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Bugfixes for gmsh extension
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* handle node tags properly
* add more examples from gmsh docs
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@j-fu
j-fu committed Nov 28, 2023
1 parent 650ffed commit 502b627
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2 changes: 1 addition & 1 deletion Project.toml
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@@ -1,7 +1,7 @@
name = "ExtendableGrids"
uuid = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
authors = ["Juergen Fuhrmann <[email protected]>", "Christian Merdon <[email protected]>", "Johannes Taraz <[email protected]>"]
version = "1.2.0"
version = "1.2.1"

[deps]
AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
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276 changes: 268 additions & 8 deletions examples/gmsh.jl
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Expand Up @@ -4,16 +4,19 @@
using ExtendableGrids
using Gmsh: gmsh

function gmsh2d()
#
# [Example t1](https://gmsh.info/doc/texinfo/gmsh.html#t1) from the GMSH docs
#
function gmsh_t1()
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
gmsh.model.add("t1")

lc = 1e-2
gmsh.model.geo.addPoint(0, 0, 0, lc, 1)
gmsh.model.geo.addPoint(0.1, 0, 0, lc, 2)
gmsh.model.geo.addPoint(0.1, 0.3, 0, lc, 3)

p4 = gmsh.model.geo.addPoint(0, 0.3, 0, lc)

gmsh.model.geo.addLine(1, 2, 1)
Expand All @@ -37,21 +40,278 @@ function gmsh2d()
gmsh.finalize()
grid
end
# ![](gmsh2d.svg)
# ![](gmsh_t1.svg)

#
# [Example t4](https://gmsh.info/doc/texinfo/gmsh.html#t4) from the GMSH docs
#
function gmsh_t4()
gmsh.initialize()

gmsh.model.add("t4")

cm = 1e-02
e1 = 4.5 * cm; e2 = 6 * cm / 2; e3 = 5 * cm / 2
h1 = 5 * cm; h2 = 10 * cm; h3 = 5 * cm; h4 = 2 * cm; h5 = 4.5 * cm
R1 = 1 * cm; R2 = 1.5 * cm; r = 1 * cm
Lc1 = 0.01
Lc2 = 0.003

function hypot(a, b)
return sqrt(a * a + b * b)
end

ccos = (-h5*R1 + e2 * hypot(h5, hypot(e2, R1))) / (h5*h5 + e2*e2)
ssin = sqrt(1 - ccos*ccos)

factory = gmsh.model.geo
factory.addPoint(-e1-e2, 0 , 0, Lc1, 1)
factory.addPoint(-e1-e2, h1 , 0, Lc1, 2)
factory.addPoint(-e3-r , h1 , 0, Lc2, 3)
factory.addPoint(-e3-r , h1+r , 0, Lc2, 4)
factory.addPoint(-e3 , h1+r , 0, Lc2, 5)
factory.addPoint(-e3 , h1+h2, 0, Lc1, 6)
factory.addPoint( e3 , h1+h2, 0, Lc1, 7)
factory.addPoint( e3 , h1+r , 0, Lc2, 8)
factory.addPoint( e3+r , h1+r , 0, Lc2, 9)
factory.addPoint( e3+r , h1 , 0, Lc2, 10)
factory.addPoint( e1+e2, h1 , 0, Lc1, 11)
factory.addPoint( e1+e2, 0 , 0, Lc1, 12)
factory.addPoint( e2 , 0 , 0, Lc1, 13)

factory.addPoint( R1 / ssin, h5+R1*ccos, 0, Lc2, 14)
factory.addPoint( 0 , h5 , 0, Lc2, 15)
factory.addPoint(-R1 / ssin, h5+R1*ccos, 0, Lc2, 16)
factory.addPoint(-e2 , 0.0 , 0, Lc1, 17)

factory.addPoint(-R2 , h1+h3 , 0, Lc2, 18)
factory.addPoint(-R2 , h1+h3+h4, 0, Lc2, 19)
factory.addPoint( 0 , h1+h3+h4, 0, Lc2, 20)
factory.addPoint( R2 , h1+h3+h4, 0, Lc2, 21)
factory.addPoint( R2 , h1+h3 , 0, Lc2, 22)
factory.addPoint( 0 , h1+h3 , 0, Lc2, 23)

factory.addPoint( 0, h1+h3+h4+R2, 0, Lc2, 24)
factory.addPoint( 0, h1+h3-R2, 0, Lc2, 25)

factory.addLine(1 , 17, 1)
factory.addLine(17, 16, 2)

factory.addCircleArc(14,15,16, 3)
factory.addLine(14,13, 4)
factory.addLine(13,12, 5)
factory.addLine(12,11, 6)
factory.addLine(11,10, 7)
factory.addCircleArc(8,9,10, 8)
factory.addLine(8,7, 9)
factory.addLine(7,6, 10)
factory.addLine(6,5, 11)
factory.addCircleArc(3,4,5, 12)
factory.addLine(3,2, 13)
factory.addLine(2,1, 14)
factory.addLine(18,19, 15)
factory.addCircleArc(21,20,24, 16)
factory.addCircleArc(24,20,19, 17)
factory.addCircleArc(18,23,25, 18)
factory.addCircleArc(25,23,22, 19)
factory.addLine(21,22, 20)

factory.addCurveLoop([17,-15,18,19,-20,16], 21)
factory.addPlaneSurface([21], 22)
factory.addCurveLoop([11,-12,13,14,1,2,-3,4,5,6,7,-8,9,10], 23)

factory.addPlaneSurface([23,21], 24)

factory.synchronize()

v = gmsh.view.add("comments")

gmsh.view.addListDataString(v, [10, -10], ["Created with Gmsh"])

gmsh.view.addListDataString(v, [0, 0.11, 0], ["Hole"],
["Align", "Center", "Font", "Helvetica"])

gmsh.view.addListDataString(v, [0, 0.09, 0], ["file://../[email protected]"],
["Align", "Center"])

gmsh.view.addListDataString(v, [-0.01, 0.09, 0],
["file://../[email protected],0,0,1,0,1,0"])

gmsh.view.addListDataString(v, [0, 0.12, 0],
["file://../[email protected]#"],
["Align", "Center"])

gmsh.view.addListDataString(v, [150, -7], ["file://../t4_image.png@20x0"])

gmsh.view.option.setString(v, "DoubleClickedCommand",
"Printf('View[0] has been double-clicked!');")
gmsh.option.setString(
"Geometry.DoubleClickedLineCommand",
"Printf('Curve %g has been double-clicked!', Geometry.DoubleClickedEntityTag);")

gmsh.model.setColor([(2, 22)], 127, 127, 127)
gmsh.model.setColor([(2, 24)], 160, 32, 240)
gmsh.model.setColor([(1, i) for i in 1:14], 255, 0, 0)
gmsh.model.setColor([(1, i) for i in 15:20], 255, 255, 0)

gmsh.model.mesh.generate(2)
grid = ExtendableGrids.simplexgrid_from_gmsh(gmsh.model)
gmsh.finalize()
grid
end

# ![](gmsh_t4.svg)

#
# [Example t5](https://gmsh.info/doc/texinfo/gmsh.html#t5) from the GMSH docs
#
function gmsh_t5()

gmsh.initialize()

gmsh.model.add("t5")

lcar1 = .1
lcar2 = .0005
lcar3 = .055

gmsh.model.geo.addPoint(0.5,0.5,0.5, lcar2, 1)
gmsh.model.geo.addPoint(0.5,0.5,0, lcar1, 2)
gmsh.model.geo.addPoint(0,0.5,0.5, lcar1, 3)
gmsh.model.geo.addPoint(0,0,0.5, lcar1, 4)
gmsh.model.geo.addPoint(0.5,0,0.5, lcar1, 5)
gmsh.model.geo.addPoint(0.5,0,0, lcar1, 6)
gmsh.model.geo.addPoint(0,0.5,0, lcar1, 7)
gmsh.model.geo.addPoint(0,1,0, lcar1, 8)
gmsh.model.geo.addPoint(1,1,0, lcar1, 9)
gmsh.model.geo.addPoint(0,0,1, lcar1, 10)
gmsh.model.geo.addPoint(0,1,1, lcar1, 11)
gmsh.model.geo.addPoint(1,1,1, lcar1, 12)
gmsh.model.geo.addPoint(1,0,1, lcar1, 13)
gmsh.model.geo.addPoint(1,0,0, lcar1, 14)

gmsh.model.geo.addLine(8,9, 1); gmsh.model.geo.addLine(9,12, 2)
gmsh.model.geo.addLine(12,11, 3); gmsh.model.geo.addLine(11,8, 4)
gmsh.model.geo.addLine(9,14, 5); gmsh.model.geo.addLine(14,13, 6)
gmsh.model.geo.addLine(13,12, 7); gmsh.model.geo.addLine(11,10, 8)
gmsh.model.geo.addLine(10,13, 9); gmsh.model.geo.addLine(10,4, 10)
gmsh.model.geo.addLine(4,5, 11); gmsh.model.geo.addLine(5,6, 12)
gmsh.model.geo.addLine(6,2, 13); gmsh.model.geo.addLine(2,1, 14)
gmsh.model.geo.addLine(1,3, 15); gmsh.model.geo.addLine(3,7, 16)
gmsh.model.geo.addLine(7,2, 17); gmsh.model.geo.addLine(3,4, 18)
gmsh.model.geo.addLine(5,1, 19); gmsh.model.geo.addLine(7,8, 20)
gmsh.model.geo.addLine(6,14, 21);

gmsh.model.geo.addCurveLoop([-11,-19,-15,-18], 22)
gmsh.model.geo.addPlaneSurface([22], 23)
gmsh.model.geo.addCurveLoop([16,17,14,15], 24)
gmsh.model.geo.addPlaneSurface([24], 25)
gmsh.model.geo.addCurveLoop([-17,20,1,5,-21,13], 26)
gmsh.model.geo.addPlaneSurface([26], 27)
gmsh.model.geo.addCurveLoop([-4,-1,-2,-3], 28)
gmsh.model.geo.addPlaneSurface([28], 29)
gmsh.model.geo.addCurveLoop([-7,2,-5,-6], 30)
gmsh.model.geo.addPlaneSurface([30], 31)
gmsh.model.geo.addCurveLoop([6,-9,10,11,12,21], 32)
gmsh.model.geo.addPlaneSurface([32], 33)
gmsh.model.geo.addCurveLoop([7,3,8,9], 34)
gmsh.model.geo.addPlaneSurface([34], 35)
gmsh.model.geo.addCurveLoop([-10,18,-16,-20,4,-8], 36)
gmsh.model.geo.addPlaneSurface([36], 37)
gmsh.model.geo.addCurveLoop([-14,-13,-12,19], 38)
gmsh.model.geo.addPlaneSurface([38], 39)

shells = []

sl = gmsh.model.geo.addSurfaceLoop([35,31,29,37,33,23,39,25,27])
push!(shells, sl)

function cheeseHole(x, y, z, r, lc, shells)
p1 = gmsh.model.geo.addPoint(x, y, z, lc)
p2 = gmsh.model.geo.addPoint(x+r,y, z, lc)
p3 = gmsh.model.geo.addPoint(x, y+r,z, lc)
p4 = gmsh.model.geo.addPoint(x, y, z+r, lc)
p5 = gmsh.model.geo.addPoint(x-r,y, z, lc)
p6 = gmsh.model.geo.addPoint(x, y-r,z, lc)
p7 = gmsh.model.geo.addPoint(x, y, z-r, lc)

c1 = gmsh.model.geo.addCircleArc(p2,p1,p7)
c2 = gmsh.model.geo.addCircleArc(p7,p1,p5)
c3 = gmsh.model.geo.addCircleArc(p5,p1,p4)
c4 = gmsh.model.geo.addCircleArc(p4,p1,p2)
c5 = gmsh.model.geo.addCircleArc(p2,p1,p3)
c6 = gmsh.model.geo.addCircleArc(p3,p1,p5)
c7 = gmsh.model.geo.addCircleArc(p5,p1,p6)
c8 = gmsh.model.geo.addCircleArc(p6,p1,p2)
c9 = gmsh.model.geo.addCircleArc(p7,p1,p3)
c10 = gmsh.model.geo.addCircleArc(p3,p1,p4)
c11 = gmsh.model.geo.addCircleArc(p4,p1,p6)
c12 = gmsh.model.geo.addCircleArc(p6,p1,p7)

l1 = gmsh.model.geo.addCurveLoop([c5,c10,c4])
l2 = gmsh.model.geo.addCurveLoop([c9,-c5,c1])
l3 = gmsh.model.geo.addCurveLoop([c12,-c8,-c1])
l4 = gmsh.model.geo.addCurveLoop([c8,-c4,c11])
l5 = gmsh.model.geo.addCurveLoop([-c10,c6,c3])
l6 = gmsh.model.geo.addCurveLoop([-c11,-c3,c7])
l7 = gmsh.model.geo.addCurveLoop([-c2,-c7,-c12])
l8 = gmsh.model.geo.addCurveLoop([-c6,-c9,c2])

s1 = gmsh.model.geo.addSurfaceFilling([l1])
s2 = gmsh.model.geo.addSurfaceFilling([l2])
s3 = gmsh.model.geo.addSurfaceFilling([l3])
s4 = gmsh.model.geo.addSurfaceFilling([l4])
s5 = gmsh.model.geo.addSurfaceFilling([l5])
s6 = gmsh.model.geo.addSurfaceFilling([l6])
s7 = gmsh.model.geo.addSurfaceFilling([l7])
s8 = gmsh.model.geo.addSurfaceFilling([l8])

sl = gmsh.model.geo.addSurfaceLoop([s1, s2, s3, s4, s5, s6, s7, s8])
v = gmsh.model.geo.addVolume([sl])
push!(shells, sl)
return v
end

x = 0
y = 0.75; z = 0; r = 0.09
for t in 1:5
x += 0.166
z += 0.166
v = cheeseHole(x, y, z, r, lcar3, shells)
gmsh.model.geo.addPhysicalGroup(3, [v], t)
end

gmsh.model.geo.addVolume(shells, 186);

gmsh.model.geo.synchronize()

gmsh.model.addPhysicalGroup(3, [186], 10);

gmsh.model.mesh.generate(3)
grid = ExtendableGrids.simplexgrid_from_gmsh(gmsh.model)
gmsh.finalize()
grid
end
# ![](gmsh_t5.svg)


# ## CI callbacks for [ExampleJuggler.jl](https://github.com/j-fu/ExampleJuggler.jl)
# Unit tests
using Test
function runtests()
grid = gmsh2d()
@test num_nodes(grid) > 0 && num_cells(grid) > 0 && num_bfaces(grid) > 0
ok(grid)= num_nodes(grid) > 0 && num_cells(grid) > 0 && num_bfaces(grid) > 0
@test ok(gmsh_t1())
@test ok(gmsh_t4())
@test ok(gmsh_t5())
end

# Plot generation
using GridVisualize
function generateplots(picdir; Plotter = nothing)
if isdefined(Plotter, :Makie)
size = (300, 300)
Plotter.save(joinpath(picdir, "gmsh2d.svg"), gridplot(gmsh2d(); Plotter, size))
size = (500, 500)
Plotter.save(joinpath(picdir, "gmsh_t1.svg"), gridplot(gmsh_t1(); Plotter, size))
Plotter.save(joinpath(picdir, "gmsh_t4.svg"), gridplot(gmsh_t4(); Plotter, size))
Plotter.save(joinpath(picdir, "gmsh_t5.svg"), gridplot(gmsh_t5(); Plotter, size))
end
end
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@j-fu j-fu commented on 502b627 Nov 28, 2023

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Registration pull request created: JuliaRegistries/General/96101

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v1.2.1 -m "<description of version>" 502b627d529bec772472f5ef7ba48dafe5155c08
git push origin v1.2.1

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