Add AM3 specific run docs

.github/workflows/lychee_config.toml

@@ -129,6 +129,7 @@ glob_ignore_case = false
     '^https://cds\.climate\.copernicus\.eu/', # EU Copernicus - has firewalls that block link-checkers
     '^https://www\.nrc\.gov/', # Gov website - has firewalls that block link-checkers
     '^https://www\.education\.gov\.au/', # AU Gov website - has firewalls that block link-checkers
+    '^https://github\.com/ACCESS-NRI/access-am3-configs', # Private GitHub repo
   ]
 
 # Exclude paths from getting checked. The values are treated as regular expressions

docs/css/access-nri.css

@@ -461,6 +461,11 @@ h1.homepage {
 /* =============================================================== 
   Admonitions 
   (https://squidfunk.github.io/mkdocs-material/reference/admonitions/)
+*/
+
+.admonition > ul li {
+  list-style-type: disc !important;
+}
 
 /* General style admonition (In markdown --> `!!! ...`) */
 .admonition {
@@ -1448,4 +1453,4 @@ div.release-table td:nth-child(3) {
 }
 div.release-table td:nth-child(4) {
   background-color: var(--success-bg) 
-}
+}

docs/models/access_models/access-am.md

@@ -0,0 +1,32 @@
+!!! release
+    This is an [**Alpha Release**](/about/releases), intended for use by experienced users and collaborators. Any model configuration and related source code information on this page may change during the release process.
+
+# ACCESS-AM
+
+![ACCESS AM model](/assets/model-config-logos/configurations-without-titles/access-am.png){: class="img-contain white-background round-edges with-padding intro-img" loading="lazy"}
+
+The ACCESS Atmosphere Model (ACCESS-AM) is a global coupled atmospheric model that can include [atmosphere](/models/model_components/atmosphere), [aerosols and atmospheric chemistry](/models/model_components/aerosols_atmospheric_chemsitry), [land](/models/model_components/land) and [land biogeochemistry](/models/model_components/bgc_land), depending on the configuration.
+
+{% set model = "ACCESS-AM3" %}
+## {{ model }}
+
+{{ model }} is a set of coupled atmosphere-land configurations developed by the ACCESS-NRI, the [Commonwealth Science and Industrial Research Organisation (CSIRO)](https://www.csiro.au/en/research/natural-environment?start=0&count=12) and the [ARC Centre of Excellence for Weather in the 21st Century](https://21centuryweather.org.au/).
+
+ACCESS-NRI has released [{{ model }} configurations](https://github.com/ACCESS-NRI/access-am3-configs).
+
+!!! tip
+    The configurations GitHub repository is private. To request access to it, follow the related instructions in the [Run {{ model }} page](/models/run_a_model/run_access-am3/#request-access).
+
+<!-- TODO: Fill in configurations for beta release. -->
+
+### Model Components {: #model-components-{{model}} }
+
+- **Atmosphere**: [UM13.1](/models/model_components/atmosphere#unified-model-um).
+
+- **Aerosols and Atmospheric Chemistry**: [GLOMAP](/models/model_components/aerosols_atmospheric_chemistry#glomap) and [UKCA](/models/model_components/aerosols_atmospheric_chemistry#UKCA).
+
+- **Land**: [CABLE](/models/model_components/land#cable) and [JULES](/models/model_components/land#jules).
+
+- **Land Biogeochemistry**: [CASA-CNP](/models/model_components/bgc_land#casa_cnp).
+
+[Run ACCESS-AM](/models/run_a_model/run_access-am3){: class="text-card"}

docs/models/access_models/index.md

@@ -6,6 +6,18 @@ Developed in collaboration with international climate modeling institutions, the
 Below is a list of ACCESS models supported by ACCESS-NRI.
 
 <div class="card-container">
+    <!-- ACCESS-AM -->
+    <a href="access-am/" class="horizontal-card">
+        <div class="card-image-container">
+            <img src="/assets/model-config-logos/configurations-without-titles/access-am.png" class="white-background img-contain"></img> 
+        </div>
+        <div class="card-text-container">
+            <span class="bold" >ACCESS-AM</span>
+            <span>
+                A global atmospheric model that includes atmosphere, land, atmospheric chemistry, aerosols and land biogeochemistry components.
+            </span>
+        </div>
+    </a>
     <!-- ACCESS-CM -->
     <a href="access-cm/" class="horizontal-card">
         <div class="card-image-container">
@@ -53,4 +65,4 @@ Below is a list of ACCESS models supported by ACCESS-NRI.
             </span>
         </div>
     </a>
-</div>
+</div>

docs/models/model_components/aerosols_atmospheric_chemistry.md

@@ -7,11 +7,13 @@
 The [UK Chemistry-Aerosol model (UKCA)](https://www.ukca.ac.uk/wiki/index.php/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.
 
 ### Models that use UKCA
-- [ACCESS-CM2](/models/access_models/access-cm#access-cm2) (optional).
+- [ACCESS-AM3](/models/access_models/access-am#access-am3) (optional)
+- [ACCESS-CM2](/models/access_models/access-cm#access-cm2) (optional)
 
 ## GLOMAP
 
 UKCA contains the [GLObal Model of Aerosol Processes (GLOMAP)](https://www.ukca.ac.uk/wiki/index.php/Aerosol_Subproject) aerosol scheme, that can also 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.
 
 ### Models that use GLOMAP
-- [ACCESS-CM2](/models/access_models/access-cm#access-cm2).
+- [ACCESS-AM3](/models/access_models/access-am#access-am3)
+- [ACCESS-CM2](/models/access_models/access-cm#access-cm2)

docs/models/model_components/atmosphere.md

@@ -7,6 +7,7 @@
 The UK Met Office [Unified Model (UM)](https://www.metoffice.gov.uk/research/approach/modelling-systems/unified-model) is a numerical model of the atmosphere used for both weather and climate applications across a wide range of temporal scales (nowcasting to centennial) and spatial scales (sub km convective scale to global). The UM includes solutions of the equations of atmospheric fluid dynamics with advanced parameterisations of physical processes like convection, cloud formation and atmospheric radiation. 
 
 ### Models that use the UM
+- [ACCESS-AM3](/models/access_models/access-am#access-am3)
 - [ACCESS-CM2](/models/access_models/access-cm#access-cm2)
 - [ACCESS-ESM1.5](/models/access_models/access-esm#access-esm15)
 - [ACCESS-rAM3](/models/access_models/access-ram#access-ram3)

docs/models/model_components/bgc_land.md

@@ -8,5 +8,6 @@
 The [Carnegie-Ames-Stanford Approach with Carbon-Nitrogen-Phosphorus (CASA-CNP)](https://carbonwaterobservatory.csiro.au/casa.html) is the biogeochemical module implemented in the ACCESS land surface model [CABLE](/models/model_components/land#cable). It models the dynamics of carbon pools and the dependence of carbon uptake due to nitrogen and phosphorous limitations.  
 
 ### Models that use CASA-CNP
+- [ACCESS-AM3](/models/access_models/access-am) (enabled within [CABLE](/models/model_components/land#cable))
 - [ACCESS-ESM1.5](/models/access_models/access-esm) (enabled within [CABLE](/models/model_components/land#cable))
 

docs/models/model_components/land.md

@@ -11,6 +11,7 @@ Refer to [CABLE documentation](https://cable.readthedocs.io/en/latest/user_guide
 
 ### Models that use CABLE
 
+- [ACCESS-AM3](/models/access_models/access-am#access-am3) (coupled into [JULES](/models/model_components/land#jules))
 - [ACCESS-CM2](/models/access_models/access-cm#access-cm2) (directly coupled into the [UM](/models/model_components/atmosphere#unified-model-um))
 - [ACCESS-ESM1.5](/models/access_models/access-esm#access-esm15) (directly coupled into the [UM](/models/model_components/atmosphere#unified-model-um))
 
@@ -35,6 +36,7 @@ To learn more about _benchcab_, its functionalities and limitations, refer to [_
 The [Joint UK Land Environment System (JULES)](https://jules.jchmr.org/) 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, for example the impact of climate change on hydrology.
 
 ### Models that use JULES
+- [ACCESS-AM3](/models/access_models/access-am#access-am3) (complementing [CABLE](/models/model_components/land#cable))
 - [ACCESS-rAM3](/models/access_models/access-ram#access-ram3)
 
 Other ACCESS models used for weather simulations, not supported by ACCESS-NRI, use JULES. Examples are ACCESS-S and ACCESS-C developed by the [Bureau of Meteorology (BoM)](https://www.bom.gov.au/).

docs/models/run_a_model/index.md

@@ -13,6 +13,15 @@ If you are unsure which ACCESS model is the best fit for your application, you c
             Run models using Rose/Cylc
         </div>
     </a>
+    <!-- Run ACCESS-AM3 -->
+    <a href="run_access-am3" 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_esm_model_visualisation.png" alt="ACCESS-AM">
+        </div>
+        <div class="card-text-container bold">   
+            Run ACCESS-AM3
+        </div>
+    </a>
     <!-- Run ACCESS-CM -->
     <a href="run_access-cm2" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">

docs/models/run_a_model/run_access-am3.md

@@ -0,0 +1,84 @@
+{% set model = "ACCESS-AM3" %}
+{% set github_configs = "https://github.com/ACCESS-NRI/access-am3-configs" %}
+{% set github_ssh = "git@github.com:ACCESS-NRI/access-am3-configs.git" %}
+{% set configs_docs = "https://access-am3-configs.access-hive.org.au" %}
+{% set example_branch = "main" %}
+{% set release_notes = "https://forum.access-hive.org.au/t/access-am3-release-information/5446" %}
+
+!!! release
+    This is an [**Alpha Release**](/about/releases), intended for use by experienced users and collaborators. Any model configuration and related source code information on this page may change during the release process.
+
+<div class="text-card-group" markdown>
+[:fontawesome-brands-github:{: class="twemoji icon-before-text"} {{ model }} configurations]({{github_configs}}){: class="text-card"}
+[![Hive](/assets/ACCESS_icon_HIVE.png){: class="icon-before-text"} {{ model }} configs docs]({{configs_docs}}){: class="text-card"}
+[:notepad_spiral:{: class="twemoji icon-before-text"} Release notes]({{release_notes}}){: class="text-card"}
+</div>
+
+# Run {{ model }}
+
+## About
+
+The instructions below outline how to run {{ model }} using ACCESS-NRI's software deployment pipeline, specifically designed to run on the [National Computational Infrastructure (NCI)](https://nci.org.au/about-us/who-we-are) supercomputer [_Gadi_](https://nci.org.au/our-systems/hpc-systems).
+
+If you are unsure whether {{ model }} is the right choice for your experiment, take a look at the overview of [ACCESS Models](/models).
+
+All {{model}} configurations are licensed under the UKMO's Momentum licence. {{model}} is delivered to the community through private GitHub repositories. See the [Request access prerequisite](#request-access) for details.
+
+{{ model }} release notes are [available on the ACCESS-Hive Forum]({{release_notes}}) and are updated when new releases are made available.
+
+## Prerequisites
+
+!!! warning
+    Before continuing, make sure you have read the guide on [running models using _Rose/Cylc_](/models/run-a-model/rose-cylc.md).
+
+In addition to the [prerequisites for _Rose/Cylc_](/models/run_a_model/rose_cylc/#prerequisites), you will need:
+
+- **Request access to the configurations**<br>
+    To request access to the configurations repository (and associated model component repositories), please contact us [through the ACCESS-Hive Forum](https://forum.access-hive.org.au/t/request-access-to-am3-configurations/5580/13). This step will also allow us to check you are properly licensed to use the software.
+    {: #request-access }
+
+- **Join NCI projects**<br>
+    Join the following projects by requesting membership on their respective NCI project pages:
+
+    - [access](https://my.nci.org.au/mancini/project/access/join)
+    - [ki32](https://my.nci.org.au/mancini/project/ki32/join)
+    - [ki32_mosrs](https://my.nci.org.au/mancini/project/ki32_mosrs/join)
+    - [vk83](https://my.nci.org.au/mancini/project/vk83/join)
+    - [xp65](https://my.nci.org.au/mancini/project/xp65/join)
+
+    !!! tip
+        To request membership for the _ki32_mosrs_ subproject, you need to:
+
+        - already be member of the _ki32_ project
+        - have a [MOSRS account](/models/run_a_model/rose_cylc/#mosrs-account)
+
+    !!! warning
+        You will not be granted access to some of the projects listed here before we have checked you are properly licensed to use the software. Ensure you [request access to the configurations](#request-access) first.
+
+    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).
+
+## Get {{model}} configuration
+
+Follow the instructions for [Model configurations stored on _GitHub_](/models/run_a_model/rose_cylc/#model-configurations-stored-on-github) using the following specific information:
+
+- [Repository](/models/run-a-model/rose-cylc/#model-configurations-stored-on-github): {{ github_ssh }}
+- [Branch](/models/run-a-model/rose-cylc/#model-configurations-stored-on-github): {{ example_branch }}
+
+## Initial Setup
+
+Before you can run {{ model }} configuration, you need to specify which projects you want to use for data storage and compute resources. For this, in the configuration directory open the `rose-suite.conf_nci_gadi` file and change:
+
+- `root_dir` to the path you want to use as a work directory for running the simulation. A space under `/scratch/<project>` is ideal, where `<project>` is the project associated with the current work. The directory will be created by the suite if it does not exist.
+- `STORAGE_PROJECT` must be the same project as used in the `root_dir` path.
+- `COMPUTE_PROJECT` to any project you want to be charged for the compute resources.
+
+Now the configuration can be run using the [Run the model configuration](/models/run_a_model/rose_cylc/#run-the-model-configuration) instructions.
+
+## Inspecting the outputs
+
+The netCDF outputs are placed in `~/cylc-run/<suite-id>/share/data/History_Data/netCDF`.
+The outputs in [UM Fieldsfiles format](https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_F03.pdf) are placed in `~/cylc-run/<suite-id>/share/data/History_Data`.
+
+## Further Information
+
+See [{{ model }} configuration documentation](https://access-nri.github.io/access-am3-configs-doc/) for more detailed information about {{ model }} configuration.

mkdocs.yml

@@ -1,11 +1,8 @@
-# This file uses the following environment variables set within the build workflow:
-# - SITE_URL: the URL of the site (Falls back to a default URL)
-# For example, for PR-previews, SITE_URL is set to <default_URL>/pr-previews/pr-NUM
-
 site_name: ACCESS-Hive Docs
 
 # Site URL
-site_url: !ENV [SITE_URL, "https://docs.access-hive.org.au/"]
+site_url: !ENV READTHEDOCS_CANONICAL_URL
+# READTHEDOCS_CANONICAL_URL is set within the website build (GitHub worflow or ReadTheDocs)
 
 # Git repository (Adds a link to the GitHub repository at the top)
 repo_url: https://github.com/ACCESS-NRI/ACCESS-Hive-Docs
@@ -107,6 +104,7 @@ nav:
     - models/index.md
     - ACCESS Models:
       - models/access_models/index.md
+      - ACCESS-AM: models/access_models/access-am.md
       - ACCESS-CM: models/access_models/access-cm.md
       - ACCESS-ESM: models/access_models/access-esm.md
       - ACCESS-OM: models/access_models/access-om.md
@@ -124,6 +122,7 @@ nav:
     - Run a Model: 
       - models/run_a_model/index.md
       - Run models using Rose/Cylc: models/run_a_model/rose_cylc.md
+      - Run ACCESS-AM3: models/run_a_model/run_access-am3.md
       - Run ACCESS-CM2: models/run_a_model/run_access-cm2.md
       - Run ACCESS-ESM: models/run_a_model/run_access-esm.md
       - Run ACCESS-OM2: models/run_a_model/run_access-om2.md