[CIG-SHORT] RuntimeError: Determinant of Jacobian
Brad Aagaard
baagaard at usgs.gov
Thu May 22 19:46:12 PDT 2014
Changing mesh format and getting a negative Jacobian most likely means
the cell ordering if reversed. The magnitude of your Jacobian is large
and negative consistent with this.
Regards,
Brad
On 5/22/14, 7:47 PM, Marcelo Contreras wrote:
> Hi Charles,
>
> Now I have a working example and fixed with your suggestions
> (attached image) and now I have another error /using the same pylith
> problem and mesh/ but I wrote the mesh in gmv ascii format… following
> the example in ~/src/pylith/examples/3d/tet4/step03.cfg
>
> meshiolagrit = 1
> psetfile = 1
>
> [pylithapp.mesh_generator]
> reader = pylith.meshio.MeshIOLagrit
>
> [pylithapp.mesh_generator.reader]
> filename_gmv = subduccion_05.1.gmv
> filename_pset = subduccion_05.1.pset
>
>
> Now the error is :
>
> RuntimeError: Determinant of Jacobian (-4.7916e+15) for cell 0 is
> smaller than minimum permissible value (1e-06)!
> The two most likely causes of this are highly distorted cells and
> nondimensionalization with a length scale that is much larger than the
> dimensions of the cells.
>
>
> Do you know why I have this error with the same pylith problem and only
> changing the mesh format ? I need another instructions in my
> pylithapp.cfg? … for me is more simple write an ascii gmv mesh.
>
> best regards
> Marcelo.
>
>
>
>
> E 07-05-2014, a las 19:51, Charles Williams <willic3 at gmail.com
> <mailto:willic3 at gmail.com>> escribió:
>
>> I’m glad that was helpful. The error you’re getting now seems to
>> indicate that you have applied Dirichlet boundary conditions to a
>> fault node. You can fix this within Cubit by removing fault nodes
>> from the nodeset to which BC are being applied, or vice-versa.
>>
>> Good luck,
>> Charles
>>
>> p.s. In the future, could you please make sure your e-mails are also
>> sent to cig-short? Many users have these sorts of problems, and it
>> makes the information available to others.
>>
>>
>> On 8/05/2014, at 9:24 am, Marcelo Contreras <marcontk at gmail.com
>> <mailto:marcontk at gmail.com>> wrote:
>>
>>> Hi Charles,
>>>
>>> Perfect, your suggestions were great help. Now I have another error
>>> but I think can solve it …
>>>
>>> RuntimeError: Vertex with label '2885' on negative side of fault
>>> 'FAULT' is constrained.
>>> Fault vertices cannot be constrained.
>>>
>>> best regards
>>> Marcelo.
>>>
>>> El 06-05-2014, a las 17:18, Charles Williams <willic3 at gmail.com
>>> <mailto:willic3 at gmail.com>> escribió:
>>>
>>>> Hi Marcelo,
>>>>
>>>> The smallest Jacobian (1.5e-3) is pretty small, especially if you’re
>>>> still using the default normalization (1 km) for PyLith. It’s hard
>>>> to know how to improve your mesh quality without knowing how you
>>>> generated it. Also, what are the dimensions of your mesh? There
>>>> are many strategies for improving mesh quality, and I believe I
>>>> discussed one or two the other day on this list.
>>>>
>>>> I think you have two options at this point:
>>>>
>>>> 1. Improve the mesh quality in Cubit (look in the manual and on
>>>> this list for strategies).
>>>> 2. Change the default normalization in PyLith (this is described in
>>>> the PyLith manual).
>>>>
>>>> In either case, you should make sure your mesh is of sufficient
>>>> quality. I think the simplest (and probably most diagnostic) metric
>>>> to use is condition number. Ideally, you would like each cell to
>>>> have a condition number less than 2, but in some cases slightly
>>>> larger values can still work.
>>>>
>>>> Cheers,
>>>> Charles
>>>>
>>>>
>>>> On 7/05/2014, at 9:09 am, Marcelo Contreras <marcontk at gmail.com
>>>> <mailto:marcontk at gmail.com>> wrote:
>>>>
>>>>> Hi Charles,
>>>>>
>>>>> Ok, from cubit’s menu “validate the mesh <— metric :
>>>>> Jacobian” there isn't bad elements (attached figure). I tried
>>>>> with some comand to smooth the mesh but without success, in most
>>>>> cases some elements were eliminated. I don't know how should I do
>>>>> it. ¿Do you know?
>>>>>
>>>>> best regards
>>>>> Marcelo.
>>>>>
>>>>> <Captura de pantalla 2014-05-06 a la(s) 16.42.00.png>
>>>>>
>>>>>
>>>>> El 06-05-2014, a las 1:05, Charles Williams <willic3 at gmail.com
>>>>> <mailto:willic3 at gmail.com>> escribió:
>>>>>
>>>>>> Hi Marcelo,
>>>>>>
>>>>>> The first thing I would do is check the mesh quality in Cubit. It
>>>>>> seems likely you have at least one poorly-formed element. If you
>>>>>> do, you should try smoothing the mesh to improve the quality. Let
>>>>>> me know what happens.
>>>>>>
>>>>>> Cheers,
>>>>>> Charles
>>>>>>
>>>>>>
>>>>>> On 6/05/2014, at 4:38 pm, Marcelo Contreras <marcontk at gmail.com
>>>>>> <mailto:marcontk at gmail.com>> wrote:
>>>>>>
>>>>>>>
>>>>>>> Hi Charles,
>>>>>>>
>>>>>>> I’m following examples/3d/tet4 in the version 1.9. I
>>>>>>> generated a mesh like in attached figure and in pylith1.9 can’t
>>>>>>> fix de error :
>>>>>>>
>>>>>>> RuntimeError: Determinant of Jacobian (2.20698e-11) for cell 4857
>>>>>>> is smaller than minimum permissible value (1e-06)!
>>>>>>> The two most likely causes of this are highly distorted cells and
>>>>>>> nondimensionalization with a length scale that is much larger
>>>>>>> than the dimensions of the cells.
>>>>>>>
>>>>>>> ¿Do you know the problem? ¿How can I fix it? … I attached some
>>>>>>> files for give you more details.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> best regards
>>>>>>> Marcelo.
>>>>>>>
>>>>>>> <step03.cfg>
>>>>>>> <pylithapp.cfg>
>>>>>>> <falla_cortical_3d_07.1_02.exo>
>>>>>>>
>>>>>>> <Captura de pantalla 2014-05-06 a la(s) 0.20.30.png>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> marcont at OSXmate~/pylith190/modelos/test_viscoelastic: pylith
>>>>>>> step03.cfg
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
>>>>>>> -- petsc(info)
>>>>>>> -- Initialized PETSc.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:94:main
>>>>>>> -- pylithapp(debug)
>>>>>>> -- [0] CPU time: 0:01.14, Memory usage: 31.27 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading finite-element mesh
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:142:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading 2349 vertices.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:197:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading 10395 cells in 3 blocks.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:257:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Found 8 node sets.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'BOUNDARY_XM' with id 1 containing 177 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'BOUNDARY_XP' with id 2 containing 173 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'BOUNDARY_YM' with id 3 containing 168 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'BOUNDARY_YP' with id 4 containing 167 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'BOUNDARY_ZM' with id 5 containing 391 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'BOUNDARY_ZP' with id 6 containing 424 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'FAULT' with id 7 containing 140 nodes.
>>>>>>> >> meshio/MeshIOCubit.cc <http://meshiocubit.cc/>:285:<unknown>
>>>>>>> -- meshiocubit(info)
>>>>>>> -- Reading node set 'LIM_VISCOELAST' with id 8 containing 395 nodes.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/topology/MeshImporter.py:119:create
>>>>>>> -- meshimporter(info)
>>>>>>> -- Adjusting topology.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:115:_adjustTopology
>>>>>>> -- meshimporter(info)
>>>>>>> -- Counting vertices for fault 'FAULT'.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:125:_adjustTopology
>>>>>>> -- meshimporter(info)
>>>>>>> -- Adjusting topology for fault 'FAULT' with 140 vertices.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:106:main
>>>>>>> -- pylithapp(debug)
>>>>>>> -- [0] CPU time: 0:01.40, Memory usage: 39.05 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:92:preinitialize
>>>>>>> -- timedependent(info)
>>>>>>> -- Pre-initializing problem.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:390:_setupMaterials
>>>>>>> -- implicit(info)
>>>>>>> -- Pre-initializing materials.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:391:_setupMaterials
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.40, Memory usage: 39.12 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>>>>>>> -- fiatsimplex(info)
>>>>>>> -- Cell geometry:
>>>>>>> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig
>>>>>>> Object of type 'pylith::feassemble::GeometryTet3D *' at
>>>>>>> 0x1053a8480> >
>>>>>>> -- Vertices:
>>>>>>> -- [[-1. -1. -1.]
>>>>>>> [ 1. -1. -1.]
>>>>>>> [-1. 1. -1.]
>>>>>>> [-1. -1. 1.]]
>>>>>>> -- Quad pts:
>>>>>>> -- [[-0.5 -0.5 -0.5]]
>>>>>>> -- Quad wts:
>>>>>>> -- [ 1.33333333]
>>>>>>> -- Basis fns @ quad pts ):
>>>>>>> -- [[ 0.25 0.25 0.25 0.25]]
>>>>>>> -- Basis fn derivatives @ quad pts:
>>>>>>> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>>>>>>> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>>>>>>> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>>>>>>> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.48, Memory usage: 40.24 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>>>>>>> -- implicit(info)
>>>>>>> -- Added elasticity integrator for material 'ELASTICO1'.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>>>>>>> -- fiatsimplex(info)
>>>>>>> -- Cell geometry:
>>>>>>> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig
>>>>>>> Object of type 'pylith::feassemble::GeometryTet3D *' at
>>>>>>> 0x105950930> >
>>>>>>> -- Vertices:
>>>>>>> -- [[-1. -1. -1.]
>>>>>>> [ 1. -1. -1.]
>>>>>>> [-1. 1. -1.]
>>>>>>> [-1. -1. 1.]]
>>>>>>> -- Quad pts:
>>>>>>> -- [[-0.5 -0.5 -0.5]]
>>>>>>> -- Quad wts:
>>>>>>> -- [ 1.33333333]
>>>>>>> -- Basis fns @ quad pts ):
>>>>>>> -- [[ 0.25 0.25 0.25 0.25]]
>>>>>>> -- Basis fn derivatives @ quad pts:
>>>>>>> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>>>>>>> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>>>>>>> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>>>>>>> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.49, Memory usage: 40.25 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>>>>>>> -- implicit(info)
>>>>>>> -- Added elasticity integrator for material 'ELASTICO2'.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>>>>>>> -- fiatsimplex(info)
>>>>>>> -- Cell geometry:
>>>>>>> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig
>>>>>>> Object of type 'pylith::feassemble::GeometryTet3D *' at
>>>>>>> 0x105950b70> >
>>>>>>> -- Vertices:
>>>>>>> -- [[-1. -1. -1.]
>>>>>>> [ 1. -1. -1.]
>>>>>>> [-1. 1. -1.]
>>>>>>> [-1. -1. 1.]]
>>>>>>> -- Quad pts:
>>>>>>> -- [[-0.5 -0.5 -0.5]]
>>>>>>> -- Quad wts:
>>>>>>> -- [ 1.33333333]
>>>>>>> -- Basis fns @ quad pts ):
>>>>>>> -- [[ 0.25 0.25 0.25 0.25]]
>>>>>>> -- Basis fn derivatives @ quad pts:
>>>>>>> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>>>>>>> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>>>>>>> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>>>>>>> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.51, Memory usage: 40.28 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>>>>>>> -- implicit(info)
>>>>>>> -- Added elasticity integrator for material 'VISCOSO'.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:420:_setupBC
>>>>>>> -- implicit(info)
>>>>>>> -- Pre-initializing boundary conditions.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:421:_setupBC
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.51, Memory usage: 40.28 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:439:_setupBC
>>>>>>> -- implicit(info)
>>>>>>> -- Added boundary condition 'BOUNDARY_XP' as a constraint.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:439:_setupBC
>>>>>>> -- implicit(info)
>>>>>>> -- Added boundary condition 'BOUNDARY_XM' as a constraint.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:444:_setupBC
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.52, Memory usage: 40.29 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:459:_setupInterfaces
>>>>>>> -- implicit(info)
>>>>>>> -- Pre-initializing interior interfaces.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py:108:preinitialize
>>>>>>> -- faultcohesivekin(info)
>>>>>>> -- Pre-initializing fault 'FAULT'.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>>>>>>> -- fiatsimplex(info)
>>>>>>> -- Cell geometry:
>>>>>>> -- <pylith.feassemble.CellGeometry.GeometryTri3D; proxy of <Swig
>>>>>>> Object of type 'pylith::feassemble::GeometryTri3D *' at
>>>>>>> 0x105958810> >
>>>>>>> -- Vertices:
>>>>>>> -- [[-1. -1.]
>>>>>>> [ 1. -1.]
>>>>>>> [-1. 1.]]
>>>>>>> -- Quad pts:
>>>>>>> -- [[-1. -1.]
>>>>>>> [ 1. -1.]
>>>>>>> [-1. 1.]]
>>>>>>> -- Quad wts:
>>>>>>> -- [ 0.66666667 0.66666667 0.66666667]
>>>>>>> -- Basis fns @ quad pts ):
>>>>>>> -- [[ 1.00000000e+00 2.77555756e-17 0.00000000e+00]
>>>>>>> [ 2.77555756e-17 1.00000000e+00 0.00000000e+00]
>>>>>>> [ 5.55111512e-17 5.55111512e-17 1.00000000e+00]]
>>>>>>> -- Basis fn derivatives @ quad pts:
>>>>>>> -- [[[-0.5 -0.5]
>>>>>>> [ 0.5 0. ]
>>>>>>> [ 0. 0.5]]
>>>>>>>
>>>>>>> [[-0.5 -0.5]
>>>>>>> [ 0.5 0. ]
>>>>>>> [ 0. 0.5]]
>>>>>>>
>>>>>>> [[-0.5 -0.5]
>>>>>>> [ 0.5 0. ]
>>>>>>> [ 0. 0.5]]]
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:468:_setupInterfaces
>>>>>>> -- implicit(info)
>>>>>>> -- Added interface condition 'FAULT' as an integrator.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:479:_setupInterfaces
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.53, Memory usage: 40.36 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:188:preinitialize
>>>>>>> -- implicit(info)
>>>>>>> -- Pre-initializing output.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:112:main
>>>>>>> -- pylithapp(debug)
>>>>>>> -- [0] CPU time: 0:01.54, Memory usage: 40.36 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
>>>>>>> -- timedependent(info)
>>>>>>> -- Verifying compatibility of problem configuration.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:117:initialize
>>>>>>> -- timedependent(info)
>>>>>>> -- Initializing problem.
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:497:_initialize
>>>>>>> -- implicit(debug)
>>>>>>> -- [0] CPU time: 0:01.55, Memory usage: 40.44 MB
>>>>>>> >>
>>>>>>> /Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py:500:_initialize
>>>>>>> -- implicit(info)
>>>>>>> -- Initializing integrators.
>>>>>>> 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 116, in main
>>>>>>> self.problem.initialize()
>>>>>>> File
>>>>>>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/TimeDependent.py",
>>>>>>> line 119, in initialize
>>>>>>> self.formulation.initialize(self.dimension, self.normalizer)
>>>>>>> File
>>>>>>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Implicit.py",
>>>>>>> line 127, in initialize
>>>>>>> self._initialize(dimension, normalizer)
>>>>>>> File
>>>>>>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/problems/Formulation.py",
>>>>>>> line 504, in _initialize
>>>>>>> integrator.initialize(totalTime, numTimeSteps, normalizer)
>>>>>>> File
>>>>>>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/feassemble/ElasticityImplicit.py",
>>>>>>> line 56, in initialize
>>>>>>> ModuleElasticityImplicit.initialize(self, self.mesh())
>>>>>>> File
>>>>>>> "/Users/marcont/pylith190/lib/python2.7/site-packages/pylith/feassemble/feassemble.py",
>>>>>>> line 420, in initialize
>>>>>>> def initialize(self, *args): return
>>>>>>> _feassemble.IntegratorElasticity_initialize(self, *args)
>>>>>>> RuntimeError: Determinant of Jacobian (2.20698e-11) for cell 4857
>>>>>>> is smaller than minimum permissible value (1e-06)!
>>>>>>> The two most likely causes of this are highly distorted cells and
>>>>>>> nondimensionalization with a length scale that is much larger
>>>>>>> than the dimensions of the cells.
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> Charles A. Williams
>>>>>> Scientist
>>>>>> GNS Science
>>>>>> 1 Fairway Drive, Avalon
>>>>>> PO Box 30368
>>>>>> Lower Hutt 5040
>>>>>> New Zealand
>>>>>> ph (office): 0064-4570-4566
>>>>>> fax (office): 0064-4570-4600
>>>>>> C.Williams at gns.cri.nz <mailto:C.Williams at gns.cri.nz>
>>>>>>
>>>>>
>>>>
>>>> Charles A. Williams
>>>> Scientist
>>>> GNS Science
>>>> 1 Fairway Drive, Avalon
>>>> PO Box 30368
>>>> Lower Hutt 5040
>>>> New Zealand
>>>> ph (office): 0064-4570-4566
>>>> fax (office): 0064-4570-4600
>>>> C.Williams at gns.cri.nz <mailto:C.Williams at gns.cri.nz>
>>>>
>>>
>>
>> Charles A. Williams
>> Scientist
>> GNS Science
>> 1 Fairway Drive, Avalon
>> PO Box 30368
>> Lower Hutt 5040
>> New Zealand
>> ph (office): 0064-4570-4566
>> fax (office): 0064-4570-4600
>> C.Williams at gns.cri.nz <mailto:C.Williams at gns.cri.nz>
>>
>
>
>
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