[firedrake] Possible bug with perturbed extruded mesh?

Andrew McRae a.mcrae12 at imperial.ac.uk
Wed Apr 15 16:45:49 BST 2015 

Okay.

In UFL, you'll need the branch fd_bendy
In FFC, you'll need the branch fd_bendy

This will give the *functionality*, but the performance may suck for
complicated expressions.

To recover decent performance:
In FFC, you also need the changes on the coffee-support-rhs branch, so e.g.
merge this branch into the fd_bendy branch (locally)
In COFFEE, use the not_all_left_hand_sides branch

Unless you use CellSize, it's not necessary to switch Firedrake branch to
bendy_changes (though, on master, a couple of the tests will fail, and a
couple of other tests 'unexpectedly' pass).

Oh, and don't forget to clean your form cache - ./scripts/firedrake-clean
from the firedrake directory.

On 15 April 2015 at 16:09, Tuomas Karna <tuomas.karna at gmail.com> wrote:

>  Nice! Yes, I'd like to try that out if possible. The only repositories
> I've pip-installed are petsc and petsc4py, others are cloned.
>
>
> On 04/15/2015 03:56 AM, Andrew McRae wrote:
>
>  Also works with 'bendy' (non-affine support):
>
> atm112 at ubuntu:~$ python tuomas.py
> pyop2:INFO Solving linear variational problem...
> pyop2:INFO Solving linear variational problem...done
> a == L: 0.999999885647 1.00000011385
> pyop2:INFO Solving linear variational problem...
> pyop2:INFO Solving linear variational problem...done
> a == L2: 0.999999999999 1.0
>
>  Do you want more details?  It's a small-to-moderate PITA to enable this
> functionality, depending on exactly which repositories you've checked out
> and which ones you've only pip-installed.
>
> On 15 April 2015 at 02:11, Tuomas Karna <tuomas.karna at gmail.com> wrote:
>
>> 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 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()
>>>>
>>>>
>>>> _______________________________________________
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>>>> firedrake at imperial.ac.uk
>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>>
>>>
>>>
>>>
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>>>
>>>
>>>
>>
>>
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