Refactor how model parameters are stored and passed

OpenThermochronology · Nov 12, 2022 · f99c528 · f99c528 · brenhinkeller · Nov 12, 2022
1 parent 98f1372
commit f99c528
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Showing 8 changed files with 364 additions and 351 deletions.
diff --git a/examples/ZrnHeInversionVartCryst.jl b/examples/ZrnHeInversionVartCryst.jl
diff --git a/src/Thermochron.jl b/src/Thermochron.jl
@@ -6,7 +6,7 @@ module Thermochron
     using ProgressMeter: @showprogress
 
     include("minerals.jl")
-    include("ZrnHe.jl")
+    include("zirconhelium.jl")
     include("inversion.jl")
 
 end
diff --git a/src/inversion.jl b/src/inversion.jl
@@ -15,9 +15,8 @@
         sigma = sqrt(sigma_analytical^2 + sigma_annealing^2)
 
     """
-    function simannealsigma(n, sigma_analytical; params=(25.0, 35.0, 10/10^5))
-        σₘ, σᵢ, λ = params
-        sigma_annealing = σᵢ*exp(-λ*n) + σₘ
-        return sqrt(sigma_analytical^2 + sigma_annealing^2)
+    function simannealsigma(n, sigma_analytical; params=(σModel=25.0, σAnnealing=35.0, λAnnealing=10/10^5))
+        sigma_combined = params.σAnnealing * exp(-params.λAnnealing*n) + params.σModel
+        return sqrt(sigma_analytical^2 + sigma_combined^2)
     end
     export simannealsigma
diff --git a/src/ZrnHe.jl → src/zirconhelium.jl b/src/ZrnHe.jl → src/zirconhelium.jl
@@ -1,25 +1,26 @@
 
 """
 ```julia
-ρᵣ = DamageAnnealing(dt::Number, tSteps::Vector, TSteps::Matrix)
+ρᵣ = anneal(dt::Number, tSteps::Vector, TSteps::Matrix, [model::Symbol])
 ```
 Zircon damage annealing model as in Guenthner et al. 2013 (AJS)
 """
-function DamageAnnealing(dt::Number, tSteps::DenseVector, TSteps::DenseVector)
+function anneal(dt::Number, tSteps::DenseVector, TSteps::DenseVector, model=:zrdaam)
     # Allocate matrix to hold reduced track lengths for all previous timesteps
     ρᵣ = zeros(length(tSteps),length(tSteps))
     # In=-place version
-    DamageAnnealing!(ρᵣ, dt, tSteps, TSteps)
+    anneal!(ρᵣ, dt, tSteps, TSteps, model)
 end
-export DamageAnnealing
+export anneal
 
 """
 ```julia
-DamageAnnealing!(ρᵣ::Matrix, dt::Number, tSteps::Vector, TSteps::Vector)
+anneal!(ρᵣ::Matrix, dt::Number, tSteps::Vector, TSteps::Vector, [model::Symbol])
 ```
-In-place version of `DamageAnnealing`
+In-place version of `anneal`
 """
-function DamageAnnealing!(ρᵣ::DenseMatrix, dt::Number, tSteps::DenseVector, TSteps::DenseVector)
+anneal!(ρᵣ::DenseMatrix, dt::Number, tSteps::DenseVector, TSteps::DenseVector, model::Symbol) = anneal!(ρᵣ, dt, tSteps, TSteps, Val(model))
+function anneal!(ρᵣ::DenseMatrix, dt::Number, tSteps::DenseVector, TSteps::DenseVector, ::Val{:zrdaam})
     # Annealing model constants
     B=-0.05721
     C0=6.24534
@@ -63,7 +64,7 @@ function DamageAnnealing!(ρᵣ::DenseMatrix, dt::Number, tSteps::DenseVector, T
 
     return ρᵣ
 end
-export DamageAnnealing!
+export anneal!
 
 
 """

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -2,6 +2,6 @@ using Thermochron
 using LinearAlgebra
 using Test
 
-@testset "Zircon helium" begin include("testZrnHe.jl") end
+@testset "Zircon helium" begin include("testzirconhelium.jl") end
 @testset "Inversion" begin include("testinversion.jl") end
 @testset "Integrated Examples" begin include("testexamples.jl") end