Refactor ThermalDiffusionLithiumDensity to remove hardcoded parameters

examples/example_config_files/ThermalDiffusionLithiumDensity/Thermal_Diffusion_Config.yml

@@ -0,0 +1,19 @@
+model: ThermalDiffusionLithiumDensity
+material: HPGe
+
+impurity_density_profile: 
+  annealing_temperature_ranges:
+      low_T:
+        T_min: 473K
+        T_max: 873K
+        D0: 2.5e-7m^2/s
+        H: 11800cal
+      high_T:
+        T_min: 873K
+        T_max: 1273K
+        D0: 1.3e-7m^2/s
+        H: 10700cal    
+
+experimental_parameters:
+  a: 21.27
+  b: 2610

src/ImpurityDensities/ThermalDiffusionLithiumDensity.jl

@@ -31,24 +31,49 @@ struct ThermalDiffusionLithiumDensity{T <: SSDFloat} <: AbstractImpurityDensity{
     lithium_diffusivity_in_germanium::T
 end
 
-function calculate_lithium_diffusivity_in_germanium(lithium_annealing_temperature::T)::T where {T <: SSDFloat}
+struct LithiumDiffusionBranch{T <: SSDFloat}
+    T_min::T
+    T_max::T
+    D0::T
+    H::T
+end
+
+struct LithiumDiffusionParameters{T <: SSDFloat}
+    lowT::LithiumDiffusionBranch{T}
+    highT::LithiumDiffusionBranch{T}
+end
+
+struct LithiumSaturationParameters{T <: SSDFloat}
+    a::T
+    b::T
+end
+
+struct ThermalDiffusionLithiumDensityParameters{T <: SSDFloat}
+    diffusion::LithiumDiffusionParameters{T}
+    saturation::LithiumSaturationParameters{T}
+end
+
+include("ThermalDiffusionLithiumDensityParameters.jl")
+
+function calculate_lithium_diffusivity_in_germanium(lithium_annealing_temperature::T,parameters)::LithiumDiffusionParameters::T where {T <: SSDFloat}
     # D0 [m^2*s^-1]
     # H [cal]
-    D0::T, H::T = ifelse(lithium_annealing_temperature <= 873, T.((2.5e-7, 11800)), T.((1.3e-7, 10700)))
+    D0::T, H::T = ifelse(lithium_annealing_temperature <= parameters.lowT.T_max, T.((parameters.lowT.D0, parameters.lowT.H)), T.((parameters.highT.D0, parameters.highT.H)))
     D0 * exp(-H/(R_gas*lithium_annealing_temperature))
 end
-function calculate_lithium_saturated_density(lithium_annealing_temperature::T)::T where {T <: SSDFloat}
-    exp10(27.27 - 2610.0/lithium_annealing_temperature)
+function calculate_lithium_saturated_density(lithium_annealing_temperature::T,parameters::LithiumSaturationParameters)::T where {T <: SSDFloat}
+    exp10(parameters.a - parameters.b/lithium_annealing_temperature)
 end
 
 function ThermalDiffusionLithiumDensity{T}(
+    modelParameters::ThermalDiffusionLithiumDensityParameters{T} = ThermalDiffusionLithiumParameters(), 
     lithium_annealing_temperature::T,
     lithium_annealing_time::T,
     contact_with_lithium_doped::G,
     inactive_contact_id::Int;
     distance_to_contact::Function = pt::AbstractCoordinatePoint{T} -> ConstructiveSolidGeometry.distance_to_surface(pt, contact_with_lithium_doped),
-    lithium_density_on_contact::T = calculate_lithium_saturated_density(lithium_annealing_temperature),
-    lithium_diffusivity_in_germanium::T = calculate_lithium_diffusivity_in_germanium(lithium_annealing_temperature),
+    lithium_density_on_contact::T = calculate_lithium_saturated_density(lithium_annealing_temperature,modelParameters.saturation),
+    lithium_diffusivity_in_germanium::T = calculate_lithium_diffusivity_in_germanium(lithium_annealing_temperature,modelParameters.diffusion),
 ) where {T <: SSDFloat, G <: Union{<:AbstractGeometry, Nothing}}
     ThermalDiffusionLithiumDensity{T}(lithium_annealing_temperature, lithium_annealing_time, inactive_contact_id, distance_to_contact, lithium_density_on_contact, lithium_diffusivity_in_germanium)
 end

src/ImpurityDensities/ThermalDiffusionLithiumDensityParameters.jl

@@ -0,0 +1,96 @@
+
+
+
+function _ThermalDiffusionLithiumParameters(
+    config::AbstractDict;
+    T::Type = Float32,
+    lowT_Tmin::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["low_T"]["T_min"],
+    lowT_Tmax::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["low_T"]["T_max"],
+    lowT_D0::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["low_T"]["D0"],
+    lowT_H::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["low_T"]["H"],
+    highT_Tmin::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["high_T"]["T_min"],
+    highT_Tmax::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["high_T"]["T_max"],
+    highT_D0::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["high_T"]["D0"],
+    highT_H::Union{RealQuantity, String} =
+        config["impurity_density_profile"]["annealing_temperature_ranges"]["high_T"]["H"],
+    a::Union{Real, String} =
+        config["experimental_parameters"]["a"],
+    b::Union{Real, String} =
+        config["experimental_parameters"]["b"],
+    input_units::Union{Missing, NamedTuple} = missing
+)
+
+    temperature_unit = !ismissing(input_units) ? input_units.temperature : u"K"
+    diffusivity_unit = !ismissing(input_units) ?
+        input_units.length^2 / internal_time_unit : u"m^2/s"
+
+    lowT = LithiumDiffusionBranch{T}(
+        _parse_value(T, lowT_Tmin, temperature_unit),
+        _parse_value(T, lowT_Tmax, temperature_unit),
+        _parse_value(T, lowT_D0,  diffusivity_unit),
+        _parse_value(T, lowT_H,   u"cal")
+    )
+
+    highT = LithiumDiffusionBranch{T}(
+        _parse_value(T, highT_Tmin, temperature_unit),
+        _parse_value(T, highT_Tmax, temperature_unit),
+        _parse_value(T, highT_D0,  diffusivity_unit),
+        _parse_value(T, highT_H,   u"cal")
+    )
+
+    diffusion_params = LithiumDiffusionParameters{T}(lowT, highT)
+
+    saturation_params = LithiumSaturationParameters{T}(
+        T(a),
+        T(b)
+    )
+
+    return ThermalDiffusionLithiumDensityParameters{T}(
+        diffusion_params,
+        saturation_params
+    )
+end
+
+
+function ThermalDiffusionLithiumParameters(config::AbstractDict, input_units::Union{Missing, NamedTuple} = missing; kwargs...)
+    if !haskey(config, "impurity_density_profile") 
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'impurity_density_profile'.")) 
+    elseif !haskey(config["impurity_density_profile"], "annealing_temperature_ranges") 
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'impurity_density_profile/annealing_temperature_ranges'.")) 
+    elseif !haskey(config["impurity_density_profile"]["annealing_temperature_ranges"], "low_T")
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'impurity_density_profile/annealing_temperature_ranges/low_T'."))
+    elseif !haskey(config["impurity_density_profile"]["annealing_temperature_ranges"], "high_T")
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'impurity_density_profile/annealing_temperature_ranges/high_T'."))
+    end
+
+    for axis in ("T_min", "T_max", "D0", "H")
+        if !haskey(config["impurity_density_profile"]["annealing_temperature_ranges"]["low_T"], axis)
+            throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'impurity_density_profile/annealing_temperature_ranges/low_T/$(axis)'."))
+        end
+        if !haskey(config["impurity_density_profile"]["annealing_temperature_ranges"]["high_T"], axis)
+            throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'impurity_density_profile/annealing_temperature_ranges/high_T/$(axis)'."))
+        end
+    end
+
+    if !haskey(config, "experimental_parameters") 
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'experimental_parameters'.")) 
+    elseif !haskey(config["experimental_parameters"], "a") 
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'experimental_parameters/a'.")) 
+    elseif !haskey(config["experimental_parameters"], "b") 
+        throw(ConfigFileError("ThermalDiffusionLithiumDensity config file needs entry 'experimental_parameters/b'.")) 
+    end
+
+    _ThermalDiffusionLithiumParameters(config; input_units = input_units, kwargs...)
+end
+
+const default_ThermalDiffusionLithiumDensity_config_file = joinpath(get_path_to_example_config_files(), "ThermalDiffusionLithiumDensity/Thermal_Diffusion_Config.yaml")
+function ThermalDiffusionLithiumParameters(config_filename::AbstractString = default_ThermalDiffusionLithiumDensity_config_file, input_units::Union{Missing, NamedTuple} = missing; kwargs...)
+    ThermalDiffusionLithiumParameters(parse_config_file(config_filename), input_units; kwargs...)
+end