Merge pull request #24 from PALEOtoolkit/add_romaniello2010

Add ICBM global ocean and Black Sea examples from Romeniello & Derry (2010)

.gitignore

@@ -7,3 +7,4 @@ LocalPreferences.toml
 *.nc
 *.zip
 examples/shelf1D/S2P3_transport_20240614
+examples/romglb/romaniello2010_transport

docs/src/PALEOocean_Reactions.md

@@ -9,8 +9,9 @@ CurrentModule = PALEOocean.Ocean
 OceanNoTransport.ReactionOceanNoTransport
 OceanTransport3box.ReactionOceanTransport3box
 OceanTransport6box.ReactionOceanTransport6box
-OceanTransportTMM.ReactionOceanTransportTMM
 OceanTransportColumn.ReactionOceanTransportColumn
+OceanTransportRomaniello2010.ReactionOceanTransportRomanielloICBM
+OceanTransportTMM.ReactionOceanTransportTMM
 ```
 
 ## Vertical Transport

docs/src/paleo_references.bib

@@ -151,6 +151,29 @@ @article{Ridgwell2007
 	pages = {87--104},
 }
 
+@article{Romaniello2010a,
+author = {Romaniello, Stephen J. and Derry, Louis A},
+doi = {10.1029/2009GC002712},
+journal = {Geochemistry Geophysics Geosystems},
+month = {aug},
+number = {8},
+pages = {1--18},
+title = {{Validation of an intermediate-complexity model for simulating marine biogeochemistry under anoxic conditions in the modern Black Sea}},
+volume = {11},
+year = {2010}
+}
+
+@article{Romaniello2010,
+author = {Romaniello, Stephen J. and Derry, Louis A},
+doi = {10.1029/2009GC002711},
+journal = {Geochemistry Geophysics Geosystems},
+month = {aug},
+number = {8},
+pages = {1--33},
+title = {{An intermediate-complexity model for simulating marine biogeochemistry in deep time: Validation against the modern global ocean}},
+volume = {11},
+year = {2010}
+}
 
 @article{Sarmiento1984,
 author = {Sarmiento, Jorge L and Toggweiler, J. R.},

examples/blacksea/PALEO_examples_blacksea_O2_only.jl

@@ -0,0 +1,58 @@
+using Logging
+using DiffEqBase
+using Sundials
+
+using Plots
+
+import PALEOboxes as PB
+import PALEOmodel
+import PALEOocean
+
+
+global_logger(ConsoleLogger(stderr,Logging.Info))
+
+include("config_ocean_blacksea_expts.jl")
+include("plot_ocean_blacksea.jl")
+
+# abiotic atmosphere-ocean, O2 only
+model = PB.create_model_from_config(
+    joinpath(@__DIR__, "PALEO_examples_blacksea_cfg.yaml"), "blacksea_abiotic_O2",
+    modelpars=Dict(
+        "matdir"=>joinpath(@__DIR__, "../romglb/romaniello2010_transport") # assume zip file has been downloaded and unpacked in this subfolder
+    )
+)
+
+config_ocean_blacksea_expts(model, ["baseline"]); tspan=(0, 1e4)
+
+initial_state, modeldata = PALEOmodel.initialize!(model)
+
+paleorun = PALEOmodel.Run(model=model, output = PALEOmodel.OutputWriters.OutputMemory())
+
+# No carbonate system, so can integrate as an ODE
+PALEOmodel.ODE.integrateForwardDiff(
+    paleorun, initial_state, modeldata, tspan,
+    solvekwargs=(reltol=1e-5,),
+)
+
+
+########################################
+# Plot output
+########################################
+
+# individual plots
+# plotlyjs(size=(750, 565))
+# pager = PALEOmodel.DefaultPlotPager()
+
+# assemble plots onto screens with 6 subplots
+gr(size=(1200, 900))
+pager=PALEOmodel.PlotPager((2, 3), (legend_background_color=nothing, margin=(5, :mm)))
+
+plot_totals(paleorun.output; species=["T", "O2"], pager=pager)
+plot_airsea(paleorun.output; species=["O2"], pager=pager)
+plot_ocean_tracers(
+    paleorun.output; 
+    tracers=["insol", "T_conc", "O2_conc"],
+    tcol=[-Inf, 10.0, 100.0, 1000.0, 1e4, 1e5],
+    pager=pager
+)
+pager(:newpage) # flush output

examples/blacksea/PALEO_examples_blacksea_P_O2.jl

@@ -0,0 +1,59 @@
+using Logging
+using DiffEqBase
+using Sundials
+
+using Plots
+
+import PALEOboxes as PB
+import PALEOmodel
+import PALEOocean
+
+
+global_logger(ConsoleLogger(stderr,Logging.Info))
+
+include("config_ocean_blacksea_expts.jl")
+include("plot_ocean_blacksea.jl")
+
+# abiotic atmosphere-ocean, O2 only
+model = PB.create_model_from_config(
+    joinpath(@__DIR__, "PALEO_examples_blacksea_cfg.yaml"), "blacksea_P_O2",
+    modelpars=Dict(
+        "matdir"=>joinpath(@__DIR__, "../romglb/romaniello2010_transport") # assume zip file has been downloaded and unpacked in this subfolder
+    )
+)
+
+config_ocean_blacksea_expts(model, ["baseline"]); tspan=(0, 1e5)
+
+initial_state, modeldata = PALEOmodel.initialize!(model)
+
+paleorun = PALEOmodel.Run(model=model, output = PALEOmodel.OutputWriters.OutputMemory())
+
+# No carbonate system, so can integrate as an ODE
+PALEOmodel.ODE.integrateForwardDiff(
+    paleorun, initial_state, modeldata, tspan,
+    solvekwargs=(reltol=1e-5,),
+)
+
+
+########################################
+# Plot output
+########################################
+
+# individual plots
+# plotlyjs(size=(750, 565))
+# pager = PALEOmodel.DefaultPlotPager()
+
+# assemble plots onto screens with 6 subplots
+gr(size=(1200, 900))
+pager=PALEOmodel.PlotPager((2, 3), (legend_background_color=nothing, margin=(5, :mm)))
+
+plot_totals(paleorun.output; species=["T", "O2", "P"], pager=pager)
+plot_airsea(paleorun.output; species=["O2"], pager=pager)
+pager(:newpage)
+plot_ocean_tracers(
+    paleorun.output; 
+    tracers=["insol", "T_conc", "O2_conc", "P_conc"],
+    tcol=[-Inf, 10.0, 100.0, 1000.0, 1e4, 1e5],
+    pager=pager
+)
+pager(:newpage) # flush output

examples/blacksea/PALEO_examples_blacksea_P_O2_SO4.jl

@@ -0,0 +1,58 @@
+using Logging
+using DiffEqBase
+using Sundials
+
+using Plots
+
+import PALEOboxes as PB
+import PALEOmodel
+import PALEOocean
+
+
+global_logger(ConsoleLogger(stderr,Logging.Info))
+
+include("config_ocean_blacksea_expts.jl")
+include("plot_ocean_blacksea.jl")
+
+model = PB.create_model_from_config(
+    joinpath(@__DIR__, "PALEO_examples_blacksea_cfg.yaml"), "blacksea_P_O2_SO4",
+    modelpars=Dict(
+        "matdir"=>joinpath(@__DIR__, "../romglb/romaniello2010_transport") # assume zip file has been downloaded and unpacked in this subfolder
+    )
+)
+
+config_ocean_blacksea_expts(model, ["baseline"]); tspan=(0, 1e5)
+
+initial_state, modeldata = PALEOmodel.initialize!(model)
+
+paleorun = PALEOmodel.Run(model=model, output = PALEOmodel.OutputWriters.OutputMemory())
+
+# No carbonate system, so can integrate as an ODE
+PALEOmodel.ODE.integrateForwardDiff(
+    paleorun, initial_state, modeldata, tspan,
+    solvekwargs=(reltol=1e-5,),
+)
+
+
+########################################
+# Plot output
+########################################
+
+# individual plots
+# plotlyjs(size=(750, 565))
+# pager = PALEOmodel.DefaultPlotPager()
+
+# assemble plots onto screens with 6 subplots
+gr(size=(1200, 900))
+pager=PALEOmodel.PlotPager((2, 3), (legend_background_color=nothing, margin=(5, :mm)))
+
+plot_totals(paleorun.output; species=["T", "O2", "P", "S"], pager=pager)
+plot_airsea(paleorun.output; species=["O2"], pager=pager)
+pager(:newpage)
+plot_ocean_tracers(
+    paleorun.output; 
+    tracers=["insol", "T_conc", "O2_conc", "P_conc", "SO4_conc", "H2S_conc"],
+    tcol=[-Inf, 10.0, 100.0, 1000.0, 1e4, 1e5],
+    pager=pager
+)
+pager(:newpage) # flush output