Merge pull request #50 from BattModels/shhh

add option for overpotential not to warn as it makes phase diagram co…

Project.toml

@@ -1,7 +1,7 @@
 name = "ElectrochemicalKinetics"
 uuid = "a2c6e634-85ca-418a-9c67-9b5417ce2d04"
 authors = ["Rachel Kurchin <[email protected]>", "Holden Parks <[email protected]>", "Dhairya Gandhi <[email protected]>"]
-version = "0.1.2"
+version = "0.1.3"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"

src/fitting.jl

@@ -45,7 +45,7 @@ Given values for current/rate constant and specified model parameters, find the
 
 NOTE that this currently only solves for net reaction rates.
 """
-function overpotential(k, model::KineticModel, guess = _get_guess(k, model); T = 298, loss = janky_log_loss, autodiff = true, verbose=false, kwargs...)
+function overpotential(k, model::KineticModel, guess = _get_guess(k, model); T = 298, loss = janky_log_loss, autodiff = true, verbose=false, warn=true, kwargs...)
     # wherever k=0 we can shortcut since the answer has to be 0
     k_solve = k
     if k==0 # scalar k=0, possibly vector model
@@ -91,7 +91,7 @@ function overpotential(k, model::KineticModel, guess = _get_guess(k, model); T =
     else
         Vs = nlsolve(compare_k!, guess, show_trace=verbose)
     end
-    if !converged(Vs)
+    if !converged(Vs) && warn
         @warn "Overpotential fit not fully converged...you may have fed in an unreachable reaction rate!"
     end
     sol = Vs.zero

src/phase_diagrams.jl

@@ -23,18 +23,18 @@ prefactor(x, intercalate::Bool) = intercalate ? (1 .- x) : x
 These functions return single-argument functions (to easily use common-tangent function below while
 still being able to swap out model parameters by calling "function-builders" with different arguments).
 """
-function µ_kinetic(I, km::KineticModel; intercalate=true, kwargs...)
+function µ_kinetic(I, km::KineticModel; intercalate=true, warn=true, kwargs...)
     thermo_term(x) = μ_thermo(x; kwargs...)
-    μ(x::Real) = thermo_term(x) .+ overpotential(I, prefactor(x, intercalate)*km)
-    μ(x::AbstractVector) = thermo_term(x) .+ overpotential(I, prefactor(x, intercalate).*Ref(km))
+    μ(x::Real) = thermo_term(x) .+ overpotential(I, prefactor(x, intercalate)*km, warn=warn)
+    μ(x::AbstractVector) = thermo_term(x) .+ overpotential(I, prefactor(x, intercalate).*Ref(km), warn=warn)
     return μ
 end
 
-function g_kinetic(I, km::KineticModel; intercalate=true, kwargs...)
+function g_kinetic(I, km::KineticModel; intercalate=true, warn=true, kwargs...)
     thermo_term(x) = g_thermo(x; kwargs...)
     #TODO: gradient of this term is just value of overpotential(x)
     function kinetic_term(x)
-        f(x) = ElectrochemicalKinetics.overpotential(I, prefactor(x, intercalate) * km)
+        f(x) = ElectrochemicalKinetics.overpotential(I, prefactor(x, intercalate) * km, warn=warn)
         n, w = ElectrochemicalKinetics.scale_coarse(zero.(x), x)
         map((w, n) -> sum(w .* f(n)), eachcol(w), eachcol(n))
     end