Mailman 3 - SfePy - python.org

.mesh file documentation
by Ryan Krauss 23 Jun '08

23 Jun '08

I am trying to create a .mesh file as an input to SfePy, and all the links I can find for it in google are broken, for example: http://www-rocq.inria.fr/gamma/medit Looking at simple.mesh, the format seems fairly straight forward. After a couple of header lines, it seems to contain coordinates of vertices. I assume this are X Y Z, but I don't understand the 4th column which is always 0. Then there are a bunch of lines describing tetrahedrons. I assume these are being described based on numbers assigned to vertices. But again there is an extra final column I don't understand. One tetrahedron row seems to contain 4 vertices and then the number 6. What does the 6 represent? So, I am slightly stuck. Can anyone direct me to documentation on .mesh files? Also, are there free utilities or Python scripts for generating them? I don't want to reinvent the wheel and might go a little crazy trying to visualize too many tetrahedra. I don't want to reinvent the wheel. Ryan

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installation/testing problem
by RyanGT 16 May '08

16 May '08

I have correctly installed and tested SfePy on my desktop. I am having issues on my laptop. Both are running Ubuntu Gutsy. I think I followed the same procedure on both. make finishes on both machines without errors. Here is the output of trying to run "python simple.py input/poisson.py": ryan@ryan-duo-laptop:~/siue/Research/SfePy_build/sfepy- release-00.41.03$ python simple.py input/poisson.py sfe: warning: other missing: ['functions', 'modules', 'epbc_[0-9]+| epbcs', 'lcbc_[0-9]+|lcbcs', 'nbc_[0-9]+|nbcs'] sfe: reading mesh... sfe: ...done in 0.03 s sfe: setting up domain edges... sfe: ...done in 0.02 s sfe: setting up domain faces... sfe: ...done in 0.01 s sfe: creating regions... sfe: leaf Gamma_Right region_4 sfe: leaf Omega region_1000 sfe: leaf Gamma_Left region_03 sfe: ...done in 0.04 s sfe: equation "Temperature": sfe: dw_laplace.i1.Omega( coef.val, s, t ) = 0 Traceback (most recent call last): File "simple.py", line 106, in <module> main() File "simple.py", line 98, in main dpb, vecDP, data = solveDirect( conf, options ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/solvers/generic.py", line 155, in solveDirect pb, state, data = solveStationary( conf, saveNames = saveNames ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/solvers/generic.py", line 55, in solveStationary problem = ProblemDefinition.fromConf( conf ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/fem/problemDef.py", line 67, in fromConf obj.setEquations( conf.equations ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/fem/problemDef.py", line 133, in setEquations equations.parseTerms( self.domain.regions ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/fem/equations.py", line 147, in parseTerms eq.parseTerms( regions, self.caches ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/fem/equations.py", line 230, in parseTerms terms = parseTerms( regions, self.desc, self.itps ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/fem/equations.py", line 26, in parseTerms bnf = createBNF( termDescs, itps ) File "/home/ryan/siue/Research/SfePy_build/sfepy-release-00.41.03/ sfe/fem/parseEq.py", line 79, in createBNF default = [] )( "args" ) + ")" TypeError: 'Optional' object is not callable So, it seems like something is missing, but I don't know what sfe: warning: other missing: ['functions', 'modules', 'epbc_[0-9]+| epbcs', 'lcbc_[0-9]+|lcbcs', 'nbc_[0-9]+|nbcs'] means. Here is the output of "python runTests.py": ryan@ryan-duo-laptop:~/siue/Research/SfePy_build/sfepy- release-00.41.03$ python runTests.py <<< directory: tests, test files: 18 tests/test_input_kostka.py --- test_input: failed! tests/test_input_octahedron.py nodes: 100% | ###################################################| Time: 00:00:00 elements: 100% | ################################################| Time: 00:00:01 --- test_input: failed! tests/test_input_navier_stokes.py --- test_input: failed! tests/test_input_poisson.py --- test_input: failed! tests/test_elasticity_small_strain.py --- test_get_solution: failed! +++ test_linear_terms: ok tests/test_quadratures.py --- test_problemCreation: failed! tests/test_io.py +++ test_recursiveDictHDF5: ok --- test_sparseMatrixHDF5: failed! tests/test_parsing.py --- test_parseEquations: failed! +++ test_parseRegions: ok tests/test_periodic_bc_3d.py +++ test_pbc: ok tests/test_input_pfdpm_permeability.py --- test_input: failed! tests/test_lcbc_2d.py --- test_linearRigidBodyBC: failed! tests/test_periodic_bc_2d.py +++ test_pbc: ok tests/test_input_le.py --- test_input: failed! tests/test_input_time_poisson.py --- test_input: failed! tests/test_base.py +++ test_structAdd: ok +++ test_structIAdd: ok tests/test_lcbc_3d.py --- test_linearRigidBodyBC: failed! tests/test_input_sinbc.py --- test_input: failed! tests/test_meshio.py nodes: 100% | ###################################################| Time: 00:00:00 elements: 100% | ################################################| Time: 00:00:01 +++ test_readMeshes: ok +++ test_compareSameMeshes: ok 18 test file(s) executed in 7.65 s, 14 failure(s) of 23 test(s) What do I need to do to get this fixed? Thanks, Ryan

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ANN: SfePy 00.41.03
by Robert Cimrman 26 Mar '08

26 Mar '08

Greetings, I'm pleased to announce the release 00.41.03 of SfePy (formerly SFE) SfePy is a finite element analysis software in Python, based primarily on Numpy and SciPy. Mailing lists, issue tracking, mercurial repository: http://code.google.com/p/sfepy/ Home page: http://sfepy.kme.zcu.cz Major improvements: - works on 64 bits - support for various mesh formats - Schroedinger equation solver - see http://code.google.com/p/sfepy/wiki/Examples - new solvers: - generic time-dependent problem solver - pysparse, symeig, scipy-based eigenproblem solvers - scipy-based iterative solvers - many new terms For information on this release, see http://sfepy.googlecode.com/svn/web/releases/004103_RELEASE_NOTES.txt Best regards, r.

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sfepy build on 64 bit gutsy using gfortran for numpy scipy.
by osman 17 Mar '08

17 Mar '08

Robert, Please disregard my last email. Now sfepy builds ok on my 64 bit gutsy. I just had to do make clean and remake. stargate:/home/osman/sfepy-bash-> ./runTests.py --filter-more /usr/lib/python2.5/site-packages/scipy/sparse/linalg/dsolve/ linsolve.py:20: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead ' install scikits.umfpack instead', DeprecationWarning ) <<< directory: tests, test files: 17 --- test_recursiveDictHDF5: failed! --- test_sparseMatrixHDF5: failed! +++ test_pbc: ok +++ test_pbc: ok +++ test_linearRigidBodyBC: ok +++ test_linearRigidBodyBC: ok nodes: 100% | ##################################################################################| Time: 00:00:00 elements: 100% | ###############################################################################| Time: 00:00:00 +++ test_input: ok +++ test_parseEquations: ok +++ test_parseRegions: ok +++ test_input: ok +++ test_input: ok +++ test_input: ok +++ test_input: ok nodes: 100% | ##################################################################################| Time: 00:00:00 elements: 100% | ###############################################################################| Time: 00:00:00 +++ test_readMeshes: ok +++ test_compareSameMeshes: ok +++ test_linear_terms: ok +++ test_structAdd: ok +++ test_structIAdd: ok +++ test_input: ok +++ test_problemCreation: ok +++ test_input: ok 17 test file(s) executed in 17.25 s, 2 failure(s) of 21 test(s) stargate:/home/osman/sfepy-bash-> Thanks Robert! -osman

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Getting started with FEM using sfepy
by Sergey Dolgov 08 Mar '08

08 Mar '08

Hi Robert, Ondrej, others. For some time now I've been planing to learn finite element method with the purpose of applying it to electrostatic problems arising in field emission calculations. I'm also fond of free software tools. I've been thinking of using libmesh, which seems to be rather powerful, but currently I would say that it is too hardcore for me, given how weak my knowledge of C++ is; plus I don't yet need advanced capabilities like parallel computation. So while reading about sympy, I've stumbled upon sfepy, and I feel optimistic about it because 1) it looks like a still relatively simple implementation, and 2) it is wrtten mostly in Python (I've got some experience with Python, numpy, scipy, matplotlib). What sfepy is lacking is of course documentation. I've read some introductory texts on FEM, but certainly don't feel knowledgeable enough to figure how to use sfepy right away. I wold say I need to close the gap between pure theory and sfepy implementation. Thus I've got two questions: * Do you think that using sfepy to learn FEM in general is a good idea? (By "using sfepy to learn FEM" I mean 1) learning how to describe the problem so that sfepy can solve it and 2) learning how sfepy actually works so that I can actually make modifications myself) * What book would you recommend as a guide to studying FEM (is there one that sfepy implementation follows more closely than the others)? Sorry if my questions look silly -- they certainly do to me :) Nonetheless, thanks for the great work! -- Sergey

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Google Summer of Code 2008
by Robert Cimrman 27 Feb '08

27 Feb '08

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 13 Feb '08

13 Feb '08

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/) :)

1 0

mesh class, automatic mesh generation, boundary conditions
by Ondrej Certik 12 Feb '08

12 Feb '08

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 06 Feb '08

06 Feb '08

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 06 Feb '08

06 Feb '08

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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