Merge branch 'main' into adm/powerlaw

JuliaGeodynamics · Oct 19, 2024 · aa97968 · aa97968
2 parents 9917eca + 2b4f474
commit aa97968
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diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml
@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.24.3
+        uses: crate-ci/typos@v1.25.0
diff --git a/.github/workflows/blank.yml b/.github/workflows/blank.yml
@@ -7,6 +7,11 @@ on:
     tags: '*'
   pull_request:
 
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   run_tests:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -15,17 +20,29 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.7'
-          - '1.8'
           - '1.9'
           - '1.10'
+          - '1.11'
           - 'nightly'
         os:
           - ubuntu-latest
-          - macOS-latest
+          - macOS-13
           - windows-latest
         arch:
           - x64
+        include:
+          - os: macOS-latest
+            arch: aarch64
+            version: '1.9'
+          - os: macOS-latest
+            arch: aarch64
+            version: '1.10'
+          - os: macOS-latest
+            arch: aarch64
+            version: '1.11'
+          - os: macOS-latest
+            arch: aarch64
+            version: 'nightly'
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "GeoParams"
 uuid = "e018b62d-d9de-4a26-8697-af89c310ae38"
 authors = ["Boris Kaus <kaus@uni-mainz.de>, Albert De Montserrat <albertdemontserratnavarro@erdw.ethz.ch>"]
-version = "0.6.4"
+version = "0.6.5"
 
 [deps]
 BibTeX = "7b0aa2c9-049f-5cec-894a-2b6b781bb25e"
@@ -15,7 +15,6 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Loess = "4345ca2d-374a-55d4-8d30-97f9976e7612"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
@@ -46,7 +45,6 @@ LinearAlgebra = "1.0"
 Loess = "0.5,0.6"
 MuladdMacro = "0.2.4"
 Parameters = "0.12"
-Requires = "0.5.0, 0.6, 0.7, 0.8, 1.0 - 1.3"
 Roots = "1.0, 2.0"
 Setfield = "0.5.1, 0.6, 0.7, 0.8, 1.0"
 SpecialFunctions = "2.0"
@@ -62,3 +60,7 @@ julia = "1.7"
 [extras]
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test", "Statistics"]
diff --git a/README.md b/README.md
@@ -19,15 +19,20 @@ We also implement some typically used creep law parameters, together with tools
 NOTE: The package remains under development and the API is not yet fully fixed. Therefore feel free to look at it, but be aware that things may still change when you incorporate it into your codes. Comments/ideas/suggestions are highly apprecciated!
 
 ### Contents
-* [1. Nondimensionalization](#1-nondimensionalization)
-* [2. Material parameters](#2-material-parameters)
-* [3. Plotting and output](#3-plotting-and-output)
-* [4. Computational engine](#4-computational-engine)
-* [5. Installation](#5-installation)
-* [6. Documentation](#6-documentation)
-* [7. Dependencies](#7-dependencies)
-* [8. Contributing](#8-contributing)
-* [9. Funding](#9-funding)
+- [Contents](#contents)
+- [1. Nondimensionalization](#1-nondimensionalization)
+- [2. Material parameters](#2-material-parameters)
+  - [2.1 Constant density, constant linear viscosity](#21-constant-density-constant-linear-viscosity)
+  - [2.2 Nonlinear creep laws](#22-nonlinear-creep-laws)
+- [3. Plotting and output](#3-plotting-and-output)
+  - [3.1 Plotting](#31-plotting)
+  - [3.2 Automatically create data tables](#32-automatically-create-data-tables)
+- [4. Computational engine](#4-computational-engine)
+- [5. Installation](#5-installation)
+- [6. Documentation](#6-documentation)
+- [7. Dependencies](#7-dependencies)
+- [8. Contributing](#8-contributing)
+- [9. Funding](#9-funding)
 
 ### 1. Nondimensionalization
 Typical geodynamic simulations involve dimensions on the order of 10's-1000's of kilometers, and viscosities on the order of ~1e20 Pas. If such values are directly employed in numerical solvers, they may result in roundoff errors. It is therefore common practice to nondimensionalize the input parameters by dividing them by typical values such that the result gives numbers that are closer to one.
@@ -126,23 +131,30 @@ Phase 2 : Viscous Sinker
 You can add pre-defined non-linear creep laws as:
 ```julia
 julia> Phase = SetMaterialParams(Name="Viscous Matrix", Phase=2,
-                                                  Density   = ConstantDensity(),
-                                                  CreepLaws = (SetDislocationCreep("Wet Olivine | Hirth & Kohlstedt (2003)"),
-                                                              LinearViscous(η=1e23Pa*s)) )
+                                 Density   = ConstantDensity(),
+                                 CompositeRheology = CompositeRheology(
+                                                        SetDislocationCreep(Dislocation.wet_olivine_Hirth_2003),  
+                                                        LinearViscous(η=1e23Pa*s))
+                                )
 Phase 2 : Viscous Matrix
         | [dimensional units]
-        |
-        |-- Density           : Constant density: ρ=2900.0 kg m⁻³·⁰
-        |-- Gravity           : Gravitational acceleration: g=9.81 m s⁻²·⁰
-        |-- CreepLaws         : DislocationCreep: Name = Wet Olivine | Hirth & Kohlstedt (2003), n=3.5, r=1.2, A=90.0, E=480.0, V=1.1e-5, Apparatus=1
-        |                       Linear viscosity: η=1.0e23
+        | 
+        |-- Name              : Viscous Matrix 
+        |-- Density           : Constant density: ρ=2900.0 kg m⁻³·⁰ 
+        |-- Gravity           : Gravitational acceleration: g=9.81 m s⁻²·⁰ 
+        |-- CompositeRheology : --⟦▪̲̅▫̲̅▫̲̅▫̲̅----⟦▪̲̅▫̲̅▫̲̅▫̲̅--
 ```
-Note that the dictionary `DislocationCreep_info` has all pre-defined creep laws, so for an overview type:
+Note that the functions `dislocation_law_list()` and `diffusion_law_list()` list all pre-defined creep laws, so for an overview type:
 ```julia
-julia> DislocationCreep_info
-Dict{String, DislocationCreep} with 2 entries:
-  "Dry Olivine | Hirth & Kohlstedt (2003)" => DislocationCreep: n=3.05, r=0, A=110000.0 MPa⁻³·⁰⁵ s⁻¹, E…
-  "Wet Olivine | Hirth & Kohlstedt (2003)" => DislocationCreep: n=3.5, r=1.2, A=90 MPa⁻³·⁵ s⁻¹, E=480 k…
+julia> dislocation_law_list()
+40-element Vector{Function}:
+ dry_anorthite_Rybacki_2000 (generic function with 1 method)
+ dry_olivine_Hirth_2003 (generic function with 1 method)
+ dry_olivine_Karato_2003 (generic function with 1 method)
+ dry_quartzite_Jaoul_1984 (generic function with 1 method)
+ ⋮
+ wet_omphacite_Zhang_2006 (generic function with 1 method)
+ wet_quartzite_Hirth_2001 (generic function with 1 method)
 ```
 
 ### 3. Plotting and output
@@ -164,9 +176,10 @@ When writing scientific papers that describes numerical modelling results, it is
 That is why we provide routines that fully automatize this process:
 First, we need to define a phase.
 ```julia
-julia> MatParam = (SetMaterialParams(Name="Viscous Matrix", Phase=1, Density=ConstantDensity(),CreepLaws = SetDislocationCreep("Quartz Diorite | Hansen & Carter (1982)")),
+julia> import GeoParams.Dislocation
+julia> MatParam = (SetMaterialParams(Name="Viscous Matrix", Phase=1, Density=ConstantDensity(),CreepLaws = SetDislocationCreep(Dislocation.quartz_diorite_HansenCarter_1982)),
                    SetMaterialParams(Name="Viscous Sinker", Phase=2, Density= PT_Density(),CreepLaws = LinearViscous(η=1e21Pa*s)),
-                   SetMaterialParams(Name="Viscous Bottom", Phase=3, Density= PT_Density(),CreepLaws = SetDislocationCreep("Diabase | Caristan (1982)")))
+                   SetMaterialParams(Name="Viscous Bottom", Phase=3, Density= PT_Density(),CreepLaws = SetDislocationCreep(Dislocation.diabase_Caristan_1982)))
 ```
 Next, you can create a LaTeX table for the defined phase ...
 ```julia

diff --git a/ext/GeoParamsGLMakieExt.jl b/ext/GeoParamsGLMakieExt.jl
@@ -1,6 +1,8 @@
 # Package extension for adding GLMakie-based features to GeoParams.jl
 module GeoParamsGLMakieExt
 
+using GeoParams
+
 # We do not check `isdefined(Base, :get_extension)` as recommended since
 # Julia v1.9.0 does not load package extensions when their dependency is
 # loaded from the main environment.

diff --git a/src/Energy/Shearheating.jl b/src/Energy/Shearheating.jl
@@ -172,7 +172,7 @@ end
 
 function compute_shearheating(s::AbstractMaterialParamsStruct, args::Vararg{Any,N}) where N
     if isempty(s.ShearHeat)
-        return 0.0  # return zero if not specified
+        return 0e0  # return zero if not specified
     else
         return compute_shearheating(s.ShearHeat[1], args...)
     end

diff --git a/src/GeoParams.jl b/src/GeoParams.jl
@@ -15,7 +15,6 @@ module GeoParams
 using Parameters         # helps setting default parameters in structures
 using Unitful            # Units
 using BibTeX             # references of creep laws
-using Requires: @require # To only add plotting routines if GLMakie is loaded
 using StaticArrays
 using LinearAlgebra
 using ForwardDiff
@@ -335,6 +334,18 @@ export compute_meltfraction,
     Vector_MeltingParam,
     SmoothMelting
 
+
+using .MaterialParameters.Permeability
+export compute_permeability,
+    compute_permeability!,
+    compute_permeability_ratio,
+    param_info,
+    AbstractPermeability,
+    ConstantPermeability,
+    HazenPermeability,
+    PowerLawPermeability,
+    CarmanKozenyPermeability
+
 include("Traits/rheology.jl")
 export RheologyTrait
 export islinear, LinearRheologyTrait, NonLinearRheologyTrait
@@ -363,18 +374,18 @@ function creeplaw_list(m::Module)
     out = string.(names(m; all=true, imported=true))
     filter!(x -> !startswith(x, "#"), out)
     return [getfield(m, Symbol(x)) for x in out if !isnothing(tryparse(Int, string(x[end]))) || endswith(x, "a") || endswith(x, "b")]
-end 
+end
 
 diffusion_law_list() = creeplaw_list(Diffusion)
 dislocation_law_list() = creeplaw_list(Dislocation)
 grainboundarysliding_law_list() = creeplaw_list(GBS)
 nonlinearpeierls_law_list() = creeplaw_list(NonLinearPeierls)
 peierls_law_list() = creeplaw_list(Peierls)
 
-export diffusion_law_list, 
-       dislocation_law_list, 
-       grainboundarysliding_law_list, 
-       nonlinearpeierls_law_list, 
+export diffusion_law_list,
+       dislocation_law_list,
+       grainboundarysliding_law_list,
+       nonlinearpeierls_law_list,
        peierls_law_list
 
 # Define Table output functions
@@ -420,18 +431,6 @@ export PlotStrainrateStress,
     PlotPressureStressTime_0D,
     StrengthEnvelopePlot
 
-# We do not check `isdefined(Base, :get_extension)` as recommended since
-# Julia v1.9.0 does not load package extensions when their dependency is
-# loaded from the main environment.
-function __init__()
-    @static if !(VERSION >= v"1.9.1")
-        @require GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" begin
-            print("Adding plotting routines of GeoParams through GLMakie \n")
-            @eval include("../ext/GeoParamsGLMakieExt.jl")
-        end
-    end
-end
-
 #Set functions aliases using @use
 include("aliases.jl")
 export ntuple_idx
@@ -454,4 +453,4 @@ export get_G, get_Kb
 const get_shearmodulus = get_G
 const get_bulkmodulus  = get_Kb
 
-end # module GeoParams
+end # module GeoParams