[Nek5000-users] n2to3 mesh size error

Tue Nov 14 10:30:05 CST 2017

Thanks a lot Marco!

On Tue, Nov 14, 2017 at 11:27 AM <nek5000-users at lists.mcs.anl.gov> wrote:

> It works for 2D and 3D meshes. Sideset ids should be set in the package
> you use to create the mesh. Then in the subroutine usrdat (inside the *.usr
> file), you will have to loop over the faces of each element and set the
> boundary conditions:
>
>       do i=1,nelt
>         do j=1,2*ndim
>           !write(6,*) bc(5,j,i,1)
>           if(bc(5,j,i,1).eq.1) then
>             cbc(j,i,1)='mv '
>             !write(6,*) 'mv bc'
>           elseif(bc(5,j,i,1).eq.2) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.3) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.4) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.5) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.6) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.7) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.8) then
>             cbc(j,i,1)='W  '
>           elseif(bc(5,j,i,1).eq.9) then
>             cbc(j,i,1)='W  '
>           else
>             cbc(j,i,1)='E  '
>           endif
>         enddo
>       enddo
>
> The installation of the exo2nek script is not that complicated if you
> follow the instructions in the README file.
>
> Marco
>
>
> On Nov 14, 2017, at 10:15 AM, nek5000-users at lists.mcs.anl.gov wrote:
>
> Does exo2nek support 3D conversion? Also, someone should consider updating
> the README for the exo2nek tools. Its not quite clear for someone who is
> starting out with nek5000, what exactly sideset ids are and how fluidic bcs
> are actually assigned. I will however give it a go.
>
> Thanks for your help everyone.
>
> On Tue, Nov 14, 2017 at 9:39 AM <nek5000-users at lists.mcs.anl.gov> wrote:
>
>> can you generate the same mesh in a exodus format? If you can, use the
>> exo2nek script to convert the mesh in a re2 file.
>>
>> Marco
>>
>> On Nov 14, 2017, at 9:36 AM, nek5000-users at lists.mcs.anl.gov wrote:
>>
>> Note, this converter is not part of Nek5000 and not support by us. Yes
>> this converter does not output the correct BC.
>>
>> On 14 Nov 2017, at 08:13, "nek5000-users at lists.mcs.anl.gov" <
>> nek5000-users at lists.mcs.anl.gov> wrote:
>>
>> So your mesh has more than 1000 elements. I think that the way the python
>> script is written the boundary conditions in a rea file is not correct. I
>> had this issue in the past.
>>
>> On Nov 14, 2017, at 9:02 AM, nek5000-users at lists.mcs.anl.gov wrote:
>>
>> Its a 25X25 square grid in 2D. Im trying to extrude this with 10 elements
>> in the z direction.
>>
>> On Tue, Nov 14, 2017 at 8:13 AM <nek5000-users at lists.mcs.anl.gov> wrote:
>>
>>> What is the number of elements in your mesh?
>>>
>>> On Nov 13, 2017, at 11:40 PM, nek5000-users at lists.mcs.anl.gov wrote:
>>>
>>> Gmsh to .rea using CPraveen's python mesh converter.
>>>
>>> On Mon, Nov 13, 2017, 10:52 PM <nek5000-users at lists.mcs.anl.gov> wrote:
>>>
>>>> Looks like the boundary conditions in your .rea file are somehow messed
>>>> up. How do you generate you .rea?
>>>>
>>>> -----Original message-----
>>>> > From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov
>>>> >
>>>> > Sent: Tuesday 14th November 2017 4:47
>>>> > To: nek5000-users at lists.mcs.anl.gov
>>>> > Subject: [Nek5000-users] n2to3 mesh size error
>>>> >
>>>> > Hi all,
>>>> >
>>>> > I keep running into an error whenever I want to use n2to3 to extrude
>>>> my mesh from 2 dimensions to 3. My workflow is as follows:
>>>> >
>>>> > gmsh .geo file -> gmsh .msh file -> .rea file -> n2to3 > .rea (3D)
>>>> file.
>>>> >
>>>> > Now if the original 2D .rea file obtained from gmsh contains less
>>>> than 1000 elements, n2to3 fails with the error
>>>> >
>>>> > At line 651 of file n2to3.f (unit = 10, file = msh_test.rea)
>>>> > Fortran runtime error: Bad value during integer read
>>>> >
>>>> > However, should this not be the case (mesh size > 1000) its all
>>>> smooth sailing. The trouble is with a mesh of that size my processor and
>>>> memory requirements quickly blow up.
>>>> >
>>>> > Incidentally, genmap fails under almost exactly the same conditions.
>>>> >
>>>> > Is there a lower limit to mesh size issue for nek5000 that Im missing
>>>> here?
>>>> >
>>>> > Sincerely,
>>>> > --
>>>> > Amitvikram Dutta
>>>> > Graduate Research Assistant
>>>> > Fluid Mechanics Research Lab
>>>> > University of Waterloo
>>>> > _______________________________________________
>>>> > Nek5000-users mailing list
>>>> > Nek5000-users at lists.mcs.anl.gov
>>>> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>> _______________________________________________
>>>> Nek5000-users mailing list
>>>> Nek5000-users at lists.mcs.anl.gov
>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>>
>>> --
>>>
>>> *Amitvikram Dutta*
>>>
>>> Graduate Research Assistant
>>>
>>> Fluid Mechanics Research Lab
>>>
>>> University of Waterloo
>>> _______________________________________________
>>> Nek5000-users mailing list
>>> Nek5000-users at lists.mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>
>>>
>>> _______________________________________________
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>>> Nek5000-users at lists.mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>
>> --
>>
>> *Amitvikram Dutta*
>>
>> Graduate Research Assistant
>>
>> Fluid Mechanics Research Lab
>>
>> University of Waterloo
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>
>>
>> _______________________________________________
>>
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>>
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>> Nek5000-users at lists.mcs.anl.gov
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>>
> --
>
> *Amitvikram Dutta*
>
> Graduate Research Assistant
>
> Fluid Mechanics Research Lab
>
> University of Waterloo
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
>
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
-- 

*Amitvikram Dutta*

Graduate Research Assistant

Fluid Mechanics Research Lab

University of Waterloo
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