SfePy September 2019

sfepy@python.org

3 participants
3 discussions

by Guillaume GB

Hello, To get the Cauchy stress, we have to evaluate the term *ev_cauchy_stress*, however, it does not seem to be compatible with a shell10X term-based problem. Is there a way to get Cauchy stress and strain when dealing with a shell model? Best regards. Guillaume Gbikpi-Benissan -- Junior Researcher (Postdoc) RUDN University Moscow, Russian Federation

3 months

ANN: SfePy 2019.3

by Robert Cimrman

I am pleased to announce release 2019.3 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method or by the isogeometric analysis (limited support). It is distributed under the new BSD license. Home page: http://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - interface to eigenvalue problem solvers in SLEPc - new Python 3 enabled Timer class and other Python 3 compatibility fixes For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Vladimir Lukes

3 months, 4 weeks

Output for running failed test_homogenization_perfusion.py in raise mode

by Roshan Suresh Kumar

Hi, During my installation of the latest version of sfepy from source (GitHub repo) in Windows, I ran the command to test the various modules. I found that one test had failed, the one for test_homogenization_perfusion.py. I ran the test in raise mode and the output is show below. P.S.: I installed all of the optional dependencies except igakit, petsc4py, slepc4py, pymetis, scikits.umfpack and pysparse. I hope this helps. Let me know if you need any other details. Thanks. Roshan Suresh Kumar <<< directory: tests, test files: 1 <<< [1] tests\test_homogenization_perfusion.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'print_function', 'absolute_import', 'six', 'input_name', 'TestCommon', 'verbose', '_filename'] >>> test instance prepared (1 test(s)) run_tests.py:105: DeprecationWarning: time.clock has been deprecated in Python 3.3 and will be removed from Python 3.8: use time.perf_counter or time.process_time instead tt = time.clock() ../examples/homogenization/perfusion_micro.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'absolute_import', 'match_x_plane', 'match_y_plane', 'cb', 'nm', 'data_dir', 'six', 'range', 'get_mats', 'recovery_perf', 'geoms', 'pb_def', 'eps0', 'param_h', 'aux', 'ch', 'val', 'all_periodicYM', 'all_periodicY', 'reg_io', 'ebcs_eta', 'ebcs_gamma', 'ch2', 'val2', 'aux_bY', 'i_io', 'io', 'ion', 'matk1', 'matk2', 'ipm', 'ireg', 'coefs', 'requirements', 'ipm2', 'get_channel', 'set_corrpis', 'set_corr_S', 'set_corr_cc', 'i_io2', 'io2', 'io12', 'verbose', '_filename'] homogen: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\meshes\3d\perfusion_micro3d.mesh)... homogen: ...done in 0.12 s homogen: creating regions... homogen: Y homogen: YM homogen: Pl homogen: Pr homogen: Pn homogen: Pf homogen: bYm homogen: bYp homogen: YA homogen: fixedYA homogen: YB homogen: fixedYB homogen: PlYM homogen: PrYM homogen: PnYM homogen: PfYM homogen: bYMA homogen: PlYA homogen: PrYA homogen: PnYA homogen: PfYA homogen: bYA_1 homogen: bYA_2 homogen: bYA_3 homogen: bYMB homogen: PlYB homogen: PrYB homogen: PnYB homogen: PfYB homogen: bYB_1 homogen: bYB_2 homogen: bYB_3 homogen: bYMp homogen: bYMm homogen: bYA homogen: bYB homogen: bYMpm homogen: bYMchs homogen: bYA_n1 homogen: bYA_n2 homogen: bYA_n3 homogen: bYB_n1 homogen: bYB_n2 homogen: bYB_n3 homogen: YMmchs homogen: ...done in 0.25 s homogen: using solvers: ts: no ts nls: newton ls: ls he: computing dependency corrs_gamma_m... he: equation "eq_gamma_pm": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 1.000000e+00 * dw_surface_integrate.iS.bYMm(qM) he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.01 s he: matrix shape: (1992, 1992) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 25154 (6.34e-03% fill) he: updating materials... he: mat2M he: ...done in 0.03 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: updating variables... he: ...done he: updating materials... he: mat2M he: ...done in 0.00 s he: nls: iter: 0, residual: 6.480876e-02 (rel: 1.000000e+00) he: residual: 0.04 [s] he: matrix: 0.03 [s] he: solve: 0.09 [s] he: nls: iter: 1, residual: 3.816937e-16 (rel: 5.889539e-15) he: solved in 1 steps in 0.38 seconds he: ...done he: computing Volume_total... he: equation "tmp": he: d_volume.iV.Y(vol_all) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_one... he: ...done he: computing Volume_bYMp... he: equation "tmp": he: d_surface.iS.bYMp(pM) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYp... he: equation "tmp": he: d_surface.iS.bYp(vol_all) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYMm... he: equation "tmp": he: d_surface.iS.bYMm(pM) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYm... he: equation "tmp": he: d_surface.iS.bYm(vol_all) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYA_1... he: equation "tmp": he: d_surface.iS.bYA_1(pA) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYA_2... he: equation "tmp": he: d_surface.iS.bYA_2(pA) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYA_3... he: equation "tmp": he: d_surface.iS.bYA_3(pA) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYB_1... he: equation "tmp": he: d_surface.iS.bYB_1(pB) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYB_2... he: equation "tmp": he: d_surface.iS.bYB_2(pB) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Volume_bYB_3... he: equation "tmp": he: d_surface.iS.bYB_3(pB) he: updating materials... he: ...done in 0.00 s he: ...done he: computing Hmp... he: equation "tmp": he: ev_surface_integrate.iS.bYMp(corr_M) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_gamma_p... he: equation "eq_gamma_pm": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 1.000000e+00 * dw_surface_integrate.iS.bYMp(qM) he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: matrix shape: (1992, 1992) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 25154 (6.34e-03% fill) he: updating materials... he: mat2M he: ...done in 0.03 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: updating variables... he: ...done he: updating materials... he: mat2M he: ...done in 0.00 s he: nls: iter: 0, residual: 7.140562e-02 (rel: 1.000000e+00) he: residual: 0.01 [s] he: matrix: 0.04 [s] he: solve: 0.09 [s] he: nls: iter: 1, residual: 3.887365e-16 (rel: 5.444059e-15) he: solved in 1 steps in 0.37 seconds he: ...done he: computing Hpm... he: equation "tmp": he: ev_surface_integrate.iS.bYMm(corr_M) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_etaA... he: equation "eq_eta": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0 he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: matrix shape: (1992, 1992) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 25154 (6.34e-03% fill) he: updating materials... he: mat2M he: ...done in 0.02 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: updating variables... he: ...done he: updating materials... he: mat2M he: ...done in 0.00 s he: nls: iter: 0, residual: 1.862908e-01 (rel: 1.000000e+00) he: residual: 0.01 [s] he: matrix: 0.03 [s] he: solve: 0.09 [s] he: nls: iter: 1, residual: 4.052551e-16 (rel: 2.175390e-15) he: solved in 1 steps in 0.35 seconds he: ...done he: computing EmA... he: equation "tmp": he: ev_surface_integrate.iS.bYMm(corr_M) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_gamma_B_1... he: equation "eq_gamma": he: dw_diffusion.iV.YB(mat2B.k, qB, pB) + dw_volume_dot.iV.YB(qB, lsB) = 1.000000e+00 * dw_surface_integrate.iS.bYB_1(qB) he: equation "eq_imv": he: dw_volume_dot.iV.YB(lvB, pB) = 0 he: updating variables... he: ...done he: setting up dof connectivities... he: ...done in 0.00 s he: lcbc: imvB he: dofs: total 1406, free 694, constrained 712, new 1 he: -> active 695 he: matrix shape: (1406, 1406) he: assembling matrix graph... he: ...done in 0.01 s he: matrix structural nonzeros: 22052 (1.12e-02% fill) he: updating materials... he: mat2B he: ...done in 0.01 s he: using solvers: ts: no ts nls: newton ls: ls he: updating variables... he: ...done he: lcbc: imvB he: dofs: total 1406, free 694, constrained 712, new 1 he: -> active 695 he: updating variables... he: ...done he: lcbc: imvB he: dofs: total 1406, free 694, constrained 712, new 1 he: -> active 695 he: updating materials... he: mat2B he: ...done in 0.00 s he: nls: iter: 0, residual: 9.945233e-03 (rel: 1.000000e+00) he: residual: 0.01 [s] he: matrix: 0.01 [s] he: solve: 0.01 [s] he: nls: iter: 1, residual: 2.133885e-16 (rel: 2.145636e-14) he: solved in 1 steps in 0.13 seconds he: ...done he: computing RB_2_1... he: equation "tmp": he: ev_surface_integrate.iS.bYB_2(corr1_B) he: updating materials... he: ...done in 0.00 s he: ...done he: computing dependency corrs_oneB... he: ...done he: computing dependency corrs_etaB... he: equation "eq_eta": he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0 >>> <class 'ValueError'> Traceback (most recent call last): File "run_tests.py", line 234, in <module> sys.exit(main()) File "run_tests.py", line 223, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 144, in run_tests stats[0] + 1) File "run_tests.py", line 108, in run_test ifile=ifile) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\base\testing.py", line 67, in run ret = test_method() File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\tests\test_homogenization_perfusion.py", line 51, in test_solution coefs = app() File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\applications\application.py", line 29, in call_basic return self.call(**kwargs) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\homogen_app.py", line 174, in call aux = self.he(ret_all=ret_all, time_tag=time_tag) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\applications\application.py", line 29, in call_basic return self.call(**kwargs) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 729, in call self.app_options.store_micro_idxs, time_tag) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 107, in __call__ time_tag) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 281, in calculate_req chunk_tab, 'reqs', proc_id) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 149, in calculate val = mini_app(data=data) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\coefs_base.py", line 459, in __call__ problem.set_equations(self.equations) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\problem.py", line 525, in set_equations user=user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\equations.py", line 66, in from_conf materials, integrals, user=user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\equations.py", line 772, in from_desc terms.assign_args(variables, materials, user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\terms\terms.py", line 299, in assign_args term.assign_args(variables, materials, user) File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\terms\terms.py", line 512, in assign_args raise ValueError('argument %s not found!' % arg_name) ValueError: argument qM not found! 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4 months, 2 weeks

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SfePy September 2019