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Changed input style for add_polygon! #119

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Oct 9, 2024
Merged

Changed input style for add_polygon! #119

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f933def
Easier handling
TatjanaWeiler May 28, 2024
41b06b6
Update Setup_geometry.jl
TatjanaWeiler May 28, 2024
fd39d65
Making it time stable
TatjanaWeiler Jun 3, 2024
3c5027d
Update Setup_geometry.jl
TatjanaWeiler Jun 18, 2024
e0a2be1
change nicer handling
TatjanaWeiler Jun 19, 2024
db96858
Update Tutorial_polygon_geometry.jl
TatjanaWeiler Oct 9, 2024
c82028d
Update .typos.toml
TatjanaWeiler Oct 9, 2024
6c597cf
Merge branch 'main' into main
boriskaus Oct 9, 2024
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2 changes: 2 additions & 0 deletions .typos.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@
MOR = "MOR"
dum = "dum"
Shepard = "Shepard"
arange = "arange"
iy = "iy"
nin = "nin"

[files]
Expand Down
32 changes: 16 additions & 16 deletions docs/src/man/Tutorial_NumericalModel_2D.md
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Original file line number Diff line number Diff line change
Expand Up @@ -47,13 +47,13 @@ Temp = fill(1350.0, nx, 1, nz);
We will start with a simple subduction setup, which consists of a horizontal part:

```julia
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1));
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1));
```

And with the inclined part:

```julia
add_box!(Phases, Temp, Grid2D; xlim=(0,300), zlim=(-80.0, 0.0), phase = ConstantPhase(1), DipAngle=30);
add_box!(Phases, Temp, Grid2D; xlim=(0.0,300.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1), DipAngle=30);
```

Add them to the `CartData` dataset:
Expand Down Expand Up @@ -100,8 +100,8 @@ LithosphericPhases([15 55], [1 2], nothing)
and set the slab again:

```julia
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-80.0, 0.0), phase = lith);
add_box!(Phases, Temp, Grid2D; xlim=(0,300), zlim=(-80.0, 0.0), phase = lith, DipAngle=30);
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = lith);
add_box!(Phases, Temp, Grid2D; xlim=(0.0,300.0), zlim=(-80.0, 0.0), phase = lith, DipAngle=30);
```

Which looks like:
Expand All @@ -124,8 +124,8 @@ We can do that by specifying a thermal structure. For example, we can use the ha

```julia
therm = HalfspaceCoolingTemp(Age=40)
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-80.0, 0.0), phase = lith, T=therm);
add_box!(Phases, Temp, Grid2D; xlim=(0,300), zlim=(-80.0, 0.0), phase = lith, T = therm, DipAngle=30);
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = lith, T=therm);
add_box!(Phases, Temp, Grid2D; xlim=(0.0,300.0), zlim=(-80.0, 0.0), phase = lith, T = therm, DipAngle=30);
```

Which looks like:
Expand Down Expand Up @@ -159,13 +159,13 @@ a spreading velocity (note that this simply relates to the thermal structure and

```julia
lith = LithosphericPhases(Layers=[15 55], Phases=[1 2], Tlab=1250)
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
```

For the subduction we use a thermal structure of a slab heated by hot asthenosphere

```julia
add_box!(Phases, Temp, Grid2D; xlim=(0,300), zlim=(-80.0, 0.0), phase = lith, T = McKenzie_subducting_slab(Tsurface=0,v_cm_yr=3), DipAngle=30);
add_box!(Phases, Temp, Grid2D; xlim=(0.0,300.0), zlim=(-80.0, 0.0), phase = lith, T = McKenzie_subducting_slab(Tsurface=0,v_cm_yr=3), DipAngle=30);
```

We can set the mantle lithosphere that is hotter > 1250 C to mantle:
Expand All @@ -186,25 +186,25 @@ Saved file: Grid2D_SubductionRidge.vts
![Mechanical2D_Tutorial_4](../assets/img/Mechanical2D_Tutorial_4.png)

#### Overriding slab and weak layer
Ok, lets add an overriding slab as well. For this, we use the `AddLayer!` function
Ok, lets add an overriding slab as well. For this, we use the `add_layer!` function

```julia
lith = LithosphericPhases(Layers=[15 20 55], Phases=[3 4 5], Tlab=1250)
add_box!(Phases, Temp, Grid2D; xlim=(0,1000), zlim=(-80.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80));
add_box!(Phases, Temp, Grid2D; xlim=(0.0,1000.0), zlim=(-80.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80));
```

The oceanic plate is as before

```julia
lith = LithosphericPhases(Layers=[15 55], Phases=[1 2], Tlab=1250)
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
```

For the inclined part, we set a layer above the slab (the "weak" layer to facilitate subduction initiation )

```julia
lith = LithosphericPhases(Layers=[10 15 55], Phases=[6 1 2], Tlab=1250)
add_box!(Phases, Temp, Grid2D; xlim=(0,300), zlim=(-80.0, 10.0), phase = lith, T = McKenzie_subducting_slab(Tsurface=0,v_cm_yr=3), DipAngle=30);
add_box!(Phases, Temp, Grid2D; xlim=(0.0,300.0), zlim=(-80.0, 10.0), phase = lith, T = McKenzie_subducting_slab(Tsurface=0,v_cm_yr=3), DipAngle=30);
```

Lithosphere-asthenosphere boundary:
Expand Down Expand Up @@ -236,7 +236,7 @@ z = range(-660,0, nz);
Grid2D = CartData(xyz_grid(x,0,z))
Phases = zeros(Int64, nx, 1, nz);
Temp = fill(1350.0, nx, 1, nz);
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1));
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1));
```

Next, we should define a `Trench` structure, which contains info about the trench which goes in 3D from `Start` - `End` coordinates (`x`,`y`)-coordinates respectively. As we are dealing with a 2D model, we set the `y`-coordinates to -100.0 and 100.0 respectively.
Expand Down Expand Up @@ -284,16 +284,16 @@ LithosphericPhases([15 20 55], [3 4 5], 1250)
Lets start with defining the horizontal part of the overriding plate. Note that we define this twice with different thickness to deal with the bending subduction area:

```julia
add_box!(Phases, Temp, Grid2D; xlim=(200,1000), zlim=(-150.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80));
add_box!(Phases, Temp, Grid2D; xlim=(0,200), zlim=(-50.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80));
add_box!(Phases, Temp, Grid2D; xlim=(200.0,1000.0), zlim=(-150.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80));
add_box!(Phases, Temp, Grid2D; xlim=(0.0,200.0), zlim=(-50.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80));
```

The horizontal part of the oceanic plate is as before:

```julia
v_spread_cm_yr = 3 #spreading velocity
lith = LithosphericPhases(Layers=[15 55], Phases=[1 2], Tlab=1250)
add_box!(Phases, Temp, Grid2D; xlim=(-800,0.0), zlim=(-150.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=v_spread_cm_yr));
add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-150.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=v_spread_cm_yr));
```

Yet, now we add a trench as well. The starting thermal age at the trench is that of the horizontal part of the oceanic plate:
Expand Down
26 changes: 13 additions & 13 deletions docs/src/man/Tutorial_NumericalModel_3D.md
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Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,15 @@ Note that if the lowermost layer has the same phase as the mantle, you can defin

```julia
lith = LithosphericPhases(Layers=[15 45 10], Phases=[0 1 2], Tlab=1250)
add_box!(Phases, Temp, Grid; xlim=(-800,0.0), ylim=(-400, 400.0), zlim=(-80.0, 0.0), phase = lith,
add_box!(Phases, Temp, Grid; xlim=(-800.0,0.0), ylim=(-400, 400.0), zlim=(-80.0, 0.0), phase = lith,
Origin=(-0,0,0),
T=SpreadingRateTemp(SpreadingVel=3, MORside="right"), StrikeAngle=30);
```

And an an inclined part:

```julia
add_box!(Phases, Temp, Grid; xlim=(0,300), ylim=(-400, 400.0), zlim=(-80.0, 0.0), phase = lith,
add_box!(Phases, Temp, Grid; xlim=(0.0,300.0), ylim=(-400.0, 400.0), zlim=(-80.0, 0.0), phase = lith,
Origin=(-0,0,0),
T=McKenzie_subducting_slab(Tsurface=0,v_cm_yr=3), DipAngle=30, StrikeAngle=30);
```
Expand Down Expand Up @@ -104,27 +104,27 @@ Overriding plate with a 30 km crust and mantle lithosphere that where T<1250 cel

```julia
lith_cont = LithosphericPhases(Layers=[30 200 50], Phases=[3 4 2], Tlab=1250)
add_box!(Phases, Temp, Grid; xlim=(400,1000), ylim=(-1000, 0.0), zlim=(-240.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=150));
add_box!(Phases, Temp, Grid; xlim=(200,1000), ylim=(-1000, 0.0), zlim=(-80.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=150));
add_box!(Phases, Temp, Grid; xlim=(400.0,1000.0), ylim=(-1000.0, 0.0), zlim=(-240.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=150));
add_box!(Phases, Temp, Grid; xlim=(200.0,1000.0), ylim=(-1000.0, 0.0), zlim=(-80.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=150));

lith_cont = LithosphericPhases(Layers=[30 200 10], Phases=[5 6 2], Tlab=1250)
add_box!(Phases, Temp, Grid; xlim=(400,1000), ylim=(0, 1000), zlim=(-240.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=200));
add_box!(Phases, Temp, Grid; xlim=(200,1000), ylim=(0, 1000), zlim=( -80.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=200));
add_box!(Phases, Temp, Grid; xlim=(400.0,1000.0), ylim=(0.0, 1000.0), zlim=(-240.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=200));
add_box!(Phases, Temp, Grid; xlim=(200.0,1000.0), ylim=(0.0, 1000.0), zlim=( -80.0, 0.0), phase = lith_cont, T=HalfspaceCoolingTemp(Age=200));
```

Define an oceanic plate with ridge

```julia
v_spread_cm_yr = 3 #spreading velocity
lith = LithosphericPhases(Layers=[15 45 10], Phases=[0 1 2], Tlab=1250)
add_box!(Phases, Temp, Grid; xlim=(-800 , 200), ylim=(-1000, -400.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid; xlim=(-1000,-800), ylim=(-1000, -400.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3,MORside="right"));
add_box!(Phases, Temp, Grid; xlim=(-800.0 , 200.0), ylim=(-1000.0, -400.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid; xlim=(-1000.0,-800.0), ylim=(-1000.0, -400.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3,MORside="right"));

add_box!(Phases, Temp, Grid; xlim=(-700, 200), ylim=(-400, 200.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid; xlim=(-1000,-700), ylim=(-400, 200.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3,MORside="right"));
add_box!(Phases, Temp, Grid; xlim=(-700.0, 200.0), ylim=(-400.0, 200.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid; xlim=(-1000.0,-700.0), ylim=(-400.0, 200.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3,MORside="right"));

add_box!(Phases, Temp, Grid; xlim=(-650, 200), ylim=(200, 1000.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid; xlim=(-1000,-650), ylim=(200, 1000.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3,MORside="right"));
add_box!(Phases, Temp, Grid; xlim=(-650.0, 200.0), ylim=(200.0, 1000.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3));
add_box!(Phases, Temp, Grid; xlim=(-1000.0,-650.0), ylim=(200.0, 1000.0), zlim=(-80.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=3,MORside="right"));
```

Subducting parts of the oceanic plate
Expand Down Expand Up @@ -153,7 +153,7 @@ T_slab = LinearWeightedTemperature( F1=HalfspaceCoolingTemp(Age=AgeTrench_Myrs)
add_slab!(Phases, Temp, Grid, trench1, phase = lith, T=T_slab);
```

Finally, it is often nice to see the deformation of the plate when it subducts. A simple way to do that is to put a `stripes` on top using `addStripes`, which has the same phase as the subducting crust.
Finally, it is often nice to see the deformation of the plate when it subducts. A simple way to do that is to put a `stripes` on top using `add_stripes!`, which has the same phase as the subducting crust.

```julia
add_stripes!(Phases, Grid; stripAxes = (1,1,0), phase = ConstantPhase(0), stripePhase = ConstantPhase(9), stripeWidth=50, stripeSpacing=200)
Expand Down
14 changes: 7 additions & 7 deletions docs/src/man/tutorial_Polygon_structures.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@ z = LinRange(-660,50,nz)
Cart = CartData(xyz_grid(x, y, z))

# initialize phase and temperature matrix
Phase = ones(Int32,size(X))
Temp = ones(Float64,size(X))*1350
Phase = fill(1,nx,ny,nz);
Temp = fill(1350.0, nx,ny,nz);

# add different phases: crust->2, Mantle Lithosphere->3 Mantle->1
add_box!(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))
Expand All @@ -47,22 +47,22 @@ To include the geological structures of a passive margin into the model, we use
# unlimited number of points possible to create the polygon

# add sediment basin
add_polygon!(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_polygon!(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
add_polygon!(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_polygon!(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
add_polygon!(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));
add_polygon!(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");
Cart = addfield(Cart,(;Phase, Temp))
write_paraview(Cart, "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.
Expand Down
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