Added an option for --part-only-overlapping which produces an overlapping...

Added an option for --part-only-overlapping which produces an overlapping series of patches for post-processing purposes

library/LibUtilities/BasicUtils/MeshPartition.cpp

@@ -92,7 +92,8 @@ namespace Nektar
 
         }
 
-        void MeshPartition::PartitionMesh(int nParts, bool shared)
+        void MeshPartition::PartitionMesh(int nParts, bool shared,
+                                          bool overlapping)
         {
             ASSERTL0(m_meshElements.size() >= nParts,
                      "Too few elements for this many processes.");
@@ -103,7 +104,7 @@ namespace Nektar
                 WeightElements();
             }
             CreateGraph(m_mesh);
-            PartitionGraph(m_mesh, nParts, m_localPartition);
+            PartitionGraph(m_mesh, nParts, m_localPartition, overlapping);
         }
 
         void MeshPartition::WriteLocalPartition(LibUtilities::SessionReaderSharedPtr& pSession)
@@ -1067,7 +1068,8 @@ namespace Nektar
 
         void MeshPartition::PartitionGraph(BoostSubGraph& pGraph,
                                            int nParts,
-                                           std::vector<BoostSubGraph>& pLocalPartition)
+                                           std::vector<BoostSubGraph>& pLocalPartition,
+                                           bool overlapping)
         {
             int i;
             int nGraphVerts = boost::num_vertices(pGraph);
@@ -1075,6 +1077,7 @@ namespace Nektar
 
             // Convert boost graph into CSR format
             BoostVertexIterator    vertit, vertit_end;
+            BoostAdjacencyIterator adjvertit, adjvertit_end;
             Array<OneD, int> part(nGraphVerts,0);
 
             if (m_comm->GetRowComm()->TreatAsRankZero())
@@ -1082,7 +1085,6 @@ namespace Nektar
                 int acnt = 0;
                 int vcnt = 0;
                 int nWeight = nGraphVerts;
-                BoostAdjacencyIterator adjvertit, adjvertit_end;
                 Array<OneD, int> xadj(nGraphVerts+1,0);
                 Array<OneD, int> adjncy(2*nGraphEdges);
                 Array<OneD, int> vwgt(nWeight, 1);
@@ -1180,8 +1182,27 @@ namespace Nektar
                 pGraph[*vertit].partition = part[i];
                 boost::add_vertex(i, pLocalPartition[part[i]]);
             }
-        }
 
+            if(overlapping)
+            {
+                // 
+                for ( boost::tie(vertit, vertit_end) = boost::vertices(pGraph);
+                      vertit != vertit_end;
+                      ++vertit)
+                {
+                    for (boost::tie(adjvertit, adjvertit_end) = boost::adjacent_vertices(*vertit,pGraph);
+                         adjvertit != adjvertit_end; ++adjvertit)
+                    {
+                        if(part[*adjvertit] != part[*vertit])
+                        {
+                            boost::add_vertex(*adjvertit, pLocalPartition[part[*vertit]]);
+                            
+                        }
+                    }
+                }
+            }
+        }
+        
 
         void MeshPartition::CheckPartitions(int nParts, Array<OneD, int> &pPart)
         {

library/LibUtilities/BasicUtils/MeshPartition.h

@@ -66,7 +66,7 @@ namespace Nektar
             LIB_UTILITIES_EXPORT MeshPartition(const SessionReaderSharedPtr& pSession);
             LIB_UTILITIES_EXPORT virtual ~MeshPartition();
 
-            LIB_UTILITIES_EXPORT void PartitionMesh(int nParts, bool shared = false);
+            LIB_UTILITIES_EXPORT void PartitionMesh(int nParts, bool shared = false, bool overlapping = false);
             LIB_UTILITIES_EXPORT void WriteLocalPartition(
                     SessionReaderSharedPtr& pSession);
             LIB_UTILITIES_EXPORT void WriteAllPartitions(
@@ -213,7 +213,8 @@ namespace Nektar
             void CreateGraph(BoostSubGraph& pGraph);
             void PartitionGraph(BoostSubGraph& pGraph,
                                 int nParts,
-                                std::vector<BoostSubGraph>& pLocalPartition);
+                                std::vector<BoostSubGraph>& pLocalPartition,
+                                bool overlapping = false);
 
             virtual void PartitionGraphImpl(
                     int&                              nVerts,

library/LibUtilities/BasicUtils/SessionReader.cpp

@@ -338,6 +338,8 @@ namespace Nektar
                                  "number of slices in Z-dir")
                 ("part-only",    po::value<int>(),
                                  "only partition mesh into N partitions.")
+                ("part-only-overlapping",    po::value<int>(),
+                                 "only partition mesh into N overlapping partitions.")
                 ("part-info",    "Output partition information")
             ;
 
@@ -1600,7 +1602,8 @@ namespace Nektar
             // Mesh has not been partitioned so do partitioning if required.
             // Note in the serial case nothing is done as we have already loaded
             // the mesh.
-            if (DefinesCmdLineArgument("part-only"))
+            if (DefinesCmdLineArgument("part-only")||
+                DefinesCmdLineArgument("part-only-overlapping"))
             {
                 // Perform partitioning of the mesh only. For this we insist
                 // the code is run in serial (parallel execution is pointless).
@@ -1608,12 +1611,21 @@ namespace Nektar
                         "The 'part-only' option should be used in serial.");
 
                 // Number of partitions is specified by the parameter.
-                int nParts = GetCmdLineArgument<int>("part-only");
+                int nParts; 
                 SessionReaderSharedPtr vSession     = GetSharedThisPtr();
                 MeshPartitionSharedPtr vPartitioner =
                         GetMeshPartitionFactory().CreateInstance(
                                             vPartitionerName, vSession);
-                vPartitioner->PartitionMesh(nParts, true);
+                if(DefinesCmdLineArgument("part-only"))
+                {
+                    nParts = GetCmdLineArgument<int>("part-only");
+                    vPartitioner->PartitionMesh(nParts, true);
+                }
+                else  
+                {
+                    nParts = GetCmdLineArgument<int>("part-only-overlapping");
+                    vPartitioner->PartitionMesh(nParts, true, true);
+                }
                 vPartitioner->WriteAllPartitions(vSession);
                 vPartitioner->GetCompositeOrdering(m_compOrder);
                 vPartitioner->GetBndRegionOrdering(m_bndRegOrder);