Re: [petsc-dev] DMPlex + Cohesive Cells Setup

Wed, 02 Sep 2020 10:45:13 -0700

I’m getting an argument out of bounds error (attached) but I suspect it’s because I’m feeding in bad input to either calls (I am marking __all__ vertices in the mesh in my input label to DMPlexLabelCohesiveComplete). Are the cohesive grains allowed to intersect? Does a cohesive region have to be closed? Does it have to be entirely enclosed by the mesh, i.e. not touching any of the boundaries?

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)
Cell: (312) 694-3391
[0]PETSC ERROR: --------------------- Error Message 
--------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: Cone point 2146435072 is not in the valid range [0, 7771)
[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for 
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.13.4-873-g0490b72f82  GIT 
Date: 2020-08-31 18:21:33 +0000
[0]PETSC ERROR: ./cohes_create on a arch-darwin-c-debug named 
Jacobs-MBP.fios-router.home by jacobfaibussowitsch Wed Sep  2 13:37:46 2020
[0]PETSC ERROR: Configure options 
--DATAFILESPATH=/Users/jacobfaibussowitsch/NoSync/datafiles --with-blaslapack 
--with-chaco-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-ctetgen-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-debugger=lldb --with-debugging=1 
--with-exodusii-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages --with-gmp 
--with-hdf5-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-med-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-metis-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages --with-mpfr 
--with-mpi-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-mumps-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-netcdf-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-parmetis-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-pnetcdf-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-python-dir=/usr/local/opt/python/libexec/bin 
--with-scalapack-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-triangle-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages 
--with-zlib-dir=/Users/jacobfaibussowitsch/NoSync/petscpackages --with-zstd 
PETSC_ARCH=arch-darwin-c-debug
[0]PETSC ERROR: #1 DMPlexSetCone() line 1971 in 
/Users/jacobfaibussowitsch/NoSync/petsc/src/dm/impls/plex/plex.c
[0]PETSC ERROR: #2 DMPlexConstructCohesiveCells_Internal() line 1389 in 
/Users/jacobfaibussowitsch/NoSync/petsc/src/dm/impls/plex/plexsubmesh.c
[0]PETSC ERROR: #3 DMPlexConstructCohesiveCells() line 1647 in 
/Users/jacobfaibussowitsch/NoSync/petsc/src/dm/impls/plex/plexsubmesh.c
[0]PETSC ERROR: #4 main() line 34 in 
/Users/jacobfaibussowitsch/NoSync/warp3d/meshes/cohes_create.c
[0]PETSC ERROR: No PETSc Option Table entries
[0]PETSC ERROR: ----------------End of Error Message -------send entire error 
message to [email protected]

On Sep 2, 2020, at 09:28, Matthew Knepley <[email protected]> wrote:

On Mon, Aug 31, 2020 at 5:39 PM Jacob Faibussowitsch <[email protected]> wrote:
Hello All,

What is the simplest possible configuration required to insert cohesive cells into a plex? Plex/tests/ex5.c would be the example to ape here but there is a lot there that I don’t (think) I need like a DS or any kind of physics. For now, I am essentially looking to:

1. Read the mesh
2. Perform some mesh analysis
3. Slap some cohesive cells along one/multiple areas identified in the previous step (maybe even everywhere?)
4. Save the new mesh

This doesn’t even have to parallel. 

You can try it out easily. If it does not give you what you want, we can fix that up.

with the cohesive cells inserted. For input, you need a suitable label.

with a label marking vertices on an internal surface and creates the label needed by the call above.

Let me know if that works.

  Thanks,

     Matt
 
Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)
Cell: (312) 694-3391



--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener


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