4 CSIEM : model

4.1 Overview

This chapter describes the technical specification of the numerical model component of the CSIEM platform. This includes the coupled hydrodynamic-biogeochemical modelling framework, and a high level overview ofthe simulation domain and mesh design, the suite of boundary conditions that drive the model, the approach to benthic zonation, and the repository structure used for version control and collaborative model development. Together, these elements define the core model architecture that underpins all simulations presented in subsequent chapters.

Whereas earlier chapters have introduced the broader context of Cockburn Sound environmental management (Chapter 1), the overall organisational structure of the CSIEM platform (Chapter 2), the data integration framework (Chapter 3), and the visualisation and analytics toolkit (Chapter 5), the focus here is to describe the model configuration and its modular nature – how the model is constructed, what inputs it requires, and how the model files are organised and maintained. More detailed scientific descriptions of the individual model components, their calibration, and performance assessments are provided in Chapters 7–17, which cover ocean climatology, hydrodynamics, catchment inflows, sediment biogeochemistry, water quality, light climate, and seagrass habitat modelling.

4.2 Water quality model : TUFLOW-FV – AED

The base model used in the CSIEM platform is the finite volume hydrodynamic model TUFLOW-FV, developed by BMT Global Pty Ltd (BMTWBM, 2023). The model adopts a flexible-mesh and accounts for variations in water level, salinity, temperature, and density in response to tides, inflows and surface thermodynamics. At the ocean-side (western) boundary the model is driven by conditions predicted by the regional ROMS model (see Section 8.4). At the water surface, the model is driven by spatially-variable outputs from various weather data-sets (see Section 7.2).

The model was selected as it includes enhanced useability features including integration with geospatial data formats and QGIS, optimisation for operation on GPUs, multiple turbulence closure and numerical schemes, and ability for including a complex array of industry-relevant boundary conditions (e.g., for resolving aspects such as dredging, shipping, discharges and coastal infrastructure). The model has been previously validated in a range of coastal areas around Australia, including in Cockburn Sound during assessment of the Perth Seawater Desalination Plant (PSDP) infrastructure. The hydrodynamic component of the model is termed “HD” and readers can refer to Chapter 9 for a detailed description of the model application in Cockburn Sound.

The TUFLOW-FV model additionally includes a “Sediment Transport Module” (termed ST), which is used to simulate the physical controls on sediment movement within the domain. This module has been developed specifically by BMT Global Pty Ltd for assessment of port options and dredge managerment applications within Cockburn Sound and Owen Anchorage, and documentation for this aspect is forthcoming.

To simulate the water quality and benthic habitat within Cockburn Sound and surrounding waters, the AED water quality model is used and is dynamically (two-way) linked with TUFLOW-FV. AED is a community-driven library of modules and algorithms for simulation of “aquatic eco-dynamics” - water quality, aquatic biogeochemistry, biotic habitat and aquatic ecosystem dynamics, developed by the Centre for Water and Spatial Science at UWA (Hipsey et al., 2022). Each module has options for resolving key aquatic processes sourced from a wide variety of scientific literature, making the library one of the most advanced available to aquatic ecosystem modellers. The model can be run in a simple and advanced modes, termed “WQ” and “ECO”, respectively, which are described further below.

4.2.1 What does the model simulate?

Depending on the selection of the HD, ST, WQ, or ECO model configuration, a simulation will include a range of physical, chemical and biological variables. A summary of the variables that are simulated by the coupled platform is presented in Table 4.1, and the specifics of these are described in more detail in subsequent chapters (as linked to from the table).

Table 4.1: Summary of CSIEM simulated (state) variables (current as of v1.7).

Abbreviation	Unit	Common Name	Process Description	Notes
Physical variables
\[U, V, W\]	\[\small{m/s}\]	Current velocity	Velocities simulated by the hydrodynamic model, subject to boundary forcing	Chapter 9 HD,ST,WQ,ECO
\[T\]	\[\small{^{\circ}C}\]	Temperature	Temperature dynamics subject to surface heating and cooling	Chapter 9 HD,ST,WQ,ECO
\[S\]	\[\small{psu}\]	Salinity	Salinity dynamics subject to inputs, rainfall dilution and evapo-concentration	Chapter 9 HD,ST,WQ,ECO
\[EC, \rho\]	\[\small{\mu S\: cm^{-1} ; kg\:m^{-3}}\]	Electrical conductivity; Density	Derived from salinity and temperature variables	Chapter 9 HD,ST,WQ,ECO
Light variables
\[I_{PAR}\]	\[\small{\mu E\: m^{-2}\: s^{-1}}\]	PAR light intensity	Incident light attenuated as a function of depth	Chapter 15 WQ,ECO
\[K_d\]	\[\small{m^{-1}}\]	PAR extinction coefficient	Extinction coefficient based on chl-a, organic matter and suspended solids	Chapter 15 WQ,ECO
\[E_\lambda\]	\[\small{W\: m^{-2}}\]	Spectral light energy	Light spectra: incoming surface light and direct/diffuse below-water profiles	Chapter 15 ECO
\[\kappa_\lambda\]	\[\small{m^{-1}}\]	Bandwidth-specific attenuation	Wavelength-specific attenuation through the water column	Chapter 15 ECO
Biogeochemical variables
\[DO\]	\[\small{mmol\: O_2\: m^{-3}}\]	Dissolved oxygen	Impacted by photosynthesis, organic decomposition, nitrification, surface exchange, and sediment oxygen demand	Chapter 13 WQ,ECO
\[RSi\]	\[\small{mmol\: Si\: m^{-3}}\]	Reactive silica	Algal uptake, sediment flux	Chapter 13 ECO
\[FRP\]	\[\small{mmol\: P\: m^{-3}}\]	Filterable reactive phosphorus	Algal uptake, organic mineralisation, sediment flux	Chapter 13 WQ,ECO
\[PIP\]	\[\small{mmol\: P\: m^{-3}}\]	Particulate inorganic phosphorus	Adsorption/desorption of/to free FRP	Chapter 13 WQ,ECO
\[NH_4^+\]	\[\small{mmol\: N\: m^{-3}}\]	Ammonium	Algal uptake, nitrification, organic mineralisation, sediment flux	Chapter 13 WQ,ECO
\[NO_3^-\]	\[\small{mmol\: N\: m^{-3}}\]	Nitrate	Algal uptake, nitrification, denitrification, sediment flux	Chapter 13 WQ,ECO
\[DOC\]	\[\small{mmol\: C\: m^{-3}}\]	Dissolved organic carbon	Mineralisation, algal mortality/excretion, photolysis	Chapter 13 WQ,ECO
\[DON\]	\[\small{mmol\: N\: m^{-3}}\]	Dissolved organic nitrogen	Mineralisation, algal mortality/excretion, photolysis	Chapter 13 WQ,ECO
\[DOP\]	\[\small{mmol\: P\: m^{-3}}\]	Dissolved organic phosphorus	Mineralisation, algal mortality/excretion, photolysis	Chapter 13 WQ,ECO
\[POC\]	\[\small{mmol\: C\: m^{-3}}\]	Particulate organic carbon	Breakdown, settling, algal mortality/excretion, resuspension	Chapter 13 WQ,ECO
\[PON\]	\[\small{mmol\: N\: m^{-3}}\]	Particulate organic nitrogen	Breakdown, settling, algal mortality/excretion, resuspension	Chapter 13 WQ,ECO
\[POP\]	\[\small{mmol\: P\: m^{-3}}\]	Particulate organic phosphorus	Breakdown, settling, algal mortality/excretion, resuspension	Chapter 13 WQ,ECO
\[TP\]	\[\small{mmol\: P\: m^{-3}}\]	Total phosphorus	Sum of all phosphorus state variables	Chapter 13 WQ,ECO
\[TN\]	\[\small{mmol\: N\: m^{-3}}\]	Total nitrogen	Sum of all nitrogen state variables	Chapter 13 WQ,ECO
\[CANDI\]	\[\small{various}\]	Sediment concentrations (various)	Numerous porewater and particulate consituents associated with sediment biogeochemistry	Chapter 12 ECO
Planktonic variables
\[PHY_{mixed}\]	\[\small{mmol\: C\: m^{-3}}\]	Mixed phytoplankton	Photosynthesis, nutrient uptake, respiration, sedimentation	Chapter 13 WQ,ECO
\[PHY_{pico}\]	\[\small{mmol\: C\: m^{-3}}\]	Picophytoplankton	Photosynthesis, nutrient uptake, respiration, sedimentation	Chapter 13 WQ,ECO
\[PHY_{diatom}\]	\[\small{mmol\: C\: m^{-3}}\]	Diatoms	Photosynthesis, nutrient uptake, respiration, sedimentation	Chapter 13 WQ,ECO
\[PHY_{dino}\]	\[\small{mmol\: C\: m^{-3}}\]	Dinoflagellates	Photosynthesis, nutrient uptake, respiration, sedimentation (ECO includes mixotrophy)	Chapter 13 WQ,ECO
\[TCHLA\]	\[\small{\mu g\: L^{-1}}\]	Total chlorophyll-a	Sum of planktonic algal groups, converted to chlorophyll-a	Chapter 13 WQ,ECO
\[ZOO_{grazer}\]	\[\small{mmol\: C\: m^{-3}}\]	Grazing zooplankton (e.g. cladocerans)	Ingestion, nutrient excretion, respiration, egestion	Chapter 13 ECO
\[ZOO_{predator}\]	\[\small{mmol\: C\: m^{-3}}\]	Predatory zooplankton (e.g. copepods)	Ingestion, nutrient excretion, respiration, egestion	Chapter 13 ECO
Sediment & Turbidity
\[SED_{1:N}\]	\[\small{g\: SS\: m^{-3}}\]	Suspended sediment	Sedimentation, resuspension, cohesion, bedload	Refer to BMT (2026)
\[SS_{1:2}\]	\[\small{g\: SS\: m^{-3}}\]	Suspended sediment	Sedimentation, resuspension	Chapter 13 WQ,ECO
\[Turbidity\]	\[\small{NTU}\]	Turbidity	Derived from particulate components in suspension (excluding ST SED components)	Chapter 13 WQ,ECO
Benthic & Habitat variables
\[MPB\]	\[\small{mmol\: C\: m^{-2}}\]	Benthic microalgae (MPB)	Benthic photosynthesis and respiration, resuspension, burial	Chapter 13; Chapter 16 WQ,ECO
\[MAC_A\]	\[\small{mmol\: C\: m^{-2}}\]	Above-ground seagrass biomass	Benthic photosynthesis, nutrient uptake, respiration, translocation	Chapter 16 WQ,ECO
\[MAC_B\]	\[\small{mmol\: C\: m^{-2}}\]	Below-ground seagrass biomass	Root growth, respiration, translocation	Chapter 16 WQ,ECO
\[MAC_F\]	\[\small{mmol\: C\: m^{-2}}\]	Seagrass seed biomass	Fruit development & release	Chapter 16 WQ,ECO
\[HSI\]	\[\small{-}\]	Posidonia seagrass habitat suitability index	Composite index based on light, temperature, substrate, wave stress, current stress	Chapter 17 WQ,ECO
\[BIV_{suspfeeder}\]	\[\small{mmol\: C\: m^{-2}}\]	Benthic invertebrate biomass	Filtration and ingestion, excretion, egestion, respiration, mortality	Chapter 16 ECO

4.2.2 WQ vs ECO?

The base TUFLOW-FV – AED model configurations simulate the full suite of state variables listed in Table 4.1, but the level of detail in resolving the biogeochemical and ecological compnentns is seprated into a core and advanced configuration, termed “WQ” and “ECO”, respectively. This is because the data and computational demands of the full ecosystem model are higher than the water quality model, and therefore in some cases users may wish to run the WQ model for a longer period or more scenarios, and then use the ECO model for a subset of simulations. The WQ model includes a simplified representation of the ecosystem, with a focus on key water quality variables and their interactions, whereas the ECO model includes a more detailed representation of the ecosystem, including more functional groups of biota and their interactions.

The choice of simulation type depends on the research question being addressed, and users can choose to run either or both types of simulations as needed. Specifically:

• WQ : designed to resolve nutirents, turbidity, chlorophyll-a and seagrass dynamics;
• ECO : designed to resolve the above, plus a more detailed representation of the food web and trophic interactions, including more advanced phytoplankton ecophysiology, zooplankton groups, benthic invertebrates, and a spectrally-resolved light climate model. In subsequent chapters, several bespoke modifications for Cockburn Sound that were made to AED modules are outlined.

Users select either a WQ or ECO configuration rather than both. ECO includes all WQ variables, plus additional components and functionality.

4.3 Model simulation domain

The geographical extent of the CSIEM domain is centred around Cockburn Sound, extending from Mandurah at the south to Quinns Rocks at the north (32.677°S – 31.669°S), and from outer Rottnest Island at the west to Narrows Bridge at the east (115.323°E - 115.858°E) (Figure 4.1). The model adopted a flexible-mesh (finite-volume) approach, in which the mesh consists of triangular and quadrilateral elements of different sizes that are suited to simulating areas of complex morphometry, with the model resolution generally increases from the offshore areas to the nearshore areas.

The model domain bathymetry was derived from a 10m DEM product and a range of other data sources (Gunaratne et al., 2023). The vertical mesh discretization adopted a hybrid σ-z coordinate allowing multiple surface Lagrangian layers to respond to tidal elevation changes. The layer thickness was 0.5 m at depths of 3.0–4.0 m, 1.0 m at depths of 4.0-23.0 m, that gradually increased to 50 m in deeper water, and then four uniformly distributed sigma layers were added above the fixed thickness layers.

There are three “base” mesh options (namely coarse, optimised, and fine resolutions) available to support different research and management needs, plus a fourth “WEM” that has been developed for specific application to study the post-2030 Westport coastal development (follow this link for futher information).

The mesh structures can be seen in Figure 4.1. All mesh configurations are designed so that all CSIEM simulations share the same boundary conditions, when modellers use the MARVL platform for visualisations and analysis of results (Chapter 5), then plotting and assessment works in an identical way regardless of the chosen mesh. This is an advanced feature of CSIEM modelling platform in that users can choose a mesh option that is suitable to their needs depending on the resolution and run time requirements, where different meshes can be used in different stages of model development. Simulations on different mesh resolutions have also been compared and benchmarked against each other in terms of computational efficiency and accuracy.

Figure 4.1: Plan-view of the three base CSIEM model meshes around the Cockburn Sound region, showing the B (optimized), C (fine) options, and A (coarse) mesh options.

4.4 Boundary conditions

Regardless of the model mesh option that is chosen, the CSIEM system manages several standard boundary conditions to allow the model to be forced by tidal, meteorological and inflow information, which is brought together from various data sources (Figure 4.2).

The CSIEM boundary conditions include:

• Meteorology: Meteorological conditions are collected from a range of sources. For the years before 2019, the spatially resolved Bureau of Meteorology Atmospheric High-Resolution Regional Reanalysis for Australia (BARRA-PH) climate product is used. Beyond 2019, users can choose to use results from either the high-resolution Weather Research and Forecasting (WRF) model setup that has been developed, or the coarser scale BARRA-C2 is also available (see Chapter 7).

• Wave conditions: Set on the surface of model domain, the wave conditions (significant wave heights, periods, directions) are specified based on the integration of the WWMSP WWM outputs, or BMT’s SWAN outputs, as outlined in Chapter 7.

• Ocean physical conditions: Set on the ocean side, an open boundary is specified based on the integration with WWMSP ROMS modelling outputs. Water level, velocity, water temperature and salinity are specified along the boundary extent.

• Ocean biogeochemical conditions: In addition to the variables needed for CSIEM hydrodynamic predictions, numerous water quality variables are specified using a ‘monthly climatology’ approach that is described in detail in Chapter 8.

• Swan-Canning and Peel-Harvey inflows: Inflows to the CSIEM model domain from the local catchment via Swan-Canning River and Peel-Harvey Estuary was set based on available flow data from Water Information Reporting (WIR) portal (https://wir.water.wa.gov.au/Pages/Water-Information-Reporting.aspx). The nutrient boundary condition inputs are extrapolated based on field measurements at the nearest sites to the model boundaries and described in detail in Chapter 10.

• Groundwater inputs: At the coastal interface between Kwinana and Cockburn Sound, groundwater fluxes and their associated nutrient loads are specified based on the integration with groundwater model outputs. More details of linkage between the groundwater inputs and CSIEM are provided in Chapter 11.

• Wastewater treatment plants (WWTPs) inputs: The discharge rates of the WWTPs and their water quality were obtained from the National Outfall Database (https://nod.org.au/), which included data of Alkimos, Beenyup, East Rockingham, Point Peron, Subiaco, and Woodman Point from Jan/2015 at monthly intervals. Outside the reporting period, mean values of water quality in the corresponding months were used.

• Industrial operational discharges and intakes: these inputs were set according to the BMT development (Gunaratne et al., 2023) assuming a constant rate and water quality for each input.

Figure 4.2: Overview of the CSIEM model integration ecosystem, depicting the links of the main hydrodynamic-water quality with other dependent model and data products that are required to run an integrated simulation. Down the list represents disicplinary integration and left to right represents spatio-temporal down-scaling.

4.5 Benthic (bottom) zonation

The CSIEM platform has been designed to accommodate horizontal variation in benthic substrates. This is needed to be able to resolve:

• the effect of bottom “roughness” on flow dynamics
• the variation of sediment physical properties, as relevant to sediment transport dynamics
• variability in the dynamics of sediment biogeochemical processes, and
• the dynamics of bottom biotic communities, and their associated feedbacks to water column properties.

Bottom properties are configured via setting of a) material zones and b) relevant benthic or sediment properties. This is done via loading shapefiles, and/or cell-specific properties into the model configuration.

Refer to Appendix B for an overview of the data sources and approach to setup of benthic areas within the CSIEM platform.

4.6 Model repository and version management

4.6.1 csiem-model repository

The organisation of the CSIEM model system is via a set of version-controlled, cloud-based repositories managed under the SEAF-CS GitHub organisation. The top-level csiem-model repository links to specific model simulation repositories using the Git sub-module feature. Each model is a standalone version-controlled repository that can be cloned in isolation, or the entire compatible model set can be cloned at key version/release points via the high-level csiem-model repository. The linked model repositories include:

• csiem_model_tfvaed_1.7: the current generation of the TUFLOW-FV – AED hydrodynamic-biogeochemical model;
• csiem_model_tfvaed_2.0: the next-generation model configuration under development;
• csiem_model_ecopath_1.0: the EcoPath food-web and trophic pathways model;
• csiem_model_candi_1.0: the CANDI-AED sediment biogeochemistry model;
• csiem_model_wrf_1.0: the WRF weather model configuration for Perth;
• csiem_model_tools: utility scripts for boundary condition processing, model setup and plotting.

Major “generations” of model setup are each stored as a separate repository with a version number suffix, and each maintains its own version control and release history. New models can be added to the collection as they are developed.

In addition to the model repositories, the separately managed environment_repo (also referred to as bc_repo in earlier versions) contains boundary condition files spanning multiple decades. Due to the large volume of data (~1 Tb for the period 1990–2024), these files are not stored on GitHub but are archived on the Pawsey Acacia S3 server and the SEAF Azure platform, and are accessible via fetch scripts provided in csiem_model_tools.

Beyond the models developed within the WAMSI Westport Research program, there is also a range of supporting environmental models – including meteorology, wave and hydrodynamic products – that are available and able to be used as boundary conditions or reference simulations for Cockburn Sound. These environmental models are outlined in Table 4.2.

Table 4.2: Summary of existing environmental models for Westport.

Model	Model Description	Agency / Organisation	Agency ID	Program	Program Code	Start	End	Domain Extent	Storage Location	Status
Meteorology
WRF	South-western Australia Downscaled Weather Model	Murdoch University	MU	SW Climate	SWWA-WRF	1970	2020	SWWA	Pawsey	Completed
WRF Perth Coast	Perth Coast Downscaled Weather Model	Western Australian Marine Science Institution	WAMSI	WAMSI Theme 1	WRF-PERTH	2018	2024	Perth Coast	Pawsey/SEAF	Completed
BARRA	BARRA Reanalysis	Bureau of Meteorology	BOM	BARRA-PR	BARRA-PR	1990	2019	Perth	NCI	Completed
Wave
SWAN	Cockburn Sound Breakwater Wave Model	BMT	BMT	Westport Breakwater Wave Assessment	W-BW	2011	2021	Cockburn Sound	BMT	Completed
WWM	Cockburn Sound Wave Model	Western Australian Marine Science Institution	WAMSI	WAMSI Westport Marine Science Program	WWMSP5.2	2011	2021	Cockburn Sound	Pawsey	Ongoing
Hydrodynamics
ROMS	WA Regional Ocean Model	Western Australian Marine Science Institution	WAMSI	WAMSI Westport Marine Science Program	WWMSP5.1	2000	2022.5	WA	Pawsey	Completed
TFV-AED	PSDP2 Environmental Assessment Model	BMT	BMT	PSDP2	PSDP2	2005	2015	Cockburn Sound	BMT	Completed
Hydrodynamics-Biogeochemistry
TFV-AED	Swan-Canning Esturaine Response Model	University of Western Australia	UWA	SCCM-SCERM	SCERM	2007	2020	Swan-Canning	UWA	Completed
TFV-AED	Cockburn Sound Integrated Ecosystem Model	Western Australian Marine Science Institution	WAMSI	WAMSI Westport Marine Science Program	WWMSP1.2	2010	2021	Cockburn Sound	Pawsey	Ongoing
Ecology
EcoPath	Cockburn Sound Food Web Model	Western Australian Marine Science Institution	WAMSI	WAMSI Westport Marine Science Program	WWMSP1.3	TBC	TBC	Cockburn Sound	Pawsey	Ongoing

4.6.2 CSIEM TUFLOW-FV-AED model file organisation

The main 3D hydrodynamic-biogeochemical simulation configuration files are stored in the csiem_model_tfvaed repositories. The current version is csiem_model_tfvaed_1.7. This repository contains a carefully structured folder tree with the input files needed for a TUFLOW-FV – AED model simulation. Note that the environment_repo (boundary condition files) and model outputs are not stored in this repository; they are separately archived on the Pawsey Acacia server or the SEAF Azure platform (see also Hipsey et al., 2025).

The repository is assembled around the following structure:

csiem_model_tfvaed_1.7/
|
|-- model_components/
|   |-- includes/                   # Model configuration files
|   |   |-- bc/                     # Boundary condition includes
|   |   |-- ic/                     # Initial condition includes
|   |   |-- domain/                 # Domain configuration
|   |   |-- turbulence/             # Turbulence parameters
|   |   |-- roughness/              # Roughness settings
|   |   |-- wq/                     # Water quality configuration
|   |   |-- wq-eco/                 # Water quality-ecosystem coupling
|   |   +-- output/                 # Output definitions
|   |
|   +-- gis_repo/                   # GIS files for model setup
|       |-- 1_domain/               # Mesh and bathymetry files
|       |-- 2_benthic/              # Benthic substrate maps
|       |-- 3_output/               # Output extraction points
|       +-- 4_gw/                   # Groundwater zone definitions
|
|-- model_runs/                     # Main simulation configurations (.fvc)
|   |-- HD/                         # Hydrodynamic simulations
|   |-- WQ/                         # Water quality simulations
|   |-- ST/                         # Sediment transport simulations
|   +-- ECO/                        # Ecosystem simulations
|
|-- model_modifier_library/         # Scenario modifiers for human activities
|   |-- discharges/
|   |-- dredging/
|   |-- intakes/
|   |-- shipping/
|   +-- modifier_catalogue.xlsx     # Catalogue of available modifiers
|
+-- environment_repo/  (external, on Pawsey S3)
    |-- 1_ocean/                    # ROMS-derived ocean boundaries
    |-- 2_weather/                  # Meteorological forcing (BARRA/WRF)
    |-- 3_waves/                    # Wave forcing (WWM/SWAN)
    |-- 4_sce/                      # Swan-Canning Estuary inflows
    |-- 5_phe/                      # Peel-Harvey Estuary inflows
    +-- 6_gw/                       # Groundwater inputs (SGD by zone)

The model_components/ directory contains all modular configuration and geospatial files required by simulations. The model_runs/ directory holds the main model configuration files (.fvc files) for each simulation type. The model_modifier_library/ houses configuration “modifiers” that represent specific human activities or scenarios that can be applied on top of the base environmental model.

The environment_repo (boundary condition files) is managed separately due to its large size (~1 Tb for 1990–2024), and is stored on Pawsey S3 storage rather than in the GitHub repository. It is organised with a standard file naming convention, with files generally grouped by year.

4.6.3 Simulation naming conventions

Model configuration files follow standardised naming conventions that encode the model generation, mesh resolution, simulation period, and simulation type. The main configuration file naming convention is:

csiem_{model generation ID}_{mesh option}_{model period}_{simulation type}.fvc

For example, the file csiem_v1_B009_20130101_20131231_WQ.fvc specifies a Generation 1 model on the B009 (optimised) mesh, covering the year 2013, configured for a coupled water quality simulation. The simulation type codes are:

• WQ: coupled TUFLOW-FV – AED water quality simulation;
• HD: TUFLOW-FV hydrodynamic-only simulation;
• ST: TUFLOW-FV sediment transport simulation;
• ECO: ecosystem simulation.

Include files referenced within the main configuration adopt their own conventions depending on boundary type. For example, meteorological boundary files follow the pattern met_{data source}_{domain}_{data period}.fvc, and initial condition files follow initial_conditions_{model version}.fvc.

Users tailor their simulation by engaging specific “include” files, in the appropriate sequence, within the main model configuration file. The model requires an active TUFLOW-FV binary and license with a pre-compiled AED plugin. The current model is built with:

• TUFLOW-FV: Build version 2025.2.1
• AED: Build version 2.3.6

TUFLOW-FV can be downloaded from the BMT TUFLOW website, and the compatible AED plugin from the UWA AED website. Input and model output files can be processed using the csiem-marvl repository, which includes supporting scripts for model assessment, reporting and visualisation.

4.6.4 Accessing model results

Model runs of the “WQ” and “ECO” types are run for select years and archived for downstream analyses. The outputs are organised by model generation, mesh option, simulation period, and simulation type, following the same naming conventions as the input configuration files. Refer to Appendix D for a list of available model outputs. Contact the WAMSI SEAF team for access to the model outputs.

4.7 Summary

The CSIEM platform provides a flexible simulation framework built around the coupled TUFLOW-FV – AED modelling system. Users can select from four mesh resolutions and domain configurations (coarse, optimised, fine, and the Westport-specific WEM mesh) depending on the spatial detail and computational budget required for their application. Four simulation templates are available — hydrodynamic-only (HD), sediment transport (ST), water quality (WQ), and the full ecosystem model (ECO) — allowing the level of biogeochemical and ecological complexity to be matched to the research question. All configurations share a common set of modular boundary conditions and a standardised repository structure, ensuring consistency and reproducibility across simulations. Pre-computed model results for select years are archived and accessible for downstream analysis via the MARVL platform, while custom simulations can be configured by selecting the desired mesh, simulation type, and time period from the available options.