Merge pull request #6 from PALEOtoolkit/sync_PALEOboxes

Update to PALEOboxes v0.18
PALEOtoolkit · May 12, 2022 · 85d1b18 · 85d1b18 · sjdaines · May 12, 2022
2 parents 0d139c0 + 7c915e3
commit 85d1b18
Show file tree

Hide file tree

Showing 9 changed files with 138 additions and 108 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "PALEOcopse"
 uuid = "4a6ed817-0e58-48c6-8452-9e9afc8cb508"
 authors = ["sd336 "]
-version = "0.2.1"
+version = "0.2.2"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -19,7 +19,7 @@ Documenter = "0.27"
 Infiltrator = "1.0"
 Interpolations = "0.13"
 MAT = "0.10"
-PALEOboxes = "0.17"
+PALEOboxes = "0.18"
 PALEOmodel = "0.14"
 Plots = "1.0"
 Roots = "1.0, 2.0"

diff --git a/src/COPSE/MapAtmOceanReservoirs.jl b/src/COPSE/MapAtmOceanReservoirs.jl
@@ -117,14 +117,18 @@ Base.@kwdef mutable struct ReactionAtmOcean_A{P} <:  PB.AbstractReaction
             description="calculate d13CO2, d13DIC relative to A"),
         PB.ParBool("fix_cisotopefrac_T", false,
             description="remove temperature dependence of d13CO2, d13DIC relative to A"),
+        PB.ParType(PB.AbstractData, "CIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable carbon isotopes and specify isotope type"),
     )
 
     norm_value::Float64 = NaN
 end
 
 function PB.register_methods!(rj::ReactionAtmOcean_A)
 
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", rj.external_parameters; default=PB.ScalarData)
+    CIsotopeType = rj.pars.CIsotope.v
 
     vars = [
         PB.VarStateExplicitScalar("A",          "mol",      "atm-ocean inorganic carbon (CO2 + DIC)",

diff --git a/src/Forcings/LipForcing.jl b/src/Forcings/LipForcing.jl
@@ -245,6 +245,10 @@ Base.@kwdef mutable struct ReactionForce_LIPs{P} <:  PB.AbstractReaction
             description="smooth LIP basalt emplacement"),
         PB.ParString("co2releasefield", "NoCO2", allowed_values=["NoCO2", "CO2min", "CO2max"],
             description="LIP CO2 release"),
+        PB.ParType(PB.AbstractData, "CIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable carbon isotopes and specify isotope type"),
     )
 
     LIP_data = nothing
@@ -262,8 +266,8 @@ function PB.register_methods!(rj::ReactionForce_LIPs)
 
     rj.LIP_data = read_lips_xlsx(lipfile)
 
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", rj.external_parameters; default=PB.ScalarData)    
-    @info "    CIsotopeType=$(CIsotopeType) from CIsotope in external_parameters"
+    CIsotopeType = rj.pars.CIsotope.v
+    @info "    CIsotopeType=$(CIsotopeType)"
 
     vars = [
         PB.VarDepScalar("tforce",     "yr",  "historical time at which to apply forcings, present = 0 yr"),

diff --git a/src/biogeochem/Strontium.jl b/src/biogeochem/Strontium.jl
@@ -127,20 +127,26 @@ Base.@kwdef mutable struct ReactionSrSed{P} <: PB.AbstractReaction
             description="functional form for sediment Sr metamorphic loss"),
         PB.ParDouble("k_Sr_metam", 13e9, units="mol yr-1",
             description="rate of metamorphic loss of Sr from sedimentary reservoir"),
+
+        # Isotopes
+        PB.ParType(PB.AbstractData, "SrIsotope", SrIsotopeDefault,
+            external=true,
+            allowed_values=[PB.ScalarData, PB.IsotopeLinear],
+            description="disable / enable Sr isotopes and specify isotope type"),
     )
 end
 
 function PB.register_methods!(rj::ReactionSrSed)
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
+    SrIsotopeType = rj.pars.SrIsotope.v
 
     vars = [
         PB.VarDepScalar("global.tforce", "yr",  "historical time at which to apply forcings, present = 0 yr"),
         PB.VarDepScalar("global.DEGASS", "",  "normalized DEGASS forcing"),
 
-        PB.VarDepScalar("Sr_sed", "mol",  "sedimentary Sr", attributes=(:field_data=>SrIsotopeType, )),
+        PB.VarDepScalar("Sr_sed", "mol",  "sedimentary Sr"),
         PB.VarDepScalar("Sr_sed_delta", "",  "d87Sr of sedimentary Sr"),
         PB.VarDepScalar("Sr_sed_norm", "",  "normalized sedimentary Sr"),    
-        PB.VarContribScalar("Sr_sed_sms", "mol yr-1",  "sedimentary Sr source minus sink flux", attributes=(:field_data=>SrIsotopeType, ))
+        PB.VarContribScalar("Sr_sed_sms", "mol yr-1",  "sedimentary Sr source minus sink flux")
     ]
 
     PB.add_method_do!(
@@ -153,18 +159,6 @@ function PB.register_methods!(rj::ReactionSrSed)
     return nothing
 end
 
-function PB.check_configuration(rj::ReactionSrSed, model::PB.Model)
-    configok = true
-
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
-
-    if !(SrIsotopeType in (PB.ScalarData, PB.IsotopeLinear))
-        @warn "ReactionSrSed.check_configuration unsupported IsotopeType $SrIsotopeType"
-        configok = false
-    end
-
-    return configok
-end
 
 function do_Sr_sed(
     m::PB.ReactionMethod,
@@ -229,12 +223,18 @@ Base.@kwdef mutable struct ReactionSrLand{P} <: PB.AbstractReaction
             description="functional form for sediment Sr weathering"),
         PB.ParDouble("k_Sr_sedw", 17e9, units="mol yr-1",
             description="Sr weathering rate constant from sediments"),
+
+        # Isotopes
+        PB.ParType(PB.AbstractData, "SrIsotope", SrIsotopeDefault,
+            external=true,
+            allowed_values=[PB.ScalarData, PB.IsotopeLinear],
+            description="disable / enable Sr isotopes and specify isotope type"),
     )
 end
 
 
 function PB.register_methods!(rj::ReactionSrLand)
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
+    SrIsotopeType = rj.pars.SrIsotope.v
 
     vars = [
         PB.VarDepScalar("basw_relative", "",  "Basalt weathering normalized to present"),
@@ -327,12 +327,18 @@ Base.@kwdef mutable struct ReactionSrOceanfloor{P} <: PB.AbstractReaction
             description="Sr burial output"),
         PB.ParDouble("k_mccb_0", NaN, units="mol yr-1",
             description="Carbonate burial rate to normalize Sr burial output for f_Sr_sedb=\"carbburial\""),
+
+        # Isotopes
+        PB.ParType(PB.AbstractData, "SrIsotope", SrIsotopeDefault,
+            external=true,
+            allowed_values=[PB.ScalarData, PB.IsotopeLinear],
+            description="disable / enable Sr isotopes and specify isotope type"),
     )
 end
 
 
 function PB.register_methods!(rj::ReactionSrOceanfloor)
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
+    SrIsotopeType = rj.pars.SrIsotope.v
 
     vars = [
         PB.VarDepScalar("global.DEGASS",        "",         "normalized DEGASS forcing"),

diff --git a/src/landsurface/LandBergman2004.jl b/src/landsurface/LandBergman2004.jl
@@ -56,6 +56,15 @@ Base.@kwdef mutable struct ReactionLandBergman2004{P} <: PB.AbstractReaction
 
         # Organic carbon burial
         PB.ParString("f_locb",      "original", allowed_values=["original", "Prescribed"]),
+
+        PB.ParType(PB.AbstractData, "CIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable carbon isotopes and specify isotope type"),
+        PB.ParType(PB.AbstractData, "SIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable sulphur isotopes and specify isotope type"),
     )
 
 end
@@ -142,28 +151,22 @@ function PB.register_methods!(rj::ReactionLandBergman2004)
             ("eps_eqbw",    "per mil", "approximate atmosphere-runoff d13C")
         ])
 
-    # isotopes with defaults
-    isotope_data = merge(
-        Dict("CIsotope"=>PB.ScalarData, "SIsotope"=>PB.ScalarData),
-        rj.external_parameters
-    )
+    # isotope Types
+    CIsotopeType = rj.pars.CIsotope.v
+    SIsotopeType = rj.pars.SIsotope.v
 
     # Add flux couplers
     fluxAtoLand = PB.Fluxes.FluxContribScalar(
-        "fluxAtoLand.flux_", ["CO2::CIsotope", "O2"],
-        isotope_data=isotope_data)
+        "fluxAtoLand.flux_", ["CO2::$CIsotopeType", "O2"],
+        isotope_data=Dict())
 
     fluxRtoOcean = PB.Fluxes.FluxContribScalar(
-        "fluxRtoOcean.flux_", ["DIC::CIsotope", "TAlk", "Ca", "P", "SO4::SIsotope"],
-        isotope_data=isotope_data)
+        "fluxRtoOcean.flux_", ["DIC::$CIsotopeType", "TAlk", "Ca", "P", "SO4::$SIsotopeType"],
+        isotope_data=Dict())
 
     fluxLandtoSedCrust = PB.Fluxes.FluxContribScalar(
-        "fluxLandtoSedCrust.flux_", ["Ccarb::CIsotope", "Corg::CIsotope", "GYP::SIsotope", "PYR::SIsotope"],
-        isotope_data=isotope_data)
-
-    # isotope Types
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", isotope_data)
-    _, SIsotopeType = PB.split_nameisotope("::SIsotope", isotope_data)
+        "fluxLandtoSedCrust.flux_", ["Ccarb::$CIsotopeType", "Corg::$CIsotopeType", "GYP::$SIsotopeType", "PYR::$SIsotopeType"],
+        isotope_data=Dict())    
 
     PB.add_method_do!(
         rj,

diff --git a/src/landsurface/LandCOPSEReloaded.jl b/src/landsurface/LandCOPSEReloaded.jl
@@ -495,6 +495,16 @@ Base.@kwdef mutable struct ReactionLandWeatheringFluxes{P} <: PB.AbstractReactio
             description="fraction of locb assumed to occur in aquatic settings (not coals)"),
         PB.ParDouble("CPland0",        1000.0,     units="",
             description="present-day C/P land burial"),
+
+        # Isotopes
+        PB.ParType(PB.AbstractData, "CIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable carbon isotopes and specify isotope type"),
+        PB.ParType(PB.AbstractData, "SIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable sulphur isotopes and specify isotope type"),
     )
 
 end
@@ -580,28 +590,22 @@ function PB.register_methods!(rj::ReactionLandWeatheringFluxes)
         ]
     )
 
-    # isotopes with defaults
-    isotope_data = merge(
-        Dict("CIsotope"=>PB.ScalarData, "SIsotope"=>PB.ScalarData),
-        rj.external_parameters
-    )
+    # isotope Types
+    CIsotopeType = rj.pars.CIsotope.v
+    SIsotopeType = rj.pars.SIsotope.v
 
     # Add flux couplers
     fluxAtoLand = PB.Fluxes.FluxContribScalar(
-        "fluxAtoLand.flux_", ["CO2::CIsotope", "O2"],
-        isotope_data=isotope_data)
+        "fluxAtoLand.flux_", ["CO2::$CIsotopeType", "O2"],
+        isotope_data=Dict())
 
     fluxRtoOcean = PB.Fluxes.FluxContribScalar(
-        "fluxRtoOcean.flux_", ["DIC::CIsotope", "TAlk", "Ca", "P", "SO4::SIsotope"],
-        isotope_data=isotope_data)
+        "fluxRtoOcean.flux_", ["DIC::$CIsotopeType", "TAlk", "Ca", "P", "SO4::$SIsotopeType"],
+        isotope_data=Dict())
 
     fluxLandtoSedCrust = PB.Fluxes.FluxContribScalar(
-        "fluxLandtoSedCrust.flux_", ["Ccarb::CIsotope", "Corg::CIsotope", "GYP::SIsotope", "PYR::SIsotope"],
-        isotope_data=isotope_data)
-
-    # isotope Types
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", isotope_data)
-    _, SIsotopeType = PB.split_nameisotope("::SIsotope", isotope_data)
+        "fluxLandtoSedCrust.flux_", ["Ccarb::$CIsotopeType", "Corg::$CIsotopeType", "GYP::$SIsotopeType", "PYR::$SIsotopeType"],
+        isotope_data=Dict())
 
     PB.add_method_do!(
         rj,

diff --git a/src/ocean/OceanCOPSE.jl b/src/ocean/OceanCOPSE.jl
@@ -96,40 +96,51 @@ Base.@kwdef mutable struct ReactionOceanCOPSE{P} <: PB.AbstractReaction
         PB.ParString("f_sisotopefrac","fixed",  allowed_values=["fixed", "copse_O2"],
             description="S isotope fractionation calculation."),
 
+        # Isotopes
+        PB.ParType(PB.AbstractData, "CIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable carbon isotopes and specify isotope type"),
+        PB.ParType(PB.AbstractData, "SIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable sulphur isotopes and specify isotope type"),
     )
 
 end
 
 
 function PB.register_methods!(rj::ReactionOceanCOPSE)
 
-    # isotopes with defaults
-    isotope_data = merge(
-        Dict("CIsotope"=>PB.ScalarData, "SIsotope"=>PB.ScalarData),
-        rj.external_parameters
-    )
-
+
     # TODO - not the right place for this ? 
     # define a 1 cell grid
     rj.domain.grid = PB.Grids.UnstructuredVectorGrid(ncells=1)
     PB.Grids.set_subdomain!(rj.domain.grid, "oceansurface", PB.Grids.BoundarySubdomain([1]), true)
     PB.Grids.set_subdomain!(rj.domain.grid, "oceanfloor",   PB.Grids.BoundarySubdomain([1]), true)
 
-
+    # isotope Types
+    CIsotopeType = rj.pars.CIsotope.v
+    if rj.pars.enableS.v
+        SIsotopeType = rj.pars.SIsotope.v
+    else
+        SIsotopeType = PB.ScalarData
+    end
+
     state_varnames = [
-        ("P",               "mol P",    "Marine phosphorus"),         
-        ("O",               "mol O2",   "Atm-ocean oxygen"),
-        ("(DIC::CIsotope)",    "mol C",    "ocean inorganic carbon"),
-        ("(CAL)",             "mol Ca",   "Marine calcium"),
+        ("P",                   "mol P",    "Marine phosphorus"),         
+        ("O",                   "mol O2",   "Atm-ocean oxygen"),
+        ("(DIC::$CIsotopeType)",    "mol C",    "ocean inorganic carbon"),
+        ("(CAL)",               "mol Ca",   "Marine calcium"),
     ]
     if rj.pars.enableS.v
-        push!(state_varnames, ("S::SIsotope",      "mol S",    "Marine sulphate"))
+        push!(state_varnames, ("S::$SIsotopeType",      "mol S",    "Marine sulphate"))
     end
     if rj.pars.f_ncycle.v
         push!(state_varnames, ("N",               "mol N",    "Marine nitrogen"))
     end
     vars_res, vars_sms, vars_dep_res = PB.Reservoirs.ReservoirLinksVector(
-        isotope_data, state_varnames
+        Dict(), state_varnames
     )
 
     # dependencies required in do_react
@@ -184,26 +195,18 @@ function PB.register_methods!(rj::ReactionOceanCOPSE)
 
     # Define flux coupler (a NamedTuple of Variables)
     burial_fluxnames = [   
-        "Corg::CIsotope", "Ccarb::CIsotope", 
+        "Corg::$CIsotopeType", "Ccarb::$CIsotopeType", 
         "Porg", "Pauth", "PFe", "P", 
     ]
     if rj.pars.enableS.v
-        push!(burial_fluxnames, "GYP::SIsotope", "PYR::SIsotope")
+        push!(burial_fluxnames, "GYP::$SIsotopeType", "PYR::$SIsotopeType")
     end
 
     fluxOceanBurial = PB.Fluxes.FluxContrib( # Scalar ?
         "fluxOceanBurial.flux_",
         burial_fluxnames,
-        isotope_data=isotope_data
+        isotope_data=Dict(),
     ) 
-
-    # isotope Types
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", isotope_data)
-    if rj.pars.enableS.v
-        _, SIsotopeType = PB.split_nameisotope("::SIsotope", isotope_data)
-    else
-        SIsotopeType = PB.ScalarData
-    end
 
     # Now assemble these lists into properties and dependencies for each method,
     # following the Matlab COPSE convention that:

diff --git a/src/oceanfloor/Weathering.jl b/src/oceanfloor/Weathering.jl
@@ -47,17 +47,19 @@ Base.@kwdef mutable struct ReactionSeafloorWeathering{P} <: PB.AbstractReaction
 
         PB.ParString("f_sfw_d13C",   "delta_DIC",  allowed_values=["delta_DIC", "delta_mccb"],
             description="d13C delta"),
+
+        # Isotopes
+        PB.ParType(PB.AbstractData, "CIsotope", PB.ScalarData,
+            external=true,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable carbon isotopes and specify isotope type"),
     )
 end
 
 
 function PB.register_methods!(rj::ReactionSeafloorWeathering)
-    # isotopes with defaults
-    isotope_data = merge(
-        Dict("CIsotope"=>PB.ScalarData, ),
-        rj.external_parameters
-    )
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", isotope_data)
+
+    CIsotopeType = rj.pars.CIsotope.v
 
     vars = [
         PB.VarDep("global.RHOSFW",          "", "seafloor weathering-specific additional forcing (usually 1.0)"),
@@ -77,13 +79,13 @@ function PB.register_methods!(rj::ReactionSeafloorWeathering)
     # flux couplers
     fluxOceanBurial = PB.Fluxes.FluxContrib(
         "fluxOceanBurial.flux_",
-        ["Ccarb::CIsotope"],
-        isotope_data=isotope_data)
+        ["Ccarb::$CIsotopeType"],
+        isotope_data=Dict())
 
     fluxOceanfloorSolute = PB.Fluxes.FluxContrib(
         "fluxOceanfloor.soluteflux_",
-        ["DIC::CIsotope"],
-        isotope_data=isotope_data)
+        ["DIC::$CIsotopeType"],
+        isotope_data=Dict())
 
     if rj.pars.sfw_distribution_method.v == "Depth"
         grid_vars = [