTop = 0;
+    }
+    
+    scrollToBottom() {
+        // Scroll to the bottom of the container.
+        this.container.scrollTop = this.container.scrollHeight;
+    }
+    
+    scrollOneLine(line) {
+        const nPix = parseInt(getComputedStyle(line).height);
+        this.container.scrollBy(0,nPix);
+    }
+
+    generateObservers() {
+        const intersectionFunction = entry => {
+            if (entry.intersectionRatio == 1) {
+                intersectionObserver.unobserve(entry.target);
+            } else {
+                if (entry.target.nextSibling) {
+                    this.scrollOneLine(entry.target);
+                }
+                intersectionObserver.unobserve(entry.target);
+            }
+        }
+           
+        let margin = `${parseInt(getComputedStyle(this.container).marginBottom) - 5}px` // Margin of the intersectionObserver computed as bottom margin - 5px (5px padding)
+        let intersectionObserver = new IntersectionObserver(entries => {
+            entries.forEach(entry => {
+                console.log(entry.intersectionRatio)
+                console.log(this.container.scrollTop)
+                intersectionFunction(entry)
+            })
+        },
+        {
+            root: this.container,
+            rootMargin: `0px 0px ${margin} 0px`,
+        })
+        
+        const mutationFunction = entry => {
+            if (entry.target.nextSibling) {
+                intersectionObserver.observe(entry.target.nextSibling)
+            } else {
+                this.scrollToBottom();
+            }
+        }
+
+        this.mutationObserver = new MutationObserver(entries => {
+            entries.forEach(entry => {
+                if (entry.oldValue?.includes("isBeingTyped")) {
+                    mutationFunction(entry)
+                }
+            })
+        })
+    }
+    
+    autoScroll() {
+        /**
+        * Auto scrolls 1 line if the terminal content exceeds the terminal max-height.
+        */
+        this.lines.forEach(line => {
+            this.mutationObserver.observe(line,{
+                attributes: true,
+                attributeOldValue: true,
+                attributeFilter: ["class"]
+            })
+        });
+
+        this.addEventListener('wheel', e => {
+            this.mutationObserver.disconnect();
+        })
+
+        this.addEventListener('keydown', e => {
+            if (['ArrowDown','Space','ArrowUp'].includes(e.code)) {
+                this.mutationObserver.disconnect();
+            }
+        })
+    }
+}
+
+/* =============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ ===============================================================================================================
+ =============================================================================================================== */
+
+ /* Terminal line */
+const lineTemplate = document.createElement('template');
+lineTemplate.innerHTML = `
+    <style>
+        :host {
+            --color-text-prompt: #a2a2a2;
+            --color-text-directory: #A6CE39;
+            --color-text-symlink: #06AEEF;
+            --color-text-inputchar: #FAA619;
+            display: grid;
+        }
+        
+        div.terminal-line {
+            min-height: 2em;
+            line-height: 2;
+            display: inline;
+            align-self: center;
+        }
+        
+        span.directory {
+            color: var(--color-text-directory);
+        }
+        
+        span.inputChar {
+            color: var(--color-text-inputchar);
+        }
+    </style>
+    
+    <body>
+        <div class='terminal-line'><slot></slot></div>
+    </body>
+    
+`
+
+class TerminalLine extends HTMLElement {
+    /**
+     * Defining custom attributes for <terminal-line> component
+    //  * @param {string} data - Type of prompt for the current line. Choices can be:
+    //  *   - 'output': Output of the terminal. Written all at once; (default)
+    //  *   - 'input': Input to the terminal. Written with typing animation after 'directory' and 'inputChar' attributes;
+    //  *   - 'prompt': Same as input, but with written with typing animation after 'promptChar' attribute;
+    //  *   - 'progress' Line with progress bar animation.
+    //  * @param {number} lineDelay - Delay before the start of the line animation, in ms.
+    //  * @param {number} typingDelay - Delay between each typed character in the line, in ms.
+    //  * @param {string} progressChar – Character to use for progress bar in the line, defaults to █.
+	//  * @param {number} progressPercent - Max percent of progress in the line, default 100%.
+    //  * @param {string} cursor – Character to use for cursor in the line, defaults to ▋.
+    //  * @param {string} inputChar – Character(s) to use before the 'input' prompt in the line, defaults to '$'.
+    //  * @param {string} directory – Directory to write in the 'input' prompt before the input character in the line.
+    //  * @param {string} promptChar – Character(s) to use before the 'prompt' prompt in the line, defaults to '>>>'.
+    //  * @param {string} PS1 – String to write in the 'input' prompt before the actual line. 
+            If present, any 'directory' or 'input' attribute will be disregarded.
+            Accepts HTML format. E.g.: "This is a <span style='color: green;'>valid</span> PS1 attribute"
+    //  */
+    constructor() {
+        super();
+        const shadow = this.attachShadow({ mode: "open" });
+        shadow.appendChild(lineTemplate.content.cloneNode(true));
+        this.ALLOWED_NODES = ["span"];
+        this.line = this.shadowRoot.querySelector(".terminal-line");
+        this.setCursorChar();
+        this.keepNodes();
+        this.generatePS1AndPromptCharElements();
+        this.resetDelays();
+        this.container.addFocusOnTerminalContainerOnClick(this);
+    }
+    
+    get container() {
+        if (this.parentElement.tagName.toLowerCase() != 'terminal-animation') {
+            throw new Error("A 'terminal-line' tag can only be placed inside a 'terminal-animation' tag.");
+        }
+        return this.parentElement;
+    }
+
+    get data() {
+        /**
+        * Getter for the data property
+        */
+        if (this.hasAttribute('data')) {
+            let attr = this.getAttribute('data');
+            if (this.container.DATA_TYPES.includes(attr)) {
+                return attr;
+            } else {
+                return 'output';
+            }
+        } else {
+            return this.container.data;
+        }
+    }
+    
+    get _lineDelay() {
+        /**
+        * Resets lineDelay property.
+        */
+        if (this.hasAttribute('lineDelay')) {
+            this.lineDelay = parseFloat(this.getAttribute('lineDelay'));
+        } else if (this.container.hasAttribute('lineDelay')) {
+            this.lineDelay = parseFloat(this.container.getAttribute('lineDelay'));
+        } else if (["input","prompt"].includes(this.data)) {
+            this.lineDelay = 600;
+        } else {
+            this.lineDelay = 100;
+        }
+    }
+
+    set _lineDelay(time) {
+        /**
+        * Sets lineDelay property.
+        */
+        this.lineDelay = time;
+    }
+    
+    get _typingDelay() {
+        /**
+        * Resets typingDelay property.
+        */
+        if (this.hasAttribute('typingDelay')) {
+            this.typingDelay = parseFloat(this.getAttribute('typingDelay'));
+        } else if (this.container.hasAttribute('typingDelay')) {
+            this.typingDelay = parseFloat(this.container.getAttribute('typingDelay'));
+        } else if (["progress"].includes(this.data)) {
+            this.typingDelay = 30;
+        } else {
+            this.typingDelay = 80;
+        }
+    }
+    
+    set _typingDelay(time) {
+        /**
+        * Sets typingDelay property.
+        */
+        this.typingDelay = time;
+    }
+
+    resetDelays() {
+        this._lineDelay;
+        this._typingDelay;
+    } 
+    
+    get progressChar() {
+        /**
+        * Getter for the progressChar property
+        */
+        return this.getAttribute('progressChar')?.toString() || this.container.progressChar;
+    }
+    
+    get progressPercent() {
+        /**
+        * Getter for the progressPercent property
+        */
+        return parseFloat(this.getAttribute('progressPercent')) || this.container.progressPercent;
+    }
+    
+    get cursor() {
+        /**
+        * Getter for the cursor property
+        */
+        return this.getAttribute('cursor')?.toString() || this.container.cursor;
+    }
+    
+    get inputChar() {
+        /**
+        * Getter for the inputChar property
+        */
+        if (this.hasAttribute('PS1')) {
+            return '';
+        } else {
+            return this.getAttribute('inputChar')?.toString() || this.container.inputChar;
+        }
+    }
+    
+    get promptChar() {
+        /**
+        * Getter for the promptChar property
+        */
+        return this.getAttribute('promptChar')?.toString() || this.container.promptChar;
+    }
+    
+    get directory() {
+        /**
+        * Getter for the directory property
+        */
+        if (this.hasAttribute('PS1')) {
+            return '';
+        } else {
+            return this.getAttribute('directory')?.toString() || this.container.directory;
+        }
+    }
+
+    get PS1() {
+        /**
+        * Getter for the PS1 property
+        */
+        if (this.hasAttribute('PS1')) {
+            return this.getAttribute('PS1');
+        } else if (this.hasAttribute('directory') || this.hasAttribute('inputChar')) {
+            return `<span class="directory" part='directory'>${this.directory}</span><span class="inputChar" part="input-character">${this.inputChar}&nbsp;</span>`;
+        } else {
+            return this.container.PS1;
+        }
+    }
+    
+    setCursorChar() {
+        const style = document.createElement('style');
+        style.innerHTML=`
+            .cursor::after {
+                content: '${this.cursor}';
+                font-family: monospace;
+                -webkit-animation: blink 1s infinite;
+                        animation: blink 1s infinite;
+            }
+            
+            @-webkit-keyframes blink {
+                50% {
+                    opacity: 0;
+                }
+            }
+    
+            @keyframes blink {
+                50% {
+                    opacity: 0;
+                }
+            }
+        `
+        this.shadowRoot.appendChild(style);
+    }
+
+    keepNodes(elementList=this.ALLOWED_NODES) {
+        /*
+        * Delete all line nodes whose tags are not within the elementList, 
+        * create <span> tags around textNodes,
+        * and create the nodes property with the kept ones.
+        */
+        for (let i=0; i<this.childNodes.length; i++) {
+            let node = this.childNodes[i];
+            if (node.nodeType == 3) {
+                let span = document.createElement('span');
+                this.insertBefore(span,node);
+                span.appendChild(node);
+            } else if (!elementList.includes(node.tagName.toLowerCase())) {
+                node.remove();
+                i--;
+            }
+        }
+        this.nodes = Array.from(this.childNodes);
+    }
+    
+    hide(element=this) {
+        /**
+        * Change element's style to 'hidden'
+        */
+        element.style.visibility = 'hidden';
+    }
+    
+    show(element=this) {
+        /**
+        * Change element's style to 'visible'
+        */
+        element.style.visibility = 'visible';
+    }
+
+    sleep(time) {
+        /**
+        * Sleep for an amount of time
+        */
+        return new Promise(resolve => setTimeout(resolve, time));
+    }
+
+    showPS1() {
+        this.show(this.shadowRoot.querySelector('.ps1'));
+    }
+    
+    showPromptChar() {
+        this.show(this.shadowRoot.querySelector('.promptChar'));
+    }
+
+    async type() {
+        /**
+        * Function that handles the animation of the current line based on its data property
+        */
+        if (this.data == 'input') {
+            this.showPS1();
+            await this.typeInput();
+        } else if (this.data == 'progress') {
+            await this.sleep(this.lineDelay);
+            await this.typeProgress();
+            return;
+        } else if (this.data == 'prompt') {
+            this.showPromptChar();
+            await this.typeInput();
+        } else {
+            await this.sleep(this.lineDelay);
+            this.show()
+        }
+
+    }
+
+    measureChar(char=this.progressChar) {
+        const ruler = document.createElement('span');
+        ruler.innerHTML = char;
+        ruler.style.whiteSpace = 'pre';
+        this.appendChild(ruler);
+        const width = ruler.offsetWidth;
+        this.removeChild(ruler);
+        return width;
+    }
+
+    async typeProgress() {
+        /**
+        * Animate a progress bar.
+        */
+        const progressCharWidth = this.measureChar();
+        const progressSteps = Math.round((parseInt(getComputedStyle(this).width)*0.8*(this.progressPercent/100))/progressCharWidth);
+        let percent = 0;
+        this.textContent = '0%';
+        this.show();
+        for (let i=1; i<=progressSteps; i++) {
+            await this.sleep(this.typingDelay);
+            percent = Math.round(this.progressPercent/progressSteps*i)
+            this.textContent = `${this.progressChar.repeat(i)} ${percent}%`;
+        }
+    }
+
+    generateProgress() {
+        const progressCharWidth = this.measureChar();
+        const progressLength = Math.round((parseInt(getComputedStyle(this).width)*0.8*(this.progressPercent/100))/progressCharWidth);
+        this.textContent = `${this.progressChar.repeat(progressLength)} ${this.progressPercent}%`;
+    }
+
+    async typeInput() {
+         /**
+         * Animate an input line.
+         */
+        let textArray = this.getAndRemoveTextContent();
+        this.show();
+        this.addCursor();
+        await this.sleep(this.lineDelay);
+        for (let i=0; i<this.nodes.length; i++) {
+            let node = this.nodes[i];
+            let text = textArray[i];
+            for (let char of text) {
+                await this.sleep(this.typingDelay);
+                node.textContent += char;
+            }
+        }
+        this.removeCursor();
+    }
+
+    getAndRemoveTextContent() {
+        let textArray = [];
+        for (let node of this.nodes) {
+            textArray.push(node.textContent);
+            node.textContent = "";
+        }
+        return textArray;
+    }
+
+    addCursor() {
+        this.line.classList.add('cursor');
+    }
+    
+    removeCursor() {
+        this.line.classList.remove('cursor');
+    }
+
+    generatePS1AndPromptCharElements() {
+        let elem = document.createElement('div');
+        elem.style.display="inline";
+        if (this.data == 'input') {
+            elem.innerHTML = this.PS1;
+            elem.classList.add('ps1');
+            this.PS1Element = elem;
+            this.line.prepend(elem)
+        } else if (this.data == 'prompt') {
+            elem.innerHTML = `${this.promptChar} `;
+            elem.classList.add('promptChar');
+            elem.setAttribute('part','prompt-character');
+            this.promptCharElement = elem;
+            this.line.prepend(elem)
+        }
+        if (!this.parentElement.static) {
+            this.hide(elem);
+        }
+    }
+}
+
+customElements.define("terminal-animation", TerminalAnimation)
+customElements.define("terminal-line", TerminalLine)
\ No newline at end of file
diff --git a/pr-preview/pr-396/model_evaluation/index.html b/pr-preview/pr-396/model_evaluation/index.html
index a518d2871..811ffb413 100644
--- a/pr-preview/pr-396/model_evaluation/index.html
+++ b/pr-preview/pr-396/model_evaluation/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://access-hive.org.au/model_evaluation/">
       
       
-        <link rel="prev" href="../models/running-a-model/running-access-om/">
+        <link rel="prev" href="../models/run-a-model/run-access-om/">
       
       
         <link rel="next" href="model_evaluation_getting_started/">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../css/termynal.css">
-    
       <link rel="stylesheet" href="../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../models/running-a-model/" class="md-tabs__link">
+      <a href="../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../models/running-a-model/">Run a Model</a>
+          <a href="../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2276,8 +2274,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2344,11 +2343,11 @@ <h1 id="model-evaluation-and-diagnostics-med">Model Evaluation and Diagnostics (
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2462,7 +2461,7 @@ <h1 id="model-evaluation-and-diagnostics-med">Model Evaluation and Diagnostics (
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../js/termynal.js"></script>
+        <script src="../js/terminal_animation.js"></script>
       
         <script src="../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_data_processing/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_data_processing/index.html
index f6c88682e..c261da810 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_data_processing/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_data_processing/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2290,8 +2288,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2335,18 +2334,18 @@ <h1 id="data-processing-tools">Data Processing Tools</h1>
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
 <p>On this page, we will provide you a list of currated data processing tools.</p>
-<p>While we are still ramping up this service, please take a look at the gallery of community tools on <a href="../../community_resources/community_data_processing/">Community Resources -&gt; Community Data Processing Tools</a> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>.</p>
+<p>While we are still ramping up this service, please take a look at the gallery of community tools on <a href="../../community_resources/community_data_processing/">Community Resources -&gt; Community Data Processing Tools</a> {{ community }}.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2460,7 +2459,7 @@ <h1 id="data-processing-tools">Data Processing Tools</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/index.html
index bc53fdbaf..446f79e51 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1222,7 +1220,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1245,7 +1243,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1259,7 +1257,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1273,7 +1271,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1287,7 +1285,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1301,7 +1299,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -1437,8 +1435,9 @@
         Computing Access (Gadi@NCI)
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2386,8 +2385,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" hidden>
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2728,11 +2728,11 @@ <h4 id="pbs-jobs">PBS Jobs</h4>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2848,7 +2848,7 @@ <h4 id="pbs-jobs">PBS Jobs</h4>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/index.html
index b3e0dd891..5443fbf1e 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2278,8 +2276,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2329,11 +2328,11 @@ <h1 id="getting-started-with-model-evaluation-at-nci">Getting Started with Model
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2447,7 +2446,7 @@ <h1 id="getting-started-with-model-evaluation-at-nci">Getting Started with Model
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/index.html
index 1eab14170..2b997b158 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -1449,8 +1447,9 @@
         Model Evaluation on Gadi
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2342,8 +2341,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2446,11 +2446,11 @@ <h3 id="25-model-evaluation">2.5) Model Evaluation</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2564,7 +2564,7 @@ <h3 id="25-model-evaluation">2.5) Model Evaluation</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_live_diagnostics/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_live_diagnostics/index.html
index 1eb8cbc3a..7517175b0 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_live_diagnostics/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_live_diagnostics/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2340,11 +2339,11 @@ <h1 id="live-diagnostics-on-gadi">Live Diagnostics on Gadi</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2458,7 +2457,7 @@ <h1 id="live-diagnostics-on-gadi">Live Diagnostics on Gadi</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/index.html
index fbbaf2f33..6bccfa6c7 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2280,8 +2278,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2342,47 +2341,47 @@ <h1 id="access-nri-intake-model-catalog">ACCESS-NRI intake Model Catalog</h1>
 ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself.
 
-## [NCI datasets][NCI-geonetwork] <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+## [NCI datasets][NCI-geonetwork] {{ recommended }}
 
 NCI has an extensive catalog of datasets of interest to the weather and climate community. These datasets are directly available on the NCI supercomputer and the [Australian Research Environment][ARE-opus]
 
-## [CLEX NCI Data Collection Intake Catalogue][Intake-CLEX] <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+## [CLEX NCI Data Collection Intake Catalogue][Intake-CLEX] {{ recommended }}
 
 This is an Intake catalogue maintained by the ARC Centre of Excellence for Climate Extremes [(CLEX)][CLEX-web].
 Only datasets from the NCI Catalog are referenced.
 The catalogue is available in intake's default catalogue list in the CLEX Conda environment.
 Two notebooks are provided in the docs folder showing how to access the ERA5 and CIP6 datasets.
 
-## [Australia Climate Data Guide Catalogue][ACDG-Catalog] <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+## [Australia Climate Data Guide Catalogue][ACDG-Catalog] {{ recommended }}
 
 *A one-stop catalogue to discover Climate Data in Australia*
 
 The ACDG portal is a metadata portal listing climate research resources available in Australia from multiple data repositories.
 This is a community based project managed by the ACDG Single Access working group. This is a group of Australian climate community self-nominated representatives. Anyone is welcome to join the group or to contribute independently to the metadata portal the group is developing.
 
-## [Australian Ocean Data Network][AODN-Network] <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+## [Australian Ocean Data Network][AODN-Network] {{ recommended }}
 
 The Australian Ocean Data Network (AODN) is an interoperable online network of marine and climate data resources.  IMOS and the 6 Australian Commonwealth agencies ([see AODN Partners](https://imos.org.au/facilities/aodn/aodn-data-management/aodn-partners)) form the core of the AODN. Increasingly, though, universities and State government offices are offering up data resources to the AODN, and delivery of data to the AODN is being written in to significant research programs e.g. [National Environmental Science Program Marine Biodiversity Hub](http://www.nespmarine.edu.au/) and the [Great Australian Bight research program](http://www.misa.net.au/GAB).
 
-## [Intake-Ilamb Catalog][Intake-Ilamb] <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>
+## [Intake-Ilamb Catalog][Intake-Ilamb] {{ supported }}
 
 The Intake-Ilamb catalog provides an yaml-style intake catalog of the reference data used for ESM model benchmarking in the International Land Model Benchmarking [(ILAMB)][ILAMB-web] effort.
 
-## [FLUXNET][FLUXNET-web] <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>
+## [FLUXNET][FLUXNET-web] {{ community }}
 
 FLUXNET is an international “network of networks,” tying together regional networks of earth system scientists. FLUXNET scientists use the eddy covariance technique to measure the cycling of carbon, water, and energy between the biosphere and atmosphere. Scientists use these data to better understand ecosystem functioning, and to detect trends in climate, greenhouse gases, and air pollution.
 
-## [CEDA Archive][CEDA-Archive-Web] <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>
+## [CEDA Archive][CEDA-Archive-Web] {{ community }}
 
 The CEDA Archive forms part of NERC's Environmental Data Service (EDS) and is responsible for looking after data from atmospheric and earth observation research. They host over 18 Petabytes of data from climate models, satellites, aircraft, met observations, and other sources.
 
-### [OZFlux][OZFlux-web] <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a>
+### [OZFlux][OZFlux-web] {{ community }}
 
 OzFlux is an ecosystem research network set up to provide Australian, New Zealand and global ecosystem modelling communities with consistent observations of energy, carbon and water exchange between the atmosphere and key Australian and New Zealand ecosystems.
 
-## [Australian Community Reference Climate Data Collection][AusRefClimData] <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a>
+## [Australian Community Reference Climate Data Collection][AusRefClimData] {{ recommended }}
 
-<a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> [Australian Community Reference Climate Data Collection @ NCI]
+{{ community }} [Australian Community Reference Climate Data Collection @ NCI]
 
 This collection is a collaborative effort between the Australian Climate Service (ACS), ARC Centre of Excellence for Climate Extremes (CLEX) and the wider Australian climate research community to re-establish and maintain a reference dataset collection at NCI.
 
@@ -2407,11 +2406,11 @@ <h1 id="access-nri-intake-model-catalog">ACCESS-NRI intake Model Catalog</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2525,7 +2524,7 @@ <h1 id="access-nri-intake-model-catalog">ACCESS-NRI intake Model Catalog</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_add_models/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_add_models/index.html
index ceba8c735..6d4911555 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_add_models/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_add_models/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2290,8 +2288,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2332,18 +2331,18 @@
 
 <h1 id="add-your-model-data-to-the-access-nri-intake-catalog">Add your model data to the ACCESS-NRI intake Catalog</h1>
 <p>You've just run a new experiment, now you want to create an intake-esm catalog for that experiment?</p>
-<p>Look at this <a href="https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/how_tos/building_intake-esm_catalogs.ipynb">Tutorial</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> to learn how to add your own models.</p>
+<p>Look at this <a href="https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/how_tos/building_intake-esm_catalogs.ipynb">Tutorial</a> {{ supported }} to learn how to add your own models.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2457,7 +2456,7 @@ <h1 id="add-your-model-data-to-the-access-nri-intake-catalog">Add your model dat
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/index.html
index 6847261d4..7696b34d2 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2290,8 +2288,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2331,10 +2330,10 @@
 
 
 <h1 id="search-for-a-model-in-the-access-nri-intake-catalog">Search for a model in the ACCESS-NRI intake Catalog</h1>
-<p>To have the huge amount of data from different experiments on the NCI storage at the palm of your hand, we provide a ("meta") catalog for you to query via python as part of the <code class="highlight"><span class="n">intake</span></code> package with our curated catalog plugin <code class="highlight"><span class="n">intake</span><span class="o">.</span><span class="n">cat</span><span class="o">.</span><span class="n">access_nri</span></code> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>.</p>
-<p>To use this catalog, you need access to NCI's Gadi. Check out our <a href="../../model_evaluation_getting_started/">Get Started with ACCESS at NCI</a>  <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> guide on how to get access.</p>
-<p>Once logged in to Gadi, you will need to add the <code class="highlight"><span class="n">access</span><span class="o">-</span><span class="n">nri</span><span class="o">-</span><span class="n">catalog</span></code> to your <code class="highlight"><span class="n">conda</span></code> environments and start an <a href="https://are.nci.org.au/pun/sys/dashboard">ARE JupyterLab Session</a>. Check out our <a href="https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/getting_started/index.rst">ACCESS-NRI Intake Catalog</a> guide <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> for the specific setup (note that you can only read in data from specific experiments if they are loaded through the <em>Storage</em> keyword).</p>
-<p>Once your JupyterLab session started, you can access the <code class="highlight"><span class="n">intake</span></code> catalog to load the data. Take a look at this <a href="https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/how_tos/example_usage.ipynb">Tutorial</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a>.</p>
+<p>To have the huge amount of data from different experiments on the NCI storage at the palm of your hand, we provide a ("meta") catalog for you to query via python as part of the <code class="highlight"><span class="n">intake</span></code> package with our curated catalog plugin <code class="highlight"><span class="n">intake</span><span class="o">.</span><span class="n">cat</span><span class="o">.</span><span class="n">access_nri</span></code> {{ supported }}.</p>
+<p>To use this catalog, you need access to NCI's Gadi. Check out our <a href="../../model_evaluation_getting_started/">Get Started with ACCESS at NCI</a>  {{ supported }} guide on how to get access.</p>
+<p>Once logged in to Gadi, you will need to add the <code class="highlight"><span class="n">access</span><span class="o">-</span><span class="n">nri</span><span class="o">-</span><span class="n">catalog</span></code> to your <code class="highlight"><span class="n">conda</span></code> environments and start an <a href="https://are.nci.org.au/pun/sys/dashboard">ARE JupyterLab Session</a>. Check out our <a href="https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/getting_started/index.rst">ACCESS-NRI Intake Catalog</a> guide {{ supported }} for the specific setup (note that you can only read in data from specific experiments if they are loaded through the <em>Storage</em> keyword).</p>
+<p>Once your JupyterLab session started, you can access the <code class="highlight"><span class="n">intake</span></code> catalog to load the data. Take a look at this <a href="https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/how_tos/example_usage.ipynb">Tutorial</a> {{ supported }}.</p>
 <div class="highlight"><pre><span></span><code><span class="c1"># Impport packages for searching/loading/plotting</span>
 <span class="kn">import</span> <span class="nn">intake</span>
 <span class="kn">from</span> <span class="nn">distributed</span> <span class="kn">import</span> <span class="n">Client</span>
@@ -2375,11 +2374,11 @@ <h1 id="search-for-a-model-in-the-access-nri-intake-catalog">Search for a model
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2493,7 +2492,7 @@ <h1 id="search-for-a-model-in-the-access-nri-intake-catalog">Search for a model
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_observational_catalogs/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_observational_catalogs/index.html
index a4bed7936..712e7171b 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_observational_catalogs/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_observational_catalogs/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2288,8 +2286,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2945,11 +2944,11 @@ <h1 id="todo-tier3">ToDo Tier3</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -3063,7 +3062,7 @@ <h1 id="todo-tier3">ToDo Tier3</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/index.html
index 7953f88fb..44ec81a25 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2278,8 +2276,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2328,11 +2327,11 @@ <h1 id="model-evaluation-on-gadi">Model Evaluation on Gadi</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2446,7 +2445,7 @@ <h1 id="model-evaluation-on-gadi">Model Evaluation on Gadi</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool/index.html
index 65f54f1eb..662f5c41d 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2290,8 +2288,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2341,11 +2340,11 @@ <h1 id="tutorial-for-using-esmvaltool-on-gadinci">Tutorial for using <code>esmva
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2459,7 +2458,7 @@ <h1 id="tutorial-for-using-esmvaltool-on-gadinci">Tutorial for using <code>esmva
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/index.html
index 1b768566f..9c3137ad0 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -1704,8 +1702,9 @@
         ILAMB
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2499,8 +2498,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -3046,11 +3046,11 @@ <h2 id="6-fix-your-setup-with-ilamb_doctor">6. Fix your setup with ilamb_doctor<
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -3164,7 +3164,7 @@ <h2 id="6-fix-your-setup-with-ilamb_doctor">6. Fix your setup with ilamb_doctor<
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima/index.html
index da7909ed2..1af34d13f 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../../models/running-a-model/">Run a Model</a>
+          <a href="../../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2290,8 +2288,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2342,11 +2341,11 @@ <h1 id="tutorial-for-using-pangeo-cosima-on-gadinci">Tutorial for using <code>pa
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2460,7 +2459,7 @@ <h1 id="tutorial-for-using-pangeo-cosima-on-gadinci">Tutorial for using <code>pa
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/model_evaluation/model_evaluation_recipe_gallery/index.html b/pr-preview/pr-396/model_evaluation/model_evaluation_recipe_gallery/index.html
index a50008586..939f05529 100644
--- a/pr-preview/pr-396/model_evaluation/model_evaluation_recipe_gallery/index.html
+++ b/pr-preview/pr-396/model_evaluation/model_evaluation_recipe_gallery/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -355,7 +353,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../models/running-a-model/" class="md-tabs__link">
+      <a href="../../models/run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1220,7 +1218,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../models/running-a-model/">Run a Model</a>
+          <a href="../../models/run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1243,7 +1241,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../models/run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1257,7 +1255,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1271,7 +1269,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1285,7 +1283,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1299,7 +1297,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../models/running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../models/run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -1765,8 +1763,9 @@
         Evaluation Recipe Gallery
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1782,8 +1781,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#link-to-our-med-recipe-gallery" class="md-nav__link">
-     Link to our MED Recipe Gallery  
+  <a href="#link-to-our-med-recipe-gallery-supported" class="md-nav__link">
+     Link to our MED Recipe Gallery {{ supported }} 
   </a>
   
 </li>
@@ -2321,8 +2320,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2338,8 +2338,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#link-to-our-med-recipe-gallery" class="md-nav__link">
-     Link to our MED Recipe Gallery  
+  <a href="#link-to-our-med-recipe-gallery-supported" class="md-nav__link">
+     Link to our MED Recipe Gallery {{ supported }} 
   </a>
   
 </li>
@@ -2380,9 +2380,9 @@ <h1 id="model-evaluation-and-diagnostics-med-recipe-gallery">Model Evaluation an
 <!-- ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
-<p>While we are still building this gallery, please have a look at the Community MED Recipes listed at <a href="../community_resources/community_med_recipes.md">Community Resources -&gt; Community Model Evaluation Recipes</a> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a></p>
+<p>While we are still building this gallery, please have a look at the Community MED Recipes listed at <a href="../community_resources/community_med_recipes.md">Community Resources -&gt; Community Model Evaluation Recipes</a> {{ community }}</p>
 <p>Here, we plan to provide you with an embedded link to our actively maintained Model Evaluation and Dianostics (MED) Recipe Gallery, hosted at <a href="https://medportal.herokuapp.com/models/published">medportal.herokuapp.com</a>. For now, we provide a placeholder image with link and pointers to useful Model Evaluation and Dianostics (MED) resources.</p>
-<h2 id="link-to-our-med-recipe-gallery"><div class="center-icons"> <a href="https://medportal.herokuapp.com/models/published">Link to our MED Recipe Gallery</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="link-to-our-med-recipe-gallery-supported"><div class="center-icons"> <a href="https://medportal.herokuapp.com/models/published">Link to our MED Recipe Gallery</a> {{ supported }} </div></h2>
 <p><a href="https://medportal.herokuapp.com/models/published">
     <img align="center" width="90%" src="../../assets/model_evaluation/model_evaluation_recipe_gallery_placeholder.jpg"></img>
 </a></p>
@@ -2392,11 +2392,11 @@ <h2 id="link-to-our-med-recipe-gallery"><div class="center-icons"> <a href="http
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2510,7 +2510,7 @@ <h2 id="link-to-our-med-recipe-gallery"><div class="center-icons"> <a href="http
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/configurations/access-am/index.html b/pr-preview/pr-396/models/configurations/access-am/index.html
index 249db2830..19e43a0fc 100644
--- a/pr-preview/pr-396/models/configurations/access-am/index.html
+++ b/pr-preview/pr-396/models/configurations/access-am/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -97,7 +95,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#access-am" class="md-skip">
+        <a href="#access-am-supported" class="md-skip">
           Skip to content
         </a>
       
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1171,8 +1169,9 @@
         ACCESS-AM
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1281,7 +1280,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1360,7 +1359,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2335,8 +2334,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2404,7 +2404,7 @@
   
 
 
-<h1 id="access-am"><div class="center-icons"> ACCESS-AM <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h1>
+<h1 id="access-am-supported"><div class="center-icons"> ACCESS-AM {{ supported }} </div></h1>
 <!-- ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
@@ -2423,11 +2423,11 @@ <h3 id="experiments">Experiments</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2541,7 +2541,7 @@ <h3 id="experiments">Experiments</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/configurations/access-cm/index.html b/pr-preview/pr-396/models/configurations/access-cm/index.html
index 4e7403a80..1e7faeffd 100644
--- a/pr-preview/pr-396/models/configurations/access-cm/index.html
+++ b/pr-preview/pr-396/models/configurations/access-cm/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -97,7 +95,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#access-cm" class="md-skip">
+        <a href="#access-cm-supported" class="md-skip">
           Skip to content
         </a>
       
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1157,8 +1155,9 @@
         ACCESS-CM
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1181,8 +1180,8 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#access-cm2" class="md-nav__link">
-     ACCESS-CM2  
+  <a href="#access-cm2-recommended" class="md-nav__link">
+     ACCESS-CM2 {{ recommended }} 
   </a>
   
 </li>
@@ -1274,7 +1273,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1297,7 +1296,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1311,7 +1310,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1325,7 +1324,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1339,7 +1338,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1353,7 +1352,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2328,8 +2327,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2352,8 +2352,8 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#access-cm2" class="md-nav__link">
-     ACCESS-CM2  
+  <a href="#access-cm2-recommended" class="md-nav__link">
+     ACCESS-CM2 {{ recommended }} 
   </a>
   
 </li>
@@ -2390,7 +2390,7 @@
   
 
 
-<h1 id="access-cm"><div class="center-icons"> ACCESS-CM <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h1>
+<h1 id="access-cm-supported"><div class="center-icons"> ACCESS-CM {{ supported }} </div></h1>
 <div style="text-align: justify">
 ACCESS-CM2 (ACCESS Coupled Model 2) is a global fully-coupled climate model that includes the atmosphere, ocean and sea-ice components, and produces physical climate simulations. ACCESS-CM2 is one of the two models run by the Australian climate community for the 
 <a href = "https://www.wcrp-climate.org/wgcm-cmip" target="_blank"> Coupled Model Intercomparison Project, CMIP</a>.
@@ -2450,7 +2450,7 @@ <h2 id="access-cm2-configurations">ACCESS-CM2 configurations</h2>
 </li>
 </ul>
 <p>ACCESS-NRI will release an ACCESS-CM model configuration. The first release of ACCESS-CM will be derived from the <a href="#access-cm2">CSIRO ACCESS-CM2 configuration</a> and will include <a href="../../model_components/atmosphere/">atmosphere</a>, <a href="../../model_components/land/">land</a>, <a href="../../model_components/ocean/">ocean</a> and <a href="../../model_components/sea-ice/">sea ice</a> components.</p>
-<h2 id="access-cm2"><div class="center-icons"> <a href="https://research.csiro.au/access/about/cm2/">ACCESS-CM2</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="access-cm2-recommended"><div class="center-icons"> <a href="https://research.csiro.au/access/about/cm2/">ACCESS-CM2</a> {{ recommended }} </div></h2>
 <p><a href="https://www.publish.csiro.au/es/ES19040"><strong>Citation</strong> <sup id="fnref:1"><a class="footnote-ref" href="#fn:1">1</a></sup></a> |
 <a href="https://nespclimate.com.au/wp-content/uploads/2020/10/Instruction-document-Getting_started_with_ACCESS.pdf"><strong>Tutorial</strong></a></p>
 <p>ACCESS-CM2 <sup id="fnref2:1"><a class="footnote-ref" href="#fn:1">1</a></sup> is one of Australia’s contributions to the World Climate Research Programme’s Coupled Model Intercomparison Project Phase 6 (CMIP6). The component models are: UM10.6 GA7.1 for the atmosphere, CABLE2.5 for the land surface, MOM5 for the ocean, and CICE5.1.2 for the sea ice. Compared to previous model versions ACCESS-CM2 shows better global hydrological balance, more realistic ocean water properties (in terms of spatial distribution) and meridional overturning circulation in the Southern Ocean but a poorer simulation of the Antarctic sea ice and a larger energy imbalance at the top of atmosphere. This energy imbalance reflects a noticeable warming trend of the global ocean over the spin-up period.</p>
@@ -2470,11 +2470,11 @@ <h2 id="access-cm2"><div class="center-icons"> <a href="https://research.csiro.a
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2588,7 +2588,7 @@ <h2 id="access-cm2"><div class="center-icons"> <a href="https://research.csiro.a
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/configurations/access-esm/index.html b/pr-preview/pr-396/models/configurations/access-esm/index.html
index 55bb4660e..7dccb8864 100644
--- a/pr-preview/pr-396/models/configurations/access-esm/index.html
+++ b/pr-preview/pr-396/models/configurations/access-esm/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -97,7 +95,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#access-esm" class="md-skip">
+        <a href="#access-esm-supported" class="md-skip">
           Skip to content
         </a>
       
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1143,8 +1141,9 @@
         ACCESS-ESM
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1160,8 +1159,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#access-esm15" class="md-nav__link">
-     ACCESS-ESM1.5  
+  <a href="#access-esm15-recommended" class="md-nav__link">
+     ACCESS-ESM1.5 {{ recommended }} 
   </a>
   
 </li>
@@ -1267,7 +1266,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1290,7 +1289,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2321,8 +2320,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2338,8 +2338,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#access-esm15" class="md-nav__link">
-     ACCESS-ESM1.5  
+  <a href="#access-esm15-recommended" class="md-nav__link">
+     ACCESS-ESM1.5 {{ recommended }} 
   </a>
   
 </li>
@@ -2376,13 +2376,13 @@
   
 
 
-<h1 id="access-esm"><div class="center-icons"> ACCESS-ESM <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h1>
+<h1 id="access-esm-supported"><div class="center-icons"> ACCESS-ESM {{ supported }} </div></h1>
 <!-- ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
 <p>ACCESS-ESM stands for ACCESS <strong>E</strong>arth <strong>S</strong>ystem <strong>M</strong>odel. Earth system model means it is a fully-coupled model that includes carbon cycle components.</p>
 <p>ACCESS-NRI will release an ACCESS-ESM model configuration. The first release of ACCESS-ESM will be derived from the <a href="#access-esm15">CSIRO ACCESS-ESM1.5 configuration</a> and will include <a href="../../model_components/atmosphere/">atmosphere</a>, <a href="../../model_components/land/">land</a> and <a href="../../model_components/bgc_land/">land biogeochemistry</a>, <a href="../../model_components/ocean/">ocean</a> and <a href="../../model_components/bgc_ocean/">ocean biogeochemistry</a>, and <a href="../../model_components/sea-ice/">sea ice</a> components.</p>
-<h2 id="access-esm15"><div class="center-icons"> <a href="https://research.csiro.au/access/about/esm1-5/">ACCESS-ESM1.5</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="access-esm15-recommended"><div class="center-icons"> <a href="https://research.csiro.au/access/about/esm1-5/">ACCESS-ESM1.5</a> {{ recommended }} </div></h2>
 <p><a href="https://www.publish.csiro.au/es/ES19035"><strong>Citation</strong> <sup id="fnref:1"><a class="footnote-ref" href="#fn:1">1</a></sup></a></p>
 <p><a href="https://confluence.csiro.au/display/ACCESS/Setting+up+for+ACCESS-ESM1.5"><strong>ACCESS Training Workshop (AMOS 2021)</strong></a></p>
 <p><a href="https://nespclimate.com.au/wp-content/uploads/2020/10/Webinar-slides-Getting_started_with_ACCESS.pdf"><strong>Webinar: <em>Getting Started with ACCESS-CM2 and ACCESS-ESM1.5</em> </strong></a></p>
@@ -2401,11 +2401,11 @@ <h2 id="access-esm15"><div class="center-icons"> <a href="https://research.csiro
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2519,7 +2519,7 @@ <h2 id="access-esm15"><div class="center-icons"> <a href="https://research.csiro
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/configurations/access-om/index.html b/pr-preview/pr-396/models/configurations/access-om/index.html
index 722948ad4..0c62da814 100644
--- a/pr-preview/pr-396/models/configurations/access-om/index.html
+++ b/pr-preview/pr-396/models/configurations/access-om/index.html
@@ -14,7 +14,7 @@
         <link rel="prev" href="../access-am/">
       
       
-        <link rel="next" href="../../running-a-model/">
+        <link rel="next" href="../../run-a-model/">
       
       <link rel="icon" href="../../../assets/ACCESS_icon_HIVE.png">
       <meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.8">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -97,7 +95,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#access-om" class="md-skip">
+        <a href="#access-om-supported" class="md-skip">
           Skip to content
         </a>
       
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1185,8 +1183,9 @@
         ACCESS-OM
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1202,8 +1201,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#access-om2" class="md-nav__link">
-     ACCESS-OM2  
+  <a href="#access-om2-recommended" class="md-nav__link">
+     ACCESS-OM2 {{ recommended }} 
   </a>
   
 </li>
@@ -1267,7 +1266,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1290,7 +1289,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2321,8 +2320,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2338,8 +2338,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#access-om2" class="md-nav__link">
-     ACCESS-OM2  
+  <a href="#access-om2-recommended" class="md-nav__link">
+     ACCESS-OM2 {{ recommended }} 
   </a>
   
 </li>
@@ -2376,16 +2376,16 @@
   
 
 
-<h1 id="access-om"><div class="center-icons"> ACCESS-OM <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h1>
+<h1 id="access-om-supported"><div class="center-icons"> ACCESS-OM {{ supported }} </div></h1>
 <!-- ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
-<p>ACCESS-OM stands for ACCESS <strong>O</strong>cean <strong>M</strong>odel. There is more than just an ocean model, but it indicates that this is not a fully-coupled model, i.e. not coupled with a model atmosphere, the atmospheric fields that drive the model are provided by a data product, usually derived from reanalysis.</p>
-<p>ACCESS-NRI will release an ACCESS-OM model configuration. The first release of ACCESS-OM will be derived from the COSIMA ACCESS-OM2 suite and will include <a href="../../model_components/ocean/">ocean</a> and <a href="../../model_components/sea-ice/">sea ice</a> components.</p>
-<h2 id="access-om2"><div class="center-icons"> <a href="http://cosima.org.au/index.php/models/">ACCESS-OM2</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> </div></h2>
+<p>The ACCESS <strong>O</strong>cean <strong>M</strong>odel, ACCESS-OM, is a global coupled ocean and sea ice configuration. It couples the ocean and sea ice components via a coupler. The atmospheric fields that drive the model are provided by a data product, usually derived from reanalysis.</p>
+<p>ACCESS-NRI will release supported ACCESS-OM configurations. The first release will be derived from the COSIMA <a href="http://cosima.org.au/index.php/models/">ACCESS-OM2</a> suite and will include <a href="../../model_components/ocean/">ocean</a> and <a href="../../model_components/sea-ice/">sea ice</a> components.</p>
+<h2 id="access-om2-recommended"><div class="center-icons"> <a href="http://cosima.org.au/index.php/models/">ACCESS-OM2</a> {{ recommended }} </div></h2>
 <p><a href="https://gmd.copernicus.org/articles/13/401/2020/"><strong>Citation</strong> <sup id="fnref:1"><a class="footnote-ref" href="#fn:1">1</a></sup></a> |
 <a href="https://github.com/COSIMA/access-om2/wiki"><strong>Documentation</strong></a></p>
-<p>ACCESS-OM2 <sup id="fnref2:1"><a class="footnote-ref" href="#fn:1">1</a></sup> is a suite of coupled ocean-sea ice models developed by the <a href="http://cosima.org.au/">Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)</a>. All models use the <a href="https://github.com/mom-ocean/MOM5">MOM5</a> ocean model coupled to the <a href="https://github.com/COSIMA/cice5">CICE5</a> sea ice model via OASIS3-MCT.</p>
+<p>ACCESS-OM2 <sup id="fnref2:1"><a class="footnote-ref" href="#fn:1">1</a></sup> is a suite of coupled ocean-sea ice models developed by the Consortium for Ocean-Sea Ice Modelling in Australia (<a href="http://cosima.org.au/">COSIMA</a>). All models use the <a href="https://github.com/mom-ocean/MOM5">MOM5</a> ocean model coupled to the <a href="https://github.com/COSIMA/cice5">CICE5</a> sea ice model via an OASIS3-MCT coupler.</p>
 <p>The models in the ACCESS-OM2 suite differ by their grid spatial resolution:</p>
 <ul>
 <li><a href="http://cosima.org.au/index.php/models/access-om2/">ACCESS-OM2</a> at 1° with 50 vertical levels</li>
@@ -2406,11 +2406,11 @@ <h2 id="access-om2"><div class="center-icons"> <a href="http://cosima.org.au/ind
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2524,7 +2524,7 @@ <h2 id="access-om2"><div class="center-icons"> <a href="http://cosima.org.au/ind
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/configurations/access-s/index.html b/pr-preview/pr-396/models/configurations/access-s/index.html
index 973eb9fda..5bb757cbd 100644
--- a/pr-preview/pr-396/models/configurations/access-s/index.html
+++ b/pr-preview/pr-396/models/configurations/access-s/index.html
@@ -40,8 +40,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -93,7 +91,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#access-s" class="md-skip">
+        <a href="#access-s-community" class="md-skip">
           Skip to content
         </a>
       
@@ -351,7 +349,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1213,7 +1211,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1236,7 +1234,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1250,7 +1248,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1264,7 +1262,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1278,7 +1276,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1292,7 +1290,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2267,8 +2265,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2307,7 +2306,7 @@
   
 
 
-<h1 id="access-s"><div class="highlight-bg center-icons"> <a href="http://www.bom.gov.au/research/projects/ACCESS-S/">ACCESS-S</a> <a href="https://access-hive.org.au/about/support"><span class="heart center-icons"><i class="heart fa-regular fa-heart" title="Community Contributed"></i></span></a> </div></h1>
+<h1 id="access-s-community"><div class="highlight-bg center-icons"> <a href="http://www.bom.gov.au/research/projects/ACCESS-S/">ACCESS-S</a> {{ community }} </div></h1>
 <!-- ???+ warning "The documentation on Hive is work in progress!"
     The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself. -->
 
@@ -2326,11 +2325,11 @@ <h1 id="access-s"><div class="highlight-bg center-icons"> <a href="http://www.bo
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2444,7 +2443,7 @@ <h1 id="access-s"><div class="highlight-bg center-icons"> <a href="http://www.bo
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/configurations/index.html b/pr-preview/pr-396/models/configurations/index.html
index fcbd266c5..ec2d4b295 100644
--- a/pr-preview/pr-396/models/configurations/index.html
+++ b/pr-preview/pr-396/models/configurations/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../running-a-model/" class="md-tabs__link">
+      <a href="../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1224,7 +1222,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../running-a-model/">Run a Model</a>
+          <a href="../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1247,7 +1245,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1261,7 +1259,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1275,7 +1273,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1289,7 +1287,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1303,7 +1301,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2278,8 +2276,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2329,11 +2328,11 @@ <h1 id="access-configurations">ACCESS Configurations</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2447,7 +2446,7 @@ <h1 id="access-configurations">ACCESS Configurations</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/index.html b/pr-preview/pr-396/models/index.html
index bd3fa738d..3015c039a 100644
--- a/pr-preview/pr-396/models/index.html
+++ b/pr-preview/pr-396/models/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../css/termynal.css">
-    
       <link rel="stylesheet" href="../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="running-a-model/" class="md-tabs__link">
+      <a href="run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1222,7 +1220,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="running-a-model/">Run a Model</a>
+          <a href="run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1245,7 +1243,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1259,7 +1257,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1273,7 +1271,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1287,7 +1285,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-a-model/running-access-am/" class="md-nav__link">
+      <a href="run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1301,7 +1299,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-a-model/running-access-om/" class="md-nav__link">
+      <a href="run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2276,8 +2274,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2446,11 +2445,11 @@ <h2 id="access-model-configurations">ACCESS Model Configurations</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2564,7 +2563,7 @@ <h2 id="access-model-configurations">ACCESS Model Configurations</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../js/termynal.js"></script>
+        <script src="../js/terminal_animation.js"></script>
       
         <script src="../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/aerosols_atmospheric_chemistry/index.html b/pr-preview/pr-396/models/model_components/aerosols_atmospheric_chemistry/index.html
index 681591c30..c78301af8 100644
--- a/pr-preview/pr-396/models/model_components/aerosols_atmospheric_chemistry/index.html
+++ b/pr-preview/pr-396/models/model_components/aerosols_atmospheric_chemistry/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1031,8 +1029,9 @@
         Aerosols and Atmospheric Chemistry
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1048,11 +1047,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#ukca" class="md-nav__link">
-     UKCA  
+  <a href="#ukca-supported" class="md-nav__link">
+     UKCA {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" UKCA  ">
+    <nav class="md-nav" aria-label=" UKCA {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1068,11 +1067,11 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#glomap" class="md-nav__link">
-     GLOMAP  
+  <a href="#glomap-supported" class="md-nav__link">
+     GLOMAP {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" GLOMAP  ">
+    <nav class="md-nav" aria-label=" GLOMAP {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1300,7 +1299,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1323,7 +1322,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1337,7 +1336,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1351,7 +1350,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1365,7 +1364,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1379,7 +1378,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2354,8 +2353,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2371,11 +2371,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#ukca" class="md-nav__link">
-     UKCA  
+  <a href="#ukca-supported" class="md-nav__link">
+     UKCA {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" UKCA  ">
+    <nav class="md-nav" aria-label=" UKCA {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -2391,11 +2391,11 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#glomap" class="md-nav__link">
-     GLOMAP  
+  <a href="#glomap-supported" class="md-nav__link">
+     GLOMAP {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" GLOMAP  ">
+    <nav class="md-nav" aria-label=" GLOMAP {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -2449,14 +2449,14 @@ <h1 id="aerosol-and-atmospheric-chemistry-components"><div class="highlight-bg">
 <!-- ![Atmospheric Component Logo](../../assets/component-logos/components-without-titles/ACCESS%20icon%20AEROSOLS.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/aerosol-chemistry-component-map.png" class="white-img-bg"></img></p>
-<h2 id="ukca"><div class="center-icons"> <a href="https://www.ukca.ac.uk/wiki/index.php/UKCA">UKCA</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="ukca-supported"><div class="center-icons"> <a href="https://www.ukca.ac.uk/wiki/index.php/UKCA">UKCA</a> {{ supported }} </div></h2>
 <p>The <a href="https://www.ukca.ac.uk/wiki/index.php/UKCA">UK Chemistry-Aerosol model (UKCA)</a> is a community atmospheric chemistry-aerosol global model  developed in the United Kingdom. It is suitable for a range of topics in climate and environmental change research.</p>
 <h3 id="how-is-ukca-used">How is UKCA used?</h3>
 <p>UKCA chemistry model is enabled in ACCESS-CM2-Chem.</p>
 <!-- 
 ![Atmospheric Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon ATMOSPHERIC CHEMISTRY.png){align=right width=40%} -->
 
-<h2 id="glomap"><div class="center-icons"> <a href="https://www.ukca.ac.uk/wiki/index.php/Aerosol_Subproject">GLOMAP</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="glomap-supported"><div class="center-icons"> <a href="https://www.ukca.ac.uk/wiki/index.php/Aerosol_Subproject">GLOMAP</a> {{ supported }} </div></h2>
 <p>UKCA contains an aerosol scheme <a href="https://www.ukca.ac.uk/wiki/index.php/Aerosol_Subproject">GLObal Model of Aerosol Processes (GLOMAP)</a> that can be used independently. The multi-component, multi-modal GLOMAP model allows simulation of aerosol number, size and concentrations of individual components such as sulphate,sea salt and different types of carbon.</p>
 <h3 id="how-is-glomap-used">How is GLOMAP used?</h3>
 <p>GLOMAP is used in ACCESS-CM2 and ACCESS-CM2-Chem.</p>
@@ -2466,11 +2466,11 @@ <h3 id="how-is-glomap-used">How is GLOMAP used?</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2584,7 +2584,7 @@ <h3 id="how-is-glomap-used">How is GLOMAP used?</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/atmosphere/index.html b/pr-preview/pr-396/models/model_components/atmosphere/index.html
index 4f2d9e82d..6822832ea 100644
--- a/pr-preview/pr-396/models/model_components/atmosphere/index.html
+++ b/pr-preview/pr-396/models/model_components/atmosphere/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -975,8 +973,9 @@
         Atmosphere
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -992,8 +991,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#the-unified-model-um" class="md-nav__link">
-     The Unified Model (UM)  
+  <a href="#the-unified-model-um-supported" class="md-nav__link">
+     The Unified Model (UM) {{ supported }} 
   </a>
   
 </li>
@@ -1281,7 +1280,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1360,7 +1359,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2335,8 +2334,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2352,8 +2352,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#the-unified-model-um" class="md-nav__link">
-     The Unified Model (UM)  
+  <a href="#the-unified-model-um-supported" class="md-nav__link">
+     The Unified Model (UM) {{ supported }} 
   </a>
   
 </li>
@@ -2411,7 +2411,7 @@ <h1 id="atmospheric-model-component"><div class="highlight-bg"> Atmospheric Mode
 <!-- ![Atmosphere Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon ATMOSPHERE.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/atmosphere-component-map.png" class="white-img-bg"></img></p>
-<h2 id="the-unified-model-um"><div class="center-icons"> The Unified Model (UM) <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="the-unified-model-um-supported"><div class="center-icons"> The Unified Model (UM) {{ supported }} </div></h2>
 <p><a href="https://www.metoffice.gov.uk/research/approach/modelling-systems/unified-model">The Unified Model (UM)</a> is a numerical model of the atmosphere used for both weather and climate applications, developed by the <a href="https://www.metoffice.gov.uk/research/approach/collaboration/unified-model/partnership">Met Office</a> in the United Kingdom (UK). It includes solutions of the equations of atmospheric fluid dynamics with advanced parameterizations of subgrid-scale physical processes like convection, cloud formation and atmospheric radiation.</p>
 <p>The Unified Model gets its name because a single model is used across a wide range of both timescales (nowcasting to centennial) and spatial scales (sub km convective scale to global climate modelling).</p>
 <p>The UM is used by several international operational meteorology and research organizations and these contribute towards its development through the UM partnership.</p>
@@ -2431,11 +2431,11 @@ <h2 id="useful-links">Useful links</h2>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2549,7 +2549,7 @@ <h2 id="useful-links">Useful links</h2>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/bgc_land/index.html b/pr-preview/pr-396/models/model_components/bgc_land/index.html
index a51373e0d..8f8388676 100644
--- a/pr-preview/pr-396/models/model_components/bgc_land/index.html
+++ b/pr-preview/pr-396/models/model_components/bgc_land/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1045,8 +1043,9 @@
         Biogeochemistry Land
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1062,11 +1061,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#casa-cnp" class="md-nav__link">
-     CASA-CNP  
+  <a href="#casa-cnp-supported" class="md-nav__link">
+     CASA-CNP {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" CASA-CNP  ">
+    <nav class="md-nav" aria-label=" CASA-CNP {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1280,7 +1279,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1303,7 +1302,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1317,7 +1316,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1331,7 +1330,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1345,7 +1344,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1359,7 +1358,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2334,8 +2333,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2351,11 +2351,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#casa-cnp" class="md-nav__link">
-     CASA-CNP  
+  <a href="#casa-cnp-supported" class="md-nav__link">
+     CASA-CNP {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" CASA-CNP  ">
+    <nav class="md-nav" aria-label=" CASA-CNP {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -2409,7 +2409,7 @@ <h1 id="biogeochemistry-land"><div class="highlight-bg"> Biogeochemistry Land </
 <!-- ![BGC Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon BGC LAND.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/bgc-land-component-map.png" class="white-img-bg"></img></p>
-<h2 id="casa-cnp"><div class="center-icons"> <a href="https://carbonwaterobservatory.csiro.au/casa.html">CASA-CNP</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="casa-cnp-supported"><div class="center-icons"> <a href="https://carbonwaterobservatory.csiro.au/casa.html">CASA-CNP</a> {{ supported }} </div></h2>
 <p>CASA (Carnegie-Ames-Stanford Approach)-CNP (Carbon-Nitrogen-Phosphorous) is the land biogeochemistry model developed in CABLE.</p>
 <p>CASA-CNP models the dynamics of carbon pools and nitrogen and phosphorous limitations. It is directly coupled with the CABLE land surface model.</p>
 <h3 id="how-is-casa-cnp-used">How is CASA-CNP used?</h3>
@@ -2420,11 +2420,11 @@ <h3 id="how-is-casa-cnp-used">How is CASA-CNP used?</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2538,7 +2538,7 @@ <h3 id="how-is-casa-cnp-used">How is CASA-CNP used?</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/bgc_ocean/index.html b/pr-preview/pr-396/models/model_components/bgc_ocean/index.html
index 79763e944..4ba1906db 100644
--- a/pr-preview/pr-396/models/model_components/bgc_ocean/index.html
+++ b/pr-preview/pr-396/models/model_components/bgc_ocean/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1059,8 +1057,9 @@
         Biogeochemistry Ocean
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1076,11 +1075,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#wombat" class="md-nav__link">
-     WOMBAT  
+  <a href="#wombat-supported" class="md-nav__link">
+     WOMBAT {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" WOMBAT  ">
+    <nav class="md-nav" aria-label=" WOMBAT {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1280,7 +1279,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1303,7 +1302,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1317,7 +1316,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1331,7 +1330,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1345,7 +1344,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1359,7 +1358,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2334,8 +2333,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2351,11 +2351,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#wombat" class="md-nav__link">
-     WOMBAT  
+  <a href="#wombat-supported" class="md-nav__link">
+     WOMBAT {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" WOMBAT  ">
+    <nav class="md-nav" aria-label=" WOMBAT {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -2409,7 +2409,7 @@ <h1 id="biogeochemistry-ocean"><div class="highlight-bg"> Biogeochemistry Ocean
 <!-- ![BGC Ocean Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon BGC OCEAN.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/bgc-ocean-component-map.png" class="white-img-bg"></img></p>
-<h2 id="wombat"><div class="center-icons"> WOMBAT <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="wombat-supported"><div class="center-icons"> WOMBAT {{ supported }} </div></h2>
 <p>WOMBAT is the ocean carbon model (World Ocean Model of Biogeochemistry And Trophic-dynamics), developed in Australia. It calculates the carbon fluxes of the ocean, by simulating the evolution of phosphate, oxygen, dissolved inorganic carbon, alkalinity and iron with one class of phytoplankton and zooplankton.</p>
 <p>WOMBAT is a Nutrient, Phytoplankton, Zooplankton and Detritus (NPZD) model, with one zooplankton and one phytoplankton class.</p>
 <h3 id="how-is-wombat-used">How is WOMBAT used?</h3>
@@ -2420,11 +2420,11 @@ <h3 id="how-is-wombat-used">How is WOMBAT used?</h3>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2538,7 +2538,7 @@ <h3 id="how-is-wombat-used">How is WOMBAT used?</h3>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/coupler/index.html b/pr-preview/pr-396/models/model_components/coupler/index.html
index d6b0c0508..bd55a2cd1 100644
--- a/pr-preview/pr-396/models/model_components/coupler/index.html
+++ b/pr-preview/pr-396/models/model_components/coupler/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -97,7 +95,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#coupler" class="md-skip">
+        <a href="#coupler-supported" class="md-skip">
           Skip to content
         </a>
       
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1073,8 +1071,9 @@
         Coupler
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1090,15 +1089,15 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#oasis3-mct" class="md-nav__link">
-     OASIS3-MCT  
+  <a href="#oasis3-mct-supported" class="md-nav__link">
+     OASIS3-MCT {{ supported }} 
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#nuopc-interoperability-layer" class="md-nav__link">
-     NUOPC Interoperability Layer  
+  <a href="#nuopc-interoperability-layer-recommended" class="md-nav__link">
+     NUOPC Interoperability Layer {{ recommended }} 
   </a>
   
 </li>
@@ -1274,7 +1273,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1297,7 +1296,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1311,7 +1310,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1325,7 +1324,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1339,7 +1338,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1353,7 +1352,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2328,8 +2327,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2345,15 +2345,15 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#oasis3-mct" class="md-nav__link">
-     OASIS3-MCT  
+  <a href="#oasis3-mct-supported" class="md-nav__link">
+     OASIS3-MCT {{ supported }} 
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#nuopc-interoperability-layer" class="md-nav__link">
-     NUOPC Interoperability Layer  
+  <a href="#nuopc-interoperability-layer-recommended" class="md-nav__link">
+     NUOPC Interoperability Layer {{ recommended }} 
   </a>
   
 </li>
@@ -2390,31 +2390,33 @@
   
 
 
-<h1 id="coupler"><div class="highlight-bg center-icons"> Coupler <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h1>
+<h1 id="coupler-supported"><div class="highlight-bg center-icons"> Coupler {{ supported }} </div></h1>
 <!-- ![Coupler Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon COUPLER.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/coupler-component-map.png" class="white-img-bg"></img></p>
-<p>A coupler is a software that allows synchronised exchanges of coupling information between numerical codes representing different components of the climate system.</p>
-<h2 id="oasis3-mct"><div class="center-icons"> <a href="https://oasis.cerfacs.fr/en/">OASIS3-MCT</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
-<p><a href="https://oasis.cerfacs.fr/en/">OASIS3-MCT</a> is the version of the Ocean Atmosphere Sea Ice Soil (OASIS) coupler interfaced with the Model Coupling Toolkit (MCT) from the Argonne National Laboratory. OASIS3-MCT is the coupler used in the configurations:
-- ACCESS-ESM1.5
-- ACCESS-CM2 
-- ACCESS-OM2
-- ACCESS-S</p>
-<h2 id="nuopc-interoperability-layer"><div class="center-icons"> <a href="https://earthsystemmodeling.org/nuopc/">NUOPC Interoperability Layer</a> <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> </div></h2>
+<p>A coupler is a software package that allows synchronised exchanges of coupling information between numerical codes representing different components of the climate system.</p>
+<h2 id="oasis3-mct-supported"><div class="center-icons"> <a href="https://oasis.cerfacs.fr/en/">OASIS3-MCT</a> {{ supported }} </div></h2>
+<p><a href="https://oasis.cerfacs.fr/en/">OASIS3-MCT</a> is the version of the Ocean Atmosphere Sea Ice Soil (OASIS) coupler interfaced with the Model Coupling Toolkit (MCT) from the Argonne National Laboratory. OASIS3-MCT is the coupler used in the configurations:</p>
+<ul>
+<li>ACCESS-ESM1.5</li>
+<li>ACCESS-CM2 </li>
+<li>ACCESS-OM2</li>
+<li>ACCESS-S</li>
+</ul>
+<h2 id="nuopc-interoperability-layer-recommended"><div class="center-icons"> <a href="https://earthsystemmodeling.org/nuopc/">NUOPC Interoperability Layer</a> {{ recommended }} </div></h2>
 <p><a href="https://earthsystemmodeling.org/nuopc/">NUOPC</a> (National Unified Operational Prediction Capability) Interoperability Layer defines conventions and a set of generic components for building coupled models using the Earth System Modeling Framework (ESMF).</p>
-<p>ACCESS-OM3, a configuration currently under development, uses NUOPC to couple its MOM6 and CICE6 model components as there are no respective OASIS coupling interfaces for these components.</p>
+<p>ACCESS-OM3, a configuration currently under development, uses <a href="https://github.com/COSIMA/access-om3/discussions/7">NUOPC to couple its MOM6 and CICE6 model components</a> as there are no respective OASIS coupling interfaces for these components.</p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2528,7 +2530,7 @@ <h2 id="nuopc-interoperability-layer"><div class="center-icons"> <a href="https:
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/index.html b/pr-preview/pr-396/models/model_components/index.html
index a60d84362..6ad26de16 100644
--- a/pr-preview/pr-396/models/model_components/index.html
+++ b/pr-preview/pr-396/models/model_components/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../running-a-model/" class="md-tabs__link">
+      <a href="../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1224,7 +1222,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../running-a-model/">Run a Model</a>
+          <a href="../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1247,7 +1245,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1261,7 +1259,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1275,7 +1273,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1289,7 +1287,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1303,7 +1301,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2278,8 +2276,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2392,11 +2391,11 @@ <h1 id="model-components"><div class="highlight-bg"> Model Components </div></h1
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2510,7 +2509,7 @@ <h1 id="model-components"><div class="highlight-bg"> Model Components </div></h1
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/land/index.html b/pr-preview/pr-396/models/model_components/land/index.html
index e49712a84..4200ed306 100644
--- a/pr-preview/pr-396/models/model_components/land/index.html
+++ b/pr-preview/pr-396/models/model_components/land/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -989,8 +987,9 @@
         Land
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1006,11 +1005,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#cable" class="md-nav__link">
-     CABLE  
+  <a href="#cable-supported" class="md-nav__link">
+     CABLE {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" CABLE  ">
+    <nav class="md-nav" aria-label=" CABLE {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -1026,8 +1025,8 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#jules" class="md-nav__link">
-     JULES  
+  <a href="#jules-supported" class="md-nav__link">
+     JULES {{ supported }} 
   </a>
   
 </li>
@@ -1287,7 +1286,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1310,7 +1309,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1324,7 +1323,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1338,7 +1337,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1352,7 +1351,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1366,7 +1365,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2341,8 +2340,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2358,11 +2358,11 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#cable" class="md-nav__link">
-     CABLE  
+  <a href="#cable-supported" class="md-nav__link">
+     CABLE {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" CABLE  ">
+    <nav class="md-nav" aria-label=" CABLE {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
@@ -2378,8 +2378,8 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#jules" class="md-nav__link">
-     JULES  
+  <a href="#jules-supported" class="md-nav__link">
+     JULES {{ supported }} 
   </a>
   
 </li>
@@ -2423,12 +2423,12 @@ <h1 id="land-model-components"><div class="highlight-bg"> Land Model Components
 <!-- ![Land Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon LAND SURFACE.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/land-component-map.png" class="white-img-bg"></img></p>
-<h2 id="cable"><div class="center-icons"> <a href="https://trac.nci.org.au/trac/cable/wiki">CABLE</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="cable-supported"><div class="center-icons"> <a href="https://trac.nci.org.au/trac/cable/wiki">CABLE</a> {{ supported }} </div></h2>
 <p><a href="https://www.cawcr.gov.au/research/cable/">Community Atmosphere Biosphere Land Exchange (CABLE)</a> is a land surface model, used to calculate the fluxes of momentum, energy, water and carbon between the land surface and the atmosphere. It also models the main biogeochemical cycles of the land ecosystem when used in conjunction with <a href="../bgc_land/#casa-cnp">the CASA-CNP module</a>. </p>
 <h3 id="how-is-cable-used">How is CABLE used?</h3>
 <p>CABLE can be run as a standalone model, for a single location, a region or globally. Coupled to the Met Office <a href="um-web">Unified Model (UM)</a>, CABLE provides the land surface component of the ACCESS Earth System Model (ACCESS-ESM) and ACCESS Coupled Model (ACCESS-CM).</p>
 <p>CABLE is an open source model developed by a community of Australian climate science researchers. <a href="https://trac.nci.org.au/trac/cable/wiki">Registration</a> is required to access the CABLE code repository.</p>
-<h2 id="jules"><div class="center-icons"> <a href="https://jules.jchmr.org/">JULES</a> <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="jules-supported"><div class="center-icons"> <a href="https://jules.jchmr.org/">JULES</a> {{ supported }} </div></h2>
 <p>The <a href="jules-web">Joint UK Land Environment System (JULES)</a> is a community land surface model that can be used both as a standalone model and as the land surface component in the UM model. By modelling different land surface processes (surface energy balance, hydrological cycle, carbon cycle, dynamic vegetation, etc.) and their interaction with each other, JULES provides a framework to assess the impact of modifying a particular process on the ecosystem as a whole, e.g., the impact of climate change on hydrology.</p>
 <!---
 Some of the ACCESS models used for weather simulations use JULES instead of CABLE. For example, the Bureau of Meteorology (BoM) uses the JULES land surface scheme in its numerical weather prediction models such as ACCESS S (Seasonal) and C (City).
@@ -2439,11 +2439,11 @@ <h2 id="jules"><div class="center-icons"> <a href="https://jules.jchmr.org/">JUL
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2557,7 +2557,7 @@ <h2 id="jules"><div class="center-icons"> <a href="https://jules.jchmr.org/">JUL
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/ocean/index.html b/pr-preview/pr-396/models/model_components/ocean/index.html
index 8d2d4675e..68bb38041 100644
--- a/pr-preview/pr-396/models/model_components/ocean/index.html
+++ b/pr-preview/pr-396/models/model_components/ocean/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1003,8 +1001,9 @@
         Ocean
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1020,23 +1019,23 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#modular-ocean-model-mom" class="md-nav__link">
-     Modular Ocean Model (MOM)   
+  <a href="#modular-ocean-model-mom-supported" class="md-nav__link">
+     Modular Ocean Model (MOM)  {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" Modular Ocean Model (MOM)   ">
+    <nav class="md-nav" aria-label=" Modular Ocean Model (MOM)  {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#mom5" class="md-nav__link">
-     MOM5  
+  <a href="#mom5-supported" class="md-nav__link">
+     MOM5 {{ supported }} 
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#mom6" class="md-nav__link">
-     MOM6  
+  <a href="#mom6-recommended" class="md-nav__link">
+     MOM6 {{ recommended }} 
   </a>
   
 </li>
@@ -1287,7 +1286,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1310,7 +1309,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1324,7 +1323,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1338,7 +1337,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1352,7 +1351,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1366,7 +1365,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2341,8 +2340,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2358,23 +2358,23 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#modular-ocean-model-mom" class="md-nav__link">
-     Modular Ocean Model (MOM)   
+  <a href="#modular-ocean-model-mom-supported" class="md-nav__link">
+     Modular Ocean Model (MOM)  {{ supported }} 
   </a>
   
-    <nav class="md-nav" aria-label=" Modular Ocean Model (MOM)   ">
+    <nav class="md-nav" aria-label=" Modular Ocean Model (MOM)  {{ supported }} ">
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#mom5" class="md-nav__link">
-     MOM5  
+  <a href="#mom5-supported" class="md-nav__link">
+     MOM5 {{ supported }} 
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#mom6" class="md-nav__link">
-     MOM6  
+  <a href="#mom6-recommended" class="md-nav__link">
+     MOM6 {{ recommended }} 
   </a>
   
 </li>
@@ -2423,12 +2423,12 @@ <h1 id="ocean-model-component"><div class="highlight-bg"> Ocean Model Component
 <!-- ![Ocean Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon OCEAN.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/ocean-component-map.png" class="white-img-bg"></img></p>
-<h2 id="modular-ocean-model-mom"><div class="center-icons"> <a href="https://mom-ocean.github.io/">Modular Ocean Model (MOM)</a>  <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="modular-ocean-model-mom-supported"><div class="center-icons"> <a href="https://mom-ocean.github.io/">Modular Ocean Model (MOM)</a>  {{ supported }} </div></h2>
 <p>The <a href="https://mom-ocean.github.io/">Modular Ocean Model (MOM)</a> is one of the ocean components of the ACCESS climate model system. Used to simulate ocean currents at both regional and global scales, MOM is an invaluable tool for studying the global ocean climate system, as well as capabilities for regional and coastal applications. </p>
-<h3 id="mom5"><div class="center-icons"> MOM5 <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h3>
+<h3 id="mom5-supported"><div class="center-icons"> MOM5 {{ supported }} </div></h3>
 <p><a href="https://github.com/mom-ocean/MOM5"><strong>Source Code</strong></a></p>
 <p>MOM5 is used in supported climate ACCESS configurations.</p>
-<h3 id="mom6"><div class="center-icons"> MOM6 <a href="https://access-hive.org.au/about/support"><span class="icon-recommended center-icons"><i class="fa fa-star" title="Recommended by ACCESS-NRI"></i></span></a> </div></h3>
+<h3 id="mom6-recommended"><div class="center-icons"> MOM6 {{ recommended }} </div></h3>
 <p><a href="https://github.com/mom-ocean/MOM6"><strong>Source Code</strong></a> |
 <a href="https://github.com/NOAA-GFDL/MOM6-examples/wiki/Tutorials"><strong>Tutorials</strong></a></p>
 <p>The most recent version, <a href="https://www.gfdl.noaa.gov/mom-ocean-model/">MOM6</a>, is an open source development by a consortium of scientists across several government agencies and academic institutions with critical contributions provided by researchers worldwide.</p>
@@ -2438,11 +2438,11 @@ <h3 id="mom6"><div class="center-icons"> MOM6 <a href="https://access-hive.org.a
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2556,7 +2556,7 @@ <h3 id="mom6"><div class="center-icons"> MOM6 <a href="https://access-hive.org.a
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/model_components/sea-ice/index.html b/pr-preview/pr-396/models/model_components/sea-ice/index.html
index f2fafe41c..33e2eafed 100644
--- a/pr-preview/pr-396/models/model_components/sea-ice/index.html
+++ b/pr-preview/pr-396/models/model_components/sea-ice/index.html
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -358,7 +356,7 @@
   <!-- Recurse, if the first item has further nested items -->
   
   <li class="md-tabs__item">
-      <a href="../../running-a-model/" class="md-tabs__link">
+      <a href="../../run-a-model/" class="md-tabs__link">
         Run a Model
       </a>
     </li>
@@ -1017,8 +1015,9 @@
         Sea Ice
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1034,8 +1033,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#cice" class="md-nav__link">
-     CICE  
+  <a href="#cice-supported" class="md-nav__link">
+     CICE {{ supported }} 
   </a>
   
 </li>
@@ -1267,7 +1266,7 @@
         
         
         <div class="md-nav__link md-nav__link--index ">
-          <a href="../../running-a-model/">Run a Model</a>
+          <a href="../../run-a-model/">Run a Model</a>
           
             <label for="__nav_3">
               <span class="md-nav__icon md-icon"></span>
@@ -1290,7 +1289,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
+      <a href="../../run-a-model/getting_started/access_to_gadi_at_nci/" class="md-nav__link">
         Computing Access (Gadi@NCI)
       </a>
     </li>
@@ -1304,7 +1303,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-esm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1318,7 +1317,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-cm/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1332,7 +1331,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-am/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1346,7 +1345,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-a-model/running-access-om/" class="md-nav__link">
+      <a href="../../run-a-model/run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2321,8 +2320,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2338,8 +2338,8 @@
       <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
         
           <li class="md-nav__item">
-  <a href="#cice" class="md-nav__link">
-     CICE  
+  <a href="#cice-supported" class="md-nav__link">
+     CICE {{ supported }} 
   </a>
   
 </li>
@@ -2383,7 +2383,7 @@ <h1 id="sea-ice-model-component"><div class="highlight-bg"> Sea-Ice Model Compon
 <!-- ![Sea-Ice Component Logo](../../assets/component-logos/components-without-titles/ACCESS icon SEA ICE.png){align=right width=40%} -->
 
 <p><img src = "../../../assets/component-logos/component-maps/sea-ice-component-map.png" class="white-img-bg"></img></p>
-<h2 id="cice"><div class="center-icons"> CICE <a href="https://access-hive.org.au/about/support"><span class="icon-supported center-icons"><i class="fa fa-check" title="Supported by ACCESS-NRI"></i></span></a> </div></h2>
+<h2 id="cice-supported"><div class="center-icons"> CICE {{ supported }} </div></h2>
 <p>CICE is a numerical model for simulating the growth, melting and movement of polar sea ice. This software package was developed by researchers at <a href="https://www.lanl.gov/">Los Alamos National Laboratory team</a> and is currently managed by the <a href="https://github.com/CICE-Consortium/About-Us/wiki">CICE Consortium</a>, an international group of institutions formed to maintain and develop CICE in the public domain.</p>
 <p><a href="https://github.com/CICE-Consortium/CICE-svn-trunk/wiki">CICE5</a> is the current version used in ACCESS model configurations.</p>
 <p><a href="https://github.com/CICE-Consortium/CICE/wiki">CICE6</a> is currently under development.</p>
@@ -2393,11 +2393,11 @@ <h2 id="cice"><div class="center-icons"> CICE <a href="https://access-hive.org.a
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2511,7 +2511,7 @@ <h2 id="cice"><div class="center-icons"> CICE <a href="https://access-hive.org.a
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/getting_started/access_to_gadi_at_nci/index.html b/pr-preview/pr-396/models/run-a-model/getting_started/access_to_gadi_at_nci/index.html
similarity index 98%
rename from pr-preview/pr-396/models/running-a-model/getting_started/access_to_gadi_at_nci/index.html
rename to pr-preview/pr-396/models/run-a-model/getting_started/access_to_gadi_at_nci/index.html
index b981dadf7..4b2c4f36d 100644
--- a/pr-preview/pr-396/models/running-a-model/getting_started/access_to_gadi_at_nci/index.html
+++ b/pr-preview/pr-396/models/run-a-model/getting_started/access_to_gadi_at_nci/index.html
@@ -8,13 +8,13 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/getting_started/access_to_gadi_at_nci/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/getting_started/access_to_gadi_at_nci/">
       
       
         <link rel="prev" href="../../">
       
       
-        <link rel="next" href="../../running-access-esm/">
+        <link rel="next" href="../../run-access-esm/">
       
       <link rel="icon" href="../../../../assets/ACCESS_icon_HIVE.png">
       <meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.8">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -1265,8 +1263,9 @@
         Computing Access (Gadi@NCI)
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1365,7 +1364,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-access-esm/" class="md-nav__link">
+      <a href="../../run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1379,7 +1378,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-access-cm/" class="md-nav__link">
+      <a href="../../run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1393,7 +1392,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-access-am/" class="md-nav__link">
+      <a href="../../run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1407,7 +1406,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../running-access-om/" class="md-nav__link">
+      <a href="../../run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2384,8 +2383,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" hidden>
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2484,7 +2484,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/getting_started/access_to_gadi_at_nci.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/getting_started/access_to_gadi_at_nci.md" title="Edit this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25Z"/></svg>
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@@ -2493,7 +2493,7 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/getting_started/access_to_gadi_at_nci.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/getting_started/access_to_gadi_at_nci.md" title="View source of this page" class="md-content__button md-icon">
       
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     </a>
@@ -2726,11 +2726,11 @@ <h4 id="pbs-jobs">PBS Jobs</h4>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2846,7 +2846,7 @@ <h4 id="pbs-jobs">PBS Jobs</h4>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../../js/termynal.js"></script>
+        <script src="../../../../js/terminal_animation.js"></script>
       
         <script src="../../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/getting_started/index.html b/pr-preview/pr-396/models/run-a-model/getting_started/index.html
similarity index 98%
rename from pr-preview/pr-396/models/running-a-model/getting_started/index.html
rename to pr-preview/pr-396/models/run-a-model/getting_started/index.html
index 07dc9a469..4cb15c31b 100644
--- a/pr-preview/pr-396/models/running-a-model/getting_started/index.html
+++ b/pr-preview/pr-396/models/run-a-model/getting_started/index.html
@@ -8,7 +8,7 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/getting_started/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/getting_started/">
       
       
       
@@ -40,8 +40,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -1250,7 +1248,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-esm/" class="md-nav__link">
+      <a href="../run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1264,7 +1262,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-cm/" class="md-nav__link">
+      <a href="../run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1278,7 +1276,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-am/" class="md-nav__link">
+      <a href="../run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1292,7 +1290,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-om/" class="md-nav__link">
+      <a href="../run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2267,8 +2265,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2291,7 +2290,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/getting_started/index.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/getting_started/index.md" title="Edit this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25Z"/></svg>
     </a>
@@ -2300,7 +2299,7 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/getting_started/index.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/getting_started/index.md" title="View source of this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0 8a5 5 0 0 1-5-5 5 5 0 0 1 5-5 5 5 0 0 1 5 5 5 5 0 0 1-5 5m0-12.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5Z"/></svg>
     </a>
@@ -2311,21 +2310,21 @@ <h1 id="getting-started-to-run-a-model"><div class="highlight-bg"> Getting Start
 <p>If <em>Model</em>, <em>Model Component</em> or <em>Model Configuration</em> are not familiar terms for you, please check out our <a href="../">Model overview</a>.</p>
 <p>If you have not run a model before, our <a href="access_to_gadi_at_nci/">Getting Started Guide</a> will give you the basics to access the Model infrastructure on the high-performance-computing facility Gadi@NCI.</p>
 <p>Detailed guides for the different Model configurations can then be found on the following pages:<br />
--  <a href="../running-access-esm/">Run ACCESS-ESM</a> for the ACCESS Earth System Model configurations<br />
--  <a href="../running-access-cm/">Run ACCESS-CM</a> for the ACCESS Coupled Model configurations<br />
--  <a href="../running-access-am/">Run ACCESS-AM</a> for the ACCESS Atmosphere Model configurations<br />
--  <a href="../running-access-om/">Run ACCESS-OM</a> for the ACCESS Ocean Model configurations  </p>
+-  <a href="../running-access-esm.md">Run ACCESS-ESM</a> for the ACCESS Earth System Model configurations<br />
+-  <a href="../running-access-cm.md">Run ACCESS-CM</a> for the ACCESS Coupled Model configurations<br />
+-  <a href="../running-access-am.md">Run ACCESS-AM</a> for the ACCESS Atmosphere Model configurations<br />
+-  <a href="../running-access-om.md">Run ACCESS-OM</a> for the ACCESS Ocean Model configurations  </p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2439,7 +2438,7 @@ <h1 id="getting-started-to-run-a-model"><div class="highlight-bg"> Getting Start
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/index.html b/pr-preview/pr-396/models/run-a-model/index.html
similarity index 98%
rename from pr-preview/pr-396/models/running-a-model/index.html
rename to pr-preview/pr-396/models/run-a-model/index.html
index 52ca848a6..26b20500e 100644
--- a/pr-preview/pr-396/models/running-a-model/index.html
+++ b/pr-preview/pr-396/models/run-a-model/index.html
@@ -8,7 +8,7 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/">
       
       
         <link rel="prev" href="../configurations/access-om/">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -1259,7 +1257,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-access-esm/" class="md-nav__link">
+      <a href="run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1273,7 +1271,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-access-cm/" class="md-nav__link">
+      <a href="run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1287,7 +1285,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-access-am/" class="md-nav__link">
+      <a href="run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1301,7 +1299,7 @@
   
   
     <li class="md-nav__item">
-      <a href="running-access-om/" class="md-nav__link">
+      <a href="run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2276,8 +2274,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2300,7 +2299,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/index.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/index.md" title="Edit this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25Z"/></svg>
     </a>
@@ -2309,7 +2308,7 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/index.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/index.md" title="View source of this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0 8a5 5 0 0 1-5-5 5 5 0 0 1 5-5 5 5 0 0 1 5 5 5 5 0 0 1-5 5m0-12.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5Z"/></svg>
     </a>
@@ -2321,21 +2320,21 @@ <h1 id="running-a-model">Running a Model</h1>
 <p>If <em>Model</em>, <em>Model Component</em> or <em>Model Configuration</em> are not familiar terms for you, please check out our <a href="../">Model overview</a>.</p>
 <p>If you have not run a model before, our <a href="getting_started/access_to_gadi_at_nci/">Getting Started Guide</a> will give you the basics to access the Model infrastructure on the high-performance-computing facility Gadi@NCI.</p>
 <p>Detailed guides for the different Model configurations can then be found on the following pages:<br />
--  <a href="running-access-esm/">Run ACCESS-ESM</a> for the ACCESS Earth System Model configurations<br />
--  <a href="running-access-cm/">Run ACCESS-CM</a> for the ACCESS Coupled Model configurations<br />
--  <a href="running-access-am/">Run ACCESS-AM</a> for the ACCESS Atmosphere Model configurations<br />
--  <a href="running-access-om/">Run ACCESS-OM</a> for the ACCESS Ocean Model configurations  </p>
+-  <a href="./running-access-esm.md">Run ACCESS-ESM</a> for the ACCESS Earth System Model configurations<br />
+-  <a href="./running-access-cm.md">Run ACCESS-CM</a> for the ACCESS Coupled Model configurations<br />
+-  <a href="./running-access-am.md">Run ACCESS-AM</a> for the ACCESS Atmosphere Model configurations<br />
+-  <a href="./running-access-om.md">Run ACCESS-OM</a> for the ACCESS Ocean Model configurations  </p>
 
   <hr>
 <div class="md-source-file">
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2449,7 +2448,7 @@ <h1 id="running-a-model">Running a Model</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../js/termynal.js"></script>
+        <script src="../../js/terminal_animation.js"></script>
       
         <script src="../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/running-access-am/index.html b/pr-preview/pr-396/models/run-a-model/run-access-am/index.html
similarity index 98%
rename from pr-preview/pr-396/models/running-a-model/running-access-am/index.html
rename to pr-preview/pr-396/models/run-a-model/run-access-am/index.html
index fa7b9ef6b..eee0107de 100644
--- a/pr-preview/pr-396/models/running-a-model/running-access-am/index.html
+++ b/pr-preview/pr-396/models/run-a-model/run-access-am/index.html
@@ -8,13 +8,13 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/running-access-am/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/run-access-am/">
       
       
-        <link rel="prev" href="../running-access-cm/">
+        <link rel="prev" href="../run-access-cm/">
       
       
-        <link rel="next" href="../running-access-om/">
+        <link rel="next" href="../run-access-om/">
       
       <link rel="icon" href="../../../assets/ACCESS_icon_HIVE.png">
       <meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.8">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -1254,7 +1252,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-esm/" class="md-nav__link">
+      <a href="../run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1268,7 +1266,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-cm/" class="md-nav__link">
+      <a href="../run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1304,7 +1302,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-om/" class="md-nav__link">
+      <a href="../run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2279,8 +2277,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2301,7 +2300,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/running-access-am.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/run-access-am.md" title="Edit this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25Z"/></svg>
     </a>
@@ -2310,7 +2309,7 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/running-access-am.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/run-access-am.md" title="View source of this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0 8a5 5 0 0 1-5-5 5 5 0 0 1 5-5 5 5 0 0 1 5 5 5 5 0 0 1-5 5m0-12.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5Z"/></svg>
     </a>
@@ -2326,11 +2325,11 @@ <h1>Run ACCESS-AM</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2444,7 +2443,7 @@ <h1>Run ACCESS-AM</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/running-access-cm/index.html b/pr-preview/pr-396/models/run-a-model/run-access-cm/index.html
similarity index 98%
rename from pr-preview/pr-396/models/running-a-model/running-access-cm/index.html
rename to pr-preview/pr-396/models/run-a-model/run-access-cm/index.html
index 938d38be4..aec78c78b 100644
--- a/pr-preview/pr-396/models/running-a-model/running-access-cm/index.html
+++ b/pr-preview/pr-396/models/run-a-model/run-access-cm/index.html
@@ -8,13 +8,13 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/running-access-cm/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/run-access-cm/">
       
       
-        <link rel="prev" href="../running-access-esm/">
+        <link rel="prev" href="../run-access-esm/">
       
       
-        <link rel="next" href="../running-access-am/">
+        <link rel="next" href="../run-access-am/">
       
       <link rel="icon" href="../../../assets/ACCESS_icon_HIVE.png">
       <meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.8">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -1259,7 +1257,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-esm/" class="md-nav__link">
+      <a href="../run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1291,8 +1289,9 @@
         Run ACCESS-CM
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -1390,7 +1389,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-am/" class="md-nav__link">
+      <a href="../run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1404,7 +1403,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-om/" class="md-nav__link">
+      <a href="../run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2379,8 +2378,9 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
@@ -2478,7 +2478,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/running-access-cm.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/run-access-cm.md" title="Edit this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25Z"/></svg>
     </a>
@@ -2487,7 +2487,7 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/running-access-cm.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/run-access-cm.md" title="View source of this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0 8a5 5 0 0 1-5-5 5 5 0 0 1 5-5 5 5 0 0 1 5 5 5 5 0 0 1-5 5m0-12.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5Z"/></svg>
     </a>
@@ -2504,7 +2504,7 @@ <h2 id="getting-started"><strong>Getting Started</strong></h2>
 <li>A Linux/Mac/Unix computer with an internet connection and a command line terminal (e.g., MacOS with XQuartz and command line tools installed, or Putty Cygwin/MobaXterm/similar X-Windows compatible program on a PC). </li>
 </ul>
 <h3 id="requirements-for-running-access-cm-suites">Requirements for running ACCESS-CM suites</h3>
-<p>Here, we assume that you already have access to Gadi, the supercomputer hosted by the National Computational Infrastructure (NCI). If needed, you can go back to our guide on how to get <a href="../getting_started/access_to_gadi_at_nci/">access to Gadi</a>.</p>
+<p>Here, we assume that you already have access to Gadi, the supercomputer hosted by the National Computational Infrastructure (NCI). If needed, you can go back to our guide on how to get <a href="../running-a-model/getting_started/access_to_gadi_at_nci.md">access to Gadi</a>.</p>
 <h4 id="basic-setup">Basic Setup</h4>
 <p>To run an ACCESS-CM suite, new users will need to:</p>
 <ul>
@@ -2531,7 +2531,7 @@ <h4 id="logging-in-to-gadi-and-accessdev">Logging in to Gadi and accessdev</h4>
 <hr />
 <h1 id="copy-edit-and-run-an-access-cm2-suite">Copy, Edit, and Run an ACCESS-CM2 suite</h1>
 <div style="text-align: justify">
-ACCESS-CM2 is a set of sub-models (eg. UM, MOM, CICE, CABLE, OASIS) with a range of model parameters, input data, and computer related information, that need to be packaged together as a <i>suite</i> in order to run.
+ACCESS-CM2 is a set of submodels (eg. UM, MOM, CICE, CABLE, OASIS) with a range of model parameters, input data, and computer related information, that need to be packaged together as a <i>suite</i> in order to run.
 <br>
 Each ACCESS-CM2 suite has an ID, in the format <code>u-&lt;suite-name&gt;</code>, with <code>&lt;suite-name&gt;</code> being a unique identifier (e.g. <code>u-br565</code> is the CMIP6 release preindustrial experiment suite).
 <br>
@@ -2659,11 +2659,11 @@ <h2 id="run-an-access-cm2-suite">Run an ACCESS-CM2 suite</h2>
 <br>
 ACCESS-CM2 suites run on <a href="https://opus.nci.org.au/display/Help/0.+Welcome+to+Gadi#id-0.WelcometoGadi-Overview" target="_blank">Gadi</a> through a PBS job submission.
 <br>
-When the suite gets run, the suite configuration files are copied on Gadi under <code>/scratch/&lt;$PROJECT&gt;/$USER/cylc-run/&lt;suite-ID&gt;</code>, and a symbolic link to this folder is also created in the <code>$USER</code>'s home directory under <code>~/cylc-run/&lt;suite-ID&gt;</code>.
+When the suite gets run, its configuration files are copied on Gadi under <code>/scratch/$PROJECT/$USER/cylc-run/&lt;suite-ID&gt;</code>, and a symbolic link to this folder is also created in the <code>$USER</code>'s home directory under <code>~/cylc-run/&lt;suite-ID&gt;</code>.
 <br>
 An ACCESS-CM2 suite is constituted by several tasks (such as checking out code repositories, compiling and building the different model components, running the model, etc.). The workflow of these tasks is controlled by Cylc.
 <br>
-<a href="https://cylc.github.io/cylc-doc/7.8.8/html/index.html" target="_blank">Cylc</a> (pronounced ‘silk’), is a workflow manager that automatically executes tasks according to the model main cycle script <code>suite.rc</code>. Cylc deals with how the job will be run and manages the time steps of each sub-model, as well as monitoring all the tasks and reporting any error that might occur.
+<a href="https://cylc.github.io/cylc-doc/7.8.8/html/index.html" target="_blank">Cylc</a> (pronounced ‘silk’), is a workflow manager that automatically executes tasks according to the model main cycle script <code>suite.rc</code>. Cylc deals with how the job will be run and manages the time steps of each submodel, as well as monitoring all the tasks and reporting any error that might occur.
 <br>
 To run an ACCESS-CM2 suite, on <i>accessdev</i>:
 <ol>
@@ -2950,7 +2950,7 @@ <h2 id="suite-output-files">Suite output files</h2>
 <!-- References -->
 <p><br></p>
 <h6>References</h6>
-<ul style="font-size:0.8em;">
+<ul class="references">
     <li>
         <a href = "https://confluence.csiro.au/display/ACCESS/Using+CM2+suites+in+Rose+and+Cylc" target="_blank">https://confluence.csiro.au/display/ACCESS/Using+CM2+suites+in+Rose+and+Cylc</a>
     </li>
@@ -2970,11 +2970,11 @@ <h6>References</h6>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -3088,7 +3088,7 @@ <h6>References</h6>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/running-access-esm/index.html b/pr-preview/pr-396/models/run-a-model/run-access-esm/index.html
similarity index 64%
rename from pr-preview/pr-396/models/running-a-model/running-access-esm/index.html
rename to pr-preview/pr-396/models/run-a-model/run-access-esm/index.html
index 5d399e409..8075fadc6 100644
--- a/pr-preview/pr-396/models/running-a-model/running-access-esm/index.html
+++ b/pr-preview/pr-396/models/run-a-model/run-access-esm/index.html
@@ -8,13 +8,13 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/running-access-esm/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/run-access-esm/">
       
       
         <link rel="prev" href="../getting_started/access_to_gadi_at_nci/">
       
       
-        <link rel="next" href="../running-access-cm/">
+        <link rel="next" href="../run-access-cm/">
       
       <link rel="icon" href="../../../assets/ACCESS_icon_HIVE.png">
       <meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.8">
@@ -44,8 +44,6 @@
       
     
     
-      <link rel="stylesheet" href="../../../css/termynal.css">
-    
       <link rel="stylesheet" href="../../../css/fontello.css">
     
       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -96,6 +94,11 @@
     <label class="md-overlay" for="__drawer"></label>
     <div data-md-component="skip">
       
+        
+        <a href="#run-access-esm" class="md-skip">
+          Skip to content
+        </a>
+      
     </div>
     <div data-md-component="announce">
       
@@ -1260,11 +1263,169 @@
       <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
       
       
+        
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          Run ACCESS-ESM
+          <span class="md-nav__icon md-icon"></span>
+        </label>
       
       <a href="./" class="md-nav__link md-nav__link--active">
         Run ACCESS-ESM
       </a>
       
+        
+  
+    
+  
+  <nav class="md-nav md-nav--secondary" aria-label="On this page">
+    
+    
+    
+      
+    
+    
+      <label class="md-nav__title" for="__toc">
+        <span class="md-nav__icon md-icon"></span>
+        On this page
+      </label>
+      <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+        
+          <li class="md-nav__item">
+  <a href="#requirements" class="md-nav__link">
+    Requirements
+  </a>
+  
+    <nav class="md-nav" aria-label="Requirements">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#general-requirements" class="md-nav__link">
+    General requirements
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#model-specific-requirements" class="md-nav__link">
+    Model-specific requirements
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#get-access-esm-configuration" class="md-nav__link">
+    Get ACCESS-ESM configuration
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#edit-access-esm-configuration" class="md-nav__link">
+    Edit ACCESS-ESM configuration
+  </a>
+  
+    <nav class="md-nav" aria-label="Edit ACCESS-ESM configuration">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#payu" class="md-nav__link">
+    Payu
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#edit-the-master-configuration-file" class="md-nav__link">
+    Edit the Master Configuration file
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#run-access-esm-configuration" class="md-nav__link">
+    Run ACCESS-ESM configuration
+  </a>
+  
+    <nav class="md-nav" aria-label="Run ACCESS-ESM configuration">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#payu-setup-optional" class="md-nav__link">
+    Payu setup (optional)
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#run-configuration" class="md-nav__link">
+    Run configuration
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#run-configuration-for-multiple-years" class="md-nav__link">
+    Run configuration for multiple years
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#understand-runtime-runspersub-and-n-parameters" class="md-nav__link">
+    Understand runtime, runspersub, and -n parameters
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#monitor-runs" class="md-nav__link">
+    Monitor runs
+  </a>
+  
+    <nav class="md-nav" aria-label="Monitor runs">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#check-the-output-and-error-log-files" class="md-nav__link">
+    Check the output and error log files
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#model-outputs" class="md-nav__link">
+    Model outputs
+  </a>
+  
+</li>
+        
+      </ul>
+    
+  </nav>
+  
+      
     </li>
   
 
@@ -1276,7 +1437,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-cm/" class="md-nav__link">
+      <a href="../run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
       </a>
     </li>
@@ -1290,7 +1451,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-am/" class="md-nav__link">
+      <a href="../run-access-am/" class="md-nav__link">
         Run ACCESS-AM
       </a>
     </li>
@@ -1304,7 +1465,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-om/" class="md-nav__link">
+      <a href="../run-access-om/" class="md-nav__link">
         Run ACCESS-OM
       </a>
     </li>
@@ -2279,13 +2440,153 @@
               <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
     
     
+      
+    
+    
+      <label class="md-nav__title" for="__toc">
+        <span class="md-nav__icon md-icon"></span>
+        On this page
+      </label>
+      <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+        
+          <li class="md-nav__item">
+  <a href="#requirements" class="md-nav__link">
+    Requirements
+  </a>
+  
+    <nav class="md-nav" aria-label="Requirements">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#general-requirements" class="md-nav__link">
+    General requirements
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#model-specific-requirements" class="md-nav__link">
+    Model-specific requirements
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#get-access-esm-configuration" class="md-nav__link">
+    Get ACCESS-ESM configuration
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#edit-access-esm-configuration" class="md-nav__link">
+    Edit ACCESS-ESM configuration
+  </a>
+  
+    <nav class="md-nav" aria-label="Edit ACCESS-ESM configuration">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#payu" class="md-nav__link">
+    Payu
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#edit-the-master-configuration-file" class="md-nav__link">
+    Edit the Master Configuration file
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#run-access-esm-configuration" class="md-nav__link">
+    Run ACCESS-ESM configuration
+  </a>
+  
+    <nav class="md-nav" aria-label="Run ACCESS-ESM configuration">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#payu-setup-optional" class="md-nav__link">
+    Payu setup (optional)
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#run-configuration" class="md-nav__link">
+    Run configuration
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#run-configuration-for-multiple-years" class="md-nav__link">
+    Run configuration for multiple years
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#understand-runtime-runspersub-and-n-parameters" class="md-nav__link">
+    Understand runtime, runspersub, and -n parameters
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#monitor-runs" class="md-nav__link">
+    Monitor runs
+  </a>
+  
+    <nav class="md-nav" aria-label="Monitor runs">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#check-the-output-and-error-log-files" class="md-nav__link">
+    Check the output and error log files
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#model-outputs" class="md-nav__link">
+    Model outputs
+  </a>
+  
+</li>
+        
+      </ul>
     
   </nav>
   
@@ -2301,7 +2602,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/running-access-esm.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/run-access-esm.md" title="Edit this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25Z"/></svg>
     </a>
@@ -2310,27 +2611,432 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/running-access-esm.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/run-access-esm.md" title="View source of this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0 8a5 5 0 0 1-5-5 5 5 0 0 1 5-5 5 5 0 0 1 5 5 5 5 0 0 1-5 5m0-12.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5Z"/></svg>
     </a>
   
 
 
-  <h1>Run ACCESS-ESM</h1>
+<h1 id="run-access-esm"><span class="highlight-bg"> Run ACCESS-ESM </span></h1>
+<!-- <div class="page-summary">
+    <h4>On this page</h4>
+    <ol>
+        <li><a href="#runESM-1.0.0">Requirements</a>
+            <ol>
+                <li><a href="#runESM-1.2.0">General requirements</a></li>
+                <li><a href="#runESM-1.2.0">Model-specific requirements</a></li>
+            </ol>
+        </li>
+        <li><a href="#runESM-2.0.0">Get ACCESS-ESM configuration</a></li>
+        <li><a href="#runESM-3.0.0">Edit ACCESS-ESM configuration</a>
+            <ol>
+                <li><a href="#runESM-3.1.0">Payu</a></li>
+                <li><a href="#runESM-3.2.0">Edit the Master Configuration file</a></li>
+            </ol>
+        </li>
+        <li><a href="#runESM-4.0.0">Run ACCESS-ESM configuration</a>
+            <ol>
+                <li><a href="#runESM-4.1.0">Payu setup (optional)</a></li>
+                <li><a href="#runESM-4.2.0">Run configuration</a></li>
+                <li><a href="#runESM-4.3.0">Run configuration for multiple years</a></li>
+                <li><a href="#runESM-4.4.0">Understand <code>runtime</code>, <code>runspersub</code>, and <code>-n</code> parameters</a></li>
+            </ol>
+        </li>
+        <li><a href="#runESM-5.0.0">Monitor runs</a>
+            <ol>
+                <li><a href="#runESM-5.1.0">Check the output and error log files</a></li>
+            </ol>
+        </li>
+        <li><a href="#runESM-6.0.0">Model outputs</a></li>
+    </ol>
+</div> -->
+
+<h2 id="requirements"><span id="runESM-1.0.0">Requirements</span></h2>
+<div class="justified">
+Before running ACCESS-ESM, you need to make sure to possess the right tools and to have an account with specific institutions. 
+</div>
+
+<h3 id="general-requirements"><span id="runESM-1.1.0">General requirements</span></h3>
+<div class="justified">
+For the general requirements needed to run all ACCESS models, please refer to the <a href="TO DO">Getting Started (TO DO check link)</a> page.
+</div>
+
+<h3 id="model-specific-requirements"><span id="runESM-1.2.0">Model-specific requirements</span></h3>
+<div class="justified">
+<ul>
+    <li>
+        <b>Payu</b>
+        <br>
+        To get <i>payu</i> on Gadi, run:
+        <pre><code>module use /g/data/hh5/public/modules
+            module load conda/analysis3
+        </code></pre>
+    </li>
+</ul>
+</div>
+<hr />
+<h2 id="get-access-esm-configuration"><span id="runESM-2.0.0">Get ACCESS-ESM configuration</span></h2>
+<div class="justified">
+A suitable ACCESS-ESM pre-industrial configuration is avaible on the <a href="https://github.com/coecms/esm-pre-industrial" target="_blank">coecms GitHub</a>.
+<br>
+In order to get it, on Gadi, create a directory where to keep the model configuration, and clone the GitHub repo in it by running: 
+<pre><code>git clone https://github.com/coecms/esm-pre-industrial</code></pre>
+<terminal-animation>
+    <terminal-line data="input">mkdir -p ~/access-esm</terminal-line>
+    <terminal-line data="input">cd ~/access-esm</terminal-line>
+    <terminal-line data="input" directory="~/access-esm">git clone https://github.com/coecms/esm-pre-industrial</terminal-line>
+    <terminal-line>Cloning into 'esm-pre-industrial'...</terminal-line>
+    <terminal-line lineDelay=1000>remote: Enumerating objects: 767, done.</terminal-line>
+    <terminal-line>remote: Counting objects: 100% (295/295), done.</terminal-line>
+    <terminal-line>remote: Compressing objects: 100% (138/138), done.</terminal-line>
+    <terminal-line>remote: Total 767 (delta 173), reused 274 (delta 157), pack-reused 472</terminal-line>
+    <terminal-line>Receiving objects: 100% (767/767), 461.57 KiB | 5.24 MiB/s, done.</terminal-line>
+    <terminal-line>Resolving deltas: 100% (450/450), done.</terminal-line>
+</terminal-animation>
+<b>Note:</b> Some modules might interfere with the <code>git</code> commands (for example matlab/R2018a). If you are running into issues during the cloning of the repository, it might be a good idea to run <pre><code>module purge</code></pre> first, before trying again.
+</div>
+<hr />
+<h2 id="edit-access-esm-configuration"><span id="runESM-3.0.0">Edit ACCESS-ESM configuration</span></h2>
+<div class="justified">
+In order to modify an ACCESS-ESM configuration, it is worth understanding a bit more how its job scheduler <i>payu</i> works.
+</div>
+
+<h3 id="payu"><span id="runESM-3.1.0">Payu</span></h3>
+<div class="justified">
+<a href="https://payu.readthedocs.io/en/latest/" target="_blank"><i>Payu</i></a> is a workflow management tool for running numerical models in supercomputing environments.
+<br>
+The general layout of a <i>payu</i>-supported model run consists of two main directories:
+<ul>
+    <li>
+        The <b>laboratory</b> is the directory where all parts of the model are kept. For ACCESS-ESM, it is typically <code>/scratch/$PROJECT/$USER/access-esm</code>.
+    </li>
+    <li>
+        The <b>control</b> directory, where the model configuration is kept and from where the model is run (in our case is the cloned directory <code>~/access-esm/esm-pre-industrial</code>).
+    </li>
+</ul>
+This distinction of directories keeps the small-size configuration files separated from the larger binary outputs and inputs. In this way, we can place the configuration files in the <code>$HOME</code> directory (being the only filesystem on Gadi that is actively backed up), without overloading it with too much data.
+<br>
+Moreover, this separation allows to run multiple self-resubmitting experiments simultaneously that might share common executables and input data.
+<br>
+To proceed with the setup of the <i>laboratory</i> directory, from the <i>control</i> directory run:
+<pre><code>payu init</code></pre> 
+This will create the <i>laboratory</i> directory, along with other subdirectories (depending on the configuration). The main subdirectories we are interested in are: 
+<ul>
+    <li><code>work</code> &rarr; temporary directory where the model is actually run. It gets cleaned after each run.</li>
+    <li><code>archive</code> &rarr; directory where the output is placed after each run.</li>
+    <terminal-animation>
+        <terminal-line data="input">cd ~/access-esm/esm-pre-industrial</terminal-line>
+        <terminal-line data="input" directory="~/access-esm/esm-pre-industrial">payu init</terminal-line>
+        <terminal-line>laboratory path:  /scratch/$PROJECT/$USER/access-esm</terminal-line>
+        <terminal-line>binary path:  /scratch/$PROJECT/$USER/access-esm/bin</terminal-line>
+        <terminal-line>input path:  /scratch/$PROJECT/$USER/access-esm/input</terminal-line>
+        <terminal-line>work path:  /scratch/$PROJECT/$USER/access-esm/work</terminal-line>
+        <terminal-line>archive path:  /scratch/$PROJECT/$USER/access-esm/archive</terminal-line>
+    </terminal-animation>
+</ul>
+</div>
+
+<h3 id="edit-the-master-configuration-file"><span id="runESM-3.2.0">Edit the Master Configuration file</span></h3>
+<div class="justified">
+The <code>config.yaml</code> file, located in the <i>control</i> directory, is the Master Configuration file. 
+<br>
+This file controls the general model configuration and if we open it in a text editor, we can see different parts:
+<ul>
+    <li>
+        <b>PBS resources</b>
+        <br>
+        <pre><code>jobname: pre-industrial
+            queue: normal
+            walltime: 20:00:00
+        </code></pre>
+        These are settings for the PBS scheduler. Edit lines in this section to change any of the PBS resources. 
+        <br>
+        For example, to run ACCESS-ESM under the <code>tm70</code> <a href="TO DO">project (TO DO add Getting started, join a NCI Project link)</a>, add the following line to this section:
+        <pre><code>project: tm70</code></pre>
+    </li>
+    <li>
+        <b>Link to the laboratory directory</b>
+        <br>
+        <pre><code># note: if laboratory is relative path, it is relative to /scratch/$PROJECT/$USER
+            laboratory: access-esm
+        </code></pre>
+        This will set the laboratory directory. Relative paths are relative to <code>/scratch/$PROJECT/$USER</code>. Absolute paths can be specified as well.
+    </li>
+    <li>
+        <b>Model</b>
+        <pre><code>model: access</code></pre>
+        The main model. This tells <i>payu</i> which driver to use (<i>access</i> stands for ACCESS-ESM).
+    </li>
+    <li>
+        <b>Submodels</b>
+        <br>
+        <pre><code>submodels:
+            &nbsp;&nbsp;- name: atmosphere
+            &nbsp;&nbsp;&nbsp;&nbsp;model: um
+            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 192
+            &nbsp;&nbsp;&nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/coe/um7.3x
+            &nbsp;&nbsp;&nbsp;&nbsp;input:
+            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/atmosphere
+            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/start_dump<br>
+            &nbsp;&nbsp;- name: ocean
+            &nbsp;&nbsp;&nbsp;&nbsp;model: mom
+            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 180
+            &nbsp;&nbsp;&nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/coe/mom5xx
+            &nbsp;&nbsp;&nbsp;&nbsp;input:
+            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/ocean/common
+            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/ocean/pre-industrial<br>
+            &nbsp;&nbsp;- name: ice
+            &nbsp;&nbsp;&nbsp;&nbsp;model: cice
+            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 12
+            &nbsp;&nbsp;&nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/coe/cicexx
+            &nbsp;&nbsp;&nbsp;&nbsp;input:
+            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/ice<br>
+            &nbsp;&nbsp;- name: coupler
+            &nbsp;&nbsp;&nbsp;&nbsp;model: oasis
+            &nbsp;&nbsp;&nbsp;&nbsp;ncpus: 0
+            &nbsp;&nbsp;&nbsp;&nbsp;input:
+            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- /g/data/access/payu/access-esm/input/pre-industrial/coupler
+        </code></pre>
+        ACCESS-ESM is a coupled model, which means it has multiple submodels (i.e. model components). 
+        <br>
+        This section specifies the submodels and contains configuration options (for example the directories of input files) that are required to ensure the model can execute correctly. Each submodel also has additional configuration options that are read in when the submodel is running. These specific configuration options are found in the subdirectory of the <i>control</i> directory having the <i>name</i> of the submodel (e.g. in our case the configuration for the atmosphere submodel, i.e. the UM, will be in the directory <code>~/access-esm/esm-pre-industrial/atmosphere</code>).
+    </li>
+    <li>
+        <b>collate</b>
+        <br>
+        <pre><code>collate:
+            &nbsp;&nbsp;exe: /g/data/access/payu/access-esm/bin/mppnccombine
+            &nbsp;&nbsp;restart: true
+            &nbsp;&nbsp;mem: 4GB
+        </code></pre>
+        The <i>collate</i> process joins a number of smaller files, which contain different parts of the model grid, together into target output files. The restart files are typically tiled in the same way and will also be joined together if the <i>restart</i> option is set to <code>true</code>.
+    </li>
+    <li>
+        <b>restart</b>
+        <br>
+        <pre><code>restart: /g/data/access/payu/access-esm/restart/pre-industrial</code></pre>
+        The location of the files used for a warm restart.
+    </li>
+    <li>
+        <b>Start date and internal run length</b>
+        <br>
+        <pre><code>calendar:
+            &nbsp;&nbsp;start:
+            &nbsp;&nbsp;&nbsp;&nbsp;year: 101
+            &nbsp;&nbsp;&nbsp;&nbsp;month: 1
+            &nbsp;&nbsp;&nbsp;&nbsp;days: 1<br>
+            &nbsp;&nbsp;runtime:
+            &nbsp;&nbsp;&nbsp;&nbsp;years: 1
+            &nbsp;&nbsp;&nbsp;&nbsp;months: 0
+            &nbsp;&nbsp;&nbsp;&nbsp;days: 0
+        </code></pre>
+        This section specifies the start date and internal run length.
+        <br>
+        <b>Note:</b> The internal run length (controlled by <code>runtime</code>) can be different from the total run length. Also, the <code>runtime</code> value can be lowered, but should not be increased to a total of more than 1 year, to avoid errors. If you want to know more about the difference between internal run and total run lenghts, or if you want to run the model for more than 1 year, check <a href="#runESM-4.3.0">Run configuration for multiple years</a>.
+    </li>
+    <li>
+        <b>Number of runs per PBS submission</b>
+        <br>
+        <pre><code>runspersub: 5</code></pre>
+        ACCESS-ESM configurations are often run in multiple steps (or cycles), with <i>payu</i> running a maximum of <code>runspersub</code> internal runs for every PBS job submission.
+        <br>
+        <b>Note:</b> If we increase <code>runspersub</code>, we might need to increase the <i>walltime</i> in the PBS resources.
+    </li>
+</ul>
+To know more about other configuration settings for the <code>config.yaml</code> file, please check <a href="https://payu.readthedocs.io/en/latest/config.html" target="_blank">how to configure your experiment with <i>payu</i></a>.
+</div>
+<hr />
+<h2 id="run-access-esm-configuration"><span id="runESM-4.0.0">Run ACCESS-ESM configuration</span></h2>
+<p>After editing the configuration, we are ready to run ACCESS-ESM. 
+<br>
+ACCESS-ESM suites run on <a href="https://opus.nci.org.au/display/Help/0.+Welcome+to+Gadi#id-0.WelcometoGadi-Overview" target="_blank">Gadi</a> through a PBS job submission managed by <i>payu</i>.</p>
+<h3 id="payu-setup-optional"><span id="runESM-4.1.0">Payu setup (optional)</span></h3>
+<div class="justified">
+As a first step, from the control directory, is good practice to run:
+<pre><code>payu setup</code></pre>
+This will prepare the model run, based on the experiment configuration.
+<terminal-animation>
+    <terminal-line data="input">payu setup</terminal-line>
+    <terminal-line>laboratory path:  /scratch/$PROJECT/$USER/access-esm</terminal-line>
+    <terminal-line>binary path:  /scratch/$PROJECT/$USER/access-esm/bin</terminal-line>
+    <terminal-line>input path:  /scratch/$PROJECT/$USER/access-esm/input</terminal-line>
+    <terminal-line>work path:  /scratch/$PROJECT/$USER/access-esm/work</terminal-line>
+    <terminal-line>archive path:  /scratch/$PROJECT/$USER/access-esm/archive</terminal-line>
+    <terminal-line>Loading input manifest: manifests/input.yaml</terminal-line>
+    <terminal-line>Loading restart manifest: manifests/restart.yaml</terminal-line>
+    <terminal-line>Loading exe manifest: manifests/exe.yaml</terminal-line>
+    <terminal-line>Setting up atmosphere</terminal-line>
+    <terminal-line>Setting up ocean</terminal-line>
+    <terminal-line>Setting up ice</terminal-line>
+    <terminal-line>Setting up coupler</terminal-line>
+    <terminal-line>Checking exe and input manifests</terminal-line>
+    <terminal-line>Updating full hashes for 3 files in manifests/exe.yaml</terminal-line>
+    <terminal-line>Creating restart manifest</terminal-line>
+    <terminal-line>Updating full hashes for 30 files in manifests/restart.yaml</terminal-line>
+    <terminal-line>Writing manifests/restart.yaml</terminal-line>
+    <terminal-line>Writing manifests/exe.yaml</terminal-line>
+</terminal-animation>
+<b>Note:</b> You can skip this step as it is included also in the run command. However, runnning it explicitly helps to check for errors and make sure executable and restart directories are accessible.
+</div>
 
+<h3 id="run-configuration"><span id="runESM-4.2.0">Run configuration</span></h3>
+<div class="justified">
+To run ACCESS-ESM configuration for one internal run length (controlled by <code>runtime</code> in the <code>config.yaml</code> file), run:
+<pre><code>payu run -f</code></pre>
+This will submit a single job to the queue with a total run length of <code>runtime</code>. It there is no previous run, it will start from the <code>start</code> date indicated in the <code>config.yaml</code> file, otherwise it will perform a warm restart from a precedently saved restart file.
+<br>
+<b>Note:</b>The <code>-f</code> option ensures that <i>payu</i> will run even if there is an existing non-empty <i>work</i> directory, which happens if a run crashes.
+<terminal-animation>
+    <terminal-line data="input">payu run -f</terminal-line>
+    <terminal-line>Loading input manifest: manifests/input.yaml</terminal-line>
+    <terminal-line>Loading restart manifest: manifests/restart.yaml</terminal-line>
+    <terminal-line>Loading exe manifest: manifests/exe.yaml</terminal-line>
+    <terminal-line>payu: Found modules in /opt/Modules/v4.3.0</terminal-line>
+    <terminal-line>qsub -q normal -P &lt;project&gt; -l walltime=11400 -l ncpus=384 -l mem=1536GB -N pre-industrial -l wd -j n -v PAYU_PATH=/g/data/hh5/public/apps/miniconda3/envs/analysis3-23.01/bin,MODULESHOME=/opt/Modules/v4.3.0,MODULES_CMD=/opt/Modules/v4.3.0/libexec/modulecmd.tcl,MODULEPATH=/g/data3/hh5/public/modules:/etc/scl/modulefiles:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/modulefiles:/apps/Modules/modulefiles -W umask=027 -l storage=gdata/access+gdata/hh5 -- /g/data/hh5/public/apps/miniconda3/envs/analysis3-23.01/bin/python3.9 /g/data/hh5/public/apps/miniconda3/envs/analysis3-23.01/bin/payu-run</terminal-line>
+    <terminal-line>&lt;job-ID&gt;.gadi-pbs</terminal-line>
+</terminal-animation>
+</div>
 
+<h3 id="run-configuration-for-multiple-years"><span id="runESM-4.3.0">Run configuration for multiple years</span></h3>
+<div class="justified">
+If you want to run ACCESS-ESM configuration for multiple internal run lengths (controlled by <code>runtime</code> in the <code>config.yaml</code> file), you can use the option <code>-n</code>:
+<pre><code>payu run -n &lt;number-of-runs&gt;</code></pre>
+This will run the configuration <code>number-of-runs</code> times with a total run length of <code>runtime * number-of-runs</code>. The number of consecutive PBS jobs submitted to the queue depends on the <code>runspersub</code> value specified in the <code>config.yaml</code> file.
+</div>
+
+<h3 id="understand-runtime-runspersub-and-n-parameters"><span id="runESM-4.4.0">Understand <code>runtime</code>, <code>runspersub</code>, and <code>-n</code> parameters</span></h3>
+<div class="justified">
+With the correct use of <code>runtime</code>, <code>runspersub</code>, and <code>-n</code> parameters, we can have full control of our run.
+<br>
+<ul>
+    <li>
+        <code>runtime</code> defines the internal run length.
+    </li>
+    <li>
+        <code>runspersub</code> defines the maximum number of internal runs for every PBS job submission.
+    </li>
+    <li>
+        <code>-n</code> sets the number of internal runs to be performed.
+    </li>
+</ul>
+Let's have some practical examples:
+<ul>
+    <li>
+        <b>Run 20 years of simulation, with resubmission every 5 years</b>
+        <br>
+        To have a total run length of 20 years, with a resubmition cycle of 5 years, we can leave <code>runtime</code> to the default value of <code>1 year</code>, set <code>runspersub</code> to <code>5</code>, and run the configuration using <code>-n 20</code>:
+        <pre><code>payu run -n 20</code></pre>
+        This will submit subsequent jobs for the following years: 1 to 5, 6 to 10, 11 to 15, and 16 to 20. With a total of 4 PBS jobs.
+    </li>
+    <li>
+        <b>Run 7 years of simulation, with resubmission every 3 years</b>
+        <br>
+        To have a total run length of 7 years, with a resubmition cycle of 3 years, we can leave <code>runtime</code> to the default value of <code>1 year</code>, set <code>runspersub</code> to <code>3</code>, and run the configuration using <code>-n 7</code>:
+        <pre><code>payu run -n 7</code></pre>
+        This will submit subsequent jobs for the following years: 1 to 3, 4 to 6, and 7. With a total of 3 PBS jobs.
+    </li>
+    <li>
+        <b>Run 3 months and 10 days of simulation, in one single submission</b>
+        <br>
+        To have a total run length of 3 months and 10 days, all in a single submission, we have to set <code>runtime</code> to:
+        <pre><code>years: 0
+            months: 3
+            days: 10
+        </code></pre>
+        set <code>runspersub</code> to <code>1</code> (or any value > 1), and run the configuration without <code>-n</code> (or with <code>-n</code> equals <code>1</code>):
+        <pre><code>payu run</code></pre>
+    </li>
+    <li>
+        <b>Run 1 year and 4 months of simulation, with resubmission every 4 months</b>
+        <br>
+        To have a total run length of 1 year and 4 months (16 months), we will have to split it into multiple internal runs. For example, we can have 4 internal runs of 4 months each. Therefore, we will have to set <code>runtime</code> to:
+        <pre><code>years: 0
+            months: 4
+            days: 0
+        </code></pre>
+        Since the internal run length is set to 4 months, to resubmit our jobs every 4 months (i.e. every internal run), we have to set <code>runspersub</code> to <code>1</code>. Finally, we will perform 4 internal runs by running the configuration with <code>-n 4</code>:
+        <pre><code>payu run -n 4</code></pre>
+    </li>
+</ul>
+</div>
+<hr />
+<h2 id="monitor-runs"><span id="runESM-5.0.0">Monitor runs</span></h2>
+<div class="justified">
+Currently, there is no specific tool to monitor ACCESS-ESM runs. 
+<br>
+One way to check the status of our run is running:
+<pre><code>qstat -u $USER</code></pre>
+This will show the status of all your PBS jobs (if there is any PBS job submitted):
+<terminal-animation>
+    <terminal-line data="input">qstat -u $USER</terminal-line>
+    <terminal-line linedelay=500>Job id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;User&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Time Use&nbsp;S Queue</terminal-line>
+    <terminal-line linedelay=0>---------------------  ---------------- ----------------  -------- - -----</terminal-line>
+    <terminal-line linedelay=0>&lt;job-ID&gt;.gadi-pbs&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pre-industrial&nbsp;&nbsp;&nbsp;&lt;$USER&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;time&gt;&nbsp;R&nbsp;normal-exec</terminal-line>
+    <terminal-line linedelay=0>&lt;job-ID&gt;.gadi-pbs&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;other-job-name&gt;&nbsp;&lt;$USER&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;time&gt;&nbsp;R&nbsp;normal-exec</terminal-line>
+    <terminal-line linedelay=0>&lt;job-ID&gt;.gadi-pbs&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;other-job-name&gt;&nbsp;&lt;$USER&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;time&gt;&nbsp;R&nbsp;normal-exec</terminal-line>
+</terminal-animation>
+If you changed the <code>jobname</code> in the PBS resources of the <a href="#runESM-3.2.0">Master Configuration file</a>, that will be your job's <i>Name</i> instead of <code>pre-industrial</code>.
+<br>
+<i>S</i> indicates the status of your run:
+<ul>
+    <li>Q &rarr; Job waiting in the queue to start</li>
+    <li>R &rarr; Job running</li>
+    <li>E &rarr; Job ending</li>
+</ul>
+If there is no listed job with your <code>jobname</code> (or if there is no job submitted at all), your run might have successfully completed, or might have been terminated due to an error.
+</div>
+
+<h3 id="check-the-output-and-error-log-files"><span id="runESM-5.1.0">Check the output and error log files</span></h3>
+<div class="justified">
+While the model is running, <i>payu</i> saves the standard output and standard error into the files <code>access.out</code> and <code>access.err</code> in the <i>control</i> directory. You can examine these files, as the run progresses, to check on it's status.
+<br>
+After the model has completed its run, or if it crashed, the output and error log files, respectively, are renamed by default into <code>jobname.o&lt;job-ID&gt;</code> and <code>jobname.e&lt;job-ID&gt;</code>.
+</div>
+<hr />
+<h2 id="model-outputs"><span id="runESM-6.0.0">Model outputs</span></h2>
+<div class="justified">
+While the configuration is running, output files (as well as restart files) are moved from the <code>work</code> directory to the <code>archive</code> directory, under <code>/scratch/$PROJECT/$USER/access-esm/archive</code> (also symlinked in the <i>control</i> directory under <code>~/access-esm/esm-pre-industrial/archive</code>).
+<br>
+Both outputs and restarts are stored into subfolders for each different configuration (<code>esm-pre-industrial</code> in our case), and inside the configuration folder, they are subdivided for each internal run.
+<br>
+The format of a typical output folder is <code>outputXXX</code>, whereas the typical restart folder is usually formatted as <code>restartXXX</code>, with <i>XXX</i> being the number of internal run, starting from <code>000</code>.
+<br>
+In the respective folders, outputs and restarts are separated for each model component.
+<br>
+For the atmospheric output data, each file it is usually a <a href = "https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_F03.pdf" target="_blank">UM fieldsfile</a>, formatted as <code>&lt;UM-suite-identifier&gt;a.p&lt;output-stream-identifier&gt;&lt;time-identifier&gt;</code>.
+<terminal-animation>
+    <terminal-line data="input">cd /scratch/$PROJECT/$USER/access-esm/archive/esm-pre-industrial</terminal-line>
+    <terminal-line data="input" directory="/scratch/$PROJECT/$USER/access-esm/archive/esm-pre-industrial">ls</terminal-line>
+    <terminal-line class="ls-output-format">output000 pbs_logs restart000</terminal-line>
+    <terminal-line data="input" directory="/scratch/$PROJECT/$USER/access-esm/archive/esm-pre-industrial">ls output000/atmosphere</terminal-line>
+    <terminal-line class="ls-output-format">aiihca.daa1210 aiihca.daa1810 aiihca.paa1apr aiihca.paa1jun aiihca.pea1apr aiihca.pea1jun aiihca.pga1apr aiihca.pga1jun atm.fort6.pe0 exstat ihist prefix.CNTLGEN UAFLDS_A aiihca.daa1310  aiihca.daa1910  aiihca.paa1aug aiihca.paa1mar aiihca.pea1aug aiihca.pea1mar aiihca.pga1aug aiihca.pga1mar cable.nml fort.57 INITHIS prefix.PRESM_A um_env.py aiihca.daa1410 aiihca.daa1a10 aiihca.paa1dec aiihca.paa1may aiihca.pea1dec aiihca.pea1may aiihca.pga1dec aiihca.pga1may CNTLALL ftxx input_atm.nml SIZES xhist aiihca.daa1510 aiihca.daa1b10 aiihca.paa1feb aiihca.paa1nov aiihca.pea1feb aiihca.pea1nov aiihca.pga1feb aiihca.pga1nov CONTCNTL ftxx.new namelists STASHC aiihca.daa1610 aiihca.daa1c10 aiihca.paa1jan aiihca.paa1oct aiihca.pea1jan aiihca.pea1oct aiihca.pga1jan aiihca.pga1oct debug.root.01 ftxx.vars nout.000000 thist aiihca.daa1710 aiihca.daa2110 aiihca.paa1jul aiihca.paa1sep aiihca.pea1jul aiihca.pea1sep aiihca.pga1jul aiihca.pga1sep errflag hnlist prefix.CNTLATM UAFILES_A</terminal-line>
+</terminal-animation>
+
+</div>
+
+<!-- References -->
+<p><br></p>
+<h6>References</h6>
+<ul class="references">
+    <li>
+        <a href = "https://github.com/coecms/esm-pre-industrial" target="_blank">https://github.com/coecms/esm-pre-industrial</a>
+    </li>
+    <li>
+        <a href = "https://payu.readthedocs.io/en/latest/usage.html" target="_blank">https://payu.readthedocs.io/en/latest/usage.html</a>
+    </li>
+</ul>
 
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-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
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         Created:
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+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
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diff --git a/pr-preview/pr-396/models/running-a-model/running-access-om/index.html b/pr-preview/pr-396/models/run-a-model/run-access-om/index.html
similarity index 98%
rename from pr-preview/pr-396/models/running-a-model/running-access-om/index.html
rename to pr-preview/pr-396/models/run-a-model/run-access-om/index.html
index ef98097ef..1afcb46fa 100644
--- a/pr-preview/pr-396/models/running-a-model/running-access-om/index.html
+++ b/pr-preview/pr-396/models/run-a-model/run-access-om/index.html
@@ -8,10 +8,10 @@
       
       
       
-        <link rel="canonical" href="https://access-hive.org.au/models/running-a-model/running-access-om/">
+        <link rel="canonical" href="https://access-hive.org.au/models/run-a-model/run-access-om/">
       
       
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+        <link rel="prev" href="../run-access-am/">
       
       
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       <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
@@ -1259,7 +1257,7 @@
   
   
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-      <a href="../running-access-esm/" class="md-nav__link">
+      <a href="../run-access-esm/" class="md-nav__link">
         Run ACCESS-ESM
       </a>
     </li>
@@ -1273,7 +1271,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-cm/" class="md-nav__link">
+      <a href="../run-access-cm/" class="md-nav__link">
         Run ACCESS-CM
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@@ -1287,7 +1285,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../running-access-am/" class="md-nav__link">
+      <a href="../run-access-am/" class="md-nav__link">
         Run ACCESS-AM
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@@ -1319,8 +1317,9 @@
         Run ACCESS-OM
       </a>
       
-        <!--  -->
+        
   
+    
   
   <nav class="md-nav md-nav--secondary" aria-label="On this page">
     
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                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
-                    <!--  -->
+                    
   
+    
   
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@@ -2426,7 +2426,7 @@
                   
 
   
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/running-a-model/running-access-om.md" title="Edit this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/edit/main/docs/models/run-a-model/run-access-om.md" title="Edit this page" class="md-content__button md-icon">
       
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     </a>
@@ -2435,7 +2435,7 @@
     
       
     
-    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/running-a-model/running-access-om.md" title="View source of this page" class="md-content__button md-icon">
+    <a href="https://github.com/ACCESS-Hive/access-hive.github.io/raw/main/docs/models/run-a-model/run-access-om.md" title="View source of this page" class="md-content__button md-icon">
       
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 9a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0 8a5 5 0 0 1-5-5 5 5 0 0 1 5-5 5 5 0 0 1 5 5 5 5 0 0 1-5 5m0-12.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5Z"/></svg>
     </a>
@@ -2465,11 +2465,11 @@ <h1 id="references">References</h1>
   <small>
     
       Last update:
-      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+      <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
         <br>
         Created:
-        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 5, 2023</span>
+        <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">July 10, 2023</span>
       
     
   </small>
@@ -2583,7 +2583,7 @@ <h1 id="references">References</h1>
       
         <script src="https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js"></script>
       
-        <script src="../../../js/termynal.js"></script>
+        <script src="../../../js/terminal_animation.js"></script>
       
         <script src="../../../js/miscellaneous.js"></script>
       
diff --git a/pr-preview/pr-396/models/running-a-model/running-access-s/index.html b/pr-preview/pr-396/models/running-a-model/running-access-s/index.html
deleted file mode 100644
index a8c804251..000000000
--- a/pr-preview/pr-396/models/running-a-model/running-access-s/index.html
+++ /dev/null
@@ -1,2436 +0,0 @@
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-      <meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.8">
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diff --git a/pr-preview/pr-396/search/search_index.json b/pr-preview/pr-396/search/search_index.json
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You can contribute to this part of the Hive too!</p> <p>Currently, we provide pointers to the following categories: - Working Groups  - Glossaries - Variables - Model Evaluation Links - Training - Events </p>"},{"location":"community_resources/community_data_processing/","title":"Community Processing Data Processing Tools","text":""},{"location":"community_resources/community_data_processing/#tools","title":"Tools","text":""},{"location":"community_resources/community_data_processing/#kerchunk","title":"Kerchunk","text":"<p>Documentation |  Sources</p> <p>Kerchunk is a library that provides a unified way to represent a variety of chunked, compressed data formats (e.g. NetCDF/HDF5, GRIB2, TIFF, \u2026), allowing efficient access to the data from traditional file systems or cloud object storage. It also provides a flexible way to create virtual datasets from multiple files.</p>"},{"location":"community_resources/community_data_processing/#cmor3","title":"CMOR3","text":"<p>Climate Model Output Rewriter Version 3</p> <p>Documentation |  Sources</p> <p>CMOR is used to produce CF-compliant netCDF files. The structure of the files created by CMOR and the metadata they contain fulfill the requirements of many of the climate community\u2019s standard model experiments (which are referred to here as \u201cMIPs\u201d and include, for example, AMIP, PMIP, APE, and IPCC scenario runs).</p>"},{"location":"community_resources/community_data_processing/#xmip","title":"xMIP","text":"<p>Documentation | Tutorial on NCI | Sources</p> <p>This package facilitates the cleaning, organization and interactive analysis of Model Intercomparison Projects (MIPs) within the Pangeo software stack.</p>"},{"location":"community_resources/community_data_processing/#app4-the-access-post-processor","title":"APP4 (The ACCESS Post Processor)","text":"<p>Documentation |  Sources</p> <p>The APP4 is a CMORisation tool designed to convert ACCESS model output to ESGF-compliant formats, primarily for publication to CMIP6. The code was originally built for CMIP5, and was further developed for CMIP6-era activities. Uses CMOR3 and files created with the CMIP6 data request to generate CF-compliant files according to the CMIP6 data standards.</p>"},{"location":"community_resources/community_data_processing/#access-archiver","title":"ACCESS-Archiver","text":"<p>Documentation |  Sources</p> <p>The ACCESS Archiver is designed to archive model output from ACCESS simulations. It's focus is to copy ACCESS model output from its initial location to a secondary location (typically from <code>/scratch</code> to <code>/g/data</code>), while converting UM files to netCDF, compressing MOM/CICE files, and culling restart files to 10-yearly. Saves 50-80% of storage space due to conversion and compression.</p>"},{"location":"community_resources/community_data_processing/#synda","title":"Synda","text":"<p>synda is a command line tool to search and download files from the Earth System Grid Federation (ESGF) archive.</p>"},{"location":"community_resources/community_data_processing/#fluxnetlsm","title":"FluxnetLSM","text":"<p>Citation 1 | Sources</p> <p>R package for post-processing FLUXNET datasets for use in land surface modelling. Performs quality control and data conversion of FLUXNET data and collated site metadata. Supports FLUXNET2015, La Thuile, OzFlux and ICOS data releases.</p>"},{"location":"community_resources/community_data_processing/#metpy","title":"Metpy","text":"<p>https://unidata.github.io/MetPy/latest/examples/formats/index.html</p> <p>Documentation | Sources</p> <p>MetPy is a collection of tools in Python for reading, visualizing, and performing calculations with weather data. MetPy supports Python &gt;= 3.8 and is freely available under a permissive open source license.</p> <p>Format types are: GINI Water Vapor Imagery, NEXRAD Level 3 File, and NEXRAD Level 2 File.</p>"},{"location":"community_resources/community_data_processing/#xskillscore","title":"xskillscore","text":"<p>Documentation | Sources</p> <p>xskillscore is a Python library for computing a wide variety of skill metrics. Its typical application is to verify deterministic and probabilistic forecasts relative to observations.</p>"},{"location":"community_resources/community_data_processing/#analysis-blogposts-and-tutorials","title":"Analysis blogposts and tutorials","text":"<p>Accessing NetCDF and GRIB file collections as cloud-native virtual datasets using Kerchunk, Peter March, Sep 2022</p> <ol> <li> <p>A. M. Ukkola, N. Haughton, M. G. De Kauwe, G. Abramowitz, and A. J. Pitman. Fluxnetlsm r package (v1.0): a community tool for processing fluxnet data for use in land surface modelling. Geoscientific Model Development, 10(9):3379\u20133390, 2017. URL: https://gmd.copernicus.org/articles/10/3379/2017/, doi:10.5194/gmd-10-3379-2017.\u00a0\u21a9</p> </li> </ol>"},{"location":"community_resources/community_med_recipes/","title":"Community Model Evaluation and Diagnostics (MED) Recipe Gallery","text":"<p>We are trying to ingest more and more model evaluation and diagnostics recipes in your currated recipe gallery on this website . While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community :</p> MED Recipe Components Description ESMValTool  (Earth System Model EValuation Tool) Documentation |         Tutorial |         Source Code COSIMA Cookbook / Recipes (Consortium for Ocean-Sea Ice Modelling in Australia) Documentation |         Tutorial |         Source Code |         Recipes iLAMB (international Land Model Benchmarking) Documentation |         Tutorial |         Source Code iOMB (international Ocean Model Benchmarking) Documentation |         Tutorial |         Source Code METPlus (Model Evaluation Tool Plus) Tutorial |         Paper PMP (PCMDI Metrics Package) Documentation |         Source Code climpred  Documentation |         Tutorial |         Source Code |         Paper FREVA (Free Evaluation System Framework) Documentation |         Source Code TECA (Toolkit for Extremes Climate Analysis) Documentation |         Tutorial |         Source Code MONET (Model and ObservatioN Evaluation Toolkit) Documentation |         Tutorial |         Source Code |         Paper LIVVkit (land ice verification &amp; validation toolkit) Documentation |         Tutorial |         Source Code CSET (Convective Scale Evaluation Tool ) Documentation |         Tutorial |         Source Code |          MetPy (Model Evaluation Tool Plus) Tutorial |         Source Code |         Recipes         MetPy is a collection of tools in Python for reading, visualizing, and performing calculations with weather data. MetPy supports Python &gt;= 3.8 and is freely available under a permissive open source license.      Afterburner  Documentation |         Source"},{"location":"community_resources/community_model_catalogs/","title":"Community Model Data Catalogs","text":"<p>We are trying to ingest more and more model data catalogs in your currated catalog on this website. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us () or may be interesting for the community ():</p> Model Catalog Comp. Description NCI datasets          NCI has an extensive catalog of datasets of interest to the weather and climate community. These datasets are directly available on the NCI supercomputer and the [Australian Research Environment](https://opus.nci.org.au/display/Help/ARE+User+Guide)          CLEX NCI Data Collection Intake Catalogue          This is an Intake catalogue maintained by the ARC Centre of Excellence for Climate Extremes [(CLEX)](https://climateextremes.org.au/).         Only datasets from the NCI Catalog are referenced.         The catalogue is available in intake's default catalogue list in the CLEX Conda environment.         Two notebooks are provided in the docs folder showing how to access the ERA5 and CIP6 datasets.          Australia Climate Data Guide Catalogue          *A one-stop catalogue to discover Climate Data in Australia*         The ACDG portal is a metadata portal listing climate research resources available in Australia from multiple data repositories.         This is a community based project managed by the ACDG Single Access working group. This is a group of Australian climate community self-nominated representatives. Anyone is welcome to join the group or to contribute independently to the metadata portal the group is developing.          Australian Ocean Data Network          The Australian Ocean Data Network (AODN) is an interoperable online network of marine and climate data resources.  IMOS and the 6 Australian Commonwealth agencies ([see AODN Partners](https://imos.org.au/facilities/aodn/aodn-data-management/aodn-partners)) form the core of the AODN. Increasingly, though, universities and State government offices are offering up data resources to the AODN, and delivery of data to the AODN is being written in to significant research programs e.g. [National Environmental Science Program Marine Biodiversity Hub](http://www.nespmarine.edu.au/) and the [Great Australian Bight research program](http://www.misa.net.au/GAB).          Intake-Ilamb Catalog          The Intake-Ilamb catalog provides an yaml-style intake catalog of the reference data used for ESM model benchmarking in the International Land Model Benchmarking [(ILAMB)](https://www.ilamb.org/) effort.          FLUXNET          FLUXNET is an international \u201cnetwork of networks,\u201d tying together regional networks of earth system scientists. FLUXNET scientists use the eddy covariance technique to measure the cycling of carbon, water, and energy between the biosphere and atmosphere. Scientists use these data to better understand ecosystem functioning, and to detect trends in climate, greenhouse gases, and air pollution.          CEDA Archive          The CEDA Archive forms part of NERC's Environmental Data Service (EDS) and is responsible for looking after data from atmospheric and earth observation research. They host over 18 Petabytes of data from climate models, satellites, aircraft, met observations, and other sources.          OZFlux          OzFlux is an ecosystem research network set up to provide Australian, New Zealand and global ecosystem modelling communities with consistent observations of energy, carbon and water exchange between the atmosphere and key Australian and New Zealand ecosystems.          Australian Community Reference Climate Data Collection          This collection is a collaborative effort between the Australian Climate Service (ACS), ARC Centre of Excellence for Climate Extremes (CLEX) and the wider Australian climate research community to re-establish and maintain a reference dataset collection at NCI.         An [intake-esm catalogue](https://github.com/aus-ref-clim-data-nci/acs-replica-intake) is also available to facilitate data access."},{"location":"community_resources/community_observational_catalogs/","title":"Community Observational Data Catalogs","text":"<p>We are trying to ingest more and more model data catalogs in your currated catalog on this website. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us () or may be interesting for the community ():</p> Data Catalog Comp. Description Copernicus Climate Change Service (C3S) Data Store (CDS)          The Copernicus Climate Change Service (C3S) combines observations of the climate system with the latest science to develop authoritative, quality-assured information about the past, current and future states of the climate in Europe and worldwide. C3S data is provided via its Climate Data Store (CDS).         You can search its available datasets via this interface.         You can use the CDS API as well as command line tools to download data. To download ERA5 from CDS, you can use for example this era5cli command line tool.          Catalogue Search at CEDA (Centre for Environmental Data Analysis)           The CEDA (Centre for Environmental Data Analysis) Archive hosts atmospheric and earth observation data.         It provids an interactive Catalogue Search and Tools for downloading data.         It holds environmental data related to atmospheric and earth observation fields. Our remit covers the following areas (see linked examples to some of our most popular datasets):          - Climate - e.g. HadUK Grid, CMIP, CRU          - Composition - e.g. CCI          - Observations - e.g. MIDAS Open          - Numerical weather prediction - e.g. Met Office NWP          - Airborne - e.g. FAAM          - Satellite data and imagery - e.g. Sentinel"},{"location":"community_resources/community_working_groups/","title":"Community Working Groups","text":"<p>The ACCESS Community and the ACCESS-NRI have established Community Working Groups to assess and prioritise the needs of the modelling community as well as encourage collaboration within. These working groups are open to the community and welcome new members.</p> <p>The working group activities are coordinated through the ACCESS Hive Community Forum:</p>              Atmospheric Modelling                       Land Surface Modelling                       COSIMA(Ocean and Sea-Ice)                       Forecasting and Prediction                       Earth System Modelling                       Cryosphere          <p>To join a working group follow the instructions on the ACCESS-NRI website, and to participate in the activities of the working group visit the ACCESS-hive forum.</p>"},{"location":"community_resources/events/","title":"Workshops and Conferences","text":"<p>TODO get the liquid working {{ events_content }}</p>"},{"location":"community_resources/events/add_event/","title":"Workshops and Conferences: Add Event","text":"<p>We encourage members of the community to list any workshops, tutorials, conferences that might be of interest to the community.</p>"},{"location":"community_resources/events/add_event/#how-to-add-your-event","title":"How to add your event","text":""},{"location":"community_resources/events/add_event/#add-an-issue","title":"Add an issue","text":"<p>The easiest way for you to add your event is to make an issue with the template provided. This provides a form which guides you through the process of providing the required information.</p>"},{"location":"community_resources/events/add_event/#create-a-pull-request-to-add-your-event","title":"Create a pull-request to add your event","text":"<p>This process requires some knowledge of git, GitHub and Markdown. If you do not feel comfortable doing this then it is sufficient to just add an issue as above. The issue will be assigned to someone else to finish.</p> <p>If you do feel confident adding your event to the list, then create a Markdown text file, identified with the <code>.md</code> extension, to the correct subdirectory in the <code>events</code> folder of the ACCESS-Hive repository. The subdirectories are named by year, put your new file in the year in which the event will take place. Avoid spaces in your filename: use an underscore <code>_</code> where you would normally have a space. e.g. <code>regional_dowscaling_cordex.md</code></p> <p>The file must contain a header with the metadata as in the example below:</p> <pre><code>---\ntitle: Regional climate downscaling for Australia within the CORDEX framework\nstart_date: 27/11/2022\nend_date: 27/11/2022\nlocation: Adelaide, SA\nlink: https://www.amos2022.org.au/\ndescription: This workshop is relevant for those performing regional climate simulations or downscaling with empirical/statistical downscaling approaches including machine learning, as well as those using regional climate projection data in their work. The focus will be on CORDEX related data and modelling. The workshop will have some presentations with extended discussion.\n---\n</code></pre> <p>Make sure to follow all the steps described in the contribution guidelines to submit this addition for approval for publication.</p>"},{"location":"community_resources/events/events/2022/CORDEXAmos2022/","title":"Regional climate downscaling for Australia within the CORDEX framework","text":"<p>This workshop is relevant for those performing regional climate simulations or downscaling with empirical/statistical downscaling approaches including machine learning, as well as those using regional climate projection data in their work. The focus will be on CORDEX related data and modelling. The workshop will have some presentations with extended discussion. Some topics to be covered include: - Accessing the existing CORDEX-CMIP5 data. How to access and use the data - Explain the CORDEX-CMIP6 protocol - What does it say? How can you contribute? - Who is planning to contribute (or is already working on contributions) to the Australasia domain?</p>"},{"location":"community_resources/events/events/2022/GC5Workshop/","title":"GC5 Assessment Workshop","text":"<p>The UM Partnership Team and GC Programme Team are running a GC5 assessment workshop, to assess the latest configuration of the Global Coupled model.</p> <p>The workshop will be a hybrid event with an option to attend online or in-person at Met Office Collaboration Building, Exeter. We will discuss the assessment of the latest GC5 configuration in a range of model simulations in a seamless context and sessions will broadly consist of: - Summary of GC5 physics changes - General model assessment - Summary from Priority Evaluation Groups (PEGs) - Summary from Collaboration Groups (CoGs) - Upcoming changes in GC science and tools - Discussions</p> <p>Please fill in the registration form to confirm attendance by 21st October</p> <p>For any further questions please contact Luke Roberts, Prince Xavier or Charline Marzin at the Met Office.</p>"},{"location":"community_resources/events/events/2022/GroundTruthingClimateChange/","title":"Ground truthing future climate change","text":"<p>Scientific ocean drilling provides the robust baseline data on global climate evolution over extended geologic time periods that are critical for improving climate model performance. By targeting how the climate system operates across a wide array of past climate states, scientific ocean drilling has, and continues to, obtain the data necessary to calibrate and improve numerical models used to project future climate impacts and inform mitigation strategies.</p> <p>Join us in this session where we aim to connect climate and ocean modellers to our rich (50+ years of drilling) database and unanswered questions in scientific ocean drilling. By addressing key questions about Earth\u2019s past, present, and future through interdisciplinary research, we are aiming to spark new collaborations and proposals that will lead to a more profound understanding of Earth as one integrated, interconnected system.</p>"},{"location":"community_resources/events/events/2022/SWOTAmos2022/","title":"The Surface Water and Ocean Topography (SWOT) satellite: A primer","text":"<p>The Surface Water and Ocean Topography (SWOT) satellite, which will launch in November 2022, is a ground-breaking wide-swath altimetry mission that will observe fine details of the ocean dynamics at a resolution 10 times finer than current satellites. SWOT is jointly developed by NASA and CNES with contributions from researchers around the world, including Australia. The Australian government, the Integrated Marine Observing System, and the Australian marine science community are investing in SWOT through calibration/validation and synergistic in situ measurements of fine-scale ocean dynamics in the Australian region. This workshop will present a primer on the principles of the satellite and instrument, how it works, and what are its possibilities and limitations compared to existing altimetry products. This will be complemented with a brief summary of ocean research related to and enabled by SWOT, including internal waves and tides, sub-mesoscale dynamics, the geoid, and mean dynamic topography. The goal of the workshop is to provide oceanographers, hydrologists and other users of altimetry data with the information they need to prepare for the arrival of SWOT data in late 2023.</p>"},{"location":"community_resources/glossaries/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p> <p> CMIP(6):  </p> <p> ERA(5):  </p> <p> UM: </p>"},{"location":"community_resources/glossaries/glossary_access_nri/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_cmip/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_cssr/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_era/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_ipcc/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_um/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p> ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p> IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p> CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/training/","title":"Training and Policies","text":"<p>This space is intended to promote training material relevant to ACCESS and its community. The training material can be directly relevant to ACCESS and its model components, such as:</p> <ul> <li>using coupled models and model components</li> <li>using configurations</li> <li>using model evaluation tools and workflows</li> </ul> <p>It is also intended for training material around more peripheral topics that are essential for the community, such as:</p> <ul> <li>HPC</li> <li>version control</li> <li>essential software packages</li> </ul> <p>ACCESS-NRI encourages the members of the community to contact us to share their suggestions.</p> <p>Finally, you will also find ACCESS-NRI's policies in this space.</p>"},{"location":"community_resources/training/ACCESS_training/","title":"ACCESS Training Material","text":"<p>This page is intended to provide access to training material directly related to ACCESS models and model components. This material can cover topics such as but not limited to:</p> <ul> <li>how to use a specific model</li> <li>how to modify a model configuration</li> <li>how to test a model modification or validate a model run</li> </ul>"},{"location":"community_resources/training/ACCESS_training/#jules-tutorials","title":"JULES tutorials","text":"<p>The JULES tutorials explain how to use FCM, Rose and Cylc both for using the model and for development work. They can be useful to ACCESS users as practical demonstrations of the Rose and Cylc infrastructure.</p>"},{"location":"community_resources/training/additional_training/","title":"Additional training material","text":"<p>To learn the basics of Git and GitHub. It also includes ACCESS-NRI's recommendations to setup GitHub. </p> <p></p> <p>The National Computational Infrastructure (NCI) provides training resources and in-person training courses throughout the year to help develop the skills of the NCI user community.  </p> <p>A full calendar of upcoming training opportunities can be found on their Opus page.</p> <p>Users can find important information and resources about using NCI systems and services in the NCI User Guides.</p>"},{"location":"contribute/","title":"How to Contribute","text":"<p>ACCESS-Hive is a community supported site, as such contributions to the ACCESS-Hive site are encouraged by any member of the community. Members of the ACCESS community are also welcome to become reviewers. Please refer to the following contribution guidelines to learn how you can help the ACCESS community build a documentation database useful to everyone.</p> <p>Although we encourage everyone to get involved and contribute to the ACCESS-Hive in order to adequately represent the needs of the entire ACCESS community, we recognise not everyone will have the time to do so. In case you do not have a lot of time, please consider sharing your ideas via issues on the ACCESS-Hive GitHub repository so someone might be able to add them to the ACCESS-Hive site for you.1</p> Abstract <p>The aim of this how-to is to enable you to:</p> <ul> <li>add or modify a link to a new documentation in an existing page</li> <li>contribute complex modifications, eg., add pages, modify the navigation, modify an existing page in depth etc.</li> <li>how to deal with relevant documentation that is not currently on a website</li> </ul>"},{"location":"contribute/#become-a-member-of-the-access-hive-organisation","title":"Become a member of the ACCESS-Hive organisation","text":"<p>The ACCESS-Hive organisation is open to any member of the ACCESS community. Furthermore, organisation members have write access to the ACCESS-Hive repository which simplifies the process to contribute. Members can work from branches that contain their modifications instead of creating and maintaining their own forks. </p> <p>As such, we encourage you to become a member of the organisation by replying to this issue and ask to be invited to join the organisation.</p>"},{"location":"contribute/#process-to-contribute","title":"Process to contribute","text":"<p>This documentation is based on the Material for Mkdocs theme. Please see the documentation for the theme or for Mkdocs for a full explanation of all the capabilities.</p> <p>The documentation is written in Markdown format. Please see this cheat sheet for a quick reference to the base syntax. Please note that Material for Mkdocs extends that syntax.</p> <p>Additionally, ACCESS-Hive is a portal for documentation hosted elsewhere. The documentation you want to add needs to be available from an existing website. We realise people might have standalone files or other information to share, please see our Standalone documentation page for ways to easily upload your documentation to a site.</p> <p>There are two main ways to contribute to the site:</p> <ul> <li>you can modify an existing page directly from GitHub without any knowledge of Git. This is a simple way suitable to light modifications.</li> <li>you can work on your local computer and use Git to manage your modifications. This is recommended for more involved modifications. It is the easiest way to modify the categories and menu structure used to navigate the site.</li> </ul> <ol> <li> <p>Image by pch.vector on Freepik\u00a0\u21a9</p> </li> </ol>"},{"location":"contribute/change-the-navigation/","title":"Change the navigation","text":""},{"location":"contribute/change-the-navigation/#structure-of-the-repository","title":"Structure of the repository","text":"<p>The important elements of the repository to know about before modifying the navigation are:</p> <ul> <li><code>docs/</code> folder: this folder contains all the documentation pages. There is an <code>index.md</code> file for the About page, one folder per tab on the site, an <code>assets/</code> folder to store images used in the documentation and some customisation folders such as <code>css/</code> or <code>font/</code>.</li> <li><code>mkdocs.yml</code>: it is a YAML formatted file, hence the <code>.yml</code> extension. The site navigation is defined in this file as well as options for the styling of the site.</li> </ul> YAML <p>YAML is a popular choice for configuration files, as it is a simple way of encoding data structures in a text file. See this short tutorial.</p>"},{"location":"contribute/change-the-navigation/#a-simple-example","title":"A simple example","text":"<p>The easiest way to explain how the navigation is defined is to look at an example. Let's say <code>mkdocs.yml</code> contains:</p> <pre><code>nav:\n- Welcome: index.md\n- ACCESS-NRI: ACCESS-NRI/ACCESS-NRI.md\n- Community: - Generate Bathymetry: community/bathymetry.md\n- How to contribute: - How to contribute: help/how_to_contribute.md\n- Setup: help/contribution_setup.md\n- Modify the documentation: help/modify_documentation.md\n- Change the navigation: help/change_navigation.md\n</code></pre> <p>The top level category names define the tabs in the header bar. So here we have the tabs: \"Welcome\", \"ACCESS-NRI\", \"Community\" and \"How to contribute\". It is also the name of the top section under each tab.</p> <p></p> <p>The second level of categories indicate the name of each page under that section. So the \"ACCESS-NRI\" tab has the text directly under the section \"ACCESS-NRI\". The \"Community\" tab has a section called \"Community\" that contains one page: \"Generate Bathymetry\". Finally, the \"How to contribute\" tab has 1 section \"How to contribute\" with 4 pages.</p> <p>The filenames indicate the path to the file relative to the <code>docs/</code> folder containing the text for each page. It is recommended to use the title of each file (i.e. the heading level 1) or an abbreviation of it as the name of the page and the filename.</p> <p></p>"},{"location":"contribute/change-the-navigation/#add-sections-to-a-tab","title":"Add sections to a tab","text":"<p>It is possible to define several sections per tab by using more levels of indentation. For example, to add a \"My example\" section to the \"How to contribute\" tab:</p> <pre><code>nav:\n- Welcome: index.md\n- ACCESS-NRI: ACCESS-NRI/ACCESS-NRI.md\n- Community: - Generate Bathymetry: community/bathymetry.md\n- How to contribute: - How to contribute: help/how_to_contribute.md\n- Setup: help/contribution_setup.md\n- Modify the documentation: help/modify_documentation.md\n- Change the navigation: help/change_navigation.md\n- My example:\n- Beautiful example: help/beautiful_example.md\n</code></pre> <p>will create this navigation: </p>"},{"location":"contribute/edit-locally/","title":"Edit locally on your computer","text":"<p>If you want to submit a substantial contribution to ACCESS-Hive, it might be easier to do so from your own computer. Especially, it is a lot easier to proceed locally if you need to modify several files or want to modify the navigation of the site.</p> <p>You can avoid creating your own fork for the repository by first becoming a member of ACCESS-Hive organisation. To become a member, please reply to this issue and ask to be invited to join the organisation.</p> <p>To work locally, you will need git and a text editor installed on your computer.</p>"},{"location":"contribute/edit-locally/#open-an-issue","title":"Open an issue","text":"<p>For all additions or modifications to the ACCESS-Hive site, it is recommended to start by opening an Issue in the ACCESS-Hive GitHub repository. Consider assigning the Issue to yourself in the right-hand side panel if you intend on working on the issue and you are a member of the ACCESS-Hive organisation.</p>"},{"location":"contribute/edit-locally/#obtaining-the-source-files","title":"Obtaining the source files","text":"<p>Everything is stored within the ACCESS-Hive repository on GitHub and you simply need to clone this repository to your local machine:</p> <pre><code>git clone git@github.com:ACCESS-Hive/access-hive.github.io.git\n</code></pre>"},{"location":"contribute/edit-locally/#edit-to-access-hive","title":"Edit to ACCESS-Hive","text":"<p>Once you have installed all you need, you will need to follow the usual series of steps when contributing to Open Source developments:</p> <ul> <li>open an Issue</li> <li>clone the repository locally</li> <li>start a branch to work on, linked to the Issue</li> <li>commit your modifications to that branch and push to GitHub</li> <li>open a pull request between the <code>main</code> branch and your branch, follow the instructions from the Pull request template.</li> <li>ask for reviews by tagging the ACCESS-Hive/reviewers team and reply to requests for changes</li> </ul> <p>If you don't know how to do these steps, please refer to our Git and GitHub training.</p> What page to edit <p>If you have problems finding the page you need to edit, the easiest way is to head to the ACCESS-Hive site. If you click on the pen icon  at the top right of each page title, you will open a GitHub page showing you the path to the file you want to edit.</p> Headers and table of content <p>The level 1 headers are reserved for the title of the page and are ignored from the pages' table of contents. Only use level 2 headers and higher to organise pages.</p>"},{"location":"contribute/edit-locally/#add-a-new-event","title":"Add a new event","text":"<p>The process to add a new event is a bit different from other updates on the site. Since you need to create a new file to contain the information about the event you are adding, it is recommended to work locally. You need to create a new Markdown file (identified by the <code>.md</code> extension) as described on this page. To record and submit your modification to the site, make sure you follow all the steps as explained in the Open Source process in the previous section.</p>"},{"location":"contribute/edit-locally/#preview-of-the-documentation","title":"Preview of the documentation","text":""},{"location":"contribute/edit-locally/#preview-from-a-pull-request","title":"Preview from a Pull Request","text":"<p>When a pull request is created or updated, GitHub will automatically build a preview of the documentation that includes the proposed changes.</p> <p>In the pull request, you will see the link to the preview appear in this fashion:</p> <p></p> Build delay <p>It can take a while for the preview to build, even after the CI check is indicated as finished. Please wait for the comment with the link to appear and allow for some time after that for the preview to be properly deployed.</p> <p>If you open the preview and it looks completely broken or if it hasn't updated from additional modifications in the pull request, it probably means the site hasn't finished building yet. If you wait a couple of minutes and refresh the page, it should fix itself.</p>"},{"location":"contribute/edit-locally/#local-preview-if-editing-on-your-own-computer","title":"Local preview (if editing on your own computer)","text":"<p>MkDocs includes a live preview server, so you can preview your changes as you write your documentation. The server will automatically rebuild the site upon saving.</p>"},{"location":"contribute/edit-locally/#software-installation","title":"Software installation","text":"<p>To build the site locally, you need to install [Material for Mkdocs][MatforMkdocs] and other plugins. You can find a full list in the <code>requirements.txt</code> file in the root of the ACCESS-Hive repository. Please use <code>pip</code> for the installation as some of packages are not updated or not available on <code>conda</code>:</p> <pre><code>pip install -r requirements.txt\n</code></pre>"},{"location":"contribute/edit-locally/#start-the-server","title":"Start the server","text":"<p>To start the server, open a terminal and navigate to your ACCESS-Hive local repository. Now type:</p> <pre><code>mkdocs serve\n</code></pre> <p>Your documentation will be built on http://127.0.0.1:8000. Open this URL in your browser to see a preview of the documentation. The URL is given in the terminal when running the <code>mkdocs serve</code> command. Make sure you keep the command running so as to see live updates on saving your modifications.</p>"},{"location":"contribute/edit-on-github/","title":"Edit directly on GitHub","text":"<p>This way to edit the site allows people with no knowledge of Git to contribute to ACCESS-Hive but is only suitable for light modifications of existing pages.</p> <ul> <li>Go to the page you want to modify on the ACCESS-Hive documentation site. At the right of the title, you will see a pen icon . When you click on this icon, your browser will open the file in GitHub allowing you to edit the file.</li> </ul> <ul> <li>Enter your modification in the main pane. All the files are written in Markdown.</li> </ul> Headers and table of content <p>The level 1 headers are reserved for the title of the page and are ignored from the pages' table of contents. Only use level 2 headers and higher to organise pages.</p> <ul> <li>Then add a commit message in the Commit changes box.</li> </ul> <ul> <li>Commit and open a pull request</li> </ul> Pull request is required <p>The <code>main</code> branch of the repository is protected and nobody can write to it directly. You will need to choose either to create a new branch (for ACCESS-Hive organisation members only) or to create a fork on your GitHub personal account (for non-members of ACCESS-Hive organisation) and then open a pull request in all cases. </p> <p>When creating the pull request, make sure to follow the instructions given to you in the pull request template. The description can be edited at any time. You can fill in the check list after creating the pull request. The pull request will automatically build a preview of the documentation with your proposed changes.</p> <ul> <li> <p>Ask for a review by tagging the <code>@ACCESS-Hive/reviewers</code> team in a comment.</p> </li> <li> <p>Reply to the review. You will be notified by email of any subsequent comment, request or action from the reviewer on this pull request. Please make sure you take any action required by the reviewer or your modification will not be accepted into the ACCESS-Hive site.</p> </li> </ul>"},{"location":"contribute/edit-on-github/#further-edits","title":"Further edits","text":"<p>During the review process, you might be requested to edit your proposed changes. For this, you will need to navigate to the branch created by GitHub. </p> <ul> <li>At the top of the Pull request window on GitHub, you should see a link to your branch, circled in red on the image:</li> </ul> <ul> <li>Once you click on this link, navigate to and open the file you need to modify, then click on the pen icon in the toolbar on the right, circled in red on the image:</li> </ul> <ul> <li> <p>Then commit your changes once again to the same branch. This will update the pull request and the preview of the site.</p> </li> <li> <p>You need to let the reviewer know once you are confident you have responded to all their concerns, so they can review again. For this, locate the \"Reviewers\" pane in the right-hand side menu list on GitHub and click the icon circled in red in the image:</p> </li> </ul>"},{"location":"contribute/reviewers/","title":"Reviewing for ACCESS-Hive","text":"<p>Any member of the ACCESS-Hive Github Community (to join) can join the reviewers team. Please ask one of the maintainers to invite you to join the reviewers team.</p>"},{"location":"contribute/reviewers/#reviewer-guidelines","title":"Reviewer Guidelines","text":"<p>Firstly, thank you so much for helping to review links submitted to the ACCESS-Hive, we\u2019re delighted to have your help. This document is designed to outline our editorial guidelines and help you understand our requirements for accepting a pull request (PR).</p>"},{"location":"contribute/reviewers/#guiding-principles","title":"Guiding principles","text":"<p>If the submitting authors have followed the contribution guidelines then the review should be rapid. An important requirement is the ACCESS-Hive is a portal to documentation, it does not host the documentation itself.</p> <p>For those PRs that don\u2019t quite meet the requirements, please try to give clear feedback on what needs fixing. Our goal is to maintain a high quality platform for exchanging links to relevant documentation and you, as a reviewer, have a key role to play.</p> <p>A review involves checking submissions against a checklist of essential features and details described at the top of each PR. This should be objective, not subjective; it should be based on the materials in the submission as perceived without distortion by personal feelings, prejudices, or interpretations.</p> <p>Some continuous tests such as hyperlink references checks and preview deployments are automatically triggered by submitting a PR.</p> <p>Reviewers should:</p> <ol> <li>Ensure that the tests are passing without errors.</li> <li>Do a visual check using the preview.</li> <li>Do a Github pull request review. See GitHub's extensive documentation</li> <li>Once you have approved the PR. Tag the editors team <code>@ACCESS-Hive/editors</code> in the discussion.</li> </ol> <p>We encourage reviewers to provide feedback from within the PR discussion.</p> <p>You can include in your review links to any new issues that you the reviewer believe to be impeding the acceptance of the pull request.</p>"},{"location":"contribute/standalone-documentation/","title":"Standalone documentation","text":"<p>You may have very valuable resources to share which are not currently available through any website, it is what we call \"standalone documentation\" in the current context.</p> <p>To contribute these resources to ACCESS-Hive, you will first need to make them available on the internet. Below are some ideas on how to do that:</p> <ol> <li>Check if your organisation has a documentation or information site suitable for your resource.</li> <li>Check if ACCESS-NRI has a documentation site suitable for your resource. Note in this case, you will be asked about ownership and license associated with your resource.</li> <li>Publish your documentation via Zenodo. This will clarify the licensing and reuse conditions.</li> </ol> <p>If none of the previous options seem suitable to you, please consult the forum.</p>"},{"location":"model_evaluation/","title":"Model Evaluation and Diagnostics (MED)","text":"<p>Model evaluation is about measuring how fit for purpose a particular model is.</p> <p>If you are new to model evaluation and diagnostics, we recommend you read our Getting Started with MED page.</p> <p>Here, we provide catalogs and pointers to observational data as well as model data that can be used for evaluation. We provide tools to process such data into a comparable format and a gallery of recipes to evaluate the formatted data.</p> Observational Data Catalog Model Data Catalog Data Format Processing Evaluation Recipe Gallery <p>Our vision: PLACEHOLDER FOR OUTCOME OF STAFF RETREAT</p>"},{"location":"model_evaluation/model_evaluation_data_processing/","title":"Data Processing Tools","text":"<p>On this page, we will provide you a list of currated data processing tools.</p> <p>While we are still ramping up this service, please take a look at the gallery of community tools on Community Resources -&gt; Community Data Processing Tools .</p>"},{"location":"model_evaluation/model_evaluation_live_diagnostics/","title":"Live Diagnostics on Gadi","text":"<p>Here, we will describe the tools we provide for \"live-diagnostics\" of the ACCESS configurations. These tools allow you to check model output/progress/failures at specified time steps while your model is running.</p>"},{"location":"model_evaluation/model_evaluation_observational_catalogs/","title":"Observational Data Catalog","text":"<p>As of June 2023, we provide the following observational data catalogs on Gadi@NCI through the project <code>kj13</code>:</p> <pre><code>/g/data/kj13/datasets\n\u251c\u2500\u2500 cmip6\n\u2502   \u2514\u2500\u2500 *.nc\n\u251c\u2500\u2500 esmvaltool\n\u2502   \u2514\u2500\u2500 obsdata-v2/\n\u2502       \u251c\u2500\u2500 Tier1\n\u2502       \u2502   \u251c\u2500\u2500 AIRS\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 *.nc\n\u2502       \u2502   \u2514\u2500\u2500  ...\n\u2502       \u251c\u2500\u2500 Tier2\n\u2502       \u2502   \u251c\u2500\u2500 BerkeleyEarth\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 *.nc\n\u2502       \u2502   \u2514\u2500\u2500  ...\n\u2502       \u2514\u2500\u2500 Tier3\n\u2502           \u251c\u2500\u2500 ERA5\n\u2502           \u2502   \u2514\u2500\u2500 OBS6_ERA5_reanaly_v1_Amon_pr_197901-202012.nc\n\u2502           \u2514\u2500\u2500  ...\n\u251c\u2500\u2500 ilamb\n\u2502   \u2514\u2500\u2500 DATA\n\u2502       \u251c\u2500\u2500 albedo\n\u2502       \u2502   \u251c\u2500\u2500 CERESed4.1\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 albedo.nc\n\u2502       \u2502   \u2514\u2500\u2500 ...\n\u2502       \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 iomb\n\u2502   \u2514\u2500\u2500 DATA\n\u2502       \u251c\u2500\u2500 silicate\n\u2502       \u2502   \u251c\u2500\u2500 GLODAP\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 *albedo*.nc\n\u2502       \u2502   \u2514\u2500\u2500 ...\n\u2502       \u2514\u2500\u2500 ...\n</code></pre> <p>If you want to use but do not have access to Gadi@NCI yet, please follow our instructions on how to Get Started with Model Evaluation.</p> Dataset name Downloaded /g/data/kj13/datasets/ AIRS 2020-12-04 Tier1/AIRS AIRS-2-0 2020-12-04 Tier1/AIRS-2-0 AIRS-2-1 2021-07-14 Tier1/AIRS-2-1 ATSR 2020-12-04 Tier1/ATSR CALIOP 2020-12-04 Tier1/CALIOP CERES-EBAF 2020-12-04 Tier1/CERES-EBAF CFSR 2020-12-04 Tier1/CFSR CloudSat 2020-12-04 Tier1/CloudSat ESACCI-GHG 2020-12-04 Tier1/ESACCI-GHG GPCP-SG 2020-12-04 Tier1/GPCP-SG ISCCP 2021-04-08 Tier1/ISCCP JRA-55 2022-11-15 Tier1/JRA-55 MODIS 2020-12-04 Tier1/MODIS SSMI 2020-12-04 Tier1/SSMI SSMI-MERIS 2021-10-19 Tier1/SSMI-MERIS TRMM-L3 2020-12-04 Tier1/TRMM-L3 ghgcci 2020-12-04 Tier1/ESACCI-GHG BerkeleyEarth 2020-12-04 Tier2/BerkeleyEarth CALIPSO-GOCCP 2023-01-28 Tier2/CALIPSO-GOCCP CERES-EBAF 2022-08-12 Tier2/CERES-EBAF CRU 2021-07-14 Tier2/CRU CT2019 2020-12-04 Tier2/CT2019 CowtanWay 2020-12-04 Tier2/CowtanWay Duveiller2018 2020-12-04 Tier2/Duveiller2018 E-OBS 2020-12-04 Tier2/E-OBS ESACCI-AEROSOL 2023-01-28 Tier2/ESACCI-AEROSOL ESACCI-CLOUD 2023-01-28 Tier2/ESACCI-CLOUD ESACCI-FIRE 2023-01-28 Tier2/ESACCI-FIRE ESACCI-LANDCOVER 2023-01-28 Tier2/ESACCI-LANDCOVER ESACCI-LST 2022-01-26 Tier2/ESACCI-LST ESACCI-OC 2022-01-26 Tier2/ESACCI-OC ESACCI-OZONE 2023-01-28 Tier2/ESACCI-OZONE ESACCI-SEA-SURFACE-SALINITY 2022-01-26 Tier2/ESACCI-SEA-SURFACE-SALINITY ESACCI-SOILMOISTURE 2023-01-28 Tier2/ESACCI-SOILMOISTURE ESACCI-SST 2023-01-28 Tier2/ESACCI-SST ESRL 2021-04-08 Tier2/ESRL Eppley-VGPM-MODIS 2020-12-05 Tier2/Eppley-VGPM-MODIS GCP2018 2021-11-08 Tier2/GCP2018 GCP2020 2021-11-08 Tier2/GCP2020 GHCN 2023-01-28 Tier2/GHCN GHCN-CAMS 2020-12-05 Tier2/GHCN-CAMS GISTEMP 2020-12-05 Tier2/GISTEMP GLODAP 2022-04-29 Tier2/GLODAP GPCC 2021-04-08 Tier2/GPCC HALOE 2023-01-28 Tier2/HALOE HadCRUT3 2023-01-28 Tier2/HadCRUT3 HadCRUT4 2023-01-28 Tier2/HadCRUT4 HadCRUT4-clim 2020-12-04 Tier2/HadCRUT4-clim HadCRUT5 2022-04-29 Tier2/HadCRUT5 HadISST 2023-01-28 Tier2/HadISST ISCCP-FH 2023-01-28 Tier2/ISCCP-FH JRA-25 2022-11-24 Tier2/JRA-25 Kadow2020 2022-08-12 Tier2/Kadow2020 Landschuetzer2016 2020-12-05 Tier2/Landschuetzer2016 Landschuetzer2020 2022-11-15 Tier2/Landschuetzer2020 MOBO-DIC_MPIM 2022-11-15 Tier2/MOBO-DIC_MPIM NCEP 2023-01-28 Tier2/NCEP NCEP-DOE-R2 2023-01-28 Tier2/NCEP-DOE-R2 NCEP-NCAR-R1 2023-01-28 Tier2/NCEP-NCAR-R1 NOAA-CIRES-20CR 2023-01-28 Tier2/NOAA-CIRES-20CR NOAAGlobalTemp 2022-08-12 Tier2/NOAAGlobalTemp OSI-450-nh 2020-12-05 Tier2/OSI-450-nh OSI-450-sh 2020-12-05 Tier2/OSI-450-sh OceanSODA-ETHZ 2022-11-17 Tier2/OceanSODA-ETHZ PATMOS-x 2023-01-28 Tier2/PATMOS-x PERSIANN-CDR 2020-12-05 Tier2/PERSIANN-CDR PHC 2020-12-05 Tier2/PHC PIOMAS 2020-12-05 Tier2/PIOMAS REGEN 2020-12-05 Tier2/REGEN Scripps-CO2-KUM 2022-04-29 Tier2/Scripps-CO2-KUM TCOM-CH4 2023-01-28 Tier2/TCOM-CH4 TCOM-N2O 2023-01-28 Tier2/TCOM-N2O WFDE5 2021-07-14 Tier2/WFDE5 WOA 2021-10-19 Tier2/WOA AURA-TES 2023-06-14 Tier3/AURA-TES CALIPSO-ICECLOUD 2023-06-14 Tier3/CALIPSO-ICECLOUD CDS-XCH4 2023-06-14 Tier3/DS-XCH4 CDS-XCO2 2023-06-14 Tier3/CDS-XCO2 ERA-Interim 2022-11-24 Tier3/ERA-Interim ERA-Interim-Land 2021-09-14 Tier3/ERA-Interim-Land ERA5 2021-02-12 Tier3/ERA5 ERA5-Land 2023-06-14 Tier3/ERA5-Land FLUXCOM 2022-01-26 Tier3/FLUXCOM HWSD 2023-06-14 Tier3/HWSD LandFlux-EVAL 2023-06-14 Tier3/LandFlux-EVAL MAC-LWP 2023-06-14 Tier3/MAC-LWP NIWA-BS 2023-06-16 Tier3/NIWA-BS"},{"location":"model_evaluation/model_evaluation_observational_catalogs/#todo-tier2","title":"ToDo Tier2","text":"Dataset name Downloaded /g/data/kj13/datasets/ ESDC Tier2/"},{"location":"model_evaluation/model_evaluation_observational_catalogs/#todo-tier3","title":"ToDo Tier3","text":"Dataset name Downloaded /g/data/kj13/datasets/ APHRO-MA Tier3/ CDS-SATELLITE-ALBEDO Tier3/ CDS-SATELLITE-LAI-FAPAR Tier3/ CDS-SATELLITE-SOIL-MOISTURE Tier3/ CDS-UERRA Tier3/ CERES-SYN1deg Tier3/ CLARA-AVHRR Tier3/ CLOUDSAT-L2 Tier3/ ESACCI-WATERVAPOUR Tier3/ GRACE Tier3/ JMA-TRANSCOM Tier3/ LAI3g Tier3/ MERRA2 Tier3/ MLS-AURA Tier3/ MTE Tier3/ NDP Tier3/ NIWA-BS Tier3/ NSIDC-0116-nh Tier3/ NSIDC-0116-sh Tier3/ UWisc Tier3/"},{"location":"model_evaluation/model_evaluation_recipe_gallery/","title":"Model Evaluation and Diagnostics (MED) Recipe Gallery","text":"<p>While we are still building this gallery, please have a look at the Community MED Recipes listed at Community Resources -&gt; Community Model Evaluation Recipes </p> <p>Here, we plan to provide you with an embedded link to our actively maintained Model Evaluation and Dianostics (MED) Recipe Gallery, hosted at medportal.herokuapp.com. For now, we provide a placeholder image with link and pointers to useful Model Evaluation and Dianostics (MED) resources.</p>"},{"location":"model_evaluation/model_evaluation_recipe_gallery/#link-to-our-med-recipe-gallery","title":"Link to our MED Recipe Gallery","text":""},{"location":"model_evaluation/model_evaluation_getting_started/","title":"Getting Started with Model Evaluation at NCI","text":"<p>Welcome to Model Evaluation and Diagnostics!</p> <p>Here, we provide you the important information to give you access to the large data that we curate at NCI's storage and show you how you can use it to figure out how fit for purpose specific models are, in particular when you compare them to osbervational data:</p> <p>1) Getting Access to NCI and relevant NCI projects 2) Setting up environments at gadi@NCI to load and evaluate observational and model data</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/","title":"Getting Started: Computing Access (Gadi@NCI)","text":"<p>Here, we provide you the important information to give you access to the large data that we curate at NCI's storage:</p> <p>1) Get an NCI Account 2) Join relevant NCI projects 3) Logging in to Gadi@NCI 4) Computing on Gadi</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#1-nci-account","title":"1) NCI Account","text":"<p>To be able to work with our data, you need an NCI account.</p> <p>If you don't have one yet, signup here.</p> <p>Note: You will need an institutional email address with an organisation that allows access to NCI (e.g., CSIRO, a university, etc.).</p> <p>Once you have signed up, you will be allocated a username. We will refer to this username (e.g. <code>kf1234</code>) as <code>$USER</code>.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#2-join-relevant-nci-projects","title":"2) Join relevant NCI projects","text":"<p>There is a plethora of NCI projects that may or may not be relevant for you.</p> <p>We recommend you have a chat with your supervisor to identify the relevant projects, but in any case suggest to join <code>xp65</code> for MED code as well as <code>kj13</code> for MED data.</p> <p>To get this conversation started, we list some possibly relevant projects below:</p> Project Description with link, * indicated compute resource ACCESS-NRI projects tm70 ACCESS-NRI Working Project * iq82 ACCESS-NRI MED Compute * kj13 ACCESS-NRI MED Data Dev ct11 ACCESS-NRI Replicated Datasets xp65 ACCESS-NRI Analysis Environments ACCESS projects access ACCESS software sharing p66 ACCESS - AOGCM / suppport development of the ACCESS modelling system * p73 ACCESS Model Output Archive (AOGCM) Data projects hh5 Climate-LIEF Data Storage ub7 Seasonal Prediction ACCESS-S1 Hindcast ux62 Seasonal Prediction ACCESS-S2 Hindcast cb20 ESGF CMIP3 Replication Data al33 ESGF CMIP5 Replication Data rr3 ESGF CMIP5 Australian Data Publication oi10 ESGF CMIP6 Replication Data fs38 ESGF CMIP6 Australian Data Publication rt52 ERA5 Replicated Data: Single and pressure-levels data uc16 ERA5 Replicated Datasets on Potential Temperature &amp; Vorticity Levels zz93 ERA5-Land Replicated Data zv2 Australian Gridded Climate Data (AGCD) Collection qv56 Reference Datasets for Climate Model Analysis/Forcing cj50 COSIMA Model Output Collection Other projects ik11 COSIMA shared working space v45 Ocean Extremes * ga6 Modelling the formation of sedimentary basins and continental margins * m18 Evolution and dynamics of the Australian lithosphere * q97 Earth dynamics and resources over the last billion years * qu79 Collaborative REAnalysis Technical Environment Intercomparison Project (CREATE-IP) <p>To join a project or find more projects, please use this NCI website.</p> <p>The first project that you join will become your default login project, e.g. <code>xp65</code>. We will refer to it as <code>$PROJECT</code> and we show you how to change it below.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#3-logging-in-to-gadinci","title":"3) Logging in to Gadi@NCI","text":"<p>If you have never logged onto Gadi before, we recommend to take a look at NCI's Welcome to Gadi website. It provides all the important commands and information for logging properly onto Gadi, like the following: \"To run jobs on Gadi, you need to first log in to the system. Users on Mac/Linux can use the built-in terminal. For Windows users, we recommend using MobaXterm as the local terminal. Logging in to Gadi happens through a Gadi login node.\"</p> <p>When you login, via the command <pre><code>ssh -Y $USER@gadi.nci.org.au\n</code></pre> you will enter your $HOME directory with your default <code>$PROJECT</code> and your default SHELL. Both are saved at <code>$HOME/.config/gadi-login.conf</code> and you can print them via <pre><code>cat $HOME/.config/gadi-login.conf\n</code></pre></p> <p>The <code>-Y</code> option is needed to run graphical tools by enabling the forwarding of trusted X protocol mesgs between X-Server on local system and X programs on Gadi.  You need to enable X Windowing system on your local system before running ssh. This can be done by running X-Server like XQuartz (Mac), MobaXterm (MS Windows), startx or similar (Linux).</p> <p>Again, for more useful information we recommend to check out NCI's Welcome to Gadi website.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#4-computing-on-gadi","title":"4) Computing on Gadi","text":""},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#gadi-resources","title":"Gadi Resources","text":"<p>Coupled climate models like ACCESS-CM involve, among other things, calculation of complex mathematical equations that explain the physics of the atmosphere and oceans. Performed at hundreds of millions of points around the Earth, these calculations require vast computing power to complete them in a reasonable amount of time, thus relying on the power of  high-performance computing (HPC) like Gadi. The Gadi supercomputer can handle more than 10 million billion (10 quadrillion) calculations per second and is connected to 100,000 Terabytes of high-performance research data storage.</p> <p>An overview of Gadi resources such as compute, storage and PBS jobs are described below. </p> <p>Useful NCI commands to check your available compute resources are:</p> Command Purpose <code>logout</code> or Ctrl+D To exit a session <code>hostname</code> Displays login node details <code>module list</code> Modules currently loaded <code>module avail</code> Available modules <code>nci_account -P [proj]</code> Compute allocation for [proj] <code>nqstat -P [proj]</code> Jobs running/queued in [proj] <code>lquota</code> Storage allocation and usage for all your projects"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#compute-hours","title":"Compute Hours","text":"<p>Compute allocations are granted to projects instead of directly to users and, hence, you need to be a member of a project in order to use its compute allocation. To run jobs on Gadi, you need to have sufficient allocated compute hours available, where the job cost depends on the resources reserved for the job and the amount of walltime it uses. </p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#storage","title":"Storage","text":"<p>Each user has a project-independent <code>$HOME</code> directory, which has a storage limit of 10 GiB. All data on <code>/home</code> is backed up.</p> <p>Through project membership, the user gets access to the storage space within the project folders <code>/scratch</code> and  <code>/g/data</code> filesystems for that particular project.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#pbs-jobs","title":"PBS Jobs","text":"<p>To run compute tasks such as an ACCESS-CM suite on Gadi, users need to submit them as jobs to queues. Within a job submission, you can specify the queue, duration and computational resources needed for your job. When a job submission is accepted, it is assigned a jobID (shown in the return message) that can then be used to monitor the job\u2019s status. </p> <p>On job completion, contents of the job\u2019s standard output/error stream gets copied to a file in the working directory with the respective format: <code>&lt;jobname&gt;.o&lt;jobid&gt;</code> and <code>&lt;jobname&gt;.e&lt;jobid&gt;</code>. Users should check these two log files before proceeding with post-processing of any output from their corresponding job.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/","title":"Getting Started with Model Evaluation at Gadi@NCI","text":"<p>At this stage of Getting Started, we assume that you already have access to Gadi@NCI. If this is not the case, please go to our instructions on how to get access to Gadi@NCI</p> <p>Here we describe where you can find, load, and evalulate observational and model data on Gadi.</p> <p>Note: You do not automatically have access to all of Gadi's storage at <code>/g/data/</code>, but need to be part of a <code>$PROJECT</code> to see files at <code>/g/data/$PROJECT</code>. Furthermore, if you use Gadi's job submission system PBS (Portable Batch System), you need to add the relevant storage to the <code>#PBS -l storage=gdata/xp65+gdata/kj13</code> (if you want the job to have access to <code>xp65</code> and <code>kj13</code> in this example).</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#21-access-med-our-currated-conda-environment-for-you-on-gadi","title":"2.1) <code>access-med</code>: Our currated <code>conda</code> environment for you on Gadi","text":"<p>To avoid running multiple (different) versions of code on Gadi, we provide you with a <code>conda</code> environment called <code>access-med</code> that we actually curate for you (version 0.1 is from June 2023).</p> <p>In order to change to this environment, please execute the following commands after loggin onto Gadi (and as part of your PBS scripts): <pre><code>$ module use /g/data/xp65/public/modules\n$ module load conda/access-med-0.1\n</code></pre></p> <p>If you are planning to run your code through JupyterLab on NCI's ARE, you need to use <code>/g/data/xp65/public/modules</code> as Module directories and <code>conda/are</code> as Modules when launching a JupyterLab session.</p> <p>You are now able to use the scripts of our currated environment, including <code>python3</code>, <code>intake</code>, <code>jupyter</code>, <code>esmvaltool</code>, or <code>ilamb</code>. The complete list of dependencies can be found in our dedicated GitHub repository.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#22-observational-data","title":"2.2) Observational Data","text":"<p>We provide an extensive collection of observational data on Gadi@NCI within the <code>/g/data/kj13/datasets</code> directory. </p> <p>Please take a look at our Observational Data Catalog for an overview.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#23-model-data","title":"2.3) Model Data","text":"<p>There are many models and data stored on Gadi, as you can imagine from the plethora of projects in Section 1.2. Downloading this data is hardly practical, so we suggest to work on Gadi instead.</p> <p>To avoid endless searches within Gadi's storage, we written a useful 'library' tool, called <code>access-nri-catalog</code>, that allows to search the Model Catalogs easily and is already loaded as part of our <code>access-med</code> <code>conda</code> environment. To find out how you can search for Model Data on Gadi, take a look at our Model Catalog.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#25-model-evaluation","title":"2.5) Model Evaluation","text":"<p>Now that you have both Observational Data and Model Data at the palm of your hand on Gadi@NCI, there are many ways to evaluate this data.</p> <p>As part of our ACCESS-NRI <code>conda</code> environment, we provide several Model Evaluation Tools, like <code>ilamb</code> or <code>esmvaltool</code>.</p> <p>Check out Model Evaluation at Gadi to find out how you can use them on Gadi.</p>"},{"location":"model_evaluation/model_evaluation_model_catalogs/","title":"ACCESS-NRI intake Model Catalog","text":"<p>ACCESS-NRI is hosting a number of calculated models for you through National Computational Infrastructure (NCI) storage.</p> <p>We have set up an ACCESS-NRI intake Catalog package that allows you to easily search and load the model data on this storage. The premise of this ACCESS-NRI intake Catalog is to provide a (\"meta\") catalog of intake-esm (\"sub\") catalogs, which each correspond to different \"experiments\".</p> Search for a model in the ACCESS-NRI intake Catalog Add your model data to the ACCESS-NRI intake Catalog"},{"location":"model_evaluation/model_evaluation_model_catalogs/model_evaluation_add_models/","title":"Add your model data to the ACCESS-NRI intake Catalog","text":"<p>You've just run a new experiment, now you want to create an intake-esm catalog for that experiment?</p> <p>Look at this Tutorial  to learn how to add your own models.</p>"},{"location":"model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/","title":"Search for a model in the ACCESS-NRI intake Catalog","text":"<p>To have the huge amount of data from different experiments on the NCI storage at the palm of your hand, we provide a (\"meta\") catalog for you to query via python as part of the <code>intake</code> package with our curated catalog plugin <code>intake.cat.access_nri</code> .</p> <p>To use this catalog, you need access to NCI's Gadi. Check out our Get Started with ACCESS at NCI  guide on how to get access.</p> <p>Once logged in to Gadi, you will need to add the <code>access-nri-catalog</code> to your <code>conda</code> environments and start an ARE JupyterLab Session. Check out our ACCESS-NRI Intake Catalog guide  for the specific setup (note that you can only read in data from specific experiments if they are loaded through the Storage keyword).</p> <p>Once your JupyterLab session started, you can access the <code>intake</code> catalog to load the data. Take a look at this Tutorial .</p> <pre><code># Impport packages for searching/loading/plotting\nimport intake\nfrom distributed import Client\nimport matplotlib.pyplot as plt\n\n# The search process is a 2-step one\n# Comparable with searching for a book in a library:\n# 1) You look for the right book/catalog sections\n# 2) You look for the right book/catalog in the these sections\n\n# Load the ACCES-NRI list of catalogs for available experiment data\n# Similar to an overview of library section\naccess_nri_catalog_sections = intake.cat.access_nri\n\n# Perform a search for names, models, variables etc.\nexample_section_search = access_nri_catalog_sections.search(name=\"cmip6_oi10\")\n\n# Once you are sufficiently happy with your search, you can load the \"section\"\ncatalog_sections = access_nri_catalog_sections.search(name=\"025deg_jra55_iaf_omip2_cycle1\").to_source()\n# and start looking for the right catalogs of interest\ncatalogs_of_interest = catalog_sections.search(filename=\"ocean_scalar.*\")\n\n# Call the client that allows use load the data efficiently\nclient = Client(threads_per_worker=1)\nclient.dashboard_link\n\n# Actually load the data\nexperiment_data = catalogs_of_interest.to_dataset_dict(progressbar=False)\n\n# Et voil\u00e0, you have loaded the data and can start plotting\nexperiment_data[\"ocean_scalar_snapshot.1day\"][\"temp_global_ave\"].plot(label=\"daily\")\nexperiment_data[\"ocean_scalar.1mon\"][\"temp_global_ave\"].plot(label=\"monthly\")\n_ = plt.legend()\n</code></pre>"},{"location":"model_evaluation/model_evaluation_on_gadi/","title":"Model Evaluation on Gadi","text":"<p>To kick-start your model evaluation efforts, we provide the following tools as part of our <code>access-med</code> <code>conda</code> environment (and tutorials for how to use them on Gadi@NCI):   - ilamb, a tool for International Land (and Ocean) Model Benchmarking.   - esmvaltool, an Earth System Model Evaluation Tool </p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool/","title":"Tutorial for using <code>esmvaltool</code> on Gadi@NCI","text":"The documentation on Hive is work in progress! <p>The ACCESS-Hive is a community resource that is a work in progress. We\u2019d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you\u2019d like us to provide but aren\u2019t able to contribute yourself.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/","title":"Tutorial for using <code>ilamb</code> on Gadi@NCI","text":"<p>This tutorial explains how you can setup and run International Land Model Benchmarking (ILAMB) and International Ocean Model Benchmarking (IOMB) tests on <code>NCI</code> infrastracture. Both projects are maintained as <code>python</code> code under the package name <code>ilamb</code>.</p> <p>The Tutorial contains: 1) Background 2) Installation guide 3) Setup details 4) Run <code>ilamb</code> 5) Run <code>liamb</code> on <code>NCI</code> 6) Fix your setup with <code>ilamb-doctor</code></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#1-background-international-land-model-benchmarking-ilamb-and-international-ocean-model-benchmarking-iomb","title":"1) Background: International Land Model Benchmarking (ILAMB) and International Ocean Model Benchmarking (IOMB)","text":"<p>As earth system models (ESMs) become increasingly complex, there is a growing need for comprehensive and multi-faceted evaluation of model projections. The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns to reduce uncertainties associated with key land surface processes.</p> <p>If you have used (and installed) <code>ilamb</code> on NCI and know the basic principle of <code>ilamb</code>, you can start from Section 5) Guide for using ilamb on NCI.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#2-installing-ilamb","title":"2) Installing <code>ilamb</code>","text":"<p>For NCI users, ACCESS-NRI is providing a <code>conda</code> environment called <code>ilamb_dev</code> through the <code>xp65</code> project, with ilamb installed. You can load and activate it via:</p> <pre><code>&gt;&gt;&gt; module use /g/data/xp65/public/modules\n&gt;&gt;&gt; module load conda/ilamb_dev\n&gt;&gt;&gt; conda activate ilamb_dev\n</code></pre> <p>We will soon add <code>ilamb</code> also to the ACCESS-NRI MED <code>conda</code> environment, <code>access-med</code> under project<code>xp65</code>.</p> <p>If you want to install <code>ilamb</code> yourself, please follow the official installation instructions at https://www.ilamb.org/doc/install.html.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#3-configuring-ilamb","title":"3) Configuring <code>ilamb</code>","text":"<p>Before you can run <code>ilamb</code>, you need to configure a few things:</p> <p>3.1. Organise the ILAMB_ROOT path 3.2. Set up a <code>config</code> file 3.3. Set up a <code>modelroute</code> and <code>regions</code> files (Optional, if you want to run only a subset of models and/or specific regions of the world) 3.4. Download a <code>shapefiles</code> files locally (Optional online, necessary offline e.g. on NCI compute nodes)</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#31-organise-the-ilamb_root-path","title":"3.1) Organise the ILAMB_ROOT path","text":"<p><code>ilamb</code> demands files to be organised in a specific directory structure of <code>DATA</code> and <code>MODELS</code>.</p> <p>If you do not have your own files yet, you can download and use example files provided as part of the  of <code>ilamb</code>'s First Steps Tutorial</p> <p>The following tree represents the organization of the contents of this extracted sample data (Note: We renamed the main directory name): <pre><code>$ILAMB_ROOT (renamed from \"ILAMB_sample\")\n\u251c\u2500\u2500 sample.cfg (see [Section 3.2](#32-set-up-a-config-file))\n\u251c\u2500\u2500 modelroute.txt (optional, see [Section 3.3](#33-set-up-modelroute-and-regions-files))\n\u251c\u2500\u2500 regions.txt (optional, see [Section 3.3](#33-set-up-modelroute-and-regions-files))\n\u251c\u2500\u2500 DATA\n\u2502   \u251c\u2500\u2500 albedo\n\u2502   \u2502   \u2514\u2500\u2500 CERES\n\u2502   \u2502       \u2514\u2500\u2500 albedo_0.5x0.5.nc\n\u2502   \u2514\u2500\u2500 rsus\n\u2502       \u2514\u2500\u2500 CERES\n\u2502           \u2514\u2500\u2500 rsus_0.5x0.5.nc\n\u2514\u2500\u2500 MODELS\n    \u2514\u2500\u2500 CLM40cn\n        \u251c\u2500\u2500 rsds\n        \u2502   \u2514\u2500\u2500 rsds_Amon_CLM40cn_historical_r1i1p1_185001-201012.nc\n        \u2514\u2500\u2500 rsus\n            \u2514\u2500\u2500 rsus_Amon_CLM40cn_historical_r1i1p1_185001-201012.nc\n</code></pre></p> <p>There are two main branches in this directory. The first is the <code>DATA</code> directory\u2013this is where we keep the observational datasets each in a subdirectory bearing the name of the variable. While not strictly necesary to follow this form, it is a convenient convention. The second branch is the <code>MODEL</code> directory in which we see a single model result from CLM.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#311-add-files-to-data","title":"3.1.1) Add files to DATA","text":"<p>There is a lot of DATA available to add. Take a look at https://www.ilamb.org/ILAMB-Data/ and https://www.ilamb.org/IOMB-Data/ for extensive lists for ILAMB-Data (land modelling) and IOMB-Data (ocean modelling).</p> <p><code>ilamb</code> has a commandline prompt to add new DATA in a substructure. To fetch all available DATA from the website, you can simply go to your $ILAMB_ROOT and type <pre><code>&gt;&gt;&gt; ilamb-fetch\n</code></pre></p> <p>The command will compare the above website with your current DATA and make suggestions for downloads: <pre><code>Comparing remote location:\n\n      https://www.ilamb.org/ILAMB-Data/\n\nTo local location:\n\n      ./\n\nI found the following files which are missing, out of date, or corrupt:\n\n      .//DATA/twsa/GRACE/twsa_0.5x0.5.nc\n      .//DATA/rlus/CERES/rlus_0.5x0.5.nc\n      ... (we have abbreviated the extensive list here)\n\nDownload replacements? [y/n]\n</code></pre></p> <p>You can use <code>ilamb-fetch -h</code> to see how you can adjust the remote and local locations. If you want to download IOMB-Data, you can for example use <pre><code>ilamb-fetch --remote_root https://www.ilamb.org/IOMB-Data/\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#312-add-files-to-model","title":"3.1.2) Add files to MODEL","text":"<p>If you want to add your own <code>MODEL</code> to <code>ilamb</code>, you can do so by following this description.</p> <p>For <code>NCI</code> users, our <code>ilamb_dev</code> <code>conda</code> enrivonment already provides all observational datasets from the <code>ilamb</code> official web and the ACCESS-ESM1_5 model result for user at <code>ILAMB_ROOT</code>. Stay tune for more observational and model data or tell us which ones we should definitely add.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#32-set-up-a-config-file","title":"3.2) Set up a <code>config</code> file","text":"<p>Now that we have the data, we need to setup a <code>config</code> file which the <code>ilamb</code> package will use to initiate a benchmark study.  </p> <p><code>ilamb</code> provides default config files here.</p> <p>Below we explain both which variables you can define, but start by showing you the minimum setup from the tutorial's. <code>sample.cfg</code> file:</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#minimum-configure-file-with-a-direct-and-a-derived-variable","title":"Minimum configure file with a direct and a derived variable","text":"<pre><code># This configure file specifies the variables\n\n[h1: Radiation and Energy Cycle]\n\n[h2: Surface Upward SW Radiation]\nvariable = \"rsus\"\n\n[CERES]\nsource   = \"DATA/rsus/CERES/rsus_0.5x0.5.nc\"\n\n[h2: Albedo]\nvariable = \"albedo\"\nderived  = \"rsus/rsds\"\n\n[CERES]\nsource   = \"DATA/albedo/CERES/albedo_0.5x0.5.nc\"\n</code></pre> <p>In brief: This file allows you to create different header descriptions of the experiments (<code>h1</code>: top level for grouping of variables, <code>h2</code>: sub-level for each variable), but most importantly the <code>variable</code>s that we will look into and their <code>source</code>. In the eaxmple, <code>rsus</code> (Surface Upward Shortwave Radiation) and <code>albedo</code> are the used variables. The latter is actually derived from two variables by dividing the Surface Upward Shortwave Radiation by the Surface Downward Shortwave Radiation, <code>derived = rsus/rsds</code>. Finally, sources are defined as <code>source</code> with a text-font header without <code>h1</code> or <code>h2</code>.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#changing-configure-file-variables","title":"Changing configure file variables","text":"<p>This is the list of all the variables you can modify in config file: <pre><code>source              = None\n#Full path to the observational dataset\n\ncmap                = \"jet\"\n#The colormap to use in rendering plots (default is 'jet')\n\nvariable            = None\n#Name of the variable to extract from the source dataset\n\nalternate_vars      = None\n#Other accepted variable names when extracting from models\n\nderived             = None\n#An algebraic expression which captures how the confrontation variable may be generated\n\nland                = False\n#Enable to force the masking of areas with no land (default is False)\n\nbgcolor             = \"#EDEDED\"\n#Background color\n\ntable_unit          = None\n#The unit to use when displaying output in tables on the HTML page\n\nplot_unit           = None\n#The unit to use when displaying output on plots on the HTML page\n\nspace_mean          = True\n#Disable to compute sums of the variable over space instead of mean values\n\nrelationships       = None\n#A list of confrontations with whose data we use to study relationships, the syntax is \"h2 tag/observational dataset\". You will see the relationship part in the output if you specify some relationship.\n\nctype               = None\n#Choose a specific Confrontion class. \n\nregions             = None\n#Specify the regions of confrontation\n\nskip_rmse           = False\n#akip rmse in program\n\nskip_iav            = True\n#Ship iav in program\n\nmass_weighting      = False\n#if switch to true, using an average data in a period to normalize\n\nweight              = 1    \n# if a dataset has no weight specified, it is implicitly 1\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#33-set-up-modelroute-and-regions-files","title":"3.3) Set up <code>modelroute</code> and <code>regions</code> files","text":"<p>If you plan to run only a specific subset of models, you can already define them in a <code>modelroute.txt</code> file. It could look like our specific example for running different versions (1, 2, and 3) of the ACCESS-ESM 1.5 suite:</p> <pre><code># Model Name                    , PATH/TO/MODELS  , EXTRA COMMANDS\nACCESS_ESM1-5-r1i1p1f1          , MODELS/r1i1p1f1 , CMIP6\nACCESS_ESM1-5-r2i1p1f1          , MODELS/r2i1p1f1 , CMIP6\nACCESS_ESM1-5-r3i1p1f1          , MODELS/r3i1p1f1 , CMIP6\n... (abbreviated)\n</code></pre>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#34-downloadlink-shapefiles-files-locally","title":"3.4) Download/link <code>shapefiles</code> files locally","text":"<p>You can download the <code>shapefiles</code> that are needed to run <code>ilamb</code> and <code>cartopy</code> offline here:</p> <ul> <li>For Land: https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_land.zip</li> <li>For Ocean: https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_ocean.zip</li> </ul> <p>Finally, you need to define that path as <code>CARTOPY_DATA_DIR</code> via  <pre><code>export CARTOPY_DATA_DIR=/absolute/path/to/shapefiles/directory\n</code></pre></p> <p>Note: For NCI, we already provide shapefiles in a directory as part of project <code>xp65</code>. After joining the project, you can thus easily use <pre><code>export CARTOPY_DATA_DIR=/g/data/xp65/public/apps/cartopy-data\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#4-run-ilamb","title":"4) Run <code>ilamb</code>","text":""},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#41-ilamb-run","title":"4.1) ilamb-run","text":"<p>Now that we have the configuration file set up, you can run the study using the <code>ilamb-run</code> script. Executing the following command at the $ILAMB_ROOT directory will run <code>ilamb</code> as specified in your <code>sample.cfg</code> for all models of the <code>model_root</code> and all regions (<code>global</code>) of the world: <pre><code>ilamb-run --config sample.cfg --model_root $ILAMB_ROOT/MODELS/ --regions global\n</code></pre> If you are on some institutional resource, you may need to launch the above command using a submission script, or request an interactive node. As the script runs, it will yield output which resembles the following: <pre><code>Searching for model results in /Users/ncf/sandbox/ILAMB_sample/MODELS/\n\n                                          CLM40cn\n\nParsing config file sample.cfg...\n\n                   SurfaceUpwardSWRadiation/CERES Initialized\n                                     Albedo/CERES Initialized\n\nRunning model-confrontation pairs...\n\n                   SurfaceUpwardSWRadiation/CERES CLM40cn              Completed  37.3 s\n                                     Albedo/CERES CLM40cn              Completed  44.7 s\n\nFinishing post-processing which requires collectives...\n\n                   SurfaceUpwardSWRadiation/CERES CLM40cn              Completed   3.3 s\n                                     Albedo/CERES CLM40cn              Completed   3.3 s\n\nCompleted in  91.8 s\n</code></pre> What happened here? First, the script looks for model results in the directory you specified in the <code>--model_root</code> option. It will treat each subdirectory of the specified directory as a separate model result. Here since we only have one such directory, <code>CLM40cn</code>, it found that and set it up as a model in the system. Next it parsed the configure file we examined earlier. We see that it found the CERES data source for both variables as we specified it. If the source data was not found or some other problem was encountered, the green <code>Initialized</code> will appear as red text which explains what the problem was (most likely <code>MisplacedData</code>). If you encounter this error, make sure that <code>ILAMB_ROOT</code> is set correctly and that the data really is in the paths you specified in the configure file.</p> <p>Next we ran all model-confrontation pairs. In our parlance, a confrontation is a benchmark observational dataset and its accompanying analsys. We have two confrontations specified in our configure file and one model, so we have two entries here. If the analysis completed without error, you will see a green <code>Completed</code> text appear along with the runtime. Here we see that <code>albedo</code> took a few seconds longer than <code>rsus</code>, presumably because we had the additional burden of reading in two datasets and combining them.</p> <p>The next stage is the post-processing. This is done as a separate loop to exploit some parallelism. All the work in a model-confrontation pair is purely local to the pair. Yet plotting results on the same scale implies that we know the maxmimum and minimum values from all models and thus requires the communcation of this information. Here, as we are plotting only over the globe and not extra regions, the plotting occurs quickly.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#42-run-specific-models-and-regions","title":"4.2) Run specific models and regions","text":"<p>As mentioned in Section 3.3, you can adjust the models and regions that <code>ilamb</code> will run on. You can find more information in the <code>ilamb</code> tutorial. Calling <code>ilamb-run</code> with both specifications, would look like: <pre><code>ilamb-run --config cmip.cfg --model_setup modelroute.txt --regions regions.txt\n</code></pre> where you call a specific config file (see Section 3.2) as well as specific model routes and regions with files (see Section 3.3).</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#43-viewing-the-benchmarking-output-in-your-browser","title":"4.3) Viewing the benchmarking output in your browser","text":"<p>The whole process generates a directory of results within ILAMB_ROOT which by default is called <code>_build</code>. To view the results locally on your computer, navigate into this directory and start a local <code>http</code> server: <pre><code>python -m http.server\n</code></pre> You should see a message similar to this (or use http://0.0.0.0:8000/): <pre><code>Serving HTTP on 0.0.0.0 port 8000 (http://0.0.0.0:8000/) ...\n</code></pre> Open this link in your browser and you will see a webpage with a summary table in the center. As we have so few variables and a single model at this point, the table will very simple:</p> <p></p> <p>As we add more variables and models, this summary table helps you understand relative differences in scores among models. For now, clicking on a row of the table will expand it to reveal the underlying datasets used. Clicking on CERES will take you to another page which presents detailed scores and plots.</p> <p></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#5-run-ilamb-on-nci","title":"5) Run <code>ilamb</code> on NCI","text":"<p>If you followed the guides above, you should be familiar with how you can setup <code>ilamb</code>.</p> <p>To run <code>ilamb</code> on NCI, you can either start an interactive setup Section 5.1 or use a non-interactive Portable Batch System (PBS) job Section 5.2.</p> <p>In both cases, you need to again define the variable <code>$ILAMB_ROOT</code></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#51-ilamb_root-and-datamodel-on-nci","title":"5.1) ILAMB_ROOT and DATA/MODEL on NCI","text":"<p>In our default setup, we will place ILAMB_ROOT and the shapefiles for cartopy directly in the home directory. First, you have to create the ILAMB_ROOT directory <pre><code>mkdir $PWD/ILAMB_ROOT\n</code></pre> You can then simply export their paths after login as: <pre><code>export ILAMB_ROOT=$PWD/ILAMB_ROOT\nexport CARTOPY_DATA_DIR=/g/data/xp65/public/apps/cartopy-data\n</code></pre></p> <p>You can of course change the path of the directory, but will need to take this into account for the PBS job by adding a command to change into the $ILAMB_ROOT directory (see PBS setup comments).</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#ilamb_rootdata-on-nci","title":"ILAMB_ROOT/DATA on NCI","text":"<p>An extensive colletion of DATA is provided in the <code>kj13</code> project. You need to have joined the project on NCI to get access to this data.</p> <p>To create a symbolic link to this data, use the bash command <pre><code>ln -s /g/data/kj13/datasets/ilamb/DATA $ILAMB_ROOT/DATA\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#ilmab_rootmodel-on-nci","title":"ILMAB_ROOT/MODEL on NCI","text":"<p>In the future, we will provide a symbolic link to a MODEL catalog for you as well.</p> <p>For now, you will need to create the directory $ILAMB_ROOT/MODEL and populate it with symbolic links to specific models yourself.</p> <p>In our example, we will use ACCESS-ESM1.5, which is provided on NCI as part of project <code>fs38</code>.  You need to have joined the project on NCI to get access to this data.</p> <p>To link the ACCESS-ESM1.5 suite files to your $ILAMB_ROOT/MODEL, simply execute the following bash command <pre><code>mkdir $ILAMB_ROOT/MODELS\nln -s /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r* $ILAMB_ROOT/MODELS\n</code></pre></p> <p>By the end of Section 5.1.1 and 5.1.2, your $ILAMB_ROOT Directory should look similar to <pre><code>$ILAMB_ROOT\n\u251c\u2500\u2500 ...\n\u251c\u2500\u2500 DATA -&gt; /g/data/kj13/datasets/ilamb/DATA\n\u2514\u2500\u2500 MODELS\n    \u251c\u2500\u2500 r10i1p1f1 -&gt; /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r10i1p1f1\n    \u251c\u2500\u2500 ... (abbreviated)\n    \u2514\u2500\u2500 r9i1p1f1 -&gt; /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r9i1p1f1\n</code></pre></p> <p>These different models have a lot of subdirectories, which are important to keep in mind when defining the <code>source</code> parameter in your <code>ilamb</code> <code>.cfg</code> file. Note that the <code>ilamb</code> files will end with <code>*.nc*. For example, one of the *rsus* files for run</code>r10i1p1f1<code>can be found (and used for</code>.cfg` under <pre><code>source = /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r1i1p1f1/Amon/rsus/gn/files/d20191115/rsus_Amon_ACCESS-ESM1-5_historical_r1i1p1f1_gn_185001-201412.nc\n</code></pre> or shorter  <pre><code>source = $ILAMB_ROOT/MODELS/r1i1p1f1/Amon/rsus/gn/files/d20191115/rsus_Amon_ACCESS-ESM1-5_historical_r1i1p1f1_gn_185001-201412.nc\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#52-portable-batch-system-pbs-jobs-on-nci","title":"5.2) Portable Batch System (PBS) jobs on NCI","text":"<p>The following default PBS file, let's call it <code>ilamb_test.sh</code> can help you to setup your own, while making sure to use the correct project (#PBS -P) to charge your computing cost to: <pre><code>#!/bin/bash\n\n#PBS -N default_ilamb\n#PBS -P tm70\n#PBS -q normalbw\n#PBS -l ncpus=1\n#PBS -l mem=32GB           \n#PBS -l jobfs=10GB        \n#PBS -l walltime=00:10:00  \n#PBS -l storage=gdata/xp65+gdata/kj13+gdata/fs38\n#PBS -l wd\n\nmodule use /g/data/xp65/public/modules\nmodule load conda/access-med-0.1\n\nexport ILAMB_ROOT=$PWD/ILAMB_ROOT\nexport CARTOPY_DATA_DIR=/g/data/xp65/public/apps/cartopy-data\n\nilamb-run --config cmip.cfg --model_setup $PWD/modelroute.txt --regions global\n</code></pre></p> <p>If you are not familiar with PBS jobs on NCI, you could find the guide here. In brief: this PBS script (which you can submit via the bash command <code>qsub ilamb_test.sh</code>), will submit a job to Gadi with the job name (#PBS -N) default_ilamb under project (#PBS -P) <code>tm70</code> with a normal queue (#PBS -q normalbw), for 1 CPU (#PBS -l ncpus=1) with 32 GB RAM (#PBS -l mem=32GB), with an walltime of 10 hours and access to 10 GB local disk space (#PBS -l jobfs=10GB) as well as data storage access to projects <code>xp65</code>, <code>kj13</code>, and <code>fs38</code> (again, note that you have to be member of both projects on NCI. Upon starting the job, it will change into to the working directory that you started the job from (#PBS -l wd) and load the access-med conda environment. Finally, it will export the $ILAMB_ROOT as well as $ARTOPY_DATA_DIR paths and start an <code>ilamb-run</code>.</p> <p>In our example, we actually run the <code>cmip.cfg</code> file from the <code>ilamb</code> config file github repository for files spec</p> <p>Note: If your ILAMB_ROOT and CARTOPY_DATA_DIR are not in your directory from where you submitted the job from, then you need to adjust the export commands to their path <pre><code>export ILAMB_ROOT=/absolute/path/where/ILAMB_ROOT/actually/is\nexport CARTOPY_DATA_DIR=/absolute/path/where/shapefiles/actually/are\n</code></pre></p> <p>Once the jobs are finished, you can again inspect the outcome as described in Section 4.3</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#6-fix-your-setup-with-ilamb_doctor","title":"6. Fix your setup with ilamb_doctor","text":"<p><code>ilamb_doctor</code> is a script you can use to diagnosing some missing model values or what is incorrect or missing from a given analysis. It takes options similar to <code>ilamb-run</code> and is used in the following way: ```[ILAMB/test]$ ilamb-doctor --config test.cfg --model_root ${ILAMB_ROOT}/MODELS/CLM</p> <p>Searching for model results in /Users/ncf/ILAMB//MODELS/CLM</p> <pre><code>                               CLM40n16r228\n                               CLM45n16r228\n                               CLM50n18r229\n</code></pre> <p>We will now look in each model for the variables in the ILAMB configure file you specified (test.cfg). The color green is used to reflect which variables were found in the model. The color red is used to reflect that a model is missing a required variable.</p> <pre><code>                       Biomass/GlobalCarbon CLM40n16r228 biomass or cVeg\n                                    ... (abbreviated)\n                        Precipitation/GPCP2 CLM50n18r229 pr\n</code></pre> <p>``` Here we have run the command on some inputs in our test directory. You will see a list of the confrontations we run and the variables which are required or their synonyms. What is missing in this tutorial is the text coloring which will indicate if a given model has the required variables.</p> <p>We have finish the introduction of basic <code>ilamb</code> usage. We believe you have some understanding of <code>ilamb</code> and cont wait to use it. if you still have any question or you want some developer level support, you can find more detail in their official tutorial.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima/","title":"Tutorial for using <code>pangeo</code> &amp; COSIMA on Gadi@NCI","text":"The documentation on Hive is work in progress! <p>The ACCESS-Hive is a community resource that is a work in progress. We\u2019d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you\u2019d like us to provide but aren\u2019t able to contribute yourself.</p> <p>https://pangeo.io</p>"},{"location":"models/","title":"ACCESS Models","text":"<p>ACCESS is a family of related computer models or components that represent different parts of the Earth system. ACCESS links various model components through software called couplers to form different Model Configurations.</p>"},{"location":"models/#access-model-components","title":"ACCESS Model Components","text":"Atmosphere Land Ocean Sea Ice Aerosols Atmospheric Chemistry Biogeochemistry Land Biogeochemistry Ocean Coupler"},{"location":"models/#access-model-configurations","title":"ACCESS Model Configurations","text":"ACCESS-CM                      ACCESS Coupled Model (CM) produces physical climate simulations by deploying the atmosphere, ocean, and sea-ice components. ACCESS-CM features improved fluid dynamics and a microphysical aerosol scheme.                  ACCESS-ESM                      ACCESS Earth System Model (ESM) simulates the carbon and other bio-chemical cycles within the climate system, by deploying the atmosphere, ocean, and sea-ice components. ACCESS-ESM is one of the two ACCESS global coupled model versions.                  ACCESS-OM                      ACCESS Ocean Model (OM) deploys the ocean and sea-ice components to provide the Australian climate community with ocean weather and climate data, including seasonal forecasting, climate variability, downscaling of climate in the marine environment around Australia, and ocean biogeochemistry."},{"location":"models/configurations/","title":"ACCESS Configurations","text":"<p>The Configurations section is still in development.</p> <p>What to expect in the next few months?</p> <p>The ACCESS-NRI will release model configurations and experiments to the community, including a reference model output for each experiment.</p> <p>The model configurations and experiments will be documented in this section as they are released by the ACCESS-NRI. The information will cover topics such as where to find a configuration or experiment, how to use a configuration to run your own experiment, where to find the data produced by a released experiment.</p>"},{"location":"models/configurations/access-am/","title":"ACCESS-AM","text":"<p>The ACCESS-AM model is a coupled model between the atmosphere and the land. The atmospheric model component is the UM model. The UM model comes by default coupled to the JULES land model. That is why the first configurations and experiments released of ACCESS-AM will be UM-JULES configurations. But the ACCESS-NRI is working to ensure subsequent releases of ACCESS-AM use the CABLE land model instead.</p>"},{"location":"models/configurations/access-am/#getting-started-information","title":"Getting started information","text":"<p>On this page, you will find information on how to gain access to the UM model and start using the model. You will also find links to various configurations and experiments you can use as a basis to design your experiment.</p>"},{"location":"models/configurations/access-am/#configurations","title":"Configurations","text":""},{"location":"models/configurations/access-am/#experiments","title":"Experiments","text":"<p>Some experiments already run with the UM are listed on:</p> <ul> <li>CLEX CMS wiki</li> </ul>"},{"location":"models/configurations/access-cm/","title":"ACCESS-CM","text":"ACCESS-CM2 (ACCESS Coupled Model 2) is a global fully-coupled climate model that includes the atmosphere, ocean and sea-ice components, and produces physical climate simulations. ACCESS-CM2 is one of the two models run by the Australian climate community for the   Coupled Model Intercomparison Project, CMIP."},{"location":"models/configurations/access-cm/#access-cm2-configurations","title":"ACCESS-CM2 configurations","text":"<ul> <li> <p>Atmosphere model (UM10.6): N96 resolution (1.875\u00b0 x 1.25\u00b0, 85 levels). Physical model only \u2013 no carbon cycle.</p> </li> <li> <p>Land surface model (CABLE2.5) </p> </li> <li> <p>Ocean model (MOM5): Tripolar grid, 1\u00b0 resolution, 50 levels.</p> </li> <li> <p>Sea ice model (CICE5.1) </p> COMPONENT MODEL VERSION Atmosphere UM 10.6 Land Surface CABLE 2.5 (integrated in UM) Ocean MOM 5 Sea Ice CICE 5.1 Coupler OASIS-MCT 3 </li> </ul> <p>ACCESS-NRI will release an ACCESS-CM model configuration. The first release of ACCESS-CM will be derived from the CSIRO ACCESS-CM2 configuration and will include atmosphere, land, ocean and sea ice components.</p>"},{"location":"models/configurations/access-cm/#access-cm2","title":"ACCESS-CM2","text":"<p>Citation 1 | Tutorial</p> <p>ACCESS-CM2 1 is one of Australia\u2019s contributions to the World Climate Research Programme\u2019s Coupled Model Intercomparison Project Phase 6 (CMIP6). The component models are: UM10.6 GA7.1 for the atmosphere, CABLE2.5 for the land surface, MOM5 for the ocean, and CICE5.1.2 for the sea ice. Compared to previous model versions ACCESS-CM2 shows better global hydrological balance, more realistic ocean water properties (in terms of spatial distribution) and meridional overturning circulation in the Southern Ocean but a poorer simulation of the Antarctic sea ice and a larger energy imbalance at the top of atmosphere. This energy imbalance reflects a noticeable warming trend of the global ocean over the spin-up period.</p> <ol> <li> <p>Daohua Bi, Martin Dix, Simon Marsland, Siobhan O'Farrell, Arnold Sullivan, Roger Bodman, Rachel Law, Ian Harman, Jhan Srbinovsky, Harun A Rashid, Peter Dobrohotoff, Chloe Mackallah, Hailin Yan, Anthony Hirst, Abhishek Savita, Fabio Boeira Dias, Matthew Woodhouse, Russell Fiedler, and Aidan Heerdegen. Configuration and spin-up of ACCESS-CM2, the new generation Australian Community Climate and Earth System Simulator coupled model. Journal of Southern Hemisphere Earth Systems Science, 70(1):225\u2013251, 2020.\u00a0\u21a9\u21a9</p> </li> </ol>"},{"location":"models/configurations/access-esm/","title":"ACCESS-ESM","text":"<p>ACCESS-ESM stands for ACCESS Earth System Model. Earth system model means it is a fully-coupled model that includes carbon cycle components.</p> <p>ACCESS-NRI will release an ACCESS-ESM model configuration. The first release of ACCESS-ESM will be derived from the CSIRO ACCESS-ESM1.5 configuration and will include atmosphere, land and land biogeochemistry, ocean and ocean biogeochemistry, and sea ice components.</p>"},{"location":"models/configurations/access-esm/#access-esm15","title":"ACCESS-ESM1.5","text":"<p>Citation 1</p> <p>ACCESS Training Workshop (AMOS 2021)</p> <p>Webinar: Getting Started with ACCESS-CM2 and ACCESS-ESM1.5 </p> <p>ACCESS-ESM1.5 1 is a fully-coupled climate model with land and ocean carbon cycle components. ACCESS-ESM1.5 has mainly been developed to enable Australia to participate in the Coupled Model Intercomparison Project Phase 6 (CMIP6) with an ESM version. An assessment of the climate response to CO2 forcing indicates that ACCESS-ESM1.5 has an equilibrium climate sensitivity of 3.87\u00b0C.</p> <ol> <li> <p>Tilo Ziehn, Matthew A Chamberlain, Rachel M Law, Andrew Lenton, Roger W Bodman, Martin Dix, Lauren Stevens, Ying-Ping Wang, and Jhan Srbinovsky. The Australian Earth System Model: ACCESS-ESM1.5. Journal of Southern Hemisphere Earth Systems Science, 70(1):193\u2013214, 2020.\u00a0\u21a9\u21a9</p> </li> </ol>"},{"location":"models/configurations/access-om/","title":"ACCESS-OM","text":"<p>ACCESS-OM stands for ACCESS Ocean Model. There is more than just an ocean model, but it indicates that this is not a fully-coupled model, i.e. not coupled with a model atmosphere, the atmospheric fields that drive the model are provided by a data product, usually derived from reanalysis.</p> <p>ACCESS-NRI will release an ACCESS-OM model configuration. The first release of ACCESS-OM will be derived from the COSIMA ACCESS-OM2 suite and will include ocean and sea ice components.</p>"},{"location":"models/configurations/access-om/#access-om2","title":"ACCESS-OM2","text":"<p>Citation 1 | Documentation</p> <p>ACCESS-OM2 1 is a suite of coupled ocean-sea ice models developed by the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA). All models use the MOM5 ocean model coupled to the CICE5 sea ice model via OASIS3-MCT.</p> <p>The models in the ACCESS-OM2 suite differ by their grid spatial resolution:</p> <ul> <li>ACCESS-OM2 at 1\u00b0 with 50 vertical levels</li> <li>ACCESS-OM2-025 at 0.25\u00b0 with 50 vertical levels</li> <li>ACCESS-OM2-01 at 0.1\u00b0 with 75 vertical levels</li> </ul> <ol> <li> <p>A. E. Kiss, A. McC. Hogg, N. Hannah, F. Boeira Dias, G. B. Brassington, M. A. Chamberlain, C. Chapman, P. Dobrohotoff, C. M. Domingues, E. R. Duran, M. H. England, R. Fiedler, S. M. Griffies, A. Heerdegen, P. Heil, R. M. Holmes, A. Klocker, S. J. Marsland, A. K. Morrison, J. Munroe, M. Nikurashin, P. R. Oke, G. S. Pilo, O. Richet, A. Savita, P. Spence, K. D. Stewart, M. L. Ward, F. Wu, and X. Zhang. ACCESS-OM2 v1.0: a global ocean\u2013sea ice model at three resolutions. Geoscientific Model Development, 13(2):401\u2013442, 2020. URL: https://gmd.copernicus.org/articles/13/401/2020/, doi:10.5194/gmd-13-401-2020.\u00a0\u21a9\u21a9</p> </li> </ol>"},{"location":"models/configurations/access-s/","title":"ACCESS-S","text":"<p>ACCESS-S is the Bureau of Meteorology's climate modelling system used for seasonal forecasting.</p> <p>This coupled model uses a different set of model components than the other ACCESS models:</p> <ul> <li>UM for the atmosphere</li> <li>JULES for the land</li> <li>NEMO for the ocean</li> <li>CICE for the sea-ice</li> <li>OASIS3-MCT for the coupler</li> </ul>"},{"location":"models/model_components/","title":"Model Components","text":"<p>ACCESS components represent different chemical, physical or biological parts of the Earth System.</p> Atmosphere Land Ocean Sea Ice Aerosols Atmospheric Chemistry Biogeochemistry Land Biogeochemistry Ocean Coupler <p>Most model components have originated from collaborations with international research groups. These include:</p> <ul> <li>UK Met Office \u2192 Unified Model (UM) atmospheric component.</li> <li>NOAA/ Geophysical Fluid Dynamics Laboratory (GFDL) \u2192 Modular Ocean Model (MOM) component.</li> <li>Los Alamos National Laboratory (LANL) \u2192 Sea ice model (CICE) component.</li> <li>Centre Europ\u00e9en de Recherche et de Formation Avanc\u00e9e en Calcul Scientifique (CERFACS) \u2192 Ocean-Atmosphere-Sea Ice-Snowpack Model Coupling Toolkit (OASIS3-MCT).</li> <li>United Kingdom Chemistry and Aerosols (UKCA) \u2192 UK community atmospheric Chemistry-Aerosol (UKCA) model.</li> <li>CSIRO, COSIMA and CLEX \u2192 Community Atmosphere Biosphere Land Exchange (CABLE),  Whole Ocean Model with Biogeochemistry And Trophic-dynamics (WOMBAT) and land biogeochemistry Carnegie\u2013Ames\u2013Stanford-Approach (CASA) models. These models have been developed in Australia.</li> </ul>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/","title":"Aerosol and Atmospheric Chemistry Components","text":""},{"location":"models/model_components/aerosols_atmospheric_chemistry/#ukca","title":"UKCA","text":"<p>The UK Chemistry-Aerosol model (UKCA) is a community atmospheric chemistry-aerosol global model  developed in the United Kingdom. It is suitable for a range of topics in climate and environmental change research.</p>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/#how-is-ukca-used","title":"How is UKCA used?","text":"<p>UKCA chemistry model is enabled in ACCESS-CM2-Chem.</p>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/#glomap","title":"GLOMAP","text":"<p>UKCA contains an aerosol scheme GLObal Model of Aerosol Processes (GLOMAP) that can be used independently. The multi-component, multi-modal GLOMAP model allows simulation of aerosol number, size and concentrations of individual components such as sulphate,sea salt and different types of carbon.</p>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/#how-is-glomap-used","title":"How is GLOMAP used?","text":"<p>GLOMAP is used in ACCESS-CM2 and ACCESS-CM2-Chem.</p>"},{"location":"models/model_components/atmosphere/","title":"Atmospheric Model Component","text":""},{"location":"models/model_components/atmosphere/#the-unified-model-um","title":"The Unified Model (UM)","text":"<p>The Unified Model (UM) is a numerical model of the atmosphere used for both weather and climate applications, developed by the Met Office in the United Kingdom (UK). It includes solutions of the equations of atmospheric fluid dynamics with advanced parameterizations of subgrid-scale physical processes like convection, cloud formation and atmospheric radiation.</p> <p>The Unified Model gets its name because a single model is used across a wide range of both timescales (nowcasting to centennial) and spatial scales (sub km convective scale to global climate modelling).</p> <p>The UM is used by several international operational meteorology and research organizations and these contribute towards its development through the UM partnership.</p>"},{"location":"models/model_components/atmosphere/#how-is-the-um-used","title":"How is the UM used?","text":"<p>The UM Model component represents the atmosphere in many of the ACCESS Models used at regional and global scales.</p> <p>The ACCESS-CM2 climate model and ACCESS-ESM1-5 earth system model use versions of the UM as their atmospheric components.</p> <p>The Australian Bureau of Meteorology operational 12 km spatial resolution global forecasting system uses the Unified Model, as part of ACCESS for:</p> <ul> <li>Forecasting of extreme events and emergencies such as heatwaves, bushfires, cyclones, floods, coral bleaching, sea-level rise, coastal inundation and more.</li> <li>Daily and seasonal weather forecasts</li> </ul>"},{"location":"models/model_components/atmosphere/#useful-links","title":"Useful links","text":"<p>STASH register: Metadata reference for the outputs variables.</p>"},{"location":"models/model_components/bgc_land/","title":"Biogeochemistry Land","text":""},{"location":"models/model_components/bgc_land/#casa-cnp","title":"CASA-CNP","text":"<p>CASA (Carnegie-Ames-Stanford Approach)-CNP (Carbon-Nitrogen-Phosphorous) is the land biogeochemistry model developed in CABLE.</p> <p>CASA-CNP models the dynamics of carbon pools and nitrogen and phosphorous limitations. It is directly coupled with the CABLE land surface model.</p>"},{"location":"models/model_components/bgc_land/#how-is-casa-cnp-used","title":"How is CASA-CNP used?","text":"<p>CASA-CNP is switched on for carbon-cycle to use in the ACCESS-ESM1.5 model.</p>"},{"location":"models/model_components/bgc_ocean/","title":"Biogeochemistry Ocean","text":""},{"location":"models/model_components/bgc_ocean/#wombat","title":"WOMBAT","text":"<p>WOMBAT is the ocean carbon model (World Ocean Model of Biogeochemistry And Trophic-dynamics), developed in Australia. It calculates the carbon fluxes of the ocean, by simulating the evolution of phosphate, oxygen, dissolved inorganic carbon, alkalinity and iron with one class of phytoplankton and zooplankton.</p> <p>WOMBAT is a Nutrient, Phytoplankton, Zooplankton and Detritus (NPZD) model, with one zooplankton and one phytoplankton class.</p>"},{"location":"models/model_components/bgc_ocean/#how-is-wombat-used","title":"How is WOMBAT used?","text":"<p>WOMBAT is coupled to the MOM5 ocean model in the ACCESS-ESM1.5 and ACCESS-OM2 models.</p>"},{"location":"models/model_components/coupler/","title":"Coupler","text":"<p>A coupler is a software that allows synchronised exchanges of coupling information between numerical codes representing different components of the climate system.</p>"},{"location":"models/model_components/coupler/#oasis3-mct","title":"OASIS3-MCT","text":"<p>OASIS3-MCT is the version of the Ocean Atmosphere Sea Ice Soil (OASIS) coupler interfaced with the Model Coupling Toolkit (MCT) from the Argonne National Laboratory. OASIS3-MCT is the coupler used in the configurations: - ACCESS-ESM1.5 - ACCESS-CM2  - ACCESS-OM2 - ACCESS-S</p>"},{"location":"models/model_components/coupler/#nuopc-interoperability-layer","title":"NUOPC Interoperability Layer","text":"<p>NUOPC (National Unified Operational Prediction Capability) Interoperability Layer defines conventions and a set of generic components for building coupled models using the Earth System Modeling Framework (ESMF).</p> <p>ACCESS-OM3, a configuration currently under development, uses NUOPC to couple its MOM6 and CICE6 model components as there are no respective OASIS coupling interfaces for these components.</p>"},{"location":"models/model_components/land/","title":"Land Model Components","text":""},{"location":"models/model_components/land/#cable","title":"CABLE","text":"<p>Community Atmosphere Biosphere Land Exchange (CABLE) is a land surface model, used to calculate the fluxes of momentum, energy, water and carbon between the land surface and the atmosphere. It also models the main biogeochemical cycles of the land ecosystem when used in conjunction with the CASA-CNP module. </p>"},{"location":"models/model_components/land/#how-is-cable-used","title":"How is CABLE used?","text":"<p>CABLE can be run as a standalone model, for a single location, a region or globally. Coupled to the Met Office Unified Model (UM), CABLE provides the land surface component of the ACCESS Earth System Model (ACCESS-ESM) and ACCESS Coupled Model (ACCESS-CM).</p> <p>CABLE is an open source model developed by a community of Australian climate science researchers. Registration is required to access the CABLE code repository.</p>"},{"location":"models/model_components/land/#jules","title":"JULES","text":"<p>The Joint UK Land Environment System (JULES) is a community land surface model that can be used both as a standalone model and as the land surface component in the UM model. By modelling different land surface processes (surface energy balance, hydrological cycle, carbon cycle, dynamic vegetation, etc.) and their interaction with each other, JULES provides a framework to assess the impact of modifying a particular process on the ecosystem as a whole, e.g., the impact of climate change on hydrology.</p>"},{"location":"models/model_components/ocean/","title":"Ocean Model Component","text":""},{"location":"models/model_components/ocean/#modular-ocean-model-mom","title":"Modular Ocean Model (MOM)","text":"<p>The Modular Ocean Model (MOM) is one of the ocean components of the ACCESS climate model system. Used to simulate ocean currents at both regional and global scales, MOM is an invaluable tool for studying the global ocean climate system, as well as capabilities for regional and coastal applications. </p>"},{"location":"models/model_components/ocean/#mom5","title":"MOM5","text":"<p>Source Code</p> <p>MOM5 is used in supported climate ACCESS configurations.</p>"},{"location":"models/model_components/ocean/#mom6","title":"MOM6","text":"<p>Source Code | Tutorials</p> <p>The most recent version, MOM6, is an open source development by a consortium of scientists across several government agencies and academic institutions with critical contributions provided by researchers worldwide.</p>"},{"location":"models/model_components/sea-ice/","title":"Sea-Ice Model Component","text":""},{"location":"models/model_components/sea-ice/#cice","title":"CICE","text":"<p>CICE is a numerical model for simulating the growth, melting and movement of polar sea ice. This software package was developed by researchers at Los Alamos National Laboratory team and is currently managed by the CICE Consortium, an international group of institutions formed to maintain and develop CICE in the public domain.</p> <p>CICE5 is the current version used in ACCESS model configurations.</p> <p>CICE6 is currently under development.</p>"},{"location":"models/running-a-model/","title":"Running a Model","text":"<p>Here, we are providing the information to run different ACCESS models.</p> <p>If Model, Model Component or Model Configuration are not familiar terms for you, please check out our Model overview.</p> <p>If you have not run a model before, our Getting Started Guide will give you the basics to access the Model infrastructure on the high-performance-computing facility Gadi@NCI.</p> <p>Detailed guides for the different Model configurations can then be found on the following pages: -  Run ACCESS-ESM for the ACCESS Earth System Model configurations -  Run ACCESS-CM for the ACCESS Coupled Model configurations -  Run ACCESS-AM for the ACCESS Atmosphere Model configurations -  Run ACCESS-OM for the ACCESS Ocean Model configurations  </p>"},{"location":"models/running-a-model/running-access-cm/","title":"Running ACCESS-CM2 Model","text":"<p>This section includes a step-by-step instruction set on how to run the ACCESS-CM2 suite.</p> <p>It is also built as a future point of reference, where you can come back and find the section containing the information you need.</p>"},{"location":"models/running-a-model/running-access-cm/#getting-started","title":"Getting Started","text":"<ul> <li>An institutional email address with an organisation that allows access to NCI (e.g., CSIRO, a university, etc.).</li> <li>Access to NCI compute/storage.</li> <li>A Linux/Mac/Unix computer with an internet connection and a command line terminal (e.g., MacOS with XQuartz and command line tools installed, or Putty Cygwin/MobaXterm/similar X-Windows compatible program on a PC). </li> </ul>"},{"location":"models/running-a-model/running-access-cm/#requirements-for-running-access-cm-suites","title":"Requirements for running ACCESS-CM suites","text":"<p>Here, we assume that you already have access to Gadi, the supercomputer hosted by the National Computational Infrastructure (NCI). If needed, you can go back to our guide on how to get access to Gadi.</p>"},{"location":"models/running-a-model/running-access-cm/#basic-setup","title":"Basic Setup","text":"<p>To run an ACCESS-CM suite, new users will need to:</p> <ul> <li>Join the ACCESS group. You can also find instructions on how to join a particular project through the NCI self-service portal. </li> <li>Connect to accessdev to complete your setup once you have your NCI credentials and are a member of the ACCESS group.  Note: At present, both accessdev and ARE run the models on Gadi. However, ARE only supports shorter-running suites (i.e., runs less than 48 hours). Work is currently in progress to fully transition the cylc workflows from accessdev virtual machine to the ARE.</li> <li>Additional steps relating to the communication between accessdev and Gadi may also be necessary.</li> </ul>"},{"location":"models/running-a-model/running-access-cm/#uk-met-office-environment-on-nci","title":"UK Met Office Environment on NCI","text":"<p>As components within the ACCESS-CM suites use the UK Met Office model code, the UK Met Office Environment is installed on NCI. This comprises the model software and tools as well as the cylc workflow system, rose suites, the Met Office MOSRS repository and our local replica repository. In order to checkout and run ACCESS-CM2 suites on Gadi using Rose/Cylc, you need to have access to a number of repositories at the Met Office as well as the local replica and local software on NCI, which will require fullfilling these prerequisites.</p>"},{"location":"models/running-a-model/running-access-cm/#met-office-science-repository-service-mosrs","title":"Met Office Science Repository Service (MOSRS)","text":"<p>Met Office Science Repository Service (MOSRS) is a Trac server run by the UK Met Office for sharing code and configurations for the climate models it runs with partners. It contains the source code and configurations for the UM and JULES amongst other things.</p> <p>To apply for a MOSRS account, you should contact your local institutional sponsor.</p>"},{"location":"models/running-a-model/running-access-cm/#preparing-to-run-an-access-cm-suite","title":"Preparing to run an ACCESS-CM suite","text":"<p>At this stage, you should be able to connect to accessdev and Gadi. </p> <p>accessdev is a frontend system where you prepare ACCESS jobs and then submit them to Gadi (the supercomputer at NCI where ACCESS is run).  </p>"},{"location":"models/running-a-model/running-access-cm/#logging-in-to-gadi-and-accessdev","title":"Logging in to Gadi and accessdev","text":"<p>To run an ACCESS-CM2 suite (i.e., job), you need to first login to Gadi with your <code>username</code> through a login node. </p> <p><code>ssh -Y username@gadi.nci.org.au</code></p> <p>Similarly, to login to accessdev: </p> <p><code>ssh -Y $USER@accessdev.nci.org.au</code></p> <p>Aliases and shortcuts can be created to simplify these commands by configuring SSH.</p>"},{"location":"models/running-a-model/running-access-cm/#copy-edit-and-run-an-access-cm2-suite","title":"Copy, Edit, and Run an ACCESS-CM2 suite","text":"ACCESS-CM2 is a set of sub-models (eg. UM, MOM, CICE, CABLE, OASIS) with a range of model parameters, input data, and computer related information, that need to be packaged together as a suite in order to run.  Each ACCESS-CM2 suite has an ID, in the format <code>u-&lt;suite-name&gt;</code>, with <code>&lt;suite-name&gt;</code> being a unique identifier (e.g. <code>u-br565</code> is the CMIP6 release preindustrial experiment suite).  Typically, an existing suite is copied and then edited as needed for a particular run."},{"location":"models/running-a-model/running-access-cm/#copy-access-cm2-suites-with-rosie","title":"Copy ACCESS-CM2 suites with Rosie","text":"Rosie is an SVN repository wrapper with a set of options to work with ACCESS-CM2 suites.  To copy an existing suite, on accessdev:  <ol> <li>         Run <code>mosrs-auth</code> to authenticate using your MOSRS credentials:          mosrs-auth Please enter the MOSRS password for &lt;MOSRS-username&gt;: Successfully authenticated with MOSRS as &lt;MOSRS-username&gt; </li> <li>         Run <code>rosie checkout &lt;suite-ID&gt;</code> to create a local copy of the <code>&lt;suite-ID&gt;</code> from the UKMO repository (used mostly for testing and examining existing suites):          rosie checkout &lt;suite-ID&gt; [INFO] create: /home/565/&lt;$USER&gt;/roses [INFO] &lt;suite-ID&gt;: local copy created at /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;          Alternatively, run <code>rosie copy &lt;suite-ID&gt;</code> to create a new full copy (local and remote in the UKMO repository) rather than just a local copy. When a new suite is created in this way, a new unique name is generated within the repository, and populated with some descriptive information about the suite along with all the initial configuration details:          rosie copy &lt;suite-ID&gt; Copy \"&lt;suite-ID&gt;/trunk@&lt;trunk-ID&gt;\" to \"u-?????\"? [y or n (default)] y [INFO] &lt;new-suite-ID&gt;: created at https://code.metoffice.gov.uk/svn/roses-u/&lt;suite-n/a/m/e/&gt; [INFO] &lt;new-suite-ID&gt;: copied items from &lt;suite-ID&gt;/trunk@&lt;trunk-ID&gt; [INFO] &lt;suite-ID&gt;: local copy created at /home/565/&lt;$USER&gt;/roses/&lt;new-suite-ID&gt; </li> </ol> For additional <code>rosie</code> options, run <code>rosie help</code>.  The suites are created in the user's accessdev home directory, under <code>~/roses/&lt;suite-ID&gt;</code>.  The suite directory usually contains 2 subdirectories and 3 files: <ul> <li><code>app</code> \u2192 directory containing the configuration files for the various tasks within the suite.</li> <li><code>meta</code> \u2192 directory containing the GUI metadata.</li> <li><code>rose-suite.conf</code> \u2192 the main suite configuration file.</li> <li><code>rose-suite.info</code> \u2192 suite information file.</li> <li><code>suite.rc</code> \u2192 the Cylc control script file (Jinja2 language).</li> ls ~/roses/&lt;suite-ID&gt; app meta rose-suite.conf rose-suite.info suite.rc </ul>"},{"location":"models/running-a-model/running-access-cm/#edit-an-access-cm2-suite-configuration-with-rose-gui","title":"Edit an ACCESS-CM2 suite configuration with Rose GUI","text":"Rose is a configuration editor which can be used to view, edit, or run an ACCESS-CM2 suite.  To edit a suite configuration, on accessdev:  <ol> <li>         Run <code>rose edit &amp;</code> (the <code>&amp;</code> is optional and keeps the terminal prompt active while runs the GUI as a separate process) from inside the relevant suite directory (e.g. <code>~/roses/&lt;suite-ID&gt;</code>) to open the Rose GUI and inspect the suite information.          cd ~/roses/&lt;suite-ID&gt; rose edit &amp; [&lt;N&gt;] &lt;PID&gt; </li> <li>         There are many settings that can be changed in a Rose GUI. However, there are a few that we definitely want to check and edit before we run a suite:         <ul> <li>                 NCI Project                                  To make sure we run the suite under the NCI project we belong to, we can navigate to suite conf \u2192 Machine and Runtime Options, edit the Compute project field, and click the Save button . (Check how to connect to a project if you have not joined one yet).                                  If, for example, we belong to the tm70 Project (ACCESS-NRI), we will insert <code>tm70</code> in the Compute project field:                  </li> <li> Total Run length / Cycling frequency                  ACCESS-CM2 suites are often run in multiple steps, each of them constituting a cycle, with the job scheduler resubmitting the suite every chosen Cycling frequency, until the Total Run length is met.                                  To modify these parameters, we can navigate to suite conf \u2192 Run Initialisation and Cycling, edit the respective fields, and click the Save button . The values are in the ISO 8601 Duration format.                                  If, for example, we want to run the suite for a total of 50 Years, and resubmit every year, we will change Total Run length to <code>P50Y</code> and Cycling frequency to <code>P1Y</code>. Note that the current maximum Cycling frequency is 2 years:                  </li> <li> Wallclock time                  The Wallclock time is the time requested by the PBS job to run a single cycle. If this time is not enough for the suite to end its cycle, our job will be terminated before the suite can complete the run.                                   If we change the Cycling frequency, we might need to change the Wallclock time accordingly.                                   The time needed for the suite to run a full cycle depends on several factors, but a good estimation can be 4 hours per simulated year.                                  To modify the Wallclock time, we can navigate to suite conf \u2192 Run Initialisation and Cycling, edit the respective field, and click the Save button . The value is in the ISO 8601 Duration format.             </li> </ul> </li> </ol>"},{"location":"models/running-a-model/running-access-cm/#run-an-access-cm2-suite","title":"Run an ACCESS-CM2 suite","text":"After completing all the modifications to the suite, we are ready to run it.  ACCESS-CM2 suites run on Gadi through a PBS job submission.  When the suite gets run, the suite configuration files are copied on Gadi under <code>/scratch/&lt;$PROJECT&gt;/$USER/cylc-run/&lt;suite-ID&gt;</code>, and a symbolic link to this folder is also created in the <code>$USER</code>'s home directory under <code>~/cylc-run/&lt;suite-ID&gt;</code>.  An ACCESS-CM2 suite is constituted by several tasks (such as checking out code repositories, compiling and building the different model components, running the model, etc.). The workflow of these tasks is controlled by Cylc.  Cylc (pronounced \u2018silk\u2019), is a workflow manager that automatically executes tasks according to the model main cycle script <code>suite.rc</code>. Cylc deals with how the job will be run and manages the time steps of each sub-model, as well as monitoring all the tasks and reporting any error that might occur.  To run an ACCESS-CM2 suite, on accessdev: <ol> <li>         Run <code>rose suite-run</code>, from inside the suite directory, to run the initial tasks.     </li> <li>         After these few small tasks get executed, the Cylc GUI will open up and you will be able to see and control all the different tasks in the suite as they are run.     </li> cd ~/roses/&lt;suite-ID&gt; rose suite-run [INFO] export CYLC_VERSION=7.8.3 [INFO] export ROSE_ORIG_HOST=accessdev.nci.org.au [INFO] export ROSE_SITE= [INFO] export ROSE_VERSION=2019.01.2 [INFO] create: /home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt; [INFO] create: log.&lt;timestamp&gt; [INFO] symlink: log.&lt;timestamp&gt; &lt;= log [INFO] create: log/suite [INFO] create: log/rose-conf [INFO] symlink: rose-conf/&lt;timestamp&gt;-run.conf &lt;= log/rose-suite-run.conf [INFO] symlink: rose-conf/&lt;timestamp&gt;-run.version &lt;= log/rose-suite-run.version [INFO] install: rose-suite.info \u2003\u2003\u2003\u2003source: /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;/rose-suite.info [INFO] create: app [INFO] install: app \u2003\u2003\u2003\u2003source: /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;/app [INFO] create: meta [INFO] install: meta \u2003\u2003\u2003\u2003source: /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;/meta [INFO] install: suite.rc [INFO] REGISTERED &lt;suite-ID&gt; -&gt; /home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt; [INFO] create: share [INFO] install: share [INFO] create: work [INFO] chdir: log/ [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009._. [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009| |\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003The Cylc Suite Engine [7.8.3] [INFO] ._____._. ._| |_____.\u2003\u2003\u2003\u2003\u2003\u2009Copyright (C) 2008-2019 NIWA [INFO] | .___| | | | | .___|\u2003&amp; British Crown (Met Office) &amp; Contributors. [INFO] | !___| !_! | | !___. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ [INFO] !_____!___. |_!_____! This program comes with ABSOLUTELY NO WARRANTY; [INFO] \u2003\u2003\u2003\u2009.___! | \u2003\u2003\u2003\u2003\u2003see `cylc warranty`. \u2009It is free software, you [INFO] \u2003\u2003\u2003\u2009!_____! \u2003\u2003\u2003\u2003\u2003\u2009are welcome to redistribute it under certain [INFO] [INFO] *** listening on https://accessdev.nci.org.au:&lt;port&gt;/ *** [INFO] [INFO] To view suite server program contact information: [INFO]  $ cylc get-suite-contact &lt;suite-ID&gt; [INFO] [INFO] Other ways to see if the suite is still running: [INFO]  $ cylc scan -n '&lt;suite-ID&gt;' accessdev.nci.org.au [INFO]  $ cylc ping -v --host=accessdev.nci.org.au &lt;suite-ID&gt; [INFO]  $ ps -opid,args &lt;PID&gt;  # on accessdev.nci.org.au TO DO --&gt; Add Rose GUI image  </ol> You are done!!  If you don't get any errors, you will be able to check the suite output files after the run is complete.  Note that, at this stage, it is possible to close the Cylc GUI.  If you want to open it again, just run <code>rose suite-gcontrol</code> from inside the suite directory."},{"location":"models/running-a-model/running-access-cm/#check-for-errors","title":"Check for errors","text":"It is quite common, especially during the first few runs, to experience errors and job failures. An ACCESS-CM2 suite is constituted by several tasks,  and each of these tasks could fail. When a task fails, the suite is halted and you will see a red icon next to the respective task name in the Cylc GUI.   To investigate the cause of a failure, we need to look at the logs (<code>job.err</code> and <code>job.out</code>) from the suite run. There are two main ways to do so: <ul> <li>         Using the Cylc GUI                  Right-click on the task that failed and click on View Job Logs (Viewer) \u2192 job.err or job.out.                  To access the specific task you might have to click on the arrow next to the task, to extend the drop-down menu with all the sub-taks.          </li> <li>         In the <code>~/cylc-run/&lt;suite-ID&gt;</code> directory                  The suite logs directories are stored inside <code>~/cylc-run/&lt;suite-ID&gt;</code> as <code>log.&lt;TIMESTAMP&gt;</code>, with the lastest set of logs also symlinked in the <code>~/cylc-run/&lt;suite-ID&gt;/log</code> directory.                  The logs for the main job are inside the <code>~/cylc-run/&lt;suite-ID&gt;/log/job</code> directory.                  Logs are separated into simulation cycles through their starting dates, and then differentiated by task.                  They are then further separated into \"attempts\" (consecutive failed/successful tasks), with <code>NN</code> being a symlink to the most recent attempt.                  In our example, the failure occurred for the 09500101 simulation cycle (starting date on 1st January 950) in the coupled task. Therefore, the directory where to find the <code>job.err</code> and <code>job.out</code> files is <code>~/cylc-run/&lt;suite-ID&gt;/log/job/09500101/coupled/NN</code>.          cd ~/cylc-run/&lt;suite-ID&gt; ls app cylc-suite.db log log.20230530T051952Z meta rose-suite.info share suite.rc suite.rc.processed work cd log ls db job rose.conf rose-suite-run.conf rose-suite-run.locs rose-suite-run.log rose-suite-run.version suite suiterc cd job ls 09500101 cd 09500101 ls coupled fcm_make2_um fcm_make_um install_warm make2_mom make_mom fcm_make2_drivers fcm_make_drivers install_ancil make2_cice make_cice cd coupled ls 01 02 03 NN cd NN ls job job-activity.log job.err job.out job.status </li> </ul>"},{"location":"models/running-a-model/running-access-cm/#stop-restart-and-reload-suites","title":"Stop, restart and reload suites","text":"Sometimes, you may want to control the running state of a suite.  If your Cylc GUI has been closed and you are unsure whether your suite is still running, you can scan for active suites and reopen the GUI if desired.  To scan for active suites run <code>cylc scan</code>.  To reopen the Cylc GUI there are 2 main ways: <ul> <li>         run <code>rose suite-gcontrol</code> from inside the suite directory     </li>     OR     <li>         run <code>gcylc &lt;suite-ID&gt;</code> </li> </ul> cylc scan &lt;suite-ID&gt; &lt;$USER&gt;@accessdev.nci.org.au:&lt;port&gt; cd ~/roses/&lt;suite-ID&gt; rose suite-gcontrol  Add Rose GUI image  --&gt;"},{"location":"models/running-a-model/running-access-cm/#stop-a-suite","title":"STOP a suite","text":"Run <code>rose suite-stop -y</code>, from inside the suite directory, to shutdown a suite in a safe manner."},{"location":"models/running-a-model/running-access-cm/#restart-a-suite","title":"RESTART a suite","text":"There are two main ways to restart a suite: <ul> <li>         'SOFT' restart                  Run <code>rose suite-run --restart</code>, from inside the suite directory, to re-install the suite and reopen Cylc in the same state as when it was stopped (you may need to manually trigger failed tasks from the Cylc GUI).          cylc cd ~/roses/&lt;suite-ID&gt; rose suite-run --restart [INFO] export CYLC_VERSION=7.8.3 [INFO] export ROSE_ORIG_HOST=accessdev.nci.org.au [INFO] export ROSE_SITE= [INFO] export ROSE_VERSION=2019.01.2 [INFO] delete: log/rose-suite-run.conf [INFO] symlink: rose-conf/&lt;timestamp&gt;-restart.conf &lt;= log/rose-suite-run.conf [INFO] delete: log/rose-suite-run.version [INFO] symlink: rose-conf/&lt;timestamp&gt;-restart.version &lt;= log/rose-suite-run.version [INFO] chdir: log/ [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009._. [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009| |\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003The Cylc Suite Engine [7.8.3] [INFO] ._____._. ._| |_____.\u2003\u2003\u2003\u2003\u2003\u2009Copyright (C) 2008-2019 NIWA [INFO] | .___| | | | | .___|\u2003&amp; British Crown (Met Office) &amp; Contributors. [INFO] | !___| !_! | | !___. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ [INFO] !_____!___. |_!_____! This program comes with ABSOLUTELY NO WARRANTY; [INFO] \u2003\u2003\u2003\u2009.___! | \u2003\u2003\u2003\u2003\u2003see `cylc warranty`. \u2009It is free software, you [INFO] \u2003\u2003\u2003\u2009!_____! \u2003\u2003\u2003\u2003\u2003\u2009are welcome to redistribute it under certain [INFO] [INFO] *** listening on https://accessdev.nci.org.au:&lt;port&gt;/ *** [INFO] [INFO] To view suite server program contact information: [INFO]  $ cylc get-suite-contact &lt;suite-ID&gt; [INFO] [INFO] Other ways to see if the suite is still running: [INFO]  $ cylc scan -n '&lt;suite-ID&gt;' accessdev.nci.org.au [INFO]  $ cylc ping -v --host=accessdev.nci.org.au &lt;suite-ID&gt; [INFO]  $ ps -opid,args &lt;PID&gt;  # on accessdev.nci.org.au TO DO --&gt; Add Rose GUI image  </li> <li>         'HARD' restart                  Run <code>rose suite-run --new</code>, from inside the suite directory, if you want to overwrite any previous runs of the suite and begin completely afresh (WARNING!! This will overwrite all existing model output and logs).     </li> </ul>"},{"location":"models/running-a-model/running-access-cm/#reload-a-suite","title":"RELOAD a suite","text":"In some cases the suite needs to be updated without necessarily having to stop it (e.g. after fixing a typo in a file). Updating an active suite is called a 'reload', where the suite is 're-installed' and Cylc is updated with the changes (this is similar to a 'soft' restart, but with the new changes installed, so you may need to manually trigger failed tasks from the Cylc GUI).  To reload a suite run <code>rose suite-run --reload</code> from inside the suite directory."},{"location":"models/running-a-model/running-access-cm/#suite-output-files","title":"Suite output files","text":"All output files (as well as work files) are available on Gadi under <code>/scratch/$PROJECT/$USER/cylc-run/&lt;suite-ID&gt;</code> (also symlinked in <code>~/cylc-run/&lt;suite-ID&gt;</code>).  While the suite is running, files move between the <code>share</code> and the <code>work</code> directories.  At the end of each cycle, model output data and restart files are moved to <code>/scratch/$PROJECT/$USER/archive/&lt;suite-name&gt;</code>.   This directory contains 2 subdirectories: <ul> <li> <code>history</code>          This is the directory where the model output data is found, separated for each model component:          <ul> <li> <code>atm</code> \u2192 atmosphere (UM)             </li> <li> <code>cpl</code> \u2192 coupler (OASIS3-MCT)             </li> <li> <code>ocn</code> \u2192 ocean (MOM)             </li> <li> <code>ice</code> \u2192 ice (CICE)             </li> </ul>         For the atmospheric output data, each file it is usually a UM fieldsfile or netCDF file, formatted as <code>&lt;suite-name&gt;a.p&lt;output-stream-identifier&gt;&lt;year&gt;&lt;month-string&gt;</code>.                  In the case of the <code>u-br565</code> suite we will have:          cd /scratch/&lt;$PROJECT&gt;/&lt;USER&gt;/archive ls br565 &lt;suite-name&gt; &lt;other-suite-name&gt; cd br565 ls history restart ls history/atm br565a.pd0950apr.nc br565a.pd0950aug.nc br565a.pd0950dec.nc br565a.pd0950feb.nc br565a.pd0950jan.nc br565a.pd0950jul.nc br565a.pd0950jun.nc br565a.pd0950mar.nc br565a.pd0950may.nc br565a.pd0950nov.nc br565a.pd0950oct.nc br565a.pd0950sep.nc br565a.pd0951apr.nc br565a.pd0951aug.nc br565a.pd0951dec.nc br565a.pm0950apr.nc br565a.pm0950aug.nc br565a.pm0950dec.nc br565a.pm0950feb.nc br565a.pm0950jan.nc br565a.pm0950jul.nc br565a.pm0950jun.nc br565a.pm0950mar.nc br565a.pm0950may.nc br565a.pm0950nov.nc br565a.pm0950oct.nc br565a.pm0950sep.nc br565a.pm0951apr.nc br565a.pm0951aug.nc br565a.pm0951dec.nc netCDF </li> <li> <code>restart</code>          This is the directory where the restart dumps are found, subdivided for each model component (see <code>history</code> folder above).                  For the atmospheric restart files, each of them is a UM fieldsfile, formatted as <code>&lt;suite-name&gt;a.da&lt;year&gt;&lt;month&gt;&lt;day&gt;_00</code>.                  In the directory there are also some files formatted as <code>&lt;suite-name&gt;a.xhist-&lt;year&gt;&lt;month&gt;&lt;day&gt;</code> containing metadata information.                   In the case of the <code>u-br565</code> suite we will have:          ls /scratch/&lt;$PROJECT&gt;/&lt;USER&gt;/archive/br565/restart/atm br565a.da09500201_00 br565a.da09510101_00 br565.xhist-09500131 br565.xhist-09501231  </li> </ul> References <ul> <li> https://confluence.csiro.au/display/ACCESS/Using+CM2+suites+in+Rose+and+Cylc </li> <li> https://confluence.csiro.au/display/ACCESS/Understanding+CM2+output </li> <li> https://nespclimate.com.au/wp-content/uploads/2020/10/Instruction-document-Getting_started_with_ACCESS.pdf </li> <li> https://code.metoffice.gov.uk/doc/um/latest/um-training/rose-gui.html </li> </ul>"},{"location":"models/running-a-model/running-access-om/","title":"Running ACCESS-OM2 Model","text":"<p>Welcome to ACCESS-OM2 \u2014 a coupled ocean-ice model and collection of configurations developed by the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA).</p> <p>ACCESS-OM2 consists of the MOM 5.1 ocean model, CICE 5.1.2 sea ice model, and a file-based atmosphere called YATM coupled together using the OASIS3-MCT v2.0 coupler. Regridding is done using ESMF and KDTREE2.</p> <p>The configurations available here are updated from the version 1.0 configurations described in Kiss et al. (2020). Further details are given in the ACCESS-OM2 technical report.</p>"},{"location":"models/running-a-model/running-access-om/#how-to-access-existing-access-om2-output","title":"How to access existing ACCESS-OM2 output","text":"<p>NCI users can access model output via the COSIMA Cookbook. A good place to start is the data explorer, which will give an overview of the data available. Also see this overview of 0.1\u00b0 IAF outputs.</p> <p>Non-NCI users can access a subset of the ACCESS-OM2 output via the COSIMA Model Output Collection.</p>"},{"location":"models/running-a-model/running-access-om/#how-to-run-access-om2","title":"How to run ACCESS-OM2","text":"<p>Start by reading the [[Quick start|Getting-started#quick-start]] guide. If you are using gadi.nci.org.au at the NCI National Facility and are happy to use our pre-compiled executables then this should be all you need. The page also provides instructions for building your own executables.</p> <p>NOTE: All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you \"watch\" this repo (see button at top of screen; ask to be notified of all conversations) and also watch all the component models, whichever configuration(s) you are using, and payu to be kept informed of updates, problems and bug fixes as they arise.</p>"},{"location":"models/running-a-model/running-access-om/#getting-help-and-reporting-issues","title":"Getting help and reporting issues","text":"<p>For all help requests and error reports please create a \"GitHub issue\" at ACCESS-OM2 issues.</p>"},{"location":"models/running-a-model/running-access-om/#for-self-help","title":"For self-help","text":"<p>Setting up and running the model is primarily supported via the [[ACCESS-OM2 wiki|Home]] (that you are already reading). It is a \"wiki\" so feel free to correct and contribute.</p>"},{"location":"models/running-a-model/running-access-om/#how-to-update-this-wiki","title":"How to update this wiki","text":"<p>The wiki attached to a public repository can be edited by anyone. Just navigate to the page you wish to edit and click on the 'edit' button on the top right hand side.</p>"},{"location":"models/running-a-model/running-access-om/#references","title":"References","text":""},{"location":"models/running-a-model/getting_started/","title":"Getting Started to Run a Model","text":"<p>If Model, Model Component or Model Configuration are not familiar terms for you, please check out our Model overview.</p> <p>If you have not run a model before, our Getting Started Guide will give you the basics to access the Model infrastructure on the high-performance-computing facility Gadi@NCI.</p> <p>Detailed guides for the different Model configurations can then be found on the following pages: -  Run ACCESS-ESM for the ACCESS Earth System Model configurations -  Run ACCESS-CM for the ACCESS Coupled Model configurations -  Run ACCESS-AM for the ACCESS Atmosphere Model configurations -  Run ACCESS-OM for the ACCESS Ocean Model configurations  </p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/","title":"Getting Started: Computing Access (Gadi@NCI)","text":"<p>Here, we provide you the important information to give you access to the large data that we curate at NCI's storage:</p> <p>1) Get an NCI Account 2) Join relevant NCI projects 3) Logging in to Gadi@NCI 4) Computing on Gadi</p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#1-nci-account","title":"1) NCI Account","text":"<p>To be able to work with our data, you need an NCI account.</p> <p>If you don't have one yet, signup here.</p> <p>Note: You will need an institutional email address with an organisation that allows access to NCI (e.g., CSIRO, a university, etc.).</p> <p>Once you have signed up, you will be allocated a username. We will refer to this username (e.g. <code>kf1234</code>) as <code>$USER</code>.</p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#2-join-relevant-nci-projects","title":"2) Join relevant NCI projects","text":"<p>There is a plethora of NCI projects that may or may not be relevant for you.</p> <p>We recommend you have a chat with your supervisor to identify the relevant projects, but in any case suggest to join <code>xp65</code> for MED code as well as <code>kj13</code> for MED data.</p> <p>To get this conversation started, we list some possibly relevant projects below:</p> Project Description with link, * indicated compute resource ACCESS-NRI projects tm70 ACCESS-NRI Working Project * iq82 ACCESS-NRI MED Compute * kj13 ACCESS-NRI MED Data Dev ct11 ACCESS-NRI Replicated Datasets xp65 ACCESS-NRI Analysis Environments ACCESS projects access ACCESS software sharing p66 ACCESS - AOGCM / suppport development of the ACCESS modelling system * p73 ACCESS Model Output Archive (AOGCM) Data projects hh5 Climate-LIEF Data Storage ub7 Seasonal Prediction ACCESS-S1 Hindcast ux62 Seasonal Prediction ACCESS-S2 Hindcast cb20 ESGF CMIP3 Replication Data al33 ESGF CMIP5 Replication Data rr3 ESGF CMIP5 Australian Data Publication oi10 ESGF CMIP6 Replication Data fs38 ESGF CMIP6 Australian Data Publication rt52 ERA5 Replicated Data: Single and pressure-levels data uc16 ERA5 Replicated Datasets on Potential Temperature &amp; Vorticity Levels zz93 ERA5-Land Replicated Data zv2 Australian Gridded Climate Data (AGCD) Collection qv56 Reference Datasets for Climate Model Analysis/Forcing cj50 COSIMA Model Output Collection Other projects ik11 COSIMA shared working space v45 Ocean Extremes * ga6 Modelling the formation of sedimentary basins and continental margins * m18 Evolution and dynamics of the Australian lithosphere * q97 Earth dynamics and resources over the last billion years * qu79 Collaborative REAnalysis Technical Environment Intercomparison Project (CREATE-IP) <p>To join a project or find more projects, please use this NCI website.</p> <p>The first project that you join will become your default login project, e.g. <code>xp65</code>. We will refer to it as <code>$PROJECT</code> and we show you how to change it below.</p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#3-logging-in-to-gadinci","title":"3) Logging in to Gadi@NCI","text":"<p>If you have never logged onto Gadi before, we recommend to take a look at NCI's Welcome to Gadi website. It provides all the important commands and information for logging properly onto Gadi, like the following: \"To run jobs on Gadi, you need to first log in to the system. Users on Mac/Linux can use the built-in terminal. For Windows users, we recommend using MobaXterm as the local terminal. Logging in to Gadi happens through a Gadi login node.\"</p> <p>When you login, via the command <pre><code>ssh -Y $USER@gadi.nci.org.au\n</code></pre> you will enter your $HOME directory with your default <code>$PROJECT</code> and your default SHELL. Both are saved at <code>$HOME/.config/gadi-login.conf</code> and you can print them via <pre><code>cat $HOME/.config/gadi-login.conf\n</code></pre></p> <p>The <code>-Y</code> option is needed to run graphical tools by enabling the forwarding of trusted X protocol mesgs between X-Server on local system and X programs on Gadi.  You need to enable X Windowing system on your local system before running ssh. This can be done by running X-Server like XQuartz (Mac), MobaXterm (MS Windows), startx or similar (Linux).</p> <p>Again, for more useful information we recommend to check out NCI's Welcome to Gadi website.</p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#4-computing-on-gadi","title":"4) Computing on Gadi","text":""},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#gadi-resources","title":"Gadi Resources","text":"<p>Coupled climate models like ACCESS-CM involve, among other things, calculation of complex mathematical equations that explain the physics of the atmosphere and oceans. Performed at hundreds of millions of points around the Earth, these calculations require vast computing power to complete them in a reasonable amount of time, thus relying on the power of  high-performance computing (HPC) like Gadi. The Gadi supercomputer can handle more than 10 million billion (10 quadrillion) calculations per second and is connected to 100,000 Terabytes of high-performance research data storage.</p> <p>An overview of Gadi resources such as compute, storage and PBS jobs are described below. </p> <p>Useful NCI commands to check your available compute resources are:</p> Command Purpose <code>logout</code> or Ctrl+D To exit a session <code>hostname</code> Displays login node details <code>module list</code> Modules currently loaded <code>module avail</code> Available modules <code>nci_account -P [proj]</code> Compute allocation for [proj] <code>nqstat -P [proj]</code> Jobs running/queued in [proj] <code>lquota</code> Storage allocation and usage for all your projects"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#compute-hours","title":"Compute Hours","text":"<p>Compute allocations are granted to projects instead of directly to users and, hence, you need to be a member of a project in order to use its compute allocation. To run jobs on Gadi, you need to have sufficient allocated compute hours available, where the job cost depends on the resources reserved for the job and the amount of walltime it uses. </p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#storage","title":"Storage","text":"<p>Each user has a project-independent <code>$HOME</code> directory, which has a storage limit of 10 GiB. All data on <code>/home</code> is backed up.</p> <p>Through project membership, the user gets access to the storage space within the project folders <code>/scratch</code> and  <code>/g/data</code> filesystems for that particular project.</p>"},{"location":"models/running-a-model/getting_started/access_to_gadi_at_nci/#pbs-jobs","title":"PBS Jobs","text":"<p>To run compute tasks such as an ACCESS-CM suite on Gadi, users need to submit them as jobs to queues. Within a job submission, you can specify the queue, duration and computational resources needed for your job. When a job submission is accepted, it is assigned a jobID (shown in the return message) that can then be used to monitor the job\u2019s status. </p> <p>On job completion, contents of the job\u2019s standard output/error stream gets copied to a file in the working directory with the respective format: <code>&lt;jobname&gt;.o&lt;jobid&gt;</code> and <code>&lt;jobname&gt;.e&lt;jobid&gt;</code>. Users should check these two log files before proceeding with post-processing of any output from their corresponding job.</p>"}]}
\ No newline at end of file
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Index","text":""},{"location":"#welcome-to-access-hive","title":"Welcome to ACCESS-Hive","text":"ACCESS-Hive is a portal to all documentation relevant to the Australian Community Climate and Earth System Simulator, ACCESS, and the wider ACCESS community. ACCESS-Hive is developed for and by the ACCESS community following an open-source development model."},{"location":"#navigating-access-hive","title":"Navigating ACCESS-Hive","text":"Models Run a Model Model Evaluation Community Resources Community Forum"},{"location":"#about","title":"About","text":"The documentation on Hive is work in progress! <p>The ACCESS-Hive is a community resource that is a work in progress. We\u2019d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you\u2019d like us to provide but aren\u2019t able to contribute yourself.</p>"},{"location":"#support","title":"Support","text":"<p>There is a system of tags to identify who supports the linked documentation or software, and the level of support you can expect:</p> <ul> <li> <p><code>Supported by ACCESS-NRI</code> {{ supported }}</p> </li> <li> <p><code>Recommended by ACCESS-NRI</code> {{ recommended }}</p> </li> <li> <p><code>Community contributed</code> {{ community }}</p> </li> </ul> <p>See the support page for details about the support levels: what is supported, by who, and how to access help.</p>"},{"location":"#contribute-to-access-hive-1","title":"Contribute to ACCESS-Hive 1","text":"Contribute Join the ACCESS-Hive team and have your contributions onboard!"},{"location":"#acknowledgement-of-country","title":"Acknowledgement of Country","text":"<p>We at ACCESS-NRI acknowledge the Traditional Owners of the land on which our research infrastructure and community operate across Australia and pay our respects to Elders past and present. We recognise the thousands of years of accumulated knowledge and deep connection they have with all the Earth systems we simulate.2</p> <p></p> <ol> <li> <p>Image by pch.vector on Freepik\u00a0\u21a9</p> </li> <li> <p>Photo by Ren\u00e9 Riegal on Unsplash \u21a9</p> </li> </ol>"},{"location":"call_contribute/","title":"Call contribute","text":"The documentation on Hive is work in progress! <p>The ACCESS-Hive is a community resource that is a work in progress. We\u2019d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you\u2019d like us to provide but aren\u2019t able to contribute yourself.</p>"},{"location":"about/License/","title":"License","text":"<p>The ACCESS-Hive is made available under the Creative Commons Attribution license. The following is a human-readable summary of (and not a substitute for) the full legal text of the CC BY 4.0 license.</p> <p>You are free:</p> <ul> <li>to Share---copy and redistribute the material in any medium or format</li> <li>to Adapt---remix, transform, and build upon the material</li> </ul> <p>for any purpose, even commercially.</p> <p>The licensor cannot revoke these freedoms as long as you follow the license terms.</p> <p>Under the following terms:</p> <ul> <li> <p>Attribution---You must give appropriate credit (mentioning that your work is   derived from work that is Copyright \u00a9 ACCESS-NRI and, where practical, linking to https://www.access-nri.org.au/), provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.</p> </li> <li> <p>No additional restrictions---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.  With the understanding that:</p> </li> </ul> <p>Notices:</p> <ul> <li>You do not have to comply with the license for elements of the   material in the public domain or where your use is permitted by an   applicable exception or limitation.</li> <li>No warranties are given. The license may not give you all of the   permissions necessary for your intended use. For example, other   rights such as publicity, privacy, or moral rights may limit how you   use the material.</li> </ul>"},{"location":"about/code_of_conduct/","title":"Code of Conduct","text":"<p>ACCESS-Hive is an open community supported effort. For it to be successful it must be a welcoming and inclusive space so that everyone in the community feels able to contribute. </p> <p>To ensure this is the case users and contributors to ACCESS-Hive and the ACCESS-Hive Forum are required to abide by the ACCESS-NRI code of conduct.</p>"},{"location":"about/contact/","title":"Contact","text":"<p>ACCESS-Hive is an initiative of the The Australian Earth-System Simulator (ACCESS-NRI).</p> <p>ACCESS-Hive is an open community supported effort. The underpinning infrastructure is provided by ACCESS-NRI but much of the content is provided by the ACCESS Community.</p> <p>If there are problems or queries about the content of ACCESS-Hive check if there is already a relevant open issue on the ACCESS-Hive GitHub repository, and open one if not.</p> <p>Check the support page for information on what is supported and by whom.</p> <p>Join the ACCESS-Hive forum and find previous related discussions about the hive or the resources listed here, or start your own and make contacts with your community.</p> <p>Otherwise, contact ACCESS-NRI directly. Full contact details for ACCESS-NRI are available on the ACCESS-NRI website contact page</p>"},{"location":"about/contact/#other-places-where-you-can-find-the-access-nri-team","title":"Other places where you can find the ACCESS-NRI team:","text":"<p>: ACCESS-Hive Forum</p> <p>: ACCESS-NRI GitHub</p> <p>: @ACCESS_NRI twitter</p> <p>: access_nri LinkedIn</p> <p>: access-nri.slack.com</p>"},{"location":"about/policies/","title":"Policies {{ supported }}","text":"<ul> <li>Procedures and Practices: Contains documents outlining how ACCESS-NRI will function. These documents describe what users can expect and justifications for the decisions against criteria that are based on the values of the organisation.</li> </ul>"},{"location":"about/support/","title":"Support","text":""},{"location":"about/support/#support-levels","title":"Support levels","text":"<p>The site uses a system of tags to identify who supports the linked documentation or software, and the level of support you can expect:</p> <code>Supported by ACCESS-NRI</code> {{ supported }} <p>Documentation that is actively maintained and supported by ACCESS-NRI. This is documentation that was either created by ACCESS-NRI, or it is existing documentation for which ACCESS-NRI has taken over responsibility.</p> <code>Recommended by ACCESS-NRI</code> {{ recommended }} <p>Documentation for third-party software that ACCESS-NRI recommends and facilitates the use of at NCI as a service to the community. This means ACCESS-NRI supports the infrastructure required to run the software, but not necessarily the software itself. </p> <code>Community contributed</code> {{ community }} <p>Documentation that is of use to the community, but is not explicitly endorsed or supported by ACCESS-NRI. </p>"},{"location":"about/support/#how-to-get-help","title":"How to get help","text":"<p>Each entry on ACCESS-Hive links to another web site. There should be information on how to get help on the linked site. If there are no obvious channels for help, or the help is not adequate consider asking for assistance from fellow members of your community on the ACCESS-Hive forum. </p> <p>In the case of ACCESS-NRI supported documentation and software, marked {{ supported }}, if there is no information on how to get help, or your query is not appropriate for the support channels provided, please either ask on the ACCESS-Hive forum or contact ACCESS-NRI directly.</p>"},{"location":"community_resources/","title":"Community Resources","text":"<p>In this area of the Hive, we collect content that is not currated by us, but may be helpful for the community. You can contribute to this part of the Hive too!</p> <p>Currently, we provide pointers to the following categories: - Working Groups  - Glossaries - Variables - Model Evaluation Links - Training - Events </p>"},{"location":"community_resources/community_data_processing/","title":"Community Processing Data Processing Tools","text":""},{"location":"community_resources/community_data_processing/#tools","title":"Tools","text":""},{"location":"community_resources/community_data_processing/#kerchunk-community","title":"Kerchunk  {{ community }}","text":"<p>Documentation |  Sources</p> <p>Kerchunk is a library that provides a unified way to represent a variety of chunked, compressed data formats (e.g. NetCDF/HDF5, GRIB2, TIFF, \u2026), allowing efficient access to the data from traditional file systems or cloud object storage. It also provides a flexible way to create virtual datasets from multiple files.</p>"},{"location":"community_resources/community_data_processing/#cmor3-community","title":"CMOR3  {{ community }}","text":"<p>Climate Model Output Rewriter Version 3</p> <p>Documentation |  Sources</p> <p>CMOR is used to produce CF-compliant netCDF files. The structure of the files created by CMOR and the metadata they contain fulfill the requirements of many of the climate community\u2019s standard model experiments (which are referred to here as \u201cMIPs\u201d and include, for example, AMIP, PMIP, APE, and IPCC scenario runs).</p>"},{"location":"community_resources/community_data_processing/#xmip-community","title":"xMIP  {{ community }}","text":"<p>Documentation | Tutorial on NCI | Sources</p> <p>This package facilitates the cleaning, organization and interactive analysis of Model Intercomparison Projects (MIPs) within the Pangeo software stack.</p>"},{"location":"community_resources/community_data_processing/#app4-the-access-post-processor-community","title":"APP4 (The ACCESS Post Processor)  {{ community }}","text":"<p>Documentation |  Sources</p> <p>The APP4 is a CMORisation tool designed to convert ACCESS model output to ESGF-compliant formats, primarily for publication to CMIP6. The code was originally built for CMIP5, and was further developed for CMIP6-era activities. Uses CMOR3 and files created with the CMIP6 data request to generate CF-compliant files according to the CMIP6 data standards.</p>"},{"location":"community_resources/community_data_processing/#access-archiver-community","title":"ACCESS-Archiver {{ community }}","text":"<p>Documentation |  Sources</p> <p>The ACCESS Archiver is designed to archive model output from ACCESS simulations. It's focus is to copy ACCESS model output from its initial location to a secondary location (typically from <code>/scratch</code> to <code>/g/data</code>), while converting UM files to netCDF, compressing MOM/CICE files, and culling restart files to 10-yearly. Saves 50-80% of storage space due to conversion and compression.</p>"},{"location":"community_resources/community_data_processing/#synda-recommended","title":"Synda  {{ recommended }}","text":"<p>synda is a command line tool to search and download files from the Earth System Grid Federation (ESGF) archive.</p>"},{"location":"community_resources/community_data_processing/#fluxnetlsm-community","title":"FluxnetLSM  {{ community }}","text":"<p>Citation 1 | Sources</p> <p>R package for post-processing FLUXNET datasets for use in land surface modelling. Performs quality control and data conversion of FLUXNET data and collated site metadata. Supports FLUXNET2015, La Thuile, OzFlux and ICOS data releases.</p>"},{"location":"community_resources/community_data_processing/#metpy-community","title":"Metpy  {{ community }}","text":"<p>https://unidata.github.io/MetPy/latest/examples/formats/index.html</p> <p>Documentation | Sources</p> <p>MetPy is a collection of tools in Python for reading, visualizing, and performing calculations with weather data. MetPy supports Python &gt;= 3.8 and is freely available under a permissive open source license.</p> <p>Format types are: GINI Water Vapor Imagery, NEXRAD Level 3 File, and NEXRAD Level 2 File.</p>"},{"location":"community_resources/community_data_processing/#xskillscore-community","title":"xskillscore  {{ community }}","text":"<p>Documentation | Sources</p> <p>xskillscore is a Python library for computing a wide variety of skill metrics. Its typical application is to verify deterministic and probabilistic forecasts relative to observations.</p>"},{"location":"community_resources/community_data_processing/#analysis-blogposts-and-tutorials-community","title":"Analysis blogposts and tutorials  {{ community }}","text":"<p>Accessing NetCDF and GRIB file collections as cloud-native virtual datasets using Kerchunk, Peter March, Sep 2022</p> <ol> <li> <p>A. M. Ukkola, N. Haughton, M. G. De Kauwe, G. Abramowitz, and A. J. Pitman. Fluxnetlsm r package (v1.0): a community tool for processing fluxnet data for use in land surface modelling. Geoscientific Model Development, 10(9):3379\u20133390, 2017. URL: https://gmd.copernicus.org/articles/10/3379/2017/, doi:10.5194/gmd-10-3379-2017.\u00a0\u21a9</p> </li> </ol>"},{"location":"community_resources/community_med_recipes/","title":"Community Model Evaluation and Diagnostics (MED) Recipe Gallery","text":"<p>We are trying to ingest more and more model evaluation and diagnostics recipes in your currated recipe gallery on this website {{ supported }}. While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community {{ community }}:</p> MED Recipe Components Description ESMValTool {{ recommended }} (Earth System Model EValuation Tool) Documentation |         Tutorial |         Source Code COSIMA Cookbook / Recipes {{ recommended }}(Consortium for Ocean-Sea Ice Modelling in Australia) Documentation |         Tutorial |         Source Code |         Recipes iLAMB {{ recommended }}(international Land Model Benchmarking) Documentation |         Tutorial |         Source Code iOMB {{ recommended }}(international Ocean Model Benchmarking) Documentation |         Tutorial |         Source Code METPlus {{ recommended }}(Model Evaluation Tool Plus) Tutorial |         Paper PMP {{ recommended }}(PCMDI Metrics Package) Documentation |         Source Code climpred {{ community }} Documentation |         Tutorial |         Source Code |         Paper FREVA {{ community }}(Free Evaluation System Framework) Documentation |         Source Code TECA {{ community }}(Toolkit for Extremes Climate Analysis) Documentation |         Tutorial |         Source Code MONET {{ community }}(Model and ObservatioN Evaluation Toolkit) Documentation |         Tutorial |         Source Code |         Paper LIVVkit {{ community }}(land ice verification &amp; validation toolkit) Documentation |         Tutorial |         Source Code CSET {{ community }}(Convective Scale Evaluation Tool ) Documentation |         Tutorial |         Source Code |          MetPy {{ community }}(Model Evaluation Tool Plus) Tutorial |         Source Code |         Recipes         MetPy is a collection of tools in Python for reading, visualizing, and performing calculations with weather data. MetPy supports Python &gt;= 3.8 and is freely available under a permissive open source license.      Afterburner {{ community }} Documentation |         Source"},{"location":"community_resources/community_model_catalogs/","title":"Community Model Data Catalogs","text":"<p>We are trying to ingest more and more model data catalogs in your currated catalog on this website}. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us ({{ recommended }}) or may be interesting for the community ({{ community }}):</p> Model Catalog Comp. Description NCI datasets {{ recommended }}               NCI has an extensive catalog of datasets of interest to the weather and climate community. These datasets are directly available on the NCI supercomputer and the [Australian Research Environment](https://opus.nci.org.au/display/Help/ARE+User+Guide)          CLEX NCI Data Collection Intake Catalogue {{ recommended }}               This is an Intake catalogue maintained by the ARC Centre of Excellence for Climate Extremes [(CLEX)](https://climateextremes.org.au/).         Only datasets from the NCI Catalog are referenced.         The catalogue is available in intake's default catalogue list in the CLEX Conda environment.         Two notebooks are provided in the docs folder showing how to access the ERA5 and CIP6 datasets.          Australia Climate Data Guide Catalogue {{ recommended }}               *A one-stop catalogue to discover Climate Data in Australia*         The ACDG portal is a metadata portal listing climate research resources available in Australia from multiple data repositories.         This is a community based project managed by the ACDG Single Access working group. This is a group of Australian climate community self-nominated representatives. Anyone is welcome to join the group or to contribute independently to the metadata portal the group is developing.          Australian Ocean Data Network {{ recommended }}               The Australian Ocean Data Network (AODN) is an interoperable online network of marine and climate data resources.  IMOS and the 6 Australian Commonwealth agencies ([see AODN Partners](https://imos.org.au/facilities/aodn/aodn-data-management/aodn-partners)) form the core of the AODN. Increasingly, though, universities and State government offices are offering up data resources to the AODN, and delivery of data to the AODN is being written in to significant research programs e.g. [National Environmental Science Program Marine Biodiversity Hub](http://www.nespmarine.edu.au/) and the [Great Australian Bight research program](http://www.misa.net.au/GAB).          Intake-Ilamb Catalog {{ supported }}               The Intake-Ilamb catalog provides an yaml-style intake catalog of the reference data used for ESM model benchmarking in the International Land Model Benchmarking [(ILAMB)](https://www.ilamb.org/) effort.          FLUXNET {{ community }}               FLUXNET is an international \u201cnetwork of networks,\u201d tying together regional networks of earth system scientists. FLUXNET scientists use the eddy covariance technique to measure the cycling of carbon, water, and energy between the biosphere and atmosphere. Scientists use these data to better understand ecosystem functioning, and to detect trends in climate, greenhouse gases, and air pollution.          CEDA Archive {{ community }}               The CEDA Archive forms part of NERC's Environmental Data Service (EDS) and is responsible for looking after data from atmospheric and earth observation research. They host over 18 Petabytes of data from climate models, satellites, aircraft, met observations, and other sources.          OZFlux {{ community }}               OzFlux is an ecosystem research network set up to provide Australian, New Zealand and global ecosystem modelling communities with consistent observations of energy, carbon and water exchange between the atmosphere and key Australian and New Zealand ecosystems.          Australian Community Reference Climate Data Collection {{ recommended }}               This collection is a collaborative effort between the Australian Climate Service (ACS), ARC Centre of Excellence for Climate Extremes (CLEX) and the wider Australian climate research community to re-establish and maintain a reference dataset collection at NCI.         An [intake-esm catalogue](https://github.com/aus-ref-clim-data-nci/acs-replica-intake) is also available to facilitate data access."},{"location":"community_resources/community_observational_catalogs/","title":"Community Observational Data Catalogs","text":"<p>We are trying to ingest more and more model data catalogs in your currated catalog on this website}. While this is a continous effort, this site is intented for a list of additional model data catalogs that are not (yet) ingested but are recommended by us ({{ recommended }}) or may be interesting for the community ({{ community }}):</p> Data Catalog Comp. Description Copernicus Climate Change Service (C3S) Data Store (CDS) {{ recommended }}               The Copernicus Climate Change Service (C3S) combines observations of the climate system with the latest science to develop authoritative, quality-assured information about the past, current and future states of the climate in Europe and worldwide. C3S data is provided via its Climate Data Store (CDS).         You can search its available datasets via this interface.         You can use the CDS API as well as command line tools to download data. To download ERA5 from CDS, you can use for example this era5cli command line tool.          Catalogue Search at CEDA (Centre for Environmental Data Analysis)  {{ recommended }}               The CEDA (Centre for Environmental Data Analysis) Archive hosts atmospheric and earth observation data.         It provids an interactive Catalogue Search and Tools for downloading data.         It holds environmental data related to atmospheric and earth observation fields. Our remit covers the following areas (see linked examples to some of our most popular datasets):          - Climate - e.g. HadUK Grid, CMIP, CRU          - Composition - e.g. CCI          - Observations - e.g. MIDAS Open          - Numerical weather prediction - e.g. Met Office NWP          - Airborne - e.g. FAAM          - Satellite data and imagery - e.g. Sentinel"},{"location":"community_resources/community_working_groups/","title":"Community Working Groups","text":"<p>The ACCESS Community and the ACCESS-NRI have established Community Working Groups to assess and prioritise the needs of the modelling community as well as encourage collaboration within. These working groups are open to the community and welcome new members.</p> <p>The working group activities are coordinated through the ACCESS Hive Community Forum:</p>              Atmospheric Modelling                       Land Surface Modelling                       COSIMA(Ocean and Sea-Ice)                       Forecasting and Prediction                       Earth System Modelling                       Cryosphere          <p>To join a working group follow the instructions on the ACCESS-NRI website, and to participate in the activities of the working group visit the ACCESS-hive forum.</p>"},{"location":"community_resources/events/","title":"Workshops and Conferences","text":"<p>TODO get the liquid working {{ events_content }}</p>"},{"location":"community_resources/events/add_event/","title":"Workshops and Conferences: Add Event","text":"<p>We encourage members of the community to list any workshops, tutorials, conferences that might be of interest to the community.</p>"},{"location":"community_resources/events/add_event/#how-to-add-your-event","title":"How to add your event","text":""},{"location":"community_resources/events/add_event/#add-an-issue","title":"Add an issue","text":"<p>The easiest way for you to add your event is to make an issue with the template provided. This provides a form which guides you through the process of providing the required information.</p>"},{"location":"community_resources/events/add_event/#create-a-pull-request-to-add-your-event","title":"Create a pull-request to add your event","text":"<p>This process requires some knowledge of git, GitHub and Markdown. If you do not feel comfortable doing this then it is sufficient to just add an issue as above. The issue will be assigned to someone else to finish.</p> <p>If you do feel confident adding your event to the list, then create a Markdown text file, identified with the <code>.md</code> extension, to the correct subdirectory in the <code>events</code> folder of the ACCESS-Hive repository. The subdirectories are named by year, put your new file in the year in which the event will take place. Avoid spaces in your filename: use an underscore <code>_</code> where you would normally have a space. e.g. <code>regional_dowscaling_cordex.md</code></p> <p>The file must contain a header with the metadata as in the example below:</p> <pre><code>---\ntitle: Regional climate downscaling for Australia within the CORDEX framework\nstart_date: 27/11/2022\nend_date: 27/11/2022\nlocation: Adelaide, SA\nlink: https://www.amos2022.org.au/\ndescription: This workshop is relevant for those performing regional climate simulations or downscaling with empirical/statistical downscaling approaches including machine learning, as well as those using regional climate projection data in their work. The focus will be on CORDEX related data and modelling. The workshop will have some presentations with extended discussion.\n---\n</code></pre> <p>Make sure to follow all the steps described in the contribution guidelines to submit this addition for approval for publication.</p>"},{"location":"community_resources/events/events/2022/CORDEXAmos2022/","title":"Regional climate downscaling for Australia within the CORDEX framework","text":"<p>This workshop is relevant for those performing regional climate simulations or downscaling with empirical/statistical downscaling approaches including machine learning, as well as those using regional climate projection data in their work. The focus will be on CORDEX related data and modelling. The workshop will have some presentations with extended discussion. Some topics to be covered include: - Accessing the existing CORDEX-CMIP5 data. How to access and use the data - Explain the CORDEX-CMIP6 protocol - What does it say? How can you contribute? - Who is planning to contribute (or is already working on contributions) to the Australasia domain?</p>"},{"location":"community_resources/events/events/2022/GC5Workshop/","title":"GC5 Assessment Workshop","text":"<p>The UM Partnership Team and GC Programme Team are running a GC5 assessment workshop, to assess the latest configuration of the Global Coupled model.</p> <p>The workshop will be a hybrid event with an option to attend online or in-person at Met Office Collaboration Building, Exeter. We will discuss the assessment of the latest GC5 configuration in a range of model simulations in a seamless context and sessions will broadly consist of: - Summary of GC5 physics changes - General model assessment - Summary from Priority Evaluation Groups (PEGs) - Summary from Collaboration Groups (CoGs) - Upcoming changes in GC science and tools - Discussions</p> <p>Please fill in the registration form to confirm attendance by 21st October</p> <p>For any further questions please contact Luke Roberts, Prince Xavier or Charline Marzin at the Met Office.</p>"},{"location":"community_resources/events/events/2022/GroundTruthingClimateChange/","title":"Ground truthing future climate change","text":"<p>Scientific ocean drilling provides the robust baseline data on global climate evolution over extended geologic time periods that are critical for improving climate model performance. By targeting how the climate system operates across a wide array of past climate states, scientific ocean drilling has, and continues to, obtain the data necessary to calibrate and improve numerical models used to project future climate impacts and inform mitigation strategies.</p> <p>Join us in this session where we aim to connect climate and ocean modellers to our rich (50+ years of drilling) database and unanswered questions in scientific ocean drilling. By addressing key questions about Earth\u2019s past, present, and future through interdisciplinary research, we are aiming to spark new collaborations and proposals that will lead to a more profound understanding of Earth as one integrated, interconnected system.</p>"},{"location":"community_resources/events/events/2022/SWOTAmos2022/","title":"The Surface Water and Ocean Topography (SWOT) satellite: A primer","text":"<p>The Surface Water and Ocean Topography (SWOT) satellite, which will launch in November 2022, is a ground-breaking wide-swath altimetry mission that will observe fine details of the ocean dynamics at a resolution 10 times finer than current satellites. SWOT is jointly developed by NASA and CNES with contributions from researchers around the world, including Australia. The Australian government, the Integrated Marine Observing System, and the Australian marine science community are investing in SWOT through calibration/validation and synergistic in situ measurements of fine-scale ocean dynamics in the Australian region. This workshop will present a primer on the principles of the satellite and instrument, how it works, and what are its possibilities and limitations compared to existing altimetry products. This will be complemented with a brief summary of ocean research related to and enabled by SWOT, including internal waves and tides, sub-mesoscale dynamics, the geoid, and mean dynamic topography. The goal of the workshop is to provide oceanographers, hydrologists and other users of altimetry data with the information they need to prepare for the arrival of SWOT data in late 2023.</p>"},{"location":"community_resources/glossaries/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p> <p>{{ community }} CMIP(6):  </p> <p>{{ community }} ERA(5):  </p> <p>{{ community }} UM: </p>"},{"location":"community_resources/glossaries/glossary_access_nri/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_cmip/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_cssr/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_era/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_ipcc/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/glossaries/glossary_um/","title":"Glossary and Useful Terms","text":"<p>Here you can find a compilation of common terms and acronyms used by the Australian Community Climate and Earth System Simulator (ACCESS)  community:</p> <p>{{ supported }} ACCESS-NRI Glossary: This includes common terms and acronyms used by the ACCESS community in research and modelling of past, present and future climate, weather and Earth-Systems.</p> <p>{{ community }} IPCC Acronyms: Contains a comprehensive list of acronyms published in the scientific report SR15 of the Intergovernmental Panel on Climate Change (IPCC). The IPCC is the United Nations body for assessing the science related to climate change.</p> <p>{{ community }} CSSR Acronyms and Units: The Climate Science Special Report (CSSR) is an assessment of the science of climate change with particular focus on the United States.</p>"},{"location":"community_resources/training/","title":"Training and Policies","text":"<p>This space is intended to promote training material relevant to ACCESS and its community. The training material can be directly relevant to ACCESS and its model components, such as:</p> <ul> <li>using coupled models and model components</li> <li>using configurations</li> <li>using model evaluation tools and workflows</li> </ul> <p>It is also intended for training material around more peripheral topics that are essential for the community, such as:</p> <ul> <li>HPC</li> <li>version control</li> <li>essential software packages</li> </ul> <p>ACCESS-NRI encourages the members of the community to contact us to share their suggestions.</p> <p>Finally, you will also find ACCESS-NRI's policies in this space.</p>"},{"location":"community_resources/training/ACCESS_training/","title":"ACCESS Training Material","text":"<p>This page is intended to provide access to training material directly related to ACCESS models and model components. This material can cover topics such as but not limited to:</p> <ul> <li>how to use a specific model</li> <li>how to modify a model configuration</li> <li>how to test a model modification or validate a model run</li> </ul>"},{"location":"community_resources/training/ACCESS_training/#jules-tutorials-recommended","title":"JULES tutorials {{ recommended }}","text":"<p>The JULES tutorials explain how to use FCM, Rose and Cylc both for using the model and for development work. They can be useful to ACCESS users as practical demonstrations of the Rose and Cylc infrastructure.</p>"},{"location":"community_resources/training/additional_training/","title":"Additional training material","text":"<p>To learn the basics of Git and GitHub. It also includes ACCESS-NRI's recommendations to setup GitHub. </p> <p></p> <p>The National Computational Infrastructure (NCI) provides training resources and in-person training courses throughout the year to help develop the skills of the NCI user community.  </p> <p>A full calendar of upcoming training opportunities can be found on their Opus page.</p> <p>Users can find important information and resources about using NCI systems and services in the NCI User Guides.</p>"},{"location":"contribute/","title":"How to Contribute","text":"<p>ACCESS-Hive is a community supported site, as such contributions to the ACCESS-Hive site are encouraged by any member of the community. Members of the ACCESS community are also welcome to become reviewers. Please refer to the following contribution guidelines to learn how you can help the ACCESS community build a documentation database useful to everyone.</p> <p>Although we encourage everyone to get involved and contribute to the ACCESS-Hive in order to adequately represent the needs of the entire ACCESS community, we recognise not everyone will have the time to do so. In case you do not have a lot of time, please consider sharing your ideas via issues on the ACCESS-Hive GitHub repository so someone might be able to add them to the ACCESS-Hive site for you.1</p> Abstract <p>The aim of this how-to is to enable you to:</p> <ul> <li>add or modify a link to a new documentation in an existing page</li> <li>contribute complex modifications, eg., add pages, modify the navigation, modify an existing page in depth etc.</li> <li>how to deal with relevant documentation that is not currently on a website</li> </ul>"},{"location":"contribute/#become-a-member-of-the-access-hive-organisation","title":"Become a member of the ACCESS-Hive organisation","text":"<p>The ACCESS-Hive organisation is open to any member of the ACCESS community. Furthermore, organisation members have write access to the ACCESS-Hive repository which simplifies the process to contribute. Members can work from branches that contain their modifications instead of creating and maintaining their own forks. </p> <p>As such, we encourage you to become a member of the organisation by replying to this issue and ask to be invited to join the organisation.</p>"},{"location":"contribute/#process-to-contribute","title":"Process to contribute","text":"<p>This documentation is based on the Material for Mkdocs theme. Please see the documentation for the theme or for Mkdocs for a full explanation of all the capabilities.</p> <p>The documentation is written in Markdown format. Please see this cheat sheet for a quick reference to the base syntax. Please note that Material for Mkdocs extends that syntax.</p> <p>Additionally, ACCESS-Hive is a portal for documentation hosted elsewhere. The documentation you want to add needs to be available from an existing website. We realise people might have standalone files or other information to share, please see our Standalone documentation page for ways to easily upload your documentation to a site.</p> <p>There are two main ways to contribute to the site:</p> <ul> <li>you can modify an existing page directly from GitHub without any knowledge of Git. This is a simple way suitable to light modifications.</li> <li>you can work on your local computer and use Git to manage your modifications. This is recommended for more involved modifications. It is the easiest way to modify the categories and menu structure used to navigate the site.</li> </ul> <ol> <li> <p>Image by pch.vector on Freepik\u00a0\u21a9</p> </li> </ol>"},{"location":"contribute/change-the-navigation/","title":"Change the navigation","text":""},{"location":"contribute/change-the-navigation/#structure-of-the-repository","title":"Structure of the repository","text":"<p>The important elements of the repository to know about before modifying the navigation are:</p> <ul> <li><code>docs/</code> folder: this folder contains all the documentation pages. There is an <code>index.md</code> file for the About page, one folder per tab on the site, an <code>assets/</code> folder to store images used in the documentation and some customisation folders such as <code>css/</code> or <code>font/</code>.</li> <li><code>mkdocs.yml</code>: it is a YAML formatted file, hence the <code>.yml</code> extension. The site navigation is defined in this file as well as options for the styling of the site.</li> </ul> YAML <p>YAML is a popular choice for configuration files, as it is a simple way of encoding data structures in a text file. See this short tutorial.</p>"},{"location":"contribute/change-the-navigation/#a-simple-example","title":"A simple example","text":"<p>The easiest way to explain how the navigation is defined is to look at an example. Let's say <code>mkdocs.yml</code> contains:</p> <pre><code>nav:\n- Welcome: index.md\n- ACCESS-NRI: ACCESS-NRI/ACCESS-NRI.md\n- Community: - Generate Bathymetry: community/bathymetry.md\n- How to contribute: - How to contribute: help/how_to_contribute.md\n- Setup: help/contribution_setup.md\n- Modify the documentation: help/modify_documentation.md\n- Change the navigation: help/change_navigation.md\n</code></pre> <p>The top level category names define the tabs in the header bar. So here we have the tabs: \"Welcome\", \"ACCESS-NRI\", \"Community\" and \"How to contribute\". It is also the name of the top section under each tab.</p> <p></p> <p>The second level of categories indicate the name of each page under that section. So the \"ACCESS-NRI\" tab has the text directly under the section \"ACCESS-NRI\". The \"Community\" tab has a section called \"Community\" that contains one page: \"Generate Bathymetry\". Finally, the \"How to contribute\" tab has 1 section \"How to contribute\" with 4 pages.</p> <p>The filenames indicate the path to the file relative to the <code>docs/</code> folder containing the text for each page. It is recommended to use the title of each file (i.e. the heading level 1) or an abbreviation of it as the name of the page and the filename.</p> <p></p>"},{"location":"contribute/change-the-navigation/#add-sections-to-a-tab","title":"Add sections to a tab","text":"<p>It is possible to define several sections per tab by using more levels of indentation. For example, to add a \"My example\" section to the \"How to contribute\" tab:</p> <pre><code>nav:\n- Welcome: index.md\n- ACCESS-NRI: ACCESS-NRI/ACCESS-NRI.md\n- Community: - Generate Bathymetry: community/bathymetry.md\n- How to contribute: - How to contribute: help/how_to_contribute.md\n- Setup: help/contribution_setup.md\n- Modify the documentation: help/modify_documentation.md\n- Change the navigation: help/change_navigation.md\n- My example:\n- Beautiful example: help/beautiful_example.md\n</code></pre> <p>will create this navigation: </p>"},{"location":"contribute/edit-locally/","title":"Edit locally on your computer","text":"<p>If you want to submit a substantial contribution to ACCESS-Hive, it might be easier to do so from your own computer. Especially, it is a lot easier to proceed locally if you need to modify several files or want to modify the navigation of the site.</p> <p>You can avoid creating your own fork for the repository by first becoming a member of ACCESS-Hive organisation. To become a member, please reply to this issue and ask to be invited to join the organisation.</p> <p>To work locally, you will need git and a text editor installed on your computer.</p>"},{"location":"contribute/edit-locally/#open-an-issue","title":"Open an issue","text":"<p>For all additions or modifications to the ACCESS-Hive site, it is recommended to start by opening an Issue in the ACCESS-Hive GitHub repository. Consider assigning the Issue to yourself in the right-hand side panel if you intend on working on the issue and you are a member of the ACCESS-Hive organisation.</p>"},{"location":"contribute/edit-locally/#obtaining-the-source-files","title":"Obtaining the source files","text":"<p>Everything is stored within the ACCESS-Hive repository on GitHub and you simply need to clone this repository to your local machine:</p> <pre><code>git clone git@github.com:ACCESS-Hive/access-hive.github.io.git\n</code></pre>"},{"location":"contribute/edit-locally/#edit-to-access-hive","title":"Edit to ACCESS-Hive","text":"<p>Once you have installed all you need, you will need to follow the usual series of steps when contributing to Open Source developments:</p> <ul> <li>open an Issue</li> <li>clone the repository locally</li> <li>start a branch to work on, linked to the Issue</li> <li>commit your modifications to that branch and push to GitHub</li> <li>open a pull request between the <code>main</code> branch and your branch, follow the instructions from the Pull request template.</li> <li>ask for reviews by tagging the ACCESS-Hive/reviewers team and reply to requests for changes</li> </ul> <p>If you don't know how to do these steps, please refer to our Git and GitHub training.</p> What page to edit <p>If you have problems finding the page you need to edit, the easiest way is to head to the ACCESS-Hive site. If you click on the pen icon  at the top right of each page title, you will open a GitHub page showing you the path to the file you want to edit.</p> Headers and table of content <p>The level 1 headers are reserved for the title of the page and are ignored from the pages' table of contents. Only use level 2 headers and higher to organise pages.</p>"},{"location":"contribute/edit-locally/#add-a-new-event","title":"Add a new event","text":"<p>The process to add a new event is a bit different from other updates on the site. Since you need to create a new file to contain the information about the event you are adding, it is recommended to work locally. You need to create a new Markdown file (identified by the <code>.md</code> extension) as described on this page. To record and submit your modification to the site, make sure you follow all the steps as explained in the Open Source process in the previous section.</p>"},{"location":"contribute/edit-locally/#preview-of-the-documentation","title":"Preview of the documentation","text":""},{"location":"contribute/edit-locally/#preview-from-a-pull-request","title":"Preview from a Pull Request","text":"<p>When a pull request is created or updated, GitHub will automatically build a preview of the documentation that includes the proposed changes.</p> <p>In the pull request, you will see the link to the preview appear in this fashion:</p> <p></p> Build delay <p>It can take a while for the preview to build, even after the CI check is indicated as finished. Please wait for the comment with the link to appear and allow for some time after that for the preview to be properly deployed.</p> <p>If you open the preview and it looks completely broken or if it hasn't updated from additional modifications in the pull request, it probably means the site hasn't finished building yet. If you wait a couple of minutes and refresh the page, it should fix itself.</p>"},{"location":"contribute/edit-locally/#local-preview-if-editing-on-your-own-computer","title":"Local preview (if editing on your own computer)","text":"<p>MkDocs includes a live preview server, so you can preview your changes as you write your documentation. The server will automatically rebuild the site upon saving.</p>"},{"location":"contribute/edit-locally/#software-installation","title":"Software installation","text":"<p>To build the site locally, you need to install [Material for Mkdocs][MatforMkdocs] and other plugins. You can find a full list in the <code>requirements.txt</code> file in the root of the ACCESS-Hive repository. Please use <code>pip</code> for the installation as some of packages are not updated or not available on <code>conda</code>:</p> <pre><code>pip install -r requirements.txt\n</code></pre>"},{"location":"contribute/edit-locally/#start-the-server","title":"Start the server","text":"<p>To start the server, open a terminal and navigate to your ACCESS-Hive local repository. Now type:</p> <pre><code>mkdocs serve\n</code></pre> <p>Your documentation will be built on http://127.0.0.1:8000. Open this URL in your browser to see a preview of the documentation. The URL is given in the terminal when running the <code>mkdocs serve</code> command. Make sure you keep the command running so as to see live updates on saving your modifications.</p>"},{"location":"contribute/edit-on-github/","title":"Edit directly on GitHub","text":"<p>This way to edit the site allows people with no knowledge of Git to contribute to ACCESS-Hive but is only suitable for light modifications of existing pages.</p> <ul> <li>Go to the page you want to modify on the ACCESS-Hive documentation site. At the right of the title, you will see a pen icon . When you click on this icon, your browser will open the file in GitHub allowing you to edit the file.</li> </ul> <ul> <li>Enter your modification in the main pane. All the files are written in Markdown.</li> </ul> Headers and table of content <p>The level 1 headers are reserved for the title of the page and are ignored from the pages' table of contents. Only use level 2 headers and higher to organise pages.</p> <ul> <li>Then add a commit message in the Commit changes box.</li> </ul> <ul> <li>Commit and open a pull request</li> </ul> Pull request is required <p>The <code>main</code> branch of the repository is protected and nobody can write to it directly. You will need to choose either to create a new branch (for ACCESS-Hive organisation members only) or to create a fork on your GitHub personal account (for non-members of ACCESS-Hive organisation) and then open a pull request in all cases. </p> <p>When creating the pull request, make sure to follow the instructions given to you in the pull request template. The description can be edited at any time. You can fill in the check list after creating the pull request. The pull request will automatically build a preview of the documentation with your proposed changes.</p> <ul> <li> <p>Ask for a review by tagging the <code>@ACCESS-Hive/reviewers</code> team in a comment.</p> </li> <li> <p>Reply to the review. You will be notified by email of any subsequent comment, request or action from the reviewer on this pull request. Please make sure you take any action required by the reviewer or your modification will not be accepted into the ACCESS-Hive site.</p> </li> </ul>"},{"location":"contribute/edit-on-github/#further-edits","title":"Further edits","text":"<p>During the review process, you might be requested to edit your proposed changes. For this, you will need to navigate to the branch created by GitHub. </p> <ul> <li>At the top of the Pull request window on GitHub, you should see a link to your branch, circled in red on the image:</li> </ul> <ul> <li>Once you click on this link, navigate to and open the file you need to modify, then click on the pen icon in the toolbar on the right, circled in red on the image:</li> </ul> <ul> <li> <p>Then commit your changes once again to the same branch. This will update the pull request and the preview of the site.</p> </li> <li> <p>You need to let the reviewer know once you are confident you have responded to all their concerns, so they can review again. For this, locate the \"Reviewers\" pane in the right-hand side menu list on GitHub and click the icon circled in red in the image:</p> </li> </ul>"},{"location":"contribute/reviewers/","title":"Reviewing for ACCESS-Hive","text":"<p>Any member of the ACCESS-Hive Github Community (to join) can join the reviewers team. Please ask one of the maintainers to invite you to join the reviewers team.</p>"},{"location":"contribute/reviewers/#reviewer-guidelines","title":"Reviewer Guidelines","text":"<p>Firstly, thank you so much for helping to review links submitted to the ACCESS-Hive, we\u2019re delighted to have your help. This document is designed to outline our editorial guidelines and help you understand our requirements for accepting a pull request (PR).</p>"},{"location":"contribute/reviewers/#guiding-principles","title":"Guiding principles","text":"<p>If the submitting authors have followed the contribution guidelines then the review should be rapid. An important requirement is the ACCESS-Hive is a portal to documentation, it does not host the documentation itself.</p> <p>For those PRs that don\u2019t quite meet the requirements, please try to give clear feedback on what needs fixing. Our goal is to maintain a high quality platform for exchanging links to relevant documentation and you, as a reviewer, have a key role to play.</p> <p>A review involves checking submissions against a checklist of essential features and details described at the top of each PR. This should be objective, not subjective; it should be based on the materials in the submission as perceived without distortion by personal feelings, prejudices, or interpretations.</p> <p>Some continuous tests such as hyperlink references checks and preview deployments are automatically triggered by submitting a PR.</p> <p>Reviewers should:</p> <ol> <li>Ensure that the tests are passing without errors.</li> <li>Do a visual check using the preview.</li> <li>Do a Github pull request review. See GitHub's extensive documentation</li> <li>Once you have approved the PR. Tag the editors team <code>@ACCESS-Hive/editors</code> in the discussion.</li> </ol> <p>We encourage reviewers to provide feedback from within the PR discussion.</p> <p>You can include in your review links to any new issues that you the reviewer believe to be impeding the acceptance of the pull request.</p>"},{"location":"contribute/standalone-documentation/","title":"Standalone documentation","text":"<p>You may have very valuable resources to share which are not currently available through any website, it is what we call \"standalone documentation\" in the current context.</p> <p>To contribute these resources to ACCESS-Hive, you will first need to make them available on the internet. Below are some ideas on how to do that:</p> <ol> <li>Check if your organisation has a documentation or information site suitable for your resource.</li> <li>Check if ACCESS-NRI has a documentation site suitable for your resource. Note in this case, you will be asked about ownership and license associated with your resource.</li> <li>Publish your documentation via Zenodo. This will clarify the licensing and reuse conditions.</li> </ol> <p>If none of the previous options seem suitable to you, please consult the forum.</p>"},{"location":"model_evaluation/","title":"Model Evaluation and Diagnostics (MED)","text":"<p>Model evaluation is about measuring how fit for purpose a particular model is.</p> <p>If you are new to model evaluation and diagnostics, we recommend you read our Getting Started with MED page.</p> <p>Here, we provide catalogs and pointers to observational data as well as model data that can be used for evaluation. We provide tools to process such data into a comparable format and a gallery of recipes to evaluate the formatted data.</p> Observational Data Catalog Model Data Catalog Data Format Processing Evaluation Recipe Gallery <p>Our vision: PLACEHOLDER FOR OUTCOME OF STAFF RETREAT</p>"},{"location":"model_evaluation/model_evaluation_data_processing/","title":"Data Processing Tools","text":"<p>On this page, we will provide you a list of currated data processing tools.</p> <p>While we are still ramping up this service, please take a look at the gallery of community tools on Community Resources -&gt; Community Data Processing Tools {{ community }}.</p>"},{"location":"model_evaluation/model_evaluation_live_diagnostics/","title":"Live Diagnostics on Gadi","text":"<p>Here, we will describe the tools we provide for \"live-diagnostics\" of the ACCESS configurations. These tools allow you to check model output/progress/failures at specified time steps while your model is running.</p>"},{"location":"model_evaluation/model_evaluation_observational_catalogs/","title":"Observational Data Catalog","text":"<p>As of June 2023, we provide the following observational data catalogs on Gadi@NCI through the project <code>kj13</code>:</p> <pre><code>/g/data/kj13/datasets\n\u251c\u2500\u2500 cmip6\n\u2502   \u2514\u2500\u2500 *.nc\n\u251c\u2500\u2500 esmvaltool\n\u2502   \u2514\u2500\u2500 obsdata-v2/\n\u2502       \u251c\u2500\u2500 Tier1\n\u2502       \u2502   \u251c\u2500\u2500 AIRS\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 *.nc\n\u2502       \u2502   \u2514\u2500\u2500  ...\n\u2502       \u251c\u2500\u2500 Tier2\n\u2502       \u2502   \u251c\u2500\u2500 BerkeleyEarth\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 *.nc\n\u2502       \u2502   \u2514\u2500\u2500  ...\n\u2502       \u2514\u2500\u2500 Tier3\n\u2502           \u251c\u2500\u2500 ERA5\n\u2502           \u2502   \u2514\u2500\u2500 OBS6_ERA5_reanaly_v1_Amon_pr_197901-202012.nc\n\u2502           \u2514\u2500\u2500  ...\n\u251c\u2500\u2500 ilamb\n\u2502   \u2514\u2500\u2500 DATA\n\u2502       \u251c\u2500\u2500 albedo\n\u2502       \u2502   \u251c\u2500\u2500 CERESed4.1\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 albedo.nc\n\u2502       \u2502   \u2514\u2500\u2500 ...\n\u2502       \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 iomb\n\u2502   \u2514\u2500\u2500 DATA\n\u2502       \u251c\u2500\u2500 silicate\n\u2502       \u2502   \u251c\u2500\u2500 GLODAP\n\u2502       \u2502   \u2502   \u2514\u2500\u2500 *albedo*.nc\n\u2502       \u2502   \u2514\u2500\u2500 ...\n\u2502       \u2514\u2500\u2500 ...\n</code></pre> <p>If you want to use but do not have access to Gadi@NCI yet, please follow our instructions on how to Get Started with Model Evaluation.</p> Dataset name Downloaded /g/data/kj13/datasets/ AIRS 2020-12-04 Tier1/AIRS AIRS-2-0 2020-12-04 Tier1/AIRS-2-0 AIRS-2-1 2021-07-14 Tier1/AIRS-2-1 ATSR 2020-12-04 Tier1/ATSR CALIOP 2020-12-04 Tier1/CALIOP CERES-EBAF 2020-12-04 Tier1/CERES-EBAF CFSR 2020-12-04 Tier1/CFSR CloudSat 2020-12-04 Tier1/CloudSat ESACCI-GHG 2020-12-04 Tier1/ESACCI-GHG GPCP-SG 2020-12-04 Tier1/GPCP-SG ISCCP 2021-04-08 Tier1/ISCCP JRA-55 2022-11-15 Tier1/JRA-55 MODIS 2020-12-04 Tier1/MODIS SSMI 2020-12-04 Tier1/SSMI SSMI-MERIS 2021-10-19 Tier1/SSMI-MERIS TRMM-L3 2020-12-04 Tier1/TRMM-L3 ghgcci 2020-12-04 Tier1/ESACCI-GHG BerkeleyEarth 2020-12-04 Tier2/BerkeleyEarth CALIPSO-GOCCP 2023-01-28 Tier2/CALIPSO-GOCCP CERES-EBAF 2022-08-12 Tier2/CERES-EBAF CRU 2021-07-14 Tier2/CRU CT2019 2020-12-04 Tier2/CT2019 CowtanWay 2020-12-04 Tier2/CowtanWay Duveiller2018 2020-12-04 Tier2/Duveiller2018 E-OBS 2020-12-04 Tier2/E-OBS ESACCI-AEROSOL 2023-01-28 Tier2/ESACCI-AEROSOL ESACCI-CLOUD 2023-01-28 Tier2/ESACCI-CLOUD ESACCI-FIRE 2023-01-28 Tier2/ESACCI-FIRE ESACCI-LANDCOVER 2023-01-28 Tier2/ESACCI-LANDCOVER ESACCI-LST 2022-01-26 Tier2/ESACCI-LST ESACCI-OC 2022-01-26 Tier2/ESACCI-OC ESACCI-OZONE 2023-01-28 Tier2/ESACCI-OZONE ESACCI-SEA-SURFACE-SALINITY 2022-01-26 Tier2/ESACCI-SEA-SURFACE-SALINITY ESACCI-SOILMOISTURE 2023-01-28 Tier2/ESACCI-SOILMOISTURE ESACCI-SST 2023-01-28 Tier2/ESACCI-SST ESRL 2021-04-08 Tier2/ESRL Eppley-VGPM-MODIS 2020-12-05 Tier2/Eppley-VGPM-MODIS GCP2018 2021-11-08 Tier2/GCP2018 GCP2020 2021-11-08 Tier2/GCP2020 GHCN 2023-01-28 Tier2/GHCN GHCN-CAMS 2020-12-05 Tier2/GHCN-CAMS GISTEMP 2020-12-05 Tier2/GISTEMP GLODAP 2022-04-29 Tier2/GLODAP GPCC 2021-04-08 Tier2/GPCC HALOE 2023-01-28 Tier2/HALOE HadCRUT3 2023-01-28 Tier2/HadCRUT3 HadCRUT4 2023-01-28 Tier2/HadCRUT4 HadCRUT4-clim 2020-12-04 Tier2/HadCRUT4-clim HadCRUT5 2022-04-29 Tier2/HadCRUT5 HadISST 2023-01-28 Tier2/HadISST ISCCP-FH 2023-01-28 Tier2/ISCCP-FH JRA-25 2022-11-24 Tier2/JRA-25 Kadow2020 2022-08-12 Tier2/Kadow2020 Landschuetzer2016 2020-12-05 Tier2/Landschuetzer2016 Landschuetzer2020 2022-11-15 Tier2/Landschuetzer2020 MOBO-DIC_MPIM 2022-11-15 Tier2/MOBO-DIC_MPIM NCEP 2023-01-28 Tier2/NCEP NCEP-DOE-R2 2023-01-28 Tier2/NCEP-DOE-R2 NCEP-NCAR-R1 2023-01-28 Tier2/NCEP-NCAR-R1 NOAA-CIRES-20CR 2023-01-28 Tier2/NOAA-CIRES-20CR NOAAGlobalTemp 2022-08-12 Tier2/NOAAGlobalTemp OSI-450-nh 2020-12-05 Tier2/OSI-450-nh OSI-450-sh 2020-12-05 Tier2/OSI-450-sh OceanSODA-ETHZ 2022-11-17 Tier2/OceanSODA-ETHZ PATMOS-x 2023-01-28 Tier2/PATMOS-x PERSIANN-CDR 2020-12-05 Tier2/PERSIANN-CDR PHC 2020-12-05 Tier2/PHC PIOMAS 2020-12-05 Tier2/PIOMAS REGEN 2020-12-05 Tier2/REGEN Scripps-CO2-KUM 2022-04-29 Tier2/Scripps-CO2-KUM TCOM-CH4 2023-01-28 Tier2/TCOM-CH4 TCOM-N2O 2023-01-28 Tier2/TCOM-N2O WFDE5 2021-07-14 Tier2/WFDE5 WOA 2021-10-19 Tier2/WOA AURA-TES 2023-06-14 Tier3/AURA-TES CALIPSO-ICECLOUD 2023-06-14 Tier3/CALIPSO-ICECLOUD CDS-XCH4 2023-06-14 Tier3/DS-XCH4 CDS-XCO2 2023-06-14 Tier3/CDS-XCO2 ERA-Interim 2022-11-24 Tier3/ERA-Interim ERA-Interim-Land 2021-09-14 Tier3/ERA-Interim-Land ERA5 2021-02-12 Tier3/ERA5 ERA5-Land 2023-06-14 Tier3/ERA5-Land FLUXCOM 2022-01-26 Tier3/FLUXCOM HWSD 2023-06-14 Tier3/HWSD LandFlux-EVAL 2023-06-14 Tier3/LandFlux-EVAL MAC-LWP 2023-06-14 Tier3/MAC-LWP NIWA-BS 2023-06-16 Tier3/NIWA-BS"},{"location":"model_evaluation/model_evaluation_observational_catalogs/#todo-tier2","title":"ToDo Tier2","text":"Dataset name Downloaded /g/data/kj13/datasets/ ESDC Tier2/"},{"location":"model_evaluation/model_evaluation_observational_catalogs/#todo-tier3","title":"ToDo Tier3","text":"Dataset name Downloaded /g/data/kj13/datasets/ APHRO-MA Tier3/ CDS-SATELLITE-ALBEDO Tier3/ CDS-SATELLITE-LAI-FAPAR Tier3/ CDS-SATELLITE-SOIL-MOISTURE Tier3/ CDS-UERRA Tier3/ CERES-SYN1deg Tier3/ CLARA-AVHRR Tier3/ CLOUDSAT-L2 Tier3/ ESACCI-WATERVAPOUR Tier3/ GRACE Tier3/ JMA-TRANSCOM Tier3/ LAI3g Tier3/ MERRA2 Tier3/ MLS-AURA Tier3/ MTE Tier3/ NDP Tier3/ NIWA-BS Tier3/ NSIDC-0116-nh Tier3/ NSIDC-0116-sh Tier3/ UWisc Tier3/"},{"location":"model_evaluation/model_evaluation_recipe_gallery/","title":"Model Evaluation and Diagnostics (MED) Recipe Gallery","text":"<p>While we are still building this gallery, please have a look at the Community MED Recipes listed at Community Resources -&gt; Community Model Evaluation Recipes {{ community }}</p> <p>Here, we plan to provide you with an embedded link to our actively maintained Model Evaluation and Dianostics (MED) Recipe Gallery, hosted at medportal.herokuapp.com. For now, we provide a placeholder image with link and pointers to useful Model Evaluation and Dianostics (MED) resources.</p>"},{"location":"model_evaluation/model_evaluation_recipe_gallery/#link-to-our-med-recipe-gallery-supported","title":"Link to our MED Recipe Gallery {{ supported }}","text":""},{"location":"model_evaluation/model_evaluation_getting_started/","title":"Getting Started with Model Evaluation at NCI","text":"<p>Welcome to Model Evaluation and Diagnostics!</p> <p>Here, we provide you the important information to give you access to the large data that we curate at NCI's storage and show you how you can use it to figure out how fit for purpose specific models are, in particular when you compare them to osbervational data:</p> <p>1) Getting Access to NCI and relevant NCI projects 2) Setting up environments at gadi@NCI to load and evaluate observational and model data</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/","title":"Getting Started: Computing Access (Gadi@NCI)","text":"<p>Here, we provide you the important information to give you access to the large data that we curate at NCI's storage:</p> <p>1) Get an NCI Account 2) Join relevant NCI projects 3) Logging in to Gadi@NCI 4) Computing on Gadi</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#1-nci-account","title":"1) NCI Account","text":"<p>To be able to work with our data, you need an NCI account.</p> <p>If you don't have one yet, signup here.</p> <p>Note: You will need an institutional email address with an organisation that allows access to NCI (e.g., CSIRO, a university, etc.).</p> <p>Once you have signed up, you will be allocated a username. We will refer to this username (e.g. <code>kf1234</code>) as <code>$USER</code>.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#2-join-relevant-nci-projects","title":"2) Join relevant NCI projects","text":"<p>There is a plethora of NCI projects that may or may not be relevant for you.</p> <p>We recommend you have a chat with your supervisor to identify the relevant projects, but in any case suggest to join <code>xp65</code> for MED code as well as <code>kj13</code> for MED data.</p> <p>To get this conversation started, we list some possibly relevant projects below:</p> Project Description with link, * indicated compute resource ACCESS-NRI projects tm70 ACCESS-NRI Working Project * iq82 ACCESS-NRI MED Compute * kj13 ACCESS-NRI MED Data Dev ct11 ACCESS-NRI Replicated Datasets xp65 ACCESS-NRI Analysis Environments ACCESS projects access ACCESS software sharing p66 ACCESS - AOGCM / suppport development of the ACCESS modelling system * p73 ACCESS Model Output Archive (AOGCM) Data projects hh5 Climate-LIEF Data Storage ub7 Seasonal Prediction ACCESS-S1 Hindcast ux62 Seasonal Prediction ACCESS-S2 Hindcast cb20 ESGF CMIP3 Replication Data al33 ESGF CMIP5 Replication Data rr3 ESGF CMIP5 Australian Data Publication oi10 ESGF CMIP6 Replication Data fs38 ESGF CMIP6 Australian Data Publication rt52 ERA5 Replicated Data: Single and pressure-levels data uc16 ERA5 Replicated Datasets on Potential Temperature &amp; Vorticity Levels zz93 ERA5-Land Replicated Data zv2 Australian Gridded Climate Data (AGCD) Collection qv56 Reference Datasets for Climate Model Analysis/Forcing cj50 COSIMA Model Output Collection Other projects ik11 COSIMA shared working space v45 Ocean Extremes * ga6 Modelling the formation of sedimentary basins and continental margins * m18 Evolution and dynamics of the Australian lithosphere * q97 Earth dynamics and resources over the last billion years * qu79 Collaborative REAnalysis Technical Environment Intercomparison Project (CREATE-IP) <p>To join a project or find more projects, please use this NCI website.</p> <p>The first project that you join will become your default login project, e.g. <code>xp65</code>. We will refer to it as <code>$PROJECT</code> and we show you how to change it below.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#3-logging-in-to-gadinci","title":"3) Logging in to Gadi@NCI","text":"<p>If you have never logged onto Gadi before, we recommend to take a look at NCI's Welcome to Gadi website. It provides all the important commands and information for logging properly onto Gadi, like the following: \"To run jobs on Gadi, you need to first log in to the system. Users on Mac/Linux can use the built-in terminal. For Windows users, we recommend using MobaXterm as the local terminal. Logging in to Gadi happens through a Gadi login node.\"</p> <p>When you login, via the command <pre><code>ssh -Y $USER@gadi.nci.org.au\n</code></pre> you will enter your $HOME directory with your default <code>$PROJECT</code> and your default SHELL. Both are saved at <code>$HOME/.config/gadi-login.conf</code> and you can print them via <pre><code>cat $HOME/.config/gadi-login.conf\n</code></pre></p> <p>The <code>-Y</code> option is needed to run graphical tools by enabling the forwarding of trusted X protocol mesgs between X-Server on local system and X programs on Gadi.  You need to enable X Windowing system on your local system before running ssh. This can be done by running X-Server like XQuartz (Mac), MobaXterm (MS Windows), startx or similar (Linux).</p> <p>Again, for more useful information we recommend to check out NCI's Welcome to Gadi website.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#4-computing-on-gadi","title":"4) Computing on Gadi","text":""},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#gadi-resources","title":"Gadi Resources","text":"<p>Coupled climate models like ACCESS-CM involve, among other things, calculation of complex mathematical equations that explain the physics of the atmosphere and oceans. Performed at hundreds of millions of points around the Earth, these calculations require vast computing power to complete them in a reasonable amount of time, thus relying on the power of  high-performance computing (HPC) like Gadi. The Gadi supercomputer can handle more than 10 million billion (10 quadrillion) calculations per second and is connected to 100,000 Terabytes of high-performance research data storage.</p> <p>An overview of Gadi resources such as compute, storage and PBS jobs are described below. </p> <p>Useful NCI commands to check your available compute resources are:</p> Command Purpose <code>logout</code> or Ctrl+D To exit a session <code>hostname</code> Displays login node details <code>module list</code> Modules currently loaded <code>module avail</code> Available modules <code>nci_account -P [proj]</code> Compute allocation for [proj] <code>nqstat -P [proj]</code> Jobs running/queued in [proj] <code>lquota</code> Storage allocation and usage for all your projects"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#compute-hours","title":"Compute Hours","text":"<p>Compute allocations are granted to projects instead of directly to users and, hence, you need to be a member of a project in order to use its compute allocation. To run jobs on Gadi, you need to have sufficient allocated compute hours available, where the job cost depends on the resources reserved for the job and the amount of walltime it uses. </p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#storage","title":"Storage","text":"<p>Each user has a project-independent <code>$HOME</code> directory, which has a storage limit of 10 GiB. All data on <code>/home</code> is backed up.</p> <p>Through project membership, the user gets access to the storage space within the project folders <code>/scratch</code> and  <code>/g/data</code> filesystems for that particular project.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/access_to_gadi_at_nci/#pbs-jobs","title":"PBS Jobs","text":"<p>To run compute tasks such as an ACCESS-CM suite on Gadi, users need to submit them as jobs to queues. Within a job submission, you can specify the queue, duration and computational resources needed for your job. When a job submission is accepted, it is assigned a jobID (shown in the return message) that can then be used to monitor the job\u2019s status. </p> <p>On job completion, contents of the job\u2019s standard output/error stream gets copied to a file in the working directory with the respective format: <code>&lt;jobname&gt;.o&lt;jobid&gt;</code> and <code>&lt;jobname&gt;.e&lt;jobid&gt;</code>. Users should check these two log files before proceeding with post-processing of any output from their corresponding job.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/","title":"Getting Started with Model Evaluation at Gadi@NCI","text":"<p>At this stage of Getting Started, we assume that you already have access to Gadi@NCI. If this is not the case, please go to our instructions on how to get access to Gadi@NCI</p> <p>Here we describe where you can find, load, and evalulate observational and model data on Gadi.</p> <p>Note: You do not automatically have access to all of Gadi's storage at <code>/g/data/</code>, but need to be part of a <code>$PROJECT</code> to see files at <code>/g/data/$PROJECT</code>. Furthermore, if you use Gadi's job submission system PBS (Portable Batch System), you need to add the relevant storage to the <code>#PBS -l storage=gdata/xp65+gdata/kj13</code> (if you want the job to have access to <code>xp65</code> and <code>kj13</code> in this example).</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#21-access-med-our-currated-conda-environment-for-you-on-gadi","title":"2.1) <code>access-med</code>: Our currated <code>conda</code> environment for you on Gadi","text":"<p>To avoid running multiple (different) versions of code on Gadi, we provide you with a <code>conda</code> environment called <code>access-med</code> that we actually curate for you (version 0.1 is from June 2023).</p> <p>In order to change to this environment, please execute the following commands after loggin onto Gadi (and as part of your PBS scripts): <pre><code>$ module use /g/data/xp65/public/modules\n$ module load conda/access-med-0.1\n</code></pre></p> <p>If you are planning to run your code through JupyterLab on NCI's ARE, you need to use <code>/g/data/xp65/public/modules</code> as Module directories and <code>conda/are</code> as Modules when launching a JupyterLab session.</p> <p>You are now able to use the scripts of our currated environment, including <code>python3</code>, <code>intake</code>, <code>jupyter</code>, <code>esmvaltool</code>, or <code>ilamb</code>. The complete list of dependencies can be found in our dedicated GitHub repository.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#22-observational-data","title":"2.2) Observational Data","text":"<p>We provide an extensive collection of observational data on Gadi@NCI within the <code>/g/data/kj13/datasets</code> directory. </p> <p>Please take a look at our Observational Data Catalog for an overview.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#23-model-data","title":"2.3) Model Data","text":"<p>There are many models and data stored on Gadi, as you can imagine from the plethora of projects in Section 1.2. Downloading this data is hardly practical, so we suggest to work on Gadi instead.</p> <p>To avoid endless searches within Gadi's storage, we written a useful 'library' tool, called <code>access-nri-catalog</code>, that allows to search the Model Catalogs easily and is already loaded as part of our <code>access-med</code> <code>conda</code> environment. To find out how you can search for Model Data on Gadi, take a look at our Model Catalog.</p>"},{"location":"model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started/#25-model-evaluation","title":"2.5) Model Evaluation","text":"<p>Now that you have both Observational Data and Model Data at the palm of your hand on Gadi@NCI, there are many ways to evaluate this data.</p> <p>As part of our ACCESS-NRI <code>conda</code> environment, we provide several Model Evaluation Tools, like <code>ilamb</code> or <code>esmvaltool</code>.</p> <p>Check out Model Evaluation at Gadi to find out how you can use them on Gadi.</p>"},{"location":"model_evaluation/model_evaluation_model_catalogs/","title":"ACCESS-NRI intake Model Catalog","text":"<p>ACCESS-NRI is hosting a number of calculated models for you through National Computational Infrastructure (NCI) storage.</p> <p>We have set up an ACCESS-NRI intake Catalog package that allows you to easily search and load the model data on this storage. The premise of this ACCESS-NRI intake Catalog is to provide a (\"meta\") catalog of intake-esm (\"sub\") catalogs, which each correspond to different \"experiments\".</p> Search for a model in the ACCESS-NRI intake Catalog Add your model data to the ACCESS-NRI intake Catalog"},{"location":"model_evaluation/model_evaluation_model_catalogs/model_evaluation_add_models/","title":"Add your model data to the ACCESS-NRI intake Catalog","text":"<p>You've just run a new experiment, now you want to create an intake-esm catalog for that experiment?</p> <p>Look at this Tutorial {{ supported }} to learn how to add your own models.</p>"},{"location":"model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models/","title":"Search for a model in the ACCESS-NRI intake Catalog","text":"<p>To have the huge amount of data from different experiments on the NCI storage at the palm of your hand, we provide a (\"meta\") catalog for you to query via python as part of the <code>intake</code> package with our curated catalog plugin <code>intake.cat.access_nri</code> {{ supported }}.</p> <p>To use this catalog, you need access to NCI's Gadi. Check out our Get Started with ACCESS at NCI  {{ supported }} guide on how to get access.</p> <p>Once logged in to Gadi, you will need to add the <code>access-nri-catalog</code> to your <code>conda</code> environments and start an ARE JupyterLab Session. Check out our ACCESS-NRI Intake Catalog guide {{ supported }} for the specific setup (note that you can only read in data from specific experiments if they are loaded through the Storage keyword).</p> <p>Once your JupyterLab session started, you can access the <code>intake</code> catalog to load the data. Take a look at this Tutorial {{ supported }}.</p> <pre><code># Impport packages for searching/loading/plotting\nimport intake\nfrom distributed import Client\nimport matplotlib.pyplot as plt\n\n# The search process is a 2-step one\n# Comparable with searching for a book in a library:\n# 1) You look for the right book/catalog sections\n# 2) You look for the right book/catalog in the these sections\n\n# Load the ACCES-NRI list of catalogs for available experiment data\n# Similar to an overview of library section\naccess_nri_catalog_sections = intake.cat.access_nri\n\n# Perform a search for names, models, variables etc.\nexample_section_search = access_nri_catalog_sections.search(name=\"cmip6_oi10\")\n\n# Once you are sufficiently happy with your search, you can load the \"section\"\ncatalog_sections = access_nri_catalog_sections.search(name=\"025deg_jra55_iaf_omip2_cycle1\").to_source()\n# and start looking for the right catalogs of interest\ncatalogs_of_interest = catalog_sections.search(filename=\"ocean_scalar.*\")\n\n# Call the client that allows use load the data efficiently\nclient = Client(threads_per_worker=1)\nclient.dashboard_link\n\n# Actually load the data\nexperiment_data = catalogs_of_interest.to_dataset_dict(progressbar=False)\n\n# Et voil\u00e0, you have loaded the data and can start plotting\nexperiment_data[\"ocean_scalar_snapshot.1day\"][\"temp_global_ave\"].plot(label=\"daily\")\nexperiment_data[\"ocean_scalar.1mon\"][\"temp_global_ave\"].plot(label=\"monthly\")\n_ = plt.legend()\n</code></pre>"},{"location":"model_evaluation/model_evaluation_on_gadi/","title":"Model Evaluation on Gadi","text":"<p>To kick-start your model evaluation efforts, we provide the following tools as part of our <code>access-med</code> <code>conda</code> environment (and tutorials for how to use them on Gadi@NCI):   - ilamb, a tool for International Land (and Ocean) Model Benchmarking.   - esmvaltool, an Earth System Model Evaluation Tool </p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool/","title":"Tutorial for using <code>esmvaltool</code> on Gadi@NCI","text":"The documentation on Hive is work in progress! <p>The ACCESS-Hive is a community resource that is a work in progress. We\u2019d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you\u2019d like us to provide but aren\u2019t able to contribute yourself.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/","title":"Tutorial for using <code>ilamb</code> on Gadi@NCI","text":"<p>This tutorial explains how you can setup and run International Land Model Benchmarking (ILAMB) and International Ocean Model Benchmarking (IOMB) tests on <code>NCI</code> infrastracture. Both projects are maintained as <code>python</code> code under the package name <code>ilamb</code>.</p> <p>The Tutorial contains: 1) Background 2) Installation guide 3) Setup details 4) Run <code>ilamb</code> 5) Run <code>liamb</code> on <code>NCI</code> 6) Fix your setup with <code>ilamb-doctor</code></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#1-background-international-land-model-benchmarking-ilamb-and-international-ocean-model-benchmarking-iomb","title":"1) Background: International Land Model Benchmarking (ILAMB) and International Ocean Model Benchmarking (IOMB)","text":"<p>As earth system models (ESMs) become increasingly complex, there is a growing need for comprehensive and multi-faceted evaluation of model projections. The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns to reduce uncertainties associated with key land surface processes.</p> <p>If you have used (and installed) <code>ilamb</code> on NCI and know the basic principle of <code>ilamb</code>, you can start from Section 5) Guide for using ilamb on NCI.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#2-installing-ilamb","title":"2) Installing <code>ilamb</code>","text":"<p>For NCI users, ACCESS-NRI is providing a <code>conda</code> environment called <code>ilamb_dev</code> through the <code>xp65</code> project, with ilamb installed. You can load and activate it via:</p> <pre><code>&gt;&gt;&gt; module use /g/data/xp65/public/modules\n&gt;&gt;&gt; module load conda/ilamb_dev\n&gt;&gt;&gt; conda activate ilamb_dev\n</code></pre> <p>We will soon add <code>ilamb</code> also to the ACCESS-NRI MED <code>conda</code> environment, <code>access-med</code> under project<code>xp65</code>.</p> <p>If you want to install <code>ilamb</code> yourself, please follow the official installation instructions at https://www.ilamb.org/doc/install.html.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#3-configuring-ilamb","title":"3) Configuring <code>ilamb</code>","text":"<p>Before you can run <code>ilamb</code>, you need to configure a few things:</p> <p>3.1. Organise the ILAMB_ROOT path 3.2. Set up a <code>config</code> file 3.3. Set up a <code>modelroute</code> and <code>regions</code> files (Optional, if you want to run only a subset of models and/or specific regions of the world) 3.4. Download a <code>shapefiles</code> files locally (Optional online, necessary offline e.g. on NCI compute nodes)</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#31-organise-the-ilamb_root-path","title":"3.1) Organise the ILAMB_ROOT path","text":"<p><code>ilamb</code> demands files to be organised in a specific directory structure of <code>DATA</code> and <code>MODELS</code>.</p> <p>If you do not have your own files yet, you can download and use example files provided as part of the  of <code>ilamb</code>'s First Steps Tutorial</p> <p>The following tree represents the organization of the contents of this extracted sample data (Note: We renamed the main directory name): <pre><code>$ILAMB_ROOT (renamed from \"ILAMB_sample\")\n\u251c\u2500\u2500 sample.cfg (see [Section 3.2](#32-set-up-a-config-file))\n\u251c\u2500\u2500 modelroute.txt (optional, see [Section 3.3](#33-set-up-modelroute-and-regions-files))\n\u251c\u2500\u2500 regions.txt (optional, see [Section 3.3](#33-set-up-modelroute-and-regions-files))\n\u251c\u2500\u2500 DATA\n\u2502   \u251c\u2500\u2500 albedo\n\u2502   \u2502   \u2514\u2500\u2500 CERES\n\u2502   \u2502       \u2514\u2500\u2500 albedo_0.5x0.5.nc\n\u2502   \u2514\u2500\u2500 rsus\n\u2502       \u2514\u2500\u2500 CERES\n\u2502           \u2514\u2500\u2500 rsus_0.5x0.5.nc\n\u2514\u2500\u2500 MODELS\n    \u2514\u2500\u2500 CLM40cn\n        \u251c\u2500\u2500 rsds\n        \u2502   \u2514\u2500\u2500 rsds_Amon_CLM40cn_historical_r1i1p1_185001-201012.nc\n        \u2514\u2500\u2500 rsus\n            \u2514\u2500\u2500 rsus_Amon_CLM40cn_historical_r1i1p1_185001-201012.nc\n</code></pre></p> <p>There are two main branches in this directory. The first is the <code>DATA</code> directory\u2013this is where we keep the observational datasets each in a subdirectory bearing the name of the variable. While not strictly necesary to follow this form, it is a convenient convention. The second branch is the <code>MODEL</code> directory in which we see a single model result from CLM.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#311-add-files-to-data","title":"3.1.1) Add files to DATA","text":"<p>There is a lot of DATA available to add. Take a look at https://www.ilamb.org/ILAMB-Data/ and https://www.ilamb.org/IOMB-Data/ for extensive lists for ILAMB-Data (land modelling) and IOMB-Data (ocean modelling).</p> <p><code>ilamb</code> has a commandline prompt to add new DATA in a substructure. To fetch all available DATA from the website, you can simply go to your $ILAMB_ROOT and type <pre><code>&gt;&gt;&gt; ilamb-fetch\n</code></pre></p> <p>The command will compare the above website with your current DATA and make suggestions for downloads: <pre><code>Comparing remote location:\n\n      https://www.ilamb.org/ILAMB-Data/\n\nTo local location:\n\n      ./\n\nI found the following files which are missing, out of date, or corrupt:\n\n      .//DATA/twsa/GRACE/twsa_0.5x0.5.nc\n      .//DATA/rlus/CERES/rlus_0.5x0.5.nc\n      ... (we have abbreviated the extensive list here)\n\nDownload replacements? [y/n]\n</code></pre></p> <p>You can use <code>ilamb-fetch -h</code> to see how you can adjust the remote and local locations. If you want to download IOMB-Data, you can for example use <pre><code>ilamb-fetch --remote_root https://www.ilamb.org/IOMB-Data/\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#312-add-files-to-model","title":"3.1.2) Add files to MODEL","text":"<p>If you want to add your own <code>MODEL</code> to <code>ilamb</code>, you can do so by following this description.</p> <p>For <code>NCI</code> users, our <code>ilamb_dev</code> <code>conda</code> enrivonment already provides all observational datasets from the <code>ilamb</code> official web and the ACCESS-ESM1_5 model result for user at <code>ILAMB_ROOT</code>. Stay tune for more observational and model data or tell us which ones we should definitely add.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#32-set-up-a-config-file","title":"3.2) Set up a <code>config</code> file","text":"<p>Now that we have the data, we need to setup a <code>config</code> file which the <code>ilamb</code> package will use to initiate a benchmark study.  </p> <p><code>ilamb</code> provides default config files here.</p> <p>Below we explain both which variables you can define, but start by showing you the minimum setup from the tutorial's. <code>sample.cfg</code> file:</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#minimum-configure-file-with-a-direct-and-a-derived-variable","title":"Minimum configure file with a direct and a derived variable","text":"<pre><code># This configure file specifies the variables\n\n[h1: Radiation and Energy Cycle]\n\n[h2: Surface Upward SW Radiation]\nvariable = \"rsus\"\n\n[CERES]\nsource   = \"DATA/rsus/CERES/rsus_0.5x0.5.nc\"\n\n[h2: Albedo]\nvariable = \"albedo\"\nderived  = \"rsus/rsds\"\n\n[CERES]\nsource   = \"DATA/albedo/CERES/albedo_0.5x0.5.nc\"\n</code></pre> <p>In brief: This file allows you to create different header descriptions of the experiments (<code>h1</code>: top level for grouping of variables, <code>h2</code>: sub-level for each variable), but most importantly the <code>variable</code>s that we will look into and their <code>source</code>. In the eaxmple, <code>rsus</code> (Surface Upward Shortwave Radiation) and <code>albedo</code> are the used variables. The latter is actually derived from two variables by dividing the Surface Upward Shortwave Radiation by the Surface Downward Shortwave Radiation, <code>derived = rsus/rsds</code>. Finally, sources are defined as <code>source</code> with a text-font header without <code>h1</code> or <code>h2</code>.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#changing-configure-file-variables","title":"Changing configure file variables","text":"<p>This is the list of all the variables you can modify in config file: <pre><code>source              = None\n#Full path to the observational dataset\n\ncmap                = \"jet\"\n#The colormap to use in rendering plots (default is 'jet')\n\nvariable            = None\n#Name of the variable to extract from the source dataset\n\nalternate_vars      = None\n#Other accepted variable names when extracting from models\n\nderived             = None\n#An algebraic expression which captures how the confrontation variable may be generated\n\nland                = False\n#Enable to force the masking of areas with no land (default is False)\n\nbgcolor             = \"#EDEDED\"\n#Background color\n\ntable_unit          = None\n#The unit to use when displaying output in tables on the HTML page\n\nplot_unit           = None\n#The unit to use when displaying output on plots on the HTML page\n\nspace_mean          = True\n#Disable to compute sums of the variable over space instead of mean values\n\nrelationships       = None\n#A list of confrontations with whose data we use to study relationships, the syntax is \"h2 tag/observational dataset\". You will see the relationship part in the output if you specify some relationship.\n\nctype               = None\n#Choose a specific Confrontion class. \n\nregions             = None\n#Specify the regions of confrontation\n\nskip_rmse           = False\n#akip rmse in program\n\nskip_iav            = True\n#Ship iav in program\n\nmass_weighting      = False\n#if switch to true, using an average data in a period to normalize\n\nweight              = 1    \n# if a dataset has no weight specified, it is implicitly 1\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#33-set-up-modelroute-and-regions-files","title":"3.3) Set up <code>modelroute</code> and <code>regions</code> files","text":"<p>If you plan to run only a specific subset of models, you can already define them in a <code>modelroute.txt</code> file. It could look like our specific example for running different versions (1, 2, and 3) of the ACCESS-ESM 1.5 suite:</p> <pre><code># Model Name                    , PATH/TO/MODELS  , EXTRA COMMANDS\nACCESS_ESM1-5-r1i1p1f1          , MODELS/r1i1p1f1 , CMIP6\nACCESS_ESM1-5-r2i1p1f1          , MODELS/r2i1p1f1 , CMIP6\nACCESS_ESM1-5-r3i1p1f1          , MODELS/r3i1p1f1 , CMIP6\n... (abbreviated)\n</code></pre>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#34-downloadlink-shapefiles-files-locally","title":"3.4) Download/link <code>shapefiles</code> files locally","text":"<p>You can download the <code>shapefiles</code> that are needed to run <code>ilamb</code> and <code>cartopy</code> offline here:</p> <ul> <li>For Land: https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_land.zip</li> <li>For Ocean: https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_ocean.zip</li> </ul> <p>Finally, you need to define that path as <code>CARTOPY_DATA_DIR</code> via  <pre><code>export CARTOPY_DATA_DIR=/absolute/path/to/shapefiles/directory\n</code></pre></p> <p>Note: For NCI, we already provide shapefiles in a directory as part of project <code>xp65</code>. After joining the project, you can thus easily use <pre><code>export CARTOPY_DATA_DIR=/g/data/xp65/public/apps/cartopy-data\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#4-run-ilamb","title":"4) Run <code>ilamb</code>","text":""},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#41-ilamb-run","title":"4.1) ilamb-run","text":"<p>Now that we have the configuration file set up, you can run the study using the <code>ilamb-run</code> script. Executing the following command at the $ILAMB_ROOT directory will run <code>ilamb</code> as specified in your <code>sample.cfg</code> for all models of the <code>model_root</code> and all regions (<code>global</code>) of the world: <pre><code>ilamb-run --config sample.cfg --model_root $ILAMB_ROOT/MODELS/ --regions global\n</code></pre> If you are on some institutional resource, you may need to launch the above command using a submission script, or request an interactive node. As the script runs, it will yield output which resembles the following: <pre><code>Searching for model results in /Users/ncf/sandbox/ILAMB_sample/MODELS/\n\n                                          CLM40cn\n\nParsing config file sample.cfg...\n\n                   SurfaceUpwardSWRadiation/CERES Initialized\n                                     Albedo/CERES Initialized\n\nRunning model-confrontation pairs...\n\n                   SurfaceUpwardSWRadiation/CERES CLM40cn              Completed  37.3 s\n                                     Albedo/CERES CLM40cn              Completed  44.7 s\n\nFinishing post-processing which requires collectives...\n\n                   SurfaceUpwardSWRadiation/CERES CLM40cn              Completed   3.3 s\n                                     Albedo/CERES CLM40cn              Completed   3.3 s\n\nCompleted in  91.8 s\n</code></pre> What happened here? First, the script looks for model results in the directory you specified in the <code>--model_root</code> option. It will treat each subdirectory of the specified directory as a separate model result. Here since we only have one such directory, <code>CLM40cn</code>, it found that and set it up as a model in the system. Next it parsed the configure file we examined earlier. We see that it found the CERES data source for both variables as we specified it. If the source data was not found or some other problem was encountered, the green <code>Initialized</code> will appear as red text which explains what the problem was (most likely <code>MisplacedData</code>). If you encounter this error, make sure that <code>ILAMB_ROOT</code> is set correctly and that the data really is in the paths you specified in the configure file.</p> <p>Next we ran all model-confrontation pairs. In our parlance, a confrontation is a benchmark observational dataset and its accompanying analsys. We have two confrontations specified in our configure file and one model, so we have two entries here. If the analysis completed without error, you will see a green <code>Completed</code> text appear along with the runtime. Here we see that <code>albedo</code> took a few seconds longer than <code>rsus</code>, presumably because we had the additional burden of reading in two datasets and combining them.</p> <p>The next stage is the post-processing. This is done as a separate loop to exploit some parallelism. All the work in a model-confrontation pair is purely local to the pair. Yet plotting results on the same scale implies that we know the maxmimum and minimum values from all models and thus requires the communcation of this information. Here, as we are plotting only over the globe and not extra regions, the plotting occurs quickly.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#42-run-specific-models-and-regions","title":"4.2) Run specific models and regions","text":"<p>As mentioned in Section 3.3, you can adjust the models and regions that <code>ilamb</code> will run on. You can find more information in the <code>ilamb</code> tutorial. Calling <code>ilamb-run</code> with both specifications, would look like: <pre><code>ilamb-run --config cmip.cfg --model_setup modelroute.txt --regions regions.txt\n</code></pre> where you call a specific config file (see Section 3.2) as well as specific model routes and regions with files (see Section 3.3).</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#43-viewing-the-benchmarking-output-in-your-browser","title":"4.3) Viewing the benchmarking output in your browser","text":"<p>The whole process generates a directory of results within ILAMB_ROOT which by default is called <code>_build</code>. To view the results locally on your computer, navigate into this directory and start a local <code>http</code> server: <pre><code>python -m http.server\n</code></pre> You should see a message similar to this (or use http://0.0.0.0:8000/): <pre><code>Serving HTTP on 0.0.0.0 port 8000 (http://0.0.0.0:8000/) ...\n</code></pre> Open this link in your browser and you will see a webpage with a summary table in the center. As we have so few variables and a single model at this point, the table will very simple:</p> <p></p> <p>As we add more variables and models, this summary table helps you understand relative differences in scores among models. For now, clicking on a row of the table will expand it to reveal the underlying datasets used. Clicking on CERES will take you to another page which presents detailed scores and plots.</p> <p></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#5-run-ilamb-on-nci","title":"5) Run <code>ilamb</code> on NCI","text":"<p>If you followed the guides above, you should be familiar with how you can setup <code>ilamb</code>.</p> <p>To run <code>ilamb</code> on NCI, you can either start an interactive setup Section 5.1 or use a non-interactive Portable Batch System (PBS) job Section 5.2.</p> <p>In both cases, you need to again define the variable <code>$ILAMB_ROOT</code></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#51-ilamb_root-and-datamodel-on-nci","title":"5.1) ILAMB_ROOT and DATA/MODEL on NCI","text":"<p>In our default setup, we will place ILAMB_ROOT and the shapefiles for cartopy directly in the home directory. First, you have to create the ILAMB_ROOT directory <pre><code>mkdir $PWD/ILAMB_ROOT\n</code></pre> You can then simply export their paths after login as: <pre><code>export ILAMB_ROOT=$PWD/ILAMB_ROOT\nexport CARTOPY_DATA_DIR=/g/data/xp65/public/apps/cartopy-data\n</code></pre></p> <p>You can of course change the path of the directory, but will need to take this into account for the PBS job by adding a command to change into the $ILAMB_ROOT directory (see PBS setup comments).</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#ilamb_rootdata-on-nci","title":"ILAMB_ROOT/DATA on NCI","text":"<p>An extensive colletion of DATA is provided in the <code>kj13</code> project. You need to have joined the project on NCI to get access to this data.</p> <p>To create a symbolic link to this data, use the bash command <pre><code>ln -s /g/data/kj13/datasets/ilamb/DATA $ILAMB_ROOT/DATA\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#ilmab_rootmodel-on-nci","title":"ILMAB_ROOT/MODEL on NCI","text":"<p>In the future, we will provide a symbolic link to a MODEL catalog for you as well.</p> <p>For now, you will need to create the directory $ILAMB_ROOT/MODEL and populate it with symbolic links to specific models yourself.</p> <p>In our example, we will use ACCESS-ESM1.5, which is provided on NCI as part of project <code>fs38</code>.  You need to have joined the project on NCI to get access to this data.</p> <p>To link the ACCESS-ESM1.5 suite files to your $ILAMB_ROOT/MODEL, simply execute the following bash command <pre><code>mkdir $ILAMB_ROOT/MODELS\nln -s /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r* $ILAMB_ROOT/MODELS\n</code></pre></p> <p>By the end of Section 5.1.1 and 5.1.2, your $ILAMB_ROOT Directory should look similar to <pre><code>$ILAMB_ROOT\n\u251c\u2500\u2500 ...\n\u251c\u2500\u2500 DATA -&gt; /g/data/kj13/datasets/ilamb/DATA\n\u2514\u2500\u2500 MODELS\n    \u251c\u2500\u2500 r10i1p1f1 -&gt; /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r10i1p1f1\n    \u251c\u2500\u2500 ... (abbreviated)\n    \u2514\u2500\u2500 r9i1p1f1 -&gt; /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r9i1p1f1\n</code></pre></p> <p>These different models have a lot of subdirectories, which are important to keep in mind when defining the <code>source</code> parameter in your <code>ilamb</code> <code>.cfg</code> file. Note that the <code>ilamb</code> files will end with <code>*.nc*. For example, one of the *rsus* files for run</code>r10i1p1f1<code>can be found (and used for</code>.cfg` under <pre><code>source = /g/data/fs38/publications/CMIP6/CMIP/CSIRO/ACCESS-ESM1-5/historical/r1i1p1f1/Amon/rsus/gn/files/d20191115/rsus_Amon_ACCESS-ESM1-5_historical_r1i1p1f1_gn_185001-201412.nc\n</code></pre> or shorter  <pre><code>source = $ILAMB_ROOT/MODELS/r1i1p1f1/Amon/rsus/gn/files/d20191115/rsus_Amon_ACCESS-ESM1-5_historical_r1i1p1f1_gn_185001-201412.nc\n</code></pre></p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#52-portable-batch-system-pbs-jobs-on-nci","title":"5.2) Portable Batch System (PBS) jobs on NCI","text":"<p>The following default PBS file, let's call it <code>ilamb_test.sh</code> can help you to setup your own, while making sure to use the correct project (#PBS -P) to charge your computing cost to: <pre><code>#!/bin/bash\n\n#PBS -N default_ilamb\n#PBS -P tm70\n#PBS -q normalbw\n#PBS -l ncpus=1\n#PBS -l mem=32GB           \n#PBS -l jobfs=10GB        \n#PBS -l walltime=00:10:00  \n#PBS -l storage=gdata/xp65+gdata/kj13+gdata/fs38\n#PBS -l wd\n\nmodule use /g/data/xp65/public/modules\nmodule load conda/access-med-0.1\n\nexport ILAMB_ROOT=$PWD/ILAMB_ROOT\nexport CARTOPY_DATA_DIR=/g/data/xp65/public/apps/cartopy-data\n\nilamb-run --config cmip.cfg --model_setup $PWD/modelroute.txt --regions global\n</code></pre></p> <p>If you are not familiar with PBS jobs on NCI, you could find the guide here. In brief: this PBS script (which you can submit via the bash command <code>qsub ilamb_test.sh</code>), will submit a job to Gadi with the job name (#PBS -N) default_ilamb under project (#PBS -P) <code>tm70</code> with a normal queue (#PBS -q normalbw), for 1 CPU (#PBS -l ncpus=1) with 32 GB RAM (#PBS -l mem=32GB), with an walltime of 10 hours and access to 10 GB local disk space (#PBS -l jobfs=10GB) as well as data storage access to projects <code>xp65</code>, <code>kj13</code>, and <code>fs38</code> (again, note that you have to be member of both projects on NCI. Upon starting the job, it will change into to the working directory that you started the job from (#PBS -l wd) and load the access-med conda environment. Finally, it will export the $ILAMB_ROOT as well as $ARTOPY_DATA_DIR paths and start an <code>ilamb-run</code>.</p> <p>In our example, we actually run the <code>cmip.cfg</code> file from the <code>ilamb</code> config file github repository for files spec</p> <p>Note: If your ILAMB_ROOT and CARTOPY_DATA_DIR are not in your directory from where you submitted the job from, then you need to adjust the export commands to their path <pre><code>export ILAMB_ROOT=/absolute/path/where/ILAMB_ROOT/actually/is\nexport CARTOPY_DATA_DIR=/absolute/path/where/shapefiles/actually/are\n</code></pre></p> <p>Once the jobs are finished, you can again inspect the outcome as described in Section 4.3</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb/#6-fix-your-setup-with-ilamb_doctor","title":"6. Fix your setup with ilamb_doctor","text":"<p><code>ilamb_doctor</code> is a script you can use to diagnosing some missing model values or what is incorrect or missing from a given analysis. It takes options similar to <code>ilamb-run</code> and is used in the following way: ```[ILAMB/test]$ ilamb-doctor --config test.cfg --model_root ${ILAMB_ROOT}/MODELS/CLM</p> <p>Searching for model results in /Users/ncf/ILAMB//MODELS/CLM</p> <pre><code>                               CLM40n16r228\n                               CLM45n16r228\n                               CLM50n18r229\n</code></pre> <p>We will now look in each model for the variables in the ILAMB configure file you specified (test.cfg). The color green is used to reflect which variables were found in the model. The color red is used to reflect that a model is missing a required variable.</p> <pre><code>                       Biomass/GlobalCarbon CLM40n16r228 biomass or cVeg\n                                    ... (abbreviated)\n                        Precipitation/GPCP2 CLM50n18r229 pr\n</code></pre> <p>``` Here we have run the command on some inputs in our test directory. You will see a list of the confrontations we run and the variables which are required or their synonyms. What is missing in this tutorial is the text coloring which will indicate if a given model has the required variables.</p> <p>We have finish the introduction of basic <code>ilamb</code> usage. We believe you have some understanding of <code>ilamb</code> and cont wait to use it. if you still have any question or you want some developer level support, you can find more detail in their official tutorial.</p>"},{"location":"model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima/","title":"Tutorial for using <code>pangeo</code> &amp; COSIMA on Gadi@NCI","text":"The documentation on Hive is work in progress! <p>The ACCESS-Hive is a community resource that is a work in progress. We\u2019d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you\u2019d like us to provide but aren\u2019t able to contribute yourself.</p> <p>https://pangeo.io</p>"},{"location":"models/","title":"ACCESS Models","text":"<p>ACCESS is a family of related computer models or components that represent different parts of the Earth system. ACCESS links various model components through software called couplers to form different Model Configurations.</p>"},{"location":"models/#access-model-components","title":"ACCESS Model Components","text":"Atmosphere Land Ocean Sea Ice Aerosols Atmospheric Chemistry Biogeochemistry Land Biogeochemistry Ocean Coupler"},{"location":"models/#access-model-configurations","title":"ACCESS Model Configurations","text":"ACCESS-CM                      ACCESS Coupled Model (CM) produces physical climate simulations by deploying the atmosphere, ocean, and sea-ice components. ACCESS-CM features improved fluid dynamics and a microphysical aerosol scheme.                  ACCESS-ESM                      ACCESS Earth System Model (ESM) simulates the carbon and other bio-chemical cycles within the climate system, by deploying the atmosphere, ocean, and sea-ice components. ACCESS-ESM is one of the two ACCESS global coupled model versions.                  ACCESS-OM                      ACCESS Ocean Model (OM) deploys the ocean and sea-ice components to provide the Australian climate community with ocean weather and climate data, including seasonal forecasting, climate variability, downscaling of climate in the marine environment around Australia, and ocean biogeochemistry."},{"location":"models/configurations/","title":"ACCESS Configurations","text":"<p>The Configurations section is still in development.</p> <p>What to expect in the next few months?</p> <p>The ACCESS-NRI will release model configurations and experiments to the community, including a reference model output for each experiment.</p> <p>The model configurations and experiments will be documented in this section as they are released by the ACCESS-NRI. The information will cover topics such as where to find a configuration or experiment, how to use a configuration to run your own experiment, where to find the data produced by a released experiment.</p>"},{"location":"models/configurations/access-am/","title":"ACCESS-AM {{ supported }}","text":"<p>The ACCESS-AM model is a coupled model between the atmosphere and the land. The atmospheric model component is the UM model. The UM model comes by default coupled to the JULES land model. That is why the first configurations and experiments released of ACCESS-AM will be UM-JULES configurations. But the ACCESS-NRI is working to ensure subsequent releases of ACCESS-AM use the CABLE land model instead.</p>"},{"location":"models/configurations/access-am/#getting-started-information","title":"Getting started information","text":"<p>On this page, you will find information on how to gain access to the UM model and start using the model. You will also find links to various configurations and experiments you can use as a basis to design your experiment.</p>"},{"location":"models/configurations/access-am/#configurations","title":"Configurations","text":""},{"location":"models/configurations/access-am/#experiments","title":"Experiments","text":"<p>Some experiments already run with the UM are listed on:</p> <ul> <li>CLEX CMS wiki</li> </ul>"},{"location":"models/configurations/access-cm/","title":"ACCESS-CM {{ supported }}","text":"ACCESS-CM2 (ACCESS Coupled Model 2) is a global fully-coupled climate model that includes the atmosphere, ocean and sea-ice components, and produces physical climate simulations. ACCESS-CM2 is one of the two models run by the Australian climate community for the   Coupled Model Intercomparison Project, CMIP."},{"location":"models/configurations/access-cm/#access-cm2-configurations","title":"ACCESS-CM2 configurations","text":"<ul> <li> <p>Atmosphere model (UM10.6): N96 resolution (1.875\u00b0 x 1.25\u00b0, 85 levels). Physical model only \u2013 no carbon cycle.</p> </li> <li> <p>Land surface model (CABLE2.5) </p> </li> <li> <p>Ocean model (MOM5): Tripolar grid, 1\u00b0 resolution, 50 levels.</p> </li> <li> <p>Sea ice model (CICE5.1) </p> COMPONENT MODEL VERSION Atmosphere UM 10.6 Land Surface CABLE 2.5 (integrated in UM) Ocean MOM 5 Sea Ice CICE 5.1 Coupler OASIS-MCT 3 </li> </ul> <p>ACCESS-NRI will release an ACCESS-CM model configuration. The first release of ACCESS-CM will be derived from the CSIRO ACCESS-CM2 configuration and will include atmosphere, land, ocean and sea ice components.</p>"},{"location":"models/configurations/access-cm/#access-cm2-recommended","title":"ACCESS-CM2 {{ recommended }}","text":"<p>Citation 1 | Tutorial</p> <p>ACCESS-CM2 1 is one of Australia\u2019s contributions to the World Climate Research Programme\u2019s Coupled Model Intercomparison Project Phase 6 (CMIP6). The component models are: UM10.6 GA7.1 for the atmosphere, CABLE2.5 for the land surface, MOM5 for the ocean, and CICE5.1.2 for the sea ice. Compared to previous model versions ACCESS-CM2 shows better global hydrological balance, more realistic ocean water properties (in terms of spatial distribution) and meridional overturning circulation in the Southern Ocean but a poorer simulation of the Antarctic sea ice and a larger energy imbalance at the top of atmosphere. This energy imbalance reflects a noticeable warming trend of the global ocean over the spin-up period.</p> <ol> <li> <p>Daohua Bi, Martin Dix, Simon Marsland, Siobhan O'Farrell, Arnold Sullivan, Roger Bodman, Rachel Law, Ian Harman, Jhan Srbinovsky, Harun A Rashid, Peter Dobrohotoff, Chloe Mackallah, Hailin Yan, Anthony Hirst, Abhishek Savita, Fabio Boeira Dias, Matthew Woodhouse, Russell Fiedler, and Aidan Heerdegen. Configuration and spin-up of ACCESS-CM2, the new generation Australian Community Climate and Earth System Simulator coupled model. Journal of Southern Hemisphere Earth Systems Science, 70(1):225\u2013251, 2020.\u00a0\u21a9\u21a9</p> </li> </ol>"},{"location":"models/configurations/access-esm/","title":"ACCESS-ESM {{ supported }}","text":"<p>ACCESS-ESM stands for ACCESS Earth System Model. Earth system model means it is a fully-coupled model that includes carbon cycle components.</p> <p>ACCESS-NRI will release an ACCESS-ESM model configuration. The first release of ACCESS-ESM will be derived from the CSIRO ACCESS-ESM1.5 configuration and will include atmosphere, land and land biogeochemistry, ocean and ocean biogeochemistry, and sea ice components.</p>"},{"location":"models/configurations/access-esm/#access-esm15-recommended","title":"ACCESS-ESM1.5 {{ recommended }}","text":"<p>Citation 1</p> <p>ACCESS Training Workshop (AMOS 2021)</p> <p>Webinar: Getting Started with ACCESS-CM2 and ACCESS-ESM1.5 </p> <p>ACCESS-ESM1.5 1 is a fully-coupled climate model with land and ocean carbon cycle components. ACCESS-ESM1.5 has mainly been developed to enable Australia to participate in the Coupled Model Intercomparison Project Phase 6 (CMIP6) with an ESM version. An assessment of the climate response to CO2 forcing indicates that ACCESS-ESM1.5 has an equilibrium climate sensitivity of 3.87\u00b0C.</p> <ol> <li> <p>Tilo Ziehn, Matthew A Chamberlain, Rachel M Law, Andrew Lenton, Roger W Bodman, Martin Dix, Lauren Stevens, Ying-Ping Wang, and Jhan Srbinovsky. The Australian Earth System Model: ACCESS-ESM1.5. Journal of Southern Hemisphere Earth Systems Science, 70(1):193\u2013214, 2020.\u00a0\u21a9\u21a9</p> </li> </ol>"},{"location":"models/configurations/access-om/","title":"ACCESS-OM {{ supported }}","text":"<p>The ACCESS Ocean Model, ACCESS-OM, is a global coupled ocean and sea ice configuration. It couples the ocean and sea ice components via a coupler. The atmospheric fields that drive the model are provided by a data product, usually derived from reanalysis.</p> <p>ACCESS-NRI will release supported ACCESS-OM configurations. The first release will be derived from the COSIMA ACCESS-OM2 suite and will include ocean and sea ice components.</p>"},{"location":"models/configurations/access-om/#access-om2-recommended","title":"ACCESS-OM2 {{ recommended }}","text":"<p>Citation 1 | Documentation</p> <p>ACCESS-OM2 1 is a suite of coupled ocean-sea ice models developed by the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA). All models use the MOM5 ocean model coupled to the CICE5 sea ice model via an OASIS3-MCT coupler.</p> <p>The models in the ACCESS-OM2 suite differ by their grid spatial resolution:</p> <ul> <li>ACCESS-OM2 at 1\u00b0 with 50 vertical levels</li> <li>ACCESS-OM2-025 at 0.25\u00b0 with 50 vertical levels</li> <li>ACCESS-OM2-01 at 0.1\u00b0 with 75 vertical levels</li> </ul> <ol> <li> <p>A. E. Kiss, A. McC. Hogg, N. Hannah, F. Boeira Dias, G. B. Brassington, M. A. Chamberlain, C. Chapman, P. Dobrohotoff, C. M. Domingues, E. R. Duran, M. H. England, R. Fiedler, S. M. Griffies, A. Heerdegen, P. Heil, R. M. Holmes, A. Klocker, S. J. Marsland, A. K. Morrison, J. Munroe, M. Nikurashin, P. R. Oke, G. S. Pilo, O. Richet, A. Savita, P. Spence, K. D. Stewart, M. L. Ward, F. Wu, and X. Zhang. ACCESS-OM2 v1.0: a global ocean\u2013sea ice model at three resolutions. Geoscientific Model Development, 13(2):401\u2013442, 2020. URL: https://gmd.copernicus.org/articles/13/401/2020/, doi:10.5194/gmd-13-401-2020.\u00a0\u21a9\u21a9</p> </li> </ol>"},{"location":"models/configurations/access-s/","title":"ACCESS-S {{ community }}","text":"<p>ACCESS-S is the Bureau of Meteorology's climate modelling system used for seasonal forecasting.</p> <p>This coupled model uses a different set of model components than the other ACCESS models:</p> <ul> <li>UM for the atmosphere</li> <li>JULES for the land</li> <li>NEMO for the ocean</li> <li>CICE for the sea-ice</li> <li>OASIS3-MCT for the coupler</li> </ul>"},{"location":"models/model_components/","title":"Model Components","text":"<p>ACCESS components represent different chemical, physical or biological parts of the Earth System.</p> Atmosphere Land Ocean Sea Ice Aerosols Atmospheric Chemistry Biogeochemistry Land Biogeochemistry Ocean Coupler <p>Most model components have originated from collaborations with international research groups. These include:</p> <ul> <li>UK Met Office \u2192 Unified Model (UM) atmospheric component.</li> <li>NOAA/ Geophysical Fluid Dynamics Laboratory (GFDL) \u2192 Modular Ocean Model (MOM) component.</li> <li>Los Alamos National Laboratory (LANL) \u2192 Sea ice model (CICE) component.</li> <li>Centre Europ\u00e9en de Recherche et de Formation Avanc\u00e9e en Calcul Scientifique (CERFACS) \u2192 Ocean-Atmosphere-Sea Ice-Snowpack Model Coupling Toolkit (OASIS3-MCT).</li> <li>United Kingdom Chemistry and Aerosols (UKCA) \u2192 UK community atmospheric Chemistry-Aerosol (UKCA) model.</li> <li>CSIRO, COSIMA and CLEX \u2192 Community Atmosphere Biosphere Land Exchange (CABLE),  Whole Ocean Model with Biogeochemistry And Trophic-dynamics (WOMBAT) and land biogeochemistry Carnegie\u2013Ames\u2013Stanford-Approach (CASA) models. These models have been developed in Australia.</li> </ul>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/","title":"Aerosol and Atmospheric Chemistry Components","text":""},{"location":"models/model_components/aerosols_atmospheric_chemistry/#ukca-supported","title":"UKCA {{ supported }}","text":"<p>The UK Chemistry-Aerosol model (UKCA) is a community atmospheric chemistry-aerosol global model  developed in the United Kingdom. It is suitable for a range of topics in climate and environmental change research.</p>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/#how-is-ukca-used","title":"How is UKCA used?","text":"<p>UKCA chemistry model is enabled in ACCESS-CM2-Chem.</p>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/#glomap-supported","title":"GLOMAP {{ supported }}","text":"<p>UKCA contains an aerosol scheme GLObal Model of Aerosol Processes (GLOMAP) that can be used independently. The multi-component, multi-modal GLOMAP model allows simulation of aerosol number, size and concentrations of individual components such as sulphate,sea salt and different types of carbon.</p>"},{"location":"models/model_components/aerosols_atmospheric_chemistry/#how-is-glomap-used","title":"How is GLOMAP used?","text":"<p>GLOMAP is used in ACCESS-CM2 and ACCESS-CM2-Chem.</p>"},{"location":"models/model_components/atmosphere/","title":"Atmospheric Model Component","text":""},{"location":"models/model_components/atmosphere/#the-unified-model-um-supported","title":"The Unified Model (UM) {{ supported }}","text":"<p>The Unified Model (UM) is a numerical model of the atmosphere used for both weather and climate applications, developed by the Met Office in the United Kingdom (UK). It includes solutions of the equations of atmospheric fluid dynamics with advanced parameterizations of subgrid-scale physical processes like convection, cloud formation and atmospheric radiation.</p> <p>The Unified Model gets its name because a single model is used across a wide range of both timescales (nowcasting to centennial) and spatial scales (sub km convective scale to global climate modelling).</p> <p>The UM is used by several international operational meteorology and research organizations and these contribute towards its development through the UM partnership.</p>"},{"location":"models/model_components/atmosphere/#how-is-the-um-used","title":"How is the UM used?","text":"<p>The UM Model component represents the atmosphere in many of the ACCESS Models used at regional and global scales.</p> <p>The ACCESS-CM2 climate model and ACCESS-ESM1-5 earth system model use versions of the UM as their atmospheric components.</p> <p>The Australian Bureau of Meteorology operational 12 km spatial resolution global forecasting system uses the Unified Model, as part of ACCESS for:</p> <ul> <li>Forecasting of extreme events and emergencies such as heatwaves, bushfires, cyclones, floods, coral bleaching, sea-level rise, coastal inundation and more.</li> <li>Daily and seasonal weather forecasts</li> </ul>"},{"location":"models/model_components/atmosphere/#useful-links","title":"Useful links","text":"<p>STASH register: Metadata reference for the outputs variables.</p>"},{"location":"models/model_components/bgc_land/","title":"Biogeochemistry Land","text":""},{"location":"models/model_components/bgc_land/#casa-cnp-supported","title":"CASA-CNP {{ supported }}","text":"<p>CASA (Carnegie-Ames-Stanford Approach)-CNP (Carbon-Nitrogen-Phosphorous) is the land biogeochemistry model developed in CABLE.</p> <p>CASA-CNP models the dynamics of carbon pools and nitrogen and phosphorous limitations. It is directly coupled with the CABLE land surface model.</p>"},{"location":"models/model_components/bgc_land/#how-is-casa-cnp-used","title":"How is CASA-CNP used?","text":"<p>CASA-CNP is switched on for carbon-cycle to use in the ACCESS-ESM1.5 model.</p>"},{"location":"models/model_components/bgc_ocean/","title":"Biogeochemistry Ocean","text":""},{"location":"models/model_components/bgc_ocean/#wombat-supported","title":"WOMBAT {{ supported }}","text":"<p>WOMBAT is the ocean carbon model (World Ocean Model of Biogeochemistry And Trophic-dynamics), developed in Australia. It calculates the carbon fluxes of the ocean, by simulating the evolution of phosphate, oxygen, dissolved inorganic carbon, alkalinity and iron with one class of phytoplankton and zooplankton.</p> <p>WOMBAT is a Nutrient, Phytoplankton, Zooplankton and Detritus (NPZD) model, with one zooplankton and one phytoplankton class.</p>"},{"location":"models/model_components/bgc_ocean/#how-is-wombat-used","title":"How is WOMBAT used?","text":"<p>WOMBAT is coupled to the MOM5 ocean model in the ACCESS-ESM1.5 and ACCESS-OM2 models.</p>"},{"location":"models/model_components/coupler/","title":"Coupler {{ supported }}","text":"<p>A coupler is a software package that allows synchronised exchanges of coupling information between numerical codes representing different components of the climate system.</p>"},{"location":"models/model_components/coupler/#oasis3-mct-supported","title":"OASIS3-MCT {{ supported }}","text":"<p>OASIS3-MCT is the version of the Ocean Atmosphere Sea Ice Soil (OASIS) coupler interfaced with the Model Coupling Toolkit (MCT) from the Argonne National Laboratory. OASIS3-MCT is the coupler used in the configurations:</p> <ul> <li>ACCESS-ESM1.5</li> <li>ACCESS-CM2 </li> <li>ACCESS-OM2</li> <li>ACCESS-S</li> </ul>"},{"location":"models/model_components/coupler/#nuopc-interoperability-layer-recommended","title":"NUOPC Interoperability Layer {{ recommended }}","text":"<p>NUOPC (National Unified Operational Prediction Capability) Interoperability Layer defines conventions and a set of generic components for building coupled models using the Earth System Modeling Framework (ESMF).</p> <p>ACCESS-OM3, a configuration currently under development, uses NUOPC to couple its MOM6 and CICE6 model components as there are no respective OASIS coupling interfaces for these components.</p>"},{"location":"models/model_components/land/","title":"Land Model Components","text":""},{"location":"models/model_components/land/#cable-supported","title":"CABLE {{ supported }}","text":"<p>Community Atmosphere Biosphere Land Exchange (CABLE) is a land surface model, used to calculate the fluxes of momentum, energy, water and carbon between the land surface and the atmosphere. It also models the main biogeochemical cycles of the land ecosystem when used in conjunction with the CASA-CNP module. </p>"},{"location":"models/model_components/land/#how-is-cable-used","title":"How is CABLE used?","text":"<p>CABLE can be run as a standalone model, for a single location, a region or globally. Coupled to the Met Office Unified Model (UM), CABLE provides the land surface component of the ACCESS Earth System Model (ACCESS-ESM) and ACCESS Coupled Model (ACCESS-CM).</p> <p>CABLE is an open source model developed by a community of Australian climate science researchers. Registration is required to access the CABLE code repository.</p>"},{"location":"models/model_components/land/#jules-supported","title":"JULES {{ supported }}","text":"<p>The Joint UK Land Environment System (JULES) is a community land surface model that can be used both as a standalone model and as the land surface component in the UM model. By modelling different land surface processes (surface energy balance, hydrological cycle, carbon cycle, dynamic vegetation, etc.) and their interaction with each other, JULES provides a framework to assess the impact of modifying a particular process on the ecosystem as a whole, e.g., the impact of climate change on hydrology.</p>"},{"location":"models/model_components/ocean/","title":"Ocean Model Component","text":""},{"location":"models/model_components/ocean/#modular-ocean-model-mom-supported","title":"Modular Ocean Model (MOM)  {{ supported }}","text":"<p>The Modular Ocean Model (MOM) is one of the ocean components of the ACCESS climate model system. Used to simulate ocean currents at both regional and global scales, MOM is an invaluable tool for studying the global ocean climate system, as well as capabilities for regional and coastal applications. </p>"},{"location":"models/model_components/ocean/#mom5-supported","title":"MOM5 {{ supported }}","text":"<p>Source Code</p> <p>MOM5 is used in supported climate ACCESS configurations.</p>"},{"location":"models/model_components/ocean/#mom6-recommended","title":"MOM6 {{ recommended }}","text":"<p>Source Code | Tutorials</p> <p>The most recent version, MOM6, is an open source development by a consortium of scientists across several government agencies and academic institutions with critical contributions provided by researchers worldwide.</p>"},{"location":"models/model_components/sea-ice/","title":"Sea-Ice Model Component","text":""},{"location":"models/model_components/sea-ice/#cice-supported","title":"CICE {{ supported }}","text":"<p>CICE is a numerical model for simulating the growth, melting and movement of polar sea ice. This software package was developed by researchers at Los Alamos National Laboratory team and is currently managed by the CICE Consortium, an international group of institutions formed to maintain and develop CICE in the public domain.</p> <p>CICE5 is the current version used in ACCESS model configurations.</p> <p>CICE6 is currently under development.</p>"},{"location":"models/run-a-model/","title":"Running a Model","text":"<p>Here, we are providing the information to run different ACCESS models.</p> <p>If Model, Model Component or Model Configuration are not familiar terms for you, please check out our Model overview.</p> <p>If you have not run a model before, our Getting Started Guide will give you the basics to access the Model infrastructure on the high-performance-computing facility Gadi@NCI.</p> <p>Detailed guides for the different Model configurations can then be found on the following pages: -  Run ACCESS-ESM for the ACCESS Earth System Model configurations -  Run ACCESS-CM for the ACCESS Coupled Model configurations -  Run ACCESS-AM for the ACCESS Atmosphere Model configurations -  Run ACCESS-OM for the ACCESS Ocean Model configurations  </p>"},{"location":"models/run-a-model/run-access-cm/","title":"Running ACCESS-CM2 Model","text":"<p>This section includes a step-by-step instruction set on how to run the ACCESS-CM2 suite.</p> <p>It is also built as a future point of reference, where you can come back and find the section containing the information you need.</p>"},{"location":"models/run-a-model/run-access-cm/#getting-started","title":"Getting Started","text":"<ul> <li>An institutional email address with an organisation that allows access to NCI (e.g., CSIRO, a university, etc.).</li> <li>Access to NCI compute/storage.</li> <li>A Linux/Mac/Unix computer with an internet connection and a command line terminal (e.g., MacOS with XQuartz and command line tools installed, or Putty Cygwin/MobaXterm/similar X-Windows compatible program on a PC). </li> </ul>"},{"location":"models/run-a-model/run-access-cm/#requirements-for-running-access-cm-suites","title":"Requirements for running ACCESS-CM suites","text":"<p>Here, we assume that you already have access to Gadi, the supercomputer hosted by the National Computational Infrastructure (NCI). If needed, you can go back to our guide on how to get access to Gadi.</p>"},{"location":"models/run-a-model/run-access-cm/#basic-setup","title":"Basic Setup","text":"<p>To run an ACCESS-CM suite, new users will need to:</p> <ul> <li>Join the ACCESS group. You can also find instructions on how to join a particular project through the NCI self-service portal. </li> <li>Connect to accessdev to complete your setup once you have your NCI credentials and are a member of the ACCESS group.  Note: At present, both accessdev and ARE run the models on Gadi. However, ARE only supports shorter-running suites (i.e., runs less than 48 hours). Work is currently in progress to fully transition the cylc workflows from accessdev virtual machine to the ARE.</li> <li>Additional steps relating to the communication between accessdev and Gadi may also be necessary.</li> </ul>"},{"location":"models/run-a-model/run-access-cm/#uk-met-office-environment-on-nci","title":"UK Met Office Environment on NCI","text":"<p>As components within the ACCESS-CM suites use the UK Met Office model code, the UK Met Office Environment is installed on NCI. This comprises the model software and tools as well as the cylc workflow system, rose suites, the Met Office MOSRS repository and our local replica repository. In order to checkout and run ACCESS-CM2 suites on Gadi using Rose/Cylc, you need to have access to a number of repositories at the Met Office as well as the local replica and local software on NCI, which will require fullfilling these prerequisites.</p>"},{"location":"models/run-a-model/run-access-cm/#met-office-science-repository-service-mosrs","title":"Met Office Science Repository Service (MOSRS)","text":"<p>Met Office Science Repository Service (MOSRS) is a Trac server run by the UK Met Office for sharing code and configurations for the climate models it runs with partners. It contains the source code and configurations for the UM and JULES amongst other things.</p> <p>To apply for a MOSRS account, you should contact your local institutional sponsor.</p>"},{"location":"models/run-a-model/run-access-cm/#preparing-to-run-an-access-cm-suite","title":"Preparing to run an ACCESS-CM suite","text":"<p>At this stage, you should be able to connect to accessdev and Gadi. </p> <p>accessdev is a frontend system where you prepare ACCESS jobs and then submit them to Gadi (the supercomputer at NCI where ACCESS is run).  </p>"},{"location":"models/run-a-model/run-access-cm/#logging-in-to-gadi-and-accessdev","title":"Logging in to Gadi and accessdev","text":"<p>To run an ACCESS-CM2 suite (i.e., job), you need to first login to Gadi with your <code>username</code> through a login node. </p> <p><code>ssh -Y username@gadi.nci.org.au</code></p> <p>Similarly, to login to accessdev: </p> <p><code>ssh -Y $USER@accessdev.nci.org.au</code></p> <p>Aliases and shortcuts can be created to simplify these commands by configuring SSH.</p>"},{"location":"models/run-a-model/run-access-cm/#copy-edit-and-run-an-access-cm2-suite","title":"Copy, Edit, and Run an ACCESS-CM2 suite","text":"ACCESS-CM2 is a set of submodels (eg. UM, MOM, CICE, CABLE, OASIS) with a range of model parameters, input data, and computer related information, that need to be packaged together as a suite in order to run.  Each ACCESS-CM2 suite has an ID, in the format <code>u-&lt;suite-name&gt;</code>, with <code>&lt;suite-name&gt;</code> being a unique identifier (e.g. <code>u-br565</code> is the CMIP6 release preindustrial experiment suite).  Typically, an existing suite is copied and then edited as needed for a particular run."},{"location":"models/run-a-model/run-access-cm/#copy-access-cm2-suites-with-rosie","title":"Copy ACCESS-CM2 suites with Rosie","text":"Rosie is an SVN repository wrapper with a set of options to work with ACCESS-CM2 suites.  To copy an existing suite, on accessdev:  <ol> <li>         Run <code>mosrs-auth</code> to authenticate using your MOSRS credentials:          mosrs-auth Please enter the MOSRS password for &lt;MOSRS-username&gt;: Successfully authenticated with MOSRS as &lt;MOSRS-username&gt; </li> <li>         Run <code>rosie checkout &lt;suite-ID&gt;</code> to create a local copy of the <code>&lt;suite-ID&gt;</code> from the UKMO repository (used mostly for testing and examining existing suites):          rosie checkout &lt;suite-ID&gt; [INFO] create: /home/565/&lt;$USER&gt;/roses [INFO] &lt;suite-ID&gt;: local copy created at /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;          Alternatively, run <code>rosie copy &lt;suite-ID&gt;</code> to create a new full copy (local and remote in the UKMO repository) rather than just a local copy. When a new suite is created in this way, a new unique name is generated within the repository, and populated with some descriptive information about the suite along with all the initial configuration details:          rosie copy &lt;suite-ID&gt; Copy \"&lt;suite-ID&gt;/trunk@&lt;trunk-ID&gt;\" to \"u-?????\"? [y or n (default)] y [INFO] &lt;new-suite-ID&gt;: created at https://code.metoffice.gov.uk/svn/roses-u/&lt;suite-n/a/m/e/&gt; [INFO] &lt;new-suite-ID&gt;: copied items from &lt;suite-ID&gt;/trunk@&lt;trunk-ID&gt; [INFO] &lt;suite-ID&gt;: local copy created at /home/565/&lt;$USER&gt;/roses/&lt;new-suite-ID&gt; </li> </ol> For additional <code>rosie</code> options, run <code>rosie help</code>.  The suites are created in the user's accessdev home directory, under <code>~/roses/&lt;suite-ID&gt;</code>.  The suite directory usually contains 2 subdirectories and 3 files: <ul> <li><code>app</code> \u2192 directory containing the configuration files for the various tasks within the suite.</li> <li><code>meta</code> \u2192 directory containing the GUI metadata.</li> <li><code>rose-suite.conf</code> \u2192 the main suite configuration file.</li> <li><code>rose-suite.info</code> \u2192 suite information file.</li> <li><code>suite.rc</code> \u2192 the Cylc control script file (Jinja2 language).</li> ls ~/roses/&lt;suite-ID&gt; app meta rose-suite.conf rose-suite.info suite.rc </ul>"},{"location":"models/run-a-model/run-access-cm/#edit-an-access-cm2-suite-configuration-with-rose-gui","title":"Edit an ACCESS-CM2 suite configuration with Rose GUI","text":"Rose is a configuration editor which can be used to view, edit, or run an ACCESS-CM2 suite.  To edit a suite configuration, on accessdev:  <ol> <li>         Run <code>rose edit &amp;</code> (the <code>&amp;</code> is optional and keeps the terminal prompt active while runs the GUI as a separate process) from inside the relevant suite directory (e.g. <code>~/roses/&lt;suite-ID&gt;</code>) to open the Rose GUI and inspect the suite information.          cd ~/roses/&lt;suite-ID&gt; rose edit &amp; [&lt;N&gt;] &lt;PID&gt; </li> <li>         There are many settings that can be changed in a Rose GUI. However, there are a few that we definitely want to check and edit before we run a suite:         <ul> <li>                 NCI Project                                  To make sure we run the suite under the NCI project we belong to, we can navigate to suite conf \u2192 Machine and Runtime Options, edit the Compute project field, and click the Save button . (Check how to connect to a project if you have not joined one yet).                                  If, for example, we belong to the tm70 Project (ACCESS-NRI), we will insert <code>tm70</code> in the Compute project field:                  </li> <li> Total Run length / Cycling frequency                  ACCESS-CM2 suites are often run in multiple steps, each of them constituting a cycle, with the job scheduler resubmitting the suite every chosen Cycling frequency, until the Total Run length is met.                                  To modify these parameters, we can navigate to suite conf \u2192 Run Initialisation and Cycling, edit the respective fields, and click the Save button . The values are in the ISO 8601 Duration format.                                  If, for example, we want to run the suite for a total of 50 Years, and resubmit every year, we will change Total Run length to <code>P50Y</code> and Cycling frequency to <code>P1Y</code>. Note that the current maximum Cycling frequency is 2 years:                  </li> <li> Wallclock time                  The Wallclock time is the time requested by the PBS job to run a single cycle. If this time is not enough for the suite to end its cycle, our job will be terminated before the suite can complete the run.                                   If we change the Cycling frequency, we might need to change the Wallclock time accordingly.                                   The time needed for the suite to run a full cycle depends on several factors, but a good estimation can be 4 hours per simulated year.                                  To modify the Wallclock time, we can navigate to suite conf \u2192 Run Initialisation and Cycling, edit the respective field, and click the Save button . The value is in the ISO 8601 Duration format.             </li> </ul> </li> </ol>"},{"location":"models/run-a-model/run-access-cm/#run-an-access-cm2-suite","title":"Run an ACCESS-CM2 suite","text":"After completing all the modifications to the suite, we are ready to run it.  ACCESS-CM2 suites run on Gadi through a PBS job submission.  When the suite gets run, its configuration files are copied on Gadi under <code>/scratch/$PROJECT/$USER/cylc-run/&lt;suite-ID&gt;</code>, and a symbolic link to this folder is also created in the <code>$USER</code>'s home directory under <code>~/cylc-run/&lt;suite-ID&gt;</code>.  An ACCESS-CM2 suite is constituted by several tasks (such as checking out code repositories, compiling and building the different model components, running the model, etc.). The workflow of these tasks is controlled by Cylc.  Cylc (pronounced \u2018silk\u2019), is a workflow manager that automatically executes tasks according to the model main cycle script <code>suite.rc</code>. Cylc deals with how the job will be run and manages the time steps of each submodel, as well as monitoring all the tasks and reporting any error that might occur.  To run an ACCESS-CM2 suite, on accessdev: <ol> <li>         Run <code>rose suite-run</code>, from inside the suite directory, to run the initial tasks.     </li> <li>         After these few small tasks get executed, the Cylc GUI will open up and you will be able to see and control all the different tasks in the suite as they are run.     </li> cd ~/roses/&lt;suite-ID&gt; rose suite-run [INFO] export CYLC_VERSION=7.8.3 [INFO] export ROSE_ORIG_HOST=accessdev.nci.org.au [INFO] export ROSE_SITE= [INFO] export ROSE_VERSION=2019.01.2 [INFO] create: /home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt; [INFO] create: log.&lt;timestamp&gt; [INFO] symlink: log.&lt;timestamp&gt; &lt;= log [INFO] create: log/suite [INFO] create: log/rose-conf [INFO] symlink: rose-conf/&lt;timestamp&gt;-run.conf &lt;= log/rose-suite-run.conf [INFO] symlink: rose-conf/&lt;timestamp&gt;-run.version &lt;= log/rose-suite-run.version [INFO] install: rose-suite.info \u2003\u2003\u2003\u2003source: /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;/rose-suite.info [INFO] create: app [INFO] install: app \u2003\u2003\u2003\u2003source: /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;/app [INFO] create: meta [INFO] install: meta \u2003\u2003\u2003\u2003source: /home/565/&lt;$USER&gt;/roses/&lt;suite-ID&gt;/meta [INFO] install: suite.rc [INFO] REGISTERED &lt;suite-ID&gt; -&gt; /home/565/&lt;$USER&gt;/cylc-run/&lt;suite-ID&gt; [INFO] create: share [INFO] install: share [INFO] create: work [INFO] chdir: log/ [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009._. [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009| |\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003The Cylc Suite Engine [7.8.3] [INFO] ._____._. ._| |_____.\u2003\u2003\u2003\u2003\u2003\u2009Copyright (C) 2008-2019 NIWA [INFO] | .___| | | | | .___|\u2003&amp; British Crown (Met Office) &amp; Contributors. [INFO] | !___| !_! | | !___. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ [INFO] !_____!___. |_!_____! This program comes with ABSOLUTELY NO WARRANTY; [INFO] \u2003\u2003\u2003\u2009.___! | \u2003\u2003\u2003\u2003\u2003see `cylc warranty`. \u2009It is free software, you [INFO] \u2003\u2003\u2003\u2009!_____! \u2003\u2003\u2003\u2003\u2003\u2009are welcome to redistribute it under certain [INFO] [INFO] *** listening on https://accessdev.nci.org.au:&lt;port&gt;/ *** [INFO] [INFO] To view suite server program contact information: [INFO]  $ cylc get-suite-contact &lt;suite-ID&gt; [INFO] [INFO] Other ways to see if the suite is still running: [INFO]  $ cylc scan -n '&lt;suite-ID&gt;' accessdev.nci.org.au [INFO]  $ cylc ping -v --host=accessdev.nci.org.au &lt;suite-ID&gt; [INFO]  $ ps -opid,args &lt;PID&gt;  # on accessdev.nci.org.au TO DO --&gt; Add Rose GUI image  </ol> You are done!!  If you don't get any errors, you will be able to check the suite output files after the run is complete.  Note that, at this stage, it is possible to close the Cylc GUI.  If you want to open it again, just run <code>rose suite-gcontrol</code> from inside the suite directory."},{"location":"models/run-a-model/run-access-cm/#check-for-errors","title":"Check for errors","text":"It is quite common, especially during the first few runs, to experience errors and job failures. An ACCESS-CM2 suite is constituted by several tasks,  and each of these tasks could fail. When a task fails, the suite is halted and you will see a red icon next to the respective task name in the Cylc GUI.   To investigate the cause of a failure, we need to look at the logs (<code>job.err</code> and <code>job.out</code>) from the suite run. There are two main ways to do so: <ul> <li>         Using the Cylc GUI                  Right-click on the task that failed and click on View Job Logs (Viewer) \u2192 job.err or job.out.                  To access the specific task you might have to click on the arrow next to the task, to extend the drop-down menu with all the sub-taks.          </li> <li>         In the <code>~/cylc-run/&lt;suite-ID&gt;</code> directory                  The suite logs directories are stored inside <code>~/cylc-run/&lt;suite-ID&gt;</code> as <code>log.&lt;TIMESTAMP&gt;</code>, with the lastest set of logs also symlinked in the <code>~/cylc-run/&lt;suite-ID&gt;/log</code> directory.                  The logs for the main job are inside the <code>~/cylc-run/&lt;suite-ID&gt;/log/job</code> directory.                  Logs are separated into simulation cycles through their starting dates, and then differentiated by task.                  They are then further separated into \"attempts\" (consecutive failed/successful tasks), with <code>NN</code> being a symlink to the most recent attempt.                  In our example, the failure occurred for the 09500101 simulation cycle (starting date on 1st January 950) in the coupled task. Therefore, the directory where to find the <code>job.err</code> and <code>job.out</code> files is <code>~/cylc-run/&lt;suite-ID&gt;/log/job/09500101/coupled/NN</code>.          cd ~/cylc-run/&lt;suite-ID&gt; ls app cylc-suite.db log log.20230530T051952Z meta rose-suite.info share suite.rc suite.rc.processed work cd log ls db job rose.conf rose-suite-run.conf rose-suite-run.locs rose-suite-run.log rose-suite-run.version suite suiterc cd job ls 09500101 cd 09500101 ls coupled fcm_make2_um fcm_make_um install_warm make2_mom make_mom fcm_make2_drivers fcm_make_drivers install_ancil make2_cice make_cice cd coupled ls 01 02 03 NN cd NN ls job job-activity.log job.err job.out job.status </li> </ul>"},{"location":"models/run-a-model/run-access-cm/#stop-restart-and-reload-suites","title":"Stop, restart and reload suites","text":"Sometimes, you may want to control the running state of a suite.  If your Cylc GUI has been closed and you are unsure whether your suite is still running, you can scan for active suites and reopen the GUI if desired.  To scan for active suites run <code>cylc scan</code>.  To reopen the Cylc GUI there are 2 main ways: <ul> <li>         run <code>rose suite-gcontrol</code> from inside the suite directory     </li>     OR     <li>         run <code>gcylc &lt;suite-ID&gt;</code> </li> </ul> cylc scan &lt;suite-ID&gt; &lt;$USER&gt;@accessdev.nci.org.au:&lt;port&gt; cd ~/roses/&lt;suite-ID&gt; rose suite-gcontrol  Add Rose GUI image  --&gt;"},{"location":"models/run-a-model/run-access-cm/#stop-a-suite","title":"STOP a suite","text":"Run <code>rose suite-stop -y</code>, from inside the suite directory, to shutdown a suite in a safe manner."},{"location":"models/run-a-model/run-access-cm/#restart-a-suite","title":"RESTART a suite","text":"There are two main ways to restart a suite: <ul> <li>         'SOFT' restart                  Run <code>rose suite-run --restart</code>, from inside the suite directory, to re-install the suite and reopen Cylc in the same state as when it was stopped (you may need to manually trigger failed tasks from the Cylc GUI).          cylc cd ~/roses/&lt;suite-ID&gt; rose suite-run --restart [INFO] export CYLC_VERSION=7.8.3 [INFO] export ROSE_ORIG_HOST=accessdev.nci.org.au [INFO] export ROSE_SITE= [INFO] export ROSE_VERSION=2019.01.2 [INFO] delete: log/rose-suite-run.conf [INFO] symlink: rose-conf/&lt;timestamp&gt;-restart.conf &lt;= log/rose-suite-run.conf [INFO] delete: log/rose-suite-run.version [INFO] symlink: rose-conf/&lt;timestamp&gt;-restart.version &lt;= log/rose-suite-run.version [INFO] chdir: log/ [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009._. [INFO] \u2003\u2003\u2003\u2003\u2003\u2003\u2009\u2009| |\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003\u2003The Cylc Suite Engine [7.8.3] [INFO] ._____._. ._| |_____.\u2003\u2003\u2003\u2003\u2003\u2009Copyright (C) 2008-2019 NIWA [INFO] | .___| | | | | .___|\u2003&amp; British Crown (Met Office) &amp; Contributors. [INFO] | !___| !_! | | !___. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ [INFO] !_____!___. |_!_____! This program comes with ABSOLUTELY NO WARRANTY; [INFO] \u2003\u2003\u2003\u2009.___! | \u2003\u2003\u2003\u2003\u2003see `cylc warranty`. \u2009It is free software, you [INFO] \u2003\u2003\u2003\u2009!_____! \u2003\u2003\u2003\u2003\u2003\u2009are welcome to redistribute it under certain [INFO] [INFO] *** listening on https://accessdev.nci.org.au:&lt;port&gt;/ *** [INFO] [INFO] To view suite server program contact information: [INFO]  $ cylc get-suite-contact &lt;suite-ID&gt; [INFO] [INFO] Other ways to see if the suite is still running: [INFO]  $ cylc scan -n '&lt;suite-ID&gt;' accessdev.nci.org.au [INFO]  $ cylc ping -v --host=accessdev.nci.org.au &lt;suite-ID&gt; [INFO]  $ ps -opid,args &lt;PID&gt;  # on accessdev.nci.org.au TO DO --&gt; Add Rose GUI image  </li> <li>         'HARD' restart                  Run <code>rose suite-run --new</code>, from inside the suite directory, if you want to overwrite any previous runs of the suite and begin completely afresh (WARNING!! This will overwrite all existing model output and logs).     </li> </ul>"},{"location":"models/run-a-model/run-access-cm/#reload-a-suite","title":"RELOAD a suite","text":"In some cases the suite needs to be updated without necessarily having to stop it (e.g. after fixing a typo in a file). Updating an active suite is called a 'reload', where the suite is 're-installed' and Cylc is updated with the changes (this is similar to a 'soft' restart, but with the new changes installed, so you may need to manually trigger failed tasks from the Cylc GUI).  To reload a suite run <code>rose suite-run --reload</code> from inside the suite directory."},{"location":"models/run-a-model/run-access-cm/#suite-output-files","title":"Suite output files","text":"All output files (as well as work files) are available on Gadi under <code>/scratch/$PROJECT/$USER/cylc-run/&lt;suite-ID&gt;</code> (also symlinked in <code>~/cylc-run/&lt;suite-ID&gt;</code>).  While the suite is running, files move between the <code>share</code> and the <code>work</code> directories.  At the end of each cycle, model output data and restart files are moved to <code>/scratch/$PROJECT/$USER/archive/&lt;suite-name&gt;</code>.   This directory contains 2 subdirectories: <ul> <li> <code>history</code>          This is the directory where the model output data is found, separated for each model component:          <ul> <li> <code>atm</code> \u2192 atmosphere (UM)             </li> <li> <code>cpl</code> \u2192 coupler (OASIS3-MCT)             </li> <li> <code>ocn</code> \u2192 ocean (MOM)             </li> <li> <code>ice</code> \u2192 ice (CICE)             </li> </ul>         For the atmospheric output data, each file it is usually a UM fieldsfile or netCDF file, formatted as <code>&lt;suite-name&gt;a.p&lt;output-stream-identifier&gt;&lt;year&gt;&lt;month-string&gt;</code>.                  In the case of the <code>u-br565</code> suite we will have:          cd /scratch/&lt;$PROJECT&gt;/&lt;USER&gt;/archive ls br565 &lt;suite-name&gt; &lt;other-suite-name&gt; cd br565 ls history restart ls history/atm br565a.pd0950apr.nc br565a.pd0950aug.nc br565a.pd0950dec.nc br565a.pd0950feb.nc br565a.pd0950jan.nc br565a.pd0950jul.nc br565a.pd0950jun.nc br565a.pd0950mar.nc br565a.pd0950may.nc br565a.pd0950nov.nc br565a.pd0950oct.nc br565a.pd0950sep.nc br565a.pd0951apr.nc br565a.pd0951aug.nc br565a.pd0951dec.nc br565a.pm0950apr.nc br565a.pm0950aug.nc br565a.pm0950dec.nc br565a.pm0950feb.nc br565a.pm0950jan.nc br565a.pm0950jul.nc br565a.pm0950jun.nc br565a.pm0950mar.nc br565a.pm0950may.nc br565a.pm0950nov.nc br565a.pm0950oct.nc br565a.pm0950sep.nc br565a.pm0951apr.nc br565a.pm0951aug.nc br565a.pm0951dec.nc netCDF </li> <li> <code>restart</code>          This is the directory where the restart dumps are found, subdivided for each model component (see <code>history</code> folder above).                  For the atmospheric restart files, each of them is a UM fieldsfile, formatted as <code>&lt;suite-name&gt;a.da&lt;year&gt;&lt;month&gt;&lt;day&gt;_00</code>.                  In the directory there are also some files formatted as <code>&lt;suite-name&gt;a.xhist-&lt;year&gt;&lt;month&gt;&lt;day&gt;</code> containing metadata information.                   In the case of the <code>u-br565</code> suite we will have:          ls /scratch/&lt;$PROJECT&gt;/&lt;USER&gt;/archive/br565/restart/atm br565a.da09500201_00 br565a.da09510101_00 br565.xhist-09500131 br565.xhist-09501231  </li> </ul> References <ul> <li> https://confluence.csiro.au/display/ACCESS/Using+CM2+suites+in+Rose+and+Cylc </li> <li> https://confluence.csiro.au/display/ACCESS/Understanding+CM2+output </li> <li> https://nespclimate.com.au/wp-content/uploads/2020/10/Instruction-document-Getting_started_with_ACCESS.pdf </li> <li> https://code.metoffice.gov.uk/doc/um/latest/um-training/rose-gui.html </li> </ul>"},{"location":"models/run-a-model/run-access-esm/","title":"Run ACCESS-ESM","text":""},{"location":"models/run-a-model/run-access-esm/#requirements","title":"Requirements","text":"Before running ACCESS-ESM, you need to make sure to possess the right tools and to have an account with specific institutions."},{"location":"models/run-a-model/run-access-esm/#general-requirements","title":"General requirements","text":"For the general requirements needed to run all ACCESS models, please refer to the Getting Started (TO DO check link) page."},{"location":"models/run-a-model/run-access-esm/#model-specific-requirements","title":"Model-specific requirements","text":"<ul> <li> Payu          To get payu on Gadi, run:         <pre><code>module use /g/data/hh5/public/modules\n            module load conda/analysis3\n        </code></pre> </li> </ul>"},{"location":"models/run-a-model/run-access-esm/#get-access-esm-configuration","title":"Get ACCESS-ESM configuration","text":"A suitable ACCESS-ESM pre-industrial configuration is avaible on the coecms GitHub.  In order to get it, on Gadi, create a directory where to keep the model configuration, and clone the GitHub repo in it by running:  <pre><code>git clone https://github.com/coecms/esm-pre-industrial</code></pre> mkdir -p ~/access-esm cd ~/access-esm git clone https://github.com/coecms/esm-pre-industrial Cloning into 'esm-pre-industrial'... remote: Enumerating objects: 767, done. remote: Counting objects: 100% (295/295), done. remote: Compressing objects: 100% (138/138), done. remote: Total 767 (delta 173), reused 274 (delta 157), pack-reused 472 Receiving objects: 100% (767/767), 461.57 KiB | 5.24 MiB/s, done. Resolving deltas: 100% (450/450), done. Note: Some modules might interfere with the <code>git</code> commands (for example matlab/R2018a). If you are running into issues during the cloning of the repository, it might be a good idea to run <pre><code>module purge</code></pre> first, before trying again."},{"location":"models/run-a-model/run-access-esm/#edit-access-esm-configuration","title":"Edit ACCESS-ESM configuration","text":"In order to modify an ACCESS-ESM configuration, it is worth understanding a bit more how its job scheduler payu works."},{"location":"models/run-a-model/run-access-esm/#payu","title":"Payu","text":"Payu is a workflow management tool for running numerical models in supercomputing environments.  The general layout of a payu-supported model run consists of two main directories: <ul> <li>         The laboratory is the directory where all parts of the model are kept. For ACCESS-ESM, it is typically <code>/scratch/$PROJECT/$USER/access-esm</code>.     </li> <li>         The control directory, where the model configuration is kept and from where the model is run (in our case is the cloned directory <code>~/access-esm/esm-pre-industrial</code>).     </li> </ul> This distinction of directories keeps the small-size configuration files separated from the larger binary outputs and inputs. In this way, we can place the configuration files in the <code>$HOME</code> directory (being the only filesystem on Gadi that is actively backed up), without overloading it with too much data.  Moreover, this separation allows to run multiple self-resubmitting experiments simultaneously that might share common executables and input data.  To proceed with the setup of the laboratory directory, from the control directory run: <pre><code>payu init</code></pre>  This will create the laboratory directory, along with other subdirectories (depending on the configuration). The main subdirectories we are interested in are:  <ul> <li><code>work</code> \u2192 temporary directory where the model is actually run. It gets cleaned after each run.</li> <li><code>archive</code> \u2192 directory where the output is placed after each run.</li> cd ~/access-esm/esm-pre-industrial payu init laboratory path:  /scratch/$PROJECT/$USER/access-esm binary path:  /scratch/$PROJECT/$USER/access-esm/bin input path:  /scratch/$PROJECT/$USER/access-esm/input work path:  /scratch/$PROJECT/$USER/access-esm/work archive path:  /scratch/$PROJECT/$USER/access-esm/archive </ul>"},{"location":"models/run-a-model/run-access-esm/#edit-the-master-configuration-file","title":"Edit the Master Configuration file","text":"The <code>config.yaml</code> file, located in the control directory, is the Master Configuration file.   This file controls the general model configuration and if we open it in a text editor, we can see different parts: <ul> <li> PBS resources <pre><code>jobname: pre-industrial\n            queue: normal\n            walltime: 20:00:00\n        </code></pre>         These are settings for the PBS scheduler. Edit lines in this section to change any of the PBS resources.                   For example, to run ACCESS-ESM under the <code>tm70</code> project (TO DO add Getting started, join a NCI Project link), add the following line to this section:         <pre><code>project: tm70</code></pre> </li> <li> Link to the laboratory directory <pre><code># note: if laboratory is relative path, it is relative to /scratch/$PROJECT/$USER\n            laboratory: access-esm\n        </code></pre>         This will set the laboratory directory. Relative paths are relative to <code>/scratch/$PROJECT/$USER</code>. Absolute paths can be specified as well.     </li> <li> Model <pre><code>model: access</code></pre>         The main model. This tells payu which driver to use (access stands for ACCESS-ESM).     </li> <li> Submodels <pre><code>submodels:\n            \u00a0\u00a0- name: atmosphere\n            \u00a0\u00a0\u00a0\u00a0model: um\n            \u00a0\u00a0\u00a0\u00a0ncpus: 192\n            \u00a0\u00a0\u00a0\u00a0exe: /g/data/access/payu/access-esm/bin/coe/um7.3x\n            \u00a0\u00a0\u00a0\u00a0input:\n            \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0- /g/data/access/payu/access-esm/input/pre-industrial/atmosphere\n            \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0- /g/data/access/payu/access-esm/input/pre-industrial/start_dump\n            \u00a0\u00a0- name: ocean\n            \u00a0\u00a0\u00a0\u00a0model: mom\n            \u00a0\u00a0\u00a0\u00a0ncpus: 180\n            \u00a0\u00a0\u00a0\u00a0exe: /g/data/access/payu/access-esm/bin/coe/mom5xx\n            \u00a0\u00a0\u00a0\u00a0input:\n            \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0- /g/data/access/payu/access-esm/input/pre-industrial/ocean/common\n            \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0- /g/data/access/payu/access-esm/input/pre-industrial/ocean/pre-industrial\n            \u00a0\u00a0- name: ice\n            \u00a0\u00a0\u00a0\u00a0model: cice\n            \u00a0\u00a0\u00a0\u00a0ncpus: 12\n            \u00a0\u00a0\u00a0\u00a0exe: /g/data/access/payu/access-esm/bin/coe/cicexx\n            \u00a0\u00a0\u00a0\u00a0input:\n            \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0- /g/data/access/payu/access-esm/input/pre-industrial/ice\n            \u00a0\u00a0- name: coupler\n            \u00a0\u00a0\u00a0\u00a0model: oasis\n            \u00a0\u00a0\u00a0\u00a0ncpus: 0\n            \u00a0\u00a0\u00a0\u00a0input:\n            \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0- /g/data/access/payu/access-esm/input/pre-industrial/coupler\n        </code></pre>         ACCESS-ESM is a coupled model, which means it has multiple submodels (i.e. model components).                   This section specifies the submodels and contains configuration options (for example the directories of input files) that are required to ensure the model can execute correctly. Each submodel also has additional configuration options that are read in when the submodel is running. These specific configuration options are found in the subdirectory of the control directory having the name of the submodel (e.g. in our case the configuration for the atmosphere submodel, i.e. the UM, will be in the directory <code>~/access-esm/esm-pre-industrial/atmosphere</code>).     </li> <li> collate <pre><code>collate:\n            \u00a0\u00a0exe: /g/data/access/payu/access-esm/bin/mppnccombine\n            \u00a0\u00a0restart: true\n            \u00a0\u00a0mem: 4GB\n        </code></pre>         The collate process joins a number of smaller files, which contain different parts of the model grid, together into target output files. The restart files are typically tiled in the same way and will also be joined together if the restart option is set to <code>true</code>.     </li> <li> restart <pre><code>restart: /g/data/access/payu/access-esm/restart/pre-industrial</code></pre>         The location of the files used for a warm restart.     </li> <li> Start date and internal run length <pre><code>calendar:\n            \u00a0\u00a0start:\n            \u00a0\u00a0\u00a0\u00a0year: 101\n            \u00a0\u00a0\u00a0\u00a0month: 1\n            \u00a0\u00a0\u00a0\u00a0days: 1\n            \u00a0\u00a0runtime:\n            \u00a0\u00a0\u00a0\u00a0years: 1\n            \u00a0\u00a0\u00a0\u00a0months: 0\n            \u00a0\u00a0\u00a0\u00a0days: 0\n        </code></pre>         This section specifies the start date and internal run length.          Note: The internal run length (controlled by <code>runtime</code>) can be different from the total run length. Also, the <code>runtime</code> value can be lowered, but should not be increased to a total of more than 1 year, to avoid errors. If you want to know more about the difference between internal run and total run lenghts, or if you want to run the model for more than 1 year, check Run configuration for multiple years.     </li> <li> Number of runs per PBS submission <pre><code>runspersub: 5</code></pre>         ACCESS-ESM configurations are often run in multiple steps (or cycles), with payu running a maximum of <code>runspersub</code> internal runs for every PBS job submission.          Note: If we increase <code>runspersub</code>, we might need to increase the walltime in the PBS resources.     </li> </ul> To know more about other configuration settings for the <code>config.yaml</code> file, please check how to configure your experiment with payu."},{"location":"models/run-a-model/run-access-esm/#run-access-esm-configuration","title":"Run ACCESS-ESM configuration","text":"<p>After editing the configuration, we are ready to run ACCESS-ESM.   ACCESS-ESM suites run on Gadi through a PBS job submission managed by payu.</p>"},{"location":"models/run-a-model/run-access-esm/#payu-setup-optional","title":"Payu setup (optional)","text":"As a first step, from the control directory, is good practice to run: <pre><code>payu setup</code></pre> This will prepare the model run, based on the experiment configuration.  payu setup laboratory path:  /scratch/$PROJECT/$USER/access-esm binary path:  /scratch/$PROJECT/$USER/access-esm/bin input path:  /scratch/$PROJECT/$USER/access-esm/input work path:  /scratch/$PROJECT/$USER/access-esm/work archive path:  /scratch/$PROJECT/$USER/access-esm/archive Loading input manifest: manifests/input.yaml Loading restart manifest: manifests/restart.yaml Loading exe manifest: manifests/exe.yaml Setting up atmosphere Setting up ocean Setting up ice Setting up coupler Checking exe and input manifests Updating full hashes for 3 files in manifests/exe.yaml Creating restart manifest Updating full hashes for 30 files in manifests/restart.yaml Writing manifests/restart.yaml Writing manifests/exe.yaml Note: You can skip this step as it is included also in the run command. However, runnning it explicitly helps to check for errors and make sure executable and restart directories are accessible."},{"location":"models/run-a-model/run-access-esm/#run-configuration","title":"Run configuration","text":"To run ACCESS-ESM configuration for one internal run length (controlled by <code>runtime</code> in the <code>config.yaml</code> file), run: <pre><code>payu run -f</code></pre> This will submit a single job to the queue with a total run length of <code>runtime</code>. It there is no previous run, it will start from the <code>start</code> date indicated in the <code>config.yaml</code> file, otherwise it will perform a warm restart from a precedently saved restart file.  Note:The <code>-f</code> option ensures that payu will run even if there is an existing non-empty work directory, which happens if a run crashes.  payu run -f Loading input manifest: manifests/input.yaml Loading restart manifest: manifests/restart.yaml Loading exe manifest: manifests/exe.yaml payu: Found modules in /opt/Modules/v4.3.0 qsub -q normal -P &lt;project&gt; -l walltime=11400 -l ncpus=384 -l mem=1536GB -N pre-industrial -l wd -j n -v PAYU_PATH=/g/data/hh5/public/apps/miniconda3/envs/analysis3-23.01/bin,MODULESHOME=/opt/Modules/v4.3.0,MODULES_CMD=/opt/Modules/v4.3.0/libexec/modulecmd.tcl,MODULEPATH=/g/data3/hh5/public/modules:/etc/scl/modulefiles:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/modulefiles:/apps/Modules/modulefiles -W umask=027 -l storage=gdata/access+gdata/hh5 -- /g/data/hh5/public/apps/miniconda3/envs/analysis3-23.01/bin/python3.9 /g/data/hh5/public/apps/miniconda3/envs/analysis3-23.01/bin/payu-run &lt;job-ID&gt;.gadi-pbs"},{"location":"models/run-a-model/run-access-esm/#run-configuration-for-multiple-years","title":"Run configuration for multiple years","text":"If you want to run ACCESS-ESM configuration for multiple internal run lengths (controlled by <code>runtime</code> in the <code>config.yaml</code> file), you can use the option <code>-n</code>: <pre><code>payu run -n &lt;number-of-runs&gt;</code></pre> This will run the configuration <code>number-of-runs</code> times with a total run length of <code>runtime * number-of-runs</code>. The number of consecutive PBS jobs submitted to the queue depends on the <code>runspersub</code> value specified in the <code>config.yaml</code> file."},{"location":"models/run-a-model/run-access-esm/#understand-runtime-runspersub-and-n-parameters","title":"Understand <code>runtime</code>, <code>runspersub</code>, and <code>-n</code> parameters","text":"With the correct use of <code>runtime</code>, <code>runspersub</code>, and <code>-n</code> parameters, we can have full control of our run.  <ul> <li> <code>runtime</code> defines the internal run length.     </li> <li> <code>runspersub</code> defines the maximum number of internal runs for every PBS job submission.     </li> <li> <code>-n</code> sets the number of internal runs to be performed.     </li> </ul> Let's have some practical examples: <ul> <li> Run 20 years of simulation, with resubmission every 5 years          To have a total run length of 20 years, with a resubmition cycle of 5 years, we can leave <code>runtime</code> to the default value of <code>1 year</code>, set <code>runspersub</code> to <code>5</code>, and run the configuration using <code>-n 20</code>:         <pre><code>payu run -n 20</code></pre>         This will submit subsequent jobs for the following years: 1 to 5, 6 to 10, 11 to 15, and 16 to 20. With a total of 4 PBS jobs.     </li> <li> Run 7 years of simulation, with resubmission every 3 years          To have a total run length of 7 years, with a resubmition cycle of 3 years, we can leave <code>runtime</code> to the default value of <code>1 year</code>, set <code>runspersub</code> to <code>3</code>, and run the configuration using <code>-n 7</code>:         <pre><code>payu run -n 7</code></pre>         This will submit subsequent jobs for the following years: 1 to 3, 4 to 6, and 7. With a total of 3 PBS jobs.     </li> <li> Run 3 months and 10 days of simulation, in one single submission          To have a total run length of 3 months and 10 days, all in a single submission, we have to set <code>runtime</code> to:         <pre><code>years: 0\n            months: 3\n            days: 10\n        </code></pre>         set <code>runspersub</code> to <code>1</code> (or any value &gt; 1), and run the configuration without <code>-n</code> (or with <code>-n</code> equals <code>1</code>):         <pre><code>payu run</code></pre> </li> <li> Run 1 year and 4 months of simulation, with resubmission every 4 months          To have a total run length of 1 year and 4 months (16 months), we will have to split it into multiple internal runs. For example, we can have 4 internal runs of 4 months each. Therefore, we will have to set <code>runtime</code> to:         <pre><code>years: 0\n            months: 4\n            days: 0\n        </code></pre>         Since the internal run length is set to 4 months, to resubmit our jobs every 4 months (i.e. every internal run), we have to set <code>runspersub</code> to <code>1</code>. Finally, we will perform 4 internal runs by running the configuration with <code>-n 4</code>:         <pre><code>payu run -n 4</code></pre> </li> </ul>"},{"location":"models/run-a-model/run-access-esm/#monitor-runs","title":"Monitor runs","text":"Currently, there is no specific tool to monitor ACCESS-ESM runs.   One way to check the status of our run is running: <pre><code>qstat -u $USER</code></pre> This will show the status of all your PBS jobs (if there is any PBS job submitted):  qstat -u $USER Job id\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Name\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0User\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Time Use\u00a0S Queue ---------------------  ---------------- ----------------  -------- - ----- &lt;job-ID&gt;.gadi-pbs\u00a0\u00a0\u00a0\u00a0\u00a0pre-industrial\u00a0\u00a0\u00a0&lt;$USER&gt;\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0&lt;time&gt;\u00a0R\u00a0normal-exec &lt;job-ID&gt;.gadi-pbs\u00a0\u00a0\u00a0\u00a0\u00a0&lt;other-job-name&gt;\u00a0&lt;$USER&gt;\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0&lt;time&gt;\u00a0R\u00a0normal-exec &lt;job-ID&gt;.gadi-pbs\u00a0\u00a0\u00a0\u00a0\u00a0&lt;other-job-name&gt;\u00a0&lt;$USER&gt;\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0&lt;time&gt;\u00a0R\u00a0normal-exec  If you changed the <code>jobname</code> in the PBS resources of the Master Configuration file, that will be your job's Name instead of <code>pre-industrial</code>.  S indicates the status of your run: <ul> <li>Q \u2192 Job waiting in the queue to start</li> <li>R \u2192 Job running</li> <li>E \u2192 Job ending</li> </ul> If there is no listed job with your <code>jobname</code> (or if there is no job submitted at all), your run might have successfully completed, or might have been terminated due to an error."},{"location":"models/run-a-model/run-access-esm/#check-the-output-and-error-log-files","title":"Check the output and error log files","text":"While the model is running, payu saves the standard output and standard error into the files <code>access.out</code> and <code>access.err</code> in the control directory. You can examine these files, as the run progresses, to check on it's status.  After the model has completed its run, or if it crashed, the output and error log files, respectively, are renamed by default into <code>jobname.o&lt;job-ID&gt;</code> and <code>jobname.e&lt;job-ID&gt;</code>."},{"location":"models/run-a-model/run-access-esm/#model-outputs","title":"Model outputs","text":"While the configuration is running, output files (as well as restart files) are moved from the <code>work</code> directory to the <code>archive</code> directory, under <code>/scratch/$PROJECT/$USER/access-esm/archive</code> (also symlinked in the control directory under <code>~/access-esm/esm-pre-industrial/archive</code>).  Both outputs and restarts are stored into subfolders for each different configuration (<code>esm-pre-industrial</code> in our case), and inside the configuration folder, they are subdivided for each internal run.  The format of a typical output folder is <code>outputXXX</code>, whereas the typical restart folder is usually formatted as <code>restartXXX</code>, with XXX being the number of internal run, starting from <code>000</code>.  In the respective folders, outputs and restarts are separated for each model component.  For the atmospheric output data, each file it is usually a UM fieldsfile, formatted as <code>&lt;UM-suite-identifier&gt;a.p&lt;output-stream-identifier&gt;&lt;time-identifier&gt;</code>.  cd /scratch/$PROJECT/$USER/access-esm/archive/esm-pre-industrial ls output000 pbs_logs restart000 ls output000/atmosphere aiihca.daa1210 aiihca.daa1810 aiihca.paa1apr aiihca.paa1jun aiihca.pea1apr aiihca.pea1jun aiihca.pga1apr aiihca.pga1jun atm.fort6.pe0 exstat ihist prefix.CNTLGEN UAFLDS_A aiihca.daa1310  aiihca.daa1910  aiihca.paa1aug aiihca.paa1mar aiihca.pea1aug aiihca.pea1mar aiihca.pga1aug aiihca.pga1mar cable.nml fort.57 INITHIS prefix.PRESM_A um_env.py aiihca.daa1410 aiihca.daa1a10 aiihca.paa1dec aiihca.paa1may aiihca.pea1dec aiihca.pea1may aiihca.pga1dec aiihca.pga1may CNTLALL ftxx input_atm.nml SIZES xhist aiihca.daa1510 aiihca.daa1b10 aiihca.paa1feb aiihca.paa1nov aiihca.pea1feb aiihca.pea1nov aiihca.pga1feb aiihca.pga1nov CONTCNTL ftxx.new namelists STASHC aiihca.daa1610 aiihca.daa1c10 aiihca.paa1jan aiihca.paa1oct aiihca.pea1jan aiihca.pea1oct aiihca.pga1jan aiihca.pga1oct debug.root.01 ftxx.vars nout.000000 thist aiihca.daa1710 aiihca.daa2110 aiihca.paa1jul aiihca.paa1sep aiihca.pea1jul aiihca.pea1sep aiihca.pga1jul aiihca.pga1sep errflag hnlist prefix.CNTLATM UAFILES_A References <ul> <li> https://github.com/coecms/esm-pre-industrial </li> <li> https://payu.readthedocs.io/en/latest/usage.html </li> </ul>"},{"location":"models/run-a-model/run-access-om/","title":"Running ACCESS-OM2 Model","text":"<p>Welcome to ACCESS-OM2 \u2014 a coupled ocean-ice model and collection of configurations developed by the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA).</p> <p>ACCESS-OM2 consists of the MOM 5.1 ocean model, CICE 5.1.2 sea ice model, and a file-based atmosphere called YATM coupled together using the OASIS3-MCT v2.0 coupler. Regridding is done using ESMF and KDTREE2.</p> <p>The configurations available here are updated from the version 1.0 configurations described in Kiss et al. (2020). Further details are given in the ACCESS-OM2 technical report.</p>"},{"location":"models/run-a-model/run-access-om/#how-to-access-existing-access-om2-output","title":"How to access existing ACCESS-OM2 output","text":"<p>NCI users can access model output via the COSIMA Cookbook. A good place to start is the data explorer, which will give an overview of the data available. Also see this overview of 0.1\u00b0 IAF outputs.</p> <p>Non-NCI users can access a subset of the ACCESS-OM2 output via the COSIMA Model Output Collection.</p>"},{"location":"models/run-a-model/run-access-om/#how-to-run-access-om2","title":"How to run ACCESS-OM2","text":"<p>Start by reading the [[Quick start|Getting-started#quick-start]] guide. If you are using gadi.nci.org.au at the NCI National Facility and are happy to use our pre-compiled executables then this should be all you need. The page also provides instructions for building your own executables.</p> <p>NOTE: All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you \"watch\" this repo (see button at top of screen; ask to be notified of all conversations) and also watch all the component models, whichever configuration(s) you are using, and payu to be kept informed of updates, problems and bug fixes as they arise.</p>"},{"location":"models/run-a-model/run-access-om/#getting-help-and-reporting-issues","title":"Getting help and reporting issues","text":"<p>For all help requests and error reports please create a \"GitHub issue\" at ACCESS-OM2 issues.</p>"},{"location":"models/run-a-model/run-access-om/#for-self-help","title":"For self-help","text":"<p>Setting up and running the model is primarily supported via the [[ACCESS-OM2 wiki|Home]] (that you are already reading). It is a \"wiki\" so feel free to correct and contribute.</p>"},{"location":"models/run-a-model/run-access-om/#how-to-update-this-wiki","title":"How to update this wiki","text":"<p>The wiki attached to a public repository can be edited by anyone. Just navigate to the page you wish to edit and click on the 'edit' button on the top right hand side.</p>"},{"location":"models/run-a-model/run-access-om/#references","title":"References","text":""},{"location":"models/run-a-model/getting_started/","title":"Getting Started to Run a Model","text":"<p>If Model, Model Component or Model Configuration are not familiar terms for you, please check out our Model overview.</p> <p>If you have not run a model before, our Getting Started Guide will give you the basics to access the Model infrastructure on the high-performance-computing facility Gadi@NCI.</p> <p>Detailed guides for the different Model configurations can then be found on the following pages: -  Run ACCESS-ESM for the ACCESS Earth System Model configurations -  Run ACCESS-CM for the ACCESS Coupled Model configurations -  Run ACCESS-AM for the ACCESS Atmosphere Model configurations -  Run ACCESS-OM for the ACCESS Ocean Model configurations  </p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/","title":"Getting Started: Computing Access (Gadi@NCI)","text":"<p>Here, we provide you the important information to give you access to the large data that we curate at NCI's storage:</p> <p>1) Get an NCI Account 2) Join relevant NCI projects 3) Logging in to Gadi@NCI 4) Computing on Gadi</p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#1-nci-account","title":"1) NCI Account","text":"<p>To be able to work with our data, you need an NCI account.</p> <p>If you don't have one yet, signup here.</p> <p>Note: You will need an institutional email address with an organisation that allows access to NCI (e.g., CSIRO, a university, etc.).</p> <p>Once you have signed up, you will be allocated a username. We will refer to this username (e.g. <code>kf1234</code>) as <code>$USER</code>.</p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#2-join-relevant-nci-projects","title":"2) Join relevant NCI projects","text":"<p>There is a plethora of NCI projects that may or may not be relevant for you.</p> <p>We recommend you have a chat with your supervisor to identify the relevant projects, but in any case suggest to join <code>xp65</code> for MED code as well as <code>kj13</code> for MED data.</p> <p>To get this conversation started, we list some possibly relevant projects below:</p> Project Description with link, * indicated compute resource ACCESS-NRI projects tm70 ACCESS-NRI Working Project * iq82 ACCESS-NRI MED Compute * kj13 ACCESS-NRI MED Data Dev ct11 ACCESS-NRI Replicated Datasets xp65 ACCESS-NRI Analysis Environments ACCESS projects access ACCESS software sharing p66 ACCESS - AOGCM / suppport development of the ACCESS modelling system * p73 ACCESS Model Output Archive (AOGCM) Data projects hh5 Climate-LIEF Data Storage ub7 Seasonal Prediction ACCESS-S1 Hindcast ux62 Seasonal Prediction ACCESS-S2 Hindcast cb20 ESGF CMIP3 Replication Data al33 ESGF CMIP5 Replication Data rr3 ESGF CMIP5 Australian Data Publication oi10 ESGF CMIP6 Replication Data fs38 ESGF CMIP6 Australian Data Publication rt52 ERA5 Replicated Data: Single and pressure-levels data uc16 ERA5 Replicated Datasets on Potential Temperature &amp; Vorticity Levels zz93 ERA5-Land Replicated Data zv2 Australian Gridded Climate Data (AGCD) Collection qv56 Reference Datasets for Climate Model Analysis/Forcing cj50 COSIMA Model Output Collection Other projects ik11 COSIMA shared working space v45 Ocean Extremes * ga6 Modelling the formation of sedimentary basins and continental margins * m18 Evolution and dynamics of the Australian lithosphere * q97 Earth dynamics and resources over the last billion years * qu79 Collaborative REAnalysis Technical Environment Intercomparison Project (CREATE-IP) <p>To join a project or find more projects, please use this NCI website.</p> <p>The first project that you join will become your default login project, e.g. <code>xp65</code>. We will refer to it as <code>$PROJECT</code> and we show you how to change it below.</p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#3-logging-in-to-gadinci","title":"3) Logging in to Gadi@NCI","text":"<p>If you have never logged onto Gadi before, we recommend to take a look at NCI's Welcome to Gadi website. It provides all the important commands and information for logging properly onto Gadi, like the following: \"To run jobs on Gadi, you need to first log in to the system. Users on Mac/Linux can use the built-in terminal. For Windows users, we recommend using MobaXterm as the local terminal. Logging in to Gadi happens through a Gadi login node.\"</p> <p>When you login, via the command <pre><code>ssh -Y $USER@gadi.nci.org.au\n</code></pre> you will enter your $HOME directory with your default <code>$PROJECT</code> and your default SHELL. Both are saved at <code>$HOME/.config/gadi-login.conf</code> and you can print them via <pre><code>cat $HOME/.config/gadi-login.conf\n</code></pre></p> <p>The <code>-Y</code> option is needed to run graphical tools by enabling the forwarding of trusted X protocol mesgs between X-Server on local system and X programs on Gadi.  You need to enable X Windowing system on your local system before running ssh. This can be done by running X-Server like XQuartz (Mac), MobaXterm (MS Windows), startx or similar (Linux).</p> <p>Again, for more useful information we recommend to check out NCI's Welcome to Gadi website.</p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#4-computing-on-gadi","title":"4) Computing on Gadi","text":""},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#gadi-resources","title":"Gadi Resources","text":"<p>Coupled climate models like ACCESS-CM involve, among other things, calculation of complex mathematical equations that explain the physics of the atmosphere and oceans. Performed at hundreds of millions of points around the Earth, these calculations require vast computing power to complete them in a reasonable amount of time, thus relying on the power of  high-performance computing (HPC) like Gadi. The Gadi supercomputer can handle more than 10 million billion (10 quadrillion) calculations per second and is connected to 100,000 Terabytes of high-performance research data storage.</p> <p>An overview of Gadi resources such as compute, storage and PBS jobs are described below. </p> <p>Useful NCI commands to check your available compute resources are:</p> Command Purpose <code>logout</code> or Ctrl+D To exit a session <code>hostname</code> Displays login node details <code>module list</code> Modules currently loaded <code>module avail</code> Available modules <code>nci_account -P [proj]</code> Compute allocation for [proj] <code>nqstat -P [proj]</code> Jobs running/queued in [proj] <code>lquota</code> Storage allocation and usage for all your projects"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#compute-hours","title":"Compute Hours","text":"<p>Compute allocations are granted to projects instead of directly to users and, hence, you need to be a member of a project in order to use its compute allocation. To run jobs on Gadi, you need to have sufficient allocated compute hours available, where the job cost depends on the resources reserved for the job and the amount of walltime it uses. </p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#storage","title":"Storage","text":"<p>Each user has a project-independent <code>$HOME</code> directory, which has a storage limit of 10 GiB. All data on <code>/home</code> is backed up.</p> <p>Through project membership, the user gets access to the storage space within the project folders <code>/scratch</code> and  <code>/g/data</code> filesystems for that particular project.</p>"},{"location":"models/run-a-model/getting_started/access_to_gadi_at_nci/#pbs-jobs","title":"PBS Jobs","text":"<p>To run compute tasks such as an ACCESS-CM suite on Gadi, users need to submit them as jobs to queues. Within a job submission, you can specify the queue, duration and computational resources needed for your job. When a job submission is accepted, it is assigned a jobID (shown in the return message) that can then be used to monitor the job\u2019s status. </p> <p>On job completion, contents of the job\u2019s standard output/error stream gets copied to a file in the working directory with the respective format: <code>&lt;jobname&gt;.o&lt;jobid&gt;</code> and <code>&lt;jobname&gt;.e&lt;jobid&gt;</code>. Users should check these two log files before proceeding with post-processing of any output from their corresponding job.</p>"}]}
\ No newline at end of file
diff --git a/pr-preview/pr-396/sitemap.xml b/pr-preview/pr-396/sitemap.xml
index 26bfe2715..ccec0513c 100644
--- a/pr-preview/pr-396/sitemap.xml
+++ b/pr-preview/pr-396/sitemap.xml
@@ -2,472 +2,467 @@
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     <url>
          <loc>https://access-hive.org.au/call_contribute/</loc>
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     <url>
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     <url>
          <loc>https://access-hive.org.au/about/policies/</loc>
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     <url>
          <loc>https://access-hive.org.au/about/support/</loc>
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     <url>
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     <url>
          <loc>https://access-hive.org.au/community_resources/community_data_processing/</loc>
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     <url>
          <loc>https://access-hive.org.au/community_resources/community_observational_catalogs/</loc>
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     <url>
          <loc>https://access-hive.org.au/community_resources/community_working_groups/</loc>
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          <loc>https://access-hive.org.au/community_resources/events/</loc>
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     <url>
          <loc>https://access-hive.org.au/community_resources/events/add_event/</loc>
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