[CIG-SHORT] RuntimeError: Error occurred while adjusting topology to create cohesive cells for fault

[Charles Williams]

Dear Marcelo,

The screen shot does not seem to show a simply connected domain.  If your fault consists of multiple segments that are not connected, each one must be represented as a separate fault.

As Brad said, the mesh quality does not appear suitable for a PyLith simulation.

Cheers,
Charles


On 6/03/2014, at 5:13 am, Brad Aagaard <baagaard at usgs.gov> wrote:

> Marcelo,
> 
> The main part of the error message is
> 
> RuntimeError: Error occurred while adjusting topology to create cohesive cells for fault 'FAULT_SEISMO'.
> Fault surface not a single connected component.
> 
> This means that PyLith did not find the fault surface to be a simply connected domain. In other words, the fault appears be made up of multiple patches that are not connected. If you think the fault is simply connected, then there may be problems with the topology, such as coincident nodes.
> 
> Based on the snapshot you included, I am not sure your mesh will be suitable for what appears to be a subduction zone problem. The element size seems quite heterogeneous with some large cells near the fault. It looks like you may also have some significantly distorted cells in the mesh too. You should use the quality improvement routines within Tetgen and/or CUBIT to improve the mesh quality. In CUBIT, we prefer the condition number smoothing and try to keep the condition number less than 2.0.
> 
> Regards,
> Brad
> 
> 
> On 03/04/2014 08:15 PM, Marcelo Contreras Kohl wrote:
>> Hello,
>>        I have a strategy for create meshes from Tetgen and then import with
>> Cubit to obtain exodusII without warning/errors (attach screenshot). But in my
>> Pylith code I have the following error below.  Do you know the problem? do you
>> can help me with some idea?  (I’m running pylith-1.9 on mac )
>> 
>> best regards
>> Marcelo
>> Universidad de Concepción
>> Chile
>> 
>>   -- Counting vertices for fault 'FAULT_SEISMO'.
>>   >>
>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:125:_adjustTopology
>>   -- meshimporter(info)
>>   -- Adjusting topology for fault 'FAULT_SEISMO' with 6367 vertices.
>> Fatal error. Calling MPI_Abort() to abort PyLith application.
>> Traceback (most recent call last):
>>    File
>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
>> line 65, in onComputeNodes
>>      self.main(*args, **kwds)
>>    File
>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
>> line 103, in main
>>      mesh = self.mesher.create(self.problem.normalizer, interfaces)
>>    File
>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/topology/MeshImporter.py",
>> line 120, in create
>>      self._adjustTopology(mesh, faults)
>>    File
>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py",
>> line 127, in _adjustTopology
>>      interface.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
>> firstFaultCell)
>>    File
>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/faults/faults.py",
>> line 367, in adjustTopology
>>      def adjustTopology(self, *args): return
>> _faults.FaultCohesive_adjustTopology(self, *args)
>> RuntimeError: Error occurred while adjusting topology to create cohesive cells
>> for fault 'FAULT_SEISMO'.
>> Fault surface not a single connected component.
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>> /Users/marcont/pylith190/bin/nemesis: mpirun: exit 255
>> /Users/marcont/pylith190/bin/pylith: /Users/marcont/pylith190/bin/nemesis: exit 1
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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>> 
> 
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Charles A. Williams
Scientist
GNS Science
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C.Williams at gns.cri.nz