Thanks everyone for the responses. I found that the mesh created using the 
GUI of Gmsh was not working for me. But using the example.geo file from 
step-49, and using the above suggestions, it seems to be working.

Thanks

On Wednesday, 10 March 2021 at 21:50:03 UTC-5 Praveen C wrote:

> In your geo file, you can check orientation of boundary normals by adding
>
> Geometry.Normals = 100; // adjust 100 if needed
>
> Then check that all normals are pointing outward. If some surface has 
> opposite normal, then flip sign
>
> for example, if
>
> Line Loop(53) = {17, 18, -1, -16};
> Ruled Surface(54) = {53};
>
> this surface has wrong normal, define it as
>
> Ruled Surface(54) = {-53};
>
> I think fixing this orientation should fix your issue.
>
> best
> praveen
>
> On 09-Mar-2021, at 11:03 PM, krishan...@gmail.com <krishan...@gmail.com> 
> wrote:
>
>
> I am wondering what meshing software produces output files that would work 
> best with deal.ii. I have tried Gmsh, but it seems when this mesh 
> (generated by Gmsh) is imported in deal.ii, it is facing the issue of 
> negative volume fraction of a cell (could be because of the order of nodes 
> written in Gmsh?). Any suggestion about any other meshing software that 
> could be used which would avoid this issue?
>
> Thanks
>
>
>

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