Ok, then does firedrake enable built-in non-uniform extrusion, i.e., of different height and number of layers in different parts of the domain? Alternatively, if I construct such an extruded mesh in gmsh, with extruded quads, would it work in firedrake? Thank you, Tomasz ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Onno Bokhove <O.Bokhove@leeds.ac.uk> Sent: 09 May 2016 17:58:01 To: firedrake Subject: Re: [firedrake] firedrake & gmsh 3d hexahedron mesh Given your set up with gravity, the logical mesh is an extruded one! ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Homolya, Miklós <m.homolya14@imperial.ac.uk> Sent: Monday, May 9, 2016 5:10:45 PM To: firedrake Subject: Re: [firedrake] firedrake & gmsh 3d hexahedron mesh My answer isn't related to your error message, but I'd just like to remind you that Firedrake doesn't support unstructured hexahedral meshes. You can read in an unstructured quadrilateral mesh, and then extrude it, and you can manipulate the coordinates as you wish. But the only hexahedral elements we have are extruded quadrilaterals. ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Tomasz Salwa [RPG] <mmtjs@leeds.ac.uk> Sent: 09 May 2016 17:04:59 To: firedrake Subject: [firedrake] firedrake & gmsh 3d hexahedron mesh Dear all, Can anybody familiar with gmsh tell me why firedrake protests when loading the attached mesh? How can it be corrected? Thank you, Tomasz Error listing: ... File "/home/tommy/work/programs/lin_coupled_3d/lib/coupled_system.py", line 23, in __init__ self.mesh = fd.Mesh("L_domain.msh") File "<decorator-gen-275>", line 2, in Mesh File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/pyop2/profiling.py", line 203, in wrapper return f(*args, **kwargs) File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/firedrake/mesh.py", line 1075, in Mesh plex = _from_gmsh(meshfile) File "/home/tommy/programs/firedrake/local/lib/python2.7/site-packages/firedrake/mesh.py", line 159, in _from_gmsh gmsh_plex = PETSc.DMPlex().createGmsh(gmsh_viewer) File "PETSc/DMPlex.pyx", line 109, in petsc4py.PETSc.DMPlex.createGmsh (src/petsc4py.PETSc.c:222051) petsc4py.PETSc.Error: error code 62 [0] DMPlexCreateGmsh() line 247 in /tmp/pip-5Zhs5M-build/src/dm/impls/plex/plexgmsh.c [0] Invalid argument [0] Could not determine Plex facet for element 913

It's just the symmetry of my problem, but it's not a strong requirement, so I'll use "extruded" tets. Thank you! ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: 10 May 2016 09:40:14 To: firedrake@imperial.ac.uk Subject: Re: [firedrake] firedrake & gmsh 3d hexahedron mesh On 10/05/16 09:29, Tomasz Salwa [RPG] wrote:

Ok, then does firedrake enable built-in non-uniform extrusion, i.e., of different height and number of layers in different parts of the domain?

Currently no.

Alternatively, if I construct such an extruded mesh in gmsh, with extruded quads, would it work in firedrake?

No, gmsh produces unstructured hexahedra in this case and you're back to the previous problem. Is there a strong requirement for you to use hexes? You can certainly ask gmsh to produce an "extruded" tet mesh. Lawrence