[cig-commits] [commit] knepley/upgrade-petsc-interface: Topology: Added optimizeClosure() to visitors - Creates a closure index associated with the DM only if one does not already exist (a9a1eb4)

[cig_noreply at geodynamics.org]

Repository : ssh://geoshell/pylith

On branch  : knepley/upgrade-petsc-interface
Link       : https://github.com/geodynamics/pylith/compare/0b9b0aaf3cbf745e5b76f3177a1ddddb5bf75fe7...5b37d1ea08e0a69bd51ffc02ad5050e32f819f3d

>---------------------------------------------------------------

commit a9a1eb44139677150c746c60dca6665e991ff671
Author: Matthew G. Knepley <knepley at gmail.com>
Date:   Mon Nov 25 19:44:47 2013 -0600

    Topology: Added optimizeClosure() to visitors
    - Creates a closure index associated with the DM only if one does not already exist


>---------------------------------------------------------------

a9a1eb44139677150c746c60dca6665e991ff671
 libsrc/pylith/topology/CoordsVisitor.hh  |  4 ++++
 libsrc/pylith/topology/CoordsVisitor.icc | 14 +++++++++++++-
 libsrc/pylith/topology/VisitorMesh.hh    |  4 ++++
 libsrc/pylith/topology/VisitorMesh.icc   | 14 +++++++++++++-
 4 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/libsrc/pylith/topology/CoordsVisitor.hh b/libsrc/pylith/topology/CoordsVisitor.hh
index e89c765..7136dd7 100644
--- a/libsrc/pylith/topology/CoordsVisitor.hh
+++ b/libsrc/pylith/topology/CoordsVisitor.hh
@@ -76,6 +76,10 @@ public :
    */
   PetscInt sectionOffset(const PetscInt point) const;
 
+  /** Optimize the closure operator by using extra storage.
+   */
+  void optimizeClosure();
+
   /** Get coordinates array associated with closure.
    *
    * @pre Must be followed by call to restoreClosure().
diff --git a/libsrc/pylith/topology/CoordsVisitor.icc b/libsrc/pylith/topology/CoordsVisitor.icc
index 1bd7898..3f9b13d 100644
--- a/libsrc/pylith/topology/CoordsVisitor.icc
+++ b/libsrc/pylith/topology/CoordsVisitor.icc
@@ -53,7 +53,6 @@ pylith::topology::CoordsVisitor::initialize(void)
   PetscInt       size;
   PetscErrorCode err;
   err = DMPlexGetCoordinateSection(_dm, &_section);PYLITH_CHECK_ERROR(err);assert(_section);
-  err = DMPlexCreateClosureIndex(_dm, _section);PYLITH_CHECK_ERROR(err);
   err = DMGetCoordinatesLocal(_dm, &_localVec);PYLITH_CHECK_ERROR(err);assert(_localVec);
   err = VecGetLocalSize(_localVec, &size);PYLITH_CHECK_ERROR(err);
   err = VecGetArray(_localVec, &_localArray);PYLITH_CHECK_ERROR(err);assert(!size || _localArray);
@@ -108,6 +107,19 @@ pylith::topology::CoordsVisitor::sectionOffset(const PetscInt point) const
 } // sectionOffset
 
 // ----------------------------------------------------------------------
+// Optimize the closure operation.
+inline
+void
+pylith::topology::CoordsVisitor::optimizeClosure()
+{ // optimizeClosure
+  PetscSection   clSection;
+  PetscErrorCode err;
+
+  err = PetscSectionGetClosureIndex(_section, (PetscObject) _dm, &clSection, NULL);PYLITH_CHECK_ERROR(err);
+  if (!clSection) {err = DMPlexCreateClosureIndex(_dm, _section);PYLITH_CHECK_ERROR(err);}
+} // optimizeClosure
+
+// ----------------------------------------------------------------------
 // Get coordinates array associated with closure.
 inline
 void
diff --git a/libsrc/pylith/topology/VisitorMesh.hh b/libsrc/pylith/topology/VisitorMesh.hh
index a86e2f0..c71c776 100644
--- a/libsrc/pylith/topology/VisitorMesh.hh
+++ b/libsrc/pylith/topology/VisitorMesh.hh
@@ -100,6 +100,10 @@ public :
    */
   PetscInt sectionOffset(const PetscInt point) const;
 
+  /** Optimize the closure operator by using extra storage.
+   */
+  void optimizeClosure();
+
   /** Get array of values associated with closure.
    *
    * @pre Must be followed by call to restoreClosure().
diff --git a/libsrc/pylith/topology/VisitorMesh.icc b/libsrc/pylith/topology/VisitorMesh.icc
index 2ee889f..429c319 100644
--- a/libsrc/pylith/topology/VisitorMesh.icc
+++ b/libsrc/pylith/topology/VisitorMesh.icc
@@ -59,7 +59,6 @@ pylith::topology::VecVisitorMesh::initialize(const Field& field)
   _localVec = field.localVector();assert(_localVec);
 
   PetscErrorCode err = VecGetArray(_localVec, &_localArray);PYLITH_CHECK_ERROR(err);
-  err = DMPlexCreateClosureIndex(_dm, _section);PYLITH_CHECK_ERROR(err);
 } // initialize
 
 // ----------------------------------------------------------------------
@@ -140,6 +139,19 @@ pylith::topology::VecVisitorMesh::sectionOffset(const PetscInt point) const
 } // sectionOffset
 
 // ----------------------------------------------------------------------
+// Optimize the closure operation.
+inline
+void
+pylith::topology::VecVisitorMesh::optimizeClosure()
+{ // optimizeClosure
+  PetscSection   clSection;
+  PetscErrorCode err;
+
+  err = PetscSectionGetClosureIndex(_section, (PetscObject) _dm, &clSection, NULL);PYLITH_CHECK_ERROR(err);
+  if (!clSection) {err = DMPlexCreateClosureIndex(_dm, _section);PYLITH_CHECK_ERROR(err);}
+} // optimizeClosure
+
+// ----------------------------------------------------------------------
 // Get coordinates array associated with closure.
 inline
 void