diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml deleted file mode 100644 index 15aba992..00000000 --- a/.github/workflows/draft-pdf.yml +++ /dev/null @@ -1,23 +0,0 @@ -on: [push] - -jobs: - paper: - runs-on: ubuntu-latest - name: Paper Draft - steps: - - name: Checkout - uses: actions/checkout@v4 - - name: Build draft PDF - uses: openjournals/openjournals-draft-action@master - with: - journal: joss - # This should be the path to the paper within your repo. - paper-path: docs/paper/paper.md - - name: Upload - uses: actions/upload-artifact@v4 - with: - name: paper - # This is the output path where Pandoc will write the compiled - # PDF. Note, this should be the same directory as the input - # paper.md - path: docs/paper/paper.pdf \ No newline at end of file diff --git a/src/Setup_geometry.jl b/src/Setup_geometry.jl index 1771c60c..9c9c7bee 100644 --- a/src/Setup_geometry.jl +++ b/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!, add_volcano!, +export add_box!, add_sphere!, add_ellipsoid!, add_cylinder!, add_layer!, add_polygon!, add_slab!, add_stripes!, add_volcano!, add_fault!, make_volc_topo, ConstantTemp, LinearTemp, HalfspaceCoolingTemp, SpreadingRateTemp, LithosphericTemp, LinearWeightedTemperature, McKenzie_subducting_slab, @@ -37,6 +37,24 @@ function flatten_index_dimensions(Phase, ind_vec::Vector{CartesianIndex{3}}) return ind2D end +""" + ind2D = flatten_index_dimensions(Phase, ind_vec::Vector{CartesianIndex{3}}) + +This converts the indices to purely 2D indices if the array `phase` is 2D +""" +function flatten_index_dimensions(Phase::AbstractArray{T, N}, ind_vec::Array{Bool, 3}) where {T,N} + if N==2 + ind2D = Vector{CartesianIndex{2}}(undef,length(ind_vec)) + for (num, ind) in enumerate(ind_vec) + ind2D[num] = CartesianIndex(ind[1], ind[3]) + end + else + ind2D = ind_vec + end + + return ind2D +end + """ add_stripes!(Phase, Grid::AbstractGeneralGrid; stripAxes = (1,1,0), @@ -792,7 +810,7 @@ function add_volcano!( end end - ind_flat = flatten_index_dimensions(Temp, ind) + ind_flat = flatten_index_dimensions(Phases, ind) # @views Temp[ind .== false] .= 0.0 Temp[ind_flat] = compute_thermal_structure(Temp[ind_flat], Grid.x.val[ind], Grid.y.val[ind], depth[ind], Phases[ind_flat], T) @@ -1929,3 +1947,103 @@ function add_slab!(Phase, Temp, Grid::AbstractGeneralGrid, trench::Trench; return nothing end + +""" + add_fault!(Phase, Temp, Grid::AbstractGeneralGrid; + Start=(20,100), End=(10,80), + Fault_thickness=10.0, + Depth_extent=nothing, + DipAngle=0e0, + phase=ConstantPhase(1), + T=nothing, + cell=false) + +Adds a fault to the given 3D grid by modifying the `Phase` and `Temp` arrays. +For a 2D grid, use `add_box` instead. + +# Arguments +- `Phase`: Phase array +- `Temp`: Temp array +- `Grid`: The grid on which the fault is to be added. +- `Start`: Tuple representing the starting coordinates of the fault (X, Y). +- `End`: Tuple representing the ending coordinates of the fault (X, Y). +- `Fault_thickness`: Thickness of the fault. +- `Depth_extent`: Depth extent of the fault. If `nothing`, the fault extends through the entire domain. +- `DipAngle`: Dip angle of the fault. +- `phase`: Phase to be assigned to the fault. +- `T`: Temperature to be assigned to the fault. If `nothing`, the temperature is not modified. + + +# Example +```julia +add_fault!(Phase, Temp, Grid; + Start=(20,100), End=(10,80), + Fault_thickness=10.0, + Depth_extent=(-25.0, 0.0), + DipAngle=-10.0, + phase=ConstantPhase(1) + ) +``` +""" +function add_fault!( + Phase, + Temp, + Grid::AbstractGeneralGrid; + Start=(20,100), + End=(10,80), + Fault_thickness=10.0, + Depth_extent=nothing, + DipAngle=0e0, + phase=ConstantPhase(1), + T=nothing, + cell=false +) + + # Extract the coordinates + X, Y, Z = coordinate_grids(Grid, cell=cell) + + # Calculate the direction vector from Start to End + direction = (End[1] - Start[1], End[2] - Start[2]) + length = sqrt(direction[1]^2 + direction[2]^2) + unit_direction = (direction[1], direction[2]) ./ length + + # Calculate the fault region based on fault thickness and length + fault_half_thickness = Fault_thickness / 2 + + # Create a mask for the fault region + fault_mask = falses(size(X)) + + for k in 1:size(Z, 3), j in 1:size(Y, 2), i in 1:size(X, 1) + # Rotate the point using the dip angle + x_rot, y_rot, z_rot = Rot3D(X[i, j, k], Y[i, j, k], Z[i, j, k], 1.0, 0.0, cosd(DipAngle), sind(DipAngle)) + + # Calculate the projection of the rotated point onto the fault line + projection_length = (x_rot - Start[1]) * unit_direction[1] + (y_rot - Start[2]) * unit_direction[2] + if 0 ≤ projection_length ≤ length + # Calculate the perpendicular distance to the fault line + perpendicular_distance = abs((x_rot - Start[1]) * unit_direction[2] - (y_rot - Start[2]) * unit_direction[1]) + if perpendicular_distance ≤ fault_half_thickness + fault_mask[i, j, k] = true + end + end + end + + ind = findall(fault_mask) + + # Apply depth extent if provided + if !isnothing(Depth_extent) + ind = ind[Z[ind] .≥ Depth_extent[1] .&& Z[ind] .≤ Depth_extent[2]] + end + + ind_flat = flatten_index_dimensions(Phase, ind) + + # Compute thermal structure accordingly + if T != nothing + Temp[ind_flat] = compute_thermal_structure(Temp[ind_flat], X[ind], Y[ind], Z[ind], Phase[ind_flat], T) + end + + # Set the phase + Phase[ind_flat] = compute_phase(Phase[ind_flat], Temp[ind_flat], X[ind], Y[ind], Z[ind], phase) + + return nothing +end diff --git a/test/test_setup_geometry.jl b/test/test_setup_geometry.jl index 7069e2ad..bd6d267b 100644 --- a/test/test_setup_geometry.jl +++ b/test/test_setup_geometry.jl @@ -6,7 +6,7 @@ Lon3D,Lat3D,Depth3D = lonlatdepth_grid(1.0:1:10.0, 11.0:1:20.0, (-20:1:-10)*km Data = zeros(size(Lon3D)); Temp = ones(Float64, size(Data))*1350; Phases = zeros(Int32, size(Data)); -Grid = GeoData(Lon3D,Lat3D,Depth3D,(DataFieldName=Data,)) +Grid = GeoData(Lon3D,Lat3D,Depth3D,(DataFieldName=Data,)) add_box!(Phases,Temp,Grid, xlim=(2,4), zlim=(-15,-10), phase=ConstantPhase(3), DipAngle=10, T=LinearTemp(Tbot=1350, Ttop=200)) @test sum(Temp[1,1,:]) ≈ 14850.0 @@ -16,12 +16,12 @@ add_ellipsoid!(Phases,Temp,Grid, cen=(4,15,-17), axes=(1,2,3), StrikeAngle=90, D -# CartData +# CartData X,Y,Z = xyz_grid(1.0:1:10.0, 11.0:1:20.0, -20:1:-10); Data = zeros(size(X)); Temp = ones(Float64, size(Data))*1350; Phases = zeros(Int32, size(Data)); -Grid = CartData(X,Y,Z,(DataFieldName=Data,)) +Grid = CartData(X,Y,Z,(DataFieldName=Data,)) add_box!(Phases,Temp,Grid, xlim=(2,4), zlim=(-15,-10), phase=ConstantPhase(3), DipAngle=10, T=LinearTemp(Tbot=1350, Ttop=200)) @test sum(Temp[1,1,:]) ≈ 14850.0 @@ -93,7 +93,7 @@ Phases = zeros(Int64, Grid.N...); # 1) horizontally layer lithosphere; UpperCrust,LowerCrust,Mantle add_box!(Phases,Temp,Grid, xlim=(-100,100), zlim=(-100,0), Origin=(0.0,0.0,0.0), - phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), + phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), DipAngle=0.0, T=LithosphericTemp(nz=201)) @test sum(Temp[Int64(nel/2),Int64(nel/2),:]) ≈ 36131.638045729735 @@ -103,7 +103,7 @@ Temp = zeros(Float64, Grid.N...); Phases = zeros(Int64, Grid.N...); add_box!(Phases,Temp,Grid, xlim=(-100,100), zlim=(-100,0), Origin=(0.0,0.0,0.0), - phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), + phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), DipAngle=30.0, T=LithosphericTemp(nz=201)) @test sum(Temp[Int64(nel/2),Int64(nel/2),:]) ≈ 41912.18172533137 @@ -113,7 +113,7 @@ Temp = zeros(Float64, Grid.N...); Phases = zeros(Int64, Grid.N...); add_box!(Phases,Temp,Grid, xlim=(-100,100), zlim=(-100,0), - phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), + phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), DipAngle=30.0, T=LithosphericTemp(nz=201)) @test sum(Temp[Int64(nel/2),Int64(nel/2),:]) ≈ 41316.11499878003 @@ -151,7 +151,7 @@ rheology = ( ); add_box!(Phases,Temp,Grid, xlim=(-100,100), zlim=(-100,0), - phase=LithosphericPhases(Layers=[20 80], Phases = [1 2], Tlab=nothing), + phase=LithosphericPhases(Layers=[20 80], Phases = [1 2], Tlab=nothing), DipAngle=30.0, T=LithosphericTemp(rheology=rheology,nz=201)) @test sum(Temp[Int64(nel/2),Int64(nel/2),:]) ≈ 40513.969831615716 @@ -161,7 +161,7 @@ Temp = zeros(Float64, Grid.N...); Phases = zeros(Int64, Grid.N...); add_box!(Phases,Temp,Grid, xlim=(-100,100), zlim=(-100,0), - phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), + phase=LithosphericPhases(Layers=[20 15 65], Phases = [1 2 3], Tlab=nothing), DipAngle=30.0, T=LithosphericTemp(lbound="flux",nz=201)) @test sum(Temp[Int64(nel/2),Int64(nel/2),:]) ≈ 37359.648604722104 @@ -188,7 +188,7 @@ TsMK = McKenzie_subducting_slab(Tsurface = 20.0, Tmantle = 1350.0, v_cm_yr = 4.0 # Add a box with a McKenzie thermal structure -# horizontal +# horizontal Temp = ones(Float64,size(Cart))*1350; add_box!(Phase, Temp, Cart; xlim=(0.0,600.0),ylim=(0.0,600.0), zlim=(-80.0, 0.0), phase = ConstantPhase(5), T=TsMK); @test sum(Temp) ≈ 3.518172093383281e8 @@ -229,7 +229,7 @@ Temp = ones(Float64,(length(x),length(y),length(z)))*1350; add_box!(Phase, Temp, Cart; xlim=(0.0,600.0),ylim=(0.0,600.0), zlim=(-80.0, 0.0), phase = ConstantPhase(5), T=T=ConstantTemp(120.0)); -# add accretionary prism +# add accretionary prism add_polygon!(Phase, Temp, Cart; xlim=(500.0, 200.0, 500.0),ylim=(100.0,400.0), zlim=(0.0,0.0,-60.0), phase = ConstantPhase(8), T=LinearTemp(Ttop=20, Tbot=30)) @test maximum(Phase) == 8 @@ -270,13 +270,13 @@ Temp = fill(1350.0,size(Cart)); add_slab!(Phase,Temp,Cart, t1, phase=phase, T = TsHC) @test extrema(Phase) == (1, 9) -#Data_Final = CartData(X,Y,Z,(Phase=Phase,Temp=Temp)) +#Data_Final = CartData(X,Y,Z,(Phase=Phase,Temp=Temp)) #write_paraview(Data_Final, "Data_Final"); Phase = ones(Int32,size(Cart)); Temp = fill(1350.0,size(Cart)); TsMK = McKenzie_subducting_slab(Tsurface = 20.0, Tmantle = 1350.0, v_cm_yr = 4.0, Adiabat = 0.0) -temp = TsMK +temp = TsMK Phase = ones(Int32,size(Cart)); Temp = fill(1350.0,size(Cart)); @@ -290,7 +290,7 @@ t1 = Trench(Start = (400.0,400.0), End = (800.0,800.0),θ_max = 90.0, direction add_slab!(Phase,Temp,Cart, t1, phase=phase, T = T_slab) @test Temp[84,84,110] ≈ 624.6682008876219 -Data_Final = CartData(X,Y,Z,(Phase=Phase,Temp=Temp)) +Data_Final = CartData(X,Y,Z,(Phase=Phase,Temp=Temp)) # 2D slab: nx,nz = 512,128 @@ -299,7 +299,7 @@ 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=(-800.0,0.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1), T=HalfspaceCoolingTemp(Age=40)); +add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-80.0, 0.0), phase = ConstantPhase(1), T=HalfspaceCoolingTemp(Age=40)); trench = Trench(Start=(0.0,-100.0), End=(0.0,100.0), Thickness=80.0, θ_max=30.0, Length=300, Lb=150); add_slab!(Phases, Temp, Grid2D, trench, phase = ConstantPhase(2), T=HalfspaceCoolingTemp(Age=40)); @@ -333,14 +333,14 @@ v_spread_cm_yr = 3 #spreading velocity lith = LithosphericPhases(Layers=[15 55], Phases=[1 2], Tlab=1250) add_box!(Phases, Temp, Grid2D; xlim=(-800.0,0.0), zlim=(-150.0, 0.0), phase = lith, T=SpreadingRateTemp(SpreadingVel=v_spread_cm_yr)); -# Yet, now we add a trench as well. +# Yet, now we add a trench as well. AgeTrench_Myrs = 800e3/(v_spread_cm_yr/1e2)/1e6 #plate age @ trench # We want to add a smooth transition from a halfspace cooling thermal profile to a slab that is heated by the surrounding mantle below a decoupling depth `d_decoupling`. T_slab = LinearWeightedTemperature( F1=HalfspaceCoolingTemp(Age=AgeTrench_Myrs), F2=McKenzie_subducting_slab(Tsurface=0,v_cm_yr=v_spread_cm_yr, Adiabat = 0.0), crit_dist=600) -# # in this case, we have a more reasonable slab thickness: -trench = Trench(Start=(0.0,-100.0), End=(0.0,100.0), Thickness=90.0, θ_max=30.0, Length=600, Lb=200, +# # in this case, we have a more reasonable slab thickness: +trench = Trench(Start=(0.0,-100.0), End=(0.0,100.0), Thickness=90.0, θ_max=30.0, Length=600, Lb=200, WeakzoneThickness=15, WeakzonePhase=6, d_decoupling=125); add_slab!(Phases, Temp, Grid2D, trench, phase = lith, T=T_slab); @@ -348,17 +348,88 @@ add_slab!(Phases, Temp, Grid2D, trench, phase = lith, T=T_slab); ind = findall(Temp .> 1250 .&& (Phases.==2 .|| Phases.==5)); Phases[ind] .= 0; -@test sum(Temp) ≈ 8.292000736425713e7 +@test sum(Temp) ≈ 8.292000736425713e7 @test extrema(Phases) == (0, 6) #Grid2D = CartData(Grid2D.x.val,Grid2D.y.val,Grid2D.z.val, (;Phases, Temp)) #write_paraview(Grid2D,"Grid2D_SubductionCurvedOverriding"); +# 2D volcano +nx,nz = 512,128 +x = range(-100e0,100e0, nx); +z = range(-60e0,5e0, nz); +Grid2D = CartData(xyz_grid(x,0,z)) +Phases = zeros(Int64, nx, 1, nz); +Temp = fill(1350.0, nx, 1, nz); +lith = LithosphericPhases(Layers=[15 20 55], Phases=[3 4 5], Tlab=1250) + +add_box!(Phases, Temp, Grid2D; xlim=(-100.0,100.0), zlim=(-60e0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80)); + +add_volcano!(Phases, Temp, Grid2D; +volcanic_phase = 1, +center = (mean(Grid2D.x.val), 0.0), +height = 3, +radius = 5, +base = 0.0, +background = nothing, +T = HalfspaceCoolingTemp(Age=20) +) + +@test any(Phases[256,1,:] .== 1) == true + +# 3D volcano +# Create CartGrid struct +x = LinRange(0.0,100.0,64); +y = LinRange(0.0,100.0,64); +z = LinRange(-60,5e0,64); +Cart = CartData(xyz_grid(x, y, z)); + +# initialize phase and temperature matrix +Phase = zeros(Int32,size(Cart)); +Temp = fill(1350.0,size(Cart)); +lith = LithosphericPhases(Layers=[15 20 55], Phases=[3 4 5], Tlab=1250) + +add_box!(Phase, Temp, Cart; xlim=(0.0,100.0),ylim=(0.0,100.0), zlim=(-60.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80)); + +add_volcano!(Phase, Temp, Cart; + volcanic_phase = 1, + center = (mean(Cart.x.val), mean(Cart.y.val), 0.0), + height = 3, + radius = 5, + base = 0.0, + background = nothing, + T = HalfspaceCoolingTemp(Age=20) +) + +@test any(Phase[32,32,:] .== 1) == true + +#3D fault +# Create CartGrid struct +x = LinRange(0.0,100.0,64); +y = LinRange(0.0,100.0,64); +z = LinRange(-60,5e0,64); +Cart = CartData(xyz_grid(x, y, z)); + +# initialize phase and temperature matrix +Phase = zeros(Int32,size(Cart)); +Temp = fill(1350.0,size(Cart)); +lith = LithosphericPhases(Layers=[15 20 55], Phases=[3 4 5], Tlab=1250) +add_box!(Phase, Temp, Cart; xlim=(0.0,100.0),ylim=(0.0,100.0), zlim=(-60.0, 0.0), phase = lith, T=HalfspaceCoolingTemp(Age=80)); +add_fault!(Phase, Temp, Cart; + Start=(0.0,0.0), End=(100,100), + Fault_thickness=1.0, + Depth_extent=(-30.0, 0.0), + DipAngle=-10e0, + phase=ConstantPhase(1), + T=ConstantTemp(1200), +) +@test any(Phase[32,32,:] .== 1) == true +@test any(Temp[32,32,:] .== 1200) == true -# Q1Data -Grid = Q1Data(xyz_grid(1.0:1:10.0, 11.0:1:20.0, -20:1:-10)) +# Q1Data +Grid = Q1Data(xyz_grid(1.0:1:10.0, 11.0:1:20.0, -20:1:-10)) PhasesC = zeros(Int64,size(Grid)); # at cell TempC = ones(Float64, size(Grid))*1350; PhasesV = zeros(Int64,size(Grid.x)); # at vertex