Merge branch 'main' into compathelper/new_version/2024-01-06-00-46-13…

…-136-00252389865

.github/workflows/CI.yml

@@ -59,9 +59,7 @@ jobs:
           julia --project=docs/ -e '
             using Pkg
             Pkg.develop([
-            PackageSpec(path=pwd()),
-            PackageSpec(url="https://github.com/cfarm6/ContinuumMechanicsBase.jl.git"),
-            PackageSpec(url="https://github.com/cfarm6/InverseLangevinApproximations.jl.git"),
+                PackageSpec(path=pwd()),
             ])
             Pkg.instantiate()
             Pkg.update()'

Project.toml

@@ -1,7 +1,7 @@
 name = "Hyperelastics"
 uuid = "c20c605d-adbe-46e4-9db6-e2b04c3ba023"
 authors = ["Carson Farmer"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -16,7 +16,6 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
 PackageExtensionCompat = "65ce6f38-6b18-4e1d-a461-8949797d7930"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
@@ -52,15 +51,14 @@ ComponentArrays = "0.15"
 ContinuumMechanicsBase = "0.1"
 DataInterpolations = "4"
 DocStringExtensions = "0.9"
-Integrals = "3"
-InverseLangevinApproximations = "0.1"
+Integrals = "4"
+InverseLangevinApproximations = "0.2"
 LabelledArrays = "1"
 LossFunctions = "0.11"
 PackageExtensionCompat = "1"
 QuadGK = "2"
-RecursiveArrayTools = "2"
 Reexport = "1"
-SciMLBase = "1, 2"
+SciMLBase = "2"
 SpecialFunctions = "2"
 StructArrays = "0.6"
 Unitful = "1"

README.md

@@ -1,5 +1,5 @@
 # Hyperelastics
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cfarm6.github.io/Hyperelastics.jl/stable) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cfarm6.github.io/Hyperelastics.jl/dev)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://TRACER-LULab.github.io/Hyperelastics.jl/stable) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://TRACER-LULab.github.io/Hyperelastics.jl/dev)
 [![codecov](https://codecov.io/gh/TRACER-LULab/Hyperelastics.jl/graph/badge.svg?token=EML9TQUEP9)](https://codecov.io/gh/TRACER-LULab/Hyperelastics.jl)
 
 

docs/Project.toml

@@ -1,26 +1,22 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
-ContinuumMechanicsBase = "3a778109-d974-46c8-ac54-09f30d605bdf"
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Hyperelastics = "c20c605d-adbe-46e4-9db6-e2b04c3ba023"
-InverseLangevinApproximations = "b82787f2-62be-403e-9078-6d9feafd7ee3"
 MakiePublication = "dde8697e-0d61-460d-88dd-856f66710dd1"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 
 [compat]
 CairoMakie = "0.10"
 ComponentArrays = "0.15"
-ContinuumMechanicsBase = "0.1"
 DataInterpolations = "4"
 Documenter = "1"
 DocumenterCitations = "1"
 ForwardDiff = "0.10"
-InverseLangevinApproximations = "0.1"
 MakiePublication = "0.3"
 Optimization = "3"
-OptimizationOptimJL = "0.1, 0.2"
+OptimizationOptimJL = "0.2"

docs/src/example.md

@@ -6,14 +6,14 @@ using Optimization, OptimizationOptimJL
 using ComponentArrays: ComponentVector
 using ForwardDiff
 using CairoMakie, MakiePublication
-set_theme!(theme_web(width = 800))
+set_theme!(theme_latexfonts())
 ```
 
 For commonly used datasets in hyperelastic modelling, such as the `Treloar1944Uniaxial` data, functions are available for getting the datasets:
 
 ```@example 1
-f = Figure()
-ax = Makie.Axis(f[1,1])
+f = Figure(size = (800,800))
+ax = Makie.Axis(f[1,1], xlabel = "Stretch [-]", ylabel = "Stress [kg/cm²]")
 treloar_data = Treloar1944Uniaxial()
 scatter!(ax, 
     getindex.(treloar_data.data.λ, 1), 
@@ -58,16 +58,15 @@ For fiting multiple models to the same dataset,
 
 ```@example 1
 models = Dict(
-    Gent => ComponentVector(μ=240e-3, Jₘ=80.0),
+    Gent => ComponentVector(μ=240e-3, J_m=80.0),
     EdwardVilgis => ComponentVector(Ns=0.10, Nc=0.20, α=0.001, η=0.001),
     NeoHookean => ComponentVector(μ=200e-3),
-    NonaffineMicroSphere => ComponentVector(μ=0.292, N=22.5, p=1.471, U=0.744, q=0.1086),
     Beda => ComponentVector(C1=0.1237, C2=0.0424, C3=7.84e-5, K1=0.0168, α=0.9, β=0.68, ζ=3.015)
 )
 
 sol = Dict{Any, SciMLSolution}()
-for (ψ, p₀) in models
-    HEProblem = HyperelasticProblem(ψ(), treloar_data, p₀,  ad_type = AutoForwardDiff())
+for (ψ, p_0) in models
+    HEProblem = HyperelasticProblem(ψ(), treloar_data, p_0,  ad_type = AutoForwardDiff())
     sol[ψ] = solve(HEProblem, NelderMead())
 end
 return sol # hide
@@ -76,8 +75,8 @@ return sol # hide
 To predict the reponse of a model to a proivded dataset and parameters, a `predict` function is provided:
 
 ```@example 1
-f = Figure()
-ax = Makie.Axis(f[1,1])
+f = Figure(size = (800,800))
+ax = Makie.Axis(f[1,1], xlabel = "Stretch [-]", ylabel = "Stress [kg/cm²]")
 for (ψ, p) in sol
     pred = predict(ψ(), treloar_data, p.u, ad_type = AutoForwardDiff())
     lines!(ax, getindex.(pred.data.λ, 1), getindex.(pred.data.s, 1), label=string(ψ))
@@ -102,8 +101,10 @@ s₁ = getindex.(treloar_data.data.s, 1)
 λ̂₁ = getindex.(pred.data.λ, 1)
 ŝ₁ = getindex.(pred.data.s, 1)
 
-
-f, ax, p = lines( 
+f = Figure(size = (800,800))
+ax = Makie.Axis(f[1,1], xlabel = "Stretch [-]", ylabel = "Stress [kg/cm²]")
+lines!(
+    ax, 
     λ̂₁, 
     ŝ₁, 
     label = "Sussman-Bathe Approximation"

examples/Project.toml

@@ -17,6 +17,7 @@ LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
+MakiePublication = "dde8697e-0d61-460d-88dd-856f66710dd1"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"

joss/paper.bib

@@ -1,18 +1,25 @@
+@software{matAdi2023,
+  author = {Andreas Dutzler},
+  title  = {matADi: Material Definition with Automatic Differentiation},
+  url    = {https://github.com/adtzlr/matadi},
+  year   = {2023}
+}
+
 @article{Bezanson2017,
-  author   = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
-  title    = {{J}ulia: A Fresh Approach to Numerical Computing},
-  journal  = {SIAM Review},
-  volume   = {59},
-  number   = {1},
-  pages    = {65-98},
-  year     = {2017},
-  doi      = {10.1137/141000671},
-  url      = {
-              https://doi.org/10.1137/141000671
-              },
-  eprint   = {
-              https://doi.org/10.1137/141000671
-              },
+  author  = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
+  title   = {{J}ulia: A Fresh Approach to Numerical Computing},
+  journal = {SIAM Review},
+  volume  = {59},
+  number  = {1},
+  pages   = {65-98},
+  year    = {2017},
+  doi     = {10.1137/141000671},
+  url     = {
+             https://doi.org/10.1137/141000671
+             },
+  eprint  = {
+             https://doi.org/10.1137/141000671
+             }
 }
 
 @article{mooney1940theory,