Update tutorial_Polygon_structures.md

Author: boriskaus

docs/src/man/tutorial_Polygon_structures.md

@@ -1,19 +1,18 @@
-# 13 - Setting up sedimentary basin, lithospheric thinning and accretionary prism
+# Adding complex geometries to a model setup including sedimentary basins, lithospheric thinning and an accretionary prism
 
 
 ## Goal
 
-This tutorial visualizes simplified geological as it is done here for a passive margin where lithospheric thinning, sedimentary basin and accretionary prism occur. The simplification is based on a polygon structure for a pseudo-3D model. While the structure can have a random shape in the x- and z-direction, in the y-direction only the extension is variable. 
+This tutorial visualizes simplified geological as it is done here for a passive margin where lithospheric thinning, sedimentary basin and accretionary prism occur. The simplification is based on a polygon structure for a pseudo-3D model. While the structure can have a random shape in the `x`- and `z`-direction, in the `y`-direction only the extent is variable. 
 
 ## Steps
 
 #### 1. Set up your simplified background model
-Before adding specific geological features, a general simplified model setup is necessary. The construction is made by using the addBox function. For the model the discontinuities are in 15, 45, 145, and 945 km depth.
+Before adding specific geological features, a general simplified model setup is necessary. The construction is made by using the `addBox!` function. For the model the discontinuities are in 15, 45, 145, and 945 km depth.
 
 ```julia
 using GeophysicalModelGenerator
 
-
 # number of cells in every direction
 nx = 100
 ny = 100
@@ -23,8 +22,7 @@ nz = 200
 x        = LinRange(0.0,800.0,nx)
 y        = LinRange(0.0,800.0,ny)
 z        = LinRange(-660,50,nz)
-X,Y,Z    = XYZGrid(x, y, z);
-Cart     = CartData(X,Y,Z, (Data=Z,))
+Cart     = CartData(XYZGrid(x, y, z))
 
 # initialize phase and temperature matrix
 Phase   = ones(Int32,size(X))
@@ -33,15 +31,13 @@ Temp    = ones(Float64,size(X))*1350
 # add different phases: crust->2, Mantle Lithosphere->3 Mantle->1
 AddBox!(Phase, Temp, Cart; xlim=(0.0,800.0),ylim=(0.0,800.0), zlim=(-800.0,0.0), phase = LithosphericPhases(Layers=[15 30 100 800], Phases=[2 3 1 5], Tlab=1300 ), T=LinearTemp(Ttop=20, Tbot=1600))
 
-
 # add air phase 0
 AddBox!(Phase, Temp, Cart; xlim=(0.0,800.0),ylim=(0.0,800.0), zlim=(0.0,50.0), phase = ConstantPhase(0), T=ConstantTemp(20.0))
-
- ```
+```
 
 
 #### 2. Add polygon structure
-For including the geological structures of a passive margin into the model via the polygon function, depths down to 150 km are focused on. With the polygon function, it is possible to create different shapes. In the example, the sediment basin shows a more trapezial (2D in x-/z-direction) shape, while the thinning of the plate is a more triangular (2D in x-/z-direction). More complex structures are possible to build in the background model due to the non-limitation number of points in the x- and z-direction. In y-direction only the length can be varied and is set by two values. The shape is not changeable. The x- and z-values of the points need to be in the same order for selecting the correct point (P1(1/3), P2(2/2) --> xlim(1,2), ylim(3,2)).
+To include the geological structures of a passive margin into the model, we use polygons for depths of up to 150 km. In the example, the sediment basin shows a more trapezoidal (2D in `x`-/`z`-direction) shape, while the thinning of the plate has a more triangular (2D in `x`-/`z`-direction). More complex structures can be build using arbitrarily sized polygons in `x`- and `z`-direction, wheraes in the `y`-direction only the length can be varied (specified by two values). The `x`- and `z`-values of the points need to be in the same order for selecting the correct point (P1(1/3), P2(2/2) --> xlim(1,2), ylim(3,2)).
 
 
 ```julia
@@ -51,28 +47,26 @@ For including the geological structures of a passive margin into the model via t
 # unlimited number of points possible to create the polygon
 
 # add sediment basin 
-addPolygon!(Phase, Temp, Cart; xlim=[0.0,0.0, 160.0, 200.0],ylim=[100.0,300.0], zlim=[0.0,-10.0,-20.0,0.0], phase = ConstantPhase(8), T=LinearTemp(Ttop=20, Tbot=30))
+addPolygon!(Phase, Temp, Cart; xlim=[0.0,0.0, 160.0, 200.0],ylim=[100.0,300.0], zlim=[0.0,-10.0,-20.0,0.0], phase = ConstantPhase(8), T=LinearTemp(Ttop=20, Tbot=30));
 
 # add thinning of the continental crust attached to the slab and its thickness 
-addPolygon!(Phase, Temp, Cart; xlim=[0.0, 200.0, 0.0],ylim=[500.0,800.0], zlim=[-100.0,-150.0,-150.0], phase = ConstantPhase(5), T=LinearTemp(Ttop=1000, Tbot=1100))
+addPolygon!(Phase, Temp, Cart; xlim=[0.0, 200.0, 0.0],ylim=[500.0,800.0], zlim=[-100.0,-150.0,-150.0], phase = ConstantPhase(5), T=LinearTemp(Ttop=1000, Tbot=1100));
 
 # add accretionary prism 
-addPolygon!(Phase, Temp, Cart; xlim=[800.0, 600.0, 800.0],ylim=[100.0,800.0], zlim=[0.0,0.0,-60.0], phase = ConstantPhase(8), T=LinearTemp(Ttop=20, Tbot=30))
-
- ```
+addPolygon!(Phase, Temp, Cart; xlim=[800.0, 600.0, 800.0],ylim=[100.0,800.0], zlim=[0.0,0.0,-60.0], phase = ConstantPhase(8), T=LinearTemp(Ttop=20, Tbot=30));
+```
 
 #### 3. Export final model setup to a paraview file
 For visualisation and comparison to actual measured data, the mode setup is saved to a paraview file.
 
 ```julia
 # # Save data to paraview:
-Data_Final      =   CartData(X,Y,Z,(Phase=Phase,Temp=Temp)) 
-Write_Paraview(Data_Final, "Sedimentary_basin")
-
- ```
+Data_Final      =   CartData(X,Y,Z,(Phase=Phase,Temp=Temp)); 
+Write_Paraview(Data_Final, "Sedimentary_basin");
+```
 
 After importing and looking at the file to paraview, some unresolved areas might be visible as they are visible in this model. That is due to the resolution and shape of the polygon. To reduce those artefacts an increase in resolution or a change of the polygon angle might help.
 
 ![Tutorial_Polygon_structures](../assets/img/Tutorial_Polygon_structures.png)
 
-If you want to run the entire example, you can find the .jl code [here](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl/blob/main/tutorial/Tutorial_polygon_geometry.jl)
+If you want to run the entire example, you can find the .jl code [here](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl/blob/main/tutorial/Tutorial_polygon_geometry.jl)