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Merge pull request #19 from PALEOtoolkit/ocean_chemistry
Move Xiyuan's ocean chemistry example to a new folder
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| solvers | ||
| error_examples | ||
| CPU | ||
| ocean_chemistry | ||
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| # Ocean chemistry | ||
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| These examples illustrate how to implement: | ||
| - a minimal model of the marine carbonate system | ||
| - air-sea exchange of CO2 between ocean and atmosphere Domains | ||
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| See `PALEOmodel` [documentation](https://paleotoolkit.github.io/PALEOmodel.jl/) for more information on analysing model output. | ||
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| ## Example 1 Minimal Alk-pH model | ||
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| Generalizing the Reaction to establish a minimal Alk-pH model. Math equations are from Richard E. Zeebe's book(2001). | ||
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| ### Additional code files | ||
| The Reaction code (file `examples/ocean_chemistry/reactions_Alk_pH.jl`) now produces calculation of different carbonic acid `HCO3_conc`, `CO3_conc`, `CO2_aq_conc`, and coeval concentrations change of `BOH4_conc`, `H_conc`, `OH_conc`, `DIC_conc` and `TAlk_conc`: | ||
| ```@eval | ||
| str = read("../../../../examples/ocean_chemistry/reactions_Alk_pH.jl", String) | ||
| str = """```julia | ||
| $str | ||
| ```""" | ||
| import Markdown | ||
| Markdown.parse(str) | ||
| ``` | ||
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| ### yaml configuration file | ||
| The model configuration (file `examples/ocean_chemistry/config_ex1.yaml`) contains two Reservoirs `DIC`, `TAlk`. | ||
| A `ReactionFluxPerturb` from the PALEOboxes.jl reaction catalog is used to add a constant TAlk flux. | ||
| ```@eval | ||
| str = read("../../../../examples/ocean_chemistry/config_ex1.yaml", String) | ||
| str = """```julia | ||
| $str | ||
| ```""" | ||
| import Markdown | ||
| Markdown.parse(str) | ||
| ``` | ||
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| ### Run script | ||
| The script to run the model (file `examples/ocean_chemistry/run_ex1.jl`) contains: | ||
| ```@eval | ||
| str = read("../../../../examples/ocean_chemistry/run_ex1.jl", String) | ||
| str = """```julia | ||
| $str | ||
| ```""" | ||
| import Markdown | ||
| Markdown.parse(str) | ||
| ``` | ||
| and produces output showing the change, if `TAlk_conc` increase, how the carbonic acid and pH change in ocean: | ||
| ```@example ex1 | ||
| include("../../../../examples/ocean_chemistry/run_ex1.jl") # hide | ||
| plot(paleorun.output, ["ocean.TAlk_conc", "ocean.DIC_conc"], (cell=1,); ylabel="TAlk, DIC conc (mol m-3)") # hide | ||
| savefig("ex1_plot1.svg"); nothing # hide | ||
| plot(paleorun.output, "ocean.pH", (cell=1,)) # hide | ||
| savefig("ex1_plot2.svg"); nothing # hide | ||
| plot(paleorun.output, ["ocean.DIC_conc", "ocean.HCO3_conc", "ocean.CO3_conc", "ocean.CO2_aq_conc"], (cell=1,); ylabel="DIC species (mol m-3)") # hide | ||
| savefig("ex1_plot3.svg"); nothing # hide | ||
| ``` | ||
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| ### Displaying model structure and variables | ||
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| All metadata for model variables can be displayed with `PB.show_variables`: | ||
| ```@example ex1 | ||
| show(PB.show_variables(model), allcols=true, allrows=true) # display in REPL | ||
| # vscodedisplay(PB.show_variables(model)) # more convenient when using VS code | ||
| ``` | ||
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| ## Example 2 Air-sea exchange | ||
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| Adds air-sea exchange of CO2 to Example 1 | ||
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| ### Additional code files | ||
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| In order to evaluate the CO2 flux change between air and sea, we add a file (file `examples/ocean_chemistry/reactions_AirSeaExchange.jl`) to achieve air-sea CO2 exchange following Henry's Law. | ||
| ```@eval | ||
| str = read("../../../../examples/ocean_chemistry/reactions_AirSeaExchange.jl", String) | ||
| str = """```julia | ||
| $str | ||
| ```""" | ||
| import Markdown | ||
| Markdown.parse(str) | ||
| ``` | ||
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| ### yaml configuration file | ||
| The model configuration (file `examples/ocean_chemistry/config_ex2.yaml`) contains three Reservoirs `DIC`, `TAlk` and `CO2`. Following `reservoirs` [Example 4 Transfer between Domains](@ref), we use `ReactionFluxTarget` and `ReactionFluxTransfer` to transfer `CO2_airsea_exchange` between `DIC` reservoir and `CO2` reservoir: | ||
| ```@eval | ||
| str = read("../../../../examples/ocean_chemistry/config_ex2.yaml", String) | ||
| str = """```julia | ||
| $str | ||
| ```""" | ||
| import Markdown | ||
| Markdown.parse(str) | ||
| ``` | ||
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| ### Run script | ||
| The script to run the model (file `examples/ocean_chemistry/run_ex2.jl`) contains: | ||
| ```@eval | ||
| str = read("../../../../examples/ocean_chemistry/run_ex2.jl", String) | ||
| str = """```julia | ||
| $str | ||
| ```""" | ||
| import Markdown | ||
| Markdown.parse(str) | ||
| ``` | ||
| and produces output showing the change, if `TAlk_conc` increase, how the carbonic acid and pH change in ocean and CO2 change in the air: | ||
| ```@example ex2 | ||
| include("../../../../examples/ocean_chemistry/run_ex2.jl") # hide | ||
| plot(paleorun.output, ["ocean.TAlk_conc", "ocean.DIC_conc"], (cell=1,); ylabel="TAlk, DIC conc (mol m-3)") # hide | ||
| savefig("ex2_plot1.svg"); nothing # hide | ||
| plot(paleorun.output, "ocean.pH", (cell=1,)) # hide | ||
| savefig("ex2_plot2.svg"); nothing # hide | ||
| plot(paleorun.output, ["ocean.DIC_conc", "ocean.HCO3_conc", "ocean.CO3_conc", "ocean.CO2_aq_conc"], (cell=1,); ylabel="DIC species (mol m-3)") # hide | ||
| savefig("ex2_plot3.svg"); nothing # hide | ||
| display(plot(paleorun.output, "atm.pCO2atm", )) # hide | ||
| savefig("ex2_plot4.svg"); nothing # hide | ||
| display(plot(paleorun.output, ["global.C_total", "atm.CO2", "ocean.DIC_total"] ; ylabel="atm-ocean carbon (mol)")) | ||
| savefig("ex2_plot5.svg"); nothing # hide | ||
| ``` | ||
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| ### Displaying model structure and variables | ||
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| All metadata for model variables can be displayed with `PB.show_variables`: | ||
| ```@example ex2 | ||
| show(PB.show_variables(model), allcols=true, allrows=true) # display in REPL | ||
| # vscodedisplay(PB.show_variables(model)) # more convenient when using VS code | ||
| ``` | ||
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| For more information and cooperation, please communicate with us! |
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| Minimal_Alk_pH: | ||
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| domains: | ||
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| global: | ||
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| reactions: | ||
| add_Alk: | ||
| # from PALEOboxes reaction catalog: constant input flux of Alk | ||
| class: ReactionFluxPerturb | ||
| parameters: | ||
| # linear interpolation for input flux - set to constant | ||
| perturb_times: [-1e30, 1e30] | ||
| # ocean volume = 3.6e14 * 3688.0 = 1.33e18 m^3 | ||
| # DIC in ocean = 2 * 1.33e18 = 2.66e18 mol | ||
| # set Alk flux so Alk = DIC after 100 yr-1 = 2.66e18/100 = 2.66e16 mol yr-1 | ||
| perturb_totals: [2.66e16, 2.66e16] | ||
| variable_links: | ||
| F: ocean.TAlk_sms # add flux to TAlk reservoir NB: works for single-box ocean only !! | ||
| # -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ||
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| ocean: | ||
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| reactions: | ||
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| oceantrasport: | ||
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| class: ReactionOceanNoTransport | ||
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| parameters: | ||
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| area: [3.6e14] | ||
| depth: [3688.0] | ||
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| reservoir_TA: | ||
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| class: ReactionReservoir | ||
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| variable_links: | ||
| R*: TAlk* | ||
| variable_attributes: | ||
| R:initial_value: 0.0 | ||
| R:norm_value: 2.4e0 | ||
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| reservoir_DIC: | ||
| class: ReactionReservoir | ||
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| variable_links: | ||
| R*: DIC* | ||
| variable_attributes: | ||
| R:initial_value: 2.0e0 | ||
| R:norm_value: 2.0e0 | ||
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| solve_Alk_pH: | ||
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| class: Reaction_Alk_pH | ||
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| parameters: | ||
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| # kappa: 1.0 | ||
| # density: 1027.0 | ||
| # TAlk_conc_change: 10.0e-7 | ||
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| K_1: 1.4e-6 | ||
| K_2: 1.2e-9 | ||
| K_w: 6.0e-14 | ||
| K_B: 2.5e-9 | ||
| B_total: 4.2e-4 | ||
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| variable_links: | ||
| density: rho_ref # OceanNoTransport provides density as rho_ref | ||
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| oceanfloor: | ||
| # unused here, set up by ReactionOceanNoTransport | ||
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| oceansurface: | ||
| # unused here, set up by ReactionOceanNoTransport |
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