Merge pull request #14 from mncrowe/main

Merge recent docs updates, fixes and additions

docs/src/Examples.md

@@ -241,7 +241,7 @@ x₀ = [0, 0]			# position of vortex center
 M = 8				# number of coefficients in Zernike expansion
 tol = 1e-8			# maximum error in solution evaluation
 cuda = false			# use CuArrays for grid
-K₀, a₀ = [4, 4], Nothing	# guesses for K and a
+K₀, a₀ = [4, 4], nothing	# guesses for K and a
 
 # create grid
 
@@ -283,7 +283,7 @@ x₀ = [0, 0]			# position of vortex center
 M = 20				# number of coefficients in Zernike expansion
 tol = 1e-6			# maximum error in solution evaluation
 cuda = false			# use CuArrays for grid
-K₀, a₀ = 8, Nothing		# guesses for K and a
+K₀, a₀ = 8, nothing		# guesses for K and a
 
 # Set grid parameters
 

docs/src/Functions.md

@@ -48,8 +48,6 @@ Eval_w_SQG
 Calc_∇
 CartesianGrid
 PolarGrid
-Base.summary
-Base.show
 ```
 
 ## `energetics.jl`
@@ -61,10 +59,30 @@ EnergySQG
 AreaInteg2
 ```
 
+## `vortex_types.jl`
+
+```@docs
+LQGParams
+SQGParams
+LQGVortex
+SQGVortex
+DefLQGParams
+DefSQGParams
+DefLQGVortex
+DefSQGVortex
+```
+
 ## `monopoles.jl`
 
 ```@docs
 CreateRankine
 CreateMonopole
 InvertVorticity1LQG
+```
+
+## `Base`
+
+```@docs
+Base.summary
+Base.show
 ```

src/QGDipoles.jl

@@ -58,7 +58,17 @@ export
 	EnstrophyLQG,
 	EnergySQG,
 	AreaInteg2,
-
+
+	# vortex_types.jl
+	LQGParams,
+	SQGParams,
+	LQGVortex,
+	SQGVortex,
+	DefLQGParams,
+	DefSQGParams,
+	DefLQGVortex,
+	DefSQGVortex,	
+
 	# monopoles.jl
 	CreateRankine,
 	CreateMonopole,
@@ -70,6 +80,7 @@ include("JJ_integ.jl")
 include("lin_sys.jl")
 include("create_modon.jl")
 include("energetics.jl")
+include("vortex_types.jl")
 include("monopoles.jl")
 
 end

src/create_modon.jl

@@ -434,7 +434,7 @@ function ΔNCalc(K²::Union{CuArray,Array}, R::Union{Number,Vector}, β::Union{N
 end
 
 """
-Function: `CreateModonLQG(grid, M, U=1, ℓ=1, R=1, β=0, ActiveLayers=1, x₀=[0, 0], α=0; K₀=Nothing, a₀=Nothing, tol=1e-6)`
+Function: `CreateModonLQG(grid, M, U=1, ℓ=1, R=1, β=0, ActiveLayers=1, x₀=[0, 0], α=0; K₀=nothing, a₀=nothing, tol=1e-6)`
 
 High level wrapper function for calculating ψ and q for the Layered QG model using given parameters
 
@@ -446,13 +446,14 @@ Arguments:
  - `ActiveLayers`: vector of 1s or 0s where 1 denotes an active layer, Number or Vector, (default: `[1,..,1]`)
  - `x₀`: position of vortex center, vector (default: `[0, 0]`)
  - `α`: initial angle of vortex, Number (default: 0)
- - `K₀`, `a₀`: initial guesses for K and a, Arrays or Nothings (default: `Nothing`)
+ - `K₀`, `a₀`: initial guesses for K and a, Arrays or nothings (default: `nothing`)
  - `tol`: error tolerance passed to `QuadGK` and `NLSolve` functions, Number (default: `1e-6`)
 
 Note: provide values of K₀ and a₀ for active layers ONLY.
 """
 function CreateModonLQG(grid, M::Int=8, U::Number=1, ℓ::Number=1, R::Union{Number,Vector}=1, β::Union{Number,Vector}=0,
-	ActiveLayers::Union{Number,Vector}=1, x₀::Vector=[0, 0], α::Number=0; K₀=Nothing, a₀=Nothing, tol=1e-6)
+	ActiveLayers::Union{Number,Vector}=1, x₀::Vector=[0, 0], α::Number=0; K₀::Union{Number,Array,Nothing}=nothing,
+	a₀::Union{Array,Nothing}=nothing, tol=1e-6)
 
 	# If ActiveLayers size does not match size of R, assume all layers are active
 
@@ -485,7 +486,7 @@ function CreateModonLQG(grid, M::Int=8, U::Number=1, ℓ::Number=1, R::Union{Num
 end
 
 """
-Function: `CreateModonSQG(grid, M, U=1, ℓ=1, R=[Inf, Inf], β=0, x₀=[0, 0], α=0; K₀=Nothing, a₀=Nothing, tol=1e-6)`
+Function: `CreateModonSQG(grid, M, U=1, ℓ=1, R=[Inf, Inf], β=0, x₀=[0, 0], α=0; K₀=nothing, a₀=nothing, tol=1e-6)`
 
 High level wrapper function for calculating ψ and b for the SQG model using given parameters
 
@@ -497,14 +498,15 @@ Arguments:
  - `β`: beta-plane (y) PV gradient, Number (default: `0`)
  - `x₀`: position of vortex center, vector (default: `[0, 0]`)
  - `α`: initial angle of vortex, Number (default: `0`)
- - `K₀`, `a₀`: initial guesses for K and a, Arrays or Nothings (default: `Nothing`)
+ - `K₀`, `a₀`: initial guesses for K and a, Arrays or nothings (default: `nothing`)
  - `tol`: error tolerance passed to `QuadGK` and `NLSolve` functions, Number (default: `1e-6`)
 
 Note: Here R is the baroclinic Rossby radius, R = NH/f, and R' = R₀²/R where R₀ is
 the barotropic Rossby radius, R₀ = √(gH)/f. For infinite depth, R' = g/(fN).
 """
 function CreateModonSQG(grid, M::Int=12, U::Number=1, ℓ::Number=1, R::Vector=[Inf, Inf], β::Number=0,
-	x₀::Vector=[0, 0], α::Number=0; K₀=Nothing, a₀=Nothing, tol=1e-6)
+	x₀::Vector=[0, 0], α::Number=0; K₀::Union{Number,Array,Nothing}=nothing,
+	a₀::Union{Array,Nothing}=nothing, tol=1e-6)
 
 	# Define intermediate variables
 
@@ -900,7 +902,6 @@ end
 
 """
 Base.summary function for custom type `GridStruct`
-
 """
 function Base.summary(g::GridStruct)
 
@@ -917,7 +918,6 @@ end
 
 """
 Base.show function for custom type `GridStruct`
-
 """
 function Base.show(io::IO, g::GridStruct)
 
@@ -932,11 +932,11 @@ function Base.show(io::IO, g::GridStruct)
 	end
 
 	return print(io, "GridStruct\n",
-               "  ├───────────────── Device: ", dev, "\n",
-               "  ├────────── size (Lx, Ly): ", (Lx, Ly), "\n",
-               "  ├──── resolution (Nx, Ny): ", (Nx, Ny), "\n",
-               "  ├── grid spacing (Δx, Δy): ", (Δx, Δy), "\n",
-               "  └───────────────── domain: x ∈ [$(g.x[1]), $(g.x[end])]", "\n",
-               "                             y ∈ [$(g.y[1]), $(g.y[end])]")    
+               "  ├────────────────────── device: ", dev, "\n",
+               "  ├─────────────── size (Lx, Ly): ", (Lx, Ly), "\n",
+               "  ├───────── resolution (Nx, Ny): ", (Nx, Ny), "\n",
+               "  ├─────── grid spacing (Δx, Δy): ", (Δx, Δy), "\n",
+               "  └────────────────────── domain: x ∈ [$(g.x[1]), $(g.x[end])]", "\n",
+               "                                  y ∈ [$(g.y[1]), $(g.y[end])]")
 
 end

src/lin_sys.jl

@@ -240,13 +240,13 @@ function IncludePassiveLayers(K::Array, a::Array, ActiveLayers::Union{Number,Vec
 end
 
 """
-Function: `SolveInhomEVP(A, B, c, d; K₀=Nothing, a₀=Nothing, tol=1e-6, method=0, m=2, sqg=false, warn=true)`
+Function: `SolveInhomEVP(A, B, c, d; K₀=nothing, a₀=nothing, tol=1e-6, method=0, m=2, sqg=false, warn=true)`
 
 Solves the inhomogeneous eigenvalue problem using nonlinear root finding
 
 Arguments:
  - `A`, `B`, `c`, `d`: inhomogeneous eigenvalue problem terms, Arrays
- - `K₀`, `a₀`: initial guesses for K and a, Arrays or Nothings (default: `Nothing`)
+ - `K₀`, `a₀`: initial guesses for K and a, Arrays or nothings (default: `nothing`)
  - `tol`: error tolerance for `nlsolve`, Number (default: `1e-6`)
  - `method`: `0` - eigensolve for N = 1 and `nlsolve` for N > 1, `1` - `nlsolve` (default: `0`)
  - `m`: exponent of K in eignevalue problem (default: `2`)
@@ -257,8 +257,9 @@ Note: setting `sqg=true` overwrites the value of `m` and is equivalent to settin
 The option to set both is included for consistency with `BuildLinSys` and more generality
 with the value of `m`.
 """
-function SolveInhomEVP(A::Array, B::Array, c::Array, d::Array; K₀=Nothing, a₀=Nothing,
-		tol::Number=1e-6, method::Int=0, m::Int=2, sqg::Bool=false, warn::Bool=true)
+function SolveInhomEVP(A::Array, B::Array, c::Array, d::Array; K₀::Union{Number,Array,Nothing}=nothing,
+		a₀::Union{Array,Nothing}=nothing, tol::Number=1e-6, method::Int=0, m::Int=2,
+		sqg::Bool=false, warn::Bool=true)
 
 	# Ensure that m is set correctly for SQG case
 
@@ -295,7 +296,7 @@ function SolveInhomEVP(A::Array, B::Array, c::Array, d::Array; K₀=Nothing, a
 
 		# Set K₀ value if none given
 
-		if K₀ == Nothing
+		if K₀ isa Nothing
 
 			K₀ = [4]
 
@@ -346,7 +347,7 @@ function SolveInhomEVP(A::Array, B::Array, c::Array, d::Array; K₀=Nothing, a
 
 		# Define a₀ if none given and reshape if given
 
-		if a₀ == Nothing
+		if a₀ isa Nothing
 
 			a₀ = vcat(-10*ones(N, 1), zeros(N*(M-1), 1))
 
@@ -358,7 +359,7 @@ function SolveInhomEVP(A::Array, B::Array, c::Array, d::Array; K₀=Nothing, a
 
 		# Define K₀ if none given and reshape if given
 
-		if K₀ == Nothing
+		if K₀ isa Nothing
 
 			K₀ = 5*ones(N, 1)