SfePy August 2016

sfepy@python.org

6 participants
11 discussions

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

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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), }

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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.

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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

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Do I generate mesh in the wrong way?
by Ronghai Wu 01 Sep '16

01 Sep '16

Hi Robert, I am using sfepy for static linear elasticity problem in 2D. The mesh size is 200*200 (mesh file is attached) and equations are as following: def D_function(self, ts, coors, mode, term=None, **kwargs): if mode != 'qp': return _, weights = term.integral.get_qp('2_4') self.n_qp = weights.shape[0] self.val_D = np.repeat(self.stiffness_tensor, self.n_qp, axis=0) return {'function' : self.val_D} def prestress_function(self,ts, coors, mode, term=None, **kwargs): if mode != 'qp': return _, weights = term.integral.get_qp('2_4') self.n_qp = weights.shape[0] self.val_pre = np.repeat(self.prestress_value, self.n_qp, axis=0) return {'function' : self.val_pre} self.m = Material('m', function=self.D_function) self.prestress_value = np.copy(self.stress_0) (self.prestress_value).shape = (-1, 3, 1) self.prestress = Material('prestress', function=self.prestress_function) integral = Integral('i', order=2) self.t1 = Term.new('dw_lin_elastic(m.function, v, u )', integral, self.omega, m=self.m, v=self.v, u=self.u) self.t2 = Term.new('dw_lin_prestress(prestress.function, v )',integral, self.omega, prestress=self.prestress, v=self.v) self.t3 = Term.new('dw_surface_ltr(traction_lef.val, v)', integral, self.lef, traction_lef=self.traction_lef, v=self.v) self.t4 = Term.new('dw_surface_ltr(traction_rig.val, v)', integral, self.rig, traction_rig=self.traction_rig, v=self.v) self.t5 = Term.new('dw_surface_ltr(traction_top.val, v)', integral, self.top, traction_top=self.traction_top, v=self.v) self.t6 = Term.new('dw_surface_ltr(traction_bot.val, v)', integral, self.bot, traction_bot=self.traction_bot, v=self.v) self.fem_eq = Equation('balance', self.t1 - self.t2 - self.t3 - self.t4 - self.t5 - self.t6) self.eqs = Equations([self.fem_eq]) self.ls = ScipyDirect({}) self.nls_status = IndexedStruct() self.nls = Newton({'i_max' : 1,'eps_a' : 1e-8,'problem' : 'nonlinear'}, lin_solver=self.ls, status=self.nls_status) self.pb = Problem('elasticity', equations=self.eqs, nls=self.nls, ls=self.ls) self.pb.time_update(ebcs=Conditions([fix_u_lef_corn])) self.pb.update_materials() self.vec = self.pb.solve() When I run the simulation, the information below are printed. I have several questions about it. I tried to find answers from source codes but failed. Could you please give me some help, thanks. (1) I do understand why "matrix shape: (79999, 79999)" and "matrix structural nonzeros: 1439965". what exactly this "matrix" is? what is its relation with mesh size (200*200)? (2) I do not understand why "updating materials..." did twice. (3) "solve: 6.18 [s]". I guess it should not take such a long time for a mesh size (200*200) problem. Is it because I generate mesh file in the wrong way or because of other reasons? (4) In which source code file the following information are printed? sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (79999, 79999) sfepy: assembling matrix graph... sfepy: ...done in 0.05 s sfepy: matrix structural nonzeros: 1439965 (2.25e-04% fill) sfepy: updating materials... sfepy: m sfepy: traction_bot sfepy: traction_rig sfepy: prestress sfepy: traction_top sfepy: traction_lef sfepy: ...done in 0.05 s sfepy: updating materials... sfepy: m sfepy: traction_bot sfepy: traction_rig sfepy: prestress sfepy: traction_top sfepy: traction_lef sfepy: ...done in 0.05 s sfepy: nls: iter: 0, residual: 4.741758e+01 (rel: 1.000000e+00) sfepy: rezidual: 0.04 [s] sfepy: solve: 6.18 [s] sfepy: matrix: 0.10 [s] sfepy: nls: iter: 1, residual: 5.936719e-14 (rel: 1.252008e-15) sfepy: equation "tmp": sfepy: ev_cauchy_strain.2.Omega(u) sfepy: updating materials... sfepy: ...done in 0.00 s Regards Ronghai

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ValueError: variable kind is 2 or 3 words! (test_field)
by Nikhil Vaidya 31 Aug '16

31 Aug '16

When I run a simulation i get the following error: Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 120, in from_conf obj.set_equations(conf.equations, user={'ts' : obj.ts}) File "C:\sfepy\sfepy\discrete\problem.py", line 411, in set_equations variables = Variables.from_conf(self.conf_variables, self.fields) File "C:\sfepy\sfepy\discrete\variables.py", line 156, in from_conf var = Variable.from_conf(key, val, fields) File "C:\sfepy\sfepy\discrete\variables.py", line 809, in from_conf raise ValueError('variable kind is 2 or 3 words! (%s)' % conf.kind) ValueError: variable kind is 2 or 3 words! (test_field) The above error message is displayed after the region definition process. Can you tell me what is causing this issue? Best regards, Nikhil

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probe.py
by Jan Heczko 31 Aug '16

31 Aug '16

Hi, I tried to test the usage of probe.py as a script according to the example [1], i.e. I called ./simple.py examples/linear_elasticity/its2D_4.py which creates its2D.h5 and then ./probe.py examples/linear_elasticity/its2D_4.py its2D.h5 which results in: probe: left over: ['refine_mesh', 'verbose', '__builtins__', 'absolute_import', '__file__', '__name__', 'stiffness_from_youngpoisson', 'data_dir', '_filename', 'refinement_level', 'young', '__package__', 'stress_strain', 'range', 'probe_hook', 'output_dir', 'poisson', 'gen_lines' , '__doc__'] probe: results in: its2D.h5 probe: loaded: [u'cauchy_stress', u'cauchy_strain', u'u'] probe: from step: 0 probe: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/media/sf_sfepy/ meshes/2d/its2D.mesh)... probe: ...done in 0.00 s probe: creating regions... probe: Top probe: Bottom probe: Omega probe: Left probe: ...done in 0.01 s probe: 0 line [[ 0. 0.], [ 75. 0.]] Traceback (most recent call last): File "./probe.py", line 272, in <module> main() File "./probe.py", line 269, in main generate_probes(filename_input, filename_results, options) File "./probe.py", line 139, in generate_probes out = probe_hook(data, probe, labels[ip], problem) File "/media/sf_sfepy/examples/linear_elasticity/its2D_4.py", line 92, in probe_hook results['u'] = get_it('u', 'u') File "/media/sf_sfepy/examples/linear_elasticity/its2D_4.py", line 87, in get_it pars, vals = probe(var) File "/media/sf_sfepy/sfepy/discrete/probes.py", line 239, in __call__ return self.probe(variable, **kwargs) File "/media/sf_sfepy/sfepy/discrete/probes.py", line 287, in probe refine_flag = self.refine_points(variable, points, cells) File "/media/sf_sfepy/sfepy/discrete/probes.py", line 322, in refine_points ed = variable.get_element_diameters(cells, 0) File "/media/sf_sfepy/sfepy/discrete/variables.py", line 1830, in get_element_diameters diameters = domain.get_element_diameters(cells, vg, mode, square=square) File "/media/sf_sfepy/sfepy/discrete/fem/domain.py", line 173, in get_element_diameters vg.get_element_diameters(diameters, gel.edges, AttributeError: 'tuple' object has no attribute 'get_element_diameters' Am I using it the right way? Is my sfepy installation broken in some way? I tried the same using an older version of sfepy, which gave a different error. [1] http://sfepy.org/doc-devel/examples/linear_elasticity/its2D_4.html?highligh… Regards Jan

2 1

Error while reading mesh
by Nikhil Vaidya 30 Aug '16

30 Aug '16

I am running a Navier stokes simulation. I observed the following output after I ran my file: simple.py RF_testcase\Vein_flow_setup.py sfepy: left over: ['__builtins__', '__file__', 'absolute_import', '__doc__', '__name__', '__package__', 'verbose', 'verify_incompressibility', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\sfepy\RF_testcase\sfepy_test_full_geom_m.mesh)... Traceback (most recent call last): File "C:\sfepy\simple.py", line 170, in <module> main() File "C:\sfepy\simple.py", line 163, in main app = PDESolverApp(conf, options, output_prefix) File "C:\sfepy\sfepy\applications\pde_solver_app.py", line 137, in __init__ self.problem = Problem.from_conf(conf, init_equations=is_eqs, **kwargs) File "C:\sfepy\sfepy\discrete\problem.py", line 88, in from_conf mesh = Mesh.from_file(conf.filename_mesh, prefix_dir=conf_dir) File "C:\sfepy\sfepy\discrete\fem\mesh.py", line 225, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 330, in read _read_cells(3, 4) File "C:\sfepy\sfepy\discrete\fem\meshio.py", line 305, in _read_cells data = read_array(fd, num, size + 1 * has_id, nm.int32) File "C:\sfepy\sfepy\base\ioutils.py", line 215, in read_array raise ValueError('(%d, %d) array reading failed!' % (n_row, n_col)) ValueError: (1376353, 5) array reading failed! I created the mesh in NETGEN and had to remove surface elements by hand. Can you tell me what is going wrong? Best regards, Nikhil

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About Mesh
by Nikhil Vaidya 22 Aug '16

22 Aug '16

Hello! I am trying to solve a problem using sfepy. It is a multiphysics problem with weakly coupled convection and conduction. There are three regions in my domain which need to be separately defined. I went through the user guide and saw the format for defining regions in the domain. The regions in my geometry are not simple enough to be described by mathematical conditions. I usually use Starccm+ for my multiphysics simulations. There I define the regions using the GUI. One region in my domain is a real blood vessel observed in a CT scan. Can anyone tell me how I should define my regions in this case? I have seen in the user guide, that regions can be defined using "groups" of cells and vertices. I would like to know how these groups are defined. Best regards, Nikhil

3 5

memory corruption error
by Nicolas DELAN 22 Aug '16

22 Aug '16

Hi, I try to launch several times sfepy using a loop but at the second iteration i have this error: glibc detected *** python: malloc(): memory corruption: 0x0000000002e2d810 *** Is there any solution ?

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