Add ICBM global ocean and Black Sea examples from Romeniello & Derry …

…(2010)

examples/romglb/
examples/blacksea/

See README.md for details including how to download data files.

These use 'ReactionOceanTransportRomanielloICBM' which reads the Matlab .mat files containing transport matrix and geometry for the
ICBM models of global ocean and Black sea from:
- Romaniello & Derry (2010) 'An intermediate-complexity model for simulating marine biogeochemistry in deep time: Validation against the modern global ocean', GGG,
  <https://dx.doi.org/10.1029/2009GC002711>
- Romaniello & Derry (2010) 'Validation of an intermediate-complexity model for simulating marine biogeochemistry under anoxic conditions in the modern Black Sea', GGG,
  <https://dx.doi.org/10.1029/2009GC002712>

.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