[cig-commits] [commit] knepley/upgrade-petsc-interface: Setup topology::StratumIS interface to take arg to filter to cells only. New functionality NOT IMPLEMENTED. (70e98ee)

[cig_noreply at geodynamics.org]

Repository : ssh://geoshell/pylith

On branch  : knepley/upgrade-petsc-interface
Link       : https://github.com/geodynamics/pylith/compare/4829f3cf356e30c9c893222f879af32b1f73a245...70e98ee8a2f7a96f12d544487cc44287b37d1496

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

commit 70e98ee8a2f7a96f12d544487cc44287b37d1496
Author: Brad Aagaard <baagaard at usgs.gov>
Date:   Mon Nov 11 19:29:17 2013 -0800

    Setup topology::StratumIS interface to take arg to filter to cells only. New functionality NOT IMPLEMENTED.


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

70e98ee8a2f7a96f12d544487cc44287b37d1496
 libsrc/pylith/feassemble/IntegratorElasticity.cc |  8 +++-----
 libsrc/pylith/materials/Material.cc              |  2 +-
 libsrc/pylith/topology/Stratum.hh                |  3 ++-
 libsrc/pylith/topology/Stratum.icc               | 11 ++++++++---
 4 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/libsrc/pylith/feassemble/IntegratorElasticity.cc b/libsrc/pylith/feassemble/IntegratorElasticity.cc
index 3478fb8..78c9a62 100644
--- a/libsrc/pylith/feassemble/IntegratorElasticity.cc
+++ b/libsrc/pylith/feassemble/IntegratorElasticity.cc
@@ -114,7 +114,7 @@ pylith::feassemble::IntegratorElasticity::initialize(const topology::Mesh& mesh)
   // Setup index set for material.
   PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
   if (!_materialIS) {
-    delete _materialIS; _materialIS = new topology::StratumIS(dmMesh, "material-id", _material->id());assert(_materialIS);
+    delete _materialIS; _materialIS = new topology::StratumIS(dmMesh, "material-id", _material->id());assert(_materialIS); // :TODO: FIX THIS
   } // if
 
   // Compute geometry for quadrature operations.
@@ -261,21 +261,19 @@ pylith::feassemble::IntegratorElasticity::verifyConfiguration(const topology::Me
   } // if
 
   PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
-  topology::StratumIS materialIS(dmMesh, "material-id", _material->id());
+  topology::StratumIS materialIS(dmMesh, "material-id", _material->id()); // :TODO: FIX THIS
   const PetscInt* cells = materialIS.points();
   const PetscInt numCells = materialIS.size();
 
   const int numCorners = _quadrature->refGeometry().numCorners();
-  PetscInt cStart, cEnd, vStart, vEnd;
+  PetscInt vStart, vEnd;
   PetscErrorCode err;
 
-  err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);PYLITH_CHECK_ERROR(err);
   err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);PYLITH_CHECK_ERROR(err);
   for(PetscInt c = 0; c < numCells; ++c) {
     const PetscInt cell = cells[c];
     PetscInt cellNumCorners = 0, closureSize, *closure = NULL;
 
-    if ((cell < cStart) || (cell >= cEnd)) continue;
     err = DMPlexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);PYLITH_CHECK_ERROR(err);
     for (PetscInt cl = 0; cl < closureSize*2; cl += 2) {
       if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++cellNumCorners;
diff --git a/libsrc/pylith/materials/Material.cc b/libsrc/pylith/materials/Material.cc
index 4ea41a0..e5aee74 100644
--- a/libsrc/pylith/materials/Material.cc
+++ b/libsrc/pylith/materials/Material.cc
@@ -128,7 +128,7 @@ pylith::materials::Material::initialize(const topology::Mesh& mesh,
 
   // Get cells associated with material
   PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
-  delete _materialIS; _materialIS = new topology::StratumIS(dmMesh, "material-id", _id);assert(_materialIS);
+  delete _materialIS; _materialIS = new topology::StratumIS(dmMesh, "material-id", _id);assert(_materialIS); // :TODO: FIX THIS
   const PetscInt numCells = _materialIS->size();
   const PetscInt* cells = _materialIS->points();
 
diff --git a/libsrc/pylith/topology/Stratum.hh b/libsrc/pylith/topology/Stratum.hh
index 1f46d61..d9abd32 100644
--- a/libsrc/pylith/topology/Stratum.hh
+++ b/libsrc/pylith/topology/Stratum.hh
@@ -106,7 +106,8 @@ public :
    */
   StratumIS(const PetscDM dmMesh,
 	    const char* label,
-	    const int id);
+	    const int id,
+	    const bool includeOnlyCells =false);
 
   /// Default destructor.
   ~StratumIS(void);
diff --git a/libsrc/pylith/topology/Stratum.icc b/libsrc/pylith/topology/Stratum.icc
index 7dc912e..f8df592 100644
--- a/libsrc/pylith/topology/Stratum.icc
+++ b/libsrc/pylith/topology/Stratum.icc
@@ -87,13 +87,18 @@ pylith::topology::Stratum::size(void) const
 inline
 pylith::topology::StratumIS::StratumIS(const PetscDM dmMesh,
 				       const char* label,
-				       const int id)
+				       const int id,
+				       const bool includeOnlyCells)
 { // constructor
   assert(dmMesh);
   PetscErrorCode err;
   err = DMPlexGetStratumIS(dmMesh, label, id, &_indexSet);PYLITH_CHECK_ERROR(err);assert(_indexSet);
-  err = ISGetSize(_indexSet, &_size);PYLITH_CHECK_ERROR(err);assert(_size >= 0);
-  err = ISGetIndices(_indexSet, &_points);PYLITH_CHECK_ERROR(err);assert(!_size || _points);
+  if (!includeOnlyCells) {
+    err = ISGetSize(_indexSet, &_size);PYLITH_CHECK_ERROR(err);assert(_size >= 0);
+    err = ISGetIndices(_indexSet, &_points);PYLITH_CHECK_ERROR(err);assert(!_size || _points);
+  } else {
+    // :TODO: Matt add stuff here
+  } // if/else
 } // constructor
 
 // ----------------------------------------------------------------------