function name changes in GMG

Project.toml

@@ -1,7 +1,7 @@
 name = "LaMEM"
 uuid = "2e889f3d-35ce-4a77-8ea2-858aecb630f7"
 authors = ["Boris Kaus <[email protected]>"]
-version = "0.2.13"
+version = "0.2.14"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
@@ -26,7 +26,7 @@ PlotsExt = "Plots"
 DelimitedFiles = "1"
 DocStringExtensions = "0.9"
 GeoParams = "0.4, 0.5"
-GeophysicalModelGenerator = "0.6"
+GeophysicalModelGenerator = "0.7"
 Glob = "1"
 LightXML = "0.9"
 MPICH_jll = "4.1 - 4.1.2"

README.md

@@ -47,7 +47,7 @@ julia> add_phase!(model, sphere, matrix)
 
 Create an initial geometry using the [GeophysicalModelGenerator](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl/tree/main) interface:
 ```Julia
-julia> addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+julia> add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 ```
 and run the simulation with:
 ```julia

docs/src/juliasetup_LaPalma.md

@@ -89,16 +89,16 @@ julia> model.Grid.Phases .= 2;
 
 Now set points above the topography to zero (will be air later), the ones above the topography but below zero to 'water` and below 40 km to mantle (if we had a Moho surface we could use that):
 ```julia
- julia> aboveSurface!(model, Topo_LaMEM, phase=0, T=0)
+ julia> above_surface!(model, Topo_LaMEM, phase=0, T=0)
  julia> model.Grid.Phases[Z.<-0 .&& model.Grid.Phases .== 0] .= 1;
  julia> model.Grid.Phases[Z.<-40] .= 3;
 ```
 
 Finally, we define some magma chambers:
 ```julia 
-julia> addSphere!(model, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200));
-julia> addEllipsoid!(model, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200));
-julia> addEllipsoid!(model, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> add_sphere!(model, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> add_ellipsoid!(model, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> add_ellipsoid!(model, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200));
 ```
 
  We can plot a cross-section through the model:

docs/src/juliasetup_TMSubduction.md

@@ -266,10 +266,10 @@ model.Grid.Phases[model.Grid.Grid.Z .> 0.0 ] .= 5;
 ```
 
 ##### Add left oceanic plate
-An oceanic plate can be added using the `addBox!()` function of the `GeophysicalModelGenerator` package (see `?GeophysicalModelGenerator.addBox!` for more information, or check out the online [help](https://juliageodynamics.github.io/GeophysicalModelGenerator.jl/dev/man/lamem/) of the package). The lithosphere to asthenosphere temperature is set to 1250°C. If temperature of the plate is > 1250°C then the material is turned to asthenosphere. The temperature profile of the plate is set using a half space cooling temperature and a spreading rate velocity of 0.5 cm/yr with the ridge prescribed to be at the "left" of the box.
+An oceanic plate can be added using the `add_box!()` function of the `GeophysicalModelGenerator` package (see `?GeophysicalModelGenerator.add_box!` for more information, or check out the online [help](https://juliageodynamics.github.io/GeophysicalModelGenerator.jl/dev/man/lamem/) of the package). The lithosphere to asthenosphere temperature is set to 1250°C. If temperature of the plate is > 1250°C then the material is turned to asthenosphere. The temperature profile of the plate is set using a half space cooling temperature and a spreading rate velocity of 0.5 cm/yr with the ridge prescribed to be at the "left" of the box.
 
 ```julia
-addBox!(model;  xlim    = (-2000.0, 0.0), 
+add_box!(model;  xlim    = (-2000.0, 0.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -286,7 +286,7 @@ addBox!(model;  xlim    = (-2000.0, 0.0),
 Same for the plate on the right:
 
 ```julia
-addBox!(model;  xlim    = (1500, 2000), 
+add_box!(model;  xlim    = (1500, 2000), 
                 ylim    = (model.Grid.coord_y..., ), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -303,7 +303,7 @@ addBox!(model;  xlim    = (1500, 2000),
 For the overriding plate margin the age is fixed to 90 Ma using `HalfspaceCoolingTemp()`.
 
 ```julia
-addBox!(model;  xlim    = (0.0, 400.0), 
+add_box!(model;  xlim    = (0.0, 400.0), 
                 ylim    = (model.Grid.coord_y[1], model.Grid.coord_y[2]), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -316,7 +316,7 @@ addBox!(model;  xlim    = (0.0, 400.0),
 ##### Add overriding plate craton
 
 ```julia
-addBox!(model;  xlim    = (400.0, 1500.0), 
+add_box!(model;  xlim    = (400.0, 1500.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -330,7 +330,7 @@ addBox!(model;  xlim    = (400.0, 1500.0),
 Here we change the dip angle of the box to 30° to initiates subduction:
 
 ```julia
-addBox!(model;  xlim    = (0.0, 300), 
+add_box!(model;  xlim    = (0.0, 300), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=30,

docs/src/juliasetup_example_sphere.md

@@ -69,7 +69,7 @@ julia> add_phase!(model, sphere, matrix)
 #### 1.3 Set initial model geometry
 We also need to specify an initial model geometry. The julia package `GeophysicalModelGenerator` has a number of functions for that, which can be used here. For the current setup, we just add a sphere: 
 ```julia
-julia> addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+julia> add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 ```
 It is often useful to plot the initial model setup. You can do this with the `heatmap` function from the `Plots.jl` package, for which we provide a LaMEM plugin that allows you to specify a cross-section through a 3D LaMEM setup:
 

docs/src/juliasetups.md

@@ -96,7 +96,7 @@ In order to run a simulation, we need to define at least 1 phase and heterogenei
 The easiest way to do that is to use routines from the `GeophyicalModelGenerator` package, for which we created simple interfaces to many of the relevant routines:
 ```julia
 julia> using GeophysicalModelGenerator
-julia> addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+julia> add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 ```
 
 For the sake of this example, lets add another phase:

notebooks/FallingSphere_1.jl

@@ -91,7 +91,7 @@ We also need to specify an initial model geometry. The julia package `Geophysica
 """
 
 # ╔═╡ a3afc50b-2fcd-4067-895d-fde7fb7f8742
-addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 
 # ╔═╡ e0411cc1-60ae-43cf-9500-93a246e62e1b
 md"""

notebooks/subduction_example.ipynb

@@ -140,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "addBox!(model, xlim=(-700,100), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=0, T=ConstantTemp(1000))"
+    "add_box!(model, xlim=(-700,100), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=0, T=ConstantTemp(1000))"
    ]
   },
   {
@@ -150,7 +150,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "addBox!(model, xlim=(100,300), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=30, T=ConstantTemp(1000))"
+    "add_box!(model, xlim=(100,300), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=30, T=ConstantTemp(1000))"
    ]
   },
   {

scripts/TM_Subduction_example.jl

@@ -62,7 +62,7 @@ model.Grid.Temp[model.Grid.Grid.Z .> 0]    .=  Tair;
 model.Grid.Phases[model.Grid.Grid.Z .> 0.0 ] .= 5;
 
 # Left ocanic plate:
-addBox!(model;  xlim    = (-2000.0, 0.0), 
+add_box!(model;  xlim    = (-2000.0, 0.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -74,7 +74,7 @@ addBox!(model;  xlim    = (-2000.0, 0.0),
                                                 AgeRidge    = 0.01;
                                                 maxAge      = 80.0      ) )
 # Add right oceanic plate:
-addBox!(model;  xlim    = (1500, 2000), 
+add_box!(model;  xlim    = (1500, 2000), 
                 ylim    = (model.Grid.coord_y..., ), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -87,7 +87,7 @@ addBox!(model;  xlim    = (1500, 2000),
                                                 maxAge      = 80.0      ) )
 
 # Add overriding plate margin
-addBox!(model;  xlim    = (0.0, 400.0), 
+add_box!(model;  xlim    = (0.0, 400.0), 
                 ylim    = (model.Grid.coord_y[1], model.Grid.coord_y[2]), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -98,7 +98,7 @@ addBox!(model;  xlim    = (0.0, 400.0),
 
 
 # Overriding plate craton
-addBox!(model;  xlim    = (400.0, 1500.0), 
+add_box!(model;  xlim    = (400.0, 1500.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -107,7 +107,7 @@ addBox!(model;  xlim    = (400.0, 1500.0),
                                                     Tmantle     = Tmantle,
                                                     Age         = 120      ) )
 #   Add pre-subducted slab                                                  
-addBox!(model;  xlim    = (0.0, 300), 
+add_box!(model;  xlim    = (0.0, 300), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=30,

src/LaMEM.jl

@@ -35,7 +35,7 @@ export  LaMEM_Model, Model, Write_LaMEM_InputFile, create_initialsetup,
         add_vbox!, rm_vbox!, rm_last_vbox!, 
         add_phase!, rm_phase!, rm_last_phase!, replace_phase!, add_petsc!, add_softening!, add_phaseaggregate!,
         add_phasetransition!, add_dike!, add_geom!, rm_geom!, set_air, copy_phase,
-        add_topography!, aboveSurface!, belowSurface!,
+        add_topography!, above_surface!, below_surface!,
         prepare_lamem, isdefault, hasplasticity,
         add_geoparams_rheologies,
         stress_strainrate_0D    

src/LaMEM_ModelGeneration/ErrorChecking.jl

@@ -19,7 +19,7 @@ function Check_LaMEM_Model(m::Model)
     end
 
     if (m.ModelSetup.msetup=="files") && diff([extrema(m.Grid.Phases)...])[1]==0 && diff([extrema(m.Grid.Temp)...])[1]==0
-        @warn "Your initial `Temp` grid is constant, as is your initial `Phases` grid. \n Is that intended? \n In most cases, you would want to set some variability in the initial conditions, \n for example with the `GeophysicalModelGenerator` function `addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.15, ))` "
+        @warn "Your initial `Temp` grid is constant, as is your initial `Phases` grid. \n Is that intended? \n In most cases, you would want to set some variability in the initial conditions, \n for example with the `GeophysicalModelGenerator` function `add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.15, ))` "
     end
 
     if (m.Solver.SolverType!="direct") &&  (m.Solver.SolverType!="multigrid")

src/LaMEM_ModelGeneration/GMG_interface.jl

@@ -2,12 +2,12 @@
 #
 # Some wrappers around GMG routines
 
-import GeophysicalModelGenerator: addBox!, addLayer!, addSphere!, addEllipsoid!, addCylinder!, aboveSurface, belowSurface
+import GeophysicalModelGenerator: add_box!, add_layer!, add_sphere!, add_ellipsoid!, add_cylinder!, above_surface, below_surface
 import GeophysicalModelGenerator: addPolygon!, addSlab!, addStripes!
-export aboveSurface!, belowSurface!
+export above_surface!, below_surface!
 
 """
-    addBox!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},
+    add_box!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},
             Origin=nothing, StrikeAngle=0, DipAngle=0,
             phase = ConstantPhase(1),
             T=nothing )
@@ -16,30 +16,30 @@ Adds a box with phase & temperature structure to a 3D model setup. This simplifi
 See the documentation of the GMG routine for the full options.
 
 """
-addBox!(model::Model; kwargs...) = addBox!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+add_box!(model::Model; kwargs...) = add_box!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
 
 """
-    addLayer!(model::Model; xlim, ylim, zlim=Tuple{2},
+    add_layer!(model::Model; xlim, ylim, zlim=Tuple{2},
             phase = ConstantPhase(1),
             T=nothing )
 
 Adds a layer with phase & temperature structure to a 3D model setup. This simplifies creating model geometries in geodynamic models
 See the documentation of the GMG routine for the full options.
 
 """
-addLayer!(model::Model; kwargs...) = addLayer!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+add_layer!(model::Model; kwargs...) = add_layer!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
 
 
 """
-    addSphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)
+    add_sphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)
 
 See the documentation of the GMG routine
 
 """
-addSphere!(model::Model; kwargs...) = addSphere!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+add_sphere!(model::Model; kwargs...) = add_sphere!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
 
 """
-    addCylinder!(model::Model;                                      # required input
+    add_cylinder!(model::Model;                                      # required input
                     base=Tuple{3}, cap=Tuple{3}, radius=Tuple{1},   # center and radius of the sphere
                     phase = ConstantPhase(1),                       # Sets the phase number(s) in the sphere
                     T=nothing )                                     # Sets the thermal structure (various fucntions are available)
@@ -48,11 +48,11 @@ addSphere!(model::Model; kwargs...) = addSphere!(model.Grid.Phases, model.Grid.T
 See the documentation of the GMG routine
 
 """
-addCylinder!(model::Model; kwargs...) = addCylinder!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+add_cylinder!(model::Model; kwargs...) = add_cylinder!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
 
 
 """
-    addEllipsoid!(model::Model;                                 # required input
+    add_ellipsoid!(model::Model;                                 # required input
                     cen=Tuple{3}, axes=Tuple{3},                # center and semi-axes of the ellpsoid
                     Origin=nothing, StrikeAngle=0, DipAngle=0,  # origin & dip/strike
                     phase = ConstantPhase(1),                   # Sets the phase number(s) in the box
@@ -61,7 +61,7 @@ addCylinder!(model::Model; kwargs...) = addCylinder!(model.Grid.Phases, model.Gr
 See the documentation of the GMG routine
 
 """
-addEllipsoid!(model::Model; kwargs...) = addEllipsoid!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+add_ellipsoid!(model::Model; kwargs...) = add_ellipsoid!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
 
 
 """
@@ -108,21 +108,21 @@ addStripes!(model::Model; kwargs...) = addStripes!(model.Grid.Phases, model.Grid
 
 
 """
-    aboveSurface(model::Model, DataSurface_Cart::CartData)
+    above_surface(model::Model, DataSurface_Cart::CartData)
 
 Returns a boolean grid that is `true` if the `Phases/Temp` grid are above the surface
 """
-aboveSurface(model::Model, DataSurface_Cart::CartData) = aboveSurface(model.Grid.Grid, DataSurface_Cart)
+above_surface(model::Model, DataSurface_Cart::CartData) = above_surface(model.Grid.Grid, DataSurface_Cart)
 
 
 """
-    aboveSurface!(model::Model, DataSurface_Cart::CartData; phase::Int64=nothing, T::Number=nothing) 
+    above_surface!(model::Model, DataSurface_Cart::CartData; phase::Int64=nothing, T::Number=nothing) 
     
 Sets the `Temp` or `Phases` above the surface `DataSurface_Cart` to a constant value.
 """
-function aboveSurface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
+function above_surface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
 
-    id = aboveSurface(model, DataSurface_Cart)
+    id = above_surface(model, DataSurface_Cart)
     if !isnothing(phase)
         model.Grid.Phases[id] .= phase
     end
@@ -137,21 +137,21 @@ end
 
 
 """
-    belowSurface(model::Model, DataSurface_Cart::CartData)
+    below_surface(model::Model, DataSurface_Cart::CartData)
 
 Returns a boolean grid that is `true` if the `Phases/Temp` grid are below the surface
 """
-belowSurface(model::Model, DataSurface_Cart::CartData) = belowSurface(model.Grid.Grid, DataSurface_Cart)
+below_surface(model::Model, DataSurface_Cart::CartData) = below_surface(model.Grid.Grid, DataSurface_Cart)
 
 
 """
-    belowSurface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
+    below_surface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
     
 Sets the `Temp` or `Phases` below the surface `DataSurface_Cart` to a constant value.
 """
-function belowSurface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
+function below_surface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
 
-    id = belowSurface(model, DataSurface_Cart)
+    id = below_surface(model, DataSurface_Cart)
     if !isnothing(phase)
         model.Grid.Phases[id] .= phase
     end

src/LaMEM_ModelGeneration/LaMEM_Model.jl

@@ -64,7 +64,7 @@ include("Model.jl")                 # main LaMEM_Model
 export Model
 
 include("GMG_interface.jl")
-export aboveSurface!, belowSurface!
+export above_surface!, below_surface!
 
 include("Utils.jl")
 export  add_phase!, rm_phase!, rm_last_phase!, add_petsc!, add_softening!, add_phaseaggregate!, 

src/LaMEM_ModelGeneration/Utils.jl

@@ -247,7 +247,7 @@ function set_geom!(model::Model, d::geom_Sphere)
     end
 
     # call a GMG routine
-    addSphere!(model.Grid.Phases,model.Grid.Temp,model.Grid.Grid, cen=cen, radius=radius, phase=phase, T=T)
+    add_sphere!(model.Grid.Phases,model.Grid.Temp,model.Grid.Grid, cen=cen, radius=radius, phase=phase, T=T)
 
     return nothing
 end

test/CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl

@@ -28,13 +28,13 @@ Phases      =   zeros(Int64, size(Grid_LaMEM.X));             # Rock numbers
 Temp        =   ones(Float64,size(Grid_LaMEM.X))*T_mantle;    # Temperature in C    
 
 # Create horizontal part of slab with crust & mantle lithosphere
-addBox!(Phases,Temp,Grid_LaMEM,
+add_box!(Phases,Temp,Grid_LaMEM,
         xlim=(Trench_x_location, Trench_x_location+Length_Horiz_Slab), 
         zlim=(-ThicknessSlab   , 0.0),
         phase=LithosphericPhases(Layers=[ThicknessCrust ThicknessML], Phases=[1 2 0]) );               
 
 # Add inclined part of slab                            
-addBox!(Phases,Temp,Grid_LaMEM,
+add_box!(Phases,Temp,Grid_LaMEM,
         xlim=(Trench_x_location-Length_Subduct_Slab, Trench_x_location), 
         zlim=(-ThicknessSlab   , 0.0),
         DipAngle=-SubductionAngle,

test/mesh_refinement_test.jl

@@ -23,7 +23,7 @@ using GeophysicalModelGenerator
     add_phase!(model, sphere, matrix)
 
     # Add an initial geometry (using GeophysicalModelGenerator routines)
-    addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+    add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 
     # run the simulation on 1 core
     run_lamem(model, 1);

test/test_compression.jl

@@ -17,7 +17,7 @@ using GeophysicalModelGenerator
         add_phase!(model, sphere, matrix)
 
         # Add an initial geometry (using GeophysicalModelGenerator routines)
-        addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+        add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 
         # run the simulation on 4 core
         run_lamem(model, 4);