[cig-commits] r14848 - in short/3D/PyLith/branches/pylith-swig: . examples/3d/hex8 libsrc/faults libsrc/problems modulesrc/problems pylith/faults unittests/pytests/faults
brad at geodynamics.org
brad at geodynamics.org
Sat May 2 13:18:43 PDT 2009
Author: brad
Date: 2009-05-02 13:18:42 -0700 (Sat, 02 May 2009)
New Revision: 14848
Modified:
short/3D/PyLith/branches/pylith-swig/TODO
short/3D/PyLith/branches/pylith-swig/examples/3d/hex8/dislocation.cfg
short/3D/PyLith/branches/pylith-swig/libsrc/faults/BruneSlipFn.cc
short/3D/PyLith/branches/pylith-swig/libsrc/faults/ConstRateSlipFn.cc
short/3D/PyLith/branches/pylith-swig/libsrc/faults/FaultCohesiveKin.cc
short/3D/PyLith/branches/pylith-swig/libsrc/faults/LiuCosSlipFn.cc
short/3D/PyLith/branches/pylith-swig/libsrc/faults/StepSlipFn.cc
short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.cc
short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.hh
short/3D/PyLith/branches/pylith-swig/libsrc/problems/SolverNonlinear.cc
short/3D/PyLith/branches/pylith-swig/modulesrc/problems/Formulation.i
short/3D/PyLith/branches/pylith-swig/pylith/faults/Fault.py
short/3D/PyLith/branches/pylith-swig/pylith/faults/FaultCohesiveKin.py
short/3D/PyLith/branches/pylith-swig/unittests/pytests/faults/TestFaultCohesiveKin.py
Log:
Fixed bugs in field names for fault output.
Modified: short/3D/PyLith/branches/pylith-swig/TODO
===================================================================
--- short/3D/PyLith/branches/pylith-swig/TODO 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/TODO 2009-05-02 20:18:42 UTC (rev 14848)
@@ -141,6 +141,7 @@
material
db -> properties_db
no need to set Quadrature type
+ CellFilterAvg Mesh/SubMesh
-- Release (v1.4) --
Modified: short/3D/PyLith/branches/pylith-swig/examples/3d/hex8/dislocation.cfg
===================================================================
--- short/3D/PyLith/branches/pylith-swig/examples/3d/hex8/dislocation.cfg 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/examples/3d/hex8/dislocation.cfg 2009-05-02 20:18:42 UTC (rev 14848)
@@ -69,7 +69,6 @@
[pylithapp.timedependent.interfaces.fault]
label = 10
-quadrature = pylith.feassemble.quadrature.Quadrature2Din3D
quadrature.cell = pylith.feassemble.FIATLagrange
quadrature.cell.dimension = 2
mat_db.iohandler.filename = mat_elastic.spatialdb
@@ -97,11 +96,11 @@
# Give basename for VTK output of state variables.
[pylithapp.timedependent.materials.elastic.output]
-cell_filter = pylith.meshio.CellFilterAvg
+cell_filter = pylith.meshio.CellFilterAvgMesh
writer.filename = dislocation-statevars-elastic.vtk
[pylithapp.timedependent.materials.viscoelastic.output]
cell_info_fields = [density,mu,lambda,maxwell_time]
-cell_filter = pylith.meshio.CellFilterAvg
+cell_filter = pylith.meshio.CellFilterAvgMesh
writer.filename = dislocation-statevars-viscoelastic.vtk
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/faults/BruneSlipFn.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/faults/BruneSlipFn.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/faults/BruneSlipFn.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -81,7 +81,7 @@
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
- _parameters->add("final slip", "final slip");
+ _parameters->add("final slip", "final_slip");
topology::Field<topology::SubMesh>& finalSlip =
_parameters->get("final slip");
finalSlip.newSection(vertices, spaceDim);
@@ -91,7 +91,7 @@
const ALE::Obj<RealSection>& finalSlipSection = finalSlip.section();
assert(!finalSlipSection.isNull());
- _parameters->add("slip time", "slip time");
+ _parameters->add("slip time", "slip_time");
topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(finalSlipSection->getChart(), 1);
slipTime.allocate();
@@ -100,7 +100,7 @@
const ALE::Obj<RealSection>& slipTimeSection = slipTime.section();
assert(!slipTimeSection.isNull());
- _parameters->add("rise time", "rise time");
+ _parameters->add("rise time", "rise_time");
topology::Field<topology::SubMesh>& riseTime = _parameters->get("rise time");
riseTime.newSection(slipTime);
riseTime.allocate();
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/faults/ConstRateSlipFn.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/faults/ConstRateSlipFn.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/faults/ConstRateSlipFn.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -79,7 +79,7 @@
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
- _parameters->add("slip rate", "slip rate");
+ _parameters->add("slip rate", "slip_rate");
topology::Field<topology::SubMesh>& slipRate = _parameters->get("slip rate");
slipRate.newSection(vertices, spaceDim);
slipRate.allocate();
@@ -88,7 +88,7 @@
const ALE::Obj<RealSection>& slipRateSection = slipRate.section();
assert(!slipRateSection.isNull());
- _parameters->add("slip time", "slip time");
+ _parameters->add("slip time", "slip_time");
topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(slipRateSection->getChart(), 1);
slipTime.allocate();
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/faults/FaultCohesiveKin.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/faults/FaultCohesiveKin.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/faults/FaultCohesiveKin.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -681,6 +681,7 @@
_allocateBufferVectorField();
assert(0 != _bufferVectorField);
_bufferVectorField->copy(dirSection);
+ _bufferVectorField->label("strike_dir");
return *_bufferVectorField;
} else if (2 == cohesiveDim && 0 == strcasecmp("dip_dir", name)) {
@@ -692,6 +693,7 @@
_allocateBufferVectorField();
assert(0 != _bufferVectorField);
_bufferVectorField->copy(dirSection);
+ _bufferVectorField->label("dip_dir");
return *_bufferVectorField;
} else if (0 == strcasecmp("normal_dir", name)) {
@@ -706,6 +708,7 @@
_allocateBufferVectorField();
assert(0 != _bufferVectorField);
_bufferVectorField->copy(dirSection);
+ _bufferVectorField->label("normal_dir");
return *_bufferVectorField;
} else if (0 == strncasecmp("final_slip_X", name, slipStrLen)) {
@@ -726,7 +729,9 @@
const topology::Field<topology::Mesh>& solution = fields->solution();
_allocateBufferVectorField();
_calcTractionsChange(_bufferVectorField, solution);
-
+ _bufferVectorField->label("traction_change");
+ return *_bufferVectorField;
+
} else {
std::ostringstream msg;
msg << "Request for unknown vertex field '" << name
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/faults/LiuCosSlipFn.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/faults/LiuCosSlipFn.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/faults/LiuCosSlipFn.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -81,7 +81,7 @@
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
- _parameters->add("final slip", "final slip");
+ _parameters->add("final slip", "final_slip");
topology::Field<topology::SubMesh>& finalSlip =
_parameters->get("final slip");
finalSlip.newSection(vertices, spaceDim);
@@ -91,7 +91,7 @@
const ALE::Obj<RealSection>& finalSlipSection = finalSlip.section();
assert(!finalSlipSection.isNull());
- _parameters->add("slip time", "slip time");
+ _parameters->add("slip time", "slip_time");
topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(finalSlipSection->getChart(), 1);
slipTime.allocate();
@@ -100,7 +100,7 @@
const ALE::Obj<RealSection>& slipTimeSection = slipTime.section();
assert(!slipTimeSection.isNull());
- _parameters->add("rise time", "rise time");
+ _parameters->add("rise time", "rise_time");
topology::Field<topology::SubMesh>& riseTime = _parameters->get("rise time");
riseTime.newSection(slipTime);
riseTime.allocate();
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/faults/StepSlipFn.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/faults/StepSlipFn.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/faults/StepSlipFn.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -77,7 +77,7 @@
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
- _parameters->add("final slip", "final slip");
+ _parameters->add("final slip", "final_slip");
topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
finalSlip.newSection(vertices, spaceDim);
finalSlip.allocate();
@@ -86,7 +86,7 @@
const ALE::Obj<RealSection>& finalSlipSection = finalSlip.section();
assert(!finalSlipSection.isNull());
- _parameters->add("slip time", "slip time");
+ _parameters->add("slip time", "slip_time");
topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(finalSlipSection->getChart(), 1);
slipTime.allocate();
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -90,15 +90,15 @@
// ----------------------------------------------------------------------
// Reform system residual.
void
-pylith::problems::Formulation::reformResidual(const PetscVec tmpResidualVec,
- const PetscVec tmpSolveSolnVec)
+pylith::problems::Formulation::reformResidual(const PetscVec* tmpResidualVec,
+ const PetscVec* tmpSolveSolnVec)
{ // reformResidual
assert(0 != _fields);
// Update section view of field.
if (0 != tmpSolveSolnVec) {
topology::Field<topology::Mesh>& solveSoln = _fields->solveSoln();
- solveSoln.scatterVectorToSection(tmpSolveSolnVec);
+ solveSoln.scatterVectorToSection(*tmpSolveSolnVec);
} // if
// Set residual to zero.
@@ -131,20 +131,20 @@
// Update PETSc view of residual
if (0 != tmpResidualVec)
- residual.scatterSectionToVector(tmpResidualVec);
+ residual.scatterSectionToVector(*tmpResidualVec);
else
residual.scatterSectionToVector();
// TODO: Move this to SolverLinear
//residual *= -1.0;
if (0 != tmpResidualVec)
- VecScale(tmpResidualVec, -1.0);
+ VecScale(*tmpResidualVec, -1.0);
} // reformResidual
// ----------------------------------------------------------------------
// Reform system Jacobian.
void
-pylith::problems::Formulation::reformJacobian(const PetscVec tmpSolveSolnVec)
+pylith::problems::Formulation::reformJacobian(const PetscVec* tmpSolveSolnVec)
{ // reformJacobian
assert(0 != _jacobian);
assert(0 != _fields);
@@ -152,7 +152,7 @@
// Update section view of field.
if (0 != tmpSolveSolnVec) {
topology::Field<topology::Mesh>& solveSoln = _fields->solveSoln();
- solveSoln.scatterVectorToSection(tmpSolveSolnVec);
+ solveSoln.scatterVectorToSection(*tmpSolveSolnVec);
} // if
// Set residual to zero.
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.hh
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.hh 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/problems/Formulation.hh 2009-05-02 20:18:42 UTC (rev 14848)
@@ -85,14 +85,14 @@
* @param tmpResidualVec Temporary PETSc vector for residual.
* @param tmpSolveSolnVec Temporary PETSc vector for solution.
*/
- void reformResidual(const PetscVec tmpResidualVec =0,
- const PetscVec tmpSolveSolnVec =0);
+ void reformResidual(const PetscVec* tmpResidualVec =0,
+ const PetscVec* tmpSolveSolnVec =0);
/* Reform system Jacobian.
*
* @param tmpSolveSolnVec Temporary PETSc vector for solution.
*/
- void reformJacobian(const PetscVec tmpSolveSolnVec =0);
+ void reformJacobian(const PetscVec* tmpSolveSolnVec =0);
// PRIVATE MEMBERS //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/problems/SolverNonlinear.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/problems/SolverNonlinear.cc 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/problems/SolverNonlinear.cc 2009-05-02 20:18:42 UTC (rev 14848)
@@ -112,7 +112,7 @@
assert(0 != formulation);
// Reform residual
- formulation->reformResidual(tmpResidualVec, tmpSolutionVec);
+ formulation->reformResidual(&tmpResidualVec, &tmpSolutionVec);
return 0;
} // reformResidual
@@ -132,7 +132,7 @@
Formulation* formulation = (Formulation*) context;
assert(0 != formulation);
- formulation->reformJacobian(tmpSolutionVec);
+ formulation->reformJacobian(&tmpSolutionVec);
return 0;
} // reformJacobian
Modified: short/3D/PyLith/branches/pylith-swig/modulesrc/problems/Formulation.i
===================================================================
--- short/3D/PyLith/branches/pylith-swig/modulesrc/problems/Formulation.i 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/modulesrc/problems/Formulation.i 2009-05-02 20:18:42 UTC (rev 14848)
@@ -65,14 +65,14 @@
* @param tmpResidualVec Temporary PETSc vector for residual.
* @param tmpSolveSolnVec Temporary PETSc vector for solution.
*/
- void reformResidual(const PetscVec tmpResidualVec =0,
- const PetscVec tmpSolveSolnVec =0);
+ void reformResidual(const PetscVec* tmpResidualVec =0,
+ const PetscVec* tmpSolveSolnVec =0);
/* Reform system Jacobian.
*
* @param tmpSolveSolnVec Temporary PETSc vector for solution.
*/
- void reformJacobian(const PetscVec tmpSolveSolnVec =0);
+ void reformJacobian(const PetscVec* tmpSolveSolnVec =0);
}; // Formulation
Modified: short/3D/PyLith/branches/pylith-swig/pylith/faults/Fault.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/faults/Fault.py 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/pylith/faults/Fault.py 2009-05-02 20:18:42 UTC (rev 14848)
@@ -72,12 +72,12 @@
import pyre.inventory
- id = pyre.inventory.int("id", default=100)
- id.meta['tip'] = "Fault identifier (must be unique across all faults " \
+ matId = pyre.inventory.int("id", default=100)
+ matId.meta['tip'] = "Fault identifier (must be unique across all faults " \
"and materials)."
- label = pyre.inventory.str("label", default="")
- label.meta['tip'] = "Name of fault."
+ faultLabel = pyre.inventory.str("label", default="")
+ faultLabel.meta['tip'] = "Name of fault."
upDir = pyre.inventory.list("up_dir", default=[0, 0, 1],
validator=validateDir)
@@ -178,7 +178,7 @@
self._logger.eventBegin(logEvent)
self._info.log("Writing fault data.")
- #self.output.writeData(t+dt, fields)
+ self.output.writeData(t+dt, fields)
self._logger.eventEnd(logEvent)
return
@@ -218,8 +218,8 @@
self.upDir = map(float, self.inventory.upDir)
self.normalDir = map(float, self.inventory.normalDir)
self.matDB = self.inventory.matDB
- ModuleFault.id(self, self.inventory.id)
- ModuleFault.label(self, self.inventory.label)
+ ModuleFault.id(self, self.inventory.matId)
+ ModuleFault.label(self, self.inventory.faultLabel)
return
Modified: short/3D/PyLith/branches/pylith-swig/pylith/faults/FaultCohesiveKin.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/faults/FaultCohesiveKin.py 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/pylith/faults/FaultCohesiveKin.py 2009-05-02 20:18:42 UTC (rev 14848)
@@ -96,7 +96,7 @@
"""
Do pre-initialization setup.
"""
- self._info.log("Pre-initializing fault '%s'." % self.label)
+ self._info.log("Pre-initializing fault '%s'." % self.label())
FaultCohesive.preinitialize(self, mesh)
Integrator.preinitialize(self, mesh)
@@ -143,7 +143,7 @@
"""
logEvent = "%sinit" % self._loggingPrefix
self._logger.eventBegin(logEvent)
- self._info.log("Initializing fault '%s'." % self.label)
+ self._info.log("Initializing fault '%s'." % self.label())
Integrator.initialize(self, totalTime, numTimeSteps, normalizer)
Modified: short/3D/PyLith/branches/pylith-swig/unittests/pytests/faults/TestFaultCohesiveKin.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/unittests/pytests/faults/TestFaultCohesiveKin.py 2009-05-02 16:48:01 UTC (rev 14847)
+++ short/3D/PyLith/branches/pylith-swig/unittests/pytests/faults/TestFaultCohesiveKin.py 2009-05-02 20:18:42 UTC (rev 14848)
@@ -104,8 +104,8 @@
mesh = importer.read(normalizer, debug=False, interpolate=False)
fault = FaultCohesiveKin()
- fault.inventory.id = 10
- fault.inventory.label = "fault"
+ fault.inventory.matId = 10
+ fault.inventory.faultLabel = "fault"
fault._configure()
fault.adjustTopology(mesh)
@@ -322,8 +322,8 @@
fault = FaultCohesiveKin()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
- fault.inventory.id = 10
- fault.inventory.label = "fault"
+ fault.inventory.matId = 10
+ fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.normalDir = [1, 0, 0]
fault.inventory.quadrature = quadrature
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