WAMSI Westport Cockburn Sound Water Quality Model — v1.8

This repository houses the hydrodynamic-biogeochemical model for Cockburn Sound, a coastal embayment located near Perth, Western Australia.
Explore the online manual »

View results archive · Report Bug · Request Feature

About The Project

In 2022, the Western Australian Marine Science Institution (WAMSI) and Westport commissioned development of an independent hydrodynamic-biogeochemical model for Cockburn Sound, located on the coast of Perth, Western Australia.

The model uses the TUFLOW-FV 3D finite-volume hydrodynamic model and the AED water quality model.

Version 1.8 is the public reference simulation set. It carries one canonical physics configuration — validated against the 1991 SMCWS field campaign and applied uniformly across every simulation — and, for the first time, extends the model back to the 1990s South Metropolitan Coastal Waters Study (SMCWS) era alongside the modern (2012–2024) years.

What changed from 1.7

• Canonical physics (validated on the 1991 hindcast, now in every fvc): stability WL limit 15 m, 3D-cell depth threshold 0.5 m, global bottom roughness 0.03, horizontal viscosity/diffusivity 0.01 (limits 0.01–10), vertical viscosity/diffusivity floors 5.0e-5 / 9.0e-6, bulk latent heat 1.5e-3, shortwave albedo 0.09, diffusivity limiter dt 10 s. (The 1992/1994 hindcasts retain their validated seasonal latent-heat coefficient of 1.4e-3.)
• Bathymetry overrides (B-mesh runs): Success and Minstrel channel depths from the 2025 EIA survey, and the Swan-mouth tidal-choke fix restoring tidal transmission through the Blackwall throat.
• 1990s SMCWS hindcasts added (B010 mesh, HD): Aug 1991, Mar–May 1992, Nov 1993–Dec 1994, with era-correct forcing (BARRA-PH weather, climatology/HYCOM ocean, corrected OBC polygons, Narrows-climatology river salinity, pre-Dawesville Peel-Harvey exchange, 1990s SDOOL flows).
• Vertical layering unified on the geometric-stretch scheme (SEP_zlayer_0p6_0p75_geo_001.csv) in all domain configurations.
• Peel-Harvey exchange now enters via both ocean entrances (Mandurah Channel + Dawesville Cut, 50:50) in all post-1994 simulations; pre-1994 simulations use the Mandurah Channel only (the Cut opened April 1994).
• B010-mesh initial conditions corrected (previously pointed at B009-mesh files).
• Mangles Bay inflow (Lake Richmond / Rockingham main drain, GLM-modelled outflow) enabled in all simulations.
• All outputs now archive under output_archive/1.8.0/.

Built With

Getting Started

This repository contains the version-controlled model configuration. The large boundary-condition forcing store (the environment repo) is not tracked in git — it is referenced by the bc include files through the $ENV_REPO environment variable (TUFLOW-FV ≥2023.1 expands $VAR in control files).

Prerequisites

• An active TUFLOW-FV binary and licence (download from BMT TUFLOW).
• The compatible AED plugin (FV-AED) from UWA-AED.

Cloning and executing the model

1. Clone this repo:

   git clone https://github.com/SEAF-CS/csiem_model_tfvaed_1.8.git

2. Obtain the forcing store and point $ENV_REPO at it:

   export ENV_REPO=/path/to/environment_repo

   Project machines: G:\CSIEM\V1.7\MODEL\csiem_model_tfvaed_1.7\model_components\environment_repo (shared on-prem mirror). External users: fetch the bc_repo from the Pawsey S3 project store (see csiem_model_tools).
3. Run a simulation from its model_runs folder with the provided launcher (sets $ENV_REPO, CPU/GPU options and the AED library):

   cd model_runs/HD
   ./run_tuflowfv_vm.sh csiem_B010_19910720_19910831.fvc

Repository structure

Folder	Content
model_components/includes	model configuration include files (domain, bc, ic, turbulence, wq, output)
model_components/gis_repo	meshes, layers, bathymetry overrides, benthic zones, projections
model_components/environment_repo	(untracked) large forcing files, referenced via $ENV_REPO
model_modifier_library	licensed-industry intakes/discharges and scenario modifiers
model_runs/HD · WQ · ECO · ST	main simulation control files + run launcher
output_archive	(untracked) simulation outputs, versioned per release (1.8.0/…)

The 1.8 reference simulation set

Period	Mesh	HD	WQ	ECO	Notes
Jul–Aug 1991	B010	✓			SMCWS winter hindcast (validated)
Feb–May 1992	B010	✓			SMCWS autumn hindcast
Nov 1993 – Dec 1994	B010	✓			SMCWS/HYCOM hindcast, pre/post Dawesville
2012–13 … 2023–24	A002	✓	✓		seven modern years
2012–13, 2020–24	B010	✓	✓		modern years on the B mesh
Nov 2022 – Apr 2024	A002/B010			✓	full ecosystem configuration

File naming: csiem_{mesh}_{start}_{end}[_WQ|_ECO].fvc; includes follow {type}_{source}_{period}.fvc.

Analysis

Model inputs and outputs are processed with the csiem-marvl validation toolbox. Please contact the developers for further information.

Contributing

Contributions from the user and developer community are welcome and greatly appreciated! Fork the repo and open a pull request, or open an issue with the tag "enhancement".

Contact

Matt Hipsey - matt.hipsey@uwa.edu.au

Project link: CSIEM online manual

Acknowledgments

• Funding from the WAMSI Westport Research Program
• Gayan Gunaratne, Louise Bruce and the BMT software team
• Brendan Busch & Peisheng Huang from the AED research group
• Oceanographic models from Ivica Janeković & Chari Pattiaratchi from the UWA Oceans Institute

(back to top)