Dear Jianan,

deal.II does have some tools that can help you to incrementally build up 
complex meshes. These helper functions include 
GridGenerator::create_triangulation_with_removed_cells 
<https://www.dealii.org/8.5.0/doxygen/deal.II/namespaceGridGenerator.html#ada140ece81bf38a23e738e0e57f89e97>
 and 
GridGenerator::merge_triangulations 
<https://www.dealii.org/8.5.0/doxygen/deal.II/namespaceGridGenerator.html#a0dace8884c1510160d7b6cbb313523e9>,
 
as well as the transformation operations demonstrated in step-49 
<https://www.dealii.org/8.5.0/doxygen/deal.II/step_49.html>. The 
GridGenerator::subdivided_hyper_rectangle 
<https://www.dealii.org/8.5.0/doxygen/deal.II/namespaceGridGenerator.html#a0e245f7c5788b6dcfcf93279a67fdbbb>
 
function could also be useful in your case. So if your mesh is regular and 
you just want to remove some cells, then this is actually quite straight 
forward to achieve. If you have cylinders in the domain, its a little more 
tricky but also might be possible. At some point you may want to weight up 
the time cost between working out how to build a more complex mesh in 
deal.II itself versus using a mesh generator.

I hope that this helps you.

Kind regards,
Jean-Paul

On Tuesday, May 9, 2017 at 5:01:53 AM UTC+2, Jianan Zhang wrote:
>
> Hi all,
>
> I've been studying deal.ii for like a month and want to use it to 
> characterize discontinuities in a rectangular waveguide. So I am using 
> FE_Nedelec elements to solve the curl-curl equation:
>
> curl(mu^(-1)curl(E)) + (-omega^2*epsilon+j*omega*sigma)*E=0,
>
> with boundary conditions: n x E = 0, on waveguide walls
>                                      n x (curl(E)) + gamma*n x (n x E) = 
> U, on port 1 
>                                      n x (curl(E)) + gamma*n x (n x E) = 
> 0,  on port 2
> where U and gamma are known.
>
> I consider that the waveguide is loaded with an obstacle of PEC, so the 
> boundary conditions will be n x E = 0 on its surfaces and inside the 
> obstacle E is zero. Since we know E is zero inside the obstacle, we can 
> ignore the its existence when we do mesh generation.
>
> So basically the mesh we need is a block (hyper rectangle in 3D) 
> subtracted by some small blocks or cylinders. Has anyone done this before 
> and can provide any hints on how to generate this kind of mesh?
> According to the topic on "How do I create the mesh for my problem?" in 
> FAQ, it seems that creating it by hand is not feasible. or maybe I can 
> generate it using Gmsh (which I am going to look into)? 
>
> Thanks in advance.
>
> Jianan Zhang 
>
>

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