From 394cc5afe7565c5dab7b7186541d57a8414ed285 Mon Sep 17 00:00:00 2001 From: Stuart Daines Date: Sun, 1 Dec 2024 13:03:17 +0000 Subject: [PATCH] sync with PALEOaqchem v0.3.16 updates --- Project.toml | 2 +- .../CONPSFeMn/PALEO_examples_sediment_NNFeMnP_cfg.yaml | 2 +- examples/CONPSFeMn/PALEO_examples_sediment_NNFeMn_cfg.yaml | 2 +- examples/FOAM/PALEO_examples_sediment_FOAM_cfg.yaml | 2 +- .../FOAM/PALEO_examples_sediment_FOAM_minimal_cfg.yaml | 2 +- examples/boudreau1996/PALEO_examples_sediment_cfg.yaml | 4 ++-- .../PALEO_examples_sediment_ironsulphur_cfg.yaml | 4 ++-- .../transport_tests/PALEO_transport_Corgdecay_cfg.yaml | 2 +- examples/transport_tests/PALEO_transport_RCmultiG_cfg.yaml | 2 +- examples/transport_tests/PALEO_transport_mudCorg_cfg.yaml | 2 +- examples/transport_tests/PALEO_transport_mud_cfg.yaml | 2 +- examples/transport_tests/PALEO_transport_sediment_cfg.yaml | 2 +- src/sediment/SedimentTransport.jl | 7 ++++--- 13 files changed, 18 insertions(+), 17 deletions(-) diff --git a/Project.toml b/Project.toml index 1571e32..965a21a 100644 --- 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 index 9fe9947..dc4b2da 100644 --- 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 index 88d5fa6..0d3b405 100644 --- 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 index 7ab2b03..c9566ce 100644 --- 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 index da508c6..3159028 100644 --- 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 index 429830c..da76857 100644 --- 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 index 2402718..d6f0094 100644 --- 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 index cbaa337..d3554c8 100644 --- 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 index ec7e296..080f745 100644 --- 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 index 47dc068..e84c699 100644 --- 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 index 81b068f..5dc8935 100644 --- 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 index 7e8286f..ae11c0c 100644 --- 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 index 8df3eff..05a59b9 100644 --- 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 `_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 @@ -832,7 +831,8 @@ 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 @@ -840,6 +840,7 @@ struct SoluteCombinedDiffusivity{M, D, B} 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]