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

[David Andrs]

> On Sep 22, 2024, at 07:26, Blaise Bourdin <bourdin at mcmaster.ca> wrote:
> 
> 
> 
>> On Sep 21, 2024, at 9:54 AM, neil liu <liufield at gmail.com <mailto: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.

I have not seen the concept of edge sets discussed in the official exodusII doc [1]. However, they have an enum called ex_entity_type which does have a EX_EDGE_SET [2] value :thinking: 
IDK, how much developed that is. I have not used this myself. Most codes I have seen just use SIDE/NODE sets… 
Just sharing something I recently spotted…

[1] https://urldefense.us/v3/__https://sandialabs.github.io/seacas-docs/exodusII-new.pdf__;!!G_uCfscf7eWS!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2ksU4efI$ 
[2] https://urldefense.us/v3/__https://sandialabs.github.io/seacas-docs/html/exodusII_8h.html*a1f649ed288d305ab55773ffd1d220490__;Iw!!G_uCfscf7eWS!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2PdimBKk$ 

—
David

> 
> Regards,
> Blaise
> 
>> 
>> Thanks,
>> 
>> Xiaodong 
>> 
>> On Fri, Sep 20, 2024 at 3:15 PM David Andrs <andrsd at gmail.com <mailto: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 <mailto: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!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2BOTP4BI$  <https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!fcN-KL0rs3WRHNRfT47zioS4djjyXM7OCr32LT2olmZHm3X1NIk-WMdU9-UR3rNotQSpINEm8NrcMtWTCFqKEg$> for trouble shooting.
>>>> [0]PETSC ERROR: Petsc Release Version 3.21.1, Apr 26, 2024
>>>> [0]PETSC ERROR: ./app on a arch-linux-c-opt named localhost.localdomain by xiaodongliu Fri Sep 20 09:36:16 2024
>>>> [0]PETSC ERROR: Configure options -download-mumps -download-scalapack --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --download-fblaslapack --download-mpich --with-scalar-type=complex --download-triangle --with-debugging=no --download-parmetis --download-metis -download-ptscotch --download-bison --download-hdf5 -download-mmg=/home/xiaodongliu/Documents/3rdPartyLib/d5c43d1bcefe598d51428f6a7fee10ec29478b79.tar.gz --download-ctetgen --download-pragmatic --download-eigen --download-netcdf=/home/xiaodongliu/Documents/3rdPartyLib/netcdf-c-4.9.2-p1.tar.gz --download-zlib --download-pnetcdf --download-exodusii
>>>> [0]PETSC ERROR: #1 ExodusGetCellType_Internal() at /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1470
>>>> [0]PETSC ERROR: #2 DMPlexCreateExodus() at /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1551
>>>> [0]PETSC ERROR: #3 DMPlexCreateExodusFromFile() at /home/xiaodongliu/Documents/petsc-with-docs-3.21.1/petsc-3.21.1/src/dm/impls/plex/plexexodusii.c:1390
>>>> 
>>>> Thanks a lot.
>>>> 
>>>> Xiaodong 
>>>> Compose:
>>>> Inquiry about reading an exodus II file from coreform Cubit
>>>> 
>>>> 
>>>> PETSc users list
>>>> 
>> <test.e>
> 
> — 
> Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1)
> Professor, Department of Mathematics & Statistics
> Hamilton Hall room 409A, McMaster University
> 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada 
> https://urldefense.us/v3/__https://www.math.mcmaster.ca/bourdin__;!!G_uCfscf7eWS!ZXJZphkaSn_4MhiE6JwD78s0zYdnwitEqgRtuh997d8-EpF-ebRBxfAqlqjCsPAyPs6UAv6MOex2EiOeyPQ$  | +1 (905) 525 9140 ext. 27243

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