dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Mon, May 15, 2006 at 04:19:04PM +0000, Alexander Jarosch wrote:
> Well the thing is that i forgot that the gmsh msh points and the VTK 
> node point numbers are not the same, as it seems. the vertex missing is 
> with the point numbers from the VTK output, because I miss the vertex 
> there. A simple python conversion tool I wrote for msh --> xml does not 
> show this behaviour, so I thougth it might be a dolfin-convert problem.
> The thing is that the vertex is not just missing in the VTK file, there 
> are wrong field values around that vertex.
> 
> How shall we proceed to debug this?
> 
> Alex

Well, post the two correct files (.msh and .xml) together with the one
that is wrong (generated with dolfin-convert) and point to where
something is different. It should be easy to fix.

You can also take a look in dolfin-config (which is also a Python
script) and see if you can spot the problem. Since you have a working
Python script yourself, you obviously know how to fix it. :-)

/Anders

> 
> 
> Anders Logg wrote:
> 
> >On Mon, May 15, 2006 at 03:41:10PM +0000, Alexander Jarosch wrote:
> > 
> >
> >>Thanks for the input Anders, I will make further testing and post 
> >>results on the list.
> >>
> >>Some other thing I mentioned earlier in a mail is that a vertex is 
> >>missing if one is converting a gmsh msh file with the dolfin-convert in 
> >>2d. here an example. The test.geo file would be:
> >>
> >>Point(1) = {0,0,0,15};
> >>Point(2) = {3000,0,0,15};
> >>Point(3) = {3000,200,0,15};
> >>Point(4) = {0,200,0,15};
> >>Line(1) = {2,1};
> >>Line(2) = {1,4};
> >>Line(3) = {4,3};
> >>Line(4) = {3,2};
> >>Line Loop(5) = {3,4,1,2};
> >>Plane Surface(6) = {5};
> >>Physical Surface(7) = {6};
> >>
> >>and if I mesh it with gmsh, ver. 1.64.0 like that
> >>
> >>#  gmsh test.geo -2 -clscale 1.0 -o test.msh
> >>
> >>and than run
> >>
> >>#  dolfin-convert test.msh test.xml
> >>
> >>the vertex with the corner points nr. 597, 1123 and 2045 is missing.
> >>
> >>can anyone reproduce that problem?
> >>
> >>cheers,
> >>
> >>Alex
> >>   
> >>
> >
> >I don't get any triangle with vertices (597, 1123, 2045) in test.msh:
> >
> >logg@gwaihir:~/tmp$ cat test.msh | grep 597 | grep 1123
> >logg@gwaihir:~/tmp$ 
> >
> >I have gmsh 1.61.3.
> >
> >Post your test.msh and I'll take a look when I get a chance.
> >
> >/Anders
> >
> >
> > 
> >
> >>Anders Logg wrote:
> >>
> >>   
> >>
> >>>On Fri, May 12, 2006 at 11:51:16AM +0000, Alexander Jarosch wrote:
> >>>
> >>>
> >>>     
> >>>
> >>>>Hello everybody,
> >>>>
> >>>>I try to do a non linear viscous Stokes problem and I use this ffc form 
> >>>>:
> >>>>
> >>>>elementE = FiniteElement("Vector Lagrange", "triangle", 1, 3)
> >>>>elementU = FiniteElement("Vector Lagrange", "triangle", 1)
> >>>>
> >>>>
> >>>>v = TestFunction(elementE)  # test function
> >>>>e = TrialFunction(elementE)  # strain (to be computed)
> >>>>u = Function(elementU)       # displacement
> >>>>
> >>>>def normal_strain(u): # eps_xx    eps_yy             eps_xy
> >>>>return [u[0].dx(0), u[1].dx(1), 0.5*(u[0].dx(1) + u[1].dx(0))]
> >>>>
> >>>>a = dot(v, e)*dx
> >>>>L = dot(v, normal_strain(u))*dx
> >>>>
> >>>>to get my strain rates from the velocity field coming out of the stokes 
> >>>>problem. Than use these strain rates to calculate new viscosities and 
> >>>>iterate the stokes problem until I converge to a non linear fluid. But 
> >>>>somehow the approach is not stable and the strain rates seems to go 
> >>>>wrong already after the initial stokes solution.
> >>>>
> >>>>Did anybody try something similar and maybe can give me some tips on 
> >>>>how to do a better approach?
> >>>>
> >>>>Thanks for any suggestions,
> >>>>
> >>>>Alex
> >>>> 
> >>>>
> >>>>       
> >>>>
> >>>There is a demo in src/demo/pde/elasticity/ for post-processing of
> >>>strain rates which computes both the normal and the shear strains.
> >>>Maybe you could compare with that demo to find out what goes wrong?
> >>>
> >>>Your variational problem looks ok and should compute the projection of
> >>>[u[0].dx(0), u[1].dx(1), 0.5*(u[0].dx(1) + u[1].dx(0))].
> >>>
> >>>Another thing you could experiment with is to project onto
> >>>discontinuous Lagrange. I think I remember I got unexpected results
> >>>when I experimented with something similar a while ago and projected
> >>>onto linears.
> >>>
> >>>/Anders
> >>>
> >>>_______________________________________________
> >>>DOLFIN-dev mailing list
> >>>DOLFIN-dev@xxxxxxxxxx
> >>>http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >>>
> >>>
> >>>
> >>>     
> >>>
> >>   
> >>
> >
> >_______________________________________________
> >DOLFIN-dev mailing list
> >DOLFIN-dev@xxxxxxxxxx
> >http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >
> > 
> >
> 
>