SfePy February 2020

sfepy@python.org

4 participants
7 discussions

Material Parameters of Individual Nodes
by derj...＠web.de 12 Apr '22

12 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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Using meshio for reading/writing mesh files in SfePy
by Vladimír Lukeš 25 Feb '20

25 Feb '20

The latest commits in the master branch on github incorporate meshio package [1] into SfePy. We use meshio to read the following file formats: abaqus, exodus, gmsh, medit, nastran, vtk, vtu, med, xdmf and tetgen. Besides these formats, we keep on maintaining own code for reading: ansys_cdb, xyz, comsol, hmascii, gambit and mesh3d. Bug fixes and improvements are welcome! Regards, Vladimír Lukeš [1] https://github.com/nschloe/meshio

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using field in postproc that was not used in equation solving
by FaTune 25 Feb '20

25 Feb '20

I want to define my own field. For example, pressure. ```python fields = { 'temperature' : ('real', 1, 'Omega', 1), 'pressure' : ('real', 1, 'Omega', 1), } variables = { 't' : ('unknown field', 'temperature', 0), 's' : ('test field', 'temperature', 't'), 'p' : ( 'parameter field', 'pressure', {'setter' : 'get_pressure'} ), } def get_pressure(ts, coors, region=None): z = coors[:,2] return z functions = { 'get_pressure': (get_pressure,), } ``` The idea is to create very primitive field that depends on z coordinates. Now I want to export the grad(p) to the output mesh. And so I add this in postprocess function: ```python p_grad = pb.evaluate('ev_grad.i.Omega(p)', mode='el_avg', verbose=False) out['p'] = Struct(name='output_data', mode='cell', data=p_grad, dofs=None) ``` But I get the following error: ValueError: argument p not found! What I'm doing wrong? And how can I export the pressure field itself (not its gradient)? The answer from Robert Cimrman: Hi, In a post-processing function, the only variables that are defined are those that are used in the equations. If p is not used, you need to create it, as shown below (also how to save p and its cell averages. def post_process(out, pb, state, extend=False): from sfepy.base.base import Struct pvar = pb.create_variables(['p'])['p'] pvar.time_update(None, pb.functions) out.update(pvar.create_output()) ap = pb.evaluate('ev_volume_integrate.i.Omega(p)', mode='el_avg', p=pvar, verbose=False) out['ap'] = Struct(name='output_data', mode='cell', data=ap, dofs=None) p_grad = pb.evaluate('ev_grad.i.Omega(p)', mode='el_avg', p=pvar, verbose=False) out['gp'] = Struct(name='output_data', mode='cell', data=p_grad, dofs=None) return out r. PS: This might be interesting to others, so, if you do not mind, you can forward it to the list.

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Re: Set groups in vtk mesh.
by Robert Cimrman 03 Feb '20

03 Feb '20

Yes, mmesh.point_data['mat_ids'] would work, but I did not see it in your mesh :) r. On 2/3/20 4:43 AM, FaTune wrote: > Your little snipped has worked like magic! Thank you so much! > > Am I right that to also save 'mat_ids' I have to change the argument > [np.zeros_like(conn[:, 0])] to mmesh.point_data['mat_ids']? > > ```python > smesh = Mesh.from_data( > 'meshio-mesh', > mmesh.points, > mmesh.point_data['node_groups'], > [conn], > mmesh.point_data['mat_ids'], > ['3_4'], > ) > ``` > > On Mon, Feb 3, 2020 at 3:45 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz> wrote: > >> I was thinking about meshio too. But because it does not write the old VTK >> format, you could try the following: >> >> ``` >> import numpy as np >> import meshio >> >> from sfepy.discrete.fem import Mesh >> >> mmesh = meshio.read('trian.vtk') >> >> conn = mmesh.cells['tetra'] >> smesh = Mesh.from_data( >> 'meshio-mesh', >> mmesh.points, >> mmesh.point_data['node_groups'], >> [conn], >> [np.zeros_like(conn[:, 0])], >> ['3_4'], >> ) >> >> smesh.write('trian2.vtk') >> ``` >> >> Then >> >> postproc.py --only-names=node_groups -b trian2.vtk --wire >> >> seems to show the regions correctly. >> >> r. >> >> On 2/2/20 1:14 PM, FaTune wrote: >>> Thank you for help. I'm not sure I know how to convert the mesh into >> older >>> format. Is there any converter? I've tried to convert trian.vtk to >>> trian.mesh using meshio-convert in ubuntu. But the resulting trian.mesh >>> doesn't have any information about node_groups. >>> >>> On Sun, Feb 2, 2020 at 9:05 PM Robert Cimrman <cimrman3(a)ntc.zcu.cz> >> wrote: >>> >>>> Can you try converting the mesh to "# vtk DataFile Version 2.0" format? >>>> Your >>>> mesh is in "# vtk DataFile Version 4.2", and the reader in sfepy does >> not >>>> read >>>> it correctly. >>>> >>>> r. >>>> >>>> On 2/2/20 1:49 AM, FaTune wrote: >>>>> I see the node_groups in paraview, but don't see it if I use your >>>> snipped: >>>>> >>>>> python postproc.py trian.vtk --all -b >>>>> >>>>> The file trian.vtk is in the attachment. Clearly something is wrong in >>>> this >>>>> mesh. >>>>> >>>>> On Sun, Feb 2, 2020 at 10:49 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz> >>>> wrote: >>>>> >>>>>> On 2/2/20 12:28 AM, FaTune wrote: >>>>>>> In addition to the previous message. I created vtk mesh with values >> in >>>>>>> field "node_groups" to be 1 or 2. When I use 'vertices of group 0' >>>> sfepy >>>>>>> works without errors, but set this region to every single vertex in >> the >>>>>>> mesh, and I don't have values 0 in 'node_groups' field. When I >> change 0 >>>>>> to >>>>>>> 1 or 2 it raises error. Apparently sfepy just ignores 'node_groups' >>>>>> field. >>>>>> >>>>>> It is possible to display the vertex and cell groups in a mesh with >> the >>>>>> following (or use any VTK viewer, such as paraview): >>>>>> >>>>>> python postproc.py meshes/3d/acoustic_wg.vtk --all -b >>>>>> >>>>>> Does it show your regions correctly? If the mesh and the node_groups >> are >>>>>> well >>>>>> defined, what you do should work. >>>>>> >>>>>> If the above does not help you finding what's wrong, send here a >> minimal >>>>>> example that demonstrates the problem. >>>>>> >>>>>> r. >>>>>> >>>>>>> On Sun, Feb 2, 2020 at 10:16 AM <fatune(a)gmail.com> wrote: >>>>>>> >>>>>>>> regions = { >>>>>>>> 'Omega' : 'all', >>>>>>>> 'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'), >>>>>>>> 'Gamma_Right' : ('vertices in (x > 99.099999)', 'facet'), >>>>>>>> 'GammaIn': ('vertices of group 0', 'edge'), >>>>>>>> } >>>>>>>> >>>>>>>> >>>>>>>> The group I am struggling with is GammaIn. I was using >>>>>> vibro_acoustic3d.py >>>>>>>> as an example when I was creating my vtk mesh. Am I right in my >>>>>> assumption >>>>>>>> that it is enough to add field "node_groups" to my vtk and sfepy >> will >>>>>>>> gather information of the group number from this field?

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Re: Set groups in vtk mesh.
by Robert Cimrman 02 Feb '20

02 Feb '20

I was thinking about meshio too. But because it does not write the old VTK format, you could try the following: ``` import numpy as np import meshio from sfepy.discrete.fem import Mesh mmesh = meshio.read('trian.vtk') conn = mmesh.cells['tetra'] smesh = Mesh.from_data( 'meshio-mesh', mmesh.points, mmesh.point_data['node_groups'], [conn], [np.zeros_like(conn[:, 0])], ['3_4'], ) smesh.write('trian2.vtk') ``` Then postproc.py --only-names=node_groups -b trian2.vtk --wire seems to show the regions correctly. r. On 2/2/20 1:14 PM, FaTune wrote: > Thank you for help. I'm not sure I know how to convert the mesh into older > format. Is there any converter? I've tried to convert trian.vtk to > trian.mesh using meshio-convert in ubuntu. But the resulting trian.mesh > doesn't have any information about node_groups. > > On Sun, Feb 2, 2020 at 9:05 PM Robert Cimrman <cimrman3(a)ntc.zcu.cz> wrote: > >> Can you try converting the mesh to "# vtk DataFile Version 2.0" format? >> Your >> mesh is in "# vtk DataFile Version 4.2", and the reader in sfepy does not >> read >> it correctly. >> >> r. >> >> On 2/2/20 1:49 AM, FaTune wrote: >>> I see the node_groups in paraview, but don't see it if I use your >> snipped: >>> >>> python postproc.py trian.vtk --all -b >>> >>> The file trian.vtk is in the attachment. Clearly something is wrong in >> this >>> mesh. >>> >>> On Sun, Feb 2, 2020 at 10:49 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz> >> wrote: >>> >>>> On 2/2/20 12:28 AM, FaTune wrote: >>>>> In addition to the previous message. I created vtk mesh with values in >>>>> field "node_groups" to be 1 or 2. When I use 'vertices of group 0' >> sfepy >>>>> works without errors, but set this region to every single vertex in the >>>>> mesh, and I don't have values 0 in 'node_groups' field. When I change 0 >>>> to >>>>> 1 or 2 it raises error. Apparently sfepy just ignores 'node_groups' >>>> field. >>>> >>>> It is possible to display the vertex and cell groups in a mesh with the >>>> following (or use any VTK viewer, such as paraview): >>>> >>>> python postproc.py meshes/3d/acoustic_wg.vtk --all -b >>>> >>>> Does it show your regions correctly? If the mesh and the node_groups are >>>> well >>>> defined, what you do should work. >>>> >>>> If the above does not help you finding what's wrong, send here a minimal >>>> example that demonstrates the problem. >>>> >>>> r. >>>> >>>>> On Sun, Feb 2, 2020 at 10:16 AM <fatune(a)gmail.com> wrote: >>>>> >>>>>> regions = { >>>>>> 'Omega' : 'all', >>>>>> 'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'), >>>>>> 'Gamma_Right' : ('vertices in (x > 99.099999)', 'facet'), >>>>>> 'GammaIn': ('vertices of group 0', 'edge'), >>>>>> } >>>>>> >>>>>> >>>>>> The group I am struggling with is GammaIn. I was using >>>> vibro_acoustic3d.py >>>>>> as an example when I was creating my vtk mesh. Am I right in my >>>> assumption >>>>>> that it is enough to add field "node_groups" to my vtk and sfepy will >>>>>> gather information of the group number from this field? >>>>>> _______________________________________________ >>>> _______________________________________________ >>>> SfePy mailing list -- sfepy(a)python.org >>>> To unsubscribe send an email to sfepy-leave(a)python.org >>>> https://mail.python.org/mailman3/lists/sfepy.python.org/ >>>> >>> >> _______________________________________________ >> SfePy mailing list -- sfepy(a)python.org >> To unsubscribe send an email to sfepy-leave(a)python.org >> https://mail.python.org/mailman3/lists/sfepy.python.org/ >> >

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Re: Set groups in vtk mesh.
by Robert Cimrman 02 Feb '20

02 Feb '20

Can you try converting the mesh to "# vtk DataFile Version 2.0" format? Your mesh is in "# vtk DataFile Version 4.2", and the reader in sfepy does not read it correctly. r. On 2/2/20 1:49 AM, FaTune wrote: > I see the node_groups in paraview, but don't see it if I use your snipped: > > python postproc.py trian.vtk --all -b > > The file trian.vtk is in the attachment. Clearly something is wrong in this > mesh. > > On Sun, Feb 2, 2020 at 10:49 AM Robert Cimrman <cimrman3(a)ntc.zcu.cz> wrote: > >> On 2/2/20 12:28 AM, FaTune wrote: >>> In addition to the previous message. I created vtk mesh with values in >>> field "node_groups" to be 1 or 2. When I use 'vertices of group 0' sfepy >>> works without errors, but set this region to every single vertex in the >>> mesh, and I don't have values 0 in 'node_groups' field. When I change 0 >> to >>> 1 or 2 it raises error. Apparently sfepy just ignores 'node_groups' >> field. >> >> It is possible to display the vertex and cell groups in a mesh with the >> following (or use any VTK viewer, such as paraview): >> >> python postproc.py meshes/3d/acoustic_wg.vtk --all -b >> >> Does it show your regions correctly? If the mesh and the node_groups are >> well >> defined, what you do should work. >> >> If the above does not help you finding what's wrong, send here a minimal >> example that demonstrates the problem. >> >> r. >> >>> On Sun, Feb 2, 2020 at 10:16 AM <fatune(a)gmail.com> wrote: >>> >>>> regions = { >>>> 'Omega' : 'all', >>>> 'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'), >>>> 'Gamma_Right' : ('vertices in (x > 99.099999)', 'facet'), >>>> 'GammaIn': ('vertices of group 0', 'edge'), >>>> } >>>> >>>> >>>> The group I am struggling with is GammaIn. I was using >> vibro_acoustic3d.py >>>> as an example when I was creating my vtk mesh. Am I right in my >> assumption >>>> that it is enough to add field "node_groups" to my vtk and sfepy will >>>> gather information of the group number from this field? >>>> _______________________________________________ >> _______________________________________________ >> SfePy mailing list -- sfepy(a)python.org >> To unsubscribe send an email to sfepy-leave(a)python.org >> https://mail.python.org/mailman3/lists/sfepy.python.org/ >> >

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Set groups in vtk mesh.
by fatune＠gmail.com 01 Feb '20

01 Feb '20

Hello. Is there a way to somehow mark some vertices in vtk mesh so I could later use them in region definition? I've tried to create my vtk mesh with vertices field "node_groups". And some vertices have this field to set to 1, and other to 2. But it doesnt work. Sfepy tell me >raise ValueError('region "%s" has no entities!' % self.name) Thank you

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SfePy February 2020