Merge branch 'development' into chrisb/om2_restart_workflow_update

Author: chrisb13

…sation/access_om_model_visualisation.png …ation/access_om2_model_visualisation.pngdocs/assets/model-config-logos/model_visualisation/access_om_model_visualisation.png renamed to docs/assets/model-config-logos/model_visualisation/access_om2_model_visualisation.png docs/assets/model-config-logos/model_visualisation/access_om_model_visualisation.png renamed to docs/assets/model-config-logos/model_visualisation/access_om2_model_visualisation.png

@@ -1,3 +1,4 @@
+[cosima]: https://cosima.org.au/
 
 # ACCESS-OM
 
@@ -6,11 +7,45 @@
 The ACCESS Ocean Model (ACCESS-OM) is a global coupled ocean model that includes [ocean](/models/model_components/ocean), [ocean biogeochemistry](/models/model_components/bgc_ocean), and [sea ice](/models/model_components/sea-ice) components, linked together by a [coupler](/models/model_components/coupler).<br>
 The atmospheric fields that drive the model are provided by a data source, usually derived from reanalysis.
 
-## ACCESS-OM2
+{% set model = "ACCESS-OM3" %}
+## {{ model }}
 
-[ACCESS-OM2](https://gmd.copernicus.org/articles/13/401/2020/) [@Kiss2020] [@ACCESS-OM2-report] [@Solodoch2022] [@Hayashida2023] [@Menviel2023] is a suite of coupled ocean-sea ice models originally developed by the [Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)](http://cosima.org.au/).<br>
+{{ model }} is a suite of coupled ocean-sea ice models developed by ACCESS-NRI and the [Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)][cosima].
 
-ACCESS-NRI has released [ACCESS-OM2 configurations](https://github.com/ACCESS-NRI/access-om2-configs) as an adaptation of those originally developed by COSIMA.
+ACCESS-NRI has released [{{ model }} configurations](https://github.com/ACCESS-NRI/access-om3-configs).
+
+There is a global configuration for **one spatial resolution**:
+
+- 0.25° or 25km horizontal resolution, 75 vertical levels.
+
+For the above resolution there is **one option of JRA55-do atmospheric forcing**:
+
+- Repeat Year Forcing (RYF): repeated 1 May 1990 - 30 April 1991 forcing
+
+Each configuration also has an optional biogeochemical (BGC) configuration that uses the [Biogeochemistry Ocean component](/models/model_components/bgc_ocean), if required.
+!!! warning
+    BGC experiments are slower and generally consume more resources (compute time and disk space).
+
+### Model Components {: #model-components-{{model}} }
+
+- **Ocean**: [MOM6](/models/model_components/ocean#mom6).<br>
+  Tripolar grid.
+
+- **Sea ice**: [CICE6](/models/model_components/sea-ice#cice6).<br>
+    Same grid as ocean.
+
+- **Ocean Biogeochemistry**: [WOMBAT](/models/model_components/bgc_ocean#wombat)  (optional).
+
+- **Coupler**: [NUOPC](/models/model_components/coupler#nuopc).
+
+[Run {{ model }}](/models/run-a-model/run-access-om3){: class="text-card"}
+
+{% set model = "ACCESS-OM2" %}
+## {{ model }}
+
+[{{ model }}](https://gmd.copernicus.org/articles/13/401/2020/) [@Kiss2020] [@ACCESS-OM2-report] [@Solodoch2022] [@Hayashida2023] [@Menviel2023] is a suite of coupled ocean-sea ice models originally developed by the [Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)][cosima].<br>
+
+ACCESS-NRI has released [{{ model }} configurations](https://github.com/ACCESS-NRI/access-om2-configs) as an adaptation of those originally developed by COSIMA.
 
 There are global configurations for **three spatial resolutions**:
 
@@ -21,21 +56,21 @@ There are global configurations for **three spatial resolutions**:
 For each resolution there are **two options of JRA55-do atmospheric forcing**:
 
 - Repeat Year Forcing (RYF): repeated 1 May 1990 - 30 April 1991 forcing
-- Interannual Forcing (IAF): 1958-2018 forcing
+- Inter-Annual Forcing (IAF): 1958-2018 forcing
 
 Each configuration also has an optional biogeochemical (BGC) configuration that uses the [Biogeochemistry Ocean component](/models/model_components/bgc_ocean), if required.
 !!! warning
     BGC experiments are slower and generally consume more resources (compute time and disk space).
 
-### Model Components
+### Model Components {: #model-components-{{model}} }
 <div class="tabLabels" label="ACCESS-OM2-versions">
-    <button id="1deg">ACCESS-OM2</button>
-    <button id="025deg">ACCESS-OM2-025</button>
-    <button id='01deg'>ACCESS-OM2-01</button>
+    <button id="{{ model }}-1deg">{{ model }}-1</button>
+    <button id="{{ model }}-025deg">{{ model }}-025</button>
+    <button id='{{ model }}-01deg'>{{ model }}-01</button>
 </div>
 
 - **Ocean**: [MOM5](/models/model_components/ocean#mom5).<br>
-  Tripolar grid, <span tabcontentfor="1deg">1</span><span tabcontentfor="025deg">0.25</span><span tabcontentfor="01deg">0.1</span>° spatial resolution, <span tabcontentfor="1deg">50</span><span tabcontentfor="025deg">50</span><span tabcontentfor="01deg">75</span> vertical levels.
+  Tripolar grid, <span tabcontentfor="{{ model }}-1deg">1</span><span tabcontentfor="{{ model }}-025deg">0.25</span><span tabcontentfor="{{ model }}-01deg">0.1</span>° spatial resolution, <span tabcontentfor="{{ model }}-1deg">50</span><span tabcontentfor="{{ model }}-025deg">50</span><span tabcontentfor="{{ model }}-01deg">75</span> vertical levels.
 
 - **Ocean Biogeochemistry**: [WOMBAT](/models/model_components/bgc_ocean#wombat) (optional).
 
@@ -46,6 +81,6 @@ Each configuration also has an optional biogeochemical (BGC) configuration that
 
 More details on the models can be found in [this ACCESS-Hive Forum post](https://forum.access-hive.org.au/t/access-om2-control-experiments/258), together with details on the extensive control experiment data already available without needing to run a new experiment.
 
-Full conditions of use for ACCESS-OM2 models and outputs can be viewed in the  [ACCESS-OM2-configs README](https://github.com/ACCESS-NRI/access-om2-configs?tab=readme-ov-file#conditions-of-use).
+Full conditions of use for {{ model }} models and outputs can be viewed in the  [{{ model }}-configs README](https://github.com/ACCESS-NRI/access-om2-configs?tab=readme-ov-file#conditions-of-use).
 
-[Run ACCESS-OM2](/models/run-a-model/run-access-om){: class="text-card"}
+[Run {{ model }}](/models/run-a-model/run-access-om2){: class="text-card"}

docs/assets/model-config-logos/model_visualisation/access_om3_model_visualisation.png

@@ -20,5 +20,5 @@ There are two MOM versions currently used in ACCESS models: [MOM5](https://githu
 - [ACCESS-OM2](/models/configurations/access-om#access-om2)
 </div>
 <div tabcontentfor="mom6" markdown>
-MOM6 is not yet included in any ACCESS-NRI-supported configuration, but will be included in ACCESS-OM3, a configuration currently under development.
-</div>
+- [ACCESS-OM3](/models/configurations/access-om#access-om3)
+</div>

docs/models/configurations/access-om.md

@@ -23,5 +23,5 @@ There are three CICE versions currently used in ACCESS models:
 - [ACCESS-OM2](/models/configurations/access-om#access-om2)
 </div>
 <div tabcontentfor="cice6" markdown>
-CICE6 is not yet included in any ACCESS-NRI-supported configuration, but will be included in ACCESS-OM3, a configuration currently under development.
-</div>
+- [ACCESS-OM3](/models/configurations/access-cm#access-om3)
+</div>

docs/models/model_components/ocean.md

@@ -22,13 +22,22 @@ If you are unsure which ACCESS model is the right choice for your experiment, ta
             Run ACCESS-ESM
         </div>
     </a>
-    <!-- Run ACCESS-OM -->
-    <a href="/models/run-a-model/run-access-om" class="vertical-card aspect-ratio1to1">
+    <!-- Run ACCESS-OM2 -->
+    <a href="/models/run-a-model/run-access-om2" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
-            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_om_model_visualisation.png" alt="ACCESS-OM">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_om2_model_visualisation.png" alt="ACCESS-OM2">
         </div>
         <div class="card-text-container bold">   
-            Run ACCESS-OM
+            Run ACCESS-OM2
+        </div>
+    </a>
+    <!-- Run ACCESS-OM3 -->
+    <a href="/models/run-a-model/run-access-om3" class="vertical-card aspect-ratio1to1">
+        <div class="card-image-container">
+            <img class="img-contain with-padding white-background" src="/assets/model-config-logos/model_visualisation/access_om3_model_visualisation.png" alt="ACCESS-OM3">
+        </div>
+        <div class="card-text-container bold">   
+            Run ACCESS-OM3
         </div>
     </a>
     <!-- Run ACCESS-rAM -->

docs/models/model_components/sea-ice.md

@@ -10,25 +10,31 @@
 
 ## Prerequisites
 
-### General prerequisites
-
-Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/set_up_nci_account).
-
-If you are unsure whether {{ model }} is the right choice for your experiment, take a look at the overview of [ACCESS Models](/models).
-
-### Model-specific prerequisites
+- **NCI Account**<br> 
+    Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/set_up_nci_account).
 
 - **_MOSRS_ account**<br>
     The [Met Office Science Repository Service (MOSRS)](https://code.metoffice.gov.uk) is a server run by the UK Met Office (UKMO) to support collaborative development with other partners organisations. MOSRS contains the source code and configurations for some model components in {{ model }} (e.g., the [UM](/models/model_components/atmosphere/#unified-model-um)).<br>
     To apply for a _MOSRS_ account, please contact your [local institutional sponsor](https://opus.nci.org.au/display/DAE/Prerequisites).
+    {: #mosrs-account}
 
-- **Join the _access_, _hr22_, _ki32_ and _ki32\_mosrs_ projects at NCI**<br>
-    To join these projects, request membership on the respective [access](https://my.nci.org.au/mancini/project/access/join), [hr22](https://my.nci.org.au/mancini/project/hr22/join), [ki32](https://my.nci.org.au/mancini/project/ki32/join) and [ki32_mosrs](https://my.nci.org.au/mancini/project/ki32_mosrs/join) NCI project pages.
+- **Join NCI projects**<br>
+    Join the following projects by requesting membership on their respective NCI project pages:
 
-    !!! tip
-        To request membership for the _ki32_mosrs_ subproject you need to have a MOSRS account and be member of the _ki32_ project.
+    - [access](https://my.nci.org.au/mancini/project/access/join)
+    - [hr22](https://my.nci.org.au/mancini/project/hr22/join)
+    - [ki32](https://my.nci.org.au/mancini/project/ki32/join)
+    - [ki32_mosrs](https://my.nci.org.au/mancini/project/ki32_mosrs/join)
 
-    For more information on how to join specific NCI projects, refer to [How to connect to a project](https://opus.nci.org.au/display/Help/How+to+connect+to+a+project).
+    !!! tip
+        To request membership for the _ki32_mosrs_ subproject, you need to:
+        
+        - already be member of the _ki32_ project
+        {: style="list-style-type: disc"}
+        - have a [MOSRS account](#mosrs-account)
+        {: style="list-style-type: disc"}
+
+    For more information on joining specific NCI projects, refer to [How to connect to a project](https://opus.nci.org.au/display/Help/How+to+connect+to+a+project).
 
 - **Connection to an ARE VDI Desktop (optional)**<br>
     To run {{ model }}, start an [Australian Research Environment (ARE) VDI Desktop](https://are.nci.org.au/pun/sys/dashboard/batch_connect/sys/desktop_vnc/ncigadi/session_contexts/new) session.<br>
@@ -380,13 +386,13 @@ rose suite-gcontrol
 It is quite common, especially during the first few runs, to experience errors and job failures. Running an {{ model }} suite involves the execution of several tasks, and any of these tasks could fail. When a task fails, the suite is halted and a red icon appears next to the respective task name in the _Cylc_ GUI.<br>
 To investigate the cause of a failure, we need to look at the logs `job.err` and `job.out` from the suite run. There are two main ways to do so:
 
-#### Using the _Cylc_ GUI
+#### Using the _Cylc_ GUI {: .no-toc }
 Right-click on the task that failed and click on _View Job Logs (Viewer) &rarr; job.err_ (or _job.out_).<br>
 To access a specific task, click on the arrow next to the task to extend the drop-down menu with all the subtasks.
 
 ![Investigate Error GUI example](/assets/run_access_cm/investigate_error_gui_are.gif){: class="example-img" loading="lazy"}
     
-#### Through the suite directory
+#### Through the suite directory {: .no-toc }
 The suite's log directories are stored in `~/cylc-run/<suite-ID>` as `log.<TIMESTAMP>`, and the latest set of logs are also symlinked in the `~/cylc-run/<suite-ID>/log` directory.<br>
 The logs for the main job can be found in the `~/cylc-run/<suite-ID>/log/job` directory.<br>
 Logs are separated into simulation cycles according to their starting dates, then divided into subdirectories according to the task name. They are then further separated into "attempts" (consecutive failed/successful tasks), where `NN` is a symlink to the most recent attempt.
@@ -457,7 +463,7 @@ qdel <job-ID>
 ### RESTART a suite
 There are two main ways to restart a suite:
 
-#### _SOFT_ restart
+#### _SOFT_ restart {: .no-toc }
 To reinstall the suite and reopen _Cylc_ in the same state it was prior to being stopped, run the following command from within the suite directory:
 ```
 rose suite-run --restart
@@ -504,7 +510,7 @@ rose suite-run --restart
     <img src="/assets/run_access_cm/Cylc_GUI_are.png" alt="Cylc GUI" imageTime="inf" loading="lazy">
 </terminal-window>
 
-#### _HARD_ restart
+#### _HARD_ restart {: .no-toc }
 To overwrite any previous runs of the suite and start afresh, run the following command from within the suite directory:
 ```
 rose suite-run --new