Merge pull request #6 from PALEOtoolkit/add_airsea

Add AirSeaExchange Reactions

Project.toml

@@ -1,47 +1,33 @@
 name = "PALEOocean"
 uuid = "41de04b1-2efd-44ae-92ae-39d71a4fd99b"
 authors = ["sd336 "]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Infiltrator = "5903a43b-9cc3-4c30-8d17-598619ec4e9b"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
-MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
 PALEOboxes = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
-Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SIMD = "fdea26ae-647d-5447-a871-4b548cad5224"
 SnoopPrecompile = "66db9d55-30c0-4569-8b51-7e840670fc0c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 TestEnv = "1e6cf692-eddd-4d53-88a5-2d735e33781b"
-XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
 
 [compat]
-DataFrames = "1.1"
 Documenter = "0.27"
-Infiltrator = "1.0"
 Interpolations = "0.13, 0.14"
-MAT = "0.10"
 PALEOboxes = "0.20.4, 0.21"
 PALEOmodel = "0.15.8"
-Plots = "1.0"
-Roots = "1.0, 2.0"
 SIMD = "3.4"
 SnoopPrecompile = "1.0"
 TestEnv = "1.0"
-XLSX = "0.7, 0.8, 0.9"
 julia = "1.6"
 
 [extras]
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
-NBInclude = "0db19996-df87-5ea3-a455-e3a50d440464"
 PALEOmodel = "bf7b4fbe-ccb1-42c5-83c2-e6e9378b660c"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["CSV", "Documenter", "Logging", "NBInclude", "PALEOmodel", "Plots", "Test"]
+test = ["Documenter", "Logging", "PALEOmodel", "Test"]

docs/src/PALEOocean Reactions.md

@@ -1,11 +1,24 @@
 # PALEOocean Reactions
 
+## Ocean geometry and transport
 ```@meta
 CurrentModule = PALEOocean.Ocean
 ```
 
-## Ocean geometry and transport
 ```@docs
 OceanNoTransport.ReactionOceanNoTransport
 ```
 
+## Ocean surface
+```@meta
+CurrentModule = PALEOocean.Oceansurface
+```
+
+### Air-sea flux
+```@docs
+AirSeaExchange.ReactionAirSea
+AirSeaExchange.ReactionAirSeaO2
+AirSeaExchange.ReactionAirSeaCO2
+AirSeaExchange.ReactionAirSeaCH4
+AirSeaExchange.ReactionAirSeaFixedSolubility
+```

examples/setup.jl

@@ -5,4 +5,5 @@ import Pkg
 
 Pkg.activate(".") # use the PALEOocean/examples environment
 Pkg.develop(path="../")   # use the local version of PALEOocean packages to allow local modifications
-Pkg.instantiate()
+Pkg.instantiate()
+Pkg.update()

examples/transport_examples/TransportExamples.jl

@@ -40,7 +40,7 @@ function PB.register_methods!(rj::ReactionTransportAdvectExample)
         rj, 
         do_setup_advect,
         (   
-            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.grid_vars_ocean)),
+            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.Ocean.grid_vars_ocean)),
         ),
     )
 
@@ -65,7 +65,7 @@ function do_setup_advect(m::PB.ReactionMethod, pars, (grid_vars, ), cellrange::P
     # advection in a loop down column 1, up column 2
     loopindices = vcat(rj.domain.grid.Icolumns[1], reverse(rj.domain.grid.Icolumns[2]), [first(rj.domain.grid.Icolumns[1])])
     @info "do_setup_advect: $(PB.fullname(rj)) adding advective flux $(pars.T[]) (m^3 s-1) around loop $loopindices"
-    PALEOocean.add_loop!(A, grid_vars.volume, pars.T[], loopindices)
+    PALEOocean.Ocean.add_loop!(A, grid_vars.volume, pars.T[], loopindices)
 
     # store the transpose as a sparse matrix for computational efficiency
     #  yr-1           s yr-1                    s-1
@@ -77,18 +77,18 @@ end
 function PB.register_dynamic_methods!(rj::ReactionTransportAdvectExample)
 
     (transport_conc_vars, transport_sms_vars, transport_input_vars) =
-        PALEOocean.find_transport_vars(rj.domain, add_transport_input_vars=true)
+        PALEOocean.Ocean.find_transport_vars(rj.domain, add_transport_input_vars=true)
 
     PB.add_method_do!(
         rj, 
         do_advect,
         (   
-            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.grid_vars_ocean)),
+            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.Ocean.grid_vars_ocean)),
             PB.VarList_components(transport_conc_vars),
             PB.VarList_components(transport_sms_vars),
             PB.VarList_components(transport_input_vars),
         ),
-        preparefn=PALEOocean.prepare_transport
+        preparefn=PALEOocean.Ocean.prepare_transport
     )
 
     return nothing
@@ -103,7 +103,7 @@ function do_advect(
 )
     rj = m.reaction
 
-    PALEOocean.do_transport_tr(
+    PALEOocean.Ocean.do_transport_tr(
         grid_vars, transport_conc_components, transport_sms_components, transport_input_components, buffer,
         rj.trspt_dtm_tr,
         cellrange
@@ -144,7 +144,7 @@ function PB.register_methods!(rj::ReactionTransportDiffuseExample)
         rj, 
         do_setup_diffuse,
         (   
-            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.grid_vars_ocean)),
+            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.Ocean.grid_vars_ocean)),
         ),
     )
 
@@ -186,7 +186,7 @@ function do_setup_diffuse(m::PB.ReactionMethod, pars, (grid_vars, ), cellrange::
             # m^3 s-1   = m^2    / m                                                   * m^2 s-1
             F           = Aintf/(grid_vars.zmid[icell_top] - grid_vars.zmid[icell_bot])*pars.Kz[]
             loopindices = (icell_top, icell_bot, icell_top)
-            PALEOocean.add_loop!(A, grid_vars.volume, F, loopindices)
+            PALEOocean.Ocean.add_loop!(A, grid_vars.volume, F, loopindices)
         end
     end
 
@@ -200,18 +200,18 @@ end
 function PB.register_dynamic_methods!(rj::ReactionTransportDiffuseExample)
 
     (transport_conc_vars, transport_sms_vars, transport_input_vars) =
-        PALEOocean.find_transport_vars(rj.domain, add_transport_input_vars=true)
+        PALEOocean.Ocean.find_transport_vars(rj.domain, add_transport_input_vars=true)
 
     PB.add_method_do!(
         rj, 
         do_diffuse,
         (   
-            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.grid_vars_ocean)),
+            PB.VarList_namedtuple(PB.VarDep.(PALEOocean.Ocean.grid_vars_ocean)),
             PB.VarList_components(transport_conc_vars),
             PB.VarList_components(transport_sms_vars),
             PB.VarList_components(transport_input_vars),
         ),
-        preparefn=PALEOocean.prepare_transport
+        preparefn=PALEOocean.Ocean.prepare_transport
     )
 
     return nothing
@@ -226,7 +226,7 @@ function do_diffuse(
 )
     rj = m.reaction
 
-    PALEOocean.do_transport_tr(
+    PALEOocean.Ocean.do_transport_tr(
         grid_vars, transport_conc_components, transport_sms_components, transport_input_components, buffer,
         rj.trspt_dtm_tr,
         cellrange
@@ -313,7 +313,7 @@ function PB.set_model_geometry(rj::ReactionOceanColumnGrid, model::PB.Model)
         cellnames=Dict(name=>i for (i, name) in enumerate(rj.grid_ocean.columnnames)))
     PB.Grids.set_subdomain!(rj.grid_oceanfloor, "ocean", PB.Grids.InteriorSubdomain(ocean_cells, ifloor), true)
 
-    PALEOocean.set_model_domains(model, rj.grid_ocean, rj.grid_oceansurface, rj.grid_oceanfloor)
+    PALEOocean.Ocean.set_model_domains(model, rj.grid_ocean, rj.grid_oceansurface, rj.grid_oceanfloor)
 
     return nothing
 end
@@ -326,7 +326,7 @@ function PB.register_methods!(rj::ReactionOceanColumnGrid)
         rj, 
         do_setup_grid,
         (   
-            PB.VarList_namedtuple(PALEOocean.grid_vars_all), 
+            PB.VarList_namedtuple(PALEOocean.Ocean.grid_vars_all), 
         ),
     )
 

examples/transport_examples/runtests.jl

@@ -0,0 +1,98 @@
+using Logging
+using Test
+
+import PALEOboxes as PB
+import PALEOmodel
+import PALEOocean
+
+include("TransportExamples.jl")
+
+@testset "transport_examples" begin
+
+skipped_testsets = [
+    # "transport_advect",
+    # "transport_diffuse",
+]
+
+!("transport_advect" in skipped_testsets) && @testset "transport_advect" begin
+
+    model = PB.create_model_from_config(
+        joinpath(@__DIR__, "TransportExamples_cfg.yaml"), "example_advect"
+    )
+
+    initial_state, modeldata = PALEOmodel.initialize!(model)
+
+    # bodge an updated initial_state for testing
+    ocean_T = PB.get_data(PB.get_variable(model, "ocean.T"), modeldata) # model data array for tracer T
+    ocean_T[1] = 2e14*200.0*1.0  # ~ 1 mol m-3 in first cell (top of first column)
+    initial_state = PALEOmodel.get_statevar(modeldata.solver_view_all)
+
+    tspan=(0.0, 5e3)
+
+    run = PALEOmodel.Run(model=model, output = PALEOmodel.OutputWriters.OutputMemory())
+
+    PALEOmodel.ODE.integrateForwardDiff(
+        run, initial_state, modeldata, tspan,
+        solvekwargs=(reltol=1e-5,),
+    )
+
+    println("conservation checks:")
+    conschecks = [
+        ("ocean",  "T_total", 1e-14),
+    ]
+    for (domname, varname, rtol) in conschecks
+        startval, endval = PB.get_data(run.output, domname*"."*varname)[[1, end]]
+        println("  check $domname.$varname $startval $endval $rtol")
+        @test isapprox(startval, endval, rtol=rtol)
+    end
+
+end
+
+!("transport_diffuse" in skipped_testsets) && @testset "transport_diffuse" begin
+
+    model = PB.create_model_from_config(
+        joinpath(@__DIR__, "TransportExamples_cfg.yaml"), "example_diffuse"
+    )
+
+    initial_state, modeldata = PALEOmodel.initialize!(model)
+
+    # bodge an updated initial_state for testing
+    ocean_T = PB.get_data(PB.get_variable(model, "ocean.T"), modeldata) # model data array for tracer T
+    ocean_T[50] = 2e14*20.0*1.0  # ~ 1 mol m-3 in middle cell of first column
+    ocean_T[100+5] = 2e13*200.0*1.0  # ~ 1 mol m-3 in middle cell of second column
+    initial_state = PALEOmodel.get_statevar(modeldata.solver_view_all)
+
+    tspan=(0.0, 1e6)
+
+    run = PALEOmodel.Run(model=model, output = PALEOmodel.OutputWriters.OutputMemory())
+
+    PALEOmodel.ODE.integrateForwardDiff(
+        run, initial_state, modeldata, tspan,
+        solvekwargs=(reltol=1e-5,),
+    )
+
+    println("conservation checks:")
+    conschecks = [
+        ("ocean",  "T_total", 1e-14),
+    ]
+    for (domname, varname, rtol) in conschecks
+        startval, endval = PB.get_data(run.output, domname*"."*varname)[[1, end]]
+        println("  check $domname.$varname $startval $endval $rtol")
+        @test isapprox(startval, endval, rtol=rtol)
+    end
+
+    println("check values at end of run:")
+    checkvals = [  
+        ("ocean", "T_conc",  0.01*ones(110),    1e-5 ),  # check uniform concentration in 110 ocean cells
+    ]    
+    for (domname, varname, checkval, rtol) in checkvals
+        outputval = PB.get_data(run.output, domname*"."*varname)[end]
+        println("  check $domname.$varname $outputval $checkval $rtol")
+        @test isapprox(outputval, checkval, rtol=rtol)
+    end
+
+end
+
+
+
+end

src/PALEOocean.jl

@@ -11,5 +11,7 @@ end
 
 include("ocean/Ocean.jl")
 
+include("oceansurface/Oceansurface.jl")
+
 
 end # module PALEOocean