Merge branch 'main' into compathelper/new_version/2024-05-18-01-03-13…

…-788-03157019633

.github/workflows/CI.yml

@@ -20,8 +20,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.9'
           - '1.10'
+          - '~1.11.0-0'
           - 'nightly'
         os:
           - ubuntu-latest

Project.toml

@@ -1,7 +1,7 @@
 name = "LaMEM"
 uuid = "2e889f3d-35ce-4a77-8ea2-858aecb630f7"
 authors = ["Boris Kaus <kaus@uni-mainz.de>"]
-version = "0.3.4"
+version = "0.4.0"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
@@ -23,24 +23,25 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PlotsExt = "Plots"
 
 [compat]
-CairoMakie = "0.11"
 DelimitedFiles = "1"
 DocStringExtensions = "0.9"
 GeoParams = "0.4, 0.5, 0.6"
 GeophysicalModelGenerator = "0.7"
 Glob = "1"
 LightXML = "0.9"
 MPICH_jll = "4.1 - 4.1.2"
+LaMEM_jll = "~2.1.4"
 Plots = "1"
 ReadVTK = "0.1, 0.2"
 Statistics = "1.0"
 WriteVTK = "1"
-julia = "1.9"
+julia = "1.10"
+
 
 [extras]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "CairoMakie", "Plots"]
+test = ["Test", "Plots"]

README.md

@@ -156,7 +156,7 @@ More details are given in the [documentation](https://juliageodynamics.github.io
 We rely on the following packages:
 - [GeophysicalModelGenerator](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl) - Data structure in which we store the info of a LaMEM timestep. The package can also be used to generate setups for LaMEM.
 - [LaMEM_jll](https://github.com/JuliaRegistries/General/tree/master/L/LaMEM_jll) - this contains the LaMEM binaries, precompiled for most systems. Note that on windows, the MUMPS parallel direct solver is not available.
-- [ReadVTK](https://github.com/JuliaVTK/ReadVTK.jl) - This reads the LaMEM `*.vtk` files (or the rectilinear and structured grid versions of it)  baxck into julia.
+- [ReadVTK](https://github.com/JuliaVTK/ReadVTK.jl) - This reads the LaMEM `*.vtk` files (or the rectilinear and structured grid versions of it)  baxck into julia. 
 
 
 ### 6. Funding

docs/src/juliasetup_TMSubduction.md

@@ -449,6 +449,7 @@ continentalLithosphere = copy_phase(    dryPeridotite,
 ```                           
 
 *Sticky air*
+
 Finally, the "air" in our model is a layer with low density and low viscosity, such that it essentially gives very low stresses compared to those within the lithosphere. We cannot give it the viscosity of real air, as this results in a too large viscosity jump at the surface (geodynamic codes cannot handle that). We therefore also often call this "sticky air". Note that we also give it a very high thermal conductivity to ensure that the temperature within the air layer remains more or less constant throughout a simulation (and equal to the temperature at the upper boundary of the model):
 
 ```julia

scripts/StrengthEnvelop.jl

@@ -1,4 +1,4 @@
-using LaMEM, CairoMakie
+using LaMEM
 
 model  = Model(Grid(nel=(4,32), x=[-1,1], z=[-30,1]), 
                Time(nstep_max=25, dt_min=1e-4, dt=1e-3, dt_max=10, time_end=100), 
@@ -24,9 +24,11 @@ run_lamem(model,1)
 
 data,_ = read_LaMEM_timestep(model, last=true)
 
-#Create plot
-fig1 = Figure(size=(800,800))
-ax = Axis(fig1[1,1], xlabel = "τII [MPa]", ylabel = "Depth [km]",title="Geotherm=$(Tgradient)°C/km")
+if 1==0
+    #Create plot
+    fig1 = Figure(size=(800,800))
+    ax = Axis(fig1[1,1], xlabel = "τII [MPa]", ylabel = "Depth [km]",title="Geotherm=$(Tgradient)°C/km")
 
-lines!(ax, data.fields.j2_dev_stress[1,1,:], data.z.val[1,1,:], label="t=$time")
-display(fig1)
+    lines!(ax, data.fields.j2_dev_stress[1,1,:], data.z.val[1,1,:], label="t=$time")
+    display(fig1)
+end

scripts/Subduction3D.jl

@@ -13,7 +13,9 @@ using LaMEM, GeophysicalModelGenerator
 # Note that a range of default values will be set, depending on the parameters you specify.
 model = Model(  
                 ## Define the grid
-                Grid(nel=(128,32,64), x=[-3960, 500], y=[0,2640], z=[-660 ,0]), 
+                Grid(   #nel=(128,32,64), 
+                        nel=(64,16,32),         # reduce resolution for CI
+                        x=[-3960, 500], y=[0,2640], z=[-660 ,0]), 
 
                 ## No slip lower boundary; the rest is free slip
                 BoundaryConditions(noslip = [0, 0, 0, 0, 1, 0]), 
@@ -29,7 +31,8 @@ model = Model(
                 Output(out_file_name="Subduction_3D", out_dir="Subduction_3D"),        
 
                 ## Timestepping etc
-                Time(nstep_max=200, nstep_out=5, time_end=100, dt_min=1e-5),           
+                Time(   nstep_max=200, 
+                        nstep_out=5, time_end=100, dt_min=1e-5),           
 
                 ## Scaling:
                 Scaling(GEO_units(length=1km, stress=1e9Pa) )       
@@ -46,8 +49,8 @@ add_box!(model, xlim=(-3000,-1000), ylim=(0,1000), zlim=(-80,0), phase=Lithosphe
 add_box!(model, xlim=(-1000,-810), ylim=(0,1000), zlim=(-80,0), phase=LithosphericPhases(Layers=[20,60], Phases=[1,2]), DipAngle=16)
 
 # There is a simple way to have a quick look at this setup by using the `Plots.jl` package:
-using Plots 
-plot_cross_section(model, y=100, field=:phase)
+#using Plots 
+#plot_cross_section(model, y=100, field=:phase)
 
 # Which will give the following plot:
 # ![2D cross section](assets/SubductionSetup_3D.png)
@@ -87,7 +90,11 @@ end
 # Add this stage, we are ready to run the simulation. On my machine it takes around 4 seconds per timestep on 8 cores: 
 try testing == true
     # if we run this as part of the test suite, use fewer timesteps
-    run_lamem(model, 8, "-nstep_max 2 -nstep_out 1")       
+    if !Sys.iswindows()
+        run_lamem(model, 8, "-nstep_max 2 -nstep_out 1")       
+    else
+        run_lamem(model, 1, "-nstep_max 2 -nstep_out 1")       
+    end
 catch
     run_lamem(model, 8)       # run on 8 cores (if possible)            
 end

scripts/TM_Subduction_example.jl

@@ -4,7 +4,13 @@ using LaMEM, GeophysicalModelGenerator
 model = Model(Grid( x   = [-2000.,2000.],
                     y   = [-2.5, 2.5],          # <- model is 2D, size in y-direction is choosen to be close to a cube shape for the cell
                     z   = [-660,40] ,
-                    nel = (512,1,128)     ),
+                    #nel = (512,1,128)
+                    nel = (256,1,64)
+
+                    ),
+
+                    ## Output filename
+                    Output(out_file_name="TMSubduction_2D", out_dir="TMSubduction_2D"),        
 
                     BoundaryConditions( temp_bot        = 1565.0,
                                         temp_top        = 20.0,
@@ -228,9 +234,17 @@ model.Solver = Solver(  SolverType      = "multigrid",
                                         ]
                     )
 
-try testing == true
+if Sys.iswindows()
+    model.Solver.MGCoarseSolver = "direct" 
+end
+
+try testing == true 
     # if we run this as part of the test suite, use fewer timesteps
-    run_lamem(model, 8, "-nstep_max 2 -nstep_out 1")       
+    if !Sys.iswindows()
+        run_lamem(model, 8, "-nstep_max 2 -nstep_out 1")       
+    else
+        run_lamem(model, 1, "-nstep_max 2 -nstep_out 1")       
+    end
 catch
     run_lamem(model, 8)       
 end

test/read_timestep.jl

@@ -20,7 +20,7 @@ pkg_dir = pkgdir(LaMEM)
     data, time = read_LaMEM_timestep(FileName,Timestep, phase=true)
 
     @test data.fields.phase[1000] == 0
-
+    #=
     # read subduction setup
     data, time = read_LaMEM_timestep("Subduction2D_FreeSlip_direct",1)
     @test data.fields.density[10000] ≈ 3200.0f0
@@ -32,15 +32,18 @@ pkg_dir = pkgdir(LaMEM)
     # Read PVD file 
     Timestep, FileNames, Time  = read_LaMEM_simulation("Subduction2D_FreeSlip_direct")
     @test Time[2] ≈ 0.055
-
+    =#
+
     # Read passive tracers 
     data, time = read_LaMEM_timestep("PlumeLithosphereInteraction",10, passive_tracers=true)
     @test data.z[100] ≈ -298.4531f0
     @test data.fields.Temperature[100] ≈ 1350.0f0
 
     # Read surface data
+    #=
     data, time = read_LaMEM_timestep("Subduction2D_FreeSurface_direct",5, surf=true)
     @test data.z[100] ≈ 0.68236357f0
     @test  sum(data.fields.topography[:,1,1]) ≈ 1.2645866f0
+    =#
 end
 

test/runLaMEM.jl

@@ -22,9 +22,9 @@ pkg_dir = pkgdir(LaMEM)
     end
 
     # Create a setup using GMG
-    include("CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl")
-    out = run_lamem(ParamFile_2, 1, "-nstep_max 1")    # 1 core
-    @test isnothing(out)
+    #include("CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl")
+    #out = run_lamem(ParamFile_2, 1, "-nstep_max 1")    # 1 core
+    #@test isnothing(out)
 
     # Try direct solvers 
     ParamFile = "input_files/FallingBlock_DirectSolver.dat";

test/runtests.jl

@@ -1,14 +1,14 @@
 using Test
 using LaMEM
 
-#include("test_julia_setups.jl")
-#include("runLaMEM.jl")
-#include("read_timestep.jl")
-#include("run_lamem_save_grid_test.jl")
-#include("mesh_refinement_test.jl")
-#include("read_logfile.jl")
-#include("test_compression.jl")
-#include("test_GeoParams_integration.jl")
+include("test_julia_setups.jl")
+include("runLaMEM.jl")
+include("read_timestep.jl")
+include("run_lamem_save_grid_test.jl")
+include("mesh_refinement_test.jl")
+include("read_logfile.jl")
+include("test_compression.jl")
+include("test_GeoParams_integration.jl")
 include("test_examples.jl")
 
 if !Sys.iswindows()

test/test_examples.jl

@@ -3,23 +3,20 @@ using Test
 
 const testing = true
 @testset "examples in /scripts" begin
-
-
-    # Subduction example
-    @testset "TM_Subduction_example" begin
-        include("../scripts/TM_Subduction_example.jl")
-        data,time = read_LaMEM_timestep(model,last=true);
-        @test time ≈ 0.001736862
-        @test sum(data.fields.velocity[3][:,:,:]) ≈ 1192.9121f0 rtol=1e-4 # check Vz
-    end
-
+    curdir = pwd()
+    pkg_dir = pkgdir(LaMEM)
+    cd(pkg_dir)
+    #cd(joinpath(pkg_dir,"test"))
+
     # 3D subduction example
-    @testset "Subduction3D" begin
-        clean_directory()
-        include("../scripts/Subduction3D.jl")
-        data,time = read_LaMEM_timestep(model,last=true);
-        @test time ≈ 0.03517227
-        @test sum(data.fields.velocity[3][:,:,:]) ≈ -33.77553f0 rtol=1e-4 # check Vz
+    if !Sys.iswindows()
+        @testset "Subduction3D" begin
+            clean_directory()
+            include("../scripts/Subduction3D.jl")
+            data,time = read_LaMEM_timestep(model,last=true);
+            @test time ≈ 0.05504613
+            @test sum(data.fields.velocity[3][:,:,:]) ≈ -51.314083f0 rtol=1e-4 # check Vz
+        end
     end
 
     # Strength envelop example
@@ -31,4 +28,19 @@ const testing = true
         @test sum(data.fields.velocity[3][:,:,:]) ≈ 14.305277f0 rtol=1e-4 # check Vz
     end
 
+
+    # Subduction example
+    if !Sys.iswindows()
+        @testset "TM_Subduction_example" begin
+            clean_directory()
+            include("../scripts/TM_Subduction_example.jl")
+            data,time = read_LaMEM_timestep(model,last=true);
+            @test time ≈ 0.0021
+            @test sum(data.fields.velocity[3][:,:,:]) ≈ 420.10352f0 rtol=1e-4 # check Vz
+        end
+
+    end
+
+    cd(curdir)
+
 end

test/test_julia_setups.jl

@@ -197,7 +197,4 @@ end
     add_geom!(model, geom_ellipsoid, geom_box, geom_layer, geom_cylinder, geom_ridge, geom_hex)
     out = run_lamem(model)
     @test isnothing(out)
-
-
-
 end