Mailman 3 March 2017 - SfePy

Material Parameters of Individual Nodes
by derj...＠web.de April 12, 2022

April 12, 2022

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 Jan. 17, 2019

Jan. 17, 2019

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 March 9, 2018

March 9, 2018

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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Unable to install sfepy 2017.1 in python 3.6 environment using anaconda3
by Emanuel Woiski March 30, 2017

March 30, 2017

Hi, I've been unable to install sfepy 2017.1 using conda-forge in the python 3.6 environment. The error was: "UnsatisfiableError: The following specifications were found to be in conflict: - python 3.6* - sfepy 2017.1* -> python 2.7* Use "conda info <package>" to see the dependencies for each package." After using conda info sfepy this is what I've got: "sfepy 2017.1 np111py35_0 ------------------------ file name : sfepy-2017.1-np111py35_0.tar.bz2 name : sfepy version : 2017.1 build string: np111py35_0 build number: 0 channel : conda-forge size : 7.3 MB arch : x86_64 has_prefix : True license : BSD-3-Clause md5 : b38a92b0ecdf0ead6b390cd984e00de1 noarch : None platform : linux requires : () subdir : linux-64 url : https://conda.anaconda.org/conda-forge/linux-64/sfepy-2017.1-np111py35_0.ta… dependencies: matplotlib mpi4py numpy 1.11* pyparsing pytables python 3.5* scipy sympy" What am I missing in order to install sfepy 2007.1 in python 3.6? Thanks, woiski

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Problem with setting up the ipython profile for sfepy
by Gary Roach March 29, 2017

March 29, 2017

Debian (stretch) Linux OS Using Anaconda3 pip and conda used for installations I created profile_sfepy directory and content by running ipython profile create sfepy from the /root/.ipython directory. This created the subdirectory profile_sfepy in the .ipython directory. In the profile_sfepy directory, I then tried to edited the ipython_config.py file as suggested in section 2.6 of the tutorial. First problem: There is no c = get_config() line in the file. The unedited file is attached. Second: exec_lines = [ ] does not exist. There is a: ## lines of code to run at IPython startup. #c.InteractiveShellApp.exec_lines = [ ] . I put the exec_lines = code directly into c.InteractiveShellApp.exec_lines "tuple?" For the rest I found places that fit. When running ipython --profile=sfepy I got the following error: ImportError: Matplotlib backend_wx and backend_wxagg require wxPython >=2.8.12 /root/anaconda3/lib/python3.5/site-packages/traits/etsconfig/etsconfig.py:429: UserWarning: Environment variable "HOME" not set, setting home directory to /tmp (environment_variable, parent_directory)) I attempted to install wxpython with conda install wxpython and got the following: UnsatisfiableError: The following specifications were found to be in conflict: - python 3.5* - wxpython I ran conda info wxpython and found that wxpython depends on python 2.7. I use python 3.5 or 6 exculsively. pip can't find the wxpython at all. What now? yours Gary R.

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balance equation in rate form and boundary conditions
by Jan Heczko March 28, 2017

March 28, 2017

Hi, everyone! I'm trying to implement an example with hypoelastic material, i.e. a material whose stress-strain relationship is given in rate-form: $$ d_stress = E : d_strain $$ The linear elastic material is a subset of this, but one can obtain different types of behavior with non-constant E. I tried two approaches (enclosed), both contain the balance equation in rate-form. The equation consists of a single `dw_lin_elastic_iso` term in both cases. When displacements are prescribed, the problem is not solved as expected: the solution is zero everywhere except where the EBCs are prescribed. The approach with two fields (displacement and velocity) works with boundary conditions prescribed for velocities. Actually, the second field (displacements) is present only to directly output displacements, since I am not interested in velocities. My questions: - Is the above described behavior correct in Sfepy? Is it a bug/feature? There is also the possibility that the formulations are not equivalent, but I can't see it now. - What is the difference between the [hypo]elastic term and e.g. diffusion? (There is a time-derivative term in `time_poisson_interactive.py` together with Dirichlet boundary conditions and everything seems to work.) Is it the fact that there is no term without time derivative in the balance equation? I guess not - I tried to add an elastic term (multiplied by either 0, 1e-4), but that doesn't change the results much. Thanks, Jan

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run_test.py failures
by Gary Roach March 23, 2017

March 23, 2017

OS Debian Linux (Stretch) Setup: Anaconda3 While testing the sfepy installation ( ./run_tests.py --debug tests/test_projections.py) the following two files errored out with "ImportError: No module named <test_projections >". as an example. The two files were: test_projections.py and test_input_navier_stokes2d_iga.py Not sure what is causing this. All of the other files passed. Gary R

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new interactive example with time stepping
by Robert Cimrman March 13, 2017

March 13, 2017

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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Two Problems: Define different node forces and calculating cauchy stress in a post process hook function
by kathrinsb...＠googlemail.com March 12, 2017

March 12, 2017

Hi, I am running the following FE simulation example (linear_elastic_tractions) as a python program. The first question is how to change the definition of the pressure traction at the surface. In my problem I have different force values for each node in the top/bottom region? The second question is about how to calculate the stress results. I extendes the traction example with a post_process_hook. My program is as follows: # coding: utf-8 from __future__ import print_function from __future__ import absolute_import from argparse import ArgumentParser import numpy as nm import time import sys sys.path.append('.') from sfepy.base.base import IndexedStruct from sfepy.discrete import (FieldVariable, Material, Integral, Equation, Equations, Problem, Function) from sfepy.discrete.fem import Mesh, FEDomain, Field from sfepy.terms import Term from sfepy.discrete.conditions import Conditions, EssentialBC from sfepy.solvers.ls import ScipyDirect from sfepy.solvers.nls import Newton from sfepy.postprocess.viewer import Viewer from sfepy.mechanics.matcoefs import stiffness_from_lame def linear_tension(ts, coor, mode=None, **kwargs): if mode == 'qp': val = nm.tile(1.0, (coor.shape[0], 1, 1)) return {'val' : val} def post_process(out, problem, state, extend=False): from sfepy.base.base import Struct # Cauchy strain averaged in elements. strain = problem.evaluate('ev_cauchy_strain.2.Omega(u)', mode='el_avg') out['cauchy_strain'] = Struct(name='output_data', mode='cell', data=strain, dofs=None) # Cauchy stress averaged in elements. stress = problem.evaluate('ev_cauchy_stress.2.Omega(solid.D, u)', mode='el_avg') out['cauchy_stress'] = Struct(name='output_data', mode='cell', data=stress, dofs=None) return out def cube_displacement_medium(): from sfepy import data_dir parser = ArgumentParser() parser.add_argument('--version', action='version', version='%(prog)s') parser.add_argument('-s', '--show', action="store_true", dest='show', default=True, help=help['show']) options = parser.parse_args() mesh = Mesh.from_file(data_dir + '/meshes/3d/cube_medium_tetra.mesh') print("Mesh number of nodes: {}, number of tetrahedrons: {}".format(mesh.n_nod, mesh.n_el)) domain = FEDomain('domain', mesh) domain.refine() omega = domain.create_region('Omega', 'all') left = domain.create_region('Left', 'vertices in (x < -0.1)', 'facet') right = domain.create_region('Right', 'vertices in (x > 0.3)', 'facet') field = Field.from_args('displacement', nm.float64, 3, omega, approx_order=1) u = FieldVariable('u', 'unknown', field, order=0) v = FieldVariable('v', 'test', field, primary_var_name='u') solid = Material('solid', values={'D': stiffness_from_lame(dim=3, lam=5.769, mu=3.846)}) load = Material('load', function=linear_tension) integral = Integral('i', order=2) t1 = Term.new('dw_lin_elastic(solid.D, v, u)', integral, omega, solid=solid, v=v, u=u) t2 = Term.new('dw_surface_ltr(load.val, v)', integral, right, load=load, v=v) eq = Equation('elasticity', t1 - t2) eqs = Equations([eq]) fixb = EssentialBC('fixb', left, {'u.all' : 0.0}) fixt = EssentialBC('fixt', right, {'u.[1,2]' : 0.0}) ls = ScipyDirect({}) nls_status = IndexedStruct() nls = Newton({ 'i_max' : 1, 'eps_a' : 1e-10, 'eps_r' : 1.0, 'macheps' : 1e-16, # Linear system error < (eps_a * lin_red). 'lin_red' : 1e-2, 'ls_red' : 0.1, 'ls_red_warp' : 0.001, 'ls_on' : 1.1, 'ls_min' : 1e-5, 'check' : 0, 'delta' : 1e-6, }, lin_solver=ls, status=nls_status) pb = Problem('linear_elastic_traction', equations=eqs, nls=nls, ls=ls) pb.save_regions_as_groups('regions') pb.time_update(ebcs=Conditions([fixb, fixt])) vec = pb.solve() print(nls_status) # calculate stress pb.save_state('linear_elastic_traction_cylinder.vtk', vec, post_process_hook=post_process) if options.show: view = Viewer('linear_elastic_traction_cylinder.vtk') view(vector_mode='warp_norm', rel_scaling=2, is_scalar_bar=True, is_wireframe=True) if __name__ == '__main__': cube_displacement_medium() When I am running the program I get the following error from the post process function: sfepy: ev_cauchy_stress.2.Omega(solid.D, u) Traceback (most recent call last): File "/home/experimental/fem/linear_elastic_traction_tetraeder.py", line 440, in <module> runtime_small_cube, nodes_small_cube = cube_displacement_medium() File "/home/experimental/fem/linear_elastic_traction_tetraeder.py", line 345, in cube_displacement_medium pb.save_state('linear_elastic_traction_cylinder.vtk', vec, post_process_hook=post_process) File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/discrete/problem.py", line 773, in save_state out = post_process_hook(out, self, state, extend=extend) File "/home/experimental/fem/linear_elastic_traction_tetraeder.py", line 85, in post_process mode='el_avg') File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/discrete/problem.py", line 1262, in evaluate verbose=verbose, **kwargs) File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/discrete/problem.py", line 1203, in create_evaluable kwargs=kwargs) File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/discrete/evaluate.py", line 213, in create_evaluable user=extra_args, verbose=verbose) File "/bin//python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/discrete/equations.py", line 66, in from_conf materials, integrals, user=user) File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/discrete/equations.py", line 751, in from_desc terms.assign_args(variables, materials, user) File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/terms/terms.py", line 295, in assign_args term.assign_args(variables, materials, user) File "/bin/python27/lib/python2.7/site-packages/sfepy-2016.3_git_f99ff34eeb05ea11e61aa3639c47537daba7cc64-py2.7-linux-x86_64.egg/sfepy/terms/terms.py", line 506, in assign_args % arg_name) ValueError: material argument solid not found! It seems that the defined material is not known in the function. Can anyone help me? Thank you.

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Usage of contact planes to model a special boundary condition
by kathrinsb...＠googlemail.com March 12, 2017

March 12, 2017

Hi, for my linear elastic problem (3d, with a fixed button or top region and some forces on the other side) I want to define another special condition: The condition is given by a direction as a normal vector of a 2d plane. Now I want to prevent node movement in that direction. I saw in the examples that I cannot use the essential boundary conditions, because I am blocking an arbitrary direction and not a dimension (x, y, z). The idea is now to use a contact plane instead. Is that a good idea for defining this condition? Thank you for your help.

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