sync with PALEOaqchem v0.3.16 updates

PALEOtoolkit · Dec 1, 2024 · 394cc5a · 394cc5a
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diff --git a/Project.toml b/Project.toml
@@ -19,7 +19,7 @@ Documenter = "1.0"
 Infiltrator = "1.0"
 LineSearches = "7.0"
 NLsolve = "4.5.1"
-PALEOaqchem = "0.3.15"
+PALEOaqchem = "0.3.16"
 PALEOboxes = "0.21.33"
 PALEOmodel = "0.15.8"
 Pkg = "1.0"

diff --git a/examples/CONPSFeMn/PALEO_examples_sediment_NNFeMnP_cfg.yaml b/examples/CONPSFeMn/PALEO_examples_sediment_NNFeMnP_cfg.yaml
@@ -175,7 +175,7 @@ sediment_Corg_O2NNMnFeSP:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/CONPSFeMn/PALEO_examples_sediment_NNFeMn_cfg.yaml b/examples/CONPSFeMn/PALEO_examples_sediment_NNFeMn_cfg.yaml
@@ -170,7 +170,7 @@ sediment_Corg_O2NNMnFeS:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/FOAM/PALEO_examples_sediment_FOAM_cfg.yaml b/examples/FOAM/PALEO_examples_sediment_FOAM_cfg.yaml
@@ -217,7 +217,7 @@ sediment_FOAM:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/FOAM/PALEO_examples_sediment_FOAM_minimal_cfg.yaml b/examples/FOAM/PALEO_examples_sediment_FOAM_minimal_cfg.yaml
@@ -157,7 +157,7 @@ sediment_Corg_Stest:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/boudreau1996/PALEO_examples_sediment_cfg.yaml b/examples/boudreau1996/PALEO_examples_sediment_cfg.yaml
@@ -129,7 +129,7 @@ sediment_Corg_O2:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute
@@ -421,7 +421,7 @@ sediment_Corg_O2_carb:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/ironsulphur/PALEO_examples_sediment_ironsulphur_cfg.yaml b/examples/ironsulphur/PALEO_examples_sediment_ironsulphur_cfg.yaml
@@ -141,7 +141,7 @@ sediment_Corg_O2_Fe:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute
@@ -524,7 +524,7 @@ sediment_Corg_O2_Fe_pyr_carb:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/transport_tests/PALEO_transport_Corgdecay_cfg.yaml b/examples/transport_tests/PALEO_transport_Corgdecay_cfg.yaml
@@ -111,7 +111,7 @@ sediment_abiotic_O2:
                         trspt_sms_ext:  _trspt_sms
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/transport_tests/PALEO_transport_RCmultiG_cfg.yaml b/examples/transport_tests/PALEO_transport_RCmultiG_cfg.yaml
@@ -144,7 +144,7 @@ sediment_abiotic_O2:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/transport_tests/PALEO_transport_mudCorg_cfg.yaml b/examples/transport_tests/PALEO_transport_mudCorg_cfg.yaml
@@ -118,7 +118,7 @@ sediment_abiotic_O2:
                         trspt_sms_ext:  _trspt_sms
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/transport_tests/PALEO_transport_mud_cfg.yaml b/examples/transport_tests/PALEO_transport_mud_cfg.yaml
@@ -118,7 +118,7 @@ sediment_abiotic_O2:
                         trspt_sms_ext:  _trspt_sms
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/examples/transport_tests/PALEO_transport_sediment_cfg.yaml b/examples/transport_tests/PALEO_transport_sediment_cfg.yaml
@@ -114,7 +114,7 @@ sediment_abiotic_O2:
                     class: ReactionSedimentTransportSolid
 
                 molecular_diffusivity:   
-                    class: ReactionAqMolecularDiffusion
+                    class: ReactionAqMolecularDiffusivity
 
                 transportsedsolute:
                     class: ReactionSedimentTransportSolute

diff --git a/src/sediment/SedimentTransport.jl b/src/sediment/SedimentTransport.jl
@@ -3,7 +3,6 @@ module SedimentTransport
 import PALEOboxes as PB
 using PALEOboxes.DocStrings
 import PALEOsediment
-import PALEOaqchem
 
 import LinearAlgebra
 import SparseArrays
@@ -324,7 +323,7 @@ Bioturbation (`diff_bioturb [m^2 yr-1]`) and bioirrigation (`alpha_bioirrig [yr-
 on the sediment grid by eg [`PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates`](@ref).
 
 Molecular diffusivity should be supplied for each species by Variables `<speciesname>_moldiff [cm^2 s-1]` eg as calculated by
-`PALEOaqchem.MolecularDiffusion.ReactionAqMolecularDiffusion` or set to a constant using `PALEOboxes.ReactionConst`.
+`PALEOaqchem.MolecularDiffusion.ReactionAqMolecularDiffusivity` or set to a constant using `PALEOboxes.ReactionConst`.
 
 ## Boundary conditions
 
@@ -832,14 +831,16 @@ end
 """
     SoluteCombinedDiffusivity(moldiff::Vector, Dfac::Vector, bioturb::Vector) -> scd
 
-calculate `scd[i]` `cm^2 s-1`, tortuoisity-corrected solute diffusivity combined with bioturbation
+Calculate `scd[i]` `m^2 yr-1`: tortuoisity-corrected solute diffusivity combined with bioturbation
+for Vector index `i`.
 """
 struct SoluteCombinedDiffusivity{M, D, B}
     moldiff::M
     Dfac::D
     bioturb::B
 end
 
+# implementation of scd[i]
 function Base.getindex(scd::SoluteCombinedDiffusivity, i)
     # m^2 yr-1  = cm^2 s-1     * s yr-1         * (cm m-1)^2
     cd = scd.moldiff[i] * PB.Constants.k_secpyr*1e-4*scd.Dfac[i] + scd.bioturb[i]