Grid and domain cleanup/documentation (#110)

* Cleanup AbstractGrid and RegRectilinearGrid

* Rename and update domains file

* Finish grids docs and create grids tests

* Finished grid tests and docs

* Finish grid documentation

* Fix bad referances

* Start domain cleanup

* Direction code cleaned up

* Remove coords field from boundaries and topography

* Boundary docs done

* Finished boundary tutorial section

* Finish boundary tests

* Clean up topography

* Finish topography tests

* Finish domain tests

* Tutorial up to date through domains

* Update test Domain API

* Finish domain API cleanup

Project.toml

@@ -50,6 +50,7 @@ julia = "1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+LibGEOS = "a90b1aa1-3769-5649-ba7e-abc5a9d163eb"
 
 [targets]
-test = ["Test"]
+test = ["LibGEOS", "Test"]

README.md

@@ -9,7 +9,7 @@
 ## _Fast and Flexible Sea Ice Dynamics_
 
 Subzero.jl is a native [Julia](https://julialang.org/) discrete-element model (DEM) for exploring fine-scale sea ice dynamics, 
-reimplementing MATLAB model [SubZero by Manucharyan and Montemuro](https://doi.org/10.1029/2022MS003247).
+reimplementing and enhancing MATLAB model [SubZero by Manucharyan and Montemuro](https://doi.org/10.1029/2022MS003247).
 
 - 🚀 Runs over **35 times faster** that original MATLAB model for title simulation!
 - 🧩 Modular simulation model makes it easy to **customize simulations**!

docs/Project.toml

@@ -1,7 +1,8 @@
 [deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
+GeoInterfaceMakie = "0edc0954-3250-4c18-859d-ec71c1660c08"
+GeometryOps = "3251bfac-6a57-4b6d-aa61-ac1fef2975ab"
+LibGEOS = "a90b1aa1-3769-5649-ba7e-abc5a9d163eb"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-
-[compat]
-Documenter = "1.5"
-Literate = "2.19"

docs/literate/tutorial.jl

@@ -7,7 +7,125 @@
 
 # ## Tutorial - copy-pasteable version
 
-# ## Core steps of an Subzero.jl simulation
+# ## Core ideas behind Subzero.jl simulations
 
 
-using Subzero # bring package into scope
+# The very first step of running a Subzero simulation is to bring the package into scope.
+using Subzero # bring Subzero into scope
+using CairoMakie, GeoInterfaceMakie # bring plotting packages into scope
+import GeoInterface as GI
+
+
+# ## Creating a Grid
+
+# Each Subzero model requires a grid object. The grid object defines the grid for the ocean
+# and atmosphere. Ocean and atmosphere vectors (like `u` and `v` velocities) and tracers
+# (like temperature) are recorded on these grid points and grid lines. The grid points are
+# then used for interpolation for coupling between the ice, ocean, and atmosphere.
+
+# All Subzero grid objects are concrete types of the abstract type [`AbstractRectilinearGrid`](@ref).
+# Right now, all grid objects must be Rectilinear. Currently the only implemented concrete type
+# is a [`RegRectilinearGrid`](@ref). If you are interested in implementing another type of
+# grid, see the [developer documentation]("devdocs.md").
+
+# Here, we will go ahead and create an instance of `RegRectilinearGrid`. We need to specify
+# the grid endpoints and either the number of grid cells in both directions, or the size of
+# the grid cells. Here we will specity the number of grid cells in the x-direction, `Nx`, and
+# in the y-direction, `Ny`.
+
+grid = RegRectilinearGrid(; x0 = -1e5, xf = 1e5, y0 = 0.0, yf = 1e5, Nx = 20, Ny = 10)
+
+# We plot a dashed box around the grid so that we can see the that the grid matches the extent given.
+# We also place tick-marks at the desired grid cell lengths. Finally, set the plot's aspect ration to `2`
+# as the x-extent is two-times larger than the y-extent.
+fig = Figure();
+Axis(fig[1, 1]; # set up axis tick marks to match grid cells
+ xticks = range(grid.x0, grid.xf, 5), xminorticks = IntervalsBetween(5),
+ xminorticksvisible = true, xminorgridvisible = true,
+ yticks = range(grid.y0, grid.yf, 3), yminorticks = IntervalsBetween(5),
+ yminorticksvisible = true, yminorgridvisible = true,
+)
+lines!( # plot boundary of grid with a dashed line
+ [grid.x0, grid.x0, grid.xf, grid.xf, grid.x0], # point x-values
+ [grid.y0, grid.yf, grid.yf, grid.y0, grid.y0]; # point y-values
+ linestyle = :dash, linewidth = 3.0)
+# Resize grid to layout
+colsize!(fig.layout, 1, Aspect(1, 2))
+resize_to_layout!(fig)
+fig # display the figure
+
+# ## Creating Boundaries
+
+# Next, each Subzero.jl model needs a `Domain`. A `Domain` defines the region of the grid that
+# the ice floes are allowed in, what happens to them when they reach the boundaries of that
+# region, and if there is any topography in the model, along with the ice, in that region.
+
+# Similarly to the `grid` above, the `Domain` will be rectilinear, defined by four boundaries,
+# one for each of the cardinal direction. You will be able to pass each of the cardinal
+# directions ([`North`](@ref), [`South`](@ref), [`East`](@ref), and [`West`](@ref)), defined as
+# types by Subzero, to the boundary constructors. Each boundary can have different behavior, allowing
+# the user to create a wide variety of domain behavior. Right now, four types of `AbstractBoundaries`
+# are implemented: [`OpenBoundary`](@ref), [`PeriodicBoundary`](@ref), [`CollisionBoundary`](@ref), and
+# [`MovingBoundary`](@ref).
+
+# In this example, we will use two `CollisionBoundary` walls and two `PeriodicBoundary` walls
+# to create a channel that the ice can infinitly flow through, from the east back to the west.
+# In the north and the south, the ice will collide with the boundaries, as if there was shoreline
+# preventing it from leaving the channel.
+
+# We will use the grid we made above to define the boundaries so that they exactly border the grid.
+
+north_bound = CollisionBoundary(North; grid)
+south_bound = CollisionBoundary(South; grid)
+east_bound = PeriodicBoundary(East; grid)
+west_bound = PeriodicBoundary(West; grid)
+
+# If we plot the polygons that are created within each boundary object, we can see that they border
+# the grid. These polygons are how we well when the ice floes are interacting with each of the
+# boundaries. We can also see that the boundaries overlap in the corners to ensure there is
+# a solid border around the grid. The `PeriodicBoundary` elements are in purple while the
+# `CollisionBoundary` elements are in teal.
+
+poly!( # plot each of the boundaries with a 50% transparent color so we can see the overlap
+ [north_bound.poly, south_bound.poly, east_bound.poly, west_bound.poly];
+ color = [(:purple, 0.5), (:purple, 0.5), (:teal, 0.5), (:teal, 0.5)],
+)
+fig # display the figure
+
+# ## Creating Topography
+# We then have the option to add in a [`TopographyField`](@ref Subzero.TopographyField), which is a collection of
+# [`TopographyElement`](@ref)s. If we want to add in topography field, we can create one using
+# the [`initialize_topography_field`](@ref) function. Here we will create two islands in the
+# channel. For simplcity, both will be triangles. I create the polygons that define the shape
+# of each island using [`GeoInterface`](https://github.com/JuliaGeo/GeoInterface.jl) and
+# defining the points with tuples:
+island1 = GI.Polygon([[(-6e4, 7.5e4), (-4e4, 5e4), (-2.5e4, 7e4), (-6e4, 7.5e4)]])
+island2 = GI.Polygon([[(5e4, 2.5e4), (5e4, 5.5e4), (7.5e4, 3e4), (5e4, 2.5e4)]])
+topo_list = [island1, island2]
+
+# We can then pass these to `initialize_topography_field` with the `polys` keyword. We could
+# also have defined them just by their coordinates and passed in the coordiantes by the `coords`
+# keyword. 
+topo_field = initialize_topography_field(; polys = topo_list)
+
+# We can now plot the topography within the domain. 
+topo_color = RGBf(115/255, 93/255, 55/255) # brown color for topography
+poly!(topo_field.poly; color = topo_color) # plot the topography
+fig # display the figure
+
+
+# ## Creating a Domian
+# We now have all of the pieces needed to create a [`Domain`](@ref). We will combine the four
+# (4) boundaries we created, and the topography, into one `Domain` object. The collection of
+# boundaries and topography define where the floes can and cannot go in the simulation and add
+# in boundary behavior.We can do that as follows:
+
+domain = Domain(; north = north_bound, south = south_bound, east = east_bound, west = west_bound, topography = topo_field)
+
+# !!! note
+# We could have skipped adding the topography to the domain. That is an optional
+# keyword and an empty topography field will be automatically created if the user does not
+# provide one.
+
+# At this point, we have already plotted all of the `Domain` objects, so we will move in to adding
+# environmental forcing from the ocean and the atmosphere.

docs/make.jl

@@ -1,12 +1,11 @@
 using Documenter, Literate
-
 using Subzero
+import GeoInterface as GI
+import GeometryOps as GO
+import LibGEOS as LG
+
 
 # Converting any files in the literate folder to markdown
-# Literate.markdown(
-# joinpath(@__DIR__, "src", "tutorial.jl"), joinpath(@__DIR__, "src");
-# credit = false
-# )
 LITERATE_INPUT = joinpath(@__DIR__, "literate")
 LITERATE_OUTPUT = joinpath(@__DIR__, "src")
 
@@ -21,13 +20,17 @@ for (root, _, files) ∈ walkdir(LITERATE_INPUT), file ∈ files
  Literate.markdown(ipath, opath)
 end
 
+# Documentation formatting
 format = Documenter.HTML(;
  repolink = "https://github.com/Caltech-OCTO/Subzero.jl",
  canonical = "https://Caltech-OCTO.github.io/SubzeroDocumentation/stable",
  mathengine = MathJax3(),
  size_threshold = 5*10^5, # 500 KiB
 )
 
+# Metadata from doc tests
+DocMeta.setdocmeta!(Subzero, :DocTestSetup, :(using Subzero); recursive=true)
+
 makedocs(;
  modules=[Subzero],
  authors="Skylar Gering and contributers",

docs/src/api.md

@@ -7,12 +7,46 @@ CurrentModule = Subzero
 !!! warning
  This page is still very much WIP!
 
-Documentation for [Subzero](https://github.com/Caltech-OCTO/Subzero.jl)'s full API (only for reference!).
+## Grids
 
-```@index
+```@docs
+AbstractRectilinearGrid
+RegRectilinearGrid
 ```
 
-## All methods
-```@autodocs
-Modules = [Subzero]
-```
+## Directions
+```@docs
+AbstractDirection
+North
+South
+East
+West
+```
+## Boundaries
+```@docs
+AbstractBoundary
+OpenBoundary
+PeriodicBoundary
+CollisionBoundary
+MovingBoundary
+```
+## Topography
+```@docs
+TopographyElement
+initialize_topography_field
+```
+## Domain
+```@docs
+Domain
+```
+
+### Model
+```@docs
+Model
+```
+
+## Developer-Used Types
+```@docs
+CellFloes
+TopographyField
+```

docs/src/assets/title.jl

@@ -10,7 +10,7 @@ const Δt = 20
 const nΔt = 15000
 
 # Model instantiation
-grid = RegRectilinearGrid((0.0, Lx), (0.0, Ly), Δgrid, Δgrid)
+grid = RegRectilinearGrid(; x0 = 0.0, xf = Lx, y0 = 0.0, yf = Ly, Δx = Δgrid, Δy = Δgrid)
 
 uvels = repeat(
  [range(0, 0.2, length = 21); range(0.2, 0, length = 20)],
@@ -24,11 +24,11 @@ ocean = Ocean(
 atmos = Atmos(grid, 0.0, 0.0, -1.0)
 
 # Domain creation
-nboundary = PeriodicBoundary(North, grid)
-sboundary = PeriodicBoundary(South, grid)
-eboundary = PeriodicBoundary(East, grid)
-wboundary = PeriodicBoundary(West, grid)
-domain = Domain(nboundary, sboundary, eboundary, wboundary)
+nboundary = PeriodicBoundary(North; grid)
+sboundary = PeriodicBoundary(South; grid)
+eboundary = PeriodicBoundary(East; grid)
+wboundary = PeriodicBoundary(West; grid)
+domain = Domain(; north = nboundary, south = sboundary, east = eboundary, west = wboundary)
 
 # Floe creation
 floe_arr = initialize_floe_field(FT, 400, [0.85], domain, hmean, Δh; rng = Xoshiro(1))