Update run-access-issm.md

Author: lawrenceabird

docs/models/run_a_model/run_access-issm.md

@@ -1,3 +1,4 @@
+{% set model = "ACCESS-ISSM" %}
 {% set model_configurations = "/models/access-issm" %}
 {% set release_notes = "https://github.com/ACCESS-NRI/ACCESS-ISSM/releases/tag/2025.11.0" %}
 
@@ -126,6 +127,7 @@ python run-mismip.py \
 ```
 
 Those arguments that accept multiple inputs (e.g. `--steps`, `--storage`, `--module_use`, and `--module_load`) are formatted internally as follows:
+
 * `--steps`: [1, 2]
 * `--storage`: `<STORAGE_LOC_1>+<STORAGE_LOC_2>+<STORAGE_LOC_n>`
 * `--module_use` and `module_load`:
@@ -172,14 +174,14 @@ The provided execution script supports 9 different experiments comprising differ
 A summary of each ice flow approximation and ice flow law is provided below:
 
 * Ice flow approximations:
-    - Shelfy Stream Approximation (SSA): Assumes that vertical shear is negligible, so ice deformation is dominated by horizonatal stretching and sliding. SSA is ideal for fast-flowing ice streams and ice shelves.
-    - Higher Order (HO): Includes both vertical and shear membrane stresses, providing a balance between accuracy and computational cost for grounded ice with moderate flow complexity.
-    - Full-stokes (FS): The complete set of Stokes equations, cpaturing all stress components and deformation modes for the most physically accurate representation of ice flow dynamics.
+    - **Shelfy Stream Approximation (SSA):** Assumes that vertical shear is negligible, so ice deformation is dominated by horizonatal stretching and sliding. SSA is ideal for fast-flowing ice streams and ice shelves.
+    - **Higher Order (HO):** Includes both vertical and shear membrane stresses, providing a balance between accuracy and computational cost for grounded ice with moderate flow complexity.
+    - **Full-stokes (FS):** The complete set of Stokes equations, cpaturing all stress components and deformation modes for the most physically accurate representation of ice flow dynamics.
 
 * Ice flow laws:
-    - Glen: Power-law relationship that links ice strain rate to stress, desribing how ice deforms under load with a stress exponent of 3.
-    - Glen (Enhanded): Applies a multiplicative enhancement factor to the standard Glen law to represent softer or damaged ice that deforms more easily.
-    - Estar: Introduces effective viscosity that blends Glen-type creep with additional physics, providing a smoother, more stable response in fast-flowing or highly-variable regions.
+    - **Glen:** Power-law relationship that links ice strain rate to stress, desribing how ice deforms under load with a stress exponent of 3.
+    - **Glen (Enhanded):** Applies a multiplicative enhancement factor to the standard Glen law to represent softer or damaged ice that deforms more easily.
+    - **Estar:** Introduces effective viscosity that blends Glen-type creep with additional physics, providing a smoother, more stable response in fast-flowing or highly-variable regions.
 
 ### Running MISMIP+ Model 1
 
@@ -220,19 +222,19 @@ Without changing any of the default options, this should generate an output simi
 Below, we provide a brief overview of the key "steps" contained in the example MISMIP configuration provided here:
 
 * **Steps 1 - 2: Model parameterisation**
-    - Step 1 - Mesh generation: This step generates an anisotropic model mesh based on the resolution requested (see Section 3.4).
-    - Step 2 - Model configuration and initial conditions: This step configures the model components and sets initial conditions based on the model requested (see Section 3.4).
+    - **Step 1 - Mesh generation:** This step generates an anisotropic model mesh based on the resolution requested (see Section 3.4).
+    - **Step 2 - Model configuration and initial conditions:** This step configures the model components and sets initial conditions based on the model requested (see Section 3.4).
 
 * **Steps 3 - 8: Model initialisation**
-    - Step 3 - Initial transient relaxation: This step performs a 200,000 year relaxation transient stress balance.
-    - Step 4 - Second transient relaxation: This step performs a second 200,000 year relaxation transient stress balance, using the final state of Step 3 as the initial conditions.
-    - Step 5 - Third transient relaxation: This step performs a third 200,000 year relaxation transient stress balance, using the final state of Step 4 as the initial conditions.
-    - Step 6 - Fourth transient relaxation: This step performs a fourth 200,000 year relaxation transient stress balance, using the final state of Step 5 as the initial conditions.
-    - Step 7 - Fifth transient relaxation: This step performs a fifth 200,000 year relaxation transient stress balance, using the final state of Step 6 as the initial conditions.
-    - Step 8 - 3D Extrusion: This steps perfoms a 3D extrusion from a 2D model mesh to a 3D model mesh, using the final stats of Step 7 as the initial conditions.
+    - **Step 3 - Initial transient relaxation:** This step performs a 200,000 year relaxation transient stress balance.
+    - **Step 4 - Second transient relaxation:** This step performs a second 200,000 year relaxation transient stress balance, using the final state of Step 3 as the initial conditions.
+    - **Step 5 - Third transient relaxation:** This step performs a third 200,000 year relaxation transient stress balance, using the final state of Step 4 as the initial conditions.
+    - **Step 6 - Fourth transient relaxation:** This step performs a fourth 200,000 year relaxation transient stress balance, using the final state of Step 5 as the initial conditions.
+    - **Step 7 - Fifth transient relaxation:** This step performs a fifth 200,000 year relaxation transient stress balance, using the final state of Step 6 as the initial conditions.
+    - **Step 8 - 3D Extrusion:** This steps perfoms a 3D extrusion from a 2D model mesh to a 3D model mesh, using the final stats of Step 7 as the initial conditions.
 
 * **Steps 9 - 17: MISMIP Model experiments**
-    - Steps 9 - 17 relate to individual MISMIP experiments, summarised in Section 4.3.
+    - **Steps 9 - 17** relate to individual MISMIP experiments, summarised in Section 4.3.
 
 #### Model parameterisation
 Steps 1 and 2 are both required for complete model parameterisation. These steps can typically be executed on a _Gadi_ login node and do not require a PBS job submission. To run steps 1 and 2, run:
@@ -263,7 +265,7 @@ Launching solution sequence on Gadi via SSH...
 Model results must be loaded manually with md = loadresultsfromcluster(md).
 ```
 
-where `<PBS_NUMBER>` will be your unique PBS job number. You can monitor the status of the PBS job using `qstat <PBS_NUMBER>`. Once the job is complete, you can retrieve the results of the model run and save these as a NetCDF file by simply running the same command and adding the `--load_only` argument, as follows:
+where `<PBS_NUMBER>` will be your unique PBS job number. You can monitor the status of the PBS job using `qstat <PBS_NUMBER>`. Once the model simulation begins, an `*.outbin` file will be created in the subdirectory. This file will grow in size as the run continues and results are saved to file. Once the model run is completed, you can retrieve the results of the model run from the `*.outbin` file and save these as a NetCDF file by simply running the same command and adding the `--load_only` argument, as follows:
 
 ```bash
 cd ~/ACCESS-ISSM/examples/mismip/
@@ -312,7 +314,7 @@ Steps 9 - 17 execute each of the MISMIP experiments, as follows:
 !!! warning
     The Full-stokes experiments are included for completeness, although they are untested and reserved for advanced users. To run the Full-stokes experiments, users must edit the `run-mismip.py` directly to remove current warnings and build upon the current implementation. See [Editing the MISMIP configuration](#editing-the-mismip-configuration) for more information.
 
-To run a given MISMIP experiment, simply execute the same commands as above, with the corresponding step number. For exaple, to run the Glen_SSA experiment, simply run:
+To run a given MISMIP experiment, simply execute the same commands as above, with the corresponding step number. For example, to run the Glen_SSA experiment, simply run:
 
 ```bash
 cd ~/ACCESS-ISSM/examples/mismip/