Mailman 3 October 2016 - 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

Calculate total force from cauchy stress
by Patricia Garcia Cañadilla 17 Jan '19

17 Jan '19

Dear Robert, I have a 2D body of hyperelastic material which contracts and I would like to compute the total force developed by the body from the cauchy stress. I am trying to follow some of your indications I found in this group, but I still couldn't make it works. Could you please help me to fix the problem? I am getting the following error: key = (region.name, integral.order, integration) AttributeError: 'dict' object has no attribute 'name' I am trying to do the following, inside stress_strain post-processing function: def stress_strain(out, problem, state, extend = False ): from sfepy.base.base import Struct from sfepy.mechanics.tensors import StressTransform from sfepy.mechanics.tensors import transform_data from sfepy.discrete.common.mappings import get_normals ev = problem.evaluate field = problem.fields['displacement'] region = problem.domain.regions['Gamma'] integral = problem.integrals['i2'] n = get_normals(field,integral,regions) stress = ev('dw_tl_fib_a.1.Omega(f1.fmax, f1.eps_opt, f1.s, f1.fdir, f1.act, v, u )',mode='qp', term_mode= 'stress'); F = ev('ev_def_grad.1.Omega(u)',mode='el_avg'); transform = StressTransform(F) Cstress = transform.get_cauchy_from_2pk(stress) T = Cstress*n; Force = ev('ev_surface_integrate.2.Gamma(T)') And here it is part of the problem configuration file. fields = { 'displacement': ('real', 'vector', 'Omega', 1), } materials = { 'solid' : (None, 'get_elastic_pars'), 'load' : (None, 'linear_tension'), 'f1' : 'get_pars_fibres1', } variables = { 'u': ('unknown field', 'displacement', 0), 'v': ('test field', 'displacement', 'u'), } regions = { 'Omega' : 'all', 'Fix1' : ('vertices in x < %.10f' % (fix_point + eps2), 'facet'), 'Fix2' : ('vertices in x > %.10f' % (fix_point - eps2), 'facet'), 'Fix' : ('r.Fix1 *v r.Fix2', 'facet'), 'Gamma' : ('vertices of surface','edge'), } ebcs = { 'fixb' : ('Fix', {'u.all' : 0.0}), } integrals = { 'i1' : ('v', 1), 'i2' : ('s', 2), }

4 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

Bending
by Alexander Stuhl 24 Oct '16

24 Oct '16

Hi, I am trying to run a programm concerning bending of a beam by terminal couples in a - more or less - complicated geometry. But SfePy calculated that there is no displacement in the entire volume. Then I reduced - step by step - the complexity of the programm in order to find the error why there is no displacement, but I cannot find it. Finally I made a simple programm concerning bending and compared it to a modified example ( linear_elasticity/linear_elastic_tractions.py ). My programm still not shows a displacement of the volume whereas the modified example does. These programms are identical regarding the code except the orientation of the beam. probe.mesh == block.mesh: Cylinder from x=-5 to x=5. Hexahedra. proby.py is a modified version of linear_elasticity/linear_elastic_tractions.py. torquefg.mesh written in Gmsh: Same cylinder, but from z=-5 to z=5. Tetrahedra I do not know the difference. Could you tell me where the fundamental error is? Best regards Alexander

2 3

output from run_tests.py
by firdaus prabowo 24 Oct '16

24 Oct '16

Hi, I'm using Ubuntu 16.04, and used anaconda python 2.7 environment to run sfepy. Only 2 errors from the testing. 96 test file(s) executed in 194.69 s, 2 failure(s) of 157 test(s) They are: +++ test_input: ok tests/test_input_balloon.py warp violation -9.511205e-01 at (iel: 196, iqp: 0)! warp violation -9.511205e-01 at (iel: 196, iqp: 1)! warp violation -9.511205e-01 at (iel: 196, iqp: 2)! warp violation -9.511205e-01 at (iel: 196, iqp: 3)! and +++ test_input: ok tests/test_input_linear_elastic_mM.py /home/fp/anaconda3/envs/py27/lib/python2.7/site-packages/scikits/umfpack/umfpack.py:718: UmfpackWarning: (almost) singular matrix! (estimated cond. number: 2.59e+12) warnings.warn(msg, UmfpackWarning) Below are the outputs using --raise argument: Error 1: (py27) fp@fp-Aspire-S7-392:~/sfepy$ python run_tests.py --raise tests/test_input_balloon.py <<< directory: tests, test files: 1 <<< tests/test_input_balloon.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', 'absolute_import', '__package__', 'TestInputEvolutionary', 'input_name', '__doc__', '__name__', 'output_name_trunk'] sfepy: left over: ['verbose', 'radius', 'bbox', 'io', 'plot', 'conf_dir', 'eps', '_filename', 'dd'] >>> test instance prepared (1 test(s)) ... solving ../examples/large_deformation/balloon.py... sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/fp/sfepy/meshes/3d/unit_ball.mesh)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Equator sfepy: Ax2 sfepy: Ax1 sfepy: Omega sfepy: Surface sfepy: ...done in 0.02 s sfepy: equation "volume": sfepy: dw_tl_volume.2.Omega(q, u) = dw_volume_dot.2.Omega(q, omega) sfepy: equation "balance": sfepy: dw_tl_he_neohook.2.Omega(solid.mu, v, u) + dw_tl_he_mooney_rivlin.2.Omega(solid.kappa, v, u) + dw_tl_membrane.2.Surface(walls.mu, walls.kappa, walls.h0, v, u) + dw_tl_bulk_pressure.2.Omega(v, u, p) = 0 sfepy: using solvers: ts: ts nls: newton ls: ls sfepy: updating variables... balloon: relative stretch: 1.0 balloon: relative volume: 1.0 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: matrix shape: (2190, 2190) sfepy: assembling matrix graph... sfepy: ...done in 0.01 s sfepy: matrix structural nonzeros: 61342 (1.28e-02% fill) sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.01 s sfepy: ====== time 0.000000e+00 (step 1 of 31) ===== sfepy: initial residual: 0.000000e+00 sfepy: ====== time 2.000000e-01 (step 2 of 31) ===== sfepy: updating variables... balloon: relative stretch: 1.2 balloon: relative volume: 1.728 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 2.989629e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.01 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.07 [s] warp violation -9.511205e-01 at (iel: 196, iqp: 0)! warp violation -9.511205e-01 at (iel: 196, iqp: 1)! warp violation -9.511205e-01 at (iel: 196, iqp: 2)! warp violation -9.511205e-01 at (iel: 196, iqp: 3)! sfepy: rezidual computation failed for iter 1 (new ls: 1.000000e-01)! sfepy: linesearch: iter 1, (7.12969e+02 < 2.98963e+02) (new ls: 5.000000e-02) sfepy: nls: iter: 1, residual: 1.773095e+02 (rel: 5.930820e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: linesearch: iter 2, (2.03446e+04 < 1.77310e+04) (new ls: 5.000000e-01) sfepy: nls: iter: 2, residual: 6.334498e+03 (rel: 2.118824e+03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.17 [s] sfepy: nls: iter: 3, residual: 1.467307e+03 (rel: 4.907989e+02) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 3.555474e+01 (rel: 1.189269e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 5, residual: 2.158173e-02 (rel: 7.218865e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 6, residual: 1.125505e-08 (rel: 3.764698e-09) sfepy: ====== time 4.000000e-01 (step 3 of 31) ===== sfepy: updating variables... balloon: relative stretch: 1.4 balloon: relative volume: 2.744 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 4.172339e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: linesearch: iter 1, (3.11750e+03 < 4.17234e+02) (new ls: 5.000000e-01) sfepy: linesearch: iter 1, (8.35338e+02 < 4.17234e+02) (new ls: 2.500000e-01) sfepy: nls: iter: 1, residual: 2.183632e+02 (rel: 5.233593e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.03 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 9.423703e+02 (rel: 2.258614e+02) sfepy: rezidual: 0.04 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 2.586064e+01 (rel: 6.198114e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 7.741878e-03 (rel: 1.855525e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 5, residual: 7.424806e-09 (rel: 1.779531e-09) sfepy: ====== time 6.000000e-01 (step 4 of 31) ===== sfepy: updating variables... balloon: relative stretch: 1.6 balloon: relative volume: 4.096 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 5.552168e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: linesearch: iter 1, (8.33815e+02 < 5.55217e+02) (new ls: 5.000000e-01) sfepy: nls: iter: 1, residual: 2.294984e+02 (rel: 4.133492e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 3.585060e+01 (rel: 6.457045e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 3.277026e-01 (rel: 5.902246e-02) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 7.096759e-06 (rel: 1.278196e-06) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 5, residual: 3.994326e-11 (rel: 7.194173e-12) sfepy: ====== time 8.000000e-01 (step 5 of 31) ===== sfepy: updating variables... balloon: relative stretch: 1.8 balloon: relative volume: 5.832 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 7.129115e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 1.627275e+02 (rel: 2.282576e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 2, residual: 4.183702e+00 (rel: 5.868473e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 1.694376e-03 (rel: 2.376699e-04) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 4, residual: 1.514653e-10 (rel: 2.124602e-11) sfepy: ====== time 1.000000e+00 (step 6 of 31) ===== sfepy: updating variables... balloon: relative stretch: 2.0 balloon: relative volume: 8.0 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 8.903180e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 5.785172e+01 (rel: 6.497871e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 2.365731e+00 (rel: 2.657175e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 7.589606e-04 (rel: 8.524601e-05) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 7.011304e-11 (rel: 7.875055e-12) sfepy: ====== time 1.200000e+00 (step 7 of 31) ===== sfepy: updating variables... balloon: relative stretch: 2.2 balloon: relative volume: 10.648 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.087436e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 1.322945e+02 (rel: 1.216572e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 3.543571e+00 (rel: 3.258647e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 7.185355e-04 (rel: 6.607609e-05) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 9.419265e-11 (rel: 8.661899e-12) sfepy: ====== time 1.400000e+00 (step 8 of 31) ===== sfepy: updating variables... balloon: relative stretch: 2.4 balloon: relative volume: 13.824 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.304267e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 1.545690e+02 (rel: 1.185103e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 3.352185e+00 (rel: 2.570169e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 4.660778e-04 (rel: 3.573485e-05) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 4, residual: 1.106934e-10 (rel: 8.487019e-12) sfepy: ====== time 1.600000e+00 (step 9 of 31) ===== sfepy: updating variables... balloon: relative stretch: 2.6 balloon: relative volume: 17.576 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.540809e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 1.570483e+02 (rel: 1.019259e+01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 2.864981e+00 (rel: 1.859401e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 3, residual: 2.835654e-04 (rel: 1.840367e-05) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 1.334972e-10 (rel: 8.664102e-12) sfepy: ====== time 1.800000e+00 (step 10 of 31) ===== sfepy: updating variables... balloon: relative stretch: 2.8 balloon: relative volume: 21.952 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.797063e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 1.519640e+02 (rel: 8.456242e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.03 [s] sfepy: matrix: 0.18 [s] sfepy: nls: iter: 2, residual: 2.376629e+00 (rel: 1.322508e-01) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 3, residual: 1.722282e-04 (rel: 9.583872e-06) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 4, residual: 1.470133e-10 (rel: 8.180757e-12) sfepy: ====== time 2.000000e+00 (step 11 of 31) ===== sfepy: updating variables... balloon: relative stretch: 3.0 balloon: relative volume: 27.0 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 2.073028e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 1.442183e+02 (rel: 6.956890e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 1.958952e+00 (rel: 9.449710e-02) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 1.063718e-04 (rel: 5.131226e-06) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 1.753168e-10 (rel: 8.457038e-12) sfepy: ====== time 2.200000e+00 (step 12 of 31) ===== sfepy: updating variables... balloon: relative stretch: 3.2 balloon: relative volume: 32.768 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 2.368706e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 1, residual: 1.358415e+02 (rel: 5.734841e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 1.618941e+00 (rel: 6.834708e-02) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 6.718124e-05 (rel: 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2.261755e-07) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 4, residual: 4.482640e-10 (rel: 1.082039e-11) sfepy: ====== time 3.400000e+00 (step 18 of 31) ===== sfepy: updating variables... balloon: relative stretch: 4.4 balloon: relative volume: 85.184 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 4.556720e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 9.563824e+01 (rel: 2.098840e+00) sfepy: rezidual: 0.03 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 6.005207e-01 (rel: 1.317879e-02) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 6.680887e-06 (rel: 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8.225571e-09) sfepy: ====== time 5.200000e+00 (step 27 of 31) ===== sfepy: updating variables... balloon: relative stretch: 6.2 balloon: relative volume: 238.328 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 9.169290e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 6.469245e+01 (rel: 7.055339e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 2, residual: 2.038528e-01 (rel: 2.223212e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 3, residual: 5.568906e-07 (rel: 6.073432e-09) sfepy: ====== time 5.400000e+00 (step 28 of 31) ===== sfepy: updating variables... balloon: relative stretch: 6.4 balloon: relative volume: 262.144 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 9.780357e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 6.243193e+01 (rel: 6.383400e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 1.845488e-01 (rel: 1.886933e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 4.428973e-07 (rel: 4.528437e-09) sfepy: ====== time 5.600000e+00 (step 29 of 31) ===== sfepy: updating variables... balloon: relative stretch: 6.6 balloon: relative volume: 287.496 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.041114e+02 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 6.032425e+01 (rel: 5.794204e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 1.676032e-01 (rel: 1.609845e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 3.548631e-07 (rel: 3.408495e-09) sfepy: ====== time 5.800000e+00 (step 30 of 31) ===== sfepy: updating variables... balloon: relative stretch: 6.8 balloon: relative volume: 314.432 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.106163e+02 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 5.835486e+01 (rel: 5.275432e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 1.526674e-01 (rel: 1.380153e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.16 [s] sfepy: nls: iter: 3, residual: 2.862193e-07 (rel: 2.587497e-09) sfepy: ====== time 6.000000e+00 (step 31 of 31) ===== sfepy: updating variables... balloon: relative stretch: 7.0 balloon: relative volume: 343.0 sfepy: data of omega set by get_volume() sfepy: ...done sfepy: lcbc: pressure sfepy: dofs: total 2190, free 1080, constrained 1110, new 1 sfepy: -> active 1081 sfepy: updating materials... sfepy: solid sfepy: walls sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.173183e+02 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 1, residual: 5.651099e+01 (rel: 4.816895e-01) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 2, residual: 1.394528e-01 (rel: 1.188671e-03) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.02 [s] sfepy: matrix: 0.15 [s] sfepy: nls: iter: 3, residual: 2.323764e-07 (rel: 1.980734e-09) ... ../examples/large_deformation/balloon.py solved +++ test_input: ok >>> all passed in 24.77 s 1 test file(s) executed in 24.77 s, 0 failure(s) of 1 test(s) Error #2: (py27) fp@fp-Aspire-S7-392:~/sfepy$ python run_tests.py --raise tests/test_input_linear_elastic_mM.py <<< directory: tests, test files: 1 <<< tests/test_input_linear_elastic_mM.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', 'absolute_import', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['get_homog_coefs_linear', 'get_elements', '__builtins__', 'get_homog', 'absolute_import', '__file__', '__doc__', '__name__', 'verbose', 'data_dir', 'nm', 'recover_micro_hook', 'regenerate', '__package__', 'save_recovery_region', '_filename', 'post_process', 'os', 'micro_filename'] >>> test instance prepared (1 test(s)) ... solving ../examples/homogenization/linear_elastic_mM.py... macro: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/fp/sfepy/meshes/3d/cylinder.mesh)... macro: ...done in 0.00 s macro: creating regions... macro: Right macro: Omega macro: Recovery macro: Left macro: ...done in 0.01 s macro: equation "balance_of_forces": macro: dw_lin_elastic.i.Omega( solid.D, v, u ) = 0 macro: using solvers: ts: no ts nls: newton ls: ls macro: updating variables... macro: ...done macro: setting up dof connectivities... macro: ...done in 0.00 s macro: matrix shape: (900, 900) macro: assembling matrix graph... macro: ...done in 0.01 s macro: matrix structural nonzeros: 31842 (3.93e-02% fill) macro: updating materials... macro: solid micro: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/fp/sfepy/meshes/3d/matrix_fiber.mesh)... micro: ...done in 0.01 s micro: creating regions... micro: Right micro: Ym micro: Bottom micro: Far micro: Corners micro: Yc micro: Near micro: Y micro: Top micro: Left micro: ...done in 0.04 s micro: using solvers: ts: no ts nls: newton ls: ls micro: volume: total = 1.00 he: computing dependency pis... he: ...done he: computing dependency corrs_rs... he: equation "pressure constraint": he: - dw_stokes.i.Y( u, q ) - dw_volume_dot.i.Y( mat.gamma, q, p ) = + dw_stokes.i.Y( Pi, q ) he: equation "balance_of_forces": he: dw_lin_elastic.i.Y( mat.D, v, u ) - dw_stokes.i.Y( v, p ) = - dw_lin_elastic.i.Y( mat.D, v, Pi ) he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: matrix shape: (7805, 7805) he: assembling matrix graph... he: ...done in 0.09 s he: matrix structural nonzeros: 568979 (9.34e-03% fill) he: updating materials... he: mat he: ...done in 0.01 s he: using solvers: ts: no ts nls: newton ls: ls he: linear problem, trying to presolve... he: presolve: 0.84 [s] he: ...done in 0.94 s he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 2.390871e+09 (rel: 1.000000e+00) /home/fp/anaconda3/envs/py27/lib/python2.7/site-packages/scikits/umfpack/umfpack.py:718: UmfpackWarning: (almost) singular matrix! (estimated cond. number: 2.59e+12) warnings.warn(msg, UmfpackWarning) he: rezidual: 0.04 [s] he: solve: 0.03 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 5.206027e-06 (rel: 2.177461e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 2.536225e+09 (rel: 1.000000e+00) he: rezidual: 0.04 [s] he: solve: 0.10 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 3.921233e-06 (rel: 1.546091e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 2.535578e+09 (rel: 1.000000e+00) he: rezidual: 0.06 [s] he: solve: 0.10 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 3.905675e-06 (rel: 1.540349e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 2.536225e+09 (rel: 1.000000e+00) he: rezidual: 0.04 [s] he: solve: 0.10 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 3.584296e-06 (rel: 1.413241e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 3.780588e+09 (rel: 1.000000e+00) he: rezidual: 0.05 [s] he: solve: 0.03 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 1.796415e-05 (rel: 4.751682e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 3.586306e+09 (rel: 1.000000e+00) he: rezidual: 0.04 [s] he: solve: 0.04 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 1.585156e-05 (rel: 4.420023e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 2.535578e+09 (rel: 1.000000e+00) he: rezidual: 0.05 [s] he: solve: 0.10 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 3.777675e-06 (rel: 1.489867e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 3.586306e+09 (rel: 1.000000e+00) he: rezidual: 0.04 [s] he: solve: 0.03 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 1.571617e-05 (rel: 4.382273e-15) he: updating materials... he: mat he: ...done in 0.00 s he: nls: iter: 0, residual: 3.780010e+09 (rel: 1.000000e+00) he: rezidual: 0.05 [s] he: solve: 0.04 [s] he: matrix: 0.00 [s] he: nls: iter: 1, residual: 2.143972e-05 (rel: 5.671868e-15) he: ...done he: computing elastic_u... he: equation "tmp": he: dw_lin_elastic.i.Y( mat.D, Pi1u, Pi2u ) he: updating materials... he: mat he: ...done in 0.02 s he: ...done he: computing elastic_p... he: equation "tmp": he: dw_volume_dot.i.Y( mat.gamma, Pi1p, Pi2p ) he: updating materials... he: mat he: ...done in 0.01 s he: ...done he: computing D... he: ...done macro: ...done in 0.18 s macro: nls: iter: 0, residual: 2.204111e+07 (rel: 1.000000e+00) macro: rezidual: 0.00 [s] macro: solve: 0.02 [s] macro: matrix: 0.01 [s] macro: nls: iter: 1, residual: 2.109222e-08 (rel: 9.569489e-16) macro: equation "tmp": macro: ev_cauchy_stress.i.Omega( solid.D, u ) macro: updating materials... macro: solid macro: ...done in 0.02 s macro: equation "tmp": macro: ev_cauchy_strain.i.Omega( u ) macro: updating materials... macro: ...done in 0.00 s macro: equation "tmp": macro: ev_cauchy_strain.i.Recovery( u ) macro: updating materials... macro: ...done in 0.00 s macro: left over: ['compute_micro_u', 'recovery_le', 'Struct', 'cb', 'absolute_import', 'compute_stress_strain_u', 'verbose', 'compute_mac_stress_part', 'requirements', 'nm', '_filename', 'data_dir', 'per', '__package__', 'add_stress_p', 'get_box_volume', 'set_elastic_u', 'expr_coefs', '__doc__', 'all_periodic', 'stiffness_from_youngpoisson_mixed', 'dim', '__builtins__', '__file__', 'equation_corrs', '__name__', 'region_lbn', 'ii', 'region_rtf', 'bulk_from_youngpoisson', 'define_box_regions', 'coefs'] macro: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/fp/sfepy/meshes/3d/matrix_fiber.mesh)... macro: ...done in 0.03 s macro: creating regions... macro: Right macro: Ym macro: Bottom macro: Far macro: Corners macro: Yc macro: Near macro: Y macro: Top macro: Left macro: ...done in 0.08 s ii: 0, iel: 50 ii: 1, iel: 150 ii: 2, iel: 250 ii: 3, iel: 350 ii: 4, iel: 450 ii: 5, iel: 550 ii: 6, iel: 650 ii: 7, iel: 750 ii: 8, iel: 850 ii: 9, iel: 950 ii: 10, iel: 1050 ii: 11, iel: 1150 ii: 12, iel: 1250 ... ../examples/homogenization/linear_elastic_mM.py solved +++ test_input: ok >>> all passed in 3.28 s 1 test file(s) executed in 3.28 s, 0 failure(s) of 1 test(s)

2 3

Problem with Iterative solver
by Nikhil Vaidya 18 Oct '16

18 Oct '16

Hello, I am trying to solve a poiseuille flow example. I want to make use of the ls.scipy_iterative sovler. I am using the cg method. The problem definition file, mesh and the vtk output are attached. Also attached is a plot of the pressure and axial flow velocity along the axis of the pipe. As you can see, the solution is completely non-physical. The same case runs fine with the scipy_direct solver. What am I doing wrong? Best regards, Nikhil

2 3

Outlet Boundary Conditions for Navier Stokes
by Nikhil Vaidya 18 Oct '16

18 Oct '16

Hello! I am solving for steady laminar flow through a pipe. The issue I am facing is the following: I have given a velocity boundary condition at the pipe inlet. For the outlet, I examined the following two cases: 1) Pressure boundary condition at outlet. 2) No boundary condition prescribed at outlet. For both cases, I get a strange jump in the velocity at the pipe outlet. In the attached files you can see the velocity and pressure plotted along the axis(from inlet to outlet) of the pipe. Why do I see a jump in the velocity for both cases? How do I specify outlet conditions in sfepy? Another observation that I have made is that for case 1, there is a jump in the pressure value at the outlet. In case 2, this pressure-jumps goes away. Best regards, Nikhil

2 7

debug on error
by Robert Cimrman 14 Oct '16

14 Oct '16

Hi, In the PR [1], all top-level scripts got --debug option that runs a post-mortem debugger when an exception occurs. The only change that might break things is that the original --debug of run_tests.py was renamed to --raise. Thoughts? I would like to merge this soon, if there are no serious objections. r. [1] https://github.com/sfepy/sfepy/pull/343

1 1

Testing fails due to pytables
by Niels Looije 10 Oct '16

10 Oct '16

Hi, While running the tests most seem to run fine except for those which rely on base.ioutils.py, e.g. running: python run_tests.py --debug tests/test_homogenization_perfusion.py fails with error: AttributeError: 'module' object has no attribute 'openFile' It seems the latest <http://www.pytables.org/MIGRATING_TO_3.x.html#major-api-changes> pytables release has started following PEP8 naming convention and function calls such as `openFile` should now be `open_file`. Can anyone confirm this? Niels

2 2