SfePy May 2010

sfepy@python.org

6 participants
22 discussions

git clone test failure
by osman 02 Jun '10

02 Jun '10

Hi Robert, I just cloned the latest snapshot. I am getting 2 failures. One is in quadrature test : ./runTests.py tests/test_quadratures.py --filter-less<<< directory: tests, test files: 1 tests/test_quadratures.py test instance prepared (2 test(s)) ... geometry: 1_2 ... order: 1 --- test_quadratures: failed! ... geometry: 1_2 ... order 1: True ... order 3: True ... order 5: True ... order 7: True ... order 9: True ... geometry: 2_3 ... order 1: True ... order 2: True ... order 3: True ... geometry: 2_4 ... order 2: True ... order 3: True ... order 5: True ... geometry: 3_4 ... order 1: True ... order 2: True ... order 3: True ... geometry: 3_8 ... order 2: True ... order 3: True ... order 5: True +++ test_weight_consistency: ok !!! 1 test failed 1 test file(s) executed in 0.22 s, 1 failure(s) of 2 test(s) ./runTests.py tests/test_input_linear_elastic_mM.py --filter-less <<< directory: tests, test files: 1 tests/test_input_linear_elastic_mM.py --- test instance creation failed !!! 1 test failed 1 test file(s) executed in 0.00 s, 1 failure(s) of 1 test(s) Now that one is due to my ubuntu karmic not having a good python tables (no hdf5 support). The first one: ./runTests.py tests/test_quadratures.py --filter-less --debug <<< directory: tests, test files: 1 <<< tests/test_quadratures.py sfepy: left over: ['get_poly', 'nm', '__builtins__', '_filename', '__file__', '__package__', '__doc__', 'sm', '__name__', 'ordered_iteritems', 'TestCommon'] >>> test instance prepared (2 test(s)) ... geometry: 1_2 ... order: 1 >>> <type 'exceptions.AttributeError'> Traceback (most recent call last): File "./runTests.py", line 225, in <module> main() File "./runTests.py", line 216, in main run_tests(stats, dirname, [filename]) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/osman/src/sfepy/sfepy/base/testing.py", line 38, in run ret = test_method() File "tests/test_quadratures.py", line 96, in test_quadratures is_simplex=is_simplex) File "tests/test_quadratures.py", line 20, in get_poly xs = sm.symarray(dim, 'x') AttributeError: 'module' object has no attribute 'symarray' Anything I can do for this failure? Regards, Osman

2 7

interesting git links
by Robert Cimrman 02 Jun '10

02 Jun '10

FYI: numpy crowd now discusses switching to git + github (finally!), and during the discussion several interesting links appeared, so let me post them here: how to compare versions of code on github (code review) [1] ipython (and nipy) development workflow [2] r. [1] http://github.com/blog/612-introducing-github-compare-view [2] https://cirl.berkeley.edu/mb312/gitwash/development_workflow.html

2 2

add output format option to script/convert_mesh.py
by Robert Cimrman 31 May '10

31 May '10

Hi all, playing with the latest Logan's patch lead me to creating a new EasyToFix issue [1]. As a matter of fact, the same applies to script/blockgen.py and script/cylindergen.py. r. [1] http://code.google.com/p/sfepy/issues/detail?id=132 -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

2 2

new implementation of conditions
by Robert Cimrman 28 May '10

28 May '10

Hi all, during the process of refactoring sfepy.fem I have "moved" boundary and initial conditions into new (documented) classes in sfepy/fem/conditions.py, see [1], [2]. Let me know about any problems. Next target are the equation mappings. r. [1] http://github.com/rc/sfepy/tree/master [2] http://docs.sfepy.org/doc-devel/src/sfepy/fem/conditions.html

1 1

Comsol mesh read/write support
by Logan Sorenson 27 May '10

27 May '10

Hi all, I added to the existing Comsol meshio faciliites to implement full read/write for SfePy suported types. Hope someone can find it useful. At the very least, it should make comparisons between Comsol and SfePy easier. The code is on the comsol_mesh branch at [1]. Regards, Logan [1] http://github.com/logansorenson/sfepy/tree/comsol_mesh -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

2 8

Postprocessing problems
by Michel Dupront 21 May '10

21 May '10

Hello, I installed mayavi-3.1.0 and sfepy-2010-1. But I have problems with the postprocessing. When the python script viewer.py executes I got the following error message: """ File "/home/ ... /sfepy-release-2010.2/sfepy/postprocess/viewer.py", line558, in call_mlab scene = gui.scene.mayavi_scene AttributeError: 'MlabSceneModel' object has no attribute 'mayavi_scene' """ After that I installed mayavi-3.3.0, but I got the same problem. Finally I installed sfe-2010-2 but unfortunately it did not help. I would really appreciate any help with this matter. Thanks Michel _________________________________________________________________ La boîte mail NOW Génération vous permet de réunir toutes vos boîtes mail dans Hotmail ! http://www.windowslive.fr/hotmail/nowgeneration/ -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

2 7

(no subject)
by Michel Dupront 20 May '10

20 May '10

Hello, I installed mayavi-3.1.0 and sfepy-2010-1. But I have problems with the postprocessing. When the python script viewer.py executes I got the following error message: """ File "/home/ ... /sfepy-release-2010.2/sfepy/postprocess/viewer.py", line558, in call_mlab scene = gui.scene.mayavi_scene AttributeError: 'MlabSceneModel' object has no attribute 'mayavi_scene' """ After that I installed mayavi-3.3.0, but I got the same problem. Finally I installed sfe-2010-2 but unfortunately it did not help. I would really appreciate any help with this matter. Thanks Michel _________________________________________________________________ Installez gratuitement les nouvelles Emoch'ticones ! http://www.ilovemessenger.fr/emoticones/telecharger-emoticones-emochticones… -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

1 0

Examples and tests using SfePy Terms
by Andre Smit 18 May '10

18 May '10

The following list was generated using the attached file (run from the sfepy/scripts folder): It shows examples or tests using the stated Term (if available). It would be nice to have examples for each of the SfePy terms if possible. Perhaps something to move onto the Easy2Fix list (although most Terms are beyond my comprehension :) Term: dq_grad ../tests/test_assembling.py Term: dw_volume_integrate_w Term: dw_laplace ../examples/acoustics/acoustics.py ../examples/diffusion/poisson.py ../examples/diffusion/time_poisson.py ../examples/diffusion/subdomains.py ../examples/diffusion/cube.py ../examples/diffusion/sinbc.py ../examples/diffusion/octahedron.py ../examples/diffusion/poisson_functions.py ../examples/diffusion/poisson_parametric_study.py ../examples/quantum/hydrogen.py ../examples/quantum/dft.py ../tests/test_laplace_unit_disk.py ../tests/test_linear_solvers.py ../tests/test_msm_symbolic.py ../tests/test_laplace_unit_square.py ../tests/test_msm_laplace.py ../tests/test_functions.py Term: dw_lin_prestress Term: dq_def_grad Term: dw_acoustic Term: dw_surface_ltr ../examples/standalone/elastic_materials/compare_elastic_materials.py Term: dw_tl_surface_traction ../examples/large_deformation/perfusion_tl.py Term: dw_biot_th Term: d_surface_integrate ../tests/test_assembling.py Term: dw_volume_integrate Term: dw_surface_mass_scalar ../examples/acoustics/acoustics.py Term: d_sd_div_grad Term: dw_point_lspring ../tests/test_elasticity_small_strain.py Term: dw_st_pspg_p ../examples/navier_stokes/stabilized_navier_stokes.py Term: dw_tl_diffusion ../examples/large_deformation/perfusion_tl.py Term: dw_adj_convect2 Term: dw_st_supg_c ../examples/navier_stokes/stabilized_navier_stokes.py Term: d_sd_convect Term: d_sd_st_grad_div Term: dw_of_ns_surf_min_d_press_diff Term: dw_st_pspg_c ../examples/navier_stokes/stabilized_navier_stokes.py Term: dw_lin_elastic ../examples/biot/biot_npbc.py ../examples/homogenization/linear_elastic_mM.py ../examples/homogenization/linear_homogenization.py ../examples/homogenization/linear_homogenization_up.py ../examples/phononic/coef_conf_elastic.py ../examples/standalone/homogenized_elasticity/rs_correctors.py ../tests/test_elasticity_small_strain.py Term: dw_tl_bulk_pressure ../examples/large_deformation/perfusion_tl.py Term: dw_st_supg_p ../examples/navier_stokes/stabilized_navier_stokes.py Term: d_of_ns_surf_min_d_press Term: dw_biot_eth Term: dw_convect Term: de_biot_stress Term: dw_st_adj_supg_c Term: dq_biot_stress Term: dw_lin_convect ../examples/navier_stokes/stabilized_navier_stokes.py Term: dw_tl_volume ../examples/large_deformation/perfusion_tl.py Term: dw_lin_elastic_th Term: dw_surface_mass_scalar_w Term: dq_lin_convect Term: dw_bc_newton Term: dw_jump ../examples/diffusion/subdomains.py ../tests/test_parsing.py Term: d_sa_acoustic_z2 Term: dw_tl_fib_a ../examples/large_deformation/active_fibres.py Term: d_sa_acoustic_alpha2 Term: di_volume_integrate ../examples/phononic/band_gaps_rigid.py ../examples/phononic/band_gaps.py Term: d_volume ../examples/homogenization/linear_homogenization.py ../examples/homogenization/linear_homogenization_up.py ../examples/phononic/band_gaps_rigid.py ../examples/phononic/band_gaps.py ../examples/standalone/homogenized_elasticity/rs_correctors.py ../tests/test_volume.py ../tests/test_parsing.py Term: dw_adj_div_grad Term: dw_stokes_w Term: dw_tl_he_neohook ../examples/large_deformation/active_fibres.py ../examples/large_deformation/perfusion_tl.py ../examples/large_deformation/hyperelastic.py ../examples/standalone/elastic_materials/compare_elastic_materials.py Term: dw_ul_bulk_penalty Term: de_cauchy_strain ../examples/homogenization/linear_elastic_mM.py ../examples/linear_elasticity/linear_elastic_probes.py ../examples/phononic/band_gaps_rigid.py ../tests/testsBasic.py Term: dw_st_adj2_supg_p Term: dw_mass_scalar_fine_coarse Term: de_average_variable Term: dq_cauchy_stress Term: dw_diffusion_r Term: dw_mass_scalar_w ../examples/diffusion/poisson_functions.py ../examples/quantum/hydrogen.py ../examples/quantum/dft.py Term: d_volume_surface ../tests/test_volume.py Term: d_volume_dot Term: dw_surface_integrate ../examples/acoustics/acoustics.py Term: dw_lin_elastic_eth Term: dw_adj_convect1 Term: dw_electric_source Term: d_acoustic_surface Term: d_of_ns_min_grad2 Term: d_of_ns_min_grad1 Term: dw_surface_integrate_w Term: dq_state_in_volume_qp Term: de_cauchy_stress ../examples/biot/biot_npbc.py ../examples/homogenization/linear_elastic_mM.py ../examples/linear_elasticity/linear_elastic_probes.py Term: dw_ul_he_mooney_rivlin Term: dw_lin_elastic_iso ../examples/biot/biot.py ../examples/linear_elasticity/linear_elastic_dynamic.py ../examples/linear_elasticity/linear_elastic.py ../examples/phononic/band_gaps_rigid.py ../examples/phononic/band_gaps.py ../examples/piezo_elasticity/piezo.py ../examples/standalone/elastic_materials/compare_elastic_materials.py ../tests/test_elasticity_small_strain.py ../tests/test_lcbc_3d.py ../tests/test_lcbc_2d.py Term: d_sa_acoustic_alpha Term: di_surface_moment Term: dw_ul_he_neohook Term: dw_tl_bulk_penalty ../examples/large_deformation/active_fibres.py ../examples/large_deformation/hyperelastic.py ../examples/standalone/elastic_materials/compare_elastic_materials.py Term: di_volume_integrate_mat Term: de_diffusion_velocity ../examples/biot/biot_npbc.py Term: dw_mass Term: dw_mass_vector ../examples/linear_elasticity/linear_elastic_dynamic.py ../examples/phononic/band_gaps_rigid.py ../examples/phononic/band_gaps.py ../examples/piezo_elasticity/piezo.py Term: d_hdpm_surfdvel ../tests/test_laplace_unit_disk.py ../tests/test_laplace_unit_square.py Term: dw_st_adj1_supg_p Term: de_grad ../tests/test_assembling.py Term: dw_st_grad_div ../examples/navier_stokes/stabilized_navier_stokes.py Term: d_sd_test_pq Term: d_sa_acoustic_z Term: dw_biot ../examples/biot/biot.py ../examples/biot/biot_npbc.py Term: dw_permeability_r Term: dq_cauchy_strain Term: dw_piezo_coupling ../examples/piezo_elasticity/piezo.py Term: d_sd_st_supg_c Term: d_surface_dot Term: dq_state_in_surface_qp Term: dw_volume_dot_w Term: dw_volume_dot_w_scalar_eth Term: d_sd_div Term: de_volume_average_mat Term: dw_acoustic_integrate Term: d_sd_st_pspg_p Term: dw_volume_dot_w_scalar_th Term: dw_diffusion ../examples/biot/biot.py ../examples/biot/biot_npbc.py ../examples/diffusion/octahedron.py ../examples/piezo_elasticity/piezo.py ../tests/test_assembling.py ../tests/test_msm_symbolic.py Term: dw_stokes ../examples/homogenization/linear_homogenization_up.py ../examples/navier_stokes/stabilized_navier_stokes.py ../examples/navier_stokes/navier_stokes.py Term: dw_volume_lvf ../examples/diffusion/poisson_parametric_study.py ../tests/test_msm_symbolic.py ../tests/test_msm_laplace.py Term: dw_tl_he_mooney_rivlin ../examples/large_deformation/hyperelastic.py ../examples/standalone/elastic_materials/compare_elastic_materials.py Term: d_surface Term: dw_div_grad ../examples/navier_stokes/stabilized_navier_stokes.py Term: d_acoustic_alpha Term: d_sd_st_pspg_c Term: dw_mass_scalar ../examples/acoustics/acoustics.py ../examples/diffusion/time_poisson.py ../examples/homogenization/linear_homogenization_up.py ../examples/quantum/hydrogen.py ../examples/quantum/dft.py -- Andre -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

3 6

improved term docs
by Robert Cimrman 18 May '10

18 May '10

Hi again, the term docs now include the term call signature, as can be seen e.g. at [1]. It is achieved using 'autodoc-process-docstring' sphinx directive, that allows editing docstrings on-the-fly, see doc/conf.py . r. [1] http://docs.sfepy.org/doc-devel/src/sfepy/terms/termsMass.html -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

2 2

EasyToFix issues
by Robert Cimrman 17 May '10

17 May '10

Hi all, Following the example of sympy and other projects, I have created a new issue label 'EasyToFix', that marks issues suitable for beginners (or go-easy old-time users ;)). There is only one of them at [1] now, but I guess we can come up with more... r. [1] http://code.google.com/p/sfepy/issues/list?q=label:EasyToFix -- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. To post to this group, send email to sfepy...(a)googlegroups.com. To unsubscribe from this group, send email to sfepy-devel...(a)googlegroups.com. For more options, visit this group at http://groups.google.com/group/sfepy-devel?hl=en.

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SfePy May 2010