[CIG-SHORT] RuntimeError: Determinant of Jacobian
Charles Williams
willic3 at gmail.com
Mon May 5 22:05:48 PDT 2014
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> 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:142:<unknown>
> -- meshiocubit(info)
> -- Reading 2349 vertices.
> >> meshio/MeshIOCubit.cc:197:<unknown>
> -- meshiocubit(info)
> -- Reading 10395 cells in 3 blocks.
> >> meshio/MeshIOCubit.cc:257:<unknown>
> -- meshiocubit(info)
> -- Found 8 node sets.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'BOUNDARY_XM' with id 1 containing 177 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'BOUNDARY_XP' with id 2 containing 173 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'BOUNDARY_YM' with id 3 containing 168 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'BOUNDARY_YP' with id 4 containing 167 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'BOUNDARY_ZM' with id 5 containing 391 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'BOUNDARY_ZP' with id 6 containing 424 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'FAULT' with id 7 containing 140 nodes.
> >> meshio/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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20140506/8c0c3852/attachment-0001.html>
More information about the CIG-SHORT
mailing list