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Biogeochemical simulation naming protocol

All simulations from 2017 onwards have the following naming structure:



GBRg     – Model grid with g = approximate grid resolution in kilometres.

Hhhh     – Hydrodynamic model, hhh = model version.

Bbbb     – Biogeochemical model, bbb = model version.

Cccc       – Catchment model, ccc = load specification.

  • fur – Furnas relationships for wet and dry tropics rivers;
  • pre – SOURCE Catchments – Pre-Industrial catchment cover;
  • bas – SOURCE Catchments – Baseline (2012/13) catchment;
  • hyd – best available forcing (2011 – Jun 30, 2014 P2R SOURCE Catchments; Jul 1, 2014 – Oct 30, 2016 – Empirical SOURCE Catchments; Oct 30, 2016 onwards Furnas relationship].
  • q2b – SOURCE catchments (Dec 1, 2010 – Oct 30, 2018 – Empirical SOURCE Catchments; Oct 31, 2018 onwards Furnas relationship].
  • q2p –SOURCE Catchments – Pre-Industrial catchment cover –  Dec 1, 2010 – Oct 31, 2018.

Scenarios undertaken using SOURCE Catchments 2019

  • q3b – P2R SOURCE Catchments with 2019 catchment condition from Dec 1, 2010 – 30/6/2018, Empirical SOURCE  with 2019 catchment condition, Jul 1, 2018 – April 30, 2019
  • q3p – P2R SOURCE Catchments with Pre-Industrial catchment condition from Dec 1, 2010 – 30/6/2018, Empirical SOURCE  with Pre-Industrial catchment , Jul 1, 2018 – April 30, 2019
  • q3R – SOURCE Catchments with 2019 catchment condition (q3b) with anthropogenic loads (q3b – q3p) reduced according to the percentage reductions of DIN, PN, PP and TSS specified in the Reef 2050 Water Quality Improvement Plan (WQIP) 2017-2022 (p54 of
  • q3A – SOURCE Catchments with 2019 catchment condition (q3b), with all D, C and B managed land improved to A management
  • q3B – SOURCE Catchments with 2019 catchment condition (q3b), with all D and C managed land improved to B management
  • q3C – SOURCE Catchments with 2019 catchment condition (q3b), with all D managed land improved to C management
  • q3T  – SOURCE Catchments with 2019 catchment condition (q3b), with Reef Trust Partnership load reductions

Note: Empirical SOURCE  uses monthly-varying concentration generation for each paddock with daily-calculated flows to generate daily-varying loads, and is used after April 30, 2019 at which time the full P2R SOURCE Catchments is unavailable.

Dddd     – Model deployment.

  • nrt – Near Real Time (-2 days, waiting for hydrodynamic forcing);
  • fct – Forecast (+2 days);
  • hnd – Hindcast (set dates);
  • crt – catchment real time (-6 months, waiting for SOURCE Catchments);
  • ran – Reanalysis (hindcast assimilating MODIS ocean colour, implemented 2017)
  • ra2 – Reanalysis (hindcast assimilating MODIS, VIIRS ocean colour, implemented 2019).

Existing configurations:

H1p85 – Hydrodynamic run for SIEF report: contained salinity errors in 2015 – grid contains only 22 rivers.

H2p0 – No known forcing problems. 70 rivers included as boundaries, but only 22 have flows and loads. Fixed a rainfall forcing issue.

B1p0 – This is the original biogeochemical model. The simulations for the SIEF report in Jan 2016, and which have been referred to previously as v926, used this version.

B1p9 – More accurate optical calculations; Normanby – particulate and dissolved loads corrected; Sediment tracer “Dust” added; Oxygen mass conservation part of diagnostics.

B2p0 – Added deep seagrass species, seagrass mortality enhanced by bottom shear stress and nutrient uptake by seagrass leaves; spectral light forcing benthic microalgae; carbon chemistry calculations in sediment and using time-varying atmospheric pCO2; distinguish carbonate and non-carbonate fine sediments; in-line calculation of simulated satellite products; VIIRS satellite comparison; implement ecological processes on boundary cells; dynamic porosity in ecological process calculations; calculation of turbidity using optical model.

B2p1 – Added new coral bleaching processes.

B3p0 – Changes from B2p0:

  • Optical properties of carbonate minerals (absoprtion, scattering and backscattering coefficients) introduced from Lucinda Jetty data set.
  • Spectrally-resolved phytoplankton backscattering.
  • Coral bleaching added using new process (coral_spectral_grow_bleach_epi.c) and new variables (Coral N, P, I reserves, xanthophyll photosynthetic and heat dissipating pigments, oxidised, reduced and inhibited reaction centres, reactive oxygen species), parameter values (ROS_threshold, ) and diagnostics (Rubisco activity, bleaching rate).
  • Coral heterotrophic feeding fixed: reserves from grazed phytoplankton now returned to water column.
  • New diagnostic variables included in optical model: simulated fluorescence, simulated turbidity, simulated normalised fluorescence line height, simulated Secchi depth, downwelling light on z-interfaces, SWR_bot_abs (the PAR weighted bottom absorption calculated by the model), OC4Me – chlorophyll algorithm for MERIS and Sentinel.
  • Optical code now has options of spectral absorption coefficients calculated through HPLC analysis, or via Gaussian approximations (previous version).
  • Separated coral growth and mortality (in coral_spectral_grow_*_epi.c) from dissolution / calcification processes (coral_spectral_carb_epi.c). Added argument to coral_spectral_carb_epi.c to apply Eyre relationship.
  • New process light_spectral_sed.c considers spectrally-resolved microphytobenthos light absorption.
  • Mass balance for oxygen includes nitrate, with stoichiometry changed for photosynthesis / respiration.
  • Seagrass growth: Small fix in partitioning of nitrate / ammonium uptake in seagrass from roots – > put new version in seagrass_spectral_grow_epi.c
  • Quadratic term for seagrass mortality added to seagrass_spectral_mortality_proto_epi.c, but zero value for all but deep seagrass.
  • Remineralisation rate of phosphorus has a separate parameter to that of C and N, requiring 2 new parameters  (r_RD_NtoP, r_DOM_NtoP)
  • New output file (ecology_setup.txt) generated (containing process list implement including options, parameter values and what was previously in spectral.txt) for improved simulation quality assurance.
  • Re-calculation of diagnostic optical properties in postcalc so they are calculated at the output time.
  • Code now Open Source, available at:, with headers improved for readability.
  • EFI now defined based on minerals present – resulting definition output into eco_setup.txt.
  • Code supports outputting solar zenith angle as either a 3D tracer (“Zenith”) or 2D epibenthic variable (“Zenith2D”).
  • New Trichodesmium processes with code updated and bug in density call fix. New process called trichodesmium_spectral_grow_wc.c
  • Introduced new sediment-water diagnostic variable.
  • Rationalisation of grid description for 2D tracers in netcdf output files.

Significant simulations:

GBR4_H1p85_B1p0_Cbas_Dhnd – The simulation run for the 2016 SIEF report that was the first publicly-available long run of the full coupled hydrodynamic – biogeochemical model (formally known as gbr926).

GBR4_H2p0_B2p0_Chyd_Dhnd – Second publicly release simulation (released mid 2017) being used for GBRF resilience and NESP TWQ Hub projects.

GBR4_H2p0_B2p0_Cpre_Dhnd – Identical to GBR4_H2p0_B2p0_Chyd_Dhnd except with Pre-Industrial loads.

GBR4_H2p0_B1p9_Chyd_Dran – First application of BGC data assimilation that is being used for GBR report card 7.

GBR4_H2p0_B3p0_Cq2b_Dhnd – Third publicly released simulation  (released Feb 7, 2019) available on NCI and RECOM.

GBR4_H2p0_B3p0_Cq2p_Dhnd – Identical to  GBR4_H2p0_B3p0_Cq2b_Dhnd except with Pre-Industrial loads.

GBR4_H2p0_B3p0_Cq2b_Dra2 – 2nd application of BGC data assimilation that is being used for GBR report card 8.