update list of functions

docs/src/man/listoffunctions.md

@@ -4,6 +4,15 @@ Here an overview of all functions:
 ```@autodocs
 Modules = [
     GeoModBox,
+    GeoModBox.Scaling,
     GeoModBox.HeatEquation.OneD,
+    GeoModBox.HeatEquation.TwoD,
+    GeoModBox.AdvectionEquation.OneD,
+    GeoModBox.AdvectionEquation.TwoD,
+    GeoModBox.InitialCondition,
+    GeoModBox.Tracers.OneD,
+    GeoModBox.Tracers.TwoD,
+    GeoModBox.MomentumEquation.OneD,
+    GeoModBox.MomentumEquation.TwoD,
 ]
 ```

src/AdvectionEquation/1Dsolvers.jl

@@ -1,7 +1,7 @@
 using Dierckx
 
-@doc raw"""
-    RK4O1D
+"""
+    RK4O1D!( x, Δt, vx, xmin, xmax )    
 
 """
 function RK4O1D!( x, Δt, vx, xmin, xmax )    
@@ -18,8 +18,8 @@ function RK4O1D!( x, Δt, vx, xmin, xmax )
 
 end
 
-@doc raw"""
-
+"""
+    upwind1D!( A, vx, Δt, Δx )
 """
 function upwind1D!( A, vx, Δt, Δx )
     Aold    =   zeros(size(A))
@@ -35,8 +35,8 @@ function upwind1D!( A, vx, Δt, Δx )
     end
 end
 
-@doc raw"""
-
+"""
+    lax1D!( A, vx, Δt, Δx )
 """
 function lax1D!( A, vx, Δt, Δx )
     Aold    =   zeros(size(A))
@@ -47,8 +47,8 @@ function lax1D!( A, vx, Δt, Δx )
             (vx*Δt/2/Δx) * ( Aold[3:end] - Aold[1:end-2])
 end
 
-@doc raw"""
-
+"""
+    slf1D!( A, Aold2, vx, Δt, Δx )
 """
 function slf1D!( A, Aold2, vx, Δt, Δx )
     # Aold2 is old time step
@@ -62,8 +62,8 @@ function slf1D!( A, Aold2, vx, Δt, Δx )
 
 end
 
-@doc raw"""
-
+"""
+    semilag1D!( A, xc, vx, Δt, Δx )
 """
 function semilag1D!( A, xc, vx, Δt, Δx )
     X       =   zeros(size(xc))

src/AdvectionEquation/2Dsolvers.jl

@@ -3,7 +3,7 @@
 # -------------------------------------------------------------------- #
 using Interpolations
 
-@doc raw"""
+"""
     upwindc2D!()
 
     Using the velocity on the centroids! 
@@ -23,7 +23,7 @@ function upwindc2D!(P,P_ex,vxc,vyc,NC,Δt,Δx,Δy)
     # ---------------------------------------------------------------- #
 end
 
-@doc raw"""
+"""
     slfc2D!
 """
 function slfc2D!(P,P_ex,P_exo,vxc,vyc,NC,Δt,Δx,Δy)
@@ -40,7 +40,7 @@ function slfc2D!(P,P_ex,P_exo,vxc,vyc,NC,Δt,Δx,Δy)
     # ---------------------------------------------------------------- #
 end
 
-@doc raw"""
+"""
     semilagc2D!()
 """
 function semilagc2D!(P,P_ex,vxc,vyc,vxo,vyo,x,y,Δt)

src/AnalyticalSolutions2D.jl

@@ -1,3 +1,6 @@
+"""
+    Dani_Solution_vec!(type,D,M,x,y,rad,mus_i,NC,NV)
+"""
 function Dani_Solution_vec!(type,D,M,x,y,rad,mus_i,NC,NV)
 # [ Vx_N,Vx_S,Vx_W,Vx_E,Vy_N,Vy_S,Vy_W,Vy_E,Pa,Vxa,Vya ]
 # ------------------------------------------------------------------------ #

src/HeatEquation/2Dsolvers.jl

@@ -1,7 +1,7 @@
 using ExtendableSparse
 
-@doc raw"""
-    ForwardEuler2Dc
+"""
+    ForwardEuler2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC)
 """
 function ForwardEuler2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC)
     # Function to solve 2D heat diffusion equation using the explicit finite
@@ -43,8 +43,8 @@ function ForwardEuler2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC)
     # ------------------------------------------------------------------- #    
 end
 
-@doc raw"""
-    ComputeResiduals2D
+"""
+    ComputeResiduals2D!(R, T, T_ex, T0, ∂T, q, ρ, Cp, k, BC, Δ, Δt)
 """
 function ComputeResiduals2D!(R, T, T_ex, T0, ∂T, q, ρ, Cp, k, BC, Δ, Δt)
     @. T_ex[2:end-1,2:end-1] = T 
@@ -59,8 +59,8 @@ function ComputeResiduals2D!(R, T, T_ex, T0, ∂T, q, ρ, Cp, k, BC, Δ, Δt)
     @. R     = ρ*Cp*(T - T0)/Δt + (q.x[2:end,:] - q.x[1:end-1,:])/Δ.x + (q.y[:,2:end] - q.y[:,1:end-1])/Δ.y  
 end
 
-@doc raw"""
-    AssembleMatrix2D
+"""
+    AssembleMatrix2D(rho, cp, k, BC, Num, nc, Δ, Δt)
 """
 function AssembleMatrix2D(rho, cp, k, BC, Num, nc, Δ, Δt)
     # Linear system of equation
@@ -111,8 +111,8 @@ function AssembleMatrix2D(rho, cp, k, BC, Num, nc, Δ, Δt)
     return flush!(K)
 end
 
-@doc raw"""
-    BackwardEuler2Dc
+"""
+    BackwardEuler2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC, rhs, K, Num)
 """
 function BackwardEuler2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC, rhs, K, Num)
 # dT/dt = kappa*d^2T_ij/dx_i^2 + Q_ij/rho/cp
@@ -178,8 +178,8 @@ D.T_ex[2:end-1,2:end-1]     .=    D.T
 # ------------------------------------------------------------------- #
 end
 
-@doc raw"""
-    CNA2Dc
+"""
+    CNA2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC, rhs, K1, K2, Num)
 """
 function CNA2Dc!(D, κ, Δx, Δy, Δt, ρ, cp, NC, BC, rhs, K1, K2, Num)
 # dT/dt = kappa*d^2T_ij/dx_i^2 + Q_ij/rho/cp
@@ -276,8 +276,8 @@ D.T_ex[2:end-1,2:end-1]     .=    D.T
 # ------------------------------------------------------------------- #
 end
 
-@doc raw"""
-    ADI2Dc
+"""
+    ADI2Dc!(T, κ, Δx, Δy, Δt, ρ, cp, NC, BC)
 """
 function ADI2Dc!(T, κ, Δx, Δy, Δt, ρ, cp, NC, BC)
     # Function to solve 2D heat diffusion equation using the alternating direct
@@ -466,8 +466,8 @@ function ADI2Dc!(T, κ, Δx, Δy, Δt, ρ, cp, NC, BC)
     T.T_ex[2:end-1,2:end-1]     .=    T.T
 end
 
-@doc raw"""
-    Poisson2Dc
+"""
+    Poisson2Dc!(D,NC,P,BC,Δ,K,rhs,Num)
 """
 function Poisson2Dc!(D,NC,P,BC,Δ,K,rhs,Num)
 # Function to solve 2D heat diffusion equation using the explicit finite
@@ -531,8 +531,8 @@ function Poisson2Dc!(D,NC,P,BC,Δ,K,rhs,Num)
 
 end
 
-@doc raw"""
-    Poisson2D
+"""
+    Poisson2D!( T, Q, kx, ky, Δx, Δy, NC, BC, K, rhs, Num ) 
 """
 function Poisson2D!( T, Q, kx, ky, Δx, Δy, NC, BC, K, rhs, Num ) 
     #  --------------------------------------------- #

src/InitialCondition/2Dini.jl

@@ -1,7 +1,7 @@
 using Base.Threads
 using GeoModBox
 
-@doc raw""" 
+""" 
     IniTemperature!(type,M,NC,D,x,y;Tb=1000,Ta=1200,Ampl=200,σ=0.05)
 
 Function to setup an initial temperature condition for a two dimensional 
@@ -115,11 +115,8 @@ Possible initial temperature conditions are:
     return D
 end    
 
-@doc raw"""
+"""
     IniVelocity!(type,D,NC,Δ,M,x,y)
-#
-#
-# ---
 """
 @views function IniVelocity!(type,D,BC,NC,NV,Δ,M,x,y;ε=1e-15)
     if type==:RigidBody
@@ -197,8 +194,8 @@ end
     return D, BC
 end
 
-@doc raw"""
-    IniPhase!
+"""
+    IniPhase!(type,D,M,x,y,NC;phase=0)
 """
 @views function IniPhase!(type,D,M,x,y,NC;phase=0)
 

src/MomentumEquation/1Dsolvers.jl

@@ -1,7 +1,7 @@
 using ExtendableSparse
 
-@doc raw"""
-    ComputeStokesResiduals1D! ()
+"""
+    ComputeStokesResiduals1D!( D, ∂P∂x, Δy, BC)
 """
 function ComputeStokesResiduals1D!( D, ∂P∂x, Δy, BC)
     @. D.vₓₑ[2:end-1]     =   D.vₓ
@@ -18,8 +18,8 @@ function ComputeStokesResiduals1D!( D, ∂P∂x, Δy, BC)
     @. D.R              =   -∂P∂x + D.∂τxy∂y
 end
 
-@doc raw"""
-    AssembleStokesMatrix1D()
+"""
+    AssembleStokesMatrix1D(nc, η, Δy, BC, K)
 """
 function AssembleStokesMatrix1D(nc, η, Δy, BC, K)
     # Zusammenstellen der Koeffizientenmatrix ------------------------------- #
@@ -49,8 +49,8 @@ function AssembleStokesMatrix1D(nc, η, Δy, BC, K)
     return flush!(K)
 end
 
-@doc raw"""
-    Stokes_1D()
+"""
+    Stokes_1D_direct(vₓ,η,Δy,nc,BC,K,rhs)
 """
 function Stokes_1D_direct(vₓ,η,Δy,nc,BC,K,rhs)
 

src/MomentumEquation/2Dsolvers.jl

@@ -1,5 +1,8 @@
 using ExtendableSparse
 
+"""
+    Assemblyc(NC, NV, Δ, η, BC, Num)
+"""
 function Assemblyc(NC, NV, Δ, η, BC, Num)
 
     # Linear system of equation ---
@@ -95,6 +98,9 @@ function Assemblyc(NC, NV, Δ, η, BC, Num)
     return flush!(K)
 end
 
+"""
+    updaterhsc(NC, NV, Δ, η, ρ, g, BC, Num)
+"""
 function updaterhsc(NC, NV, Δ, η, ρ, g, BC, Num)
 
     rhs     =   zeros(maximum(Num.Pt))  #   Right-hand Side
@@ -145,6 +151,9 @@ function updaterhsc(NC, NV, Δ, η, ρ, g, BC, Num)
     return rhs
 end
 
+"""
+    Residuals2Dc!(D,BC,ε,τ,divV,Δ,η,g,Fm,FPt)
+"""
 function Residuals2Dc!(D,BC,ε,τ,divV,Δ,η,g,Fm,FPt)
     @. D.vx[:,1]    = (BC.type.S==:freeslip)*D.vx[:,2]     + (BC.type.S==:noslip||BC.type.S==:const)*(2*BC.val.S - D.vx[:,2])
     @. D.vx[:,end]  = (BC.type.N==:freeslip)*D.vx[:,end-1] + (BC.type.N==:noslip||BC.type.N==:const)*(2*BC.val.N - D.vx[:,end-1])
@@ -166,6 +175,9 @@ function Residuals2Dc!(D,BC,ε,τ,divV,Δ,η,g,Fm,FPt)
     @. FPt             = divV
 end
 
+"""
+    Assembly(NC, NV, Δ, ηc, ηv, BC, Num)
+"""
 function Assembly(NC, NV, Δ, ηc, ηv, BC, Num)
 
     # Linear system of equation ---
@@ -281,6 +293,9 @@ function Assembly(NC, NV, Δ, ηc, ηv, BC, Num)
     return flush!(K)
 end
 
+"""
+    updaterhs(NC, NV, Δ, ηc, ηv, ρ, g, BC, Num)
+"""
 function updaterhs(NC, NV, Δ, ηc, ηv, ρ, g, BC, Num)
 
     rhs     =   zeros(maximum(Num.Pt))  #   Right-hand Side
@@ -331,6 +346,9 @@ function updaterhs(NC, NV, Δ, ηc, ηv, ρ, g, BC, Num)
     return rhs
 end
 
+"""
+    Residuals2D!(D,BC,ε,τ,divV,Δ,ηc,ηv,g,Fm,FPt)
+"""
 function Residuals2D!(D,BC,ε,τ,divV,Δ,ηc,ηv,g,Fm,FPt)
     @. D.vx[:,1]    = (BC.type.S==:freeslip)*D.vx[:,2]     + (BC.type.S==:noslip||BC.type.S==:const)*(2*BC.val.S - D.vx[:,2])
     @. D.vx[:,end]  = (BC.type.N==:freeslip)*D.vx[:,end-1] + (BC.type.N==:noslip||BC.type.N==:const)*(2*BC.val.N - D.vx[:,end-1])

src/Scaling.jl

@@ -1,3 +1,6 @@
+"""
+    Constants
+"""
 @kwdef mutable struct Constants
     hsc ::Float64 = 0.0
     tsc ::Float64 = 0.0
@@ -7,6 +10,9 @@
     Qsc ::Float64 = 0.0
 end
 
+"""
+    ScalingConstants!(M,P)
+"""
 function ScalingConstants!(M,P)
 
     S       =   Constants()
@@ -22,6 +28,9 @@ function ScalingConstants!(M,P)
 
 end
 
+"""
+    ScaleParameters!(S,M,Δ,T,P,D)
+"""
 function ScaleParameters!(S,M,Δ,T,P,D)
     # Geometry ---
     M.xmin   /=  S.hsc

src/Structures.jl

@@ -35,6 +35,9 @@ end
 #     c           ::
 # end
 
+"""
+    Physics()
+"""
 @kwdef mutable struct Physics
     # Physical parameters --- 
     # 
@@ -52,11 +55,17 @@ end
     Ra          ::Float64 = 1e5                 # Rayleigh number
 end
 
+"""
+    GridSpacing()
+"""
 @kwdef mutable struct GridSpacing
     x           ::Float64   =   0.0
     y           ::Float64   =   0.0
 end
 
+"""
+    DataFields()
+"""
 @kwdef mutable struct DataFields
     # Data fields ---
     Q           ::Matrix{Float64}   = zeros(1,1)
@@ -81,6 +90,9 @@ end
     Tmean       ::Float64           = 0.0
 end
 
+"""
+    TimeParameter()
+"""
 @kwdef mutable struct TimeParameter
     # Time Parameters ---
     const year      ::Float64   =   365.25*3600*24      #   Seconds per year

src/Tracers/1Dsolvers.jl

@@ -1,3 +1,6 @@
+"""
+    Itp1D_Centers2Markers!( Tm, xm, Tc, xc, Δx, xmin )
+"""
 function Itp1D_Centers2Markers!( Tm, xm, Tc, xc, Δx, xmin )
     # Biliniear
     for i = 1:length(xm)
@@ -7,6 +10,9 @@ function Itp1D_Centers2Markers!( Tm, xm, Tc, xc, Δx, xmin )
     end
 end
 
+"""
+    Itp1D_Markers2Centers!( Tc, xc, Tm, xm, dx, xmin )
+"""
 function Itp1D_Markers2Centers!( Tc, xc, Tm, xm, dx, xmin )
     Tc .= 0.0 
     Wc = zero(Tc)