[cig-commits] r20750 - in short/3D/PyLith/branches/v1.7-stable/libsrc/pylith: faults feassemble materials meshio problems topology
brad at geodynamics.org
brad at geodynamics.org
Thu Sep 20 09:42:15 PDT 2012
Author: brad
Date: 2012-09-20 09:42:15 -0700 (Thu, 20 Sep 2012)
New Revision: 20750
Modified:
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesive.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveDyn.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveLagrange.hh
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.hh
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticity.hh
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticityLgDeform.hh
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/ElasticMaterial.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/Material.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5Ext.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterVTK.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.hh
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/OutputSolnPoints.hh
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Explicit.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Implicit.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.cc
short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.hh
Log:
Small code cleanup, mostly checking completeness of deallocate().
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesive.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesive.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesive.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -56,6 +56,7 @@
pylith::faults::FaultCohesive::deallocate(void)
{ // deallocate
Fault::deallocate();
+ feassemble::Integrator<feassemble::Quadrature<topology::SubMesh> >::deallocate();
delete _fields; _fields = 0;
} // deallocate
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveDyn.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveDyn.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -91,10 +91,7 @@
_friction = 0; // :TODO: Use shared pointer
delete _jacobian; _jacobian = 0;
- if (_ksp) {
- PetscErrorCode err = KSPDestroy(&_ksp); _ksp = 0;
- CHECK_PETSC_ERROR(err);
- } // if
+ PetscErrorCode err = KSPDestroy(&_ksp);CHECK_PETSC_ERROR(err);
} // deallocate
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveLagrange.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveLagrange.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/faults/FaultCohesiveLagrange.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -278,16 +278,6 @@
const topology::Jacobian& jacobian,
const topology::SolutionFields& fields);
- // PROTECTED MEMBERS //////////////////////////////////////////////////
-protected :
-
- /// Array of cohesive vertex information.
- std::vector<CohesiveInfo> _cohesiveVertices;
-
- /// Map label of cohesive cell to label of cells in fault mesh.
- std::map<topology::Mesh::SieveMesh::point_type,
- topology::SubMesh::SieveMesh::point_type> _cohesiveToFault;
-
// PRIVATE METHODS ////////////////////////////////////////////////////
private :
@@ -305,6 +295,16 @@
/// Calculate fault area field.
void _calcArea(void);
+ // PROTECTED MEMBERS //////////////////////////////////////////////////
+protected :
+
+ /// Array of cohesive vertex information.
+ std::vector<CohesiveInfo> _cohesiveVertices;
+
+ /// Map label of cohesive cell to label of cells in fault mesh.
+ std::map<topology::Mesh::SieveMesh::point_type,
+ topology::SubMesh::SieveMesh::point_type> _cohesiveToFault;
+
// NOT IMPLEMENTED ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -69,8 +69,7 @@
* See governing equations section of user manual for more
* information.
*/
-class pylith::feassemble::ElasticityExplicitLgDeform :
- public IntegratorElasticityLgDeform
+class pylith::feassemble::ElasticityExplicitLgDeform : public IntegratorElasticityLgDeform
{ // ElasticityExplicitLgDeform
friend class TestElasticityExplicitLgDeform; // unit testing
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticity.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticity.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticity.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -236,15 +236,6 @@
const int numBasis,
const int numQuadPts);
-// PROTECTED MEMBERS ////////////////////////////////////////////////////
-protected :
-
- /// Elastic material associated with integrator
- materials::ElasticMaterial* _material;
-
- /// Buffers for output.
- topology::Fields<topology::Field<topology::Mesh> >* _outputFields;
-
// PROTECTED TYPEDEFS ///////////////////////////////////////////////////
protected :
@@ -255,6 +246,15 @@
typedef pylith::topology::Field<pylith::topology::Mesh>::UpdateAddVisitor UpdateAddVisitor;
typedef ALE::ISieveVisitor::IndicesVisitor<RealSection,SieveMesh::order_type,PylithInt> IndicesVisitor;
+// PROTECTED MEMBERS ////////////////////////////////////////////////////
+protected :
+
+ /// Elastic material associated with integrator
+ materials::ElasticMaterial* _material;
+
+ /// Buffers for output.
+ topology::Fields<topology::Field<topology::Mesh> >* _outputFields;
+
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticityLgDeform.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticityLgDeform.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/feassemble/IntegratorElasticityLgDeform.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -35,8 +35,7 @@
* time integration of the elasticity equation for large rigid body
* rotations and small strains.
*/
-class pylith::feassemble::IntegratorElasticityLgDeform :
- public IntegratorElasticity
+class pylith::feassemble::IntegratorElasticityLgDeform : public IntegratorElasticity
{ // IntegratorElasticityLgDeform
friend class TestIntegratorElasticityLgDeform; // unit testing
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/ElasticMaterial.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/ElasticMaterial.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/ElasticMaterial.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -70,6 +70,7 @@
void
pylith::materials::ElasticMaterial::deallocate(void)
{ // deallocate
+ Material::deallocate();
delete _initialFields; _initialFields = 0;
_dbInitialStress = 0; // :TODO: Use shared pointer.
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/Material.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/Material.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/materials/Material.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -109,9 +109,8 @@
// ----------------------------------------------------------------------
// Get physical property parameters and initial state (if used) from database.
void
-pylith::materials::Material::initialize(
- const topology::Mesh& mesh,
- feassemble::Quadrature<topology::Mesh>* quadrature)
+pylith::materials::Material::initialize(const topology::Mesh& mesh,
+ feassemble::Quadrature<topology::Mesh>* quadrature)
{ // initialize
assert(0 != _dbProperties);
assert(0 != quadrature);
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -50,8 +50,9 @@
void
pylith::meshio::DataWriterHDF5<mesh_type, field_type>::deallocate(void)
{ // deallocate
+ DataWriter<mesh_type, field_type>::deallocate();
+
PetscErrorCode err = 0;
-
err = PetscViewerDestroy(&_viewer); CHECK_PETSC_ERROR(err);
err = VecDestroy(&_tstamp); CHECK_PETSC_ERROR(err);
} // deallocate
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5Ext.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5Ext.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterHDF5Ext.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -50,12 +50,14 @@
void
pylith::meshio::DataWriterHDF5Ext<mesh_type,field_type>::deallocate(void)
{ // deallocate
+ DataWriter<mesh_type, field_type>::deallocate();
+
+ PetscErrorCode err = 0;
const typename dataset_type::const_iterator& dEnd = _datasets.end();
for (typename dataset_type::iterator d_iter=_datasets.begin();
d_iter != dEnd;
++d_iter) {
- PetscErrorCode err = PetscViewerDestroy(&d_iter->second.viewer);
- CHECK_PETSC_ERROR(err);
+ err = PetscViewerDestroy(&d_iter->second.viewer);CHECK_PETSC_ERROR(err);
} // for
} // deallocate
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterVTK.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterVTK.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/DataWriterVTK.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -67,9 +67,10 @@
void
pylith::meshio::DataWriterVTK<mesh_type, field_type>::deallocate(void)
{ // deallocate
- if (0 != _viewer)
- PetscViewerDestroy(&_viewer);
- _viewer = 0;
+ DataWriter<mesh_type, field_type>::deallocate();
+
+ PetscErrorCode err = 0;
+ err = PetscViewerDestroy(&_viewer);CHECK_PETSC_ERROR(err);
} // deallocate
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -51,10 +51,18 @@
// Destructor
pylith::meshio::ExodusII::~ExodusII(void)
{ // destructor
- close();
+ deallocate();
} // destructor
// ----------------------------------------------------------------------
+// Deallocate data structures.
+void
+pylith::meshio::ExodusII::deallocate(void)
+{ // deallocate
+ close();
+} // deallocate
+
+// ----------------------------------------------------------------------
// Set filename.
void
pylith::meshio::ExodusII::filename(const char* name)
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/ExodusII.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -56,6 +56,9 @@
/// Destructor
~ExodusII(void);
+ /// Deallocate data structures.
+ void deallocate(void);
+
/** Set filename.
*
* @param filename Name of file
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/OutputSolnPoints.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/OutputSolnPoints.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/meshio/OutputSolnPoints.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -38,8 +38,7 @@
/** @brief C++ object for managing output of finite-element data over
* a subdomain.
*/
-class pylith::meshio::OutputSolnPoints :
- public OutputManager<topology::Mesh, topology::Field<topology::Mesh> >
+class pylith::meshio::OutputSolnPoints : public OutputManager<topology::Mesh, topology::Field<topology::Mesh> >
{ // OutputSolnPoints
friend class TestOutputSolnPoints; // unit testing
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Explicit.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Explicit.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Explicit.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -36,7 +36,6 @@
// Destructor
pylith::problems::Explicit::~Explicit(void)
{ // destructor
- deallocate();
} // destructor
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Implicit.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Implicit.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/problems/Implicit.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -36,7 +36,6 @@
// Destructor
pylith::problems::Implicit::~Implicit(void)
{ // destructor
- deallocate();
} // destructor
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.cc
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.cc 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.cc 2012-09-20 16:42:15 UTC (rev 20750)
@@ -45,9 +45,17 @@
// Destructor
pylith::topology::RefineUniform::~RefineUniform(void)
{ // destructor
+ deallocate();
} // destructor
// ----------------------------------------------------------------------
+// Deallocate data structures.
+void
+pylith::topology::RefineUniform::deallocate(void)
+{ // deallocate
+} // deallocate
+
+// ----------------------------------------------------------------------
// Refine mesh.
void
pylith::topology::RefineUniform::refine(Mesh* const newMesh,
Modified: short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.hh
===================================================================
--- short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.hh 2012-09-20 14:48:26 UTC (rev 20749)
+++ short/3D/PyLith/branches/v1.7-stable/libsrc/pylith/topology/RefineUniform.hh 2012-09-20 16:42:15 UTC (rev 20750)
@@ -43,6 +43,9 @@
/// Destructor
~RefineUniform(void);
+ /// Deallocate data structures.
+ void deallocate(void);
+
/** Refine mesh.
*
* @param newMesh Refined mesh (result).
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