Merge pull request #29 from mochell/12-remove-mtk-completely

Removed Modeling toolkit from all core modules and updated basic tests

Project.toml

@@ -25,7 +25,6 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Juno = "e5e0dc1b-0480-54bc-9374-aad01c23163d"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Oceananigans = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"

examples/example_eq_v3.jl → examples/_example_eq_v3.jl

@@ -7,7 +7,7 @@ using Setfield
 using Statistics
 
 using JLD2, Printf,IfElse
-using ModelingToolkit: Num, @unpack, @register_symbolic, Symbolics, @named, ODESystem
+#using ModelingToolkit: Num, @unpack, @register_symbolic, Symbolics, @named, ODESystem
 
 # %%
 #push!(LOAD_PATH, joinpath(pwd(), "code/"))

examples/example_eq_v4.jl → examples/_example_eq_v4.jl

@@ -7,7 +7,7 @@ using Setfield
 using Statistics
 
 using JLD2, Printf,IfElse
-using ModelingToolkit: Num, @unpack, @register_symbolic, Symbolics, @named, ODESystem
+# using ModelingToolkit: Num, @unpack, @register_symbolic, Symbolics, @named, ODESystem
 
 # %%
 

src/Models/WaveGrowthModels1D.jl

@@ -4,7 +4,6 @@ export WaveGrowth1D
 export fields, reset_boundary!, show
 
 using ...Architectures
-using ModelingToolkit: get_states, ODESystem
 
 
 #using core_1D: MarkedParticleInstance
@@ -221,28 +220,28 @@ function reset_boundary!(model::WaveGrowth1D)
 end
 
 
-function Base.show(io::IO, ow::WaveGrowth1D)
-
-    if ow.ODEsystem isa ODESystem
-        sys_print = get_states(ow.ODEsystem)
-    else
-        sys_print = ow.ODEsystem
-    end
-
-    print(io, "WaveGrowth1D ", "\n",
-        "├── grid: ", ow.grid, "\n",
-        "├── layers: ", ow.layers, "\n",
-        "├── clock: ", ow.clock,
-        "├── State: ", size(ow.State), "\n",
-        "├── ParticleCollection size: ", length(ow.ParticleCollection), "\n",
-        "├── ODEs    \n",
-        "|        ├── System: ", sys_print, "\n",
-        "|        ├── Defaults: ", ow.ODEdefaults, "\n",
-        "|        └── Settings:    \n", ow.ODEsettings, "\n",
-        "├── winds ", ow.winds, "\n",
-        "├── currents ", ow.currents, "\n",
-        "└── Perdiodic Boundary ", ow.periodic_boundary, "\n")
-end
+# function Base.show(io::IO, ow::WaveGrowth1D)
+
+#     if ow.ODEsystem isa ODESystem
+#         sys_print = get_states(ow.ODEsystem)
+#     else
+#         sys_print = ow.ODEsystem
+#     end
+
+#     print(io, "WaveGrowth1D ", "\n",
+#         "├── grid: ", ow.grid, "\n",
+#         "├── layers: ", ow.layers, "\n",
+#         "├── clock: ", ow.clock,
+#         "├── State: ", size(ow.State), "\n",
+#         "├── ParticleCollection size: ", length(ow.ParticleCollection), "\n",
+#         "├── ODEs    \n",
+#         "|        ├── System: ", sys_print, "\n",
+#         "|        ├── Defaults: ", ow.ODEdefaults, "\n",
+#         "|        └── Settings:    \n", ow.ODEsettings, "\n",
+#         "├── winds ", ow.winds, "\n",
+#         "├── currents ", ow.currents, "\n",
+#         "└── Perdiodic Boundary ", ow.periodic_boundary, "\n")
+# end
 
 
 

src/Models/WaveGrowthModels2D.jl

@@ -5,7 +5,6 @@ export fields
 
 using ...Architectures
 
-using ModelingToolkit: get_states, ODESystem
 
 #using core_1D: MarkedParticleInstance
 using ...ParticleMesh: OneDGrid, OneDGridNotes, TwoDGrid, TwoDGridNotes
@@ -265,11 +264,7 @@ end
 
 function Base.show(io::IO, ow::WaveGrowth2D)
 
-    if ow.ODEsystem isa ODESystem
-        sys_print = get_states(ow.ODEsystem)
-    else
-        sys_print = ow.ODEsystem
-    end
+    sys_print = ow.ODEsystem
     print(io, "WaveGrowth2D ", "\n",
         "├── grid: ", ow.grid, "\n",
         "├── layers: ", ow.layers, "\n",

src/Operators/core_1D.jl

@@ -1,10 +1,8 @@
 module core_1D
 
 using DifferentialEquations: OrdinaryDiffEq.ODEProblem, init
-using ModelingToolkit: ODESystem ## depriciate when MTK is removed
 
 using SharedArrays
-#using ModelingToolkit: Num
 using DocStringExtensions
 # Particle-Node interaction
 export GetParticleEnergyMomentum, GetVariablesAtVertex, Get_u_FromShared, ParticleDefaults
@@ -144,8 +142,8 @@ InitParticleInstance(model::WaveGrowth1D, z_initials, pars,  ij ; cbSets=nothing
 wrapper function to initalize a particle instance
         inputs:
         model           is an initlized ODESytem
-        z_initials      is the initial state of the ODESystem
-        pars            are the parameters of the ODESystem
+        z_initials      is the initial state of the Any
+        pars            are the parameters of the Any
         ij              is the (i,j) tuple that of the initial position
         chSet           (optional) is the set of callbacks the ODE can have
 """
@@ -179,40 +177,6 @@ function InitParticleInstance(model, z_initials, ODE_settings, ij, boundary_flag
 end
 
 
-# ODESystem version, will be depriciated
-"""
-InitParticleInstance(model::WaveGrowth1D, z_initials, pars,  ij ; cbSets=nothing)
-wrapper function to initalize a particle instance
-        inputs:
-        model           is an initlized ODESytem
-        z_initials      is the initial state of the ODESystem
-        pars            are the parameters of the ODESystem
-        ij              is the (i,j) tuple that of the initial position
-        chSet           (optional) is the set of callbacks the ODE can have
-"""
-function InitParticleInstance(model::ODESystem, z_initials, ODE_settings, ij, boundary_flag, particle_on; cbSets=Nothing)
-
-    z_initials = initParticleDefaults(z_initials)
-    # create ODEProblem
-    problem = ODEProblem(model, z_initials, (0.0, ODE_settings.total_time), ODE_settings.Parameters)
-    # inialize problem
-    # works best with abstol = 1e-4,reltol=1e-3,maxiters=1e4,
-    integrator = init(
-        problem,
-        ODE_settings.solver,
-        saveat=ODE_settings.saving_step,
-        abstol=ODE_settings.abstol,
-        adaptive=ODE_settings.adaptive,
-        dt=ODE_settings.dt,
-        dtmin=ODE_settings.dtmin,
-        force_dtmin=ODE_settings.force_dtmin,
-        maxiters=ODE_settings.maxiters,
-        reltol=ODE_settings.reltol,
-        callback=ODE_settings.callbacks,
-        save_everystep=ODE_settings.save_everystep)
-    return ParticleInstance1D(ij, z_initials[3], integrator, boundary_flag, particle_on)
-end
-
 
 
 """
@@ -320,7 +284,7 @@ end
 
 """
 SeedParticle!(ParticleCollection ::Vector{Any}, State::SharedMatrix, i::Int64,
-                particle_system::ODESystem, particle_defaults::Dict{Number, Float64}, ODE_defaults::Dict{Number, Float64},
+                particle_system::Any, particle_defaults::Dict{Number, Float64}, ODE_defaults::Dict{Number, Float64},
                 GridNotes, winds, DT:: Float64, Nx:: Int, boundary::Vector{Int}, periodic_boundary::Bool)
 
 Seed Pickles to ParticleColletion and State
@@ -339,7 +303,7 @@ function SeedParticle!(
     DT::Float64,
 
     boundary::Vector{T},
-    periodic_boundary::Bool) where {T<:Union{Int,Any,Nothing,Int64},PP<:Union{ParticleDefaults,Nothing},SS<:Union{ODESystem,Any}}
+    periodic_boundary::Bool) where {T<:Union{Int,Any,Nothing,Int64},PP<:Union{ParticleDefaults,Nothing},SS<:Any}
 
     # get x position
     x = GridNotes.x[i]

src/Operators/core_1D_old.jl

@@ -14,7 +14,7 @@ using ParticleInCell
 
 using DifferentialEquations
 using ParticleMesh: OneDGrid, OneDGridNotes
-using ModelingToolkit: ODESystem
+# using ModelingToolkit: ODESystem
 
 using FetchRelations