WOMBAT-full model output from experiments investigating the effect of partial oxidation by heterotrophic bacteria at the Southern Ocean Timeseries Site.

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WOMBAT-full 1D SOTS partial oxidation experiments This repository contains the model configuration, output, restart files, executable, and initial conditions for a set of 1D WOMBAT-full experiments at the Southern Ocean Time Series (SOTS) site. The experiments investigate how partial oxidation of organic carbon by free-living heterotrophic bacteria affects dissolved organic carbon cycling and air–sea CO2 exchange. Experiments The repository contains **21 experiments**. Experiment names follow the general form: ```textom3_mom6_1D-SOTSfull_4MF_highNPP_paXpX_laXpXX``` The `pa` and `la` terms describe the degree of partial oxidation by two bacterial pathways. `pa` — particle-associated bacterial pathway `pa` controls the fate of particulate organic carbon (POC) processed by an implicit particle-associated bacterial pathway: * `pa0p0`: POC is remineralised directly to CO2.* `pa1p0`: POC is converted to dissolved organic carbon (DOC). The `pa0p0` experiment therefore represents the case without partial oxidation through this pathway. `la` — explicit sharing bacterial pathway For the `pa1p0` experiments, `la` controls the fraction of consumed DOC that is partially oxidised and transferred to an oxidised DOC pool by the explicit sharing bacterial community rather than being completely oxidised to CO2. For example: ```textla0p0 = 0% transferred to oxidised DOCla0p05 = 5% transferred to oxidised DOCla0p50 = 50% transferred to oxidised DOCla0p95 = 95% transferred to oxidised DOC``` The repository contains a sweep from `la0p0` to `la0p95` in increments of 0.05, together with the `pa0p0` reference experiment. The 21 experiments are therefore: ```textpa0p0 pa1p0_la0p0pa1p0_la0p05pa1p0_la0p10pa1p0_la0p15pa1p0_la0p20pa1p0_la0p25pa1p0_la0p30pa1p0_la0p35pa1p0_la0p40pa1p0_la0p45pa1p0_la0p50pa1p0_la0p55pa1p0_la0p60pa1p0_la0p65pa1p0_la0p70pa1p0_la0p75pa1p0_la0p80pa1p0_la0p85pa1p0_la0p90pa1p0_la0p95``` Experiment structure Each experiment contains model output and restart directories for ten successive model years, numbered from 0 to 9: ```textexperiment/├── output000/├── output001/├── ...├── output009/├── restart000/├── restart001/├── ...└── restart009/``` Output directories The `output00X` directories contain the model output from each year of the simulation. They also contain the configuration files used for that model run, including: * `field_table` — contains WOMBAT model parameters and configuration values used by the experiment.* `config.yaml` — Payu experiment configuration describing the model components, component versions, executable, input data, runtime configuration, and other information required to run the experiment. The experiments were managed using **Payu**, a workflow management tool for running numerical models on high-performance computing systems. See the official Payu documentation for information on the experiment structure and `config.yaml` configuration. https://forum.access-hive.org.au/t/payu-a-workflow-manager-for-some-access-models/1098. Restart directories The corresponding `restart00X` directories contain the model restart state produced at the end of each model year and used to initialise the subsequent year. Model executable and initial conditions The repository also contains: ```textaccess-om3-MOM6_full``` The compiled model executable used for these experiments. ```textwombatfull_ic.nc``` The WOMBAT-full biogeochemical initial-condition restart file used to initialise the experiments. Reproducibility The archived `field_table` and `config.yaml` files provide the parameterisation and model configuration associated with each individual model year. Together with the supplied model executable and `wombatfull_ic.nc` initial conditions, these files document the configuration used to produce the archived simulations. If you wish to run this model, it can be done on the Australian National Computational Infrastructure (NCI) Gadi HPC system by following the instructions at https://github.com/ACCESS-Community-Hub/om3-mom6-single-column.

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