Automatic JuliaFormatter.jl run

deprecated/flux.jl

@@ -328,7 +328,7 @@ function calc_flux!(::Val{0}, ::Val{2}, face::Face, DVM_data::DVM_Data, faceid::
     #     @show ps_data.neighbor.data[faceid][2].midpoint
     # end
     fw_test = zeros(DIM + 2)
-    for i = 1:2^(DIM-1)
+    for i = 1:(2^(DIM-1))
         nps_data = ps_data.neighbor.data[faceid][i]
         vs_data_n = nps_data.vs_data
         ds = nps_data.ds[dir]

lib/P4estTypes/src/connectivity.jl

@@ -6,6 +6,7 @@ the roots of `Pxest` quadtrees or octrees. The parameter `X` is 4 if the
 roots are quads (2D aka p4est) and 8 if they are hexes (3D aka p8est).
 
 # Fields
+
 $(DocStringExtensions.FIELDS)
 
 # Usage
@@ -15,23 +16,23 @@ $(DocStringExtensions.FIELDS)
 Construct a connectivity mesh for the roots of a forest-of-quadtrees using
 p4est's built-in mesh connectivities.  Valid values for `name` are
 
-- `:unitsquare`: the unit square.
-- `:periodic`: all-periodic unit square.
-- `:rotwrap`: periodic unit square (the left and right faces are identified,
-  and bottom and top opposite).
-- `:corner`: three-tree mesh around a corner.
-- `:pillow`: two trees on top of each other.
-- `:moebius`: a five-tree moebius band.
-- `:star`: six-tree star.
-- `:cubed`: six sides of a unit cube.
-- `:disk_nonperiodic`: five-tree flat spherical disk.
-- `:icosahedron`: for mapping the sphere using an icosahedron (see
-  `@doc P4estTypes.P4est.p4est_connectivity_new_icosahedron` for more info).
-- `:shell2d`: 2D spherical shell.
-- `:disk2d`: maps a 2D disk.
-
-
----
+  - `:unitsquare`: the unit square.
+  - `:periodic`: all-periodic unit square.
+  - `:rotwrap`: periodic unit square (the left and right faces are identified,
+    and bottom and top opposite).
+  - `:corner`: three-tree mesh around a corner.
+  - `:pillow`: two trees on top of each other.
+  - `:moebius`: a five-tree moebius band.
+  - `:star`: six-tree star.
+  - `:cubed`: six sides of a unit cube.
+  - `:disk_nonperiodic`: five-tree flat spherical disk.
+  - `:icosahedron`: for mapping the sphere using an icosahedron (see
+    `@doc P4estTypes.P4est.p4est_connectivity_new_icosahedron` for more info).
+  - `:shell2d`: 2D spherical shell.
+  - `:disk2d`: maps a 2D disk.
+
+* * *
+
     Connectivity{4}(:disk, periodic_x::Bool, periodic_y::Bool)
 
 Create a connectivity structure for a five-tree flat spherical disk.  The
@@ -40,26 +41,28 @@ the x and y directions, respectively.
 
 See `@doc P4estTypes.P4est.p4est_connectivity_new_disk` for detailed information.
 
----
+* * *
+
     Connectivity{8}(name::Symbol)
 
 Construct a connectivity mesh for the roots of a forest-of-octrees using
 p8est's built-in mesh connectivities.  Valid values for `name` are
 
-- `:unitcube`: the unit cube.
-- `:periodic`: an all-periodic unit cube.
-- `:rotcubes`: contains a few cubes (these are rotated against each other to
-  stress the topology routines).
-- `:rotwrap`: a mostly periodic unit cube (see
-  `@doc P4estTypes.P4est.p8est_connectivity_new_rotwrap`).
-- `:shell`: a spherical shell (see
-  `@doc P4estTypes.P4est.p8est_connectivity_new_shell`).
-- `:sphere`: a solid sphere (see
-  `@doc P4estTypes.P4est.p8est_connectivity_new_sphere`).
-- `:twocubes`: two cubes.
-- `:twowrap`: two cubes where the two far ends are identified periodically.
-
----
+  - `:unitcube`: the unit cube.
+  - `:periodic`: an all-periodic unit cube.
+  - `:rotcubes`: contains a few cubes (these are rotated against each other to
+    stress the topology routines).
+  - `:rotwrap`: a mostly periodic unit cube (see
+    `@doc P4estTypes.P4est.p8est_connectivity_new_rotwrap`).
+  - `:shell`: a spherical shell (see
+    `@doc P4estTypes.P4est.p8est_connectivity_new_shell`).
+  - `:sphere`: a solid sphere (see
+    `@doc P4estTypes.P4est.p8est_connectivity_new_sphere`).
+  - `:twocubes`: two cubes.
+  - `:twowrap`: two cubes where the two far ends are identified periodically.
+
+* * *
+
     Connectivity{8}(:torus, nsegments)
 
 Create a connectivity structure that builds a revolution torus.  Here
@@ -68,7 +71,8 @@ Create a connectivity structure that builds a revolution torus.  Here
 See `@doc P4estTypes.P4est.p8est_connectivity_new_torus` for detailed
 information.
 
----
+* * *
+
     Connectivity{8}(:torus, nsegments)
 
 Create a connectivity structure that builds a revolution torus.  Here
@@ -77,7 +81,8 @@ Create a connectivity structure that builds a revolution torus.  Here
 See `@doc P4estTypes.P4est.p8est_connectivity_new_torus` for detailed
 information.
 
----
+* * *
+
     Connectivity{X}(:twotrees, l_face, r_face, orientation) where {X}
 
 Create a connectivity structure (`X=4` for quadtrees and `X=8` for octrees) for
@@ -86,20 +91,22 @@ two trees being rotated with respect to each other in a user-defined way.  Here
 respectively. The argument `orientation` gives the orientation code of the
 trees with respect to each other.
 
----
+* * *
+
     Connectivity{X}(vertices, elements) where {X}
 
 Creates a connectivity from the given list of vertices and element-to-vertex
 connectivity.  The parameter set to `X=4` is for quads and `X=8` for hexes.
 
-- `vertices`: should be a number-of-vertices by 3 matrix where the columns
-  correspond to x, y, and z coordinates (typically the `z` coordinate will be
-  zero for a 2D forest).
-- `elements`: should be a number-of-vertices by 4 or 8 matrix where the columns
-  vertex indices used to define each element. Note that z-ordering should be
-  used, and it should use zero-indexing.
+  - `vertices`: should be a number-of-vertices by 3 matrix where the columns
+    correspond to x, y, and z coordinates (typically the `z` coordinate will be
+    zero for a 2D forest).
+  - `elements`: should be a number-of-vertices by 4 or 8 matrix where the columns
+    vertex indices used to define each element. Note that z-ordering should be
+    used, and it should use zero-indexing.
+
+* * *
 
----
     Connectivity{X}(filename::String) where {X}
 
 Create a connectivity from an ABAQUS input at `filename`. The parameter set to
@@ -110,9 +117,10 @@ See `@doc P4estTypes.P4est.p4est_connectivity_read_inp` and
 files.
 
 # See also
-- [`brick`](@ref): a function to create a rectangular [`Connectivity`](@ref).
-- [`connectivity`](@ref): a function to get the connectivity of a [`Pxest`](@ref).
-- [`refine`](@ref): a function to create a refined [`Connectivity`](@ref).
+
+  - [`brick`](@ref): a function to create a rectangular [`Connectivity`](@ref).
+  - [`connectivity`](@ref): a function to get the connectivity of a [`Pxest`](@ref).
+  - [`refine`](@ref): a function to create a refined [`Connectivity`](@ref).
 """
 mutable struct Connectivity{X,P}
     """The pointer (of type `P`) can be a pointer to either a

lib/P4estTypes/src/ghost.jl

@@ -6,10 +6,12 @@ for a `Pxest{X}`.  Also stores the corresponding local domain quadrants,
 mirrors, that are in other rank's ghost layers.
 
 # Fields
+
 $(DocStringExtensions.FIELDS)
 
 # See also
-- [`ghostlayer`](@ref): a function used to construct a `GhostLayer`
+
+  - [`ghostlayer`](@ref): a function used to construct a `GhostLayer`
 """
 mutable struct GhostLayer{X,P}
     """The pointer (of type `P`) can be a pointer to either a

lib/P4estTypes/src/lnodes.jl

@@ -4,10 +4,12 @@
 Stores a parallel numbering of Lobatto nodes for a `Pxest{X}`.
 
 # Fields
+
 $(DocStringExtensions.FIELDS)
 
 # See also
-- [`lnodes`](@ref): a function used to construct `LNodes`
+
+  - [`lnodes`](@ref): a function used to construct `LNodes`
 """
 mutable struct LNodes{X,P}
     """The pointer (of type `P`) can be a pointer to either a

lib/P4estTypes/src/pxest.jl

@@ -213,6 +213,7 @@ and `X=8` indicates an octant; quadrant is used both as the general
 term and the term for the 2D object).
 
 # Fields
+
 $(DocStringExtensions.FIELDS)
 """
 struct QuadrantWrapper{X,P}
@@ -308,6 +309,7 @@ end
 Stores the quadrants in a tree of a Pxest{X}.
 
 # Fields
+
 $(DocStringExtensions.FIELDS)
 """
 struct Tree{X,P,Q} <: AbstractArray{QuadrantWrapper,1}
@@ -357,19 +359,21 @@ So, each rank will only have access to the quadrants it owns.) Second, using
 forest via callback functions.
 
 # Fields
+
 $(DocStringExtensions.FIELDS)
 
 # See also
-- [`pxest`](@ref): a function that constructs a `Pxest` from a [`Connectivity`](@ref).
-- [`iterateforest`](@ref): a function to iterate over the volumes, faces, edges, and
-  corners of the forest.
-- [`refine!`](@ref): refine the quadrants of the forest.
-- [`coarsen!`](@ref): coarsen the quadrants of the forest.
-- [`balance!`](@ref): two-to-one balance the quadrants of the forest.
-- [`partition!`](@ref): partition the quadrants of the forest.
-- [`ghostlayer`](@ref): get the ghost layer of quadrants for the forest.
-- [`lnodes`](@ref): get a global node numbering.
-- [`P4estTypes.savevtk`](@ref): save a VTK representation of the forest.
+
+  - [`pxest`](@ref): a function that constructs a `Pxest` from a [`Connectivity`](@ref).
+  - [`iterateforest`](@ref): a function to iterate over the volumes, faces, edges, and
+    corners of the forest.
+  - [`refine!`](@ref): refine the quadrants of the forest.
+  - [`coarsen!`](@ref): coarsen the quadrants of the forest.
+  - [`balance!`](@ref): two-to-one balance the quadrants of the forest.
+  - [`partition!`](@ref): partition the quadrants of the forest.
+  - [`ghostlayer`](@ref): get the ghost layer of quadrants for the forest.
+  - [`lnodes`](@ref): get a global node numbering.
+  - [`P4estTypes.savevtk`](@ref): save a VTK representation of the forest.
 """
 mutable struct Pxest{X,P,C} <: AbstractArray{Tree,1}
     """The pointer (of type `P`) can be a pointer to either a

lib/P4estTypes/test/runtests.jl

@@ -39,7 +39,8 @@ mktempdir() do tmp_dir
     @test success(pipeline(cmd, stderr = stderr, stdout = stdout))
 
     @testset "$f" for f in testfiles
-        cmd = `$(mpiexec()) -n $nprocs $(Base.julia_cmd()) --startup-file=no --project=$tmp_project $(joinpath(test_dir, f))`
+        cmd =
+            `$(mpiexec()) -n $nprocs $(Base.julia_cmd()) --startup-file=no --project=$tmp_project $(joinpath(test_dir, f))`
         @test success(pipeline(cmd, stderr = stderr, stdout = stdout))
     end
 end

src/adaptive.jl

@@ -75,7 +75,7 @@ function replace_PS(::Val{1}, out_quad, in_quads, which_tree, DVM_data::DVM_Data
     )
     index = findfirst(x -> x === Odata, datas)
     deleteat!(datas, index)
-    for i = 1:2^DIM
+    for i = 1:(2^DIM)
         pw_in_quad = PointerWrapper(in_quads[i])
         dp = PointerWrapper(P4est_PS_Data, pw_in_quad.p.user_data[])
         ps_data = PS_copy(Odata)
@@ -96,7 +96,7 @@ function replace_PS(::Val{2^DIM}, out_quad, in_quads, which_tree, DVM_data::DVM_
     pw_in_quad = PointerWrapper(in_quads[1])
     dp = PointerWrapper(P4est_PS_Data, pw_in_quad.p.user_data[])
     Odatas = Vector{PS_Data}(undef, 2^DIM)
-    for i = 1:2^DIM
+    for i = 1:(2^DIM)
         pw_out_quad = PointerWrapper(out_quad[i])
         Odatas[i] = unsafe_pointer_to_objref(
             pointer(PointerWrapper(P4est_PS_Data, pw_out_quad.p.user_data[]).ps_data),
@@ -114,7 +114,7 @@ function replace_PS(::Val{2^DIM}, out_quad, in_quads, which_tree, DVM_data::DVM_
     end
     ps_data.ds .*= 2.0
     index = findfirst(x -> x === Odatas[1], datas)
-    deleteat!(datas, index:index+2^DIM-1)
+    deleteat!(datas, index:(index+2^DIM-1))
     insert!(datas, index, ps_data)
     dp[] = P4est_PS_Data(pointer_from_objref(ps_data))
 end
@@ -159,7 +159,7 @@ end
 function coarsen_flag_PS(ps_datas::Vector{PS_Data}, levels::Vector{Int}, DVM_data::DVM_Data)
     global_data = DVM_data.global_data
     flag = Cint(1)
-    for i = 1:2^DIM
+    for i = 1:(2^DIM)
         if boundary_flag(DVM_data, ps_datas[i])
             return Cint(0)
         end
@@ -181,7 +181,7 @@ function p4est_coarsen_flag(forest::Ptr{p4est_t}, which_tree, quadrants)
         quadrants_wrap = unsafe_wrap(Vector{Ptr{p4est_quadrant_t}}, quadrants, 2^DIM)
         levels = Vector{Int}(undef, 2^DIM)
         ps_datas = Vector{PS_Data}(undef, 2^DIM)
-        for i = 1:2^DIM
+        for i = 1:(2^DIM)
             qp = PointerWrapper(quadrants_wrap[i])
             dp = PointerWrapper(P4est_PS_Data, qp.p.user_data[])
             levels[i] = qp.level[]

src/connectivity.jl

@@ -2,8 +2,8 @@ function Cartesian_connectivity(Nx, Ny, xmin, xmax, ymin, ymax)
     vertices_C = Array{NTuple{2,Float64}}(undef, Nx + 1, Ny + 1)
     dx = (xmax - xmin) / Nx
     dy = (ymax - ymin) / Ny
-    for j = 1:Ny+1
-        for i = 1:Nx+1
+    for j = 1:(Ny+1)
+        for i = 1:(Nx+1)
             vertices_C[i, j] = (xmin + (i - 1) * dx, ymin + (j - 1) * dy)
         end
     end

src/flux_interp_t.jl

@@ -247,7 +247,7 @@ function calc_flux!(::Val{0}, ::Val{2}, face::Face, DVM_data::DVM_Data, faceid::
     rot = get_rot(faceid) # Left: -1, Right: 1
     gas = DVM_data.global_data.gas
     vs_data = ps_data.vs_data
-    for i = 1:2^(DIM-1)
+    for i = 1:(2^(DIM-1))
         nps_data = ps_data.neighbor.data[faceid][i]
         vs_data_n = nps_data.vs_data
         ds = nps_data.ds[dir]

src/ghost.jl

@@ -23,7 +23,7 @@ end
 function get_mirror_data_inner!(ps_data::PS_Data, vs_temp::AV)
     vs_data = ps_data.vs_data
     vs_num = vs_data.vs_num
-    vs_temp[1:NDF*vs_num] .= reshape(vs_data.df, vs_num * NDF)
+    vs_temp[1:(NDF*vs_num)] .= reshape(vs_data.df, vs_num * NDF)
 end
 function get_mirror_data(ps4est, global_data)
     GC.@preserve ps4est global_data begin
@@ -46,10 +46,10 @@ function get_mirror_data(ps4est, global_data)
             ap = Base.unsafe_wrap(Vector{Cdouble}, p, 3 * DIM + 3 + NDF * vs_num)
             offset = 0
             ap[1:(offset+=DIM)] .= ps_data.ds
-            ap[offset+1:(offset+=DIM)] .= ps_data.midpoint
-            ap[offset+1:(offset+=DIM+2)] .= ps_data.w
+            ap[(offset+1):(offset+=DIM)] .= ps_data.midpoint
+            ap[(offset+1):(offset+=DIM+2)] .= ps_data.w
             ap[offset+=1] = ps_data.vs_data.vs_num
-            vs_temp = @view(ap[offset+1:(offset+=NDF*vs_num)])
+            vs_temp = @view(ap[(offset+1):(offset+=NDF*vs_num)])
             get_mirror_data_inner!(ps_data, vs_temp)
             mirror_data_pointers[i] = p
         end
@@ -112,8 +112,8 @@ function get_mirror_structure(ps4est, global_data::Global_Data)
             p = Ptr{Cdouble}(sc_malloc(-1, vs_num * (DIM + 2) * sizeof(Cdouble)))
             ap = Base.unsafe_wrap(Vector{Cdouble}, p, vs_num * (DIM + 2))
             weight_temp = @view(ap[1:vs_num])
-            level_temp = @view(ap[vs_num+1:vs_num*2])
-            midpoint_temp = @view(ap[vs_num*2+1:vs_num*(DIM+2)])
+            level_temp = @view(ap[(vs_num+1):(vs_num*2)])
+            midpoint_temp = @view(ap[(vs_num*2+1):(vs_num*(DIM+2))])
             get_mirror_structure_inner!(ps_data, weight_temp, level_temp, midpoint_temp)
             mirror_structure_pointers[i] = p
         end
@@ -141,7 +141,7 @@ function update_mirror_data!(ps4est, DVM_data::DVM_Data)
                 mirror_data_pointers[i],
                 3 * DIM + 3 + NDF * vs_num,
             )
-            vs_temp = @view(ap[3*DIM+3+1:end])
+            vs_temp = @view(ap[(3*DIM+3+1):end])
             get_mirror_data_inner!(ps_data, vs_temp)
         end
     end