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Applied formatter.
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Johannes Markert committed Apr 8, 2024
1 parent c50b434 commit 5e18656
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4 changes: 2 additions & 2 deletions examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2e
joinpath(@__DIR__, "square_unstructured_2.inp"))

mesh = T8codeMesh(mesh_file, 2;
mapping = mapping_flag, polydeg = 3,
initial_refinement_level = 1)
mapping = mapping_flag, polydeg = 3,
initial_refinement_level = 1)

semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
boundary_conditions = boundary_conditions)
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4 changes: 2 additions & 2 deletions examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2e
joinpath(@__DIR__, "square_unstructured_2.inp"))

mesh = T8codeMesh(mesh_file, 2;
mapping = mapping_flag, polydeg = 3,
initial_refinement_level = 2)
mapping = mapping_flag, polydeg = 3,
initial_refinement_level = 2)

# A semidiscretization collects data structures and functions for the spatial discretization.
semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
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5 changes: 2 additions & 3 deletions src/auxiliary/auxiliary.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -374,11 +374,10 @@ end
abstract type MeshFile{NDIMS} end

struct GmshFile{NDIMS} <: MeshFile{NDIMS}
path :: String
path::String
end

struct AbaqusFile{NDIMS} <: MeshFile{NDIMS}
path :: String
path::String
end

end # @muladd
25 changes: 13 additions & 12 deletions src/meshes/p4est_mesh.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -392,9 +392,9 @@ end
function p4est_mesh_from_hohqmesh_abaqus(meshfile, initial_refinement_level,
n_dimensions, RealT)
connectivity, tree_node_coordinates, nodes, boundary_names = p4est_connectivity_from_hohqmesh_abaqus(meshfile,
initial_refinement_level,
n_dimensions,
RealT)
initial_refinement_level,
n_dimensions,
RealT)

p4est = new_p4est(connectivity, initial_refinement_level)

Expand All @@ -407,12 +407,12 @@ function p4est_mesh_from_standard_abaqus(meshfile, mapping, polydeg,
initial_refinement_level, n_dimensions, RealT,
boundary_symbols)
connectivity, tree_node_coordinates, nodes, boundary_names = p4est_connectivity_from_standard_abaqus(meshfile,
mapping,
polydeg,
initial_refinement_level,
n_dimensions,
RealT,
boundary_symbols)
mapping,
polydeg,
initial_refinement_level,
n_dimensions,
RealT,
boundary_symbols)

p4est = new_p4est(connectivity, initial_refinement_level)

Expand All @@ -424,7 +424,7 @@ end
# the boundary names on each tree are provided by the `meshfile` created by
# [`HOHQMesh.jl`](https://github.com/trixi-framework/HOHQMesh.jl).
function p4est_connectivity_from_hohqmesh_abaqus(meshfile, initial_refinement_level,
n_dimensions, RealT)
n_dimensions, RealT)
# Create the mesh connectivity using `p4est`
connectivity = read_inp_p4est(meshfile, Val(n_dimensions))
connectivity_pw = PointerWrapper(connectivity)
Expand Down Expand Up @@ -480,8 +480,9 @@ end
# the `mapping` passed to this function using polynomial interpolants of degree `polydeg`. All boundary
# names are given the name `:all`.
function p4est_connectivity_from_standard_abaqus(meshfile, mapping, polydeg,
initial_refinement_level, n_dimensions, RealT,
boundary_symbols)
initial_refinement_level, n_dimensions,
RealT,
boundary_symbols)
# Create the mesh connectivity using `p4est`
connectivity = read_inp_p4est(meshfile, Val(n_dimensions))
connectivity_pw = PointerWrapper(connectivity)
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62 changes: 34 additions & 28 deletions src/meshes/t8code_mesh.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ mutable struct T8codeMesh{NDIMS, RealT <: Real, IsParallel, NDIMSP2, NNODES} <:
nmpiinterfaces :: Int
nmpimortars :: Int

function T8codeMesh{NDIMS}(forest :: Ptr{t8_forest}, tree_node_coordinates, nodes,
function T8codeMesh{NDIMS}(forest::Ptr{t8_forest}, tree_node_coordinates, nodes,
boundary_names,
current_filename) where {NDIMS}
is_parallel = mpi_isparallel() ? True() : False()
Expand Down Expand Up @@ -114,7 +114,8 @@ Create a 'T8codeMesh'.
- `mapping`: a function of `NDIMS` variables to describe the mapping that transforms
the imported mesh to the physical domain. Use `nothing` for the identity map.
"""
function T8codeMesh{NDIMS, RealT}(forest :: Ptr{t8_forest}, boundary_names; polydeg = 1, mapping = nothing) where {NDIMS, RealT}
function T8codeMesh{NDIMS, RealT}(forest::Ptr{t8_forest}, boundary_names; polydeg = 1,
mapping = nothing) where {NDIMS, RealT}
# In t8code reference space is [0,1].
basis = LobattoLegendreBasis(RealT, polydeg)
nodes = 0.5 .* (basis.nodes .+ 1.0)
Expand All @@ -135,7 +136,7 @@ function T8codeMesh{NDIMS, RealT}(forest :: Ptr{t8_forest}, boundary_names; poly
# Testing for negative element volumes.
verts = zeros(3, num_corners)
for itree in 1:num_trees
veptr = t8_cmesh_get_tree_vertices(cmesh, itree-1)
veptr = t8_cmesh_get_tree_vertices(cmesh, itree - 1)

# Note, `verts = unsafe_wrap(Array, veptr, (3, 1 << NDIMS))`
# sometimes does not work since `veptr` is not necessarily properly
Expand Down Expand Up @@ -164,7 +165,8 @@ function T8codeMesh{NDIMS, RealT}(forest :: Ptr{t8_forest}, boundary_names; poly
coords_ref[1] = nodes[i]
coords_ref[2] = nodes[j]
coords_ref[3] = 0.0
t8_geometry_evaluate(cmesh, itree-1, coords_ref, 1, @view(tree_node_coordinates[:, i, j, itree]))
t8_geometry_evaluate(cmesh, itree - 1, coords_ref, 1,
@view(tree_node_coordinates[:, i, j, itree]))
end
end

Expand All @@ -174,7 +176,7 @@ function T8codeMesh{NDIMS, RealT}(forest :: Ptr{t8_forest}, boundary_names; poly
# Testing for negative element volumes.
verts = zeros(3, num_corners)
for itree in 1:num_trees
veptr = t8_cmesh_get_tree_vertices(cmesh, itree-1)
veptr = t8_cmesh_get_tree_vertices(cmesh, itree - 1)

# Note, `verts = unsafe_wrap(Array, veptr, (3, 1 << NDIMS))`
# sometimes does not work since `veptr` is not necessarily properly
Expand Down Expand Up @@ -204,7 +206,8 @@ function T8codeMesh{NDIMS, RealT}(forest :: Ptr{t8_forest}, boundary_names; poly
coords_ref[1] = nodes[i]
coords_ref[2] = nodes[j]
coords_ref[3] = nodes[k]
t8_geometry_evaluate(cmesh, itree-1, coords_ref, 1, @view(tree_node_coordinates[:, i, j, k, itree]))
t8_geometry_evaluate(cmesh, itree - 1, coords_ref, 1,
@view(tree_node_coordinates[:, i, j, k, itree]))
end
end
end
Expand Down Expand Up @@ -327,9 +330,11 @@ function T8codeMesh(trees_per_dimension; polydeg = 1,

# Note, `p*est_connectivity_new_brick` converts a domain of `[0,nx] x [0,ny] x ....`.
# Hence, transform mesh coordinates to reference space [-1,1]^NDIMS before applying user defined mapping.
mapping_(xyz...) = mapping((x * 2.0/tpd - 1.0 for (x,tpd) in zip(xyz, trees_per_dimension))...)
mapping_(xyz...) = mapping((x * 2.0 / tpd - 1.0 for (x, tpd) in zip(xyz,
trees_per_dimension))...)

return T8codeMesh{NDIMS, RealT}(forest, boundary_names; polydeg = polydeg, mapping = mapping_)
return T8codeMesh{NDIMS, RealT}(forest, boundary_names; polydeg = polydeg,
mapping = mapping_)
end

"""
Expand Down Expand Up @@ -370,7 +375,8 @@ function T8codeMesh(cmesh::Ptr{t8_cmesh};
# There's no simple and generic way to distinguish boundaries, yet. Name all of them :all.
boundary_names = fill(:all, 2 * NDIMS, t8_cmesh_get_num_trees(cmesh))

return T8codeMesh{NDIMS, RealT}(forest, boundary_names; polydeg = polydeg, mapping = mapping)
return T8codeMesh{NDIMS, RealT}(forest, boundary_names; polydeg = polydeg,
mapping = mapping)
end

"""
Expand Down Expand Up @@ -452,11 +458,11 @@ function T8codeMesh(filepath::String, NDIMS; kwargs...)
file_extension = lowercase(meshfile_suffix)

if file_extension == ".msh"
return T8codeMesh(GmshFile{NDIMS}(filepath); kwargs...)
return T8codeMesh(GmshFile{NDIMS}(filepath); kwargs...)
end

if file_extension == ".inp"
return T8codeMesh(AbaqusFile{NDIMS}(filepath); kwargs...)
return T8codeMesh(AbaqusFile{NDIMS}(filepath); kwargs...)
end

throw("Unknown file extension: " * file_extension)
Expand All @@ -482,7 +488,7 @@ mesh from a Gmsh mesh file (`.msh`).
- `RealT::Type`: The type that should be used for coordinates.
- `initial_refinement_level::Integer`: Refine the mesh uniformly to this level before the simulation starts.
"""
function T8codeMesh(meshfile::GmshFile{NDIMS}; kwargs...) where NDIMS
function T8codeMesh(meshfile::GmshFile{NDIMS}; kwargs...) where {NDIMS}
# Prevent `t8code` from crashing Julia if the file doesn't exist.
@assert isfile(meshfile.path)

Expand Down Expand Up @@ -555,9 +561,9 @@ For example, if a two-dimensional base mesh contains 25 elements then setting
If `nothing` is passed then all boundaries are named `:all`.
"""
function T8codeMesh(meshfile::AbaqusFile{NDIMS};
mapping = nothing, polydeg = 1, RealT = Float64,
initial_refinement_level = 0,
boundary_symbols = nothing) where NDIMS
mapping = nothing, polydeg = 1, RealT = Float64,
initial_refinement_level = 0,
boundary_symbols = nothing) where {NDIMS}
# Prevent `t8code` from crashing Julia if the file doesn't exist.
@assert isfile(meshfile.path)

Expand All @@ -571,30 +577,30 @@ function T8codeMesh(meshfile::AbaqusFile{NDIMS};
if header == " File created by HOHQMesh"
# Mesh curvature and boundary naming is handled with additional information available in meshfile
connectivity, tree_node_coordinates, nodes, boundary_names = p4est_connectivity_from_hohqmesh_abaqus(meshfile.path,
initial_refinement_level,
NDIMS,
RealT)
initial_refinement_level,
NDIMS,
RealT)
# Apply user defined mapping.
map_node_coordinates!(tree_node_coordinates, mapping)
else
# Mesh curvature is handled directly by applying the mapping keyword argument.
connectivity, tree_node_coordinates, nodes, boundary_names = p4est_connectivity_from_standard_abaqus(meshfile.path,
mapping,
polydeg,
initial_refinement_level,
NDIMS,
RealT,
boundary_symbols)
mapping,
polydeg,
initial_refinement_level,
NDIMS,
RealT,
boundary_symbols)
end

if typeof(connectivity) <: Ptr{p4est_connectivity}
cmesh = t8_cmesh_new_from_p4est(connectivity, mpi_comm(), 0)
cmesh = t8_cmesh_new_from_p4est(connectivity, mpi_comm(), 0)
elseif typeof(connectivity) <: Ptr{p8est_connectivity}
cmesh = t8_cmesh_new_from_p8est(connectivity, mpi_comm(), 0)
cmesh = t8_cmesh_new_from_p8est(connectivity, mpi_comm(), 0)
else
throw("`connectivity` is not of type `Ptr{p*est_connectivity}`.")
throw("`connectivity` is not of type `Ptr{p*est_connectivity}`.")
end

do_face_ghost = mpi_isparallel()
scheme = t8_scheme_new_default_cxx()
forest = t8_forest_new_uniform(cmesh, scheme, initial_refinement_level, do_face_ghost,
Expand Down

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