Hi,
I am running a quasi-static simulation using a power-law rheology and imposing slip on the fault. I am running into an error that says “Spatial database returned illegal value for physical properties.” I am using the same spatialdb files as in the set of hex8 samples. I attach the script I am using and the error log output is copy-pasted below:
thanks,
Alba
powerlaw_62.cfg (9.7 KB)
eduroam-169-233-246-98:Rheology_models absrp$ pylith powerlaw_62.cfg
./pylithapp.cfg:55:
– pyre.inventory(warning)
– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename <- ‘spatialdb/mat_elastic.spatialdb’
– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’
./pylithapp.cfg:55:
– pyre.inventory(warning)
– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename <- ‘spatialdb/mat_elastic.spatialdb’
– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’
./pylithapp.cfg:55:
– pyre.inventory(warning)
– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename <- ‘spatialdb/mat_elastic.spatialdb’
– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
– petsc(info)
– Initialized PETSc.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:103:main
– pylithapp(info)
– Running on 1 process(es).
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
– meshiocubit(info)
– Reading finite-element mesh
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:158:void pylith::meshio::MeshIOCubit::_readVertices(pylith::meshio::ExodusII &, scalar_array *, int *, int *) const
– meshiocubit(info)
– Reading 49919 vertices.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:217:void pylith::meshio::MeshIOCubit::_readCells(pylith::meshio::ExodusII &, int_array *, int_array *, int *, int *) const
– meshiocubit(info)
– Reading 255484 cells in 1 blocks.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:281:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Found 8 node sets.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_zpos’ with id 1 containing 11660 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_zneg’ with id 2 containing 1199 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_xpos’ with id 3 containing 493 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_xneg’ with id 4 containing 477 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_ypos’ with id 5 containing 577 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_yneg’ with id 6 containing 567 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘fault’ with id 7 containing 482 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘fault_edges’ with id 8 containing 43 nodes.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:93:preinitialize
– timedependent(info)
– Pre-initializing problem.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:360:_setupMaterials
– implicit(info)
– Pre-initializing materials.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:373:_setupMaterials
– implicit(info)
– Added elasticity integrator for material ‘Upper crust material’.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:389:_setupBC
– implicit(info)
– Pre-initializing boundary conditions.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC
– implicit(info)
– Added boundary condition ‘face_xpos’ as a constraint.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC
– implicit(info)
– Added boundary condition ‘face_xneg’ as a constraint.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC
– implicit(info)
– Added boundary condition ‘face_zneg’ as a constraint.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:425:_setupInterfaces
– implicit(info)
– Pre-initializing interior interfaces.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py:108:preinitialize
– faultcohesivekin(info)
– Pre-initializing fault ‘fault’.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:434:_setupInterfaces
– implicit(info)
– Added interface condition ‘fault’ as an integrator.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:162:preinitialize
– implicit(info)
– Pre-initializing output.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
– timedependent(info)
– Verifying compatibility of problem configuration.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:118:initialize
– timedependent(info)
– Initializing problem.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:466:_initialize
– implicit(info)
– Initializing integrators.
Fatal error. Calling MPI_Abort() to abort PyLith application.
Traceback (most recent call last):
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PetscApplication.py”, line 74, in onComputeNodes
self.main(*args, **kwds)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py”, line 128, in main
self.problem.initialize()
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py”, line 120, in initialize
self.formulation.initialize(self.dimension, self.normalizer)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Implicit.py”, line 121, in initialize
self._initialize(dimension, normalizer)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py”, line 470, in _initialize
integrator.initialize(totalTime, numTimeSteps, normalizer)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/ElasticityImplicit.py”, line 56, in initialize
ModuleElasticityImplicit.initialize(self, self.mesh())
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/feassemble.py”, line 359, in initialize
def initialize(self, *args): return _feassemble.IntegratorElasticity_initialize(self, *args)
RuntimeError: Spatial database returned illegal value for physical properties.
density: 2500
vp: 5291.5
vs: 3000
referenceStrainRate: 0
referenceStress: 0
powerLawExponent: 0
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: mpirun: exit 255
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/pylith: /Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: exit 1Hi,
I am running a quasistatic simulation using a power-law rheology and imposing slip on the fault. I am running into an error that says “Spatial database returned illegal value for physical properties.” I am using the same spatialdb files as in the set of hex8 samples. I attach the script I am using and the error log outputed is copy pasted below:
thanks,
Alba
eduroam-169-233-246-98:Rheology_models absrp$ pylith powerlaw_62.cfg
./pylithapp.cfg:55:
– pyre.inventory(warning)
– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename <- ‘spatialdb/mat_elastic.spatialdb’
– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’
./pylithapp.cfg:55:
– pyre.inventory(warning)
– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename <- ‘spatialdb/mat_elastic.spatialdb’
– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’
./pylithapp.cfg:55:
– pyre.inventory(warning)
– pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler.filename <- ‘spatialdb/mat_elastic.spatialdb’
– unknown component ‘pylithapp.timedependent.materials.powerlaw3d.compositedb.iohandler’
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
– petsc(info)
– Initialized PETSc.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:103:main
– pylithapp(info)
– Running on 1 process(es).
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
– meshiocubit(info)
– Reading finite-element mesh
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:158:void pylith::meshio::MeshIOCubit::_readVertices(pylith::meshio::ExodusII &, scalar_array *, int *, int *) const
– meshiocubit(info)
– Reading 49919 vertices.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:217:void pylith::meshio::MeshIOCubit::_readCells(pylith::meshio::ExodusII &, int_array *, int_array *, int *, int *) const
– meshiocubit(info)
– Reading 255484 cells in 1 blocks.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:281:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Found 8 node sets.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_zpos’ with id 1 containing 11660 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_zneg’ with id 2 containing 1199 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_xpos’ with id 3 containing 493 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_xneg’ with id 4 containing 477 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_ypos’ with id 5 containing 577 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘face_yneg’ with id 6 containing 567 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘fault’ with id 7 containing 482 nodes.
…/…/…/pylith-2.2.1/libsrc/pylith/meshio/MeshIOCubit.cc:309:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &)
– meshiocubit(info)
– Reading node set ‘fault_edges’ with id 8 containing 43 nodes.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:93:preinitialize
– timedependent(info)
– Pre-initializing problem.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:360:_setupMaterials
– implicit(info)
– Pre-initializing materials.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:373:_setupMaterials
– implicit(info)
– Added elasticity integrator for material ‘Upper crust material’.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:389:_setupBC
– implicit(info)
– Pre-initializing boundary conditions.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC
– implicit(info)
– Added boundary condition ‘face_xpos’ as a constraint.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC
– implicit(info)
– Added boundary condition ‘face_xneg’ as a constraint.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:405:_setupBC
– implicit(info)
– Added boundary condition ‘face_zneg’ as a constraint.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:425:_setupInterfaces
– implicit(info)
– Pre-initializing interior interfaces.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py:108:preinitialize
– faultcohesivekin(info)
– Pre-initializing fault ‘fault’.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:434:_setupInterfaces
– implicit(info)
– Added interface condition ‘fault’ as an integrator.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:162:preinitialize
– implicit(info)
– Pre-initializing output.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
– timedependent(info)
– Verifying compatibility of problem configuration.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:118:initialize
– timedependent(info)
– Initializing problem.
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py:466:_initialize
– implicit(info)
– Initializing integrators.
Fatal error. Calling MPI_Abort() to abort PyLith application.
Traceback (most recent call last):
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PetscApplication.py”, line 74, in onComputeNodes
self.main(*args, **kwds)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/apps/PyLithApp.py”, line 128, in main
self.problem.initialize()
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/TimeDependent.py”, line 120, in initialize
self.formulation.initialize(self.dimension, self.normalizer)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Implicit.py”, line 121, in initialize
self._initialize(dimension, normalizer)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/problems/Formulation.py”, line 470, in _initialize
integrator.initialize(totalTime, numTimeSteps, normalizer)
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/ElasticityImplicit.py”, line 56, in initialize
ModuleElasticityImplicit.initialize(self, self.mesh())
File “/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/lib/python2.7/site-packages/pylith/feassemble/feassemble.py”, line 359, in initialize
def initialize(self, *args): return _feassemble.IntegratorElasticity_initialize(self, *args)
RuntimeError: Spatial database returned illegal value for physical properties.
density: 2500
vp: 5291.5
vs: 3000
referenceStrainRate: 0
referenceStress: 0
powerLawExponent: 0
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: mpirun: exit 255
/Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/pylith: /Volumes/My Passport for Mac/pylith-2.2.1-darwin-10.11.6/bin/nemesis: exit 1