fix ReactionAreaVolumeValInRange with isotope (#26)

* fix ReactionAreaVolumeValInRange with isotope * fix ReactionWeightedMean for isotopes
PALEOtoolkit · May 19, 2022 · abecdd1 · abecdd1 · sjdaines · May 19, 2022
1 parent 8d238f0
commit abecdd1
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Showing 4 changed files with 48 additions and 6 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "PALEOboxes"
 uuid = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
 authors = ["Stuart Daines <[email protected]>"]
-version = "0.18.6"
+version = "0.18.7"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

diff --git a/src/reactioncatalog/VariableStats.jl b/src/reactioncatalog/VariableStats.jl
@@ -207,6 +207,9 @@ Base.@kwdef mutable struct ReactionWeightedMean{P} <: PB.AbstractReaction
     base::PB.ReactionBase
 
     pars::P = PB.ParametersTuple(
+        PB.ParType(PB.AbstractData, "field_data", PB.ScalarData,
+            allowed_values=PB.IsotopeTypes,
+            description="disable / enable isotopes and specify isotope type"),
     )
 
 
@@ -216,11 +219,12 @@ end
 function PB.register_methods!(rj::ReactionWeightedMean)
 
     vars = [
-        PB.VarDep(       "var", "measure-1", "variable to calculate weighted mean from"),
+        PB.VarDep(       "var", "measure-1", "variable to calculate weighted mean from",
+            attributes=(:field_data=>rj.pars.field_data.v,)),
         PB.VarDep(       "measure", "", "cell area or volume"),
         PB.VarDepScalar( "measure_total", "", "total Domain area or volume"),
         PB.VarPropScalar("var_mean", "", "weighted mean over Domain area or volume",
-            attributes=(:initialize_to_zero=>true, :atomic=>true)),
+            attributes=(:field_data=>rj.pars.field_data.v, :initialize_to_zero=>true, :atomic=>true)),
     ]
 
     PB.add_method_do!(rj, do_weighted_mean, (PB.VarList_namedtuple(vars),))
@@ -273,7 +277,8 @@ end
 function PB.register_methods!(rj::ReactionAreaVolumeValInRange)
 
     vars = [
-        PB.VarDep(       "rangevar", "mol m-3", "variable to check within range"),
+        PB.VarDep(       "rangevar", "mol m-3", "variable to check within range";
+            attributes=(:field_data=>PB.ScalarData, )), # total only, not isotope
         PB.VarDep(       "measure", "", "cell area or volume"),
         PB.VarDepScalar( "measure_total", "", "total Domain area or volume"),
         PB.VarPropScalar("frac", "", "fraction of Domain area or volume in specified range",

diff --git a/test/configreservoirs.yaml b/test/configreservoirs.yaml
@@ -49,13 +49,25 @@ model1:
         ocean:
 
             reactions:
+                grid:
+                    class: ReactionUnstructuredVectorGrid
+                    parameters:
+                        ncells: 1000
+
                 const_volume:
                     class: ReactionConst
                     parameters:
                         constnames: ["volume"]
                     variable_attributes:                       
                         volume:initial_value:        10.0
 
+                const_volume_total:
+                    class: ReactionScalarConst
+                    parameters:
+                        constnames: ["volume_total"]
+                    variable_attributes:                       
+                        volume_total:initial_value:  10000.0
+
                 reservoir_const:
                     class: ReactionReservoirConst
                     parameters:
@@ -80,4 +92,22 @@ model1:
                         vars_to_add: [volume, 2*T]
                     variable_links:
                         sum: vectorsum # 30.0
+
+                weightedmean:
+                    class: ReactionWeightedMean
+                    parameters:
+                        field_data: IsotopeLinear
+                    variable_links:
+                        var*:           const_conc*
+                        measure*:       volume*
+
+                volinrange:
+                    class: ReactionAreaVolumeValInRange
+                    parameters:
+                        range_min:         0.0
+                        range_max:         0.2
+                    variable_links:
+                        rangevar:           const_conc
+                        measure*:            volume*
+
 
diff --git a/test/runreservoirtests.jl b/test/runreservoirtests.jl
@@ -4,6 +4,7 @@ using Logging
 
 import PALEOboxes as PB
 
+import Infiltrator
 
 @testset "Reservoirs" begin
 
@@ -19,7 +20,6 @@ import PALEOboxes as PB
     @test global_domain.name == "global"
     @test  PB.get_length(global_domain) == 1
     ocean_domain =  PB.get_domain(model, "ocean")
-    ocean_domain.grid = PB.Grids.UnstructuredVectorGrid(ncells=1000)
     @test  PB.get_length(ocean_domain) == 1000
     ocean_length = PB.get_length(ocean_domain)
 
@@ -75,8 +75,10 @@ import PALEOboxes as PB
     @info "ocean host-dependent variables:\n"  ocean_hostdep_data
     @test ocean_hostdep_data["T"][1]           == 1.0*10.0    
 
+    # take a time step
     dispatchlists = modeldata.dispatchlists_all
     PB.do_deriv(dispatchlists)
+
     @info "global model-created variables:\n" global_modelcreated_vars_dict
     @test  PB.get_data(global_modelcreated_vars_dict["A_norm"], modeldata)[] == 10.0
     @test  PB.get_data(global_modelcreated_vars_dict["A_delta"], modeldata)[]== 2.0
@@ -95,7 +97,12 @@ import PALEOboxes as PB
     @test const_conc_data.v             == fill(0.1, ocean_length)
     @test const_conc_data.v_moldelta    == fill(-0.2, ocean_length)
 
-    model = nothing
+    @info "weighted mean"
+    @test PB.get_data(ocean_modelcreated_vars_dict["const_conc_mean"], modeldata)[] == PB.IsotopeLinear(0.1, -0.2)
+
+    @info "volume in range"
+    @test PB.get_data(ocean_modelcreated_vars_dict["frac"], modeldata)[] == 1.0
+
 
     @info "test complete"
     # close(logfile)