Merge pull request #121 from albert-de-montserrat/adm/volcano

Adds volcano topography with corresponding temperature field

docs/make.jl

@@ -105,7 +105,8 @@ 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",

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)

src/Setup_geometry.jl

@@ -11,7 +11,7 @@ import Base: show
 # These are routines that help to create input geometries, such as slabs with a given angle
 #
 
-export  add_box!, add_sphere!, add_ellipsoid!, add_cylinder!, add_layer!, add_polygon!, add_slab!, add_stripes!,
+export  add_box!, add_sphere!, add_ellipsoid!, add_cylinder!, add_layer!, add_polygon!, add_slab!, add_stripes!, add_volcano!,
         make_volc_topo,
         ConstantTemp, LinearTemp, HalfspaceCoolingTemp, SpreadingRateTemp, LithosphericTemp, LinearWeightedTemperature,
         McKenzie_subducting_slab,
@@ -685,7 +685,82 @@ function Rot3D(X::_T,Y::_T,Z::_T, cosStrikeAngle::_T, sindStrikeAngle::_T, cosDi
     return CoordRot[1], CoordRot[2], CoordRot[3]
 end
 
+"""
+add_volcano!(
+    Phases, Temp, Grid::CartData;
+    volcanic_phase,
+    center,
+    height,
+    radius,
+    crater,
+    base,
+    background,
+    T,
+)
+
+Adds a volcano topography (cones and truncated cones)
+
+Parameters
+====
+- Phases - Phase array (consistent with Grid)
+- Temp - Temperature array (consistent with Grid)
+- Grid - CartData
+
+Optional Parameters
+====
+- volcanic_phase - phase number of the volcano,
+- center - x- and -coordinates of center of volcano
+- height - height of volcano
+- radius - radius of volcano
+- T - temperature structure of the volcano
+- crater - this will create a truncated cone and the option defines the radius of the flat top
+- base - this sets the flat topography around the volcano
+- background - this allows loading in a topography and only adding the volcano on top (also allows stacking of several cones to get a volcano with different slopes)
+"""
+function add_volcano!(
+    Phases, 
+    Temp, 
+    Grid::CartData;
+    volcanic_phase = 1,
+    center         = (0,0,0),
+    height         = 0.0,
+    radius         = 0.0,
+    crater         = 0.0,
+    base           = 0.0,
+    background     = nothing,
+    T              = HalfspaceCoolingTemp(Age=0)
+)
+    H = make_volc_topo(Grid;
+        center     = center,
+        height     = height,
+        radius     = radius,
+        crater     = crater,
+        base       = base,
+        background = background
+    )
+
+    ni    = size(Grid.x)
+    ind   = fill(false, ni...)
+    depth = similar(Grid.z.val)
+
+    for k in axes(ind, 3)
+        for j in axes(ind, 2), i in axes(ind, 1)
+            depth[i, j, k] = max(H[i, j] - Grid.z.val[i, j, k], 0) 
+
+            if Grid.z.val[i, j, k] < H[i, j] && Grid.z.val[i, j, k] ≥ base
+                Phases[i, j, k] = volcanic_phase
+            end
+            if Phases[i, j, k] > 0
+                ind[i, j, k] = true
+            end
+        end
+    end
 
+    # @views Temp[ind .== false] .= 0.0
+    @views Temp[ind] .= compute_thermal_structure(Temp[ind], Grid.x.val[ind], Grid.y.val[ind], depth[ind], Phases[ind], T)
+
+    return nothing
+end
 
 """
 make_volc_topo(Grid::LaMEM_grid; center::Array{Float64, 1}, height::Float64, radius::Float64, crater::Float64,
@@ -797,6 +872,61 @@ function make_volc_topo(Grid::LaMEM_grid;
     return CartData(reshape(X,nx,ny,1), reshape(Y,nx,ny,1), reshape(Topo,nx,ny,1), (Topography=reshape(Topo,nx,ny,1),))
 end
 
+function make_volc_topo(Grid::CartData;
+    center         = (0,0,0),
+    height         = 0.0,
+    radius         = 0.0,
+    crater         = 0.0,
+    base           = 0.0,
+    background     = nothing
+)
+    # get node grid
+    X    = @views Grid.x.val[:,:,1]
+    Y    = @views Grid.y.val[:,:,1]
+    nx   = size(X, 1)
+    ny   = size(X, 2)
+    pos  = similar(X)
+
+    for i in eachindex(pos)
+        # compute radial distance to volcano center
+        DX   = X[i] - center[1]
+        DY   = Y[i] - center[2]
+        RD   = √(DX^2 + DY^2)
+
+        # get radial distance from crater rim
+        RD  -= crater
+
+        # find position relative to crater rim
+        dr   = radius - crater
+        pos[i]  = -RD / dr + 1
+    end
+
+    ## assign topography
+    H    = zeros(nx,ny)
+    # check if there is a background supplied
+    if background === nothing
+        H     .= base
+    else
+        # background = nondimensionalize(background, CharUnits)
+        if size(background) == size(X)
+            H .= background
+        elseif size(background) == size(reshape(X,nx,ny,1))
+            H .= @views background[:,:,1]
+        else
+            error("Size of background must be ", nx, "x", ny)
+        end
+    end
+
+    for i in eachindex(pos)
+        if 0 ≤ pos[i] < 1
+            H[i] = pos[i] * (height - base) + base
+        elseif pos[i] ≥ 1
+            H[i] = height
+        end
+    end
+
+    return H
+end
 
 abstract type AbstractThermalStructure end
 

volcano.jl

@@ -0,0 +1,66 @@
+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)
+Phases = fill(0, nx, ny, nz);
+
+# In many (geodynamic) models, one also has to define the temperature, so lets define it as well
+Temp = fill(1350.0, nx, ny, nz);
+
+lith = LithosphericPhases(Layers=[15 45 100], Phases=[1 2 3])
+
+# And an an inclined part:
+add_box!(Phases, Temp, Grid; 
+    xlim=(-100, 100), 
+    ylim=(-400, 400.0), 
+    zlim=(-110.0, 0.0), 
+    phase = lith, 
+    Origin = (0,0,0), 
+    T = HalfspaceCoolingTemp(Age=20));
+
+
+# # Add them to the `CartData` dataset:
+Grid = addfield(Grid,(;Phases, Temp))
+# heatmap(x, z, Grid.fields.Temp[:,64,:])
+
+# Which looks like
+# write_paraview(Grid,"Grid3D_FreeSubduction");
+
+center     = (0, 0, 0)
+height     = 10 # [kmm]
+radius     = 15 # [km]
+crater     = 0.0
+base       = 0.0
+background = nothing
+
+
+add_volcano!(Phases, Temp, Grid;
+    volcanic_phase  = 1,
+    center     = (0, 0, 0),
+    height     = 10,
+    radius     = 15,
+    crater     = 0.0,
+    base       = 0.0,
+    background = nothing,
+    T = HalfspaceCoolingTemp(Age=20)
+)
+
+Grid = addfield(Grid,(;Phases, Temp))
+
+write_paraview(Grid,"Grid3D_FreeSubduction");
+
+Grid.fields.Temp[Grid.fields.Temp.==0] .= NaN
+heatmap(x, z, Grid.fields.Temp[:,64,:])
+heatmap(x, z, Grid.fields.Phases[:,64,:])
+
+# heatmap(x, z, Grid.z.val[:,64,:])
+# heatmap(x, z, depth[:,64,:])
+# heatmap(x, z, ind[:,64,:])
+
+# Grid.fields.Temp[:,:,1]
+# lines(Grid.fields.Temp[64,64,:], depth[64,64,:])