Automatic JuliaFormatter.jl run

docs/make.jl

@@ -8,7 +8,7 @@ type_page = [
     "Gas"=>"type_gas.md",
     "Physical space"=>"type_physical_space.md",
     "Velocity space"=>"type_velocity_space.md",
-    "Output"=>"type_output.md"
+    "Output"=>"type_output.md",
 ]
 methods_page = [
     "Running a simulation"=>"methods_solve.md",
@@ -20,7 +20,7 @@ methods_page = [
     "Parallel"=>"methods_parallel.md",
     "Theory"=>"methods_theory.md",
     "Finalization"=>"methods_finalize.md",
-    "IO"=>"methods_io.md"
+    "IO"=>"methods_io.md",
 ]
 makedocs(;
     sitename = "KitAMR.jl",
@@ -33,13 +33,11 @@ makedocs(;
         "Tutorial"=>"tutorial.md",
         "Cluster deployment"=>"cluster_deployment.md",
         "Index"=>"index_internal.md",
-        "Limitations"=>"limitations.md"
-        ],
+        "Limitations"=>"limitations.md",
+    ],
     # format = Documenter.HTML(; collapselevel=1),
     checkdocs = :none,
-    format = Documenter.HTML()
+    format = Documenter.HTML(),
 )
 
-deploydocs(;devbranch = "main",
-    repo = "github.com/CFDML/KitAMR.jl.git",
-)
+deploydocs(; devbranch = "main", repo = "github.com/CFDML/KitAMR.jl.git")

example/Riemann_problem/rp_1D.jl

@@ -1,16 +1,17 @@
-using KitAMR,MPI
+using KitAMR, MPI
 MPI.Init()
-function Sod_init(midpoint,kinfo)
-    if midpoint[1]<0.
-        return [1.,0.,0.,0.5]
+function Sod_init(midpoint, kinfo)
+    if midpoint[1]<0.0
+        return [1.0, 0.0, 0.0, 0.5]
     else
-        return [0.125,0.,0.,0.625]
+        return [0.125, 0.0, 0.0, 0.625]
     end
 end
 
 
 solver = Solver(;
-    DIM = 2, NDF = 2,
+    DIM = 2,
+    NDF = 2,
     CFL = 0.4,
     AMR_PS_MAXLEVEL = 3,
     AMR_VS_MAXLEVEL = 3,
@@ -22,37 +23,31 @@ solver = Solver(;
     # time_marching = CIP_Marching,
     time_marching = Euler,
     # time_marching = CAIDVM_Marching,
-    max_sim_time = 20.,
+    max_sim_time = 20.0,
 )
-gas = Gas(;
-    K = 1.0,
-    Kn = 0.001,
-    ω = 0.81,
-    ωᵣ = 0.81,
-)
-output = Output(
+gas = Gas(; K = 1.0, Kn = 0.001, ω = 0.81, ωᵣ = 0.81)
+output = Output(solver;)
+udf = UDF(;)
+config = Configure(
     solver;
-)
-udf = UDF(;
-)
-config = Configure(solver;
-    geometry = [-2.,2.,-0.5,0.5],
-    trees_num = [32,8],
-    quadrature = [-7.,7.,-7.,7.],
-    vs_trees_num = [8,8],
+    geometry = [-2.0, 2.0, -0.5, 0.5],
+    trees_num = [32, 8],
+    quadrature = [-7.0, 7.0, -7.0, 7.0],
+    vs_trees_num = [8, 8],
     IC = PCoordFn(Sod_init),
     domain = [
-            Domain(UniformOutflow,1),Domain(UniformOutflow,2),
-            Domain(Period,3),Domain(Period,4)
-        ],
+        Domain(UniformOutflow, 1),
+        Domain(UniformOutflow, 2),
+        Domain(Period, 3),
+        Domain(Period, 4),
+    ],
     output = output,
     gas = gas,
-    user_defined = udf
+    user_defined = udf,
 )
 
-p4est,ka = initialize(config; prerefine_steps = 1, prerefine_recursive = true);
-solve!(p4est, ka;
-    ps_interval = 20, vs_interval = 20, partition_interval = 20)
-save_result(p4est,ka)
-finalize!(p4est,ka)
+p4est, ka = initialize(config; prerefine_steps = 1, prerefine_recursive = true);
+solve!(p4est, ka; ps_interval = 20, vs_interval = 20, partition_interval = 20)
+save_result(p4est, ka)
+finalize!(p4est, ka)
 MPI.Finalize()

example/Riemann_problem/rp_2D.jl

@@ -40,29 +40,24 @@ solver = Solver(;
     max_sim_time = 0.25,
 )
 
-gas = Gas(;
-    K = 1.0,
-    Kn = 0.001,
-    ω = 0.81,
-    ωᵣ = 0.81,
-)
+gas = Gas(; K = 1.0, Kn = 0.001, ω = 0.81, ωᵣ = 0.81)
 
-output = Output(
-    solver;
-)
+output = Output(solver;)
 
-udf = UDF(;
-)
+udf = UDF(;)
 
-config = Configure(solver;
+config = Configure(
+    solver;
     geometry = [-0.5, 0.5, -0.5, 0.5],
     trees_num = [16, 16],
     quadrature = [-5.0, 5.0, -5.0, 5.0],
     vs_trees_num = [8, 8],
     IC = PCoordFn(Riemann_2D_init),
     domain = [
-        Domain(UniformOutflow, 1), Domain(UniformOutflow, 2),
-        Domain(UniformOutflow, 3), Domain(UniformOutflow, 4),
+        Domain(UniformOutflow, 1),
+        Domain(UniformOutflow, 2),
+        Domain(UniformOutflow, 3),
+        Domain(UniformOutflow, 4),
     ],
     output = output,
     gas = gas,
@@ -71,8 +66,7 @@ config = Configure(solver;
 
 p4est, ka = initialize(config; prerefine_steps = 5, prerefine_reinit_ic = true)
 
-solve!(p4est, ka;
-    ps_interval = 40, vs_interval = 40, partition_interval = 40)
+solve!(p4est, ka; ps_interval = 40, vs_interval = 40, partition_interval = 40)
 save_result(p4est, ka)
 finalize!(p4est, ka)
 MPI.Finalize()

example/X38/X38_julia.jl

@@ -1,4 +1,4 @@
-using KitAMR,MPI
+using KitAMR, MPI
 include("./X38_udf.jl")
 
 MPI.Init() # MPI initialization. Mandatory for a paralleled program using MPI.
@@ -10,53 +10,56 @@ MPI.Init() # MPI initialization. Mandatory for a paralleled program using MPI.
 Configuration by directly construct `Configure` struct.
 =#
 solver = Solver(;
-    DIM = 3, NDF = 1,
+    DIM = 3,
+    NDF = 1,
     AMR_PS_MAXLEVEL = 4,
     AMR_DYNAMIC_PS_MAXLEVEL = 4,
     AMR_VS_MAXLEVEL = 3,
     PS_DYNAMIC_AMR = true,
     VS_DYNAMIC_AMR = true,
     flux = CAIDVM,
     time_marching = CAIDVM_Marching,
-    max_sim_time = 20.,
-)
-gas = Gas(;
-    K = 0.0,
-    Kn = 0.275,
-    ω = 0.81,
-    ωᵣ = 0.81,
-    T_ref = 273/56,
+    max_sim_time = 20.0,
 )
+gas = Gas(; K = 0.0, Kn = 0.275, ω = 0.81, ωᵣ = 0.81, T_ref = 273/56)
 output = Output(solver)
-udf = UDF(;
-    dynamic_ps_refine_flag = amr_region
-)
-config = Configure(solver;
-    geometry = [-4.0,5.0,-4.0,4.0,-4.0,4.0],
-    trees_num = [16,16,16],
-    quadrature = [-14.2,21.3,-17.75,17.75,-17.75,17.75],
-    vs_trees_num = [10,10,10],
+udf = UDF(; dynamic_ps_refine_flag = amr_region)
+config = Configure(
+    solver;
+    geometry = [-4.0, 5.0, -4.0, 4.0, -4.0, 4.0],
+    trees_num = [16, 16, 16],
+    quadrature = [-14.2, 21.3, -17.75, 17.75, -17.75, 17.75],
+    vs_trees_num = [10, 10, 10],
     IC = PCoordFn(X38_buffer_IC),
     domain = [
-            Domain(SuperSonicInflow,1,
-            [1.,8.0*sqrt(5/6),0.,0.,1.0]),Domain(UniformOutflow,2),Domain(UniformOutflow,3),
-            Domain(UniformOutflow,4),Domain(UniformOutflow,5),Domain(UniformOutflow,6)
-        ],
-    IB = [Triangles(Maxwellian,"./example/X38/X38_normalized.stl",true,1.5,[1.,0.,0.,0.,56/300])],
+        Domain(SuperSonicInflow, 1, [1.0, 8.0*sqrt(5/6), 0.0, 0.0, 1.0]),
+        Domain(UniformOutflow, 2),
+        Domain(UniformOutflow, 3),
+        Domain(UniformOutflow, 4),
+        Domain(UniformOutflow, 5),
+        Domain(UniformOutflow, 6),
+    ],
+    IB = [
+        Triangles(
+            Maxwellian,
+            "./example/X38/X38_normalized.stl",
+            true,
+            1.5,
+            [1.0, 0.0, 0.0, 0.0, 56/300],
+        ),
+    ],
     output = output,
     gas = gas,
-    user_defined = udf
+    user_defined = udf,
 )
 # ----------------------------------------------------------------------------------------------------
 
-p4est,ka = initialize(config; prerefine_steps = 0) # Initialization for `KitAMR_Data`.
+p4est, ka = initialize(config; prerefine_steps = 0) # Initialization for `KitAMR_Data`.
 #=
 Run the time-stepping loop. `max_sim_time` is set in the `Solver` above; `solve!`
 terminates (and lands the last step) exactly on it via `reached_max_time` / `limit_Δt!`.
 =#
-solve!(p4est, ka;
-    ps_interval = 40, vs_interval = 40, partition_interval = 40)
-save_result(p4est,ka) # Save converging results.
-finalize!(p4est,ka) # Finalize `p4est` things. Release the memory managed by `C`.
+solve!(p4est, ka; ps_interval = 40, vs_interval = 40, partition_interval = 40)
+save_result(p4est, ka) # Save converging results.
+finalize!(p4est, ka) # Finalize `p4est` things. Release the memory managed by `C`.
 MPI.Finalize() # MPI finalization. Mandatory for a paralleled program using MPI.
-

example/X38/X38_text.jl

@@ -1,16 +1,22 @@
-using KitAMR,MPI
+using KitAMR, MPI
 include("./X38_udf.jl")
 MPI.Init()
 config = KitAMR.read_config("./example/X38/configure_X38.txt")
-p4est,ka = KitAMR.initialize(config);
+p4est, ka = KitAMR.initialize(config);
 KitAMR.listen_for_save!()
 i = 0
 while !KitAMR.reached_max_time(ka)   # max_sim_time is read from the config file
     global i += 1
     if MPI.Comm_rank(MPI.COMM_WORLD)==0
         @show i
     end
-    KitAMR.adaptive_mesh_refinement!(p4est,ka;ps_interval = 40, vs_interval=40,partition_interval=40)
+    KitAMR.adaptive_mesh_refinement!(
+        p4est,
+        ka;
+        ps_interval = 40,
+        vs_interval = 40,
+        partition_interval = 40,
+    )
     KitAMR.limit_Δt!(ka)   # shrink Δt to land exactly on the next animation frame / max_sim_time
     KitAMR.update_slope!(ka)
     KitAMR.slope_exchange!(p4est, ka)
@@ -20,11 +26,10 @@ while !KitAMR.reached_max_time(ka)   # max_sim_time is read from the config file
     KitAMR.flux!(ka)
     KitAMR.iterate!(ka)
     KitAMR.data_exchange!(p4est, ka)
-    check_for_animsave!(p4est,ka)   # write a frame if this step landed on a frame time
+    check_for_animsave!(p4est, ka)   # write a frame if this step landed on a frame time
     KitAMR.check_for_convergence(ka)&&break
-    KitAMR.check!(p4est,ka)
+    KitAMR.check!(p4est, ka)
 end
-KitAMR.save_result(p4est,ka)
-KitAMR.finalize!(p4est,ka)
+KitAMR.save_result(p4est, ka)
+KitAMR.finalize!(p4est, ka)
 MPI.Finalize()
-

example/X38/X38_udf.jl

@@ -1,5 +1,5 @@
 using LinearAlgebra
-function amr_region(ps_data,level,ka) # dynamic
+function amr_region(ps_data, level, ka) # dynamic
     midpoint = ps_data.midpoint
     ds = ps_data.ds
     L = 1.0
@@ -8,16 +8,16 @@ function amr_region(ps_data,level,ka) # dynamic
     end
     return false
 end
-function X38_buffer_IC(midpoint::Vector{Float64},kinfo::KInfo)
+function X38_buffer_IC(midpoint::Vector{Float64}, kinfo::KInfo)
     ib = kinfo.config.IB[1]
-    Ma = 8.
+    Ma = 8.0
     T0 = 1.0
     Tw = 300/56
-    _,distance = KitAMR.nn(ib.tkdt.kdt,midpoint)
+    _, distance = KitAMR.nn(ib.tkdt.kdt, midpoint)
     R = 0.3
     if distance > R
-        return [1.0,Ma*√(5/6),0.,0.,1/T0]
+        return [1.0, Ma*√(5/6), 0.0, 0.0, 1/T0]
     else
-        return [1.0,distance*Ma*√(5/6)/R,0.,0.,1.0/(T0+(R-distance)*(Tw-T0)/R)]
+        return [1.0, distance*Ma*√(5/6)/R, 0.0, 0.0, 1.0/(T0+(R-distance)*(Tw-T0)/R)]
     end
-end
+end

example/X38/model_transform.jl

@@ -1,12 +1,12 @@
 using FileIO, MeshIO, GeometryBasics
 mesh = load("./example/X38/X38-surface-fine.stl")
-points = [x[i] for i in 1:3, x in mesh.position]
-mins = minimum(points,dims=2)
-maxes = maximum(points,dims=2)
+points = [x[i] for i = 1:3, x in mesh.position]
+mins = minimum(points, dims = 2)
+maxes = maximum(points, dims = 2)
 L = maximum(maxes-mins)
 α = -π/9# AOA 20 degrees
-Rot = [cos(α) -sin(α) 0;sin(α) cos(α) 0;0 0 1.]
-normalized_points = Rot*points./L
-normalized_position = [Point(x[1],x[2],x[3]) for x in eachcol(normalized_points)]
-new_mesh = Mesh(normalized_position,mesh.faces)
-save("./example/X38/X38_normalized.stl",new_mesh)
+Rot = [cos(α) -sin(α) 0; sin(α) cos(α) 0; 0 0 1.0]
+normalized_points = Rot*points ./ L
+normalized_position = [Point(x[1], x[2], x[3]) for x in eachcol(normalized_points)]
+new_mesh = Mesh(normalized_position, mesh.faces)
+save("./example/X38/X38_normalized.stl", new_mesh)