[cig-commits] r18265 - in short/3D/PyLith/trunk: doc/releasenotes libsrc/faults libsrc/meshio libsrc/problems libsrc/topology unittests/libtests/bc unittests/libtests/faults unittests/libtests/feassemble
brad at geodynamics.org
brad at geodynamics.org
Thu Apr 21 09:34:02 PDT 2011
Author: brad
Date: 2011-04-21 09:34:01 -0700 (Thu, 21 Apr 2011)
New Revision: 18265
Modified:
short/3D/PyLith/trunk/doc/releasenotes/announce_v1.5.2.txt
short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveDyn.cc
short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveLagrange.cc
short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5.cc
short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5Ext.cc
short/3D/PyLith/trunk/libsrc/meshio/DataWriterVTK.cc
short/3D/PyLith/trunk/libsrc/problems/Solver.cc
short/3D/PyLith/trunk/libsrc/problems/SolverLinear.cc
short/3D/PyLith/trunk/libsrc/problems/SolverNonlinear.cc
short/3D/PyLith/trunk/libsrc/topology/Field.cc
short/3D/PyLith/trunk/libsrc/topology/Jacobian.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc
Log:
Merge from stable.
Modified: short/3D/PyLith/trunk/doc/releasenotes/announce_v1.5.2.txt
===================================================================
--- short/3D/PyLith/trunk/doc/releasenotes/announce_v1.5.2.txt 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/doc/releasenotes/announce_v1.5.2.txt 2011-04-21 16:34:01 UTC (rev 18265)
@@ -11,7 +11,7 @@
You can download the source code and binaries from
- http://geodynamics.org/cig/software/packages/short/pylith
+ http://www.geodynamics.org/cig/software/pylith
Detailed installation instructions are in the User Manual with example
installation procedures for a few platforms in the bundled doc/install
@@ -27,6 +27,10 @@
building PyLith from source will need to update FIAT, PETSc, and
spatialdata.
+ * Users of the Darwin 10.6 binary version must have /usr/bin/python
+ as the Python interpreter in their path. You can verify this using
+ 'which python'.
+
* Bug fixes
- Fixed setting of elastic constants in DruckerPrager3D and
Modified: short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveDyn.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveDyn.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -87,7 +87,7 @@
delete _jacobian; _jacobian = 0;
if (0 != _ksp) {
- PetscErrorCode err = KSPDestroy(_ksp); _ksp = 0;
+ PetscErrorCode err = KSPDestroy(&_ksp); _ksp = 0;
CHECK_PETSC_ERROR(err);
} // if
} // deallocate
Modified: short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveLagrange.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveLagrange.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/faults/FaultCohesiveLagrange.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -775,7 +775,7 @@
_logger->eventEnd(updateEvent);
#endif
} // for
- err = MatDestroy(jacobianNP); CHECK_PETSC_ERROR(err);
+ err = MatDestroy(&jacobianNP); CHECK_PETSC_ERROR(err);
#else // FULL PRECONDITIONER
@@ -2074,7 +2074,7 @@
err = MatGetSubMatrices(jacobianMatrix, 1, indicesIS,
indicesIS, MAT_INITIAL_MATRIX, subMat);
CHECK_PETSC_ERROR(err);
- err = ISDestroy(indicesIS[0]); CHECK_PETSC_ERROR(err);
+ err = ISDestroy(&indicesIS[0]); CHECK_PETSC_ERROR(err);
*jacobianSub = *subMat[0];
err = PetscObjectReference((PetscObject) *subMat[0]);
Modified: short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -46,7 +46,7 @@
pylith::meshio::DataWriterHDF5<mesh_type, field_type>::deallocate(void)
{ // deallocate
if (_viewer) {
- PetscErrorCode err = PetscViewerDestroy(_viewer); CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = PetscViewerDestroy(&_viewer); CHECK_PETSC_ERROR(err);
} // if
_viewer = 0;
} // deallocate
@@ -181,7 +181,7 @@
err = VecSetBlockSize(elemVec, numCorners); CHECK_PETSC_ERROR(err);
err = VecView(elemVec, _viewer); CHECK_PETSC_ERROR(err);
err = PetscViewerHDF5PopGroup(_viewer); CHECK_PETSC_ERROR(err);
- err = VecDestroy(elemVec); CHECK_PETSC_ERROR(err);
+ err = VecDestroy(&elemVec); CHECK_PETSC_ERROR(err);
delete[] tmpVertices; tmpVertices = 0;
} catch (const std::exception& err) {
std::ostringstream msg;
@@ -203,7 +203,7 @@
pylith::meshio::DataWriterHDF5<mesh_type,field_type>::close(void)
{ // close
if (_viewer) {
- PetscViewerDestroy(_viewer);
+ PetscViewerDestroy(&_viewer);
} // if
_viewer = 0;
_timesteps.clear();
Modified: short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5Ext.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5Ext.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/meshio/DataWriterHDF5Ext.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -53,7 +53,7 @@
d_iter != dEnd;
++d_iter)
if (d_iter->second.viewer) {
- PetscViewerDestroy(d_iter->second.viewer);
+ PetscViewerDestroy(&d_iter->second.viewer);
d_iter->second.viewer = 0;
} // if
} // deallocate
@@ -142,7 +142,7 @@
err = PetscViewerBinarySetSkipHeader(binaryViewer, PETSC_TRUE);
CHECK_PETSC_ERROR(err);
err = VecView(coordinatesVector, binaryViewer); CHECK_PETSC_ERROR(err);
- err = PetscViewerDestroy(binaryViewer); CHECK_PETSC_ERROR(err);
+ err = PetscViewerDestroy(&binaryViewer); CHECK_PETSC_ERROR(err);
binaryViewer = 0;
// Create external dataset for coordinates
@@ -221,9 +221,9 @@
err = PetscViewerBinarySetSkipHeader(binaryViewer, PETSC_TRUE);
CHECK_PETSC_ERROR(err);
err = VecView(elemVec, binaryViewer); CHECK_PETSC_ERROR(err);
- err = VecDestroy(elemVec); CHECK_PETSC_ERROR(err);
+ err = VecDestroy(&elemVec); CHECK_PETSC_ERROR(err);
err = PetscFree(tmpVertices); CHECK_PETSC_ERROR(err);
- err = PetscViewerDestroy(binaryViewer); CHECK_PETSC_ERROR(err);
+ err = PetscViewerDestroy(&binaryViewer); CHECK_PETSC_ERROR(err);
binaryViewer = 0;
// Create external dataset for cells
Modified: short/3D/PyLith/trunk/libsrc/meshio/DataWriterVTK.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/meshio/DataWriterVTK.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/meshio/DataWriterVTK.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -68,7 +68,7 @@
pylith::meshio::DataWriterVTK<mesh_type, field_type>::deallocate(void)
{ // deallocate
if (0 != _viewer)
- PetscViewerDestroy(_viewer);
+ PetscViewerDestroy(&_viewer);
_viewer = 0;
} // deallocate
@@ -165,7 +165,7 @@
void
pylith::meshio::DataWriterVTK<mesh_type,field_type>::closeTimeStep(void)
{ // closeTimeStep
- PetscViewerDestroy(_viewer); _viewer = 0;
+ PetscViewerDestroy(&_viewer); _viewer = 0;
_wroteVertexHeader = false;
_wroteCellHeader = false;
} // closeTimeStep
Modified: short/3D/PyLith/trunk/libsrc/problems/Solver.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/problems/Solver.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/problems/Solver.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -86,12 +86,10 @@
_formulation = 0; // Handle only, do not manage memory.
delete _logger; _logger = 0;
if (0 != _jacobianPC) {
- PetscErrorCode err = MatDestroy(_jacobianPC); _jacobianPC = 0;
- CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = MatDestroy(&_jacobianPC);CHECK_PETSC_ERROR(err);
} // if
if (0 != _jacobianPCFault) {
- PetscErrorCode err = MatDestroy(_jacobianPCFault); _jacobianPCFault = 0;
- CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = MatDestroy(&_jacobianPCFault);CHECK_PETSC_ERROR(err);
} // if
} // deallocate
@@ -177,8 +175,7 @@
assert(!lagrangeGlobalOrder.isNull());
if (_jacobianPCFault) {
- err = MatDestroy(_jacobianPCFault); _jacobianPCFault = 0;
- CHECK_PETSC_ERROR(err);
+ err = MatDestroy(&_jacobianPCFault); CHECK_PETSC_ERROR(err);
} // if
PetscInt nrows = lagrangeGlobalOrder->getLocalSize();
PetscInt ncols = nrows;
Modified: short/3D/PyLith/trunk/libsrc/problems/SolverLinear.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/problems/SolverLinear.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/problems/SolverLinear.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -55,7 +55,7 @@
Solver::deallocate();
if (0 != _ksp) {
- PetscErrorCode err = KSPDestroy(_ksp); _ksp = 0;
+ PetscErrorCode err = KSPDestroy(&_ksp); _ksp = 0;
CHECK_PETSC_ERROR(err);
} // if
} // deallocate
@@ -75,7 +75,7 @@
PetscErrorCode err = 0;
if (0 != _ksp) {
- err = KSPDestroy(_ksp); _ksp = 0;
+ err = KSPDestroy(&_ksp); _ksp = 0;
CHECK_PETSC_ERROR(err);
} // if
err = KSPCreate(fields.mesh().comm(), &_ksp); CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/problems/SolverNonlinear.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/problems/SolverNonlinear.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/problems/SolverNonlinear.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -83,7 +83,7 @@
Solver::deallocate();
if (0 != _snes) {
- PetscErrorCode err = SNESDestroy(_snes); _snes = 0;
+ PetscErrorCode err = SNESDestroy(&_snes); _snes = 0;
CHECK_PETSC_ERROR(err);
} // if
} // deallocate
@@ -103,7 +103,7 @@
PetscErrorCode err = 0;
if (0 != _snes) {
- err = SNESDestroy(_snes); _snes = 0;
+ err = SNESDestroy(&_snes); _snes = 0;
CHECK_PETSC_ERROR(err);
} // if
err = SNESCreate(fields.mesh().comm(), &_snes); CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/topology/Field.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/topology/Field.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/topology/Field.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -76,18 +76,15 @@
s_iter != scattersEnd;
++s_iter) {
if (s_iter->second.vector) {
- err = VecDestroy(s_iter->second.vector); s_iter->second.vector = 0;
- CHECK_PETSC_ERROR(err);
+ err = VecDestroy(&s_iter->second.vector);CHECK_PETSC_ERROR(err);
} // if
if (s_iter->second.scatter) {
- err = VecScatterDestroy(s_iter->second.scatter); s_iter->second.scatter = 0;
- CHECK_PETSC_ERROR(err);
+ err = VecScatterDestroy(&s_iter->second.scatter);CHECK_PETSC_ERROR(err);
} // if
if (s_iter->second.scatterVec) {
- err = VecDestroy(s_iter->second.scatterVec); s_iter->second.scatterVec = 0;
- CHECK_PETSC_ERROR(err);
+ err = VecDestroy(&s_iter->second.scatterVec);CHECK_PETSC_ERROR(err);
} // if
} // for
} // deallocate
Modified: short/3D/PyLith/trunk/libsrc/topology/Jacobian.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/topology/Jacobian.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/libsrc/topology/Jacobian.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -91,7 +91,7 @@
pylith::topology::Jacobian::deallocate(void)
{ // deallocate
if (0 != _matrix) {
- PetscErrorCode err = MatDestroy(_matrix); _matrix = 0;
+ PetscErrorCode err = MatDestroy(&_matrix); _matrix = 0;
CHECK_PETSC_ERROR(err);
} // if
} // deallocate
@@ -175,7 +175,7 @@
CHECK_PETSC_ERROR(err);
err = MatView(_matrix, viewer); CHECK_PETSC_ERROR(err);
- err = PetscViewerDestroy(viewer); CHECK_PETSC_ERROR(err);
+ err = PetscViewerDestroy(&viewer); CHECK_PETSC_ERROR(err);
} // write
// ----------------------------------------------------------------------
@@ -227,8 +227,8 @@
isSymmetric = false;
} // if
} // for
- MatDestroy(matDense);
- MatDestroy(matSparseAIJ);
+ MatDestroy(&matDense);
+ MatDestroy(&matSparseAIJ);
if (!isSymmetric)
throw std::runtime_error("Jacobian matrix is not symmetric.");
} // verifySymmetry
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -278,8 +278,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -417,8 +417,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valE, vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
CPPUNIT_ASSERT_EQUAL(false, fault.needNewJacobian());
} // testIntegrateJacobian
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -309,8 +309,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -224,8 +224,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -306,8 +306,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -306,8 +306,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -243,8 +243,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc 2011-04-21 16:01:04 UTC (rev 18264)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc 2011-04-21 16:34:01 UTC (rev 18265)
@@ -184,8 +184,8 @@
else
CPPUNIT_ASSERT_DOUBLES_EQUAL(valsE[index], vals[index], tolerance);
} // for
- MatDestroy(jDense);
- MatDestroy(jSparseAIJ);
+ MatDestroy(&jDense);
+ MatDestroy(&jSparseAIJ);
} // testIntegrateJacobian
// ----------------------------------------------------------------------
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