[petsc-users] Inquiry about reading an exodus II file from coreform Cubit

[neil liu]

Thanks a lot, Blaise. Yes. As you said, I have to define a  node set to
find the edges we are interested in for Exodus II file.


On Sun, Sep 22, 2024 at 9:26 AM Blaise Bourdin <bourdin at mcmaster.ca> wrote:

>
>
> On Sep 21, 2024, at 9:54 AM, neil liu <liufield at gmail.com> wrote:
>
> Caution: External email.
>
> Thanks a lot, David. That works.
> Then I tried another example from Cubit. The script is defined as follows,
>
> reset
> brick x 1
> mesh vol 1
> block 1 volume 1
> sideset 1 surface 1
> block 2 surface 1 #sides of these elements can now be referenced in a
> sideset
> block 2 element type quad
> sideset 2 curve 1
>
> Then the mesh was exported as a exodus file (attached), and imported into
> Petsc.
> Here, the code was stuck by the function, DMPlexCreateExodus().
> I think maybe this is due to block 1 is 3D while block 2 is 2D.
> But this seems necessary to define an edge using sideset.
>
>
>
> That is corrrect.
> As far as I understand, one of the few assumptions in dmplex is that
> “cells” have the same topological dimension
> Here sideset 1 and 2 have different dimensions.
> As far as I remember, exodusII does not have “Edge sets”, so your best bet
> would be to define a node set for curve 1.
>
> Regards,
> Blaise
>
>
> Thanks,
>
> Xiaodong
>
> On Fri, Sep 20, 2024 at 3:15 PM David Andrs <andrsd at gmail.com> wrote:
>
>> Before you export the mesh from Cubit, change the element type to
>> something like QUAD4. PETSc does not automatically remap SHELL elements to
>> QUADs.
>>
>> --
>> David
>>
>> On Fri, Sep 20, 2024 at 8:05 AM neil liu <liufield at gmail.com> wrote:
>>
>>> Dear Petsc developers and users,
>>>
>>> I am trying to read an exodus II file from coreform cubit, but without
>>> success,
>>> Then I used petsc's built-in exodus file,
>>> /share/petsc/datafiles/meshes/sevenside.exo.
>>> This file can be read by petsc successfully.
>>>
>>> And I did a test. This file, sevenside.exo, is imported into coreform
>>> Cubit, and then is saved as a new exodus file. This new exodus file can not
>>> be read by petsc successfully.
>>>
>>> [0]PETSC ERROR: Invalid argument
>>> [0]PETSC ERROR: Unrecognized element type SHELL
>>> [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!behGY_YKaZKejR7vV7vkVTAHTWR_Y1UTNxgJ-4rMSCrvsMTFm_QsFVjhbC6HhjoPQ4ThPerrFQAqNC0N2WoY9A$ 
>>> <https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!fcN-KL0rs3WRHNRfT47zioS4djjyXM7OCr32LT2olmZHm3X1NIk-WMdU9-UR3rNotQSpINEm8NrcMtWTCFqKEg$> for
>>> trouble shooting.
>>> [0]PETSC ERROR: Petsc Release Version 3.21.1, Apr 26, 2024
>>> [0]PETSC ERROR: ./app on a arch-linux-c-opt named localhost.localdomain
>>> by xiaodongliu Fri Sep 20 09:36:16 2024
>>> [0]PETSC ERROR: Configure options -download-mumps -download-scalapack
>>> --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --download-fblaslapack
>>> --download-mpich --with-scalar-type=complex --download-triangle
>>> --with-debugging=no --download-parmetis --download-metis -download-ptscotch
>>> --download-bison --download-hdf5
>>> -download-mmg=/home/xiaodongliu/Documents/3rdPartyLib/d5c43d1bcefe598d51428f6a7fee10ec29478b79.tar.gz
>>> --download-ctetgen --download-pragmatic --download-eigen
>>> --download-netcdf=/home/xiaodongliu/Documents/3rdPartyLib/netcdf-c-4.9.2-p1.tar.gz
>>> --download-zlib --download-pnetcdf --download-exodusii
>>> [0]PETSC ERROR: #1 ExodusGetCellType_Internal() at
>>> /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1470
>>> [0]PETSC ERROR: #2 DMPlexCreateExodus() at
>>> /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1551
>>> [0]PETSC ERROR: #3 DMPlexCreateExodusFromFile() at
>>> /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1390
>>>
>>> Thanks a lot.
>>>
>>> Xiaodong
>>> Compose:
>>> Inquiry about reading an exodus II file from coreform Cubit
>>> [image: Minimize][image: Pop-out][image: Close]
>>> PETSc users list
>>>
>> <test.e>
>
>
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