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mgenet opened this issue Nov 11, 2020 · 2 comments · May be fixed by #423
Closed

physical groups #397

mgenet opened this issue Nov 11, 2020 · 2 comments · May be fixed by #423

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@mgenet
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mgenet commented Nov 11, 2020 •
edited by nschloe
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Hello,

I upgraded pygmsh to 7.1.2, and I am a little confused by the new behavior with physical groups. Basically, adding physical groups using geom.add_physical does nothing, and I am getting all points, edges and cells in the output mesh; it used to work fine. What would be the proper way to handle physical groups now? Thank you so much!

Martin

PS: Here is MWE:

R = 1
L = 3
l = 1
with pygmsh.geo.Geometry() as geom:
    p0 = geom.add_point([0, 0, 0], l)
    p1 = geom.add_point([R, 0, 0], l)
    p2 = geom.add_point([0, R, 0], l)
    p3 = geom.add_point([0, L, 0], l)
    p4 = geom.add_point([L, L, 0], l)
    p5 = geom.add_point([L, 0, 0], l)

    l1 = geom.add_circle_arc(p1, p0, p2)
    l2 = geom.add_line(p2, p3)
    l3 = geom.add_line(p3, p4)
    l4 = geom.add_line(p4, p5)
    l5 = geom.add_line(p5, p1)

    ll = geom.add_curve_loop([l1, l2, l3, l4, l5])

    s = geom.add_plane_surface(ll)
    geom.add_physical(s) # this seems to do nothing

    pygmsh_mesh = geom.generate_mesh()
pygmsh_mesh.points # this contains [0,0,0]

PPS: This worked in 6.1.1:

R = 1
L = 3
l = 1
geom = pygmsh.built_in.Geometry()
p0 = geom.add_point([0, 0, 0], l)
p1 = geom.add_point([R, 0, 0], l)
p2 = geom.add_point([0, R, 0], l)
p3 = geom.add_point([0, L, 0], l)
p4 = geom.add_point([L, L, 0], l)
p5 = geom.add_point([L, 0, 0], l)

l1 = geom.add_circle_arc(p1, p0, p2)
l2 = geom.add_line(p2, p3)
l3 = geom.add_line(p3, p4)
l4 = geom.add_line(p4, p5)
l5 = geom.add_line(p5, p1)

ll = geom.add_line_loop([l1, l2, l3, l4, l5])

s = geom.add_plane_surface(ll)
geom.add_physical(s)

pygmsh_mesh = pygmsh.generate_mesh(geom)
pygmsh_mesh.points
@beckerrh
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beckerrh commented Dec 8, 2020

Hi Martin,
for me, your code is working in the sense that I don't get a single point (using pygmesh 7.1.3 and gmsh 4.7.1 pip-installed).
However, the way to retrieve the information has changed, it is in pygmsh_mesh.cell_sets and stored differently than before.
Best, Roland

@capitalaslash capitalaslash mentioned this issue Feb 17, 2021
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@nschloe
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nschloe commented Feb 18, 2021

From what I can see, everything works as expected. You'll find the data in mesh.cell_sets, but with an empty label (''). I just deprecated no labels for physical sets in #424 to avoid such situations.

@nschloe nschloe closed this as completed Feb 18, 2021
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fix physical tags when generating the mesh capitalaslash/pygmsh
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@nschloe @mgenet @beckerrh