diff --git a/Project.toml b/Project.toml index c35ce00d..cc28fead 100644 --- a/Project.toml +++ b/Project.toml @@ -57,7 +57,8 @@ julia = "1.9" [extras] GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54" +StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [targets] -test = ["Test", "GMT"] +test = ["Test", "GMT", "StableRNGs"] diff --git a/docs/make.jl b/docs/make.jl index 17e5be69..ee827591 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -95,7 +95,7 @@ makedocs(; "11 - Read UTM data" => "man/tutorial_UTM.md", "12 - VoteMaps" => "man/Tutorial_Votemaps.md", "13 - Campi Flegrei" => "man/tutorial_local_Flegrei.md", - "14 - Cartesian Volcano Model" => "man/LaPalma_example.md", + "14 - La Palma volcano Model" => "man/Tutorial_LaPalma.md", "15 - Create movies" => "man/tutorial_time_Seismicity.md" "16 - Alpine data integration" => "man/Tutorial_AlpineData.md" ], diff --git a/docs/src/man/LaPalma_example.md b/docs/src/man/LaPalma_example.md deleted file mode 100644 index cfa201d0..00000000 --- a/docs/src/man/LaPalma_example.md +++ /dev/null @@ -1,216 +0,0 @@ -```@meta -EditURL = "../../../tutorials/LaPalma_example.jl" -``` - -# 14 - Create a Cartesian Model Setup for La Palma - -## Aim -In this tutorial, your will learn how to use real data to create a geodynamic model setup with LaMEM. -We will use the data of the Cumbre Viejo eruption in La Palma, which is a volcanic island that erupted from mid september 2021 - december 2021. -LaMEM is a cartesian geodynamic model, which implies that you will have to transfer the data from `GeoData` to `CartData`. - - -## 1. Load data -We will use two types of data to create the model - 1) Topography - 2) Earthquake locations - -We start with loading the required packages, which includes `GMT` to download topography (an optional dependency for `GeophysicalModelGenerator`) - -```julia -using GeophysicalModelGenerator, GMT -``` - -In case you managed to install GMT on your machine, you can automatically download the topography with - -```julia -Topo = ImportTopo(lon = [-18.7, -17.1], lat=[28.0, 29.2], file="@earth_relief_03s.grd") -``` - -In case you did not manage that, we have prepared a JLD2 file [here](https://seafile.rlp.net/f/03286a46a9f040a69b0f/?dl=1). -Download it, and doublecheck that you are in the same directory as the data file with: - -```julia -pwd() -``` - -Load the data: - -```julia -Topo=load("Topo_LaPalma.jld2","Topo") -``` - -Next, lets load the seismicity. We have prepared a file with earthquake locations up to early November (from [https://www.ign.es/web/ign/portal/vlc-catalogo](https://www.ign.es/web/ign/portal/vlc-catalogo)). -Download that [here](https://seafile.rlp.net/f/03286a46a9f040a69b0f/?dl=1) - -```julia -data_all_EQ = load("EQ_Data.jld2","data_all_EQ") -``` - -Write the data to paraview with - -```julia -Write_Paraview(data_all_EQ,"data_all_EQ",PointsData=true) -Write_Paraview(Topo,"Topo") -``` - -As earthquakes are point-wise data, you have to specify this. -![LaPalma_EQTopo_GeoData](../assets/img/TopoEQs_LaPalma_GeoData.png) -Note that this data is not in "easy" coordinates (see coordinate axis in the plot, where `z` is *not* pointing upwards). - -## 2. Convert data -In order to create model setups, it is helpful to first transfer the data to Cartesian. -This requires us to first determine a *projection point*, that is fixed. Often, it is helpful to use the center of the topography for this. In the present example, we will center the model around La Palma itself: - -```julia -proj = ProjectionPoint(Lon=-17.84, Lat=28.56) -``` - -Once this is done you can convert the topographic data to the cartesian reference frame - -```julia -EQ_cart = Convert2CartData(data_all_EQ, proj); -Topo_cart = Convert2CartData(Topo, proj) -``` - -It is important to realize that the cartesian coordinates of the topographic grid is no longer strictly orthogonal after this conversion. You don't notice that in the current example, as the model domain is rather small. -In other cases, however, this is quite substantial (e.g., India-Asia collision zone). -LaMEM needs an orthogonal grid of topography, which we can create with: - -```julia -Topo_LaMEM = CartData(XYZGrid(-70:.2:70,-60:.2:70,0)); -nothing #hide -``` - -In a next step, the routine `ProjectCartData` projects a `GeoData` structure to a `CartData` struct - -```julia -Topo_LaMEM = ProjectCartData(Topo_LaMEM, Topo, proj) -``` - -Let's have a look at the data: - -```julia -Write_Paraview(EQ_cart,"EQ_cart",PointsData=true) -Write_Paraview(Topo_LaMEM,"Topo_LaMEM") - - -#= -``` - -## 3. Create LaMEM setup - -In a next step, we need to read the LaMEM input file of the simulation. In particular, this will read the lateral dimensions of the grid and -the number of control volumes (elements), you want to apply in every direction. -The LaMEM input file can be downloaded [here](../scripts/LaPalma.dat). -Make sure you are in the same directory as the *.dat file & execute the following command - -```julia -Grid = ReadLaMEM_InputFile("LaPalma.dat") -``` - -The `LaMEM_grid` structure contains the number of elements in every direction and the number of markers in every cell. -It also contains `Grid.X`, `Grid.Y`, `Grid.Z`, which are the coordinates of each of the markers in the 3 directions. - -In a next step we need to give each of these points a `Phase` number (which is an integer, that indicates the type of the rock that point has), as well as the temperature (in Celsius). - -```julia -Phases = ones(Int32,size(Grid.X))*2; -Temp = ones(Float64,size(Grid.X)); -nothing #hide -``` - -In this example we set the temperature based on the depth, assuming a constant geotherm. Depth is given in kilometers - -```julia -Geotherm = 30; -Temp = -Grid.Z.*Geotherm; -nothing #hide -``` - -Since we are in La Palma, we assume that temperatures are not less than 20 degrees. Moreover, in the mantle, we have the mantle adiabat (1350 C) - -```julia -Temp[Temp.<20] .= 20; -Temp[Temp.>1350] .= 1350; -nothing #hide -``` - -Because of lacking data, we have pretty much no idea where the Moho is in La Palma. -Somewhat arbitrary, we assume it to be at 40 km depth, and set the rocks below that to "mantle": - -```julia -ind = findall( Grid.Z .< -40); -Phases[ind] .= 3; -nothing #hide -``` - -Everything above the free surface is assumed to be "air" - -```julia -ind = AboveSurface(Grid, Topo_cart); -Phases[ind] .= 0; -nothing #hide -``` - -And all "air" points that are below sea-level becomes "water" - -```julia -ind = findall( (Phases.==0) .& (Grid.Z .< 0)); -Phases[ind] .= 1; -nothing #hide -``` - -You can interpret the seismicity in different ways. If you assume that there are fully molten magma chambers, there should be no earthquakes within the magma chamber (as stresses are liklely to be very small). -If, however, this is a partially molten mush, extraction of melt of that mush will change the fluid pressure and may thus release build-up stresses. -We will assume the second option in our model setup. - -Looking at the seismicity, there is a swarm at around 35 km depth - -```julia -AddSphere!(Phases,Temp,Grid, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200)); -nothing #hide -``` - -A shallower one exists as well - -```julia -AddEllipsoid!(Phases,Temp,Grid, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200)); -nothing #hide -``` - -And there might be a mid-crustal one - -```julia -AddEllipsoid!(Phases,Temp,Grid, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200)); -nothing #hide -``` - -We can generate a 3D model setup, which must include the `Phases` and `Temp` arrays - -```julia -Model3D = CartData(Grid, (Phases=Phases,Temp=Temp)) -Write_Paraview(Model3D,"Model3D") -``` - -The model setup looks like this -![LaMEM_ModelSetup_LaPalma](../assets/img/LaMEM_ModelSetup_LaPalma.png) - -We can create a LaMEM marker file from the `Model3D` setup and the (cartesian) topography - -```julia -Save_LaMEMTopography(Topo_cart, "Topography.txt") -Save_LaMEMMarkersParallel(Model3D) -``` - -Next, you can use this to run the LaMEM model and visualize the model results in Paraview as well. -If you are interested in doing this, have a look at the LaMEM [wiki](https://bitbucket.org/bkaus/lamem/wiki/Home) pages. - -```julia -=# -``` - ---- - -*This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).* - diff --git a/docs/src/man/Tutorial_LaPalma.md b/docs/src/man/Tutorial_LaPalma.md new file mode 100644 index 00000000..0451f7a2 --- /dev/null +++ b/docs/src/man/Tutorial_LaPalma.md @@ -0,0 +1,158 @@ +```@meta +EditURL = "../../../tutorials/Tutorial_LaPalma.jl" +``` + +# Create a Cartesian Model Setup for La Palma + +## Aim +In this tutorial, your will learn how to use real data to create a geodynamic model setup in `CartData`. +We will use the data of the Cumbre Viejo eruption in La Palma, which is a volcanic island that erupted from mid september 2021 - december 2021. +The seimsicity from that time-period is used as an inspiration to set the locations of magma intrusions + +## 1. Load data +We will use two types of data to create the model + 1) Topography + 2) Earthquake locations + +We start with loading the required packages, which includes `GMT` to download topography (an optional dependency for `GeophysicalModelGenerator`) + +```julia +using GeophysicalModelGenerator, GMT, DelimitedFiles +``` + +We will use GMT to download the topography with: + +```julia +Topo = ImportTopo(lon = [-18.2, -17.5], lat=[28.4, 29.0], file="@earth_relief_15s.grd") +``` + +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") +data_EQ = readdlm("EQ_events_all_info5_LaPalma_2021.dat") +``` + +It has the following format: + +```julia +lon = data_EQ[:,1] +lat = data_EQ[:,2] +depth = -data_EQ[:,3] +Mag = data_EQ[:,10] +``` + +Create a `GeoData` structure from this: + +```julia +data_all_EQ = GeoData(lon,lat,depth, (Magnitude=Mag,)) +``` + +Next, we can write the data to paraview along with the topography. Note that we have to specify that we have `PointData`: + +```julia +Write_Paraview(data_all_EQ,"data_all_EQ",PointsData=true) +Write_Paraview(Topo,"Topo") +``` + +![LaPalma_EQTopo_GeoData](../assets/img/TopoEQs_LaPalma_GeoData.png) +Note that this data is in geographic coordinates, which makes it non-trivial to create slices through the data (see coordinate axis in the plot, where `z` is *not* pointing upwards). + +## 2. Convert data to cartesian coordinates +In order to create model setups, it is helpful to first transfer the data to Cartesian. +This requires us to first determine a *projection point*, that is fixed. Often, it is helpful to use the center of the topography for this. In the present example, we will center the model around La Palma itself: + +```julia +proj = ProjectionPoint(Lon=-17.84, Lat=28.56) +``` + +Once this is done you can convert the topographic data to the cartesian reference frame + +```julia +EQ_cart = Convert2CartData(data_all_EQ, proj); +Topo_cart = Convert2CartData(Topo, proj) +``` + +It is important to realize that the cartesian coordinates of the topographic grid is no longer strictly orthogonal after this conversion. You don't notice that in the current example, as the model domain is rather small. +In other cases, however, this is quite substantial (e.g., India-Asia collision zone). +LaMEM needs an orthogonal grid of topography, which we can create with: + +```julia +Topo_model = CartData(XYZGrid(-35:.1:30,-15:.2:45,0)); +nothing #hide +``` + +In a next step, the routine `ProjectCartData` projects a `GeoData` structure to a `CartData` struct + +```julia +Topo_model = ProjectCartData(Topo_model, Topo, proj) +``` + +Let's have a look at the data: + +```julia +Write_Paraview(EQ_cart,"EQ_cart",PointsData=true) +Write_Paraview(Topo_model,"Topo_model") +``` + +## 3. Create a volumetric earthquake plot +It is useful to plot the earthquake density in 3D, which indicates where most action is happening in the system. +For this, we first create a 3D grid of the region: + +```julia +Grid_3D = CartData(XYZGrid(-35:.3:30,-15:.25:45,-50:.5:5)) +``` + +Next we check how many earthquakes are around the grid points: + +```julia +Grid_3D =PointData2NearestGrid(EQ_cart, Grid_3D, radius_factor=3) +``` + +And we can define an array with rock types: + +```julia +Phases = zeros(Int64,size(Grid_3D.x)) +``` + +Points that are below the surface are set to one: + +```julia +Below = BelowSurface(Grid_3D, Topo_model); +Phases[Below] .= 1 +``` + +Lets assume that the crust is 15 km thick + +```julia +Phases[NumValue(Grid_3D.z) .< -15] .= 2 +``` + +And lets assume that the magma is where we have some earthquake activity: + +```julia +ind = findall( (Grid_3D.fields.Count .> 75) .&& Phases.>0) +Phases[ind] .= 3 #Magma +``` + +Add rocktypes to the grid: + +```julia +Grid_3D = AddField(Grid_3D,"Phases",Phases) +``` + +We can save this to paraview format + +```julia +Write_Paraview(Grid_3D,"Grid_3D") +``` + +The paraview statefile `/tutorials/LaPalma.pvsm` can be used to reproduce the following plot: +![LaPalma_Tutorial](../assets/img/Tutorial_LaPalma.png) + +--- + +*This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).* + diff --git a/docs/src/man/tools.md b/docs/src/man/tools.md index 7b5d2361..41aa7927 100644 --- a/docs/src/man/tools.md +++ b/docs/src/man/tools.md @@ -14,6 +14,7 @@ GeophysicalModelGenerator.InterpolateDataOnSurface GeophysicalModelGenerator.InterpolateTopographyOnPlane GeophysicalModelGenerator.ParseColumns_CSV_File GeophysicalModelGenerator.RotateTranslateScale! +GeophysicalModelGenerator.PointData2NearestGrid GeophysicalModelGenerator.Convert2UTMzone GeophysicalModelGenerator.Convert2CartData GeophysicalModelGenerator.ProjectCartData diff --git a/src/GeophysicalModelGenerator.jl b/src/GeophysicalModelGenerator.jl index 96f7534a..96e5cf6e 100644 --- a/src/GeophysicalModelGenerator.jl +++ b/src/GeophysicalModelGenerator.jl @@ -42,6 +42,7 @@ include("Setup_geometry.jl") include("stl.jl") include("ProfileProcessing.jl") include("IO.jl") +include("event_counts.jl") # Add optional routines (only activated when the packages are loaded) diff --git a/src/event_counts.jl b/src/event_counts.jl new file mode 100644 index 00000000..d75a5297 --- /dev/null +++ b/src/event_counts.jl @@ -0,0 +1,116 @@ +using NearestNeighbors + +export PointData2NearestGrid + + +""" + Grid_counts = PointData2NearestGrid(Point::CartData, Grid::CartData; radius_factor=1) + +Uses nearest neighbour interpolation to count how many points (given by `Point`) are in the vicinity of a 3D `Grid`. +The search radius is `R=radius_factor*(Δx² + Δy² + Δz²)^(1/3)` + +`Point` should have 1D coordinate vectors + +`Grid_counts` is `Grid` but with an additional field `Count` that has the number of hits +""" +function PointData2NearestGrid(Point::CartData, Grid::CartData; radius_factor=1) + + @assert length(size(Point.x)) == 1 + + # call routine + Count = PointData2NearestGrid(NumValue(Point.x),NumValue(Point.y), NumValue(Point.z), NumValue(Grid.x),NumValue(Grid.y),NumValue(Grid.z); radius_factor=radius_factor) + + # return CartGrid with added field + return AddField(Grid,"Count",Count); +end + + +""" + Grid_counts = PointData2NearestGrid(pt_x,pt_y,pt_z, Grid::CartData; radius_factor=1) + +Uses nearest neighbour interpolation to count how many points (given by `pt_x`,`pt_y`,`pt_z` coordinate vectors) are in the +vicinity of 3D `CartGrid` specified by `Grid`. The search radius is `R=radius_factor*(Δx² + Δy² + Δz²)^(1/3)` + +`Grid_counts` is `Grid` but with an additional field `Count` that has the number of hits +""" +function PointData2NearestGrid(pt_x,pt_y,pt_z, Grid::CartData; radius_factor=1) + + # call routine + Count = PointData2NearestGrid(pt_x,pt_y,pt_z, NumValue(Grid.x),NumValue(Grid.y),NumValue(Grid.z); radius_factor=radius_factor) + + # return CartGrid with added field + return AddField(Grid,"Count",Count); +end + + +""" + Grid_counts = PointData2NearestGrid(Point::GeoData, Grid::GeoData; radius_factor=1) + +Uses nearest neighbour interpolation to count how many points (given by `Point`) are in the vicinity of a 3D `Grid`. +The search radius is `R=radius_factor*(Δx² + Δy² + Δz²)^(1/3)` + +`Point` should have 1D coordinate vectors + +`Grid_counts` is `Grid` but with an additional field `Count` that has the number of hits +""" +function PointData2NearestGrid(Point::GeoData, Grid::GeoData; radius_factor=1) + + @assert length(size(Point.lon)) == 1 + + # call routine + Count = PointData2NearestGrid(NumValue(Point.lon),NumValue(Point.lat), NumValue(Point.depth), NumValue(Grid.lon),NumValue(Grid.lat),NumValue(Grid.depth); radius_factor=radius_factor) + + # return CartGrid with added field + return AddField(Grid,"Count",Count); +end + + +""" + Grid_counts = PointData2NearestGrid(pt_x,pt_y,pt_z, Grid::GeoData; radius_factor=1) + +Uses nearest neighbour interpolation to count how many points (given by `pt_x`,`pt_y`,`pt_z` coordinate vectors) are in the +vicinity of 3D `GeoData` specified by `Grid`. The search radius is `R=radius_factor*(Δx² + Δy² + Δz²)^(1/3)` + +`Grid_counts` is `Grid` but with an additional field `Count` that has the number of hits +""" +function PointData2NearestGrid(pt_x,pt_y,pt_z, Grid::GeoData; radius_factor=1) + + # call routine + Count = PointData2NearestGrid(pt_x,pt_y,pt_z, NumValue(Grid.lon),NumValue(Grid.lat),NumValue(Grid.depth); radius_factor=radius_factor) + + # return CartGrid with added field + return AddField(Grid,"Count",Count); +end + +""" + count = PointData2NearestGrid(pt_x,pt_y,pt_z, X,Y,Z; radius_factor=1) + +This uses nearest neighbour interpolation to count how many points (given by `pt_x`,`pt_y`,`pt_z` coordinate vectors) are in the +vicinity of 3D grid point specified by `X`,`Y`,`Z` 3D coordinate arrays, with regular spacing `(Δx,Δy,Δz)`. +The search radius is `R=radius_factor*(Δx² + Δy² + Δz²)^(1/3)` + +""" +function PointData2NearestGrid(pt_x,pt_y,pt_z, X,Y,Z; radius_factor=1) + + data = zeros(3,length(pt_x)); + data[1,:],data[2,:],data[3,:] = pt_x[:], pt_y[:], pt_z[:] + tree = BallTree(data) # Generate tree with EQ data + + # Grid spacing + Δx,Δy,Δz = X[2,1,1]-X[1], Y[1,2,1]-Y[1], Z[1,1,2]-Z[1] + + points = zeros(3,length(X)); + points[1,:],points[2,:],points[3,:] = X[:], Y[:], Z[:] + + radius = radius_factor*(Δx^2 + Δy^2 + Δz^2)^(1/3) # search radius + idxs = inrange(tree, points, radius) # find points (NearestNeighbors package) + le = length.(idxs) # number of points + + count = zeros(Int64,size(X)); + for i in eachindex(X) + count[i] = le[i] + end + + return count +end + diff --git a/test/runtests.jl b/test/runtests.jl index 174ada66..90ec22bc 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -44,6 +44,10 @@ end include("test_GMT.jl") end +@testset "Event counts" begin + include("test_event_counts.jl") +end + # Cleanup foreach(rm, filter(endswith(".vts"), readdir())) diff --git a/test/test_event_counts.jl b/test/test_event_counts.jl new file mode 100644 index 00000000..d8584de5 --- /dev/null +++ b/test/test_event_counts.jl @@ -0,0 +1,43 @@ +using Test + +# Create a CartGrid +Grid_cart = CartData(XYZGrid(-20:20,-20:.1:20,-30:30)) + +Lon,Lat,Depth = LonLatDepthGrid(-20:20,-20:.1:20,-30:30); +Grid_geo = GeoData(Lon,Lat,Depth,(;Depth)) + +using StableRNGs + +rng = StableRNG(123) + +# Create some random point data +pt = rand(rng, 10_000,3) .- 0.5 +pt[:,1] .*= 20 +pt[:,2] .*= 20 +pt[:,3] .*= 30 + +EQ_cart = CartData(pt[:,1],pt[:,2], pt[:,3], (z=pt[:,3],)) +EQ_geo = GeoData(pt[:,1],pt[:,2], pt[:,3], (z=pt[:,3],)) + +R = (sum(pt.^2,dims=2)).^(1/3) +ind = findall(R.< 5); + +# test the basic routine +counts = PointData2NearestGrid(pt[:,1],pt[:,2],pt[:,3], NumValue(Grid_cart.x),NumValue(Grid_cart.y), NumValue(Grid_cart.z); radius_factor=2) +@test extrema(counts) == (0, 85) + +# Test if the grid is on a CartData grid +Grid_Count = PointData2NearestGrid(pt[:,1],pt[:,2],pt[:,3], Grid_cart; radius_factor=2) +@test extrema(Grid_Count.fields.Count) == (0, 85) + +# Test in case 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tutorials/LaPalma_example.jl b/tutorials/LaPalma_example.jl deleted file mode 100644 index 81e50af4..00000000 --- a/tutorials/LaPalma_example.jl +++ /dev/null @@ -1,130 +0,0 @@ -# # Create a Cartesian Model Setup for La Palma -# -# ## Aim -# In this tutorial, your will learn how to use real data to create a geodynamic model setup with LaMEM. -# We will use the data of the Cumbre Viejo eruption in La Palma, which is a volcanic island that erupted from mid september 2021 - december 2021. -# LaMEM is a cartesian geodynamic model, which implies that you will have to transfer the data from `GeoData` to `CartData`. -# -# -# ## 1. Load data -# We will use two types of data to create the model -# 1) Topography -# 2) Earthquake locations - -# We start with loading the required packages, which includes `GMT` to download topography (an optional dependency for `GeophysicalModelGenerator`) -using GeophysicalModelGenerator, GMT - -# In case you managed to install GMT on your machine, you can automatically download the topography with -Topo = ImportTopo(lon = [-18.7, -17.1], lat=[28.0, 29.2], file="@earth_relief_03s.grd") - -# In case you did not manage that, we have prepared a JLD2 file [here](https://seafile.rlp.net/f/03286a46a9f040a69b0f/?dl=1). -# Download it, and doublecheck that you are in the same directory as the data file with: -pwd() - -# Load the data: -Topo=load("Topo_LaPalma.jld2","Topo") - -# Next, lets load the seismicity. We have prepared a file with earthquake locations up to early November (from [https://www.ign.es/web/ign/portal/vlc-catalogo](https://www.ign.es/web/ign/portal/vlc-catalogo)). -# Download that [here](https://seafile.rlp.net/f/03286a46a9f040a69b0f/?dl=1) -data_all_EQ = load("EQ_Data.jld2","data_all_EQ") - -# Write the data to paraview with -Write_Paraview(data_all_EQ,"data_all_EQ",PointsData=true) -Write_Paraview(Topo,"Topo") - -# As earthquakes are point-wise data, you have to specify this. -# ![LaPalma_EQTopo_GeoData](../assets/img/TopoEQs_LaPalma_GeoData.png) -# Note that this data is not in "easy" coordinates (see coordinate axis in the plot, where `z` is *not* pointing upwards). - -# ## 2. Convert data -# In order to create model setups, it is helpful to first transfer the data to Cartesian. -# This requires us to first determine a *projection point*, that is fixed. Often, it is helpful to use the center of the topography for this. In the present example, we will center the model around La Palma itself: -proj = ProjectionPoint(Lon=-17.84, Lat=28.56) - -# Once this is done you can convert the topographic data to the cartesian reference frame -EQ_cart = Convert2CartData(data_all_EQ, proj); -Topo_cart = Convert2CartData(Topo, proj) - -# It is important to realize that the cartesian coordinates of the topographic grid is no longer strictly orthogonal after this conversion. You don't notice that in the current example, as the model domain is rather small. -# In other cases, however, this is quite substantial (e.g., India-Asia collision zone). -# LaMEM needs an orthogonal grid of topography, which we can create with: -Topo_LaMEM = CartData(XYZGrid(-70:.2:70,-60:.2:70,0)); - -# In a next step, the routine `ProjectCartData` projects a `GeoData` structure to a `CartData` struct -Topo_LaMEM = ProjectCartData(Topo_LaMEM, Topo, proj) - -# Let's have a look at the data: -Write_Paraview(EQ_cart,"EQ_cart",PointsData=true) -Write_Paraview(Topo_LaMEM,"Topo_LaMEM") - - -#= - -# ## 3. Create LaMEM setup -# -# In a next step, we need to read the LaMEM input file of the simulation. In particular, this will read the lateral dimensions of the grid and -# the number of control volumes (elements), you want to apply in every direction. -# The LaMEM input file can be downloaded [here](../scripts/LaPalma.dat). -# Make sure you are in the same directory as the *.dat file & execute the following command -Grid = ReadLaMEM_InputFile("LaPalma.dat") - -# The `LaMEM_grid` structure contains the number of elements in every direction and the number of markers in every cell. -# It also contains `Grid.X`, `Grid.Y`, `Grid.Z`, which are the coordinates of each of the markers in the 3 directions. -# -# In a next step we need to give each of these points a `Phase` number (which is an integer, that indicates the type of the rock that point has), as well as the temperature (in Celsius). -Phases = ones(Int32,size(Grid.X))*2; -Temp = ones(Float64,size(Grid.X)); - -# In this example we set the temperature based on the depth, assuming a constant geotherm. Depth is given in kilometers -Geotherm = 30; -Temp = -Grid.Z.*Geotherm; - -# Since we are in La Palma, we assume that temperatures are not less than 20 degrees. Moreover, in the mantle, we have the mantle adiabat (1350 C) -Temp[Temp.<20] .= 20; -Temp[Temp.>1350] .= 1350; - -# Because of lacking data, we have pretty much no idea where the Moho is in La Palma. -# Somewhat arbitrary, we assume it to be at 40 km depth, and set the rocks below that to "mantle": -ind = findall( Grid.Z .< -40); -Phases[ind] .= 3; - -# Everything above the free surface is assumed to be "air" -ind = AboveSurface(Grid, Topo_cart); -Phases[ind] .= 0; - -# And all "air" points that are below sea-level becomes "water" -ind = findall( (Phases.==0) .& (Grid.Z .< 0)); -Phases[ind] .= 1; - -# You can interpret the seismicity in different ways. If you assume that there are fully molten magma chambers, there should be no earthquakes within the magma chamber (as stresses are liklely to be very small). -# If, however, this is a partially molten mush, extraction of melt of that mush will change the fluid pressure and may thus release build-up stresses. -# We will assume the second option in our model setup. -# -# Looking at the seismicity, there is a swarm at around 35 km depth -AddSphere!(Phases,Temp,Grid, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200)); - -# A shallower one exists as well -AddEllipsoid!(Phases,Temp,Grid, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200)); - -# And there might be a mid-crustal one -AddEllipsoid!(Phases,Temp,Grid, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200)); - -# We can generate a 3D model setup, which must include the `Phases` and `Temp` arrays -Model3D = CartData(Grid, (Phases=Phases,Temp=Temp)) -Write_Paraview(Model3D,"Model3D") - -# The model setup looks like this -# ![LaMEM_ModelSetup_LaPalma](../assets/img/LaMEM_ModelSetup_LaPalma.png) - -# We can create a LaMEM marker file from the `Model3D` setup and the (cartesian) topography -Save_LaMEMTopography(Topo_cart, "Topography.txt") -Save_LaMEMMarkersParallel(Model3D) - -# Next, you can use this to run the LaMEM model and visualize the model results in Paraview as well. -# If you are interested in doing this, have a look at the LaMEM [wiki](https://bitbucket.org/bkaus/lamem/wiki/Home) pages. - - -#src Note: The markdown page is generated using: -#src Literate.markdown("LaPalma_example.jl",outputdir="../man/", execute=true) - -=# \ No newline at end of file diff --git a/tutorials/Tutorial_LaPalma.jl b/tutorials/Tutorial_LaPalma.jl new file mode 100644 index 00000000..7c1d0bb7 --- /dev/null +++ b/tutorials/Tutorial_LaPalma.jl @@ -0,0 +1,94 @@ +# # Create a Cartesian Model Setup for La Palma +# +# ## Aim +# In this tutorial, your will learn how to use real data to create a geodynamic model setup in `CartData`. +# We will use the data of the Cumbre Viejo eruption in La Palma, which is a volcanic island that erupted from mid september 2021 - december 2021. +# The seimsicity from that time-period is used as an inspiration to set the locations of magma intrusions +# +# ## 1. Load data +# We will use two types of data to create the model +# 1) Topography +# 2) Earthquake locations + +# We start with loading the required packages, which includes `GMT` to download topography (an optional dependency for `GeophysicalModelGenerator`) +using GeophysicalModelGenerator, GMT, DelimitedFiles + +# We will use GMT to download the topography with: +Topo = ImportTopo(lon = [-18.2, -17.5], lat=[28.4, 29.0], file="@earth_relief_15s.grd") + +# 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: +#download_data("","EQ_events_all_info5_LaPalma_2021.dat") +data_EQ = readdlm("EQ_events_all_info5_LaPalma_2021.dat") + +# It has the following format: +lon = data_EQ[:,1] +lat = data_EQ[:,2] +depth = -data_EQ[:,3] +Mag = data_EQ[:,10] + +# Create a `GeoData` structure from this: +data_all_EQ = GeoData(lon,lat,depth, (Magnitude=Mag,)) + +# Next, we can write the data to paraview along with the topography. Note that we have to specify that we have `PointData`: +Write_Paraview(data_all_EQ,"data_all_EQ",PointsData=true) +Write_Paraview(Topo,"Topo") + +# ![LaPalma_EQTopo_GeoData](../assets/img/TopoEQs_LaPalma_GeoData.png) +# Note that this data is in geographic coordinates, which makes it non-trivial to create slices through the data (see coordinate axis in the plot, where `z` is *not* pointing upwards). + +# ## 2. Convert data to cartesian coordinates +# In order to create model setups, it is helpful to first transfer the data to Cartesian. +# This requires us to first determine a *projection point*, that is fixed. Often, it is helpful to use the center of the topography for this. In the present example, we will center the model around La Palma itself: +proj = ProjectionPoint(Lon=-17.84, Lat=28.56) + +# Once this is done you can convert the topographic data to the cartesian reference frame +EQ_cart = Convert2CartData(data_all_EQ, proj); +Topo_cart = Convert2CartData(Topo, proj) + +# It is important to realize that the cartesian coordinates of the topographic grid is no longer strictly orthogonal after this conversion. You don't notice that in the current example, as the model domain is rather small. +# In other cases, however, this is quite substantial (e.g., India-Asia collision zone). +# LaMEM needs an orthogonal grid of topography, which we can create with: +Topo_model = CartData(XYZGrid(-35:.1:30,-15:.2:45,0)); + +# In a next step, the routine `ProjectCartData` projects a `GeoData` structure to a `CartData` struct +Topo_model = ProjectCartData(Topo_model, Topo, proj) + +# Let's have a look at the data: +Write_Paraview(EQ_cart,"EQ_cart",PointsData=true) +Write_Paraview(Topo_model,"Topo_model") + +# ## 3. Create a volumetric earthquake plot +# It is useful to plot the earthquake density in 3D, which indicates where most action is happening in the system. +# For this, we first create a 3D grid of the region: +Grid_3D = CartData(XYZGrid(-35:.3:30,-15:.25:45,-50:.5:5)) + +# Next we check how many earthquakes are around the grid points: +Grid_3D =PointData2NearestGrid(EQ_cart, Grid_3D, radius_factor=3) + +# And we can define an array with rock types: +Phases = zeros(Int64,size(Grid_3D.x)) + +# Points that are below the surface are set to one: +Below = BelowSurface(Grid_3D, Topo_model); +Phases[Below] .= 1 + +# Lets assume that the crust is 15 km thick +Phases[NumValue(Grid_3D.z) .< -15] .= 2 + +# And lets assume that the magma is where we have some earthquake activity: +ind = findall( (Grid_3D.fields.Count .> 75) .&& Phases.>0) +Phases[ind] .= 3 #Magma + +# Add rocktypes to the grid: +Grid_3D = AddField(Grid_3D,"Phases",Phases) + +# We can save this to paraview format +Write_Paraview(Grid_3D,"Grid_3D") + +# The paraview statefile `/tutorials/LaPalma.pvsm` can be used to reproduce the following plot: +# ![LaPalma_Tutorial](../assets/img/Tutorial_LaPalma.png) + +#src Note: The markdown page is generated using: +#src Literate.markdown("tutorials/Tutorial_LaPalma.jl","docs/src/man",keepcomments=true, execute=false, codefence = "```julia" => "```")