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Copy file name to clipboardexpand all lines: README.md
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}
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```
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To cite a specific version of the package please also cite its [Zenode archive](https://doi.org/10.5281/zenodo.10038575).
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If on top of citing the JOSS paper above, you need to cite a specific version of the package then please cite its corresponding version from the [Zenodo archive](https://zenodo.org/doi/10.5281/zenodo.8403489).
Copy file name to clipboardexpand all lines: docs/src/index.md
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OceanBioME.jl is a fast and flexible ocean biogeochemical modelling environment. It is highly modular and is designed to make it easy to implement and use a variety of biogeochemical and physical models. OceanBioME is built to be coupled with physics models from [Oceananigans.jl](https://github.com/CliMA/Oceananigans.jl) allowing simulations across a wide range of spatial scales ranging from a global hydrostatic free surface model to non-hydrostatic large-eddy simulations. OceanBioME was designed specifically for ocean carbon dioxide removal applications. Notably, it includes active particles which allow individual-based models to be seamlessly coupled with the flow physics, ecosystem models, and carbonate chemistry.
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OceanBioME.jl currently provides a core of several biogeochemical models (Nutrient--Phytoplankton--Zooplankton--Detritus (NPZD) and [LOBSTER](https://doi.org/10.1029/2004JC002588), a medium complexity model, air-sea gas exchange models to provide appropriate top boundary conditions, and sediment models to for the benthic boundary. [PISCES](https://doi.org/10.5194/gmd-8-2465-2015) and other higher complexity models are in our future development plans.
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OceanBioME.jl currently provides a core of several biogeochemical models Nutrient--Phytoplankton--Zooplankton--Detritus (NPZD) and [LOBSTER](https://doi.org/10.1029/2004JC002588), a medium complexity model, air-sea gas exchange models to provide appropriate top boundary conditions, and sediment models to for the benthic boundary. [PISCES](https://doi.org/10.5194/gmd-8-2465-2015) and other higher complexity models are in our future development plans.
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OceanBioME.jl includes a framework for integrating the growth of biological/active Lagrangian particles which move around and can interact with the (Eulerian) tracer fields - for example, consuming nutrients and carbon dioxide while releasing dissolved organic material. A growth model for sugar kelp is currently implemented using active particles, and this model can be used in a variety of dynamical scenarios including free-floating or bottom-attached particles.
|``R_P``|`phytoplankton_redfield`| mmol C / mmol N |
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|``R_O``|`organic_redfield`| mmol C / mmol N |
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|``R_{Chl:N}``|`phytoplankton_chlorophyll_ratio`| mg Chl / mmol N |
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|``\rho_{CaCO_3}``|`organic_carbon_calcate_ratio`| mmol CaCO₃/ mmol C |
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|``R_{O_2}``|`respiraiton_oxygen_nitrogen_ratio`| mmol O / mmol N |
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|``R_{nit}``|`nitrifcation_oxygen_nitrogen_ratio`| mmol O / mmol N |
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|``R_{O_2}``|`respiration_oxygen_nitrogen_ratio`| mmol O / mmol N |
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|``R_{nit}``|`nitrification_oxygen_nitrogen_ratio`| mmol O / mmol N |
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|``f_s``|`slow_sinking_mortality_fraction`| - |
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|``\mu_{DOM}``|`disolved_organic_breakdown_rate`| 1 / s |
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|``\mu_{DOM}``|`dissolved_organic_breakdown_rate`| 1 / s |
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|``\eta``|`zooplankton_calcite_dissolution`| - |
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All default parameter values are given in [Parameters](@ref parameters); and a more thorough explanation of new terms will be included in a publication that is in prep.
Copy file name to clipboardexpand all lines: docs/src/model_implementation.md
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## Model structure
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OceanBioME BGC models are `struct`s of type `ContinuousFormBiogeochemistry`, which is of abstract type `AbstractContinuousFormBiogeochemistry` from Oceananigans. In Oceananigans this describes BGC models which are defined using continuous functions (depending continuously on ``x``, ``y``, and ``z``) rather than discrete functions (depending on ``i``, ``j``, ``k``). This allows the user to implement the BGC model equations without worrying about details of the grid or discretization, and then Oceananigans handles the rest.
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OceanBioME's `ContinuousFormBiogeochemistry` adds a layer on top of this which makes it easy to add [light attenuation models](@ref light), [sediment](@ref sediment), and [biologically active particles](@ref individuals) (or indivdiual-based models). OceanBioME's `ContinuousFormBiogeochemistry` includes parameters in which the types of these components are stored. This means that these model components will automatically be integrated into the BGC model without having to add new methods to call Oceananigans functions.
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OceanBioME's `ContinuousFormBiogeochemistry` adds a layer on top of this which makes it easy to add [light attenuation models](@ref light), [sediment](@ref sediment), and [biologically active particles](@ref individuals) (or individual-based models). OceanBioME's `ContinuousFormBiogeochemistry` includes parameters in which the types of these components are stored. This means that these model components will automatically be integrated into the BGC model without having to add new methods to call Oceananigans functions.
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