Mailman 3 February 2008 - SfePy

Google Summer of Code 2008
by Robert Cimrman Feb. 27, 2008

Feb. 27, 2008

Hi, GSoc 2008 is on, see http://code.google.com/soc/2008. Ondra, you have experience with the last GSoC, do you think we could succeed? I could be someone's mentor... I think we could use some support for our development. r.

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eigen.py update
by Robert Cimrman Feb. 13, 2008

Feb. 13, 2008

Hi, eigen.py works again, now with the new mesh io stuff. BTW, the progressbar is great! r. ps: friday is ok to go to the pub (http://www.thepub.cz/) :)

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mesh class, automatic mesh generation, boundary conditions
by Ondrej Certik Feb. 12, 2008

Feb. 12, 2008

Hi, I put my code at: http://code.google.com/p/sfepy/issues/detail?id=17 Let's discuss how to best integrate it in sfepy. The main code is in: geom/meshutils.py which converts to/from a lot of formats. It's quite long though and all in one class. My plan was to create a new class for each output/input format. So let's create some basic mesh classes, for example based on the code in sfe/fem/mesh.py. Then I'll just subclass it, implement some output/input and that's it. Another problem: how can I select some part of the geometry and assign a special boundary condition to it? In sfepy, as I understand it, it's handled by assigning a special number to each element (tetrahedron), but how can I generate such a mesh? It's not a business of sfepy. But generally I need to create a geometry (for example in gmsh), tell gmsh to mark some surface with a number. Then it is passed to tetgen, that is clever enough to assign this number to each element in the output. So all I need is to parse the output of tetgen and print the element numbers to a file for example. Sometimes, I not only need the element IDs, but I also need the set of nodes sitting at a surface. All these features are implemented in the patch attached to the issue 17. In my older FEM code, I simply read this file and assigned a correct BC to the elements in this file. How is this handled by sfepy? I think sfepy can do some things that is in the patch, but probably cannot do all of them. So let's merge it. I am waiting for your suggestions and ideas. ;) Ondrej

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time dependent problems
by Robert Cimrman Feb. 6, 2008

Feb. 6, 2008

Hi, time dependent problems are now supported by simple.py. Check input/time_poisson.py and tests/test_input_time_poisson.py. It is an initial attempt, so expect bugs and no docstrings... r.

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tests for correctness
by Ondrej Certik Feb. 6, 2008

Feb. 6, 2008

Hi, I have a question regarding tests - do some of them actually test for a correctness? It seems to me, that most of them only test, if sfepy runs for the given input and mesh, but we should also test, that the result of the calculation is actually correct. For example when I polish the schrodinger solver, the simple test is to check that all the energies are correct. For example this one: tests/test_quadratures.py Does it test for a correctness? It seems to me, that this code def test_problemCreation( self ): from sfe.solvers.generic import solveStationary problem, vec, data = solveStationary( self.conf ) ok = True return ok Always returns "ok", no matter what was returned in vec and data. Ondrej

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mailing list for issues
by Robert Cimrman Feb. 4, 2008

Feb. 4, 2008

there is now sfepy-...(a)googlegroups.com r.

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amd64 problems, scipy 0.6.0 patch
by Ondrej Certik Feb. 4, 2008

Feb. 4, 2008

Hi, To make sfepy work with the latest released scipy, use this patch: diff --git a/sfe/solvers/ls.py b/sfe/solvers/ls.py --- a/sfe/solvers/ls.py +++ b/sfe/solvers/ls.py @@ -1,7 +1,7 @@ from sfe.base.base import * from sfe.base.base import * from sfe.solvers.solvers import LinearSolver -import scipy.splinalg.dsolve.umfpack as um +import scipy.linsolve.umfpack as um um.configure( assumeSortedIndices = True ) ## However, today I discovered problems when using sfepy on amd64 (Debian): It compiles fine, but: $ ./schroedinger.py input/schroed.py warning: other missing: ['functions', 'modules', 'epbc', 'lcbc'] warning: left over: ['funV', 'options'] mesh.read = 0.04 mesh.split = 0.0 t = 0.0 Traceback (most recent call last): File "./schroedinger.py", line 110, in ? main() File "./schroedinger.py", line 107, in main evp = solveEigenProblem( conf, options ) File "./schroedinger.py", line 24, in solveEigenProblem pb = ProblemDefinition.fromConf( conf ) File "/home/ondra/sfepy/sfe/fem/problemDef.py", line 40, in fromConf domain.setupNeighbourLists() File "/home/ondra/sfepy/sfe/fem/domain.py", line 349, in setupNeighbourLists mu.sortRows( aux, nm.array( sortCols[mode], nm.int32 ) ) File "/home/ondra/sfepy/sfe/fem/extmods/meshutils.py", line 102, in sortRows return _meshutils.sortRows(*args) TypeError: array cannot be safely cast to required type This is imho related to the fact, that the 64bit system uses integers of a different default length. Ondrej

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paraview postprocessing and other stuff
by Ondrej Certik Feb. 4, 2008

Feb. 4, 2008

Hi, I greatly recommend paraview for postprocessing. We should add this to our wiki too. I created a Debian package, accessible in my repository: http://debian.certik.cz/ However, more work is needed, before it can get to the main Debian. I have a question - do you know how to save the pipeline, so that when I fix my program, calculate the result again, I don't have to fiddle with mouse in paraview and simply see the same pipeline as before but with new data? Ideally, do you have some example script how to call paraview from python? Let's add all this information to the wiki. Our first issue: http://code.google.com/p/sfepy/issues/detail?id=1 And to make things moving, I created some more issues. Now I am working on incorporating my mesh conversion utilities + automatic mesh generation using tetgen, will send a patch soon. Ondrej

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