Update from August 23, 2004

git-svn-id: http://visit.ilight.com/svn/visit/trunk/src@306 18c085ea-50e0-402c-830e-de6fd14e8384

components/Database/Database/avtGenericDatabase.h

@@ -19,6 +19,7 @@
 
 struct    avtDatasetCollection;
 struct    avtMatSpeciesMetaData;
+class     avtDomainBoundaries;
 class     avtFileFormatInterface;
 class     avtMixedVariable;
 class     avtSILRestrictionTraverser;
@@ -190,6 +191,9 @@ class     PickVarInfo;
 //    Mark C. Miller, Mon Aug  9 19:12:24 PDT 2004
 //    Added methods to get global node and zone ids
 //
+//    Hank Childs, Fri Aug 13 15:57:29 PDT 2004
+//    Beef up ghost data communication routines.
+//
 // ****************************************************************************
 
 class DATABASE_API avtGenericDatabase : public avtDatasetDatabase
@@ -290,9 +294,37 @@ class DATABASE_API avtGenericDatabase : public avtDatasetDatabase
     void                       ReadDataset(avtDatasetCollection &, 
                                   std::vector<int> &, avtDataSpecification_p &,
                                   avtSourceFromDatabase *);
-    bool                       CommunicateGhosts(avtDatasetCollection &,
-                                  std::vector<int> &, avtDataSpecification_p &,
-                                  avtSourceFromDatabase *);
+
+    avtDomainBoundaries       *GetDomainBoundaryInformation(
+                                                       avtDatasetCollection &,
+                                                       std::vector<int> &,
+                                                       avtDataSpecification_p);
+    bool                       CommunicateGhosts(avtGhostDataType,
+                                    avtDatasetCollection &, std::vector<int> &, 
+                                    avtDataSpecification_p &,
+                                    avtSourceFromDatabase *);
+    bool                       CommunicateGhostZonesFromDomainBoundaries(
+                                    avtDomainBoundaries *,
+                                    avtDatasetCollection &, std::vector<int> &,
+                                    avtDataSpecification_p &,
+                                    avtSourceFromDatabase *);
+    bool                     CommunicateGhostZonesFromDomainBoundariesFromFile(
+                                    avtDatasetCollection &, std::vector<int> &,
+                                    avtDataSpecification_p &,
+                                    avtSourceFromDatabase *);
+    bool                     CommunicateGhostNodesFromDomainBoundariesFromFile(
+                                    avtDatasetCollection &, std::vector<int> &,
+                                    avtDataSpecification_p &,
+                                    avtSourceFromDatabase *);
+    bool                       CommunicateGhostZonesFromGlobalNodeIds(
+                                    avtDatasetCollection &, std::vector<int> &,
+                                    avtDataSpecification_p &,
+                                    avtSourceFromDatabase *);
+    bool                       CommunicateGhostNodesFromGlobalNodeIds(
+                                    avtDatasetCollection &, std::vector<int> &,
+                                    avtDataSpecification_p &,
+                                    avtSourceFromDatabase *);
+
     bool                       ApplyGhostForDomainNesting(avtDatasetCollection &,
                                   std::vector<int> &, std::vector<int> &,
                                   avtDataSpecification_p &);

components/Database/Formats/avtMTSDFileFormat.C

@@ -24,6 +24,11 @@ const int avtMTSDFileFormat::MAX_FILES = 1000;
 //  Programmer:  Hank Childs
 //  Creation:    October 8, 2001
 //
+//  Modifications:
+//
+//    Hank Childs, Mon Aug 16 16:22:56 PDT 2004
+//    Initialize myDomain.
+//
 // ****************************************************************************
 
 avtMTSDFileFormat::avtMTSDFileFormat(const char * const *names, int nNames)
@@ -40,6 +45,7 @@ avtMTSDFileFormat::avtMTSDFileFormat(const char * const *names, int nNames)
     {
         filenames[i] = NULL;
     }
+    myDomain = -1;
 }
 
 

components/Database/Formats/avtMTSDFileFormat.h

@@ -52,6 +52,9 @@ class     avtIOInformation;
 //    Mark C. Miller, Tue Mar 16 14:28:42 PST 2004
 //    Added method, PopulateIOInformation
 //
+//    Hank Childs, Mon Aug 16 16:22:56 PDT 2004
+//    Allow for the domain to be set.
+//
 // ****************************************************************************
 
 class DATABASE_API avtMTSDFileFormat : public avtFileFormat
@@ -64,6 +67,8 @@ class DATABASE_API avtMTSDFileFormat : public avtFileFormat
                                             const char *type, void *args,
                                             DestructorFunction &);
 
+    void                   SetDomain(int d) { myDomain = d; };
+
     virtual void           GetCycles(std::vector<int> &);
     virtual void           GetTimes(std::vector<double> &);
     virtual int            GetNTimesteps(void);
@@ -81,6 +86,7 @@ class DATABASE_API avtMTSDFileFormat : public avtFileFormat
   protected:
     char                 **filenames;
     int                    nFiles;
+    int                    myDomain;
 
     int                    AddFile(const char *);
     static const int       MAX_FILES;

components/Database/Formats/avtMTSDFileFormatInterface.C

@@ -30,6 +30,11 @@ using std::vector;
 //  Programmer:  Hank Childs
 //  Creation:    October 8, 2001
 //
+//  Modifications:
+//
+//    Hank Childs, Mon Aug 16 16:22:56 PDT 2004
+//    Tell each file format what its domain is.
+//
 // ****************************************************************************
 
 avtMTSDFileFormatInterface::avtMTSDFileFormatInterface(avtMTSDFileFormat **lst,
@@ -37,6 +42,14 @@ avtMTSDFileFormatInterface::avtMTSDFileFormatInterface(avtMTSDFileFormat **lst,
 {
     domains  = lst;
     nDomains = nLst;
+
+    for (int i = 0 ; i < nDomains ; i++)
+    {
+        if (lst[i] != NULL)
+        {
+            lst[i]->SetDomain(i);
+        }
+    }
 }
 
 

components/Database/Ghost/avtDomainBoundaries.h

@@ -31,6 +31,9 @@ class avtMaterial;
 //    Made ExhangeVector into two methods to handle different underlying
 //    data types (int, float).
 //
+//    Hank Childs, Sat Aug 14 06:41:00 PDT 2004
+//    Added ghost nodes.
+//
 // ****************************************************************************
 class DATABASE_API avtDomainBoundaries
 {
@@ -59,6 +62,8 @@ class DATABASE_API avtDomainBoundaries
     virtual vector<avtMixedVariable*> ExchangeMixVar(vector<int>     domainNum,
                                         const vector<avtMaterial*>   mats,
                                         vector<avtMixedVariable*>    mixvars) =0;
+    virtual void                      CreateGhostNodes(vector<int>   domainNum,
+                                               vector<vtkDataSet*>   meshes)  =0;
     virtual bool                      ConfirmMesh(vector<int>      domainNum,
                                                vector<vtkDataSet*> meshes)  =0;
 };

components/Database/Ghost/avtStructuredDomainBoundaries.C

@@ -7,9 +7,11 @@
 #include <vtkCellData.h>
 #include <vtkFloatArray.h>
 #include <vtkIntArray.h>
+#include <vtkPointData.h>
 #include <vtkRectilinearGrid.h>
 #include <vtkStructuredGrid.h>
 
+#include <avtGhostData.h>
 #include <avtMaterial.h>
 #include <avtMixedVariable.h>
 
@@ -2378,6 +2380,105 @@ avtRectilinearDomainBoundaries::ExchangeMesh(vector<int>        domainNum,
     return out;
 }
 
+// ****************************************************************************
+//  Method: avtStructuredDomainBoundaries::CreateGhostNodes
+//
+//  Purpose:
+//      Creates ghost nodes.
+//
+//  Programmer: Hank Childs
+//  Creation:   August 14, 2004
+//
+// ****************************************************************************
+
+void
+avtStructuredDomainBoundaries::CreateGhostNodes(vector<int>         domainNum,
+                                                vector<vtkDataSet*> meshes)
+{
+    vector<int> domain2proc = CreateDomainToProcessorMap(domainNum);
+    CreateCurrentDomainBoundaryInformation(domain2proc);
+
+    for (int i = 0 ; i < domainNum.size() ; i++)
+    {
+        int dom = domainNum[i];
+        Boundary *bi = &boundary[dom];
+
+        vtkDataSet *ds = meshes[i];
+        int npts = ds->GetNumberOfPoints();
+
+        vtkUnsignedCharArray *gn = vtkUnsignedCharArray::New();
+        gn->SetNumberOfTuples(npts);
+        gn->SetName("vtkGhostNodes");
+        unsigned char *gnp = gn->GetPointer(0);
+   
+        for (int j = 0 ; j < npts ; j++)
+            gnp[j] = 0;
+
+        int dims[3];
+        dims[0] = bi->oldnextents[1] - bi->oldnextents[0] + 1;
+        dims[1] = bi->oldnextents[3] - bi->oldnextents[2] + 1;
+        dims[2] = bi->oldnextents[5] - bi->oldnextents[4] + 1;
+
+        if (bi->newnextents[0] < bi->oldnextents[0])
+        {
+            for (int k = 0 ; k < dims[2] ; k++)
+                for (int j = 0 ; j < dims[1] ; j++)
+                {
+                    int idx = 0 + j*dims[0] + k*dims[0]*dims[1];
+                    avtGhostData::AddGhostNodeType(gnp[idx], DUPLICATED_NODE);
+                }
+        }
+        if (bi->newnextents[1] > bi->oldnextents[1])
+        {
+            for (int k = 0 ; k < dims[2] ; k++)
+                for (int j = 0 ; j < dims[1] ; j++)
+                {
+                    int idx = dims[0]-1 + j*dims[0] + k*dims[0]*dims[1];
+                    avtGhostData::AddGhostNodeType(gnp[idx], DUPLICATED_NODE);
+                }
+        }
+        if (bi->newnextents[2] < bi->oldnextents[2])
+        {
+            for (int k = 0 ; k < dims[2] ; k++)
+                    for (int i = 0 ; i < dims[0] ; i++)
+                {
+                    int idx = i + 0*dims[0] + k*dims[0]*dims[1];
+                    avtGhostData::AddGhostNodeType(gnp[idx], DUPLICATED_NODE);
+                }
+        }
+        if (bi->newnextents[3] > bi->oldnextents[3])
+        {
+            for (int k = 0 ; k < dims[2] ; k++)
+                for (int i = 0 ; i < dims[0] ; i++)
+                {
+                    int idx = i + (dims[1]-1)*dims[0] + k*dims[0]*dims[1];
+                    avtGhostData::AddGhostNodeType(gnp[idx], DUPLICATED_NODE);
+                }
+        }
+        if (bi->newnextents[4] < bi->oldnextents[4])
+        {
+            for (int j = 0 ; j < dims[1] ; j++)
+                for (int i = 0 ; i < dims[0] ; i++)
+                {
+                        int idx = i + j*dims[0] + 0*dims[0]*dims[1];
+                    avtGhostData::AddGhostNodeType(gnp[idx], DUPLICATED_NODE);
+                }
+        }
+        if (bi->newnextents[5] > bi->oldnextents[5])
+        {
+                for (int j = 0 ; j < dims[1] ; j++)
+                for (int i = 0 ; i < dims[0] ; i++)
+                {
+                    int idx = i + j*dims[0] + (dims[2]-1)*dims[0]*dims[1];
+                    avtGhostData::AddGhostNodeType(gnp[idx], DUPLICATED_NODE);
+                }
+        }
+    
+        ds->GetPointData()->AddArray(gn);
+        gn->Delete();
+    }
+}
+
 // ****************************************************************************
 //  Method: avtStructuredDomainBoundaries::SetIndicesForRectGrid
 //

components/Database/Ghost/avtStructuredDomainBoundaries.h

@@ -161,6 +161,9 @@ class BoundaryHelperFunctions
 //    indicate this condition rather than sub-classing because the class
 //    hierarchy is more involved than was worth it.
 //
+//    Hank Childs, Sat Aug 14 06:41:00 PDT 2004
+//    Added CreateGhostNodes.
+//
 // ****************************************************************************
 
 class DATABASE_API avtStructuredDomainBoundaries :  public avtDomainBoundaries
@@ -200,6 +203,9 @@ class DATABASE_API avtStructuredDomainBoundaries :  public avtDomainBoundaries
                                         const vector<avtMaterial*>   mats,
                                         vector<avtMixedVariable*>    mixvars);
 
+    virtual void                      CreateGhostNodes(vector<int>   domainNum,
+                                               vector<vtkDataSet*> meshes);
+
     virtual bool                      ConfirmMesh(vector<int>      domainNum,
                                                vector<vtkDataSet*> meshes);
 

components/Database/Ghost/avtUnstructuredDomainBoundaries.C

+// ************************************************************************* //
+//                      avtUnstructuredDomainBoundaries.C                    //
+// ************************************************************************* //
+
 #include <avtUnstructuredDomainBoundaries.h>
 
 #include <vtkCellData.h>
 #include <vtkFloatArray.h>
 #include <vtkIdList.h>
 #include <vtkIntArray.h>
+#include <vtkPointData.h>
 #include <vtkUnsignedCharArray.h>
 #include <vtkUnstructuredGrid.h>
 
-
+#include <avtGhostData.h>
 #include <avtMaterial.h>
 #include <avtMixedVariable.h>
 
@@ -1468,3 +1473,53 @@ avtUnstructuredDomainBoundaries::CommunicateDataInformation(
     MPI_Barrier(MPI_COMM_WORLD);
 #endif
 }
+
+
+// ****************************************************************************
+//  Method: avtUnstructuredDomainBoundaries::CreateGhostNodes
+//
+//  Purpose:
+//      Creates ghost nodes.
+//
+//  Programmer: Hank Childs
+//  Creation:   August 16, 2004
+//
+// ****************************************************************************
+
+void
+avtUnstructuredDomainBoundaries::CreateGhostNodes(vector<int> domainNum,
+                                                  vector<vtkDataSet*> meshes)
+{
+    int  i, j;
+
+    for (i = 0 ; i < domainNum.size() ; i++)
+    {
+        vtkDataSet *ds = meshes[i];
+        int npts = ds->GetNumberOfPoints();
+
+        vtkUnsignedCharArray *gn = vtkUnsignedCharArray::New();
+        gn->SetNumberOfTuples(npts);
+        gn->SetName("vtkGhostNodes");
+        unsigned char *gnp = gn->GetPointer(0);
+        for (j = 0 ; j < npts ; j++)
+            gnp[j] = 0;
+
+        for (j = 0 ; j < giveIndex.size() ; j++)
+        {
+            if (giveIndex[j].first != domainNum[i])
+                continue;
+            std::map<int,int> &thisMap = sharedPointsMap[giveIndex[j].first];
+            std::map<int,int>::iterator p = thisMap.begin();
+            for (p = thisMap.begin() ; p != thisMap.end() ; p++)
+            {
+                int node = (*p).first;
+                avtGhostData::AddGhostNodeType(gnp[node], DUPLICATED_NODE);
+            }
+        }
+
+        ds->GetPointData()->AddArray(gn);
+        gn->Delete();
+    }
+}
+
+

components/Database/Ghost/avtUnstructuredDomainBoundaries.h

@@ -35,6 +35,11 @@ class avtMaterial;
 //  Programmer:  Akira Haddox
 //  Creation:    August 11, 2003
 //
+//  Modifications:
+//
+//    Hank Childs, Mon Aug 16 08:47:27 PDT 2004
+//    Added CreateGhostNodes.
+//
 // ****************************************************************************
 
 class DATABASE_API avtUnstructuredDomainBoundaries : public avtDomainBoundaries
@@ -77,6 +82,9 @@ class DATABASE_API avtUnstructuredDomainBoundaries : public avtDomainBoundaries
                                         const vector<avtMaterial*>   mats,
                                         vector<avtMixedVariable*>    mixvars);
     
+    virtual void                      CreateGhostNodes(vector<int>   domainNum,
+                                               vector<vtkDataSet*> meshes);
+
     virtual bool                      ConfirmMesh(vector<int>      domainNum,
                                         vector<vtkDataSet*> meshes);
     

config-site/mcr.llnl.gov.conf

@@ -44,7 +44,7 @@ CXXFLAGS="-Wno-deprecated $CXXFLAGS"
 ## Add parallel arguments.
 ##
 CXXFLAGS="-I/usr/lib/mpi/mpi_gnu/include $CXXFLAGS"
-MPI_LIBS="-L/usr/lib/mpi/mpi_gn/lib -Wl,-rpath=/usr/lib/mpi/mpi_gnu/lib -lmpi -lelan -lelan3 -lrmscall"
+MPI_LIBS="-L/usr/lib/mpi/mpi_gnu/lib -Wl,-rpath=/usr/lib/mpi/mpi_gnu/lib -lmpi -lelan -lelan3 -lrmscall"
 
 ##
 ## Database reader plugin support libraries

databases/Dune/Dune.xml

+<?xml version="1.0"?>
+  <Plugin name="Dune" type="database" label="Dune" version="1.0" enabled="true" dbtype="MTSD" haswriter="false">
+    <Extensions>
+      Dat
+    </Extensions>
+    <Attribute name="" purpose="" persistent="false" exportAPI="" exportInclude="">
+    </Attribute>
+  </Plugin>

databases/Dune/DuneCommonPluginInfo.C

+#include <DunePluginInfo.h>
+#include <avtDuneFileFormat.h>
+#include <avtMTSDFileFormatInterface.h>
+#include <avtGenericDatabase.h>
+
+// ****************************************************************************
+//  Method:  DuneCommonPluginInfo::GetDatabaseType
+//
+//  Purpose:
+//    Returns the type of a Dune database.
+//
+//  Programmer:  meredith -- generated by xml2info
+//  Creation:    Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+DatabaseType
+DuneCommonPluginInfo::GetDatabaseType()
+{
+    return DB_TYPE_MTSD;
+}
+
+// ****************************************************************************
+//  Method:  DuneCommonPluginInfo::GetDefaultExtensions
+//
+//  Purpose:
+//    Returns the default extensions for a Dune database.
+//
+//  Programmer:  meredith -- generated by xml2info
+//  Creation:    Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+std::vector<std::string>
+DuneCommonPluginInfo::GetDefaultExtensions()
+{
+    std::vector<std::string> defaultExtensions;
+    defaultExtensions.push_back("Dat");
+
+    return defaultExtensions;
+}
+
+// ****************************************************************************
+//  Method: DuneCommonPluginInfo::GetWriter
+//
+//  Purpose:
+//      Sets up a Dune writer.
+//
+//  Returns:    A Dune writer.
+//
+//  Programmer: meredith -- generated by xml2info
+//  Creation:   Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+avtDatabaseWriter *
+DuneCommonPluginInfo::GetWriter(void)
+{
+    return NULL;
+}
+
+// ****************************************************************************
+//  Method: DuneCommonPluginInfo::SetUpDuneDatabase
+//
+//  Purpose:
+//      Sets up a Dune database.
+//
+//  Arguments:
+//      list    A list of file names.
+//      nList   The number of timesteps in list.
+//      nBlocks The number of blocks in the list.
+//
+//  Returns:    A Dune database from list.
+//
+//  Programmer: meredith -- generated by xml2info
+//  Creation:   Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+avtDatabase *
+DuneCommonPluginInfo::SetupDatabase(const char *const *list,
+                                   int nList, int nBlock)
+{
+    avtMTSDFileFormat **ffl = new avtMTSDFileFormat*[nList];
+    for (int i = 0 ; i < nList ; i++)
+    {
+        ffl[i] = new avtDuneFileFormat(list[i]);
+    }
+    avtMTSDFileFormatInterface *inter 
+           = new avtMTSDFileFormatInterface(ffl, nList);
+    return new avtGenericDatabase(inter);
+}

databases/Dune/DuneEnginePluginInfo.C

+#include <DunePluginInfo.h>
+
+#if defined(__APPLE__)
+#define GetEngineInfo Dune_GetEngineInfo
+#endif
+
+// ****************************************************************************
+//  Function:  GetEngineInfo
+//
+//  Purpose:
+//    Return a new EnginePluginInfo for the Dune database.
+//
+//  Programmer: meredith -- generated by xml2info
+//  Creation:   Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+extern "C" EngineDatabasePluginInfo* GetEngineInfo()
+{
+    return new DuneEnginePluginInfo;
+}
+
+// this makes compilers happy... remove if we ever have functions here
+void DuneEnginePluginInfo::dummy()
+{
+}

databases/Dune/DuneMDServerPluginInfo.C

+#include <DunePluginInfo.h>
+
+#if defined(__APPLE__)
+#define GetMDServerInfo Dune_GetMDServerInfo
+#endif
+
+// ****************************************************************************
+//  Function:  GetMDServerInfo
+//
+//  Purpose:
+//    Return a new MDServerPluginInfo for the Dune database.
+//
+//  Programmer: meredith -- generated by xml2info
+//  Creation:   Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+extern "C" MDServerDatabasePluginInfo* GetMDServerInfo()
+{
+    return new DuneMDServerPluginInfo;
+}
+
+// this makes compilers happy... remove if we ever have functions here
+void DuneMDServerPluginInfo::dummy()
+{
+}

databases/Dune/DunePluginInfo.C

+// ************************************************************************* //
+//  File: DunePluginInfo.C
+// ************************************************************************* //
+
+#include <DunePluginInfo.h>
+
+#if defined(__APPLE__)
+#define GetGeneralInfo Dune_GetGeneralInfo
+#endif
+
+// ****************************************************************************
+//  Function:  GetGeneralInfo
+//
+//  Purpose:
+//    Return a new GeneralPluginInfo for the Dune database.
+//
+//  Programmer:  meredith -- generated by xml2info
+//  Creation:    Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+extern "C" GeneralDatabasePluginInfo* GetGeneralInfo()
+{
+    return new DuneGeneralPluginInfo;
+}
+
+// ****************************************************************************
+//  Method: DuneGeneralPluginInfo::GetName
+//
+//  Purpose:
+//    Return the name of the database plugin.
+//
+//  Returns:    A pointer to the name of the database plugin.
+//
+//  Programmer: meredith -- generated by xml2info
+//  Creation:   Mon Aug 23 14:39:28 PST 2004
+//
+// ****************************************************************************
+
+char *
+DuneGeneralPluginInfo::GetName() const
+{
+    return "Dune";
+}
+
+// ****************************************************************************
+//  Method: DuneGeneralPluginInfo::GetVersion
+//
+//  Purpose: