Clean physical process docs (#131)

* Remove use of coords field from tests and code

* Remove coords field from floe

* Clean up floe_utils

* Clean up geometry utils

* Wrappers for GO code

* Finish floe util cleanup

* Clean up collisions code

* Finish cleaning up collision docs

* Update comments for physical processes up through fractures

* Update ridge/raft docs

* Finish physical process docs cleanup

* Finish documentation cleanup

* Update all packages

* Decrease flow fracturing in tutorial

Author: skygering

Project.toml

@@ -36,7 +36,7 @@ Extents = "0.1"
 GeoInterfaceMakie = "0.1"
 GeometryOps = "0.1.31"
 Interpolations = "0.14, 0.15, 0.16"
-JLD2 = "0.4, 0.5"
+JLD2 = "0.4, 0.5, 0.6"
 Measures = "0.3"
 NCDatasets = "0.14"
 Rotations = "1"

docs/literate/tutorial.jl

@@ -308,7 +308,7 @@ consts = Constants()
 fracture_settings = FractureSettings(
         fractures_on = true,
         criteria = HiblerYieldCurve(floes),
-        Δt = 75,
+        Δt = 500,
         npieces = 3,
         deform_on = false,
 )
@@ -353,7 +353,7 @@ sim = Simulation(;
     model = model,
     consts = consts,
     Δt = 10, # timestep of 5 seconds
-    nΔt = 30000, # run for 10,000 timesteps
+    nΔt = 20000, # run for 20,000 timesteps
     floe_settings = floe_settings,
     fracture_settings = fracture_settings,
     writers = writers,

docs/make.jl

@@ -47,6 +47,7 @@ format = Documenter.HTML(;
     canonical = "https://Caltech-OCTO.github.io/SubzeroDocumentation/stable",
     mathengine = MathJax3(),
     size_threshold = 5*10^6,  # 500 KiB
+    collapselevel = 3,
 )
 
 # Metadata from doc tests

docs/src/api.md

@@ -4,50 +4,52 @@ CurrentModule = Subzero
 
 # Full Subzero API documentation
 
-## Grids
+## User Methods
+
+### Grids
 
 ```@docs
 AbstractRectilinearGrid
 RegRectilinearGrid
 ```
 
-## Directions
+### Directions
 ```@docs
 AbstractDirection
 North
 South
 East
 West
 ```
-## Boundaries
+### Boundaries
 ```@docs
 AbstractBoundary
 OpenBoundary
 PeriodicBoundary
 CollisionBoundary
 MovingBoundary
 ```
-## Topography
+### Topography
 ```@docs
 TopographyElement
 initialize_topography_field
 ```
-## Domain
+### Domain
 ```@docs
 Domain
 ```
 
-## Ocean
+### Ocean
 ```@docs
 Ocean
 ```
 
-## Atmosphere
+### Atmosphere
 ```@docs
 Atmos
 ```
 
-## Floes
+### Floes
 ```@docs
 Floe
 AbstractFloeFieldGenerator
@@ -56,17 +58,17 @@ VoronoiTesselationFieldGenerator
 initialize_floe_field
 ```
 
-## Model
+### Model
 ```@docs
 Model
 ```
 
-## Constants
+### Constants
 ```@docs
 Constants
 ```
 
-## Physical Process Settings
+### Physical Process Settings
 ```@docs
 FloeSettings
 CouplingSettings
@@ -81,7 +83,7 @@ RidgeRaftSettings
 WeldSettings
 ```
 
-## Output Writers
+### Output Writers
 ```@docs
 AbstractOutputWriter
 InitialStateOutputWriter
@@ -92,20 +94,20 @@ OutputWriters
 SubzeroLogger
 ```
 
-## Simulations
+### Simulations
 ```@docs
 Simulation
 run!
 restart!
 ```
 
-# Developer-Used Methods
+## Developer Methods
 
-## Simulation Methods
+### Simulation Methods
 ```@docs
 timestep_sim!
 ```
-## Output Writer Methods
+### Output Writer Methods
 ```@docs
 write_data!
 write_init_state_data!
@@ -114,10 +116,70 @@ write_floe_data!
 write_grid_data!
 calc_eulerian_data!
 ```
-
-## Developer-Used Types
+### Developer-Used Types
 ```@docs
 CellFloes
 CellStresses
 TopographyField
 ```
+
+### Collision Methods
+```@docs
+timestep_collisions!
+calc_elastic_forces
+calc_normal_force
+calc_friction_forces
+add_interactions!
+floe_floe_interaction!
+floe_domain_interaction!
+floe_domain_element_interaction!
+update_boundaries!
+add_ghosts!
+```
+
+### Coupling Methods
+```@docs
+timestep_coupling!
+calc_one_way_coupling!
+calc_two_way_coupling!
+calc_atmosphere_forcing
+calc_ocean_forcing!
+floe_to_grid_info!
+```
+
+### Fracture Methods
+```@docs
+fracture_floes!
+split_floe
+deform_floe!
+determine_fractures
+```
+
+### Ridging and Rafting Methods
+```@docs
+timestep_ridging_rafting!
+floe_floe_raft!
+floe_domain_raft!
+floe_floe_ridge!
+floe_domain_ridge!
+```
+
+### Simplify Methods
+```@docs
+simplify_floes!
+smooth_floes!
+fuse_floes!
+remove_floes!
+```
+
+### Welding Methods
+```@docs
+timestep_welding!
+```
+
+### Floe Update Methods
+```@docs
+timestep_floe_properties!
+calc_stress!
+calc_strain!
+```

docs/src/tutorial.md

@@ -356,7 +356,7 @@ The list of existing settings is:
 fracture_settings = FractureSettings(
         fractures_on = true,
         criteria = HiblerYieldCurve(floes),
-        Δt = 75,
+        Δt = 500,
         npieces = 3,
         deform_on = false,
 )
@@ -417,7 +417,7 @@ sim = Simulation(;
     model = model,
     consts = consts,
     Δt = 10, # timestep of 5 seconds
-    nΔt = 30000, # run for 10,000 timesteps
+    nΔt = 20000, # run for 20,000 timesteps
     floe_settings = floe_settings,
     fracture_settings = fracture_settings,
     writers = writers,

ext/SubzeroMakieExt.jl

@@ -18,7 +18,7 @@ heatmap and colorbar.
 ## Arguments:
 - `floe_fn::String`: $(Subzero.FLOE_FN_DEF)
 - `initial_state_fn::String`: $(Subzero.INITIAL_STATE_FN_DEF)
-- `Δt::Int`: $(Subzero.ΔT_DEF)
+- $(Subzero.ΔT_DEF)
 - `output_fn::String`: $(Subzero.MP4_OUTPUT_FN)
 """
 function plot_sim(

src/Subzero.jl

@@ -17,7 +17,7 @@ using CoordinateTransformations, Dates, Extents,
     Printf, Random, Rotations, SplitApplyCombine, Statistics, StructArrays
 
 
-
+const SIM_DEF = "`sim::Simulation`: simulation to be run"
 const FT_DEF = "`FT::Type{<:AbstractFloat}`: Float type used to run the simulation, either \
 `Float64` (default) or `Float32`."
 const POLY_DEF = "`poly::Polys{FT}`: Polygon used to represent the shape of a floe or topography"
@@ -31,8 +31,6 @@ point that is the centroid of either a floe or topography"
 const RMAX_DEF = "`rmax::FT`: Float length representing the maximum radius of a floe or topography \
 from the centroid to any given vertex"
 
-const SIM_DEF = "`sim::Simulation`: simulation to be run"
-
 
 # Types
 include("tools/geom_utils.jl")
@@ -55,9 +53,14 @@ include("simulation_components/atmos.jl")
 include("simulation_components/model.jl")
 # Outputs
 include("simulation_components/output_components/logger.jl")
-# Physical Processes
+# Process Settings
 include("simulation_components/process_settings/process_settings.jl")
 include("simulation_components/process_settings/fracture_settings.jl")
+# Simulation
+include("simulation_components/output_components/output.jl")
+include("simulation_components/constants.jl")
+include("simulation_components/simulation.jl")
+# Physical Processes
 include("physical_processes/fractures.jl")
 include("physical_processes/update_floe.jl")
 include("physical_processes/coupling.jl")
@@ -69,8 +72,4 @@ include("physical_processes/welding.jl")
 include("tools/plotting.jl")
 include("tools/conservation_em.jl")
 include("tools/compare_files.jl")
-# Simulation
-include("simulation_components/output_components/output.jl")
-include("simulation_components/constants.jl")
-include("simulation_components/simulation.jl")
 end