ENH: have ptscotch

ptscotch - compiles into ptscotchDecomp. All thirdparty decompositionMethods
now moved out of decompositionMethods so add them explicitly to link line
for programs that need them (decomposePar, snappyHexMesh etc.)

src/parallel/decompose/decompositionMethods/decompositionMethod/decompositionMethod.C

@@ -28,6 +28,9 @@ InClass
 \*---------------------------------------------------------------------------*/
 
 #include "decompositionMethod.H"
+#include "globalIndex.H"
+#include "cyclicPolyPatch.H"
+#include "syncTools.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
@@ -156,6 +159,18 @@ Foam::labelList Foam::decompositionMethod::decompose
 }
 
 
+Foam::labelList Foam::decompositionMethod::decompose
+(
+    const labelListList& globalCellCells,
+    const pointField& cc
+)
+{
+    scalarField cWeights(0);
+
+    return decompose(globalCellCells, cc, cWeights);
+}
+
+
 void Foam::decompositionMethod::calcCellCells
 (
     const polyMesh& mesh,
@@ -201,15 +216,284 @@ void Foam::decompositionMethod::calcCellCells
 }
 
 
-Foam::labelList Foam::decompositionMethod::decompose
+void Foam::decompositionMethod::calcCSR
 (
-    const labelListList& globalCellCells,
-    const pointField& cc
+    const polyMesh& mesh,
+    List<int>& adjncy,
+    List<int>& xadj
 )
 {
-    scalarField cWeights(0);
+    // Make Metis CSR (Compressed Storage Format) storage
+    //   adjncy      : contains neighbours (= edges in graph)
+    //   xadj(celli) : start of information in adjncy for celli
 
-    return decompose(globalCellCells, cc, cWeights);
+    xadj.setSize(mesh.nCells()+1);
+
+    // Initialise the number of internal faces of the cells to twice the
+    // number of internal faces
+    label nInternalFaces = 2*mesh.nInternalFaces();
+
+    // Check the boundary for coupled patches and add to the number of
+    // internal faces
+    const polyBoundaryMesh& pbm = mesh.boundaryMesh();
+
+    forAll(pbm, patchi)
+    {
+        if (isA<cyclicPolyPatch>(pbm[patchi]))
+        {
+            nInternalFaces += pbm[patchi].size();
+        }
+    }
+
+    // Create the adjncy array the size of the total number of internal and
+    // coupled faces
+    adjncy.setSize(nInternalFaces);
+
+    // Fill in xadj
+    // ~~~~~~~~~~~~
+    label freeAdj = 0;
+
+    for (label cellI = 0; cellI < mesh.nCells(); cellI++)
+    {
+        xadj[cellI] = freeAdj;
+
+        const labelList& cFaces = mesh.cells()[cellI];
+
+        forAll(cFaces, i)
+        {
+            label faceI = cFaces[i];
+
+            if
+            (
+                mesh.isInternalFace(faceI)
+             || isA<cyclicPolyPatch>(pbm[pbm.whichPatch(faceI)])
+            )
+            {
+                freeAdj++;
+            }
+        }
+    }
+    xadj[mesh.nCells()] = freeAdj;
+
+
+    // Fill in adjncy
+    // ~~~~~~~~~~~~~~
+
+    labelList nFacesPerCell(mesh.nCells(), 0);
+
+    // Internal faces
+    for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
+    {
+        label own = mesh.faceOwner()[faceI];
+        label nei = mesh.faceNeighbour()[faceI];
+
+        adjncy[xadj[own] + nFacesPerCell[own]++] = nei;
+        adjncy[xadj[nei] + nFacesPerCell[nei]++] = own;
+    }
+
+    // Coupled faces. Only cyclics done.
+    forAll(pbm, patchi)
+    {
+        if (isA<cyclicPolyPatch>(pbm[patchi]))
+        {
+            const unallocLabelList& faceCells = pbm[patchi].faceCells();
+
+            label sizeby2 = faceCells.size()/2;
+
+            for (label facei=0; facei<sizeby2; facei++)
+            {
+                label own = faceCells[facei];
+                label nei = faceCells[facei + sizeby2];
+
+                adjncy[xadj[own] + nFacesPerCell[own]++] = nei;
+                adjncy[xadj[nei] + nFacesPerCell[nei]++] = own;
+            }
+        }
+    }
+}
+
+
+// From cell-cell connections to Metis format (like CompactListList)
+void Foam::decompositionMethod::calcCSR
+(
+    const labelListList& cellCells,
+    List<int>& adjncy,
+    List<int>& xadj
+)
+{
+    // Count number of internal faces
+    label nConnections = 0;
+
+    forAll(cellCells, coarseI)
+    {
+        nConnections += cellCells[coarseI].size();
+    }
+
+    // Create the adjncy array as twice the size of the total number of
+    // internal faces
+    adjncy.setSize(nConnections);
+
+    xadj.setSize(cellCells.size()+1);
+
+
+    // Fill in xadj
+    // ~~~~~~~~~~~~
+    label freeAdj = 0;
+
+    forAll(cellCells, coarseI)
+    {
+        xadj[coarseI] = freeAdj;
+
+        const labelList& cCells = cellCells[coarseI];
+
+        forAll(cCells, i)
+        {
+            adjncy[freeAdj++] = cCells[i];
+        }
+    }
+    xadj[cellCells.size()] = freeAdj;
+}
+
+
+void Foam::decompositionMethod::calcDistributedCSR
+(
+    const polyMesh& mesh,
+    List<int>& adjncy,
+    List<int>& xadj
+)
+{
+    // Create global cell numbers
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    globalIndex globalCells(mesh.nCells());
+
+
+    //
+    // Make Metis Distributed CSR (Compressed Storage Format) storage
+    //   adjncy      : contains cellCells (= edges in graph)
+    //   xadj(celli) : start of information in adjncy for celli
+    //
+
+
+    const labelList& faceOwner = mesh.faceOwner();
+    const labelList& faceNeighbour = mesh.faceNeighbour();
+    const polyBoundaryMesh& patches = mesh.boundaryMesh();
+
+
+    // Get renumbered owner on other side of coupled faces
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    List<int> globalNeighbour(mesh.nFaces()-mesh.nInternalFaces());
+
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+
+        if (pp.coupled())
+        {
+            label faceI = pp.start();
+            label bFaceI = pp.start() - mesh.nInternalFaces();
+
+            forAll(pp, i)
+            {
+                globalNeighbour[bFaceI++] = globalCells.toGlobal
+                (
+                    faceOwner[faceI++]
+                );
+            }
+        }
+    }
+
+    // Get the cell on the other side of coupled patches
+    syncTools::swapBoundaryFaceList(mesh, globalNeighbour, false);
+
+
+    // Count number of faces (internal + coupled)
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    // Number of faces per cell
+    List<int> nFacesPerCell(mesh.nCells(), 0);
+
+    // Number of coupled faces
+    label nCoupledFaces = 0;
+
+    for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
+    {
+        nFacesPerCell[faceOwner[faceI]]++;
+        nFacesPerCell[faceNeighbour[faceI]]++;
+    }
+    // Handle coupled faces
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+
+        if (pp.coupled())
+        {
+            label faceI = pp.start();
+
+            forAll(pp, i)
+            {
+                nCoupledFaces++;
+                nFacesPerCell[faceOwner[faceI++]]++;
+            }
+        }
+    }
+
+
+    // Fill in xadj
+    // ~~~~~~~~~~~~
+
+    xadj.setSize(mesh.nCells()+1);
+
+    int freeAdj = 0;
+
+    for (label cellI = 0; cellI < mesh.nCells(); cellI++)
+    {
+        xadj[cellI] = freeAdj;
+
+        freeAdj += nFacesPerCell[cellI];
+    }
+    xadj[mesh.nCells()] = freeAdj;
+
+
+
+    // Fill in adjncy
+    // ~~~~~~~~~~~~~~
+
+    adjncy.setSize(2*mesh.nInternalFaces() + nCoupledFaces);
+
+    nFacesPerCell = 0;
+
+    // For internal faces is just offsetted owner and neighbour
+    for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
+    {
+        label own = faceOwner[faceI];
+        label nei = faceNeighbour[faceI];
+
+        adjncy[xadj[own] + nFacesPerCell[own]++] = globalCells.toGlobal(nei);
+        adjncy[xadj[nei] + nFacesPerCell[nei]++] = globalCells.toGlobal(own);
+    }
+    // For boundary faces is offsetted coupled neighbour
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+
+        if (pp.coupled())
+        {
+            label faceI = pp.start();
+            label bFaceI = pp.start()-mesh.nInternalFaces();
+
+            forAll(pp, i)
+            {
+                label own = faceOwner[faceI];
+                adjncy[xadj[own] + nFacesPerCell[own]++] =
+                    globalNeighbour[bFaceI];
+
+                faceI++;
+                bFaceI++;
+            }
+        }
+    }
 }