OK, had to pip install petsc and petsc4py to fix that.

Yes, the test works on deformed tetrahedral mesh:
a == L: 0.99999977445 1.00000019589
a == L2: 0.999999999998 1.0

- Tuomas

On 04/14/2015 05:04 PM, Tuomas Karna wrote:

Hmm, just updated all the components, still seeing the same. I'm using the mapdes firedrake branches for petsc and petsc4py. Could be linking to old petsc4py or some other lib...

- Tuomas

On 04/14/2015 02:15 PM, Andrew McRae wrote:

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@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@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@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake

_______________________________________________
firedrake mailing list
firedrake@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake

_______________________________________________
firedrake mailing list
firedrake@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake