Overview of MOM6 code structure (Paul Spence)

CITATION.cff

@@ -20,6 +20,29 @@ authors:
     email: paige.martin@anu.edu.au
     affiliation: Australia's Climate Simulator (ACCESS-NRI), Australian National University, Canberra, Australia
     orcid: 'https://orcid.org/0000-0003-3538-633X'
+  - given-names: Angus H.
+    family-names: Gibson
+    affiliation: Research School of Earth Sciences, Australian National University, Canberra, Australia
+    orcid: 'https://orcid.org/0000-0001-7577-3604'
+  - given-names: Josef I.
+    family-names: Bisits
+    affiliation: School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, Australia
+    orcid: 'https://orcid.org/0000-0002-6340-4470'
+  - given-names: Claire
+    family-names: Yung
+    email: Claire.Yung@anu.edu.au
+    affiliation: Research School of Earth Sciences, Australian National University
+    orcid: 'https://orcid.org/0000-0002-0052-7668'
+  - given-names: Dougal
+    family-names: Squire
+    email: Dougie.Squire@anu.edu.au
+    affiliation: Australia’s Climate Simulator (ACCESS-NRI), Australian National University, Canberra, Australia
+    orcid: 'https://orcid.org/0000-0003-3271-6874'
+  - given-names: Andrew
+    family-names: Kiss
+    email: Andrew.Kiss@anu.edu.au
+    affiliation: Research School of Earth Sciences, Australian National University, Canberra, Australia
+    orcid: 'https://orcid.org/0000-0001-8960-9557'
 repository-code: 'https://github.com/ACCESS-Community-Hub/decoding-om3'
 url: 'https://github.com/ACCESS-Community-Hub/decoding-om3'
 repository-artifact: >-

README.md

@@ -1,7 +1,7 @@
 # Decoding OM3
-An open source project to fearlessly peer inside OM3! Contributions _extremely_ welcome! See rendered pages at [https://decoding-access-om3.readthedocs.io/](https://decoding-access-om3.readthedocs.io/).
+An open source project to fearlessly peer inside OM3! Contributions _extremely_ welcome! See rendered pages at [https://decoding-access-om3.readthedocs.io/](https://decoding-access-om3.readthedocs.io/decoding_mom6/).
 
 Training as part of the regular Thursday 11:30 am COSIMA meetings being coordinated [here](https://docs.google.com/spreadsheets/d/1vk8m-oDRZChAFPnZ-HuF81YmiF7dkSXQkhZXekuj4fw/edit?gid=0#gid=0). Please get in touch with @chrisb13 (`chris.bull@anu.edu.au`) or @adele-morrison to get involved. Meetings are [announced on this thread](https://forum.access-hive.org.au/t/cosima-working-group-announce/238/181) and the [meeting link is this](https://utas.zoom.us/j/82678917036?from=addon).
 
 # Get started...
-All community members are welcome to contribute or correct errors/typos. To get write access, you need to create an issue and request access. You're also welcome to make a fork and put in a pull request. 
+All community members are welcome to contribute or correct errors/typos. To get write access, [create an issue and request access](https://github.com/ACCESS-Community-Hub/decoding-om3/issues/new). You're also very welcome to make a fork and put in a pull request. 

documentation/docs/pages/decoding_mom6.md

@@ -304,8 +304,68 @@ Handy resources:
  - [Another explanation of config files from MOM6 regional](https://regional-mom6.readthedocs.io/en/latest/mom6-file-structure-primer.html);
  - [AOS MOM6 tutorial 2022: Running and controlling MOM6](https://www.youtube.com/watch?v=94m3CMTwJ1E) (e.g. ~15 minutes)
 
+## Overview of MOM6 code structure 
+Presenter: Paul Spence (@PaulSpence)
+Date: 26/03/2026.
+
+Suggested resources in which this presentation was heavily based:
+
+ - [Central MOM6 code](https://github.com/mom-ocean/MOM6);
+ - [ACCESS-NRI MOM6 fork](https://github.com/acCESS-nri/mom6);
+ - [Marshall Ward's talk on the structure of the MOM6 code base](https://www.marshallward.org/mom6workshop/internals.html#/mom6-directory-tree);
+ - [Overview: MOM6 internals](https://www.youtube.com/watch?v=E8WKrESscc4).
+
+Thanks to @marshallward for some great content!
+
+Looking at the `mom6` [directory](https://github.com/aCCESS-NRI/mom6), we have:
+
+ - `src/` -- model code;
+ - `config_src/` -- configurable components;
+ - `pkg/` -- code directory but written by other people (eg. TEOS10 equation of state);
+ - `doc/` -- documentation;
+ - `ac/` -- autoconf build.
+
+See 1 minute 20 in this [Overview: MOM6 internals](https://www.youtube.com/watch?v=E8WKrESscc4) for more details.
+
+`Config_src` is particurly important. It has functions that call other model components (e.g NUOPC coupler):
+
+ - `config_src/drivers`;
+ - `solo_driver/` (example [here](https://github.com/ACCESS-NRI/MOM6/tree/2026.01/config_src/drivers/solo_driver));
+ - [NUOPC](https://github.com/ACCESS-NRI/MOM6/tree/2026.01/config_src/drivers/nuopc_cap) used in OM3 is an example of this.
+
+Other configs are:
+
+ - `config_src/memory` (e.g. [symmetric](https://github.com/ACCESS-NRI/MOM6/tree/2026.01/config_src/memory/dynamic_symmetric), [non-symmetric](https://github.com/ACCESS-NRI/MOM6/tree/2026.01/config_src/memory/dynamic_nonsymmetric), static.)
+ - `config/src_infra` FMS1, FMS2
+ - `config_src/external` BGC, data assimilation, python interface, etc.
+
+Note: `config_src/external` just contains a set of stubs (dummy interfaces) for external codebases that could be used with MOM6. For example there is no actual BGC code in there - that lives in a different repository ([here](https://github.com/ACCESS-NRI/GFDL-generic-tracers)).
+
+The `src` folder has model code and has directories:
+
+ - `core/`
+ - `parameterizations`
+ - `tracer`
+ - `ALE`
+ - `diagnostics`
+ - `user`
+
+Also see `framework/`, `equation_of_state/` etc
+
+We then watched a little of this video ([Overview: MOM6 internals](https://www.youtube.com/watch?v=E8WKrESscc4)) focusing on modules.
+
+Module Format. Here's some examples:
+
+ - [MOM_diagnostics](https://github.com/mom-ocean/MOM6/blob/main/src/diagnostics/MOM_diagnostics.F90);
+ - [MOM_diagnose_MLD](https://github.com/mom-ocean/MOM6/blob/main/src/diagnostics/MOM_diagnose_MLD.F90);
+ - A simple example is the geothermal module ([here](https://github.com/mom-ocean/MOM6/blob/08529ba87ea4ee6403446afc0c8b14f744f79c58/src/parameterizations/vertical/MOM_geothermal.F90)).
+
+Public parts of the interface are the ones that you can call elsewhere (as opposed to private ones that you can't)
+
+https://github.com/mom-ocean/MOM6/blob/08529ba87ea4ee6403446afc0c8b14f744f79c58/src/parameterizations/vertical/MOM_geothermal.F90#L25
+
+
 ## Searching through the MOM parameter docs and other output, e.g. what’s in what file, how to interpret maxCFL, truncations, warnings, errors
-## Overview of MOM6 code structure - 
 ## How to contribute code back to MOM6
 # Season 2
 ## Navier Stokes -> stacked shallow water (adiabatic)