Merge branch 'main' into main

.github/workflows/CI.yml

@@ -16,6 +16,7 @@ jobs:
         version:
           - '1.9'
           - '1.10'
+          - '~1.11.0-0'
           - 'nightly'
         os:
           - ubuntu-latest

.github/workflows/Documenter.yml

@@ -34,7 +34,7 @@ jobs:
         with:
           version: '1.9'
           show-versioninfo: true
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""

.github/workflows/SpellCheck.yml

@@ -10,6 +10,6 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.18.2
+        uses: crate-ci/typos@v1.25.0
         with:
             args: --exclude **/*.txt --exclude **/*.pvsm

.typos.toml

@@ -4,6 +4,7 @@ dum = "dum"
 Shepard = "Shepard"
 arange = "arange"
 iy = "iy"
+nin = "nin"
 
 [files]
 extend-exclude = ["tutorials/*.pvsm"]

Project.toml

@@ -1,14 +1,15 @@
 name = "GeophysicalModelGenerator"
 uuid = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 authors = ["Boris Kaus", "Marcel Thielmann"]
-version = "0.7.2"
+version = "0.7.7"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 FFMPEG = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+GDAL_jll = "a7073274-a066-55f0-b90d-d619367d196c"
 GeoParams = "e018b62d-d9de-4a26-8697-af89c310ae38"
 Geodesy = "0ef565a4-170c-5f04-8de2-149903a85f3d"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
@@ -19,13 +20,15 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MeshIO = "7269a6da-0436-5bbc-96c2-40638cbb6118"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+WhereTheWaterFlows = "ea906314-1493-4d22-a0af-f886a20c9fba"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [weakdeps]
@@ -43,7 +46,8 @@ Colors = "0.9 - 0.12"
 Downloads = "1"
 FFMPEG = "0.4"
 FileIO = "1"
-GLMakie = "0.8, 0.9"
+GDAL_jll = "300.900.0 - 301.900.0"
+GLMakie = "0.10"
 GMT = "1"
 GeoParams = "0.2 - 0.6"
 Geodesy = "1"
@@ -52,13 +56,14 @@ Glob = "1.2 - 1.3"
 GridapGmsh = "0.5 - 0.7"
 ImageIO = "0.1 - 0.6"
 Interpolations = "0.14, 0.15"
-JLD2 = "0.4"
+JLD2 = "0.4, 0.5"
 LightXML = "0.8, 0.9"
 MeshIO = "0.1 - 0.4"
 NearestNeighbors = "0.2 - 0.4"
 Parameters = "0.9 - 0.12"
 SpecialFunctions = "1.0, 2"
 StaticArrays = "1"
+WhereTheWaterFlows = "0.10"
 WriteVTK = "1"
 julia = "1.9"
 
@@ -69,4 +74,4 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "GMT", "StableRNGs","GridapGmsh"]
+test = ["Test", "GMT", "StableRNGs", "GridapGmsh"]

docs/make.jl

@@ -105,13 +105,15 @@ makedocs(;
             "19 - Jura tutorial" =>  "man/Tutorial_Jura.md",
             "20 - 2D model setups" => "man/Tutorial_NumericalModel_2D.md",
             "21 - 3D model setups" => "man/Tutorial_NumericalModel_3D.md",
-            "22 - Build geometry from polygons" =>  "man/tutorial_Polygon_structures.md"
+            "22 - 3D model setups" => "man/Tutorial_VolcanoModel_3D.md",
+            "23 - Build geometry from polygons" =>  "man/tutorial_Polygon_structures.md"
         ],
         "User Guide" => Any[
             "Installation" =>  "man/installation.md",
             "Data Structures" =>  "man/datastructures.md",
             "Data Import" =>  "man/dataimport.md",
             "Projection" =>  "man/projection.md",
+            "ASAGI" => "man/asagi_io.md",
             "Paraview output" => "man/paraview_output.md",
             "Paraview collection" => "man/paraview_collection.md",
             "Surfaces" =>  "man/surfaces.md",

docs/src/man/Tutorial_AlpineData.md

@@ -29,7 +29,7 @@ using GeophysicalModelGenerator, GMT
 When loading both packages, several `GMT` routines within `GMG` will be loaded. One of these routines is the function `import_topo`, where one simply has to provide the region for which to download the topographic data and the data source.
 
 ```julia
-Topo = import_topo([4,20,37,50], file="@earth_relief_01m.grd")
+Topo = import_topo([4,20,37,50], file="@earth_relief_01m")
 ```
 
 The data is available in different resolutions; see [here](http://gmt.soest.hawaii.edu/doc/latest/grdimage.html) for an overview. Generally, it is advisable to not use the largest resolution if you have a large area, as the files become very large.

docs/src/man/Tutorial_Jura.md

@@ -18,7 +18,7 @@ using GeophysicalModelGenerator, GMT
 Download the topography with:
 
 ```julia
-Topo = import_topo(lat=[45.5,47.7], lon=[5, 8.1], file="@earth_relief_03s.grd")
+Topo = import_topo(lat=[45.5,47.7], lon=[5, 8.1], file="@earth_relief_03s")
 ```
 
 Next, we drape the geological map on top of the geological map.

docs/src/man/Tutorial_LaPalma.md

@@ -23,15 +23,15 @@ using GeophysicalModelGenerator, GMT, DelimitedFiles
 We will use GMT to download the topography with:
 
 ```julia
-Topo = import_topo(lon = [-18.2, -17.5], lat=[28.4, 29.0], file="@earth_relief_15s.grd")
+Topo = import_topo(lon = [-18.2, -17.5], lat=[28.4, 29.0], file="@earth_relief_15s")
 ```
 
 Next, lets load the seismicity. The earthquake data is available on [https://www.ign.es/web/ign/portal/vlc-catalogo](https://www.ign.es/web/ign/portal/vlc-catalogo).
 We have filtered them and prepared a file with earthquake locations up to early November 2021 (from january 2021).
 Download that:
 
 ```julia
-#download_data("","EQ_events_all_info5_LaPalma_2021.dat")
+#download_data("https://zenodo.org/records/10738510/files/EQ_events_all_info5_LaPalma_2021.dat","EQ_events_all_info5_LaPalma_2021.dat")
 data_EQ = readdlm("EQ_events_all_info5_LaPalma_2021.dat")
 ```
 
@@ -155,4 +155,3 @@ The paraview statefile `/tutorials/LaPalma.pvsm` can be used to reproduce the fo
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-

docs/src/man/Tutorial_VolcanoModel_3D.md

@@ -0,0 +1,81 @@
+# Simple model of a magmatic chamber with a volcano on top 
+
+### Aim
+The aim of this tutorial is to show you how to create 3D numerical model setups that can be used as initial setups for other codes.
+
+### Generating the model
+
+Lets start with creating a 3D model setup in cartesian coordinates, which uses the `CartData` data structure, with a resolution of $ 128 \times 128 \times 128 $ grid points, inside the domain $\Omega \in [-100,100] \times [-100,100] \times [-110,50]$ km
+
+```julia
+using GeophysicalModelGenerator
+
+nx,ny,nz = 128, 128, 128 
+x = range(-100, 100, nx);
+y = range(-100, 100, ny);
+z = range(-110,  50, nz);
+Grid = CartData(xyz_grid(x,y,z));
+```
+
+Now we create an integer array that will hold the `Phases` information (which usually refers to the material or rock type in the simulation)
+
+```julia
+Phases = fill(0, nx, ny, nz);
+```
+
+And as in the previous tutorials we initialize the temperature field:
+```julia
+Temp = fill(1350.0, nx,ny,nz);
+```
+
+For simplicity, we will assume a model with thee horizontal layers with different rheology where later we add the volcano and the magmatic chamber. We use `add_box!` to generate the initial horizontally layered model:
+
+```julia
+lith = LithosphericPhases(Layers=[15 45 100], Phases=[1 2 3])
+add_box!(Phases, Temp, Grid; 
+    xlim=(-100, 100), 
+    ylim=(-400, 400.0), 
+    zlim=(-110.0, 0.0), 
+    phase = lith, 
+    T = HalfspaceCoolingTemp(Age=20)
+)
+```
+
+Then we can add the volcanic shape using `add_volcano!` function. In this case the base of the volcano will be centered at $x_i = (0,0,0)$, with a height of 10 km and a 15 km radius:
+```julia
+add_volcano!(Phases, Temp, Grid;
+    volcanic_phase  = 1,
+    center     = (0, 0, 0),
+    height     = 10,
+    radius     = 15,
+    base       = 0.0,
+    background = nothing,
+    T = HalfspaceCoolingTemp(Age=20)
+)
+```
+We can also add a magmatic chamber located below the volcano
+```julia
+add_ellipsoid!(Phases, Temp, Grid; 
+    cen    = (0, 0, -40), 
+    axes   = (10, 10, 10),
+    phase  = ConstantPhase(4),
+)
+```
+
+where we prescribe a constant temperature of $T=1400^{\circ}C$
+```julia
+@. Temp[Phases == 4] = 1400 
+Grid = addfield(Grid, (;Phases, Temp))
+```
+
+Finally we setup the temperature of the air to $T^{\text{air}}=0^{\circ}C$
+```julia
+@. Temp[Phases == 0] = 0 
+```
+
+```julia
+write_paraview(Grid,"VolcanoModel3D");
+```
+
+And the resulting image looks like
+![Mechanical3D_Tutorial_2](../assets/img/VolcanoModel3D.png)

docs/src/man/asagi_io.md

@@ -0,0 +1,10 @@
+# ASAGI I/O
+
+[ASAGI](https://github.com/TUM-I5/ASAGI) is a fileformat that is used by codes such as SeisSol or ExaHype. It employs the NetCDF4 data format.
+
+We can read ASAGI files into GMG, and write GMG datasets to ASAGI format, which makes it straightforward to use GMG to create a model setup or to couple the results of geodynamic simulations (e.g., produced by LaMEM) with codes that support ASAGI.
+
+```@docs
+read_ASAGI
+write_ASAGI
+```

docs/src/man/tutorial_GMT_Topography.md

@@ -15,15 +15,17 @@ The nice thing about GMT is that it automatically downloads data for you for a c
 
 ```julia
 julia> using GeophysicalModelGenerator, GMT
-julia> Topo = import_topo([4,20,37,49], file="@earth_relief_01m.grd")
+julia> Topo = import_topo([4,20,37,49], file="@earth_relief_01m")
 GeoData 
   size  : (960, 720, 1)
   lon   ϵ [ 4.0 : 19.983333333333334]
   lat   ϵ [ 37.0 : 48.983333333333334]
   depth ϵ [ -3.8725 km : 4.2495 km]
   fields: (:Topography,)
 ```
+
 The data is available in different resolutions:
+
 | Dataset                 |   Resolution |   Description                                               |
 |:----------------        | ------------ | ----------------------------------------------------------- |
 | "@earth\_relief\_01s" |	1 arc sec 	 | SRTM tiles (14297 tiles, land only, 60S-60N) [NASA/USGS]    |
@@ -54,4 +56,4 @@ The result is shown here, together with Moho data
 
 ![Tutorial_GMT_topography](../assets/img/Tutorial_GMT_topography.png)
 
-In case you are interested: we are employing the `oleron` scientific colormap [here](https://www.fabiocrameri.ch/colourmaps/).
+In case you are interested: we are employing the `oleron` scientific colormap [here](https://www.fabiocrameri.ch/colourmaps/).

docs/src/man/tutorial_GMT_Topography_GeologicalMap.md

@@ -8,7 +8,7 @@ In many cases, we want to add topographic data as well a information about tecto
 
 #### 1. Download topographic data and tectonic maps of the Alpine region
 The ETOPO1 data file used in this example can be downloaded here:  
-[https://ngdc.noaa.gov/mgg/global/global.html](https://ngdc.noaa.gov/mgg/global/global.html). For this example, we downloaded `ETOPO1_Ice_g_gmt4.grd` and stored it directly in the folder where we will be working. For the geological map, we download the data from the [SPP 4DMB repository](http://www.spp-mountainbuilding.de/data/Maps.zip) and extract the zip file (to the current folder). In this data set, a `gmt` file with the data for different tectonic units is given in `./tectonic_maps_4dmb_2020_09_17/GMT_example/alcapadi_polygons.gmt`. 
+[https://ngdc.noaa.gov/mgg/global/global.html](https://ngdc.noaa.gov/mgg/global/global.html). For this example, we downloaded `ETOPO1_Ice_g_gmt4` and stored it directly in the folder where we will be working. For the geological map, we download the data from the [SPP 4DMB repository](http://www.spp-mountainbuilding.de/data/Maps.zip) and extract the zip file (to the current folder). In this data set, a `gmt` file with the data for different tectonic units is given in `./tectonic_maps_4dmb_2020_09_17/GMT_example/alcapadi_polygons.gmt`. 
 
 #### 2. Create a tectonic map with orthogonal projection 
 To create a png with an orthogonal map projection (which we need for the png import), we do the following in julia:  
@@ -28,7 +28,7 @@ julia> using GMT, NearestNeighbors, GeoParams, GeophysicalModelGenerator
 ```
 First, define the filenames of the files you want to import:  
 ```julia
-julia> filename_topo = "./ETOPO1/ETOPO1_Ice_g_gmt4.grd" 
+julia> filename_topo = "./ETOPO1/ETOPO1_Ice_g_gmt4" 
 julia> filename_geo  = "./tectonicmap_SPP.png"
 ```
 Next, define the region that you want to visualize (note that we use the same coordinates here as we used previously for the generation of the geological map):  

docs/src/man/tutorial_GPS.md

@@ -163,7 +163,7 @@ using GMT, Interpolations
 We use the `import_topo` function to read the topography from a file:
 
 ```julia
-Elevation   =   import_topo([3,17,42,50], file="@earth_relief_01m.grd");
+Elevation   =   import_topo([3,17,42,50], file="@earth_relief_01m");
 nothing #hide
 ```