Mailman 3 August 2015 - SfePy

Material Parameters of Individual Nodes
by derj...＠web.de 11 Apr '22

11 Apr '22

Hello! It's a great tool you built there! I'd like to use it for some kind of topology optimisation. Is there an "idiomatic" way to set the material parameters of individual nodes? Thank you very much! JonnyB

3 5

Re: Torque
by Robert Cimrman 09 Mar '18

09 Mar '18

In examples/large_deformation/hyperelastic.py a rotation by displacements is applied. By using a similar function the vectors defining the force couples could be defined for dw_surface_ltr (IMHO). Does it make sense? r. ----- Reply message ----- From: "Andre Smit" <freev...(a)gmail.com> To: <sfepy...(a)googlegroups.com> Subject: Torque Date: Sat, Dec 18, 2010 05:10 What is the best way to apply a torque load to a model? -- 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.

4 7

new interactive example with time stepping
by Robert Cimrman 13 Mar '17

13 Mar '17

Hi, I have just updated the time stepping solvers in sfepy for interactive use, as demonstrated in the new example [1]. For basic use, ignore the probing code - the time stepper can be used as simply as: tss = SimpleTimeSteppingSolver({'t0' : 0.0, 't1' : 100.0, 'n_step' : 11}, problem=problem) tss.init_time() for step, time, state in tss(): pass r. [1] http://sfepy.org/doc-devel/examples/diffusion/time_poisson_interactive.html

2 8

1D line elements in SfePy
by Nimish 22 Jan '16

22 Jan '16

I am currrently looking for FEM packages to help me solve a system of beams and columns, basically a collection of 1D bernoulli/timoshenko line elements. I started reading SfePy docs and i am getting the idea that doing the above is not really possible here, am i right? Are only 2D area elements permitted in SfePy? Or is there any direct support for solving 1D line elements too.. Cheers Nimish

4 9

elastic_FE_simulation.py Broken?
by Fred Hohman 21 Aug '15

21 Aug '15

Hi sfepy-devel, The following simulation https://github.com/materialsinnovation/pymks/blob/master/pymks/datasets/ela… used to work on SfePy version `2014.4` but no longer works on version `2015.2`. Do you have any guidance on what went wrong? Below is a console printout: Traceback (most recent call last): File "/Users/fredhohman/anaconda/lib/python2.7/sitepackages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/Users/fredhohman/anaconda/lib/python2.7/sitepackages/pymks/tests/test.py", line 12, in test_elastic_FE_simulation_3D model.run(X) File "/Users/fredhohman/anaconda/lib/python2.7/site- packages/pymks/datasets/elastic_FE_simulation.py", line 190, in run strain_, displacement_, stress_ = self._solve(x) File "/Users/fredhohman/anaconda/lib/python2.7/site- packages/pymks/datasets/elastic_FE_simulation.py", line 547, in _solve mode='el_avg')) File "/Users/fredhohman/anaconda/sfepy/sfepy/discrete/problem.py", line 1245, in evaluate verbose=verbose, **kwargs) File "/Users/fredhohman/anaconda/sfepy/sfepy/discrete/problem.py", line 1186, in create_evaluable kwargs=kwargs) File "/Users/fredhohman/anaconda/sfepy/sfepy/discrete/evaluate.py", line 211, in create_evaluable user=extra_args, verbose=verbose) File "/Users/fredhohman/anaconda/sfepy/sfepy/discrete/equations.py", line 64, in from_conf materials, integrals, user=user) File "/Users/fredhohman/anaconda/sfepy/sfepy/discrete/equations.py", line 749, in from_desc terms.assign_args(variables, materials, user) File "/Users/fredhohman/anaconda/sfepy/sfepy/terms/terms.py", line 286, in assign_args term.assign_args(variables, materials, user) File "/Users/fredhohman/anaconda/sfepy/sfepy/terms/terms.py", line 497, in assign_args % arg_name) ValueError: material argument m not found! Thanks, Fred

3 3

Richards-Buckingham equation
by Serge-Étienne Parent 20 Aug '15

20 Aug '15

Hi, I'm trying to solve the Richards-Buckingham equation for single-phase water flow in unsaturated porous media. Constitutive relationships and the variational formulation are developed here: https://www.authorea.com/users/23640/articles/61529 I created a problem description file inspired from the examples in the diffusion section of the web site. However, the solution doesn't converge. Maybe the variational form wrong, maybe the equations part of the PDF is wrong, maybe its the options. I don't know. The PDF is hosted on GitHub. https://github.com/sergeetiparent/EnvGeotech/blob/master/Richards-Buckingha… Anyone interested in giving a hand on this case? My ultimate goal is to model solute transport in unsaturated soils. Thanks! Essi

2 3

Evaluating stress for the piezo coupling
by Dennis Perchak 18 Aug '15

18 Aug '15

I have been doing some modeling of a piezoelectric system and it works well. One can apply a field and see the resulting deformation. I also get how one can calculate the Cauchy strain and stress using the post-process hook and the terms 'ev_cauchy_strain.2.Omega(u)' and 'ev_cauchy_stress.2.Omega(solid.D, u)'. But since the constitutive law for the stress is the Cauchy term + the piezo-coupling term, how does one evaluate the stress and output it for given displacements and fields? Dennis

2 8

Test failures and UMFPACK_CONTROL
by David Brough 11 Aug '15

11 Aug '15

Hello, I have anaconda version 2.2.0 installed on Windows 7. After attempting to install SfePy 2015.2 from source code, but I get the following output after running the tests. python run_tests.py <<< directory: tests, test files: 91 tests\test_assembling.py --- test_assemble_matrix: failed! --- test_assemble_matrix_complex: failed! --- test_assemble_vector: failed! --- test_assemble_vector_complex: failed! tests\test_base.py +++ test_resolve_deps: ok +++ test_struct_add: ok +++ test_struct_i_add: ok +++ test_verbose_output: ok tests\test_cmesh.py --- test_cmesh_counts: failed! tests\test_domain.py --- test instance creation failed tests\test_ebcs.py --- test instance creation failed tests\test_eigenvalue_solvers.py --- test instance creation failed tests\test_elasticity_small_strain.py --- test_get_solution: failed! +++ test_linear_terms: ok tests\test_fem.py +++ test_base_functions_delta: ok +++ test_base_functions_values: ok tests\test_functions.py --- test instance creation failed tests\test_high_level.py --- test instance creation failed tests\test_homogenization_perfusion.py --- test_solution: failed! tests\test_hyperelastic_tlul.py --- test_solution: failed! tests\test_input_acoustics.py --- test_input: failed! tests\test_input_acoustics3d.py --- test_input: failed! tests\test_input_active_fibres.py --- test_input: failed! tests\test_input_biot.py --- test_input: failed! tests\test_input_biot_npbc.py --- test_input: failed! tests\test_input_biot_npbc_lagrange.py --- test_input: failed! tests\test_input_cube.py --- test_input: failed! tests\test_input_darcy_flow_multicomp.py --- test_input: failed! tests\test_input_elastic_contact_planes.py --- test_input: failed! tests\test_input_elastic_contact_sphere.py --- test_input: failed! tests\test_input_elastic_shifted_periodic.py --- test_input: failed! tests\test_input_its2D_2.py --- test_input: failed! tests\test_input_laplace_1d.py --- test_input: failed! tests\test_input_laplace_coupling_lcbcs.py --- test_input: failed! tests\test_input_laplace_time_ebcs.py --- test_input: failed! tests\test_input_linear_elastic.py --- test_input: failed! tests\test_input_linear_elastic_damping.py --- test_input: failed! tests\test_input_linear_elastic_iga.py --- test_input: failed! tests\test_input_linear_elastic_mM.py --- test_input: failed! tests\test_input_linear_elastic_probes.py --- test instance creation failed tests\test_input_linear_elastic_tractions.py --- test_input: failed! tests\test_input_linear_elastic_up.py --- test_input: failed! tests\test_input_linear_viscoelastic.py --- test_input: failed! tests\test_input_material_nonlinearity.py --- test_input: failed! tests\test_input_navier_stokes.py --- test_input: failed! tests\test_input_navier_stokes2d.py --- test_input: failed! tests\test_input_navier_stokes2d_iga.py --- test_input: failed! tests\test_input_perfusion_tl.py --- test_input: failed! tests\test_input_piezo_elasticity.py --- test_ebc: failed! --- test_input: failed! tests\test_input_poisson.py --- test_input: failed! tests\test_input_poisson_field_dependent_material.py --- test_input: failed! tests\test_input_poisson_functions.py --- test_input: failed! tests\test_input_poisson_iga.py --- test_input: failed! tests\test_input_poisson_neumann.py --- test_input: failed! tests\test_input_poisson_periodic_boundary_condition.py --- test_input: failed! tests\test_input_prestress_fibres.py --- test_input: failed! tests\test_input_sinbc.py --- test_input: failed! tests\test_input_stabilized_navier_stokes.py --- test_input: failed! tests\test_input_stokes.py --- test_input: failed! tests\test_input_stokes_slip_bc.py --- test_input: failed! tests\test_input_thermo_elasticity.py --- test_input: failed! tests\test_input_thermo_elasticity_ess.py --- test_input: failed! tests\test_input_time_poisson.py --- test_input: failed! tests\test_input_vibro_acoustic3d.py --- test_input: failed! tests\test_io.py +++ test_recursive_dict_hdf5: ok +++ test_sparse_matrix_hdf5: ok tests\test_laplace_unit_disk.py --- test instance creation failed tests\test_laplace_unit_square.py --- test instance creation failed tests\test_lcbc_2d.py --- test_linear_rigid_body_bc: failed! tests\test_lcbc_3d.py --- test_linear_rigid_body_bc: failed! tests\test_lcbcs.py --- test_laplace_shifted_periodic: failed! tests\test_linalg.py +++ test_assemble1d: ok +++ test_geometry: ok +++ test_tensors: ok +++ test_unique_rows: ok tests\test_linear_solvers.py --- test instance creation failed tests\test_linearization.py --- test_linearization: failed! tests\test_matcoefs.py +++ test_conversion_functions: ok +++ test_elastic_constants: ok +++ test_stiffness_tensors: ok tests\test_mesh_expand.py +++ test_mesh_expand: ok tests\test_mesh_generators.py +++ test_gen_block_mesh: ok +++ test_gen_cylinder_mesh: ok +++ test_gen_extended_block_mesh: ok tests\test_mesh_interp.py --- test_field_gradient: failed! --- test_interpolation: failed! --- test_interpolation_two_meshes: failed! --- test_invariance: failed! --- test_invariance_qp: failed! tests\test_mesh_smoothing.py +++ test_mesh_smoothing: ok tests\test_meshio.py +++ test_read_meshes: ok +++ test_compare_same_meshes: ok +++ test_read_dimension: ok +++ test_write_read_meshes: ok tests\test_msm_laplace.py --- test instance creation failed tests\test_msm_symbolic.py --- test instance creation failed tests\test_normals.py +++ test_normals: ok tests\test_parsing.py +++ test_parse_equations: ok +++ test_parse_regions: ok tests\test_periodic_bc_2d.py --- test instance creation failed tests\test_periodic_bc_3d.py --- test instance creation failed tests\test_permutations.py +++ test_rcm: ok tests\test_poly_spaces.py --- test_continuity: failed! --- test_gradients: failed! tests\test_projections.py --- test instance creation failed tests\test_quadratures.py +++ test_quadratures: ok +++ test_weight_consistency: ok tests\test_ref_coors.py --- test instance creation failed tests\test_regions.py +++ test_operators: ok +++ test_selectors: ok tests\test_semismooth_newton.py --- test_semismooth_newton: failed! tests\test_sparse.py +++ test_compose_sparse: ok tests\test_splinebox.py +++ test_spbox: ok tests\test_tensors.py +++ test_stress_transform: ok +++ test_tensors: ok +++ test_transform_data: ok +++ test_transform_data4: ok tests\test_term_call_modes.py --- test_term_call_modes: failed! tests\test_term_consistency.py --- test instance creation failed tests\test_units.py +++ test_consistent_sets: ok +++ test_units: ok tests\test_volume.py --- test instance creation failed 91 test file(s) executed in 17.99 s, 82 failure(s) of 123 test(s) Some of the tests don't appear to be in the test directory. Others are failing because of umfpack. For example python run_tests.py --debug tests/test_ebcs.py <<< directory: tests, test files: 1 <<< tests\test_ebcs.py sfepy: left over: ['verbose', '__builtins__', '__doc__', '__name__', 'TestCommon ', 'data_dir', 'match_y_line', '__package__', '_filename', '__file__', 'op'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\Users\m314915\Docume nts\sfepy-master\sfepy-master\meshes\2d\square_unit_tri.mesh)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Right sfepy: LeftStrip sfepy: Omega sfepy: RightStrip sfepy: Left sfepy: RightFix sfepy: LeftFix sfepy: ...done in 0.01 s sfepy: equation "eq": sfepy: dw_diffusion.2.Omega( m.K, q, p ) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (460L, 460L) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 4938 (2.33e-02% fill) sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 8.615423e+01 (rel: 1.000000e+00) --- test instance creation failed Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 83, in run_test test = conf.funmod.Test.from_conf(conf, options) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\tests\test_ebcs.py" , line 68, in from_conf problem, state = solve_pde(conf, output_dir=options.out_dir) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\applications\ pde_solver_app.py", line 55, in solve_pde return app(nls_status=nls_status) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\applications\ application.py", line 29, in call_basic return self.call(**kwargs) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\applications\ pde_solver_app.py", line 219, in call post_process_hook=self.post_process_hook): File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\solvers\ts_so lvers.py", line 29, in __call__ state = problem.solve(state0=state0, nls_status=nls_status) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\discrete\prob lem.py", line 1020, in solve vec = nls(vec0, status=self.nls_status) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\solvers\nls.p y", line 344, in __call__ eps_a=eps_a, eps_r=eps_r, mtx=mtx_a) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\solvers\ls.py ", line 45, in _standard_call **kwargs) File "C:\Users\m314915\Documents\sfepy-master\sfepy-master\sfepy\solvers\ls.py ", line 149, in __call__ return self.sls.spsolve(mtx, rhs) File "C:\Anaconda\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.py", l ine 127, in spsolve umf = umfpack.UmfpackContext(family[A.dtype.char]) File "C:\Anaconda\lib\site-packages\scikits.umfpack-5.1.0-py2.7-win32.egg\scik its\umfpack\umfpack.py", line 278, in __init__ self.control = nm.zeros( (UMFPACK_CONTROL, ), dtype = nm.double ) NameError: global name 'UMFPACK_CONTROL' is not defined Any suggestions? Thanks, David

2 3

possible bug: initial condition for a vector variable
by Yaouen 11 Aug '15

11 Aug '15

Hi, I have a vector variable u, defined over a region omega, that I'm trying to initialize to the uniform value (1,2): U = Field.from_args('U', sp.float64, 'vector', omega, approx_order=1) u = FieldVariable('u', 'unknown', U, history=1) InitialCondition('ic', omega, {'u.0': 1., 'u.1': 2.}) This, however, initializes u to (0.,2.). Is this intentional? Is there a better way to initialize a vector field? The source of this behavior seems to be at the end of sfepy.discrete.variables.FieldVariable.setup_initial_conditions: ic_vec = nm.zeros((di.n_dof[self.name],), dtype=self.dtype) ic_vec[eq] = vv self.initial_condition = ic_vec This sets every component to zero before applying the initial condition under consideration, therefore erasing any previous initial condition. Replacing the code above with if self.initial_condition==None: self.initial_condition = nm.zeros((di.n_dof[self.name],), dtype=self.dtype) self.initial_condition[eq] = vv seems to solve the problem, i.e. in my example u initializes to (1.,2.). Best, Yaouen

2 3

Installing sfepy in Anaconda for OS X
by Fred Hohman 10 Aug '15

10 Aug '15

Hi all, I'm having some difficulties installing sfepy on a mac with anaconda running OS X Yosemite. I've looked through the installation documentation but can't seem to resolve the errors. Can anyone point me to a relevant guide (if it exists) or have suggestions? I can post screenshots if needed. Thanks, Fred

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SfePy August 2015