Mailman 3 - SfePy - python.org

paraview is in Debian now
by Ondrej Certik 30 Jun '08

30 Jun '08

Hi, paraview has finally made it to Debian: http://packages.debian.org/sid/paraview thanks to Christophe Prud'homme and me. :) One more reason to use Debian, don't you think Robert? Seems like there are not so many scientists using gentoo as there are in Debian. :) Ondrej

2 2

Help with Scipy07 abstract and project planning for the summer
by Ryan Krauss 30 Jun '08

30 Jun '08

So, I have a small university grant to work on a research project this summer focused on impact dynamics. The project has two parts: 1. Designing an impact test device to extract material properties at impact speeds 2. Coming up with a Python based, FEA simulation of the impact test I have learned just enough about SfePy to believe that it is a good fit for my project. But not enough to know all that I am going to have to do to make this project work. And not even really enough to write an intelligent abstract. But the abstract is due next Monday. So, while I am still learning SfePy, I could use some help and direction in writing my abstract and planning my summer project. I am planning on trying to contribute contact modeling capabilities eventually. I believe my project will also need the following, which SfePy may or may not already be capable of: - a nonlinear material model (or at least piece-wise linear) for the stress vs. strain material behavior - modeling two bodies, one with an initial velocity and one that is initially stationary (they could initially start at the instant of contact, so that an algorithm for describing when contact happens could be put off for now) I put together a description of the problem and an high-speed video of an impact test here: http://www.siue.edu/~rkrauss/research_project3.html The entire impact event last 10 or so milliseconds. Can you help me understand what it will take to model this test, what SfePy can already do, and what I will need to contribute to make this project come together? Thanks, Ryan

3 20

release
by Robert Cimrman 30 Jun '08

30 Jun '08

Hi, we should make a release to get some attention, as both EuroScipy08 and SciPy08 conferences are approaching. Also lots of things were updated and improved since the last one (already three months ago). We are still far from 1.0, so it has not to be perfect, but are there any critical issues with the hg version that you feel should be fixed now? cheers, r.

2 9

status of testing with manufactured solutions
by Robert Cimrman 26 Jun '08

26 Jun '08

Hi, for reference, look at tests/test_msm_symbolic.py. Currently, the symbolic derivation of right-hand sides corresponding to manufactured solutions works only for scalar variables - briefly, we can test just Poisson or diffusion problems, where the symbolic description of what each term does is: Laplace term: 'c * div( grad( u ) )' (c is scalar) Diffusion term: 'div( K * grad( u ) )' (K is matrix) I would like to discuss here how to approach the problems involving vector fields, e.g. the linear elasticity. The linear elastic term is defined (LaTeX notation, summation convention - same indices sum together) as d/dx_j D_{ijkl} e_{kl}(u), or div( D e ), where e is the small strain tensor. I am thinking of two ways of describing this in SfePy: 1. matrix notation (this is used for scalar terms) expr = """ e = 1/2 * (grad( vec( u ) ) + grad( vec( u ) ).T) D = map( D_sym ) s = D * e out = div( s ) """ ... ok, but some more complex terms may be difficult to express in this was. Anyway I will try this first. 2. indicial notation """ e[i,j] = 1/2 * (der[j]( u[i] ) + der[i]( u[j] )) map = ? D[i,j,k,l] = map( D_sym ) s[i,j] = D[i,j,k,l] * e[k,l] out[i] = sum( der[j]( s[i,j] )) """ ... better in a sense that one sees immediately how the operations look. But as I would like to avoid writing for i in range( 3 ): for j in range( 3 ): e[i,j] = ... i.e. writing the cycles explicitly, some parsing would have to be included. -> my question (Ondrej) - would it be possible to add to sympy some capabilities of Einstein summation convention? maybe a module that would expand names like e_i_j into proper cycles. r.

2 3

FEA books
by Ryan Krauss 26 Jun '08

26 Jun '08

So here is the list of what I have checked out so far: Segerlind, Larry J., 1937- Applied finite element analysis. Kikuchi, Noboru. Finite element methods in mechanics / Noboru Kikuchi. Norrie, D. H. Introduction to finite element analysis, D. H. Norrie and G. de Vries. Finite element primer / published by the National Agency for Finite Element Methods and Standards. Irons, Bruce. Finite element primer / Bruce Irons and Nigel Shrive. Huebner, Kenneth H., Finite element method for engineers / Kenneth H. Huebner, Earl A. Thornton, Ted G. Byrom. What every engineer should know about finite element analysis / edited by John R. Bauer. White, R. E. (Robert E.) Introduction to the finite element method with applications to nonlinear problems / R.E. White. Becker, Eric B. Finite elements : special problems in solid mechanics / Eric B. Becker, Graham F. Carey, and J. Tinsley Oden. v.1 Becker, A. A. (Adib A.) Introductory guide to finite element analysis / A.A. Becker. Finite element methods : fifty years of the Courant element / edited by M. Krizek, P. Neittaanmaki, R. Stenberg. Bathe, Klaus-Jurgen. Finite element procedures in engineering analysis / Klaus-Jurgen Bathe. Martin, Harold Clifford, 1913- Introduction to finite element analysis: theory and application [by] Harold C. Martin [and] Graham F. Carey. Cheung, Y. K. Practical introduction to finite element analysis / Y. K. Cheung and M. F. Yeo. Norrie, D. H. Finite element method; fundamentals and applications, [by] Douglas H. Norrie [and] Gerard de Vries. If you can recommend the best starting point(s), I am open to suggestions. If you have a favorite (especially for beginners), that isn't on this list, I can almost certainly get it (we are a smallish school, but all university libraries in the state of Illinois cooperate). So, I am open to recommendations. Thanks again, Ryan

2 1

.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

3 29

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

4 16

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.

1 0

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

3 6

Getting started with FEM using sfepy
by Sergey Dolgov 07 Mar '08

07 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

4 5