That's another hack that works... glad you found one ;-) If you are looking for a free visualizer that reads Exodus and handles Quad9... use Paraview: http://www.paraview.org
Derek On Jul 27, 2009, at 8:03 AM, Boyce Griffith wrote: > Hi, Derek -- > > Thanks for the explanation --- I hacked the Exodus II I/O to > increment all block numbers by 1 and it seems to work. (Next > problem is that VisIt doesn't seem to be able to handle QUAD9 > elements, but that's a problem for another mailing list...) > > Thanks, > > -- Boyce > > Derek Gaston wrote: >> The issue is that Exodus blocks start numbering at 1 instead of >> zero.... You can loop over the elements and set their subdomain ID >> to one to fix that error... But unfortunately you will probably run >> into the next problem which is that Exodus boundary IDs start at 1 >> as well... >> The real fix is not to use the internal mesh generation of >> libmesh... And instead read an exodus mesh in (which will have >> boundary ids and block ids starting at 1). >> I have a hacked up version of libmesh's mesh generators that forces >> them to start at 1 for numbering... But its just that: a hack. It >> won't be commited. What I have on my list to do is to turn ids of >> 0 to MAX_ID when output... That way the examples will work. If I >> get a minute I'll try to do that today. >> Sorry about the trouble. >> Derek >> Sent from my iPhone >> On Jul 27, 2009, at 5:37 AM, Boyce Griffith <[email protected]> >> wrote: >>> Hi, Folks -- >>> >>> I am trying to get libMesh to output to an Exodus II file. I am >>> using a >>> recent pull of the SVN version of libMesh so that I can use >>> libMesh with >>> PETSc 3.0.0. >>> >>> (By the way, I don't really care whether it is Exodus II or not >>> --- I am >>> just trying to output data in a format which can be read by the >>> VisIt >>> visualization tool.) >>> >>> I tried modifying ex3.C to change the I/O from GMV to ExodusII, >>> i.e., I >>> simply changed the I/O from: >>> >>> // After solving the system write the solution >>> // to a GMV-formatted plot file. >>> GMVIO (mesh).write_equation_systems ("out.gmv", equation_systems); >>> >>> to: >>> >>> // After solving the system write the solution >>> // to a Exodus II-formatted plot file. >>> ExodusII_IO (mesh).write("out.exd"); >>> >>> This compiles fine but I get the following error at run time: >>> >>> [ex_put_block] Error: element block id 0 already exists in file id >>> 13 >>> exerrval = -1 >>> Error writing element block. >>> [0] src/mesh/exodusII_io_helper.C, line 118, compiled Jul 27 2009 at >>> 12:09:26 >>> terminate called after throwing an instance of 'libMesh::LogicError' >>> what(): Error in libMesh internal logic >>> [griffith-macbook-pro:62440] *** Process received signal *** >>> [griffith-macbook-pro:62440] Signal: Abort trap (6) >>> [griffith-macbook-pro:62440] Signal code: (0) >>> [griffith-macbook-pro:62440] [ 0] 2 libSystem.B.dylib >>> 0x912762bb _sigtramp + 43 >>> [griffith-macbook-pro:62440] [ 1] 3 ??? >>> 0xffffffff 0x0 + 4294967295 >>> [griffith-macbook-pro:62440] [ 2] 4 libSystem.B.dylib >>> 0x912ea23a raise + 26 >>> [griffith-macbook-pro:62440] [ 3] 5 libSystem.B.dylib >>> 0x912f6679 abort + 73 >>> [griffith-macbook-pro:62440] [ 4] 6 libstdc++.6.dylib >>> 0x035b26ef _ZN9__gnu_cxx27__verbose_terminate_handlerEv + 335 >>> [griffith-macbook-pro:62440] [ 5] 7 libstdc++.6.dylib >>> 0x035b02a9 _ZSt14set_unexpectedPFvvE + 41 >>> [griffith-macbook-pro:62440] [ 6] 8 libstdc++.6.dylib >>> 0x035b02ec _ZSt9terminatev + 28 >>> [griffith-macbook-pro:62440] [ 7] 9 libstdc++.6.dylib >>> 0x035b03eb __cxa_throw + 107 >>> [griffith-macbook-pro:62440] [ 8] 10 libmesh.dylib >>> 0x0204bb03 _ZN18ExodusII_IO_Helper9check_errEiSs + 693 >>> [griffith-macbook-pro:62440] [ 9] 11 libmesh.dylib >>> 0x02050b76 _ZN18ExodusII_IO_Helper14write_elementsERK8MeshBase + >>> 786 >>> [griffith-macbook-pro:62440] [10] 12 libmesh.dylib >>> 0x02048021 _ZN11ExodusII_IO5writeERKSs + 953 >>> [griffith-macbook-pro:62440] [11] 13 ex3-dbg >>> 0x00002e06 main + 1353 >>> [griffith-macbook-pro:62440] [12] 14 ex3-dbg >>> 0x0000275e start + 54 >>> [griffith-macbook-pro:62440] *** End of error message *** >>> >>> I get similar errors if I try to do similar things in ex4. >>> >>> What do I need to do to output to this format? >>> >>> Thanks, >>> >>> -- Boyce >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> Libmesh-devel mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/libmesh-devel ------------------------------------------------------------------------------ _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
