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Merge pull request #139 from bcube-project/improve_gen_hexa_mesh
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Improve hexa mesh generation (gmsh)
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@ghislainb
ghislainb committed Sep 20, 2024
2 parents c5d5d29 + 98b05cb commit 1754796
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Showing 3 changed files with 98 additions and 108 deletions.
191 changes: 86 additions & 105 deletions src/mesh/gmsh_utils.jl
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Expand Up @@ -641,148 +641,129 @@ end
gen_hexa_mesh(
output,
type;
recombine = false,
n = [2, 2, 2],
l = [1.0, 1.0, 1.0],
center = [0.0, 0.0, 0.0],
transfinite = false,
nx = 2,
ny = 2,
nz = 2,
lx = 1.0,
ly = 1.0,
lz = 1.0,
xc = -1.0,
yc = -1.0,
zc = -1.0,
order = 1,
kwargs...
bnd_names = ("xmin", "xmax", "ymin", "ymax", "zmin", "zmax"),
n_partitions = 0,
write_geo = false,
transfinite_lines = true,
lc = 1e-1,
kwargs...,
)
Generate a 3D mesh of a hexahedral domain and write the mesh to `output`. Use `type` to specify the element types:
`:tetra` or `:hexa`.
For kwargs, see [`gen_line_mesh`](@ref).
# Implementation
Notations from https://cgns.github.io/CGNS_docs_current/sids/conv.html
We could also use extrusion.
"""
function gen_hexa_mesh(
output,
type;
recombine = false,
n = [2, 2, 2],
l = [1.0, 1.0, 1.0],
center = [0.0, 0.0, 0.0],
nx = 2,
ny = 2,
nz = 2,
lx = 1.0,
ly = 1.0,
lz = 1.0,
xc = -1.0,
yc = -1.0,
zc = -1.0,
order = 1,
bnd_names = ("xmin", "xmax", "ymin", "ymax", "zmin", "zmax"),
n_partitions = 0,
write_geo = false,
transfinite = (type == :hexa),
transfinite_lines = (type == :hexa),
lc = 1e-1,
kwargs...,
)
@assert type ∈ (:tetra, :hexa) "`type` can only be :tetra or :hexa"
@assert !((type == :hexa) && !transfinite_lines) "Cannot mix :hexa option with transfinite_lines=false"

isHexa = type == :hexa

gmsh.initialize()
gmsh.model.add("model") # helps debugging
_apply_gmsh_options(; kwargs...)
lc = 1e-1

# Unpack
nx, ny, nz = n
lx, ly, lz = l
xc, yc, zc = center

# Points
P1 = gmsh.model.geo.addPoint(xc - lx / 2, yc - ly / 2, zc - lz / 2, lc)
P2 = gmsh.model.geo.addPoint(xc + lx / 2, yc - ly / 2, zc - lz / 2, lc)
P3 = gmsh.model.geo.addPoint(xc + lx / 2, yc + ly / 2, zc - lz / 2, lc)
P4 = gmsh.model.geo.addPoint(xc - lx / 2, yc + ly / 2, zc - lz / 2, lc)
P5 = gmsh.model.geo.addPoint(xc - lx / 2, yc - ly / 2, zc + lz / 2, lc)
P6 = gmsh.model.geo.addPoint(xc + lx / 2, yc - ly / 2, zc + lz / 2, lc)
P7 = gmsh.model.geo.addPoint(xc + lx / 2, yc + ly / 2, zc + lz / 2, lc)
P8 = gmsh.model.geo.addPoint(xc - lx / 2, yc + ly / 2, zc + lz / 2, lc)
A = gmsh.model.geo.addPoint(xc - lx / 2, yc - ly / 2, zc - lz / 2, lc)
B = gmsh.model.geo.addPoint(xc + lx / 2, yc - ly / 2, zc - lz / 2, lc)
C = gmsh.model.geo.addPoint(xc + lx / 2, yc + ly / 2, zc - lz / 2, lc)
D = gmsh.model.geo.addPoint(xc - lx / 2, yc + ly / 2, zc - lz / 2, lc)

# Lines
E1 = gmsh.model.geo.addLine(P1, P2)
E2 = gmsh.model.geo.addLine(P2, P3)
E3 = gmsh.model.geo.addLine(P3, P4)
E4 = gmsh.model.geo.addLine(P4, P1)
E5 = gmsh.model.geo.addLine(P1, P5)
E6 = gmsh.model.geo.addLine(P2, P6)
E7 = gmsh.model.geo.addLine(P3, P7)
E8 = gmsh.model.geo.addLine(P4, P8)
E9 = gmsh.model.geo.addLine(P5, P6)
E10 = gmsh.model.geo.addLine(P6, P7)
E11 = gmsh.model.geo.addLine(P7, P8)
E12 = gmsh.model.geo.addLine(P8, P5)

# Contours
F1c = gmsh.model.geo.addCurveLoop([-E4, -E3, -E2, -E1])
F2c = gmsh.model.geo.addCurveLoop([E1, E6, -E9, -E5])
F3c = gmsh.model.geo.addCurveLoop([E2, E7, -E10, -E6])
F4c = gmsh.model.geo.addCurveLoop([E3, E8, -E11, -E7])
F5c = gmsh.model.geo.addCurveLoop([E5, -E12, -E8, E4])
F6c = gmsh.model.geo.addCurveLoop([E9, E10, E11, E12])
AB = gmsh.model.geo.addLine(A, B)
BC = gmsh.model.geo.addLine(B, C)
CD = gmsh.model.geo.addLine(C, D)
DA = gmsh.model.geo.addLine(D, A)

# Surfaces
F1 = gmsh.model.geo.addPlaneSurface([F1c])
F2 = gmsh.model.geo.addPlaneSurface([F2c])
F3 = gmsh.model.geo.addPlaneSurface([F3c])
F4 = gmsh.model.geo.addPlaneSurface([F4c])
F5 = gmsh.model.geo.addPlaneSurface([F5c])
F6 = gmsh.model.geo.addPlaneSurface([F6c])
# Contour
loop = gmsh.model.geo.addCurveLoop([AB, BC, CD, DA])

# Surface loop
surfaceLoop = gmsh.model.geo.addSurfaceLoop([F1, F2, F3, F4, F5, F6])
# Surface
ABCD = gmsh.model.geo.addPlaneSurface([loop])

# Volume
volume = gmsh.model.geo.addVolume([surfaceLoop])
# Extrusion
nlayers = (transfinite || isHexa || transfinite_lines) ? [nz - 1] : []
recombine = (transfinite || isHexa)
out = gmsh.model.geo.extrude([(2, ABCD)], 0, 0, lz, nlayers, [], recombine)

# Identification
zmin = ABCD
zmax = out[1][2]
vol = out[2][2]
ymin = out[3][2]
xmax = out[4][2]
ymax = out[5][2]
xmin = out[6][2]

# Mesh settings
if (type == :hexa)
gmsh.model.geo.mesh.setTransfiniteCurve(E1, nx)
gmsh.model.geo.mesh.setTransfiniteCurve(E2, ny)
gmsh.model.geo.mesh.setTransfiniteCurve(E3, nx)
gmsh.model.geo.mesh.setTransfiniteCurve(E4, ny)
gmsh.model.geo.mesh.setTransfiniteCurve(E5, nz)
gmsh.model.geo.mesh.setTransfiniteCurve(E6, nz)
gmsh.model.geo.mesh.setTransfiniteCurve(E7, nz)
gmsh.model.geo.mesh.setTransfiniteCurve(E8, nz)
gmsh.model.geo.mesh.setTransfiniteCurve(E9, nx)
gmsh.model.geo.mesh.setTransfiniteCurve(E10, ny)
gmsh.model.geo.mesh.setTransfiniteCurve(E11, nx)
gmsh.model.geo.mesh.setTransfiniteCurve(E12, ny)

gmsh.model.geo.mesh.setTransfiniteSurface(F1)
gmsh.model.geo.mesh.setTransfiniteSurface(F2)
gmsh.model.geo.mesh.setTransfiniteSurface(F3)
gmsh.model.geo.mesh.setTransfiniteSurface(F4)
gmsh.model.geo.mesh.setTransfiniteSurface(F5)
gmsh.model.geo.mesh.setTransfiniteSurface(F6)

gmsh.model.geo.mesh.setTransfiniteVolume(volume)
end
if (recombine || type == :hexa)
gmsh.model.geo.mesh.setRecombine(2, F1)
gmsh.model.geo.mesh.setRecombine(2, F2)
gmsh.model.geo.mesh.setRecombine(2, F3)
gmsh.model.geo.mesh.setRecombine(2, F4)
gmsh.model.geo.mesh.setRecombine(2, F5)
gmsh.model.geo.mesh.setRecombine(2, F6)
if transfinite_lines
gmsh.model.geo.mesh.setTransfiniteCurve(AB, nx)
gmsh.model.geo.mesh.setTransfiniteCurve(BC, ny)
gmsh.model.geo.mesh.setTransfiniteCurve(CD, nx)
gmsh.model.geo.mesh.setTransfiniteCurve(DA, ny)
end

(transfinite || isHexa) && gmsh.model.geo.mesh.setTransfiniteSurface(ABCD)

isHexa && gmsh.model.geo.mesh.setRecombine(2, ABCD)

# Synchronize
gmsh.model.geo.synchronize()

# Define boundaries (`2` stands for 2D, i.e faces)
xmin = gmsh.model.addPhysicalGroup(2, [F5])
xmax = gmsh.model.addPhysicalGroup(2, [F3])
ymin = gmsh.model.addPhysicalGroup(2, [F2])
ymax = gmsh.model.addPhysicalGroup(2, [F4])
zmin = gmsh.model.addPhysicalGroup(2, [F1])
zmax = gmsh.model.addPhysicalGroup(2, [F6])

domain = gmsh.model.addPhysicalGroup(3, [surfaceLoop])

gmsh.model.setPhysicalName(2, xmin, "xmin")
gmsh.model.setPhysicalName(2, xmax, "xmax")
gmsh.model.setPhysicalName(2, ymin, "ymin")
gmsh.model.setPhysicalName(2, ymax, "ymax")
gmsh.model.setPhysicalName(2, zmin, "zmin")
gmsh.model.setPhysicalName(2, zmax, "zmax")
gmsh.model.setPhysicalName(3, domain, "Domain")
# Define boundaries (`1` stands for 1D, i.e lines)
gmsh.model.addPhysicalGroup(2, [xmin], -1, bnd_names[1])
gmsh.model.addPhysicalGroup(2, [xmax], -1, bnd_names[2])
gmsh.model.addPhysicalGroup(2, [ymin], -1, bnd_names[3])
gmsh.model.addPhysicalGroup(2, [ymax], -1, bnd_names[4])
gmsh.model.addPhysicalGroup(2, [zmin], -1, bnd_names[5])
gmsh.model.addPhysicalGroup(2, [zmax], -1, bnd_names[6])
gmsh.model.addPhysicalGroup(3, [vol], -1, "Domain")

# Gen mesh
gmsh.model.mesh.generate(3)
gmsh.model.mesh.setOrder(order)
gmsh.model.mesh.partition(n_partitions)

# Write result
rm(output; force = true)
gmsh.write(output)
if write_geo
output_geo = first(splitext(output)) * ".geo_unrolled"
rm(output_geo; force = true)
gmsh.write(output_geo)
end

# End
gmsh.finalize()
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13 changes: 11 additions & 2 deletions test/dof/test_assembler.jl
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Expand Up @@ -362,7 +362,7 @@

function driver_heat_solver()
mesh_path = joinpath(tempdir, "tmp1.msh")
gen_hexa_mesh(mesh_path, :tetra)
gen_hexa_mesh(mesh_path, :tetra; xc = 0.0, yc = 0.0, zc = 0.0)
mesh = read_msh(mesh_path)

λ = 100.0
Expand All @@ -376,7 +376,16 @@
@test err < 1.0e-14

mesh_path = joinpath(tempdir, "tmp2.msh")
gen_hexa_mesh(mesh_path, :hexa; n = [5, 5, 5])
gen_hexa_mesh(
mesh_path,
:hexa;
nx = 5,
ny = 5,
nz = 5,
xc = 0.0,
yc = 0.0,
zc = 0.0,
)
mesh = read_msh(mesh_path)
degree = 2
dirichlet_dict = Dict("xmin" => 260.0)
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2 changes: 1 addition & 1 deletion test/mapping/test_mapping.jl
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Expand Up @@ -472,7 +472,7 @@

# For two Hexa8 side-by-side
path = joinpath(tempdir, "mesh.msh")
gen_hexa_mesh(path, :hexa; n = [3, 2, 2])
gen_hexa_mesh(path, :hexa; nx = 3, ny = 2, nz = 2)
mesh = read_msh(path)
_check_face_parametrization(mesh)
end
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