Dissolution, physical erosion and emperical denudation impletement

Manifest.toml

@@ -1,8 +1,8 @@
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+
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@@ -361,6 +415,12 @@ version = "1.3.0"
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+
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examples/denudation/caps-miller-emp.jl

@@ -1,25 +1,21 @@
 # ~/~ begin <<docs/src/ca-with-production.md#examples/caps-osc.jl>>[init]
 using CarboKitten
-using CarboKitten.CaProdErosion
+using CarboKitten.Model.WithDenudation
 using CarboKitten.Burgess2013
-using CarboKitten.InputConfig: Input
+using CarboKitten.Model.WithDenudation: Input
 using CSV
 using DataFrames
 using Interpolations
 using Unitful
 using CarboKitten.Config: Box, Vectors, TimeProperties
 using CarboKitten.BoundaryTrait
-using CarboKitten.Denudation: Dissolution, NoDenudation, PhysicalErosionParam, EmpericalDenudationParam
+using CarboKitten.Denudation: DissolutionMod, NoDenudationMod, PhysicalErosionMod, EmpiricalDenudationMod
+using CarboKitten.Denudation: Dissolution, EmpiricalDenudation, PhysicalErosion, NoDenudation
+
 
-function sealevel_curve(t,filepath)
-    data = DataFrame(CSV.File(filepath))
-    data = hcat(collect(0:length(data[:,1]).-1)./1000, data[:,1]) #The output sealevel curve from R does not have time tab and have to add it 
-    x = linear_interpolation(data[:,1], data[:,2])
-    return x(t)
-end 
 
 const MODEL1 = [
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 500u"m/Myr",
     extinction_coefficient = 0.8u"m^-1",
@@ -28,7 +24,7 @@ const MODEL1 = [
     mass_density = 2730u"kg/m^3",
     infiltration_coefficient= 0.5),
 
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 400u"m/Myr",
     extinction_coefficient = 0.1u"m^-1",
@@ -37,7 +33,7 @@ const MODEL1 = [
     mass_density = 2730u"kg/m^3",
     infiltration_coefficient= 0.5),
 
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 100u"m/Myr",
     extinction_coefficient = 0.005u"m^-1",
@@ -47,7 +43,7 @@ const MODEL1 = [
     infiltration_coefficient= 0.5)
 ]
 
-const DENUDATION = EmpericalDenudationParam(precip = 1.0u"m")#PhysicalErosionParam(1e-3)
+const DENUDATION = EmpiricalDenudation(precip = 1.0u"m")#PhysicalErosionParam(1e-3)
 
 const INPUT = Input(
     box=Box{Shelf}(grid_size = (100, 50), phys_scale = 1.0u"km"),
@@ -61,8 +57,8 @@ const INPUT = Input(
     initial_depth = x -> x/300.0,
     facies = MODEL1,
     insolation = 400.0u"W/m^2",
-    denudationparam = DENUDATION
+    denudation = DENUDATION
   )
 
-CaProdErosion.main(INPUT, "data/caps-test.h5")
+WithDenudation.main(INPUT, "data/caps-test.h5")
 # ~/~ end

examples/denudation/caps-miller-phys.jl

@@ -1,25 +1,20 @@
 # ~/~ begin <<docs/src/ca-with-production.md#examples/caps-osc.jl>>[init]
 using CarboKitten
-using CarboKitten.CaProdErosion
+using CarboKitten.Model.WithDenudation
 using CarboKitten.Burgess2013
-using CarboKitten.InputConfig: Input
+using CarboKitten.Model.WithDenudation: Input
 using CSV
 using DataFrames
 using Interpolations
 using Unitful
 using CarboKitten.Config: Box, Vectors, TimeProperties
 using CarboKitten.BoundaryTrait
-using CarboKitten.Denudation: Dissolution, NoDenudation, PhysicalErosionParam, EmpericalDenudationParam
+using CarboKitten.Denudation: DissolutionMod, NoDenudationMod, PhysicalErosionMod, EmpiricalDenudationMod
+using CarboKitten.Denudation: Dissolution, EmpiricalDenudation, PhysicalErosion, NoDenudation
 
-function sealevel_curve(t,filepath)
-    data = DataFrame(CSV.File(filepath))
-    data = hcat(collect(0:length(data[:,1]).-1)./1000, data[:,1]) #The output sealevel curve from R does not have time tab and have to add it 
-    x = linear_interpolation(data[:,1], data[:,2])
-    return x(t)
-end 
 
 const MODEL1 = [
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 500u"m/Myr",
     extinction_coefficient = 0.8u"m^-1",
@@ -28,7 +23,7 @@ const MODEL1 = [
     mass_density = 2730u"kg/m^3",
     infiltration_coefficient= 0.5),
 
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 400u"m/Myr",
     extinction_coefficient = 0.1u"m^-1",
@@ -37,7 +32,7 @@ const MODEL1 = [
     mass_density = 2730u"kg/m^3",
     infiltration_coefficient= 0.5),
 
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 100u"m/Myr",
     extinction_coefficient = 0.005u"m^-1",
@@ -47,7 +42,7 @@ const MODEL1 = [
     infiltration_coefficient= 0.5)
 ]
 
-const DENUDATION = PhysicalErosionParam(erodability = 1e-3u"m/yr")
+const DENUDATION = PhysicalErosion(erodability = 1e-3u"m/yr")
 
 const INPUT = Input(
     box=Box{Shelf}(grid_size = (100, 50), phys_scale = 1.0u"km"),
@@ -61,8 +56,8 @@ const INPUT = Input(
     initial_depth = x -> x/300.0,
     facies = MODEL1,
     insolation = 400.0u"W/m^2",
-    denudationparam = DENUDATION
+    denudation = DENUDATION
   )
 
-CaProdErosion.main(INPUT, "data/caps-test.h5")
+WithDenudation.main(INPUT, "data/caps-test.h5")
 # ~/~ end

examples/denudation/caps-miller_diss.jl

@@ -1,25 +1,19 @@
 # ~/~ begin <<docs/src/ca-with-production.md#examples/caps-osc.jl>>[init]
 using CarboKitten
-using CarboKitten.CaProdErosion
+using CarboKitten.Model.WithDenudation
 using CarboKitten.Burgess2013
-using CarboKitten.InputConfig: Input
+using CarboKitten.Model.WithDenudation: Input
 using CSV
 using DataFrames
 using Interpolations
 using Unitful
 using CarboKitten.Config: Box, Vectors, TimeProperties
 using CarboKitten.BoundaryTrait
-using CarboKitten.Denudation: Dissolution, NoDenudation, PhysicalErosionParam, EmpericalDenudationParam
-
-function sealevel_curve(t,filepath)
-    data = DataFrame(CSV.File(filepath))
-    data = hcat(collect(0:length(data[:,1]).-1)./1000, data[:,1]) #The output sealevel curve from R does not have time tab and have to add it 
-    x = linear_interpolation(data[:,1], data[:,2])
-    return x(t)
-end 
+using CarboKitten.Denudation: DissolutionMod, NoDenudationMod, PhysicalErosionMod, EmpiricalDenudationMod
+using CarboKitten.Denudation: Dissolution, EmpiricalDenudation, PhysicalErosion, NoDenudation
 
 const MODEL1 = [
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 500u"m/Myr",
     extinction_coefficient = 0.8u"m^-1",
@@ -28,7 +22,7 @@ const MODEL1 = [
     mass_density = 2730u"kg/m^3",
     infiltration_coefficient= 0.5),
 
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 400u"m/Myr",
     extinction_coefficient = 0.1u"m^-1",
@@ -37,7 +31,7 @@ const MODEL1 = [
     mass_density = 2730u"kg/m^3",
     infiltration_coefficient= 0.5),
 
-    Burgess2013.Facies(viability_range = (4, 10),
+    WithDenudation.Facies(viability_range = (4, 10),
     activation_range = (6, 10),
     maximum_growth_rate = 100u"m/Myr",
     extinction_coefficient = 0.005u"m^-1",
@@ -47,7 +41,7 @@ const MODEL1 = [
     infiltration_coefficient= 0.5)
 ]
 
-const DENUDATION = Dissolution(temp = 273.0u"K",precip = 1.0u"mm", pco2 = 10^(-1.5)*u"atm",reactionrate = 2e-3u"m/yr")#PhysicalErosionParam(1e-3)EmpericalDenudationParam(1.0)
+const DENUDATION = Dissolution(temp = 273.0u"K",precip = 1.0u"m", pco2 = 10^(-1.5)*u"atm",reactionrate = 2e-3u"m/yr")#PhysicalErosionParam(1e-3)EmpericalDenudationParam(1.0)
 
 const INPUT = Input(
     box=Box{Shelf}(grid_size = (100, 50), phys_scale = 1.0u"km"),
@@ -61,8 +55,8 @@ const INPUT = Input(
     initial_depth = x -> x/300.0,
     facies = MODEL1,
     insolation = 400.0u"W/m^2",
-    denudationparam = DENUDATION
+    denudation = DENUDATION
   )
 
-CaProdErosion.main(INPUT, "data/caps-test2.h5")
+WithDenudation.main(INPUT, "data/caps-test2.h5")
 # ~/~ end

src/Burgess2013/Config.jl

@@ -11,27 +11,28 @@ export Facies, MODEL1
     maximum_growth_rate::typeof(1.0u"m/Myr")
     extinction_coefficient::typeof(1.0u"m^-1")
     saturation_intensity::typeof(1.0u"W/m^2")
+
 end
 
-const MODEL1 = [
-    Facies(viability_range = (4, 10),
-           activation_range = (6, 10),
-           maximum_growth_rate = 500u"m/Myr",
-           extinction_coefficient = 0.8u"m^-1",
-           saturation_intensity = 60u"W/m^2"),
-
-    Facies(viability_range = (4, 10),
-           activation_range = (6, 10),
-           maximum_growth_rate = 400u"m/Myr",
-           extinction_coefficient = 0.1u"m^-1",
-           saturation_intensity = 60u"W/m^2"),
-
-    Facies(viability_range = (4, 10),
-           activation_range = (6, 10),
-           maximum_growth_rate = 100u"m/Myr",
-           extinction_coefficient = 0.005u"m^-1",
-           saturation_intensity = 60u"W/m^2")
-]
+# const MODEL1 = [
+#     Facies(viability_range = (4, 10),
+#            activation_range = (6, 10),
+#            maximum_growth_rate = 500u"m/Myr",
+#            extinction_coefficient = 0.8u"m^-1",
+#            saturation_intensity = 60u"W/m^2"),
+
+#     Facies(viability_range = (4, 10),
+#            activation_range = (6, 10),
+#            maximum_growth_rate = 400u"m/Myr",
+#            extinction_coefficient = 0.1u"m^-1",
+#            saturation_intensity = 60u"W/m^2"),
+
+#     Facies(viability_range = (4, 10),
+#            activation_range = (6, 10),
+#            maximum_growth_rate = 100u"m/Myr",
+#            extinction_coefficient = 0.005u"m^-1",
+#            saturation_intensity = 60u"W/m^2")
+# ]
 
 end
 # ~/~ end