[firedrake] Possible bug with perturbed extruded mesh?

[Andrew McRae]

WTF?

Is your PETSc (and everything else) up to date?

I just opened an ipython session and typed
from firedrake import *
mesh = UnitCubeMesh(10, 10, 6)

and all was fine.

On 14 April 2015 at 21:51, Tuomas Karna <tuomas.karna at gmail.com> wrote:

>  Hi Andrew,
>
> I see, that could indeed be the reason.
>
> Tried UnitCubeMesh, results in an error:
>
> File "test_integration.py", line 77, in <module>
>     mesh = UnitCubeMesh(10, 10, 6)
>   File
> "/home/tuomas/.local/lib/python2.7/site-packages/firedrake/utility_meshes.py",
> line 508, in UnitCubeMesh
>     return CubeMesh(nx, ny, nz, 1, reorder=reorder)
>   File
> "/home/tuomas/.local/lib/python2.7/site-packages/firedrake/utility_meshes.py",
> line 488, in CubeMesh
>     return BoxMesh(nx, ny, nz, L, L, L, reorder=reorder)
>   File
> "/home/tuomas/.local/lib/python2.7/site-packages/firedrake/utility_meshes.py",
> line 440, in BoxMesh
>     plex = PETSc.DMPlex().generate(boundary)
>   File "PETSc/DMPlex.pyx", line 438, in petsc4py.PETSc.DMPlex.generate
> (src/petsc4py.PETSc.c:215426)
> petsc4py.PETSc.Error: error code 77
> [0] DMPlexGenerate() line 1080 in
> /home/tuomas/sources/petsc/firedrake/src/dm/impls/plex/plexgenerate.c
> [0] DMPlexGenerate_CTetgen() line 834 in
> /home/tuomas/sources/petsc/firedrake/src/dm/impls/plex/plexgenerate.c
> [0] TetGenTetrahedralize() line 21483 in
> /home/tuomas/sources/petsc/firedrake/arch-linux2-c-debug/externalpackages/ctetgen/ctetgen.c
> [0] TetGenMeshDelaunizeVertices() line 12113 in
> /home/tuomas/sources/petsc/firedrake/arch-linux2-c-debug/externalpackages/ctetgen/ctetgen.c
> [0] TetGenMeshDelaunayIncrFlip() line 12046 in
> /home/tuomas/sources/petsc/firedrake/arch-linux2-c-debug/externalpackages/ctetgen/ctetgen.c
> [0] TetGenMeshInsertVertexBW() line 11321 in
> /home/tuomas/sources/petsc/firedrake/arch-linux2-c-debug/externalpackages/ctetgen/ctetgen.c
> [0] TetGenMeshPreciseLocate() line 5781 in
> /home/tuomas/sources/petsc/firedrake/arch-linux2-c-debug/externalpackages/ctetgen/ctetgen.c
> [0] Petsc has generated inconsistent data
> [0] This is wrong
>
>
> On 04/14/2015 12:08 PM, Andrew McRae wrote:
>
>     Hi Tuomas,
>
>  It's possible that you're hitting a non-affine issue here.  At the
> moment, the Jacobian, dx_i/dX_j, of the coordinate transformation from the
> reference cell to the physical cell, x(X), is treated as being constant
> over the cell.  For non-simplex cells (i.e. quadrilaterals, triangular
> prisms, tetrahedra), this is only an approximation.  The Jacobian matrix is
> used when replacing the measure (dx == |det J|*dX) and in derivatives
> (d/dx_i == sum_j dX_j/dx_i d/dX_j).
>
>  I have some work in progress, hopefully landing in the next few weeks,
> after which the Jacobian will be calculated separately at each quadrature
> point.  This is currently spread across branches in different components of
> Firedrake.  I'll try your code tomorrow to see if the results come out the
> same (or at least much closer!).
>
>  Just checking, I assume that doing the problem on tetrahedra gives
> matching results, even with a deformed mesh?  (If so, this suggests further
> that it's a non-affine approximation issue).  I.e., replace the first four
> lines of code with
>
>  from firedrake import *
>  mesh = UnitCubeMesh(10, 10, 6)  # mesh of tetrahedra, each of the 10*10*6
> cuboids is split into 6 tets
>
>  and send it through the same deformation as before.  Replace 'ds_v + ds_t
> + ds_b' by just ds in the declaration of L2.
>
>  Best,
>  Andrew
>
> On 14 April 2015 at 19:29, Tuomas Karna <tuomas.karna at gmail.com> wrote:
>
>> Hi all,
>>
>> Encountered this issue with extruded mesh where the coordinates have
>> been deformed. The first form a==L just evaluates div(u), the second
>> a==L2 is the same but div(u) integrated in parts. Thus the results
>> should be equivalent, but that's not what I see:
>>
>> a == L: 0.999999886488 1.0000001092
>> a == L2: -0.235329928101 3.47882106918
>>
>> Without the mesh deformation the two forms give the correct solution
>> (1.0). Am I missing something?
>>
>> Cheers,
>>
>> Tuomas
>>
>> ---
>>
>> from firedrake import *
>> mesh2d = UnitSquareMesh(10,10)
>> layers = 6
>> mesh = ExtrudedMesh(mesh2d, layers, -1.0/layers)
>>
>> P1 = FunctionSpace(mesh, 'CG', 1, vfamily='CG', vdegree=1)
>> P2 = FunctionSpace(mesh, 'CG', 2, vfamily='CG', vdegree=1)
>> P1v = VectorFunctionSpace(mesh, 'CG', 1, vfamily='CG', vdegree=1)
>>
>> # deform mesh
>> scalar = Function(P1).interpolate(Expression('1.0+x[0]'))
>> coords = mesh.coordinates
>> coords.dat.data[:,2] *= scalar.dat.data[:]
>>
>> u = Function(P1v)
>> w = Function(P2)
>> u.interpolate(Expression(('x[0]', '0.0', '0.0')))
>>
>> tri = TrialFunction(P2)
>> test = TestFunction(P2)
>> normal = FacetNormal(mesh)
>>
>> a = test*tri*dx
>> L = div(u)*test*dx
>> L2 = -dot(u, grad(test))*dx + dot(u, normal)*test*(ds_v+ds_t+ds_b)
>>
>> solve(a == L, w)
>> print 'a == L:', w.dat.data.min(), w.dat.data.max()
>>
>> solve(a == L2, w)
>> print 'a == L2:', w.dat.data.min(), w.dat.data.max()
>>
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake at imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>
>
>
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