Re: [deal.II] Can GridIn read 3D quad mesh?

2018-09-19 Thread Jean-Paul Pelteret 
> Hi Shawn,


> Thank you for your help! I'd love to provide the mesh. Please let me know 
> whether the attached one would work.

You’re welcome. This second mesh is perfect. I’ll let you know when I’ve 
submitted a patch that allows this grid to be read in.

> For the boundary coloring - could you please elaborate on what that means? I 
> wasn't aware that ABAQUS has such a coloring feature but it could be me not 
> knowing this though.

This means assigning some boundary ID’s (in all of the documentation we call it 
“colouring”). Cubit allows one to do this, but I don’t know about ABAQUS itself 
(I would have thought it would be possible). I’ll try to modify the input file 
you supplied, which should be possible since the geometry is simple enough.

Best,
Jean-Paul

> 
> On Tue, Sep 18, 2018 at 10:57 PM Jean-Paul Pelteret  > wrote:
> Dear Shawn,
> 
> The GridIn::read_abaqus() function is currently not equipped to deal with the 
> codimension 1 case. I might be able to find some time to look at this in the 
> next few days though. In addition to the mesh file that you’ve already given 
> us, may you please construct and give us a fully structured grid in 
> codimension 1 (so something like a rectangle warped in the third dimension) 
> that also has some boundary colouring? That would help a great deal with 
> implementing this feature, and would also ensure that the assignment of 
> boundary ID’s is possible.
> 
> Best,
> Jean-Paul
> 
>> On 19 Sep 2018, at 01:38, Yuxiang Wang > > wrote:
>> 
>> Prof. Bangerth,
>> 
>> Thank you for the prompt response! Yes please find attached the minimal 
>> program. The main body is pretty short (see below), modified from step-49. 
>> Please let me know if you cannot reproduce it!
>> 
>> ```
>> int main ()
>> {
>>   Triangulation<2, 3> triangulation;
>> 
>>   GridIn<2, 3> gridin;
>>   gridin.attach_triangulation(triangulation);
>>   std::ifstream f("mesh.inp");
>>   gridin.read_abaqus(f);
>> 
>>   GridOut gridout;
>>   std::ofstream fout("mesh.vtu");
>>   gridout.write_vtu(triangulation, fout);
>> }
>> 
>> ```
>> 
>> 
>> Shawn
>> 
>> On Tue, Sep 18, 2018 at 4:28 PM Wolfgang Bangerth > > wrote:
>> On 09/18/2018 03:18 PM, Yuxiang Wang wrote:
>> > 
>> > Thank you for the pointer! I changed my code as you suggested and it 
>> > finished 
>> > running.
>> 
>> Great!
>> 
>> 
>> > However, when I opened the output file (mesh.vtu), the 3D mesh was 
>> > projected 
>> > to a 2D plane of z=0, and lost its 3D features. Was that expected behavior?
>> 
>> No. Are you saying that if you read a mesh, then immediately output it 
>> again, 
>> that the z-coordinate is lost? If that's correct, then that's a bug and it 
>> would be nice to have a small program and input file that demonstrates this.
>> 
>> Best
>>   W.
>> 
>> -- 
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu 
>> 
>> www: http://www.math.colostate.edu/~bangerth/ 
>> 
>> 
>> -- 
>> The deal.II project is located at http://www.dealii.org/ 
>> 
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>> 
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>> 
>> 
>> -- 
>> Yuxiang "Shawn" Wang, PhD
>> yw...@virginia.edu 
>> +1 (434) 284-0836
>> 
>> -- 
>> The deal.II project is located at http://www.dealii.org/ 
>> 
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>> 
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>> .
>> http://step-49.cc/>>
> 
> 
> -- 
> The deal.II project is located at http://www.dealii.org/ 
> 
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>

Re: [deal.II] Can GridIn read 3D quad mesh?

2018-09-19 Thread Yuxiang Wang 
Hi Jean-Paul,

Thank you for your help! I'd love to provide the mesh. Please let me know
whether the attached one would work.

For the boundary coloring - could you please elaborate on what that means?
I wasn't aware that ABAQUS has such a coloring feature but it could be me
not knowing this though.

[image: image.png]

Best,
Shawn

On Tue, Sep 18, 2018 at 10:57 PM Jean-Paul Pelteret 
wrote:

> Dear Shawn,
>
> The GridIn::read_abaqus() function is currently not equipped to deal with
> the codimension 1 case. I might be able to find some time to look at this
> in the next few days though. In addition to the mesh file that you’ve
> already given us, may you please construct and give us a fully structured
> grid in codimension 1 (so something like a rectangle warped in the third
> dimension) that also has some boundary colouring? That would help a great
> deal with implementing this feature, and would also ensure that the
> assignment of boundary ID’s is possible.
>
> Best,
> Jean-Paul
>
> On 19 Sep 2018, at 01:38, Yuxiang Wang 
> wrote:
>
> Prof. Bangerth,
>
> Thank you for the prompt response! Yes please find attached the minimal
> program. The main body is pretty short (see below), modified from step-49.
> Please let me know if you cannot reproduce it!
>
> ```
> int main ()
> {
>   Triangulation<2, 3> triangulation;
>
>   GridIn<2, 3> gridin;
>   gridin.attach_triangulation(triangulation);
>   std::ifstream f("mesh.inp");
>   gridin.read_abaqus(f);
>
>   GridOut gridout;
>   std::ofstream fout("mesh.vtu");
>   gridout.write_vtu(triangulation, fout);
> }
>
> ```
>
>
> Shawn
>
> On Tue, Sep 18, 2018 at 4:28 PM Wolfgang Bangerth 
> wrote:
>
>> On 09/18/2018 03:18 PM, Yuxiang Wang wrote:
>> >
>> > Thank you for the pointer! I changed my code as you suggested and it
>> finished
>> > running.
>>
>> Great!
>>
>>
>> > However, when I opened the output file (mesh.vtu), the 3D mesh was
>> projected
>> > to a 2D plane of z=0, and lost its 3D features. Was that expected
>> behavior?
>>
>> No. Are you saying that if you read a mesh, then immediately output it
>> again,
>> that the z-coordinate is lost? If that's correct, then that's a bug and it
>>
>> would be nice to have a small program and input file that demonstrates
>> this.
>>
>> Best
>>   W.
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
>> ---
>> You received this message because you are subscribed to a topic in the
>> Google Groups "deal.II User Group" group.
>> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/dealii/Erk7pxwTEj4/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> dealii+unsubscr...@googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
> --
> Yuxiang "Shawn" Wang, PhD
> yw...@virginia.edu
> +1 (434) 284-0836
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> 
>
>
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-- 
Yuxiang "Shawn" Wang, PhD
yw...@virginia.edu
+1 (434) 284-0836

-- 
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Job-1.inp
Description: Binary data

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-19 Thread Sambit Das 
Hi Daniel,

The third issue is fixed in https://github.com/dealii/dealii/pull/7213 
> 
> .

Thank you for creating the fix.


the first issue you observed is related to 
> https://gitlab.kitware.com/cmake/cmake/issues/17538.
> In particular, the MPI include directories might not be set correctly for 
> the CUDA compiler.
> This often happens when the CMAKE_CXX_COMPILER does not need additional 
> include directories to
> compiler MPI code, e.g. if the CMAKE_CXX_COMPILER is a MPI wrapper.

Ah, I see. 

Best,
Sambit
On Wednesday, September 19, 2018 at 4:36:46 AM UTC-5, Daniel Arndt wrote:
>
> Sambit,
>
> the first issue you observed is related to 
> https://gitlab.kitware.com/cmake/cmake/issues/17538.
> In particular, the MPI include directories might not be set correctly for 
> the CUDA compiler.
> This often happens when the CMAKE_CXX_COMPILER does not need additional 
> include directories to
> compiler MPI code, e.g. if the CMAKE_CXX_COMPILER is a MPI wrapper.
>
> The third issue is fixed in https://github.com/dealii/dealii/pull/7213.
>
> Best,
> Daniel
>

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Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-19 Thread Daniel Arndt 
Sambit,

the first issue you observed is related to 
https://gitlab.kitware.com/cmake/cmake/issues/17538.
In particular, the MPI include directories might not be set correctly for 
the CUDA compiler.
This often happens when the CMAKE_CXX_COMPILER does not need additional 
include directories to
compiler MPI code, e.g. if the CMAKE_CXX_COMPILER is a MPI wrapper.

The third issue is fixed in https://github.com/dealii/dealii/pull/7213.

Best,
Daniel

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