/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 1776 by ksteube, Tue Sep 9 06:03:53 2008 UTC revision 4800 by caltinay, Wed Mar 26 01:50:04 2014 UTC
# Line 1  Line 1 
1    
2  /* $Id$ */  /*****************************************************************************
3    *
4  /*******************************************************  * Copyright (c) 2003-2014 by University of Queensland
5   *  * http://www.uq.edu.au
6   *           Copyright 2003-2007 by ACceSS MNRF  *
7   *       Copyright 2007 by University of Queensland  * Primary Business: Queensland, Australia
8   *  * Licensed under the Open Software License version 3.0
9   *                http://esscc.uq.edu.au  * http://www.opensource.org/licenses/osl-3.0.php
10   *        Primary Business: Queensland, Australia  *
11   *  Licensed under the Open Software License version 3.0  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12   *     http://www.opensource.org/licenses/osl-3.0.php  * Development 2012-2013 by School of Earth Sciences
13   *  * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14   *******************************************************/  *
15    *****************************************************************************/
16    
17    #include <pasowrap/PasoException.h>
18    #include <pasowrap/TransportProblemAdapter.h>
19  #include "MeshAdapter.h"  #include "MeshAdapter.h"
20  #include "escript/Data.h"  #include "escript/Data.h"
21  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
22    #include "esysUtils/blocktimer.h"
23    #include "esysUtils/EsysRandom.h"
24    
25    #include <boost/python/import.hpp>
26  #ifdef USE_NETCDF  #ifdef USE_NETCDF
27  #include <netcdfcpp.h>  #include <netcdfcpp.h>
28  #endif  #endif
 extern "C" {  
 #include "escript/blocktimer.h"  
 }  
 #include <vector>  
   
 #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256  
29    
30  using namespace std;  using namespace std;
31  using namespace escript;  using namespace paso;
32    
33  namespace finley {  namespace finley {
34    
 //  
35  // define the static constants  // define the static constants
36  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
37  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
# Line 48  const int MeshAdapter::ReducedContactEle Line 48  const int MeshAdapter::ReducedContactEle
48  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49  const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;  const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Mesh* finleyMesh)
52  {  {
53     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
54     //      // need to use a null_deleter as Finley_Mesh_free deletes the pointer
55     // need to use a null_deleter as Finley_Mesh_free deletes the pointer      // for us.
56     // for us.      m_finleyMesh.reset(finleyMesh, null_deleter());
    m_finleyMesh.reset(finleyMesh,null_deleter());  
57  }  }
58    
59  //  //
60  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
61  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in) :
62  m_finleyMesh(in.m_finleyMesh)      m_finleyMesh(in.m_finleyMesh)
63  {  {
64     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
65  }  }
66    
67  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
68  {  {
69     //      // I hope the case for the pointer being zero has been taken care of
70     // I hope the case for the pointer being zero has been taken care of.      if (m_finleyMesh.unique()) {
71     //  cout << "In MeshAdapter destructor." << endl;          delete m_finleyMesh.get();
72     if (m_finleyMesh.unique()) {      }
       Finley_Mesh_free(m_finleyMesh.get());  
    }  
73  }  }
74    
75  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
76  {  {
77     return m_finleyMesh.get()->MPIInfo->size;      return m_finleyMesh.get()->MPIInfo->size;
78  }  }
79    
80  int MeshAdapter::getMPIRank() const  int MeshAdapter::getMPIRank() const
81  {  {
82     return m_finleyMesh.get()->MPIInfo->rank;      return m_finleyMesh.get()->MPIInfo->rank;
83  }  }
84    
85    void MeshAdapter::MPIBarrier() const
86    {
87    #ifdef ESYS_MPI
88        MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
89    #endif
90    }
91    
92  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  bool MeshAdapter::onMasterProcessor() const
93     return m_finleyMesh.get();  {
94        return m_finleyMesh.get()->MPIInfo->rank == 0;
95  }  }
96    
97  void MeshAdapter::write(const std::string& fileName) const  #ifdef ESYS_MPI
98    MPI_Comm
99    #else
100    unsigned int
101    #endif
102    MeshAdapter::getMPIComm() const
103  {  {
104     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;  #ifdef ESYS_MPI
105     strcpy(fName,fileName.c_str());      return m_finleyMesh->MPIInfo->comm;
106     Finley_Mesh_write(m_finleyMesh.get(),fName);  #else
107     checkFinleyError();      return 0;
108     TMPMEMFREE(fName);  #endif
109  }  }
110    
111  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  Mesh* MeshAdapter::getFinley_Mesh() const
112  {  {
113     Finley_PrintMesh_Info(m_finleyMesh.get(), full);      return m_finleyMesh.get();
114  }  }
115    
116  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
117    {
118        m_finleyMesh.get()->write(fileName);
119        checkFinleyError();
120    }
121    
122    void MeshAdapter::Print_Mesh_Info(const bool full) const
123    {
124        m_finleyMesh.get()->printInfo(full);
125    }
126    
127    void MeshAdapter::dump(const string& fileName) const
128  {  {
129  #ifdef USE_NETCDF  #ifdef USE_NETCDF
130     const NcDim* ncdims[12];      const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
131     NcVar *ids;      NcVar *ids;
132     int *int_ptr;      int *int_ptr;
133     Finley_Mesh *mesh = m_finleyMesh.get();      Mesh *mesh = m_finleyMesh.get();
134     Finley_TagMap* tag_map;      int num_Tags = 0;
135     int num_Tags = 0;      int mpi_size                         = mesh->MPIInfo->size;
136     int mpi_size             = mesh->MPIInfo->size;      int mpi_rank                         = mesh->MPIInfo->rank;
137     int mpi_rank             = mesh->MPIInfo->rank;      int numDim                           = mesh->Nodes->numDim;
138     int numDim               = mesh->Nodes->numDim;      int numNodes                         = mesh->Nodes->numNodes;
139     int numNodes             = mesh->Nodes->numNodes;      int num_Elements                     = mesh->Elements->numElements;
140     int num_Elements         = mesh->Elements->numElements;      int num_FaceElements                 = mesh->FaceElements->numElements;
141     int num_FaceElements         = mesh->FaceElements->numElements;      int num_ContactElements              = mesh->ContactElements->numElements;
142     int num_ContactElements      = mesh->ContactElements->numElements;      int num_Points                       = mesh->Points->numElements;
143     int num_Points           = mesh->Points->numElements;      int num_Elements_numNodes            = mesh->Elements->numNodes;
144     int num_Elements_numNodes        = mesh->Elements->numNodes;      int num_FaceElements_numNodes        = mesh->FaceElements->numNodes;
145     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;      int num_ContactElements_numNodes     = mesh->ContactElements->numNodes;
146     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;  #ifdef ESYS_MPI
147        MPI_Status status;
148     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),  #endif
149                                                       mpi_size, mpi_rank);  
150    /* Incoming token indicates it's my turn to write */
151     /* Figure out how much storage is required for tags */  #ifdef ESYS_MPI
152     tag_map = mesh->TagMap;      if (mpi_rank>0) {
153     if (tag_map) {          MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
154        while (tag_map) {      }
155           num_Tags++;  #endif
          tag_map=tag_map->next;  
       }  
    }  
   
    // NetCDF error handler  
    NcError err(NcError::verbose_nonfatal);  
    // Create the file.  
    NcFile dataFile(newFileName, NcFile::Replace);  
    // check if writing was successful  
    if (!dataFile.is_valid())  
       throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);  
   
    // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)  
    if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )  
       throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);  
    if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )  
       throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);  
    if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )  
       throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);  
    if (num_Elements>0)  
       if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);  
    if (num_FaceElements>0)  
       if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);  
    if (num_ContactElements>0)  
       if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);  
    if (num_Points>0)  
       if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);  
    if (num_Elements>0)  
       if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);  
    if (num_FaceElements>0)  
       if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);  
    if (num_ContactElements>0)  
       if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);  
    if (num_Tags>0)  
       if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )  
          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);  
   
    // Attributes: MPI size, MPI rank, Name, order, reduced_order  
    if (!dataFile.add_att("mpi_size", mpi_size) )  
       throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("mpi_rank", mpi_rank) )  
       throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("Name",mesh->Name) )  
       throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("numDim",numDim) )  
       throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("order",mesh->order) )  
       throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("reduced_order",mesh->reduced_order) )  
       throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("numNodes",numNodes) )  
       throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_Elements",num_Elements) )  
       throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_FaceElements",num_FaceElements) )  
       throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_ContactElements",num_ContactElements) )  
       throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_Points",num_Points) )  
       throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )  
       throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )  
       throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )  
       throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )  
       throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )  
       throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )  
       throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )  
       throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);  
    if (!dataFile.add_att("num_Tags", num_Tags) )  
       throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);  
   
    // // // // // Nodes // // // // //  
   
    // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)  
    if (numNodes>0) {  
   
       // Nodes Id  
       if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->Id[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);  
   
       // Nodes Tag  
       if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->Tag[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);  
   
       // Nodes gDOF  
       if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);  
   
       // Nodes global node index  
       if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->globalNodesIndex[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);  
   
       // Nodes grDof  
       if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);  
   
       // Nodes grNI  
       if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);  
   
       // Nodes Coordinates  
       if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);  
       if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);  
   
       // Nodes degreesOfFreedomDistribution  
       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];  
       if (! (ids->put(int_ptr, mpi_size+1)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);  
   
       // Nodes nodeDistribution  
       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];  
       if (! (ids->put(int_ptr, mpi_size+1)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);  
   
    }  
   
    // // // // // Elements // // // // //  
   
    if (num_Elements>0) {  
   
       // Temp storage to gather node IDs  
       int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);  
   
       // Elements_Id  
       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )  
          throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Elements->Id[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);  
   
       // Elements_Tag  
       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )  
          throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Elements->Tag[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);  
   
       // Elements_Owner  
       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )  
          throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Elements->Owner[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);  
   
       // Elements_Color  
       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )  
          throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Elements->Color[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);  
   
       // Elements_Nodes  
       for (int i=0; i<num_Elements; i++)  
          for (int j=0; j<num_Elements_numNodes; j++)  
             Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];  
       if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )  
          throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);  
       if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);  
   
       TMPMEMFREE(Elements_Nodes);  
   
    }  
   
    // // // // // Face_Elements // // // // //  
   
    if (num_FaceElements>0) {  
   
       // Temp storage to gather node IDs  
       int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);  
   
       // FaceElements_Id  
       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )  
          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->FaceElements->Id[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);  
   
       // FaceElements_Tag  
       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )  
          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->FaceElements->Tag[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);  
   
       // FaceElements_Owner  
       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )  
          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->FaceElements->Owner[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);  
   
       // FaceElements_Color  
       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )  
          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->FaceElements->Color[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);  
   
       // FaceElements_Nodes  
       for (int i=0; i<num_FaceElements; i++)  
          for (int j=0; j<num_FaceElements_numNodes; j++)  
             FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];  
       if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )  
          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);  
       if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
       TMPMEMFREE(FaceElements_Nodes);  
   
    }  
   
    // // // // // Contact_Elements // // // // //  
   
    if (num_ContactElements>0) {  
   
       // Temp storage to gather node IDs  
       int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);  
   
       // ContactElements_Id  
       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )  
          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->ContactElements->Id[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);  
   
       // ContactElements_Tag  
       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )  
          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->ContactElements->Tag[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);  
   
       // ContactElements_Owner  
       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )  
          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->ContactElements->Owner[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);  
   
       // ContactElements_Color  
       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )  
          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->ContactElements->Color[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);  
   
       // ContactElements_Nodes  
       for (int i=0; i<num_ContactElements; i++)  
          for (int j=0; j<num_ContactElements_numNodes; j++)  
             ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];  
       if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )  
          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
       if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )  
          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
       TMPMEMFREE(ContactElements_Nodes);  
   
    }  
   
    // // // // // Points // // // // //  
   
    if (num_Points>0) {  
   
       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");  
   
       // Temp storage to gather node IDs  
       int *Points_Nodes = TMPMEMALLOC(num_Points,int);  
   
       // Points_Id  
       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )  
          throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Points->Id[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);  
   
       // Points_Tag  
       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )  
          throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Points->Tag[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);  
   
       // Points_Owner  
       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )  
          throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Points->Owner[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);  
   
       // Points_Color  
       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
          throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Points->Color[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);  
   
       // Points_Nodes  
       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]  
       for (int i=0; i<num_Points; i++)  
          Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];  
       if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )  
          throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);  
       if (! (ids->put(&(Points_Nodes[0]), num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);  
   
       TMPMEMFREE(Points_Nodes);  
   
    }  
   
    // // // // // TagMap // // // // //  
   
    if (num_Tags>0) {  
   
       // Temp storage to gather node IDs  
       int *Tags_keys = TMPMEMALLOC(num_Tags, int);  
       char name_temp[4096];  
   
       /* Copy tag data into temp arrays */  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             Tags_keys[i++] = tag_map->tag_key;  
             tag_map=tag_map->next;  
          }  
       }  
   
       // Tags_keys  
       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
          throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);  
       int_ptr = &Tags_keys[0];  
       if (! (ids->put(int_ptr, num_Tags)) )  
          throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);  
   
       // Tags_names_*  
       // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string  
       // because the NetCDF manual doesn't tell how to do an array of strings  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             sprintf(name_temp, "Tags_name_%d", i);  
             if (!dataFile.add_att(name_temp, tag_map->name) )  
                throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);  
             tag_map=tag_map->next;  
             i++;  
          }  
       }  
156    
157        TMPMEMFREE(Tags_keys);      const std::string newFileName(esysUtils::appendRankToFileName(fileName,
158                                                         mpi_size, mpi_rank));
159    
160     }      // Figure out how much storage is required for tags
161        num_Tags = mesh->tagMap.size();
162    
163        // NetCDF error handler
164        NcError err(NcError::verbose_nonfatal);
165        // Create the file.
166        NcFile dataFile(newFileName.c_str(), NcFile::Replace);
167        string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
168        // check if writing was successful
169        if (!dataFile.is_valid())
170            throw FinleyAdapterException(msgPrefix+"Open file for output");
171    
172        // Define dimensions (num_Elements and dim_Elements are identical,
173        // dim_Elements only appears if > 0)
174        if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
175            throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
176        if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
177            throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
178        if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
179            throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
180        if (num_Elements>0)
181            if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
182                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
183        if (num_FaceElements>0)
184            if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
185                throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
186        if (num_ContactElements>0)
187            if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
188                throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
189        if (num_Points>0)
190            if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
191                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
192        if (num_Elements>0)
193            if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
194                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
195        if (num_FaceElements>0)
196            if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
197                throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
198        if (num_ContactElements>0)
199            if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
200                throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
201        if (num_Tags>0)
202            if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
203                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
204    
205        // Attributes: MPI size, MPI rank, Name, order, reduced_order
206        if (!dataFile.add_att("mpi_size", mpi_size))
207            throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
208        if (!dataFile.add_att("mpi_rank", mpi_rank))
209            throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
210        if (!dataFile.add_att("Name",mesh->m_name.c_str()))
211            throw FinleyAdapterException(msgPrefix+"add_att(Name)");
212        if (!dataFile.add_att("numDim",numDim))
213            throw FinleyAdapterException(msgPrefix+"add_att(order)");
214        if (!dataFile.add_att("order",mesh->integrationOrder))
215            throw FinleyAdapterException(msgPrefix+"add_att(order)");
216        if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder))
217            throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
218        if (!dataFile.add_att("numNodes",numNodes))
219            throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
220        if (!dataFile.add_att("num_Elements",num_Elements))
221            throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
222        if (!dataFile.add_att("num_FaceElements",num_FaceElements))
223            throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
224        if (!dataFile.add_att("num_ContactElements",num_ContactElements))
225            throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
226        if (!dataFile.add_att("num_Points",num_Points))
227            throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
228        if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes))
229            throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
230        if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
231            throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
232        if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
233            throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
234        if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
235            throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
236        if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
237            throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
238        if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
239            throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
240        if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
241            throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
242        if (!dataFile.add_att("num_Tags", num_Tags) )
243            throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
244    
245        // // // // // Nodes // // // // //
246    
247        // Nodes nodeDistribution
248        if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
249            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
250        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
251        if (! (ids->put(int_ptr, mpi_size+1)) )
252            throw FinleyAdapterException(msgPrefix+"put(Nodes_NodeDistribution)");
253    
254        // Nodes degreesOfFreedomDistribution
255        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
256            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
257        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
258        if (! (ids->put(int_ptr, mpi_size+1)) )
259            throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
260    
261        // Only write nodes if non-empty because NetCDF doesn't like empty arrays
262        // (it treats them as NC_UNLIMITED)
263        if (numNodes>0) {
264            // Nodes Id
265            if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
266                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
267            int_ptr = &mesh->Nodes->Id[0];
268            if (! (ids->put(int_ptr, numNodes)) )
269                throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
270    
271            // Nodes Tag
272            if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
273                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
274            int_ptr = &mesh->Nodes->Tag[0];
275            if (! (ids->put(int_ptr, numNodes)) )
276                throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
277    
278            // Nodes gDOF
279            if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
280                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
281            int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
282            if (! (ids->put(int_ptr, numNodes)) )
283                throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
284    
285            // Nodes global node index
286            if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
287                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
288            int_ptr = &mesh->Nodes->globalNodesIndex[0];
289            if (! (ids->put(int_ptr, numNodes)) )
290                throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
291    
292            // Nodes grDof
293            if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
294                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
295            int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
296            if (! (ids->put(int_ptr, numNodes)) )
297                throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
298    
299            // Nodes grNI
300            if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
301                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
302            int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
303            if (! (ids->put(int_ptr, numNodes)) )
304                throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
305    
306            // Nodes Coordinates
307            if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
308                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
309            if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
310                throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
311        }
312    
313        // // // // // Elements // // // // //
314        if (num_Elements>0) {
315            // Elements_Id
316            if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
317                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Id)");
318            int_ptr = &mesh->Elements->Id[0];
319            if (! (ids->put(int_ptr, num_Elements)) )
320                throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
321    
322            // Elements_Tag
323            if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
324                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
325            int_ptr = &mesh->Elements->Tag[0];
326            if (! (ids->put(int_ptr, num_Elements)) )
327                throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
328    
329            // Elements_Owner
330            if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
331                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
332            int_ptr = &mesh->Elements->Owner[0];
333            if (! (ids->put(int_ptr, num_Elements)) )
334                throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
335    
336            // Elements_Color
337            if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
338                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
339            int_ptr = &mesh->Elements->Color[0];
340            if (! (ids->put(int_ptr, num_Elements)) )
341                throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
342    
343            // Elements_Nodes
344            if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
345                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
346            if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
347                throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
348        }
349    
350        // // // // // Face_Elements // // // // //
351        if (num_FaceElements>0) {
352            // FaceElements_Id
353            if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
354                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
355            int_ptr = &mesh->FaceElements->Id[0];
356            if (! (ids->put(int_ptr, num_FaceElements)) )
357                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
358    
359            // FaceElements_Tag
360            if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
361                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
362            int_ptr = &mesh->FaceElements->Tag[0];
363            if (! (ids->put(int_ptr, num_FaceElements)) )
364                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
365    
366            // FaceElements_Owner
367            if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
368                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
369            int_ptr = &mesh->FaceElements->Owner[0];
370            if (! (ids->put(int_ptr, num_FaceElements)) )
371                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
372    
373            // FaceElements_Color
374            if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
375                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
376            int_ptr = &mesh->FaceElements->Color[0];
377            if (! (ids->put(int_ptr, num_FaceElements)) )
378                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
379    
380            // FaceElements_Nodes
381            if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
382                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
383            if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
384                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
385        }
386    
387        // // // // // Contact_Elements // // // // //
388        if (num_ContactElements>0) {
389    
390            // ContactElements_Id
391            if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
392                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
393            int_ptr = &mesh->ContactElements->Id[0];
394            if (! (ids->put(int_ptr, num_ContactElements)) )
395                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
396    
397            // ContactElements_Tag
398            if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
399                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
400            int_ptr = &mesh->ContactElements->Tag[0];
401            if (! (ids->put(int_ptr, num_ContactElements)) )
402                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
403    
404            // ContactElements_Owner
405            if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
406                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
407            int_ptr = &mesh->ContactElements->Owner[0];
408            if (! (ids->put(int_ptr, num_ContactElements)) )
409                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
410    
411            // ContactElements_Color
412            if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
413                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
414            int_ptr = &mesh->ContactElements->Color[0];
415            if (! (ids->put(int_ptr, num_ContactElements)) )
416                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
417    
418            // ContactElements_Nodes
419            if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
420                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
421            if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
422                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
423        }
424    
425        // // // // // Points // // // // //
426        if (num_Points>0) {
427            // Points_Id
428            if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
429                throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
430            int_ptr = &mesh->Points->Id[0];
431            if (! (ids->put(int_ptr, num_Points)) )
432                throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
433    
434            // Points_Tag
435            if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
436                throw FinleyAdapterException(msgPrefix+"add_var(Points_Tag)");
437            int_ptr = &mesh->Points->Tag[0];
438            if (! (ids->put(int_ptr, num_Points)) )
439                throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
440    
441            // Points_Owner
442            if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
443                throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
444            int_ptr = &mesh->Points->Owner[0];
445            if (! (ids->put(int_ptr, num_Points)) )
446                throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
447    
448            // Points_Color
449            if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
450                throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
451            int_ptr = &mesh->Points->Color[0];
452            if (! (ids->put(int_ptr, num_Points)) )
453                throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
454    
455            // Points_Nodes
456            // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
457            if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
458                throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
459            if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
460                throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
461        }
462    
463        // // // // // TagMap // // // // //
464        if (num_Tags>0) {
465            // Temp storage to gather node IDs
466            vector<int> Tags_keys;
467    
468            // Copy tag data into temp arrays
469            TagMap::const_iterator it;
470            for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++) {
471                Tags_keys.push_back(it->second);
472            }
473    
474            // Tags_keys
475            if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
476                throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
477            int_ptr = &Tags_keys[0];
478            if (! (ids->put(int_ptr, num_Tags)) )
479                throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
480    
481            // Tags_names_*
482            // This is an array of strings, it should be stored as an array but
483            // instead I have hacked in one attribute per string because the NetCDF
484            // manual doesn't tell how to do an array of strings
485            int i = 0;
486            for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++, i++) {
487                stringstream tagnamestream;
488                tagnamestream << "Tags_name_" << i;
489                const string tagname = tagnamestream.str();
490                if (!dataFile.add_att(tagname.c_str(), it->first.c_str()))
491                    throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_X)");
492            }
493        }
494    
495        // Send token to next MPI process so he can take his turn
496    #ifdef ESYS_MPI
497        if (mpi_rank<mpi_size-1) {
498            MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
499        }
500    #endif
501    
502     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
503  #else  
504     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");  #else // USE_NETCDF
505  #endif  /* USE_NETCDF */      setError(IO_ERROR, "MeshAdapter::dump: not configured with netCDF. Please contact your installation manager.");
506     checkFinleyError();  #endif // USE_NETCDF
507        checkFinleyError();
508  }  }
509    
510  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
511  {  {
512     return "FinleyMesh";      return "FinleyMesh";
513  }  }
514    
515  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
516  {  {
517     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
518     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
519     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
520        return "Invalid function space type code.";          return "Invalid function space type code.";
521     } else {      } else {
522        return loc->second;          return loc->second;
523     }      }
524  }  }
525    
526  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
527  {  {
528     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
529     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
530     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
531  }  }
532    
533  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
534  {  {
535     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
536     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
537     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
538     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
539     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
540     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
541     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
542     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
559     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
560     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
561  }  }
562    
563  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
564  {  {
565     return Nodes;      return Nodes;
566  }  }
567    
568  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
569  {  {
570     return ReducedNodes;      return ReducedNodes;
571  }  }
572    
573  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
574  {  {
575     return Elements;      return Elements;
576  }  }
577    
578  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
579  {  {
580     return ReducedElements;      return ReducedElements;
581  }  }
582    
583  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
584  {  {
585     return FaceElements;      return FaceElements;
586  }  }
587    
588  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
589  {  {
590     return ReducedFaceElements;      return ReducedFaceElements;
591  }  }
592    
593  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
594  {  {
595     return ContactElementsZero;      return ContactElementsZero;
596  }  }
597    
598  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
599  {  {
600     return ReducedContactElementsZero;      return ReducedContactElementsZero;
601  }  }
602    
603  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
604  {  {
605     return ContactElementsOne;      return ContactElementsOne;
606  }  }
607    
608  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
609  {  {
610     return ReducedContactElementsOne;      return ReducedContactElementsOne;
611  }  }
612    
613  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
614  {  {
615     return DegreesOfFreedom;      return DegreesOfFreedom;
616  }  }
617    
618  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
619  {  {
620     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
621  }  }
622    
623  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
624  {  {
625     return Points;      return Points;
626  }  }
627    
628  //  //
# Line 649  int MeshAdapter::getDiracDeltaFunctionCo Line 630  int MeshAdapter::getDiracDeltaFunctionCo
630  //  //
631  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
632  {  {
633     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());      Mesh* mesh=m_finleyMesh.get();
634     checkFinleyError();      return mesh->getDim();
    return numDim;  
635  }  }
636    
637  //  //
# Line 659  int MeshAdapter::getDim() const Line 639  int MeshAdapter::getDim() const
639  //  //
640  int MeshAdapter::getNumDataPointsGlobal() const  int MeshAdapter::getNumDataPointsGlobal() const
641  {  {
642     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);      return m_finleyMesh.get()->Nodes->getGlobalNumNodes();
643  }  }
644    
645  //  //
# Line 668  int MeshAdapter::getNumDataPointsGlobal( Line 648  int MeshAdapter::getNumDataPointsGlobal(
648  //  //
649  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
650  {  {
651     int numDataPointsPerSample=0;      int numDataPointsPerSample=0;
652     int numSamples=0;      int numSamples=0;
653     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
654     switch (functionSpaceCode) {      switch (functionSpaceCode) {
655     case(Nodes):          case Nodes:
656     numDataPointsPerSample=1;              numDataPointsPerSample=1;
657     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumNodes();
658     break;              break;
659     case(ReducedNodes):          case ReducedNodes:
660     numDataPointsPerSample=1;              numDataPointsPerSample=1;
661     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumReducedNodes();
662     break;              break;
663     case(Elements):          case Elements:
664     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
665        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
666        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
667     }              }
668     break;              break;
669     case(ReducedElements):          case ReducedElements:
670     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
671        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
672        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
673     }              }
674     break;              break;
675     case(FaceElements):          case FaceElements:
676     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
677        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
678        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
679     }              }
680     break;              break;
681     case(ReducedFaceElements):          case ReducedFaceElements:
682     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
683        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
684        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
685     }              }
686     break;              break;
687     case(Points):          case Points:
688     if (mesh->Points!=NULL) {              if (mesh->Points!=NULL) {
689        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
690        numSamples=mesh->Points->numElements;                  numSamples=mesh->Points->numElements;
691     }              }
692     break;              break;
693     case(ContactElementsZero):          case ContactElementsZero:
694     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
695        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
696        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
697     }              }
698     break;              break;
699     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
700     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
701        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
702        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
703     }              }
704     break;              break;
705     case(ContactElementsOne):          case ContactElementsOne:
706     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
707        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
708        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
709     }              }
710     break;              break;
711     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
712     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
713        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
714        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
715     }              }
716     break;              break;
717     case(DegreesOfFreedom):          case DegreesOfFreedom:
718     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
719        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
720        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumDegreesOfFreedom();
721     }              }
722     break;              break;
723     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
724     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
725        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
726        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumReducedDegreesOfFreedom();
727     }              }
728     break;              break;
729     default:          default:
730        stringstream temp;              stringstream temp;
731        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();              temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
732        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
733        break;              break;
734     }      }
735     return pair<int,int>(numDataPointsPerSample,numSamples);      return pair<int,int>(numDataPointsPerSample,numSamples);
736  }  }
737    
738  //  //
739  // adds linear PDE of second order into a given stiffness matrix and right hand side:  // adds linear PDE of second order into a given stiffness matrix and right
740    // hand side:
741  //  //
742  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
743                                   SystemMatrixAdapter& mat, escript::Data& rhs,          escript::AbstractSystemMatrix& mat, escript::Data& rhs,
744                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& A, const escript::Data& B, const escript::Data& C,
745                                   const escript::Data& d, const escript::Data& y,          const escript::Data& D, const escript::Data& X, const escript::Data& Y,
746                                   const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d, const escript::Data& y,
747  {          const escript::Data& d_contact, const escript::Data& y_contact,
748     escriptDataC _rhs=rhs.getDataC();          const escript::Data& d_dirac, const escript::Data& y_dirac) const
749     escriptDataC _A  =A.getDataC();  {
750     escriptDataC _B=B.getDataC();      SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
751     escriptDataC _C=C.getDataC();      if (!smat)
752     escriptDataC _D=D.getDataC();          throw FinleyAdapterException("finley only supports Paso system matrices.");
753     escriptDataC _X=X.getDataC();  
754     escriptDataC _Y=Y.getDataC();      Mesh* mesh=m_finleyMesh.get();
755     escriptDataC _d=d.getDataC();      Paso_SystemMatrix* S = smat->getPaso_SystemMatrix();
756     escriptDataC _y=y.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, S, rhs, A, B, C, D, X, Y);
757     escriptDataC _d_contact=d_contact.getDataC();      checkFinleyError();
758     escriptDataC _y_contact=y_contact.getDataC();  
759    
760     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, rhs,
761                escript::Data(), escript::Data(), escript::Data(), d,
762     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );              escript::Data(), y);
763     checkFinleyError();      checkFinleyError();
764    
765     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, rhs,
766     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), d_contact,
767                escript::Data(), y_contact);
768     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      checkFinleyError();
769     checkFinleyError();  
770  }      Assemble_PDE(mesh->Nodes, mesh->Points, S, rhs, escript::Data(),
771                escript::Data(), escript::Data(), d_dirac, escript::Data(), y_dirac);
772  void  MeshAdapter::addPDEToLumpedSystem(      checkFinleyError();
773                                          escript::Data& mat,  }
774                                          const escript::Data& D,  
775                                          const escript::Data& d) const  void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
776  {          const escript::Data& D, const escript::Data& d,
777     escriptDataC _mat=mat.getDataC();          const escript::Data& d_dirac, const bool useHRZ) const
778     escriptDataC _D=D.getDataC();  {
779     escriptDataC _d=d.getDataC();      Mesh* mesh=m_finleyMesh.get();
780        Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, mat, D, useHRZ);
781        checkFinleyError();
782    
783     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, mat, d, useHRZ);
784        checkFinleyError();
785    
786     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Assemble_LumpedSystem(mesh->Nodes, mesh->Points, mat, d_dirac, useHRZ);
787     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
   
    checkFinleyError();  
788  }  }
789    
   
790  //  //
791  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
792  //  //
793  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  void MeshAdapter::addPDEToRHS(escript::Data& rhs, const escript::Data& X,
794  {          const escript::Data& Y, const escript::Data& y,
795     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
796    {
797     escriptDataC _rhs=rhs.getDataC();      Mesh* mesh=m_finleyMesh.get();
798     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, 0, rhs,
799     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
800     escriptDataC _y=y.getDataC();              X, Y);
801     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
802    
803     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Assemble_PDE(mesh->Nodes, mesh->FaceElements, 0, rhs,
804     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
805                escript::Data(), y);
806     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      checkFinleyError();
807     checkFinleyError();  
808        Assemble_PDE(mesh->Nodes, mesh->ContactElements, 0, rhs,
809     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );              escript::Data(), escript::Data(), escript::Data(),
810     checkFinleyError();              escript::Data(), escript::Data(), y_contact);
811        checkFinleyError();
812    
813        Assemble_PDE(mesh->Nodes, mesh->Points, 0, rhs,
814                escript::Data(), escript::Data(), escript::Data(), escript::Data(),
815                escript::Data(), y_dirac);
816        checkFinleyError();
817  }  }
818    
819  //  //
820  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
821  //  //
822  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
823                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
824                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
825                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
826                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
827                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
828  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
829     DataArrayView::ShapeType shape;  {
830     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
831     escriptDataC _source=source.getDataC();      if (!tpa)
832     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
833     escriptDataC _A=A.getDataC();  
834     escriptDataC _B=B.getDataC();      source.expand();
835     escriptDataC _C=C.getDataC();  
836     escriptDataC _D=D.getDataC();      Mesh* mesh=m_finleyMesh.get();
837     escriptDataC _X=X.getDataC();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
838     escriptDataC _Y=Y.getDataC();  
839     escriptDataC _d=d.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix, source,
840     escriptDataC _y=y.getDataC();                          escript::Data(), escript::Data(), escript::Data(),
841     escriptDataC _d_contact=d_contact.getDataC();                          M, escript::Data(), escript::Data());
842     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
843    
844     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
845     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();                          source, A, B, C, D, X, Y);
846        checkFinleyError();
847     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );  
848     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
849                            source, escript::Data(), escript::Data(),
850     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );                          escript::Data(), d, escript::Data(), y);
851     checkFinleyError();      checkFinleyError();
852    
853     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements,
854     checkFinleyError();                          _tp->transport_matrix, source, escript::Data(),
855                            escript::Data(), escript::Data(), d_contact,
856     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );                          escript::Data(), y_contact);
857     checkFinleyError();      checkFinleyError();
858  }  
859        Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
860  //                          source, escript::Data(), escript::Data(),
861  // interpolates data between different function spaces:                          escript::Data(), d_dirac, escript::Data(), y_dirac);
862  //      checkFinleyError();
863  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  }
864  {  
865     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());  //
866     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());  // interpolates data between different function spaces
867     if (inDomain!=*this)    //
868        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
869     if (targetDomain!=*this)  {
870        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
871        const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
872     Finley_Mesh* mesh=m_finleyMesh.get();      if (inDomain!=*this)
873     escriptDataC _target=target.getDataC();          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
874     escriptDataC _in=in.getDataC();      if (targetDomain!=*this)
875     switch(in.getFunctionSpace().getTypeCode()) {          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
876     case(Nodes):  
877     switch(target.getFunctionSpace().getTypeCode()) {      Mesh* mesh=m_finleyMesh.get();
878     case(Nodes):      switch(in.getFunctionSpace().getTypeCode()) {
879     case(ReducedNodes):          case Nodes:
880     case(DegreesOfFreedom):              switch(target.getFunctionSpace().getTypeCode()) {
881     case(ReducedDegreesOfFreedom):                  case Nodes:
882     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedNodes:
883     break;                  case DegreesOfFreedom:
884     case(Elements):                  case ReducedDegreesOfFreedom:
885     case(ReducedElements):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
886     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
887     break;                  case Elements:
888     case(FaceElements):                  case ReducedElements:
889     case(ReducedFaceElements):                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in,target);
890     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      break;
891     break;                  case FaceElements:
892     case(Points):                  case ReducedFaceElements:
893     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
894     break;                      break;
895     case(ContactElementsZero):                  case Points:
896     case(ReducedContactElementsZero):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
897     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
898     break;                  case ContactElementsZero:
899     case(ContactElementsOne):                  case ReducedContactElementsZero:
900     case(ReducedContactElementsOne):                  case ContactElementsOne:
901     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsOne:
902     break;                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
903     default:                      break;
904        stringstream temp;                  default:
905        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      stringstream temp;
906        throw FinleyAdapterException(temp.str());                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
907        break;                      throw FinleyAdapterException(temp.str());
908     }                      break;
909     break;              }
910     case(ReducedNodes):              break;
911     switch(target.getFunctionSpace().getTypeCode()) {          case ReducedNodes:
912     case(Nodes):              switch(target.getFunctionSpace().getTypeCode()) {
913     case(ReducedNodes):                  case Nodes:
914     case(DegreesOfFreedom):                  case ReducedNodes:
915     case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
916     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedDegreesOfFreedom:
917     break;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
918     case(Elements):                      break;
919     case(ReducedElements):                  case Elements:
920     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case ReducedElements:
921     break;                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
922     case(FaceElements):                      break;
923     case(ReducedFaceElements):                  case FaceElements:
924     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ReducedFaceElements:
925     break;                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
926     case(Points):                      break;
927     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case Points:
928     break;                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
929     case(ContactElementsZero):                      break;
930     case(ReducedContactElementsZero):                  case ContactElementsZero:
931     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsZero:
932     break;                  case ContactElementsOne:
933     case(ContactElementsOne):                  case ReducedContactElementsOne:
934     case(ReducedContactElementsOne):                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
935     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
936     break;                  default:
937     default:                      stringstream temp;
938        stringstream temp;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
939        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException(temp.str());
940        throw FinleyAdapterException(temp.str());                      break;
941        break;              }
942     }              break;
943     break;          case Elements:
944     case(Elements):              if (target.getFunctionSpace().getTypeCode()==Elements) {
945     if (target.getFunctionSpace().getTypeCode()==Elements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
946        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
947     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_AverageElementData(mesh->Elements, target, in);
948        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);              } else {
949     } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
950        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");              }
951     }              break;
952     break;          case ReducedElements:
953     case(ReducedElements):              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
954     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
955        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else {
956     } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
957        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              }
958     }              break;
959     break;          case FaceElements:
960     case(FaceElements):              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
961     if (target.getFunctionSpace().getTypeCode()==FaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
962        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
963     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_AverageElementData(mesh->FaceElements, target, in);
964        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              } else {
965     } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
966        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              }
967     }              break;
968     break;          case ReducedFaceElements:
969     case(ReducedFaceElements):              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
970     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
971        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else {
972     } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
973        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              }
974     }              break;
975     break;          case Points:
976     case(Points):              if (target.getFunctionSpace().getTypeCode()==Points) {
977     if (target.getFunctionSpace().getTypeCode()==Points) {                  Assemble_CopyElementData(mesh->Points, target, in);
978        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              } else {
979     } else {                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
980        throw FinleyAdapterException("Error - No interpolation with data on points possible.");              }
981     }              break;
982     break;          case ContactElementsZero:
983     case(ContactElementsZero):          case ContactElementsOne:
984     case(ContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
985     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
986        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
987     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_AverageElementData(mesh->ContactElements, target, in);
988        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);              } else {
989     } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
990        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");              }
991     }              break;
992     break;          case ReducedContactElementsZero:
993     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
994     case(ReducedContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
995     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
996        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else {
997     } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
998        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");              }
999     }              break;
1000     break;          case DegreesOfFreedom:
1001     case(DegreesOfFreedom):                    switch(target.getFunctionSpace().getTypeCode()) {
1002     switch(target.getFunctionSpace().getTypeCode()) {                  case ReducedDegreesOfFreedom:
1003     case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
1004     case(DegreesOfFreedom):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1005     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1006     break;  
1007                    case Nodes:
1008     case(Nodes):                  case ReducedNodes:
1009     case(ReducedNodes):                      if (getMPISize()>1) {
1010     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in);
1011        escript::Data temp=escript::Data(in);                          in2.expand();
1012        temp.expand();                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1013        escriptDataC _in2 = temp.getDataC();                      } else {
1014        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1015     } else {                      }
1016        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1017     }                  case Elements:
1018     break;                  case ReducedElements:
1019     case(Elements):                      if (getMPISize()>1) {
1020     case(ReducedElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1021     if (getMPISize()>1) {                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1022        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1023        escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1024        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      }
1025     } else {                      break;
1026        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case FaceElements:
1027     }                  case ReducedFaceElements:
1028     break;                      if (getMPISize()>1) {
1029     case(FaceElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1030     case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1031     if (getMPISize()>1) {                      } else {
1032        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1033        escriptDataC _in2 = temp.getDataC();                      }
1034        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1035                    case Points:
1036     } else {                      if (getMPISize()>1) {
1037        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                          //escript::Data in2=escript::Data(in, continuousFunction(*this) );
1038     }                      } else {
1039     break;                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1040     case(Points):                      }
1041     if (getMPISize()>1) {                      break;
1042        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  case ContactElementsZero:
1043        escriptDataC _in2 = temp.getDataC();                  case ContactElementsOne:
1044     } else {                  case ReducedContactElementsZero:
1045        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedContactElementsOne:
1046     }                      if (getMPISize()>1) {
1047     break;                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1048     case(ContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1049     case(ContactElementsOne):                      } else {
1050     case(ReducedContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1051     case(ReducedContactElementsOne):                      }
1052     if (getMPISize()>1) {                      break;
1053        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  default:
1054        escriptDataC _in2 = temp.getDataC();                      stringstream temp;
1055        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1056     } else {                      throw FinleyAdapterException(temp.str());
1057        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              }
1058     }              break;
1059     break;          case ReducedDegreesOfFreedom:
1060     default:              switch(target.getFunctionSpace().getTypeCode()) {
1061        stringstream temp;                  case Nodes:
1062        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1063        throw FinleyAdapterException(temp.str());                  case ReducedNodes:
1064        break;                      if (getMPISize()>1) {
1065     }                          escript::Data in2=escript::Data(in);
1066     break;                          in2.expand();
1067     case(ReducedDegreesOfFreedom):                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1068     switch(target.getFunctionSpace().getTypeCode()) {                      } else {
1069     case(Nodes):                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1070     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      }
1071     break;                      break;
1072     case(ReducedNodes):                  case DegreesOfFreedom:
1073     if (getMPISize()>1) {                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1074        escript::Data temp=escript::Data(in);                      break;
1075        temp.expand();                  case ReducedDegreesOfFreedom:
1076        escriptDataC _in2 = temp.getDataC();                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1077        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                      break;
1078     } else {                  case Elements:
1079        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedElements:
1080     }                      if (getMPISize()>1) {
1081     break;                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1082     case(DegreesOfFreedom):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1083     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                      } else {
1084     break;                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1085     case(ReducedDegreesOfFreedom):                      }
1086     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1087     break;                  case FaceElements:
1088     case(Elements):                  case ReducedFaceElements:
1089     case(ReducedElements):                      if (getMPISize()>1) {
1090     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1091        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1092        escriptDataC _in2 = temp.getDataC();                      } else {
1093        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1094     } else {                      }
1095        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
1096     }                  case Points:
1097     break;                      if (getMPISize()>1) {
1098     case(FaceElements):                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1099     case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->Points, in2, target);
1100     if (getMPISize()>1) {                      } else {
1101        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1102        escriptDataC _in2 = temp.getDataC();                      }
1103        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1104     } else {                  case ContactElementsZero:
1105        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ContactElementsOne:
1106     }                  case ReducedContactElementsZero:
1107     break;                  case ReducedContactElementsOne:
1108     case(Points):                      if (getMPISize()>1) {
1109     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1110        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1111        escriptDataC _in2 = temp.getDataC();                      } else {
1112        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1113     } else {                      }
1114        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      break;
1115     }                  default:
1116     break;                      stringstream temp;
1117     case(ContactElementsZero):                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1118     case(ContactElementsOne):                      throw FinleyAdapterException(temp.str());
1119     case(ReducedContactElementsZero):                      break;
1120     case(ReducedContactElementsOne):              }
1121     if (getMPISize()>1) {              break;
1122        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );          default:
1123        escriptDataC _in2 = temp.getDataC();              stringstream temp;
1124        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1125     } else {              throw FinleyAdapterException(temp.str());
1126        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              break;
1127     }      }
1128     break;      checkFinleyError();
    default:  
       stringstream temp;  
       temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1129  }  }
1130    
1131  //  //
1132  // copies the locations of sample points into x:  // copies the locations of sample points into x
1133  //  //
1134  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1135  {  {
1136     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1137     if (argDomain!=*this)      if (argDomain!=*this)
1138        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1139     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1140     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1141     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1142        escriptDataC _arg=arg.getDataC();          Assemble_NodeCoordinates(mesh->Nodes, arg);
1143        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);      } else {
1144     } else {          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1145        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          Assemble_NodeCoordinates(mesh->Nodes, tmp_data);
1146        escriptDataC _tmp_data=tmp_data.getDataC();          // this is then interpolated onto arg:
1147        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          interpolateOnDomain(arg, tmp_data);
1148        // this is then interpolated onto arg:      }
1149        interpolateOnDomain(arg,tmp_data);      checkFinleyError();
    }  
    checkFinleyError();  
1150  }  }
1151    
1152  //  //
1153  // return the normal vectors at the location of data points as a Data object:  // return the normal vectors at the location of data points as a Data object
1154  //  //
1155  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1156  {  {
1157     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1158     if (normalDomain!=*this)      if (normalDomain!=*this)
1159        throw FinleyAdapterException("Error - Illegal domain of normal locations");          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1160     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1161     escriptDataC _normal=normal.getDataC();      switch(normal.getFunctionSpace().getTypeCode()) {
1162     switch(normal.getFunctionSpace().getTypeCode()) {          case Nodes:
1163     case(Nodes):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1164     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");              break;
1165     break;          case ReducedNodes:
1166     case(ReducedNodes):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1167     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");              break;
1168     break;          case Elements:
1169     case(Elements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1170     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");              break;
1171     break;          case ReducedElements:
1172     case(ReducedElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1173     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");              break;
1174     break;          case FaceElements:
1175     case (FaceElements):          case ReducedFaceElements:
1176     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              Assemble_getNormal(mesh->Nodes, mesh->FaceElements, normal);
1177     break;              break;
1178     case (ReducedFaceElements):          case Points:
1179     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1180     break;              break;
1181     case(Points):          case ContactElementsOne:
1182     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ContactElementsZero:
1183     break;          case ReducedContactElementsOne:
1184     case (ContactElementsOne):          case ReducedContactElementsZero:
1185     case (ContactElementsZero):              Assemble_getNormal(mesh->Nodes, mesh->ContactElements, normal);
1186     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              break;
1187     break;          case DegreesOfFreedom:
1188     case (ReducedContactElementsOne):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1189     case (ReducedContactElementsZero):              break;
1190     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case ReducedDegreesOfFreedom:
1191     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1192     case(DegreesOfFreedom):              break;
1193     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");          default:
1194     break;              stringstream temp;
1195     case(ReducedDegreesOfFreedom):              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1196     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              throw FinleyAdapterException(temp.str());
1197     break;              break;
1198     default:      }
1199        stringstream temp;      checkFinleyError();
1200        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  }
1201        throw FinleyAdapterException(temp.str());  
1202        break;  //
1203     }  // interpolates data to other domain
1204     checkFinleyError();  //
1205  }  void MeshAdapter::interpolateACross(escript::Data& target, const escript::Data& source) const
1206    {
1207  //      throw FinleyAdapterException("Error - Finley does not allow interpolation across domains.");
1208  // interpolates data to other domain:  }
1209  //  
1210  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  //
1211  {  // calculates the integral of a function defined on arg
1212     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());  //
1213     if (targetDomain!=*this)  void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1214        throw FinleyAdapterException("Error - Illegal domain of interpolation target");  {
1215        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1216     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");      if (argDomain!=*this)
1217  }          throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1218    
1219  //      double blocktimer_start = blocktimer_time();
1220  // calculates the integral of a function defined of arg:      Mesh* mesh=m_finleyMesh.get();
1221  //      switch(arg.getFunctionSpace().getTypeCode()) {
1222  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const          case Nodes:
1223  {              {
1224     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());                  escript::Data temp(arg, escript::function(*this));
1225     if (argDomain!=*this)                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1226        throw FinleyAdapterException("Error - Illegal domain of integration kernel");              }
1227                break;
1228     double blocktimer_start = blocktimer_time();          case ReducedNodes:
1229     Finley_Mesh* mesh=m_finleyMesh.get();              {
1230     escriptDataC _temp;                  escript::Data temp(arg, escript::function(*this));
1231     escript::Data temp;                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1232     escriptDataC _arg=arg.getDataC();              }
1233     switch(arg.getFunctionSpace().getTypeCode()) {              break;
1234     case(Nodes):          case Elements:
1235     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );          case ReducedElements:
1236     _temp=temp.getDataC();              Assemble_integrate(mesh->Nodes, mesh->Elements, arg, &integrals[0]);
1237     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              break;
1238     break;          case FaceElements:
1239     case(ReducedNodes):          case ReducedFaceElements:
1240     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );              Assemble_integrate(mesh->Nodes, mesh->FaceElements, arg, &integrals[0]);
1241     _temp=temp.getDataC();              break;
1242     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);          case Points:
1243     break;              throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1244     case(Elements):              break;
1245     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ContactElementsZero:
1246     break;          case ReducedContactElementsZero:
1247     case(ReducedElements):          case ContactElementsOne:
1248     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ReducedContactElementsOne:
1249     break;              Assemble_integrate(mesh->Nodes, mesh->ContactElements, arg, &integrals[0]);
1250     case(FaceElements):              break;
1251     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);          case DegreesOfFreedom:
1252     break;          case ReducedDegreesOfFreedom:
1253     case(ReducedFaceElements):              {
1254     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);                  escript::Data temp(arg, escript::function(*this));
1255     break;                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1256     case(Points):              }
1257     throw FinleyAdapterException("Error - Integral of data on points is not supported.");              break;
1258     break;          default:
1259     case(ContactElementsZero):              stringstream temp;
1260     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1261     break;              throw FinleyAdapterException(temp.str());
1262     case(ReducedContactElementsZero):              break;
1263     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);      }
1264     break;      checkFinleyError();
1265     case(ContactElementsOne):      blocktimer_increment("integrate()", blocktimer_start);
1266     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  }
1267     break;  
1268     case(ReducedContactElementsOne):  //
1269     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  // calculates the gradient of arg
1270     break;  //
1271     case(DegreesOfFreedom):  void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1272     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );  {
1273     _temp=temp.getDataC();      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1274     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);      if (argDomain!=*this)
1275     break;          throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1276     case(ReducedDegreesOfFreedom):      const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1277     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );      if (gradDomain!=*this)
1278     _temp=temp.getDataC();          throw FinleyAdapterException("Error - Illegal domain of gradient");
1279     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
1280     break;      Mesh* mesh=m_finleyMesh.get();
1281     default:      escript::Data nodeData;
1282        stringstream temp;      if (getMPISize()>1) {
1283        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();          if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1284        throw FinleyAdapterException(temp.str());              nodeData=escript::Data(arg, continuousFunction(*this));
1285        break;          } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1286     }              nodeData=escript::Data(arg, reducedContinuousFunction(*this));
1287     checkFinleyError();          } else {
1288     blocktimer_increment("integrate()", blocktimer_start);              nodeData = arg;
1289  }          }
1290        } else {
1291  //          nodeData = arg;
1292  // calculates the gradient of arg:      }
1293  //      switch(grad.getFunctionSpace().getTypeCode()) {
1294  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const          case Nodes:
1295  {              throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1296     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());              break;
1297     if (argDomain!=*this)          case ReducedNodes:
1298        throw FinleyAdapterException("Error - Illegal domain of gradient argument");              throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1299     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());              break;
1300     if (gradDomain!=*this)          case Elements:
1301        throw FinleyAdapterException("Error - Illegal domain of gradient");          case ReducedElements:
1302                Assemble_gradient(mesh->Nodes, mesh->Elements, grad, nodeData);
1303     Finley_Mesh* mesh=m_finleyMesh.get();              break;
1304     escriptDataC _grad=grad.getDataC();          case FaceElements:
1305     escriptDataC nodeDataC;          case ReducedFaceElements:
1306     escript::Data temp;              Assemble_gradient(mesh->Nodes, mesh->FaceElements, grad, nodeData);
1307     if (getMPISize()>1) {              break;
1308        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {          case Points:
1309           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );              throw FinleyAdapterException("Error - Gradient at points is not supported.");
1310           nodeDataC = temp.getDataC();              break;
1311        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {          case ContactElementsZero:
1312           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );          case ReducedContactElementsZero:
1313           nodeDataC = temp.getDataC();          case ContactElementsOne:
1314        } else {          case ReducedContactElementsOne:
1315           nodeDataC = arg.getDataC();              Assemble_gradient(mesh->Nodes, mesh->ContactElements, grad, nodeData);
1316        }              break;
1317     } else {          case DegreesOfFreedom:
1318        nodeDataC = arg.getDataC();              throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1319     }              break;
1320     switch(grad.getFunctionSpace().getTypeCode()) {          case ReducedDegreesOfFreedom:
1321     case(Nodes):              throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1322     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");              break;
1323     break;          default:
1324     case(ReducedNodes):              stringstream temp;
1325     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");              temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1326     break;              throw FinleyAdapterException(temp.str());
1327     case(Elements):              break;
1328     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);      }
1329     break;      checkFinleyError();
    case(ReducedElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(FaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedFaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(Points):  
    throw FinleyAdapterException("Error - Gradient at points is not supported.");  
    break;  
    case(ContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(DegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");  
    break;  
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1330  }  }
1331    
1332  //  //
1333  // returns the size of elements:  // returns the size of elements
1334  //  //
1335  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1336  {  {
1337     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1338     escriptDataC tmp=size.getDataC();      switch(size.getFunctionSpace().getTypeCode()) {
1339     switch(size.getFunctionSpace().getTypeCode()) {          case Nodes:
1340     case(Nodes):              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1341     throw FinleyAdapterException("Error - Size of nodes is not supported.");              break;
1342     break;          case ReducedNodes:
1343     case(ReducedNodes):              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1344     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              break;
1345     break;          case Elements:
1346     case(Elements):          case ReducedElements:
1347     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);              Assemble_getSize(mesh->Nodes, mesh->Elements, size);
1348     break;              break;
1349     case(ReducedElements):          case FaceElements:
1350     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedFaceElements:
1351     break;              Assemble_getSize(mesh->Nodes, mesh->FaceElements, size);
1352     case(FaceElements):              break;
1353     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case Points:
1354     break;              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1355     case(ReducedFaceElements):              break;
1356     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case ContactElementsZero:
1357     break;          case ContactElementsOne:
1358     case(Points):          case ReducedContactElementsZero:
1359     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsOne:
1360     break;              Assemble_getSize(mesh->Nodes,mesh->ContactElements,size);
1361     case(ContactElementsZero):              break;
1362     case(ContactElementsOne):          case DegreesOfFreedom:
1363     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1364     break;              break;
1365     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1366     case(ReducedContactElementsOne):              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1367     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              break;
1368     break;          default:
1369     case(DegreesOfFreedom):              stringstream temp;
1370     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");              temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1371     break;              throw FinleyAdapterException(temp.str());
1372     case(ReducedDegreesOfFreedom):              break;
1373     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");      }
1374     break;      checkFinleyError();
    default:  
       stringstream temp;  
       temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1375  }  }
1376    
1377  // sets the location of nodes:  //
1378    // sets the location of nodes
1379    //
1380  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1381  {  {
1382     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1383     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1384     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());      if (newDomain!=*this)
1385     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1386        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1387     tmp = new_x.getDataC();          mesh->setCoordinates(new_x);
1388     Finley_Mesh_setCoordinates(mesh,&tmp);      } else {
1389     checkFinleyError();          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1390  }      }
1391        checkFinleyError();
1392  // saves a data array in openDX format:  }
1393  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  
1394  {  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1395     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;  {
1396     const int num_data=boost::python::extract<int>(arg.attr("__len__")());      if (getMPISize() > 1) {
1397     /* win32 refactor */  #ifdef ESYS_MPI
1398     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;          int myFirstNode=0, myLastNode=0, k=0;
1399     for(int i=0;i<num_data;i++)          int* globalNodeIndex=0;
1400     {          Mesh* mesh_p=m_finleyMesh.get();
1401        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;          /*
1402     }           * this method is only used by saveDataCSV which would use the returned
1403             * values for reduced nodes wrongly so this case is disabled for now
1404     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;          if (fs_code == FINLEY_REDUCED_NODES) {
1405     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;              myFirstNode = NodeFile_getFirstReducedNode(mesh_p->Nodes);
1406                myLastNode = NodeFile_getLastReducedNode(mesh_p->Nodes);
1407     boost::python::list keys=arg.keys();              globalNodeIndex = NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1408     for (int i=0;i<num_data;++i) {          } else
1409        std::string n=boost::python::extract<std::string>(keys[i]);          */
1410        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);          if (fs_code == FINLEY_NODES) {
1411        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)              myFirstNode = mesh_p->Nodes->getFirstNode();
1412           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");              myLastNode = mesh_p->Nodes->getLastNode();
1413        data[i]=d.getDataC();              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1414        ptr_data[i]= &(data[i]);          } else {
1415        if (n.length()>MAX_namelength-1) {              throw FinleyAdapterException("Unsupported function space type for ownSample()");
1416           strncpy(names[i],n.c_str(),MAX_namelength-1);          }
1417           names[i][MAX_namelength-1]='\0';  
1418        } else {          k=globalNodeIndex[id];
1419           strcpy(names[i],n.c_str());          return ((myFirstNode <= k) && (k < myLastNode));
       }  
    }  
    Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0;i<num_data;i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
   
    return;  
 }  
   
 // saves a data array in openVTK format:  
 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  
 {  
    unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;  
    const int num_data=boost::python::extract<int>(arg.attr("__len__")());  
    /* win32 refactor */  
    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
    for(int i=0;i<num_data;i++)  
    {  
       names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
    }  
   
    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  
    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
    boost::python::list keys=arg.keys();  
    for (int i=0;i<num_data;++i) {  
       std::string n=boost::python::extract<std::string>(keys[i]);  
       escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
       if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
          throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
       data[i]=d.getDataC();  
       ptr_data[i]=&(data[i]);  
       if (n.length()>MAX_namelength-1) {  
          strncpy(names[i],n.c_str(),MAX_namelength-1);  
          names[i][MAX_namelength-1]='\0';  
       } else {  
          strcpy(names[i],n.c_str());  
       }  
    }  
    Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);  
   
    checkFinleyError();  
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0;i<num_data;i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
   
    return;  
 }  
                                                                                                                                                                       
                                                                                                                                                                       
 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  
 SystemMatrixAdapter MeshAdapter::newSystemMatrix(  
                                                  const int row_blocksize,  
                                                  const escript::FunctionSpace& row_functionspace,  
                                                  const int column_blocksize,  
                                                  const escript::FunctionSpace& column_functionspace,  
                                                  const int type) const  
 {  
    int reduceRowOrder=0;  
    int reduceColOrder=0;  
    // is the domain right?  
    const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());  
    if (row_domain!=*this)  
       throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");  
    const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());  
    if (col_domain!=*this)  
       throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");  
    // is the function space type right  
    if (row_functionspace.getTypeCode()==DegreesOfFreedom) {  
       reduceRowOrder=0;  
    } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {  
       reduceRowOrder=1;  
    } else {  
       throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
    }  
    if (column_functionspace.getTypeCode()==DegreesOfFreedom) {  
       reduceColOrder=0;  
    } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {  
       reduceColOrder=1;  
    } else {  
       throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
    }  
    // generate matrix:  
   
    Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  
    checkFinleyError();  
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
 #ifdef TRILINOS  
       /* Allocation Epetra_VrbMatrix here */  
1420  #endif  #endif
1421     }      }
1422     else {      return true;
       fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);  
    }  
    checkPasoError();  
    Paso_SystemMatrixPattern_free(fsystemMatrixPattern);  
    return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1423  }  }
1424  // creates a TransportProblemAdapter  
1425  TransportProblemAdapter MeshAdapter::newTransportProblem(  
1426                                                           const double theta,  //
1427                                                           const int blocksize,  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1428                                                           const escript::FunctionSpace& functionspace,  //
1429                                                           const int type) const  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1430  {                              const escript::FunctionSpace& row_functionspace,
1431     int reduceOrder=0;                              const int column_blocksize,
1432     // is the domain right?                              const escript::FunctionSpace& column_functionspace,
1433     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());                              const int type) const
1434     if (domain!=*this)  {
1435        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      // is the domain right?
1436     // is the function space type right      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1437     if (functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_domain!=*this)
1438        reduceOrder=0;          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1439     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1440        reduceOrder=1;      if (col_domain!=*this)
1441     } else {          throw FinleyAdapterException("Error - domain of column function space does not match the domain of matrix generator.");
1442        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
1443     }      int reduceRowOrder=0;
1444     // generate matrix:      int reduceColOrder=0;
1445        // is the function space type right?
1446     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1447     checkFinleyError();          reduceRowOrder=1;
1448     Paso_FCTransportProblem* transportProblem;      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1449     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1450     checkPasoError();      }
1451     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1452     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);          reduceColOrder=1;
1453        } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1454            throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1455        }
1456    
1457        // generate matrix:
1458        paso::SystemMatrixPattern* fsystemMatrixPattern=
1459            getFinley_Mesh()->getPattern(reduceRowOrder, reduceColOrder);
1460        checkFinleyError();
1461        Paso_SystemMatrix* fsystemMatrix;
1462        const int trilinos = 0;
1463        if (trilinos) {
1464    #ifdef TRILINOS
1465            // FIXME: Allocation Epetra_VrbMatrix here...
1466    #endif
1467        } else {
1468            fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1469                    row_blocksize, column_blocksize, FALSE);
1470        }
1471        checkPasoError();
1472        paso::SystemMatrixPattern_free(fsystemMatrixPattern);
1473        SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1474        return escript::ASM_ptr(sma);
1475  }  }
1476    
1477  //  //
1478  // vtkObject MeshAdapter::createVtkObject() const  // creates a TransportProblemAdapter
 // TODO:  
1479  //  //
1480    escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1481            const escript::FunctionSpace& functionspace, const int type) const
1482    {
1483        // is the domain right?
1484        const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1485        if (domain!=*this)
1486            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1487    
1488        // is the function space type right?
1489        int reduceOrder=0;
1490        if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1491            reduceOrder=1;
1492        } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1493            throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1494        }
1495    
1496        // generate transport problem:
1497        paso::SystemMatrixPattern* fsystemMatrixPattern=
1498            getFinley_Mesh()->getPattern(reduceOrder, reduceOrder);
1499        checkFinleyError();
1500        Paso_TransportProblem* transportProblem;
1501        transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1502        checkPasoError();
1503        paso::SystemMatrixPattern_free(fsystemMatrixPattern);
1504        TransportProblemAdapter* tpa=new TransportProblemAdapter(
1505                transportProblem, blocksize, functionspace);
1506        return escript::ATP_ptr(tpa);
1507    }
1508    
1509  //  //
1510  // returns true if data at the atom_type is considered as being cell centered:  // returns true if data on functionSpaceCode is considered as being cell centered
1511    //
1512  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1513  {  {
1514     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1515     case(Nodes):          case Nodes:
1516     case(DegreesOfFreedom):          case DegreesOfFreedom:
1517     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1518     return false;              return false;
1519     break;          case Elements:
1520     case(Elements):          case FaceElements:
1521     case(FaceElements):          case Points:
1522     case(Points):          case ContactElementsZero:
1523     case(ContactElementsZero):          case ContactElementsOne:
1524     case(ContactElementsOne):          case ReducedElements:
1525     case(ReducedElements):          case ReducedFaceElements:
1526     case(ReducedFaceElements):          case ReducedContactElementsZero:
1527     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1528     case(ReducedContactElementsOne):              return true;
1529     return true;          default:
1530     break;              stringstream temp;
1531     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1532        stringstream temp;              throw FinleyAdapterException(temp.str());
1533        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1534        throw FinleyAdapterException(temp.str());      }
1535        break;      return false;
1536     }  }
1537     checkFinleyError();  
1538     return false;  bool
1539  }  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1540    {
1541  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const      /* The idea is to use equivalence classes. [Types which can be interpolated
1542  {         back and forth]:
1543     switch(functionSpaceType_source) {          class 1: DOF <-> Nodes
1544     case(Nodes):          class 2: ReducedDOF <-> ReducedNodes
1545     switch(functionSpaceType_target) {          class 3: Points
1546     case(Nodes):          class 4: Elements
1547     case(ReducedNodes):          class 5: ReducedElements
1548     case(ReducedDegreesOfFreedom):          class 6: FaceElements
1549     case(DegreesOfFreedom):          class 7: ReducedFaceElements
1550     case(Elements):          class 8: ContactElementZero <-> ContactElementOne
1551     case(ReducedElements):          class 9: ReducedContactElementZero <-> ReducedContactElementOne
1552     case(FaceElements):  
1553     case(ReducedFaceElements):      There is also a set of lines. Interpolation is possible down a line but
1554     case(Points):      not between lines.
1555     case(ContactElementsZero):      class 1 and 2 belong to all lines so aren't considered.
1556     case(ReducedContactElementsZero):          line 0: class 3
1557     case(ContactElementsOne):          line 1: class 4,5
1558     case(ReducedContactElementsOne):          line 2: class 6,7
1559     return true;          line 3: class 8,9
1560     default:  
1561        stringstream temp;      For classes with multiple members (eg class 2) we have vars to record if
1562        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      there is at least one instance.
1563        throw FinleyAdapterException(temp.str());      e.g. hasnodes is true if we have at least one instance of Nodes.
1564     }      */
1565     break;      if (fs.empty())
1566     case(ReducedNodes):          return false;
1567     switch(functionSpaceType_target) {  
1568     case(ReducedNodes):      vector<int> hasclass(10);
1569     case(ReducedDegreesOfFreedom):      vector<int> hasline(4);    
1570     case(Elements):      bool hasnodes=false;
1571     case(ReducedElements):      bool hasrednodes=false;
1572     case(FaceElements):      bool hascez=false;
1573     case(ReducedFaceElements):      bool hasrcez=false;
1574     case(Points):      for (int i=0;i<fs.size();++i) {
1575     case(ContactElementsZero):          switch(fs[i]) {
1576     case(ReducedContactElementsZero):              case Nodes:
1577     case(ContactElementsOne):                  hasnodes=true; // fall through
1578     case(ReducedContactElementsOne):              case DegreesOfFreedom:
1579     return true;                  hasclass[1]=1;
1580     case(Nodes):                  break;
1581     case(DegreesOfFreedom):              case ReducedNodes:
1582     return false;                  hasrednodes=true; // fall through
1583     default:              case ReducedDegreesOfFreedom:
1584        stringstream temp;                  hasclass[2]=1;
1585        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                  break;
1586        throw FinleyAdapterException(temp.str());              case Points:
1587     }                  hasline[0]=1;
1588     break;                  hasclass[3]=1;
1589     case(Elements):                  break;
1590     if (functionSpaceType_target==Elements) {              case Elements:
1591        return true;                  hasclass[4]=1;
1592     } else if (functionSpaceType_target==ReducedElements) {                  hasline[1]=1;
1593        return true;                  break;
1594     } else {              case ReducedElements:
1595        return false;                  hasclass[5]=1;
1596     }                  hasline[1]=1;
1597     case(ReducedElements):                  break;
1598     if (functionSpaceType_target==ReducedElements) {              case FaceElements:
1599        return true;                  hasclass[6]=1;
1600     } else {                  hasline[2]=1;
1601        return false;                  break;
1602     }              case ReducedFaceElements:
1603     case(FaceElements):                  hasclass[7]=1;
1604     if (functionSpaceType_target==FaceElements) {                  hasline[2]=1;
1605        return true;                  break;
1606     } else if (functionSpaceType_target==ReducedFaceElements) {              case ContactElementsZero:
1607        return true;                  hascez=true; // fall through
1608     } else {              case ContactElementsOne:
1609        return false;                  hasclass[8]=1;
1610     }                  hasline[3]=1;
1611     case(ReducedFaceElements):                  break;
1612     if (functionSpaceType_target==ReducedFaceElements) {              case ReducedContactElementsZero:
1613        return true;                  hasrcez=true; // fall through
1614     } else {              case ReducedContactElementsOne:
1615        return false;                  hasclass[9]=1;
1616     }                  hasline[3]=1;
1617     case(Points):                  break;
1618     if (functionSpaceType_target==Points) {              default:
1619        return true;                  return false;
1620     } else {          }
1621        return false;      }
1622     }      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1623     case(ContactElementsZero):  
1624     case(ContactElementsOne):      // fail if we have more than one leaf group
1625     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {      if (totlines>1)
1626        return true;          return false; // there are at least two branches we can't interpolate between
1627     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {      else if (totlines==1) {
1628        return true;          if (hasline[0]==1)              // we have points
1629     } else {              resultcode=Points;
1630        return false;          else if (hasline[1]==1) {
1631     }              if (hasclass[5]==1)
1632     case(ReducedContactElementsZero):                  resultcode=ReducedElements;
1633     case(ReducedContactElementsOne):              else
1634     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {                  resultcode=Elements;
1635        return true;          } else if (hasline[2]==1) {
1636     } else {              if (hasclass[7]==1)
1637        return false;                  resultcode=ReducedFaceElements;
1638     }              else
1639     case(DegreesOfFreedom):                  resultcode=FaceElements;
1640     switch(functionSpaceType_target) {          } else {   // so we must be in line3
1641     case(ReducedDegreesOfFreedom):              if (hasclass[9]==1) {
1642     case(DegreesOfFreedom):                  // need something from class 9
1643     case(Nodes):                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1644     case(ReducedNodes):              } else {
1645     case(Elements):                  // something from class 8
1646     case(ReducedElements):                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1647     case(Points):              }
1648     case(FaceElements):          }
1649     case(ReducedFaceElements):      } else { // totlines==0
1650     case(ContactElementsZero):          if (hasclass[2]==1) {
1651     case(ReducedContactElementsZero):              // something from class 2
1652     case(ContactElementsOne):              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1653     case(ReducedContactElementsOne):          } else {
1654     return true;              // something from class 1
1655     default:              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1656        stringstream temp;          }
1657        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      }
1658        throw FinleyAdapterException(temp.str());      return true;
1659     }  }
1660     break;  
1661     case(ReducedDegreesOfFreedom):  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1662     switch(functionSpaceType_target) {                                               int functionSpaceType_target) const
1663     case(ReducedDegreesOfFreedom):  {
1664     case(ReducedNodes):      switch(functionSpaceType_source) {
1665     case(Elements):          case Nodes:
1666     case(ReducedElements):              switch(functionSpaceType_target) {
1667     case(FaceElements):                  case Nodes:
1668     case(ReducedFaceElements):                  case ReducedNodes:
1669     case(Points):                  case ReducedDegreesOfFreedom:
1670     case(ContactElementsZero):                  case DegreesOfFreedom:
1671     case(ReducedContactElementsZero):                  case Elements:
1672     case(ContactElementsOne):                  case ReducedElements:
1673     case(ReducedContactElementsOne):                  case FaceElements:
1674     return true;                  case ReducedFaceElements:
1675     case(Nodes):                  case Points:
1676     case(DegreesOfFreedom):                  case ContactElementsZero:
1677     return false;                  case ReducedContactElementsZero:
1678     default:                  case ContactElementsOne:
1679        stringstream temp;                  case ReducedContactElementsOne:
1680        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      return true;
1681        throw FinleyAdapterException(temp.str());                  default:
1682     }                      stringstream temp;
1683     break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1684     default:                      throw FinleyAdapterException(temp.str());
1685        stringstream temp;              }
1686        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;              break;
1687        throw FinleyAdapterException(temp.str());          case ReducedNodes:
1688        break;              switch(functionSpaceType_target) {
1689     }                  case ReducedNodes:
1690     checkFinleyError();                  case ReducedDegreesOfFreedom:
1691     return false;                  case Elements:
1692  }                  case ReducedElements:
1693                    case FaceElements:
1694  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const                  case ReducedFaceElements:
1695  {                  case Points:
1696     return false;                  case ContactElementsZero:
1697  }                  case ReducedContactElementsZero:
1698                    case ContactElementsOne:
1699  bool MeshAdapter::operator==(const AbstractDomain& other) const                  case ReducedContactElementsOne:
1700  {                      return true;
1701     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);                  case Nodes:
1702     if (temp!=0) {                  case DegreesOfFreedom:
1703        return (m_finleyMesh==temp->m_finleyMesh);                      return false;
1704     } else {                  default:
1705        return false;                      stringstream temp;
1706     }                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1707  }                      throw FinleyAdapterException(temp.str());
1708                }
1709  bool MeshAdapter::operator!=(const AbstractDomain& other) const              break;
1710  {          case Elements:
1711     return !(operator==(other));              if (functionSpaceType_target==Elements) {
1712  }                  return true;
1713                } else if (functionSpaceType_target==ReducedElements) {
1714  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const                  return true;
1715  {              } else {
1716     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);                  return false;
1717     checkPasoError();              }
1718     return out;          case ReducedElements:
1719                if (functionSpaceType_target==ReducedElements) {
1720                    return true;
1721                } else {
1722                    return false;
1723                }
1724            case FaceElements:
1725                if (functionSpaceType_target==FaceElements) {
1726                    return true;
1727                } else if (functionSpaceType_target==ReducedFaceElements) {
1728                    return true;
1729                } else {
1730                    return false;
1731                }
1732            case ReducedFaceElements:
1733                if (functionSpaceType_target==ReducedFaceElements) {
1734                    return true;
1735                } else {
1736                    return false;
1737                }
1738            case Points:
1739                if (functionSpaceType_target==Points) {
1740                    return true;
1741                } else {
1742                    return false;
1743                }
1744            case ContactElementsZero:
1745            case ContactElementsOne:
1746                if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1747                    return true;
1748                } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1749                    return true;
1750                } else {
1751                    return false;
1752                }
1753            case ReducedContactElementsZero:
1754            case ReducedContactElementsOne:
1755                if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1756                    return true;
1757                } else {
1758                    return false;
1759                }
1760            case DegreesOfFreedom:
1761                switch(functionSpaceType_target) {
1762                    case ReducedDegreesOfFreedom:
1763                    case DegreesOfFreedom:
1764                    case Nodes:
1765                    case ReducedNodes:
1766                    case Elements:
1767                    case ReducedElements:
1768                    case Points:
1769                    case FaceElements:
1770                    case ReducedFaceElements:
1771                    case ContactElementsZero:
1772                    case ReducedContactElementsZero:
1773                    case ContactElementsOne:
1774                    case ReducedContactElementsOne:
1775                        return true;
1776                    default:
1777                        stringstream temp;
1778                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1779                        throw FinleyAdapterException(temp.str());
1780                }
1781                break;
1782            case ReducedDegreesOfFreedom:
1783                switch(functionSpaceType_target) {
1784                    case ReducedDegreesOfFreedom:
1785                    case ReducedNodes:
1786                    case Elements:
1787                    case ReducedElements:
1788                    case FaceElements:
1789                    case ReducedFaceElements:
1790                    case Points:
1791                    case ContactElementsZero:
1792                    case ReducedContactElementsZero:
1793                    case ContactElementsOne:
1794                    case ReducedContactElementsOne:
1795                        return true;
1796                    case Nodes:
1797                    case DegreesOfFreedom:
1798                        return false;
1799                    default:
1800                        stringstream temp;
1801                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1802                        throw FinleyAdapterException(temp.str());
1803                }
1804                break;
1805            default:
1806                stringstream temp;
1807                temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1808                throw FinleyAdapterException(temp.str());
1809                break;
1810        }
1811        return false;
1812    }
1813    
1814    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1815    {
1816        if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1817            return 1;
1818    
1819        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1820            return -1;
1821    
1822        return 0;
1823    }
1824    
1825    bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1826            const escript::AbstractDomain& targetDomain,
1827            int functionSpaceType_target) const
1828    {
1829        return false;
1830    }
1831    
1832    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1833    {
1834        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1835        if (temp) {
1836            return (m_finleyMesh==temp->m_finleyMesh);
1837        } else {
1838            return false;
1839        }
1840    }
1841    
1842    bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1843    {
1844        return !(operator==(other));
1845    }
1846    
1847    int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1848    {
1849        Mesh* mesh=m_finleyMesh.get();
1850        return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1851                   package, symmetry, mesh->MPIInfo);
1852    }
1853    
1854    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1855    {
1856        Mesh* mesh=m_finleyMesh.get();
1857        return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1858                    package, symmetry, mesh->MPIInfo);
1859  }  }
1860    
1861  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1862  {  {
1863     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1864  }  }
1865    
1866  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1867  {  {
1868     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1869  }  }
1870    
1871  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1872  {  {
1873     return function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1874  }  }
1875    
1876  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1877  {  {
1878     int *out = NULL;      int *out = NULL;
1879     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1880     switch (functionSpaceType) {      switch (functionSpaceType) {
1881     case(Nodes):          case Nodes:
1882     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1883     break;              break;
1884     case(ReducedNodes):          case ReducedNodes:
1885     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1886     break;              break;
1887     case(Elements):          case Elements:
1888     out=mesh->Elements->Id;          case ReducedElements:
1889     break;              out=mesh->Elements->Id;
1890     case(ReducedElements):              break;
1891     out=mesh->Elements->Id;          case FaceElements:
1892     break;          case ReducedFaceElements:
1893     case(FaceElements):              out=mesh->FaceElements->Id;
1894     out=mesh->FaceElements->Id;              break;
1895     break;          case Points:
1896     case(ReducedFaceElements):              out=mesh->Points->Id;
1897     out=mesh->FaceElements->Id;              break;
1898     break;          case ContactElementsZero:
1899     case(Points):          case ReducedContactElementsZero:
1900     out=mesh->Points->Id;          case ContactElementsOne:
1901     break;          case ReducedContactElementsOne:
1902     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1903     out=mesh->ContactElements->Id;              break;
1904     break;          case DegreesOfFreedom:
1905     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1906     out=mesh->ContactElements->Id;              break;
1907     break;          case ReducedDegreesOfFreedom:
1908     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1909     out=mesh->ContactElements->Id;              break;
1910     break;          default:
1911     case(ReducedContactElementsOne):              stringstream temp;
1912     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1913     break;              throw FinleyAdapterException(temp.str());
1914     case(DegreesOfFreedom):              break;
1915     out=mesh->Nodes->degreesOfFreedomId;      }
1916     break;      return out;
    case(ReducedDegreesOfFreedom):  
    out=mesh->Nodes->reducedDegreesOfFreedomId;  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    return out;  
1917  }  }
1918  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1919  {  {
1920     int out=0;      int out=0;
1921     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1922     switch (functionSpaceType) {      switch (functionSpaceType) {
1923     case(Nodes):          case Nodes:
1924     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1925     break;              break;
1926     case(ReducedNodes):          case ReducedNodes:
1927     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1928     break;              break;
1929     case(Elements):          case Elements:
1930     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1931     break;              out=mesh->Elements->Tag[sampleNo];
1932     case(ReducedElements):              break;
1933     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1934     break;          case ReducedFaceElements:
1935     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1936     out=mesh->FaceElements->Tag[sampleNo];              break;
1937     break;          case Points:
1938     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1939     out=mesh->FaceElements->Tag[sampleNo];              break;
1940     break;          case ContactElementsZero:
1941     case(Points):          case ReducedContactElementsZero:
1942     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
1943     break;          case ReducedContactElementsOne:
1944     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
1945     out=mesh->ContactElements->Tag[sampleNo];              break;
1946     break;          case DegreesOfFreedom:
1947     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1948     out=mesh->ContactElements->Tag[sampleNo];              break;
1949     break;          case ReducedDegreesOfFreedom:
1950     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1951     out=mesh->ContactElements->Tag[sampleNo];              break;
1952     break;          default:
1953     case(ReducedContactElementsOne):              stringstream temp;
1954     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1955     break;              throw FinleyAdapterException(temp.str());
1956     case(DegreesOfFreedom):              break;
1957     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
1958     break;      return out;
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    return out;  
1959  }  }
1960    
1961    
1962  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1963  {  {
1964     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1965     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
1966     switch(functionSpaceType) {          case Nodes:
1967     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
1968     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
1969     break;          case ReducedNodes:
1970     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1971     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
1972     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1973     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
1974     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1975     break;          case Elements:
1976     case(ReducedDegreesOfFreedom):          case ReducedElements:
1977     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
1978     break;              break;
1979     case(Elements):          case FaceElements:
1980     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
1981     break;              mesh->FaceElements->setTags(newTag, mask);
1982     case(ReducedElements):              break;
1983     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
1984     break;              mesh->Points->setTags(newTag, mask);
1985     case(FaceElements):              break;
1986     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
1987     break;          case ReducedContactElementsZero:
1988     case(ReducedFaceElements):          case ContactElementsOne:
1989     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
1990     break;              mesh->ContactElements->setTags(newTag, mask);
1991     case(Points):              break;
1992     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
1993     break;              stringstream temp;
1994     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1995     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
1996     break;      }
1997     case(ReducedContactElementsZero):      checkFinleyError();
1998     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
1999     break;  
2000     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
2001     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
2002     break;      Mesh* mesh=m_finleyMesh.get();
2003     case(ReducedContactElementsOne):      mesh->addTagMap(name.c_str(), tag);
2004     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2005     break;  }
2006     default:  
2007        stringstream temp;  int MeshAdapter::getTag(const string& name) const
2008        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  {
2009        throw FinleyAdapterException(temp.str());      Mesh* mesh=m_finleyMesh.get();
2010     }      int tag = mesh->getTag(name.c_str());
2011     checkFinleyError();      checkFinleyError();
2012     return;      return tag;
2013  }  }
2014    
2015  void MeshAdapter::setTagMap(const std::string& name,  int tag)  bool MeshAdapter::isValidTagName(const string& name) const
2016  {  {
2017     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2018     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);      return mesh->isValidTagName(name.c_str());
2019     checkPasoError();  }
2020     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2021  }  string MeshAdapter::showTagNames() const
2022    {
2023  int MeshAdapter::getTag(const std::string& name) const      stringstream temp;
2024  {      Mesh* mesh=m_finleyMesh.get();
2025     Finley_Mesh* mesh=m_finleyMesh.get();      TagMap::const_iterator it = mesh->tagMap.begin();
2026     int tag=0;      while (it != mesh->tagMap.end()) {
2027     tag=Finley_Mesh_getTag(mesh, name.c_str());          temp << it->first;
2028     checkPasoError();          ++it;
2029     // throwStandardException("MeshAdapter::getTag is not implemented.");          if (it != mesh->tagMap.end())
2030     return tag;              temp << ", ";
2031  }      }
2032        return temp.str();
 bool MeshAdapter::isValidTagName(const std::string& name) const  
 {  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    return Finley_Mesh_isValidTagName(mesh,name.c_str());  
 }  
   
 std::string MeshAdapter::showTagNames() const  
 {  
    stringstream temp;  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    Finley_TagMap* tag_map=mesh->TagMap;  
    while (tag_map) {  
       temp << tag_map->name;  
       tag_map=tag_map->next;  
       if (tag_map) temp << ", ";  
    }  
    return temp.str();  
2033  }  }
2034    
2035  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2036  {  {
2037    Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2038    dim_t numTags=0;      switch(functionSpaceCode) {
2039    switch(functionSpaceCode) {          case Nodes:
2040     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2041            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2042            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2043     case(ReducedNodes):          case DegreesOfFreedom:
2044            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2045            break;          case ReducedDegreesOfFreedom:
2046     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2047            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2048            break;          case ReducedElements:
2049     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2050            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2051            break;          case ReducedFaceElements:
2052     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2053     case(ReducedElements):          case Points:
2054            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2055            break;          case ContactElementsZero:
2056     case(FaceElements):          case ReducedContactElementsZero:
2057     case(ReducedFaceElements):          case ContactElementsOne:
2058            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2059            break;              return mesh->ContactElements->tagsInUse.size();
2060     case(Points):          default:
2061            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2062            break;              ss << "Finley does not know anything about function space type "
2063     case(ContactElementsZero):                   << functionSpaceCode;
2064     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2065     case(ContactElementsOne):      }
2066     case(ReducedContactElementsOne):      return 0;
2067            numTags=mesh->ContactElements->numTagsInUse;  }
2068            break;  
2069     default:  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2070        stringstream temp;  {
2071        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;      Mesh* mesh=m_finleyMesh.get();
2072        throw FinleyAdapterException(temp.str());      switch(functionSpaceCode) {
2073    }          case Nodes:
2074    return numTags;              return &mesh->Nodes->tagsInUse[0];
2075  }          case ReducedNodes:
2076  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2077  {          case DegreesOfFreedom:
2078    Finley_Mesh* mesh=m_finleyMesh.get();              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2079    index_t* tags=NULL;          case ReducedDegreesOfFreedom:
2080    switch(functionSpaceCode) {              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2081     case(Nodes):          case Elements:
2082            tags=mesh->Nodes->tagsInUse;          case ReducedElements:
2083            break;              return &mesh->Elements->tagsInUse[0];
2084     case(ReducedNodes):          case FaceElements:
2085            throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case ReducedFaceElements:
2086            break;              return &mesh->FaceElements->tagsInUse[0];
2087     case(DegreesOfFreedom):          case Points:
2088            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              return &mesh->Points->tagsInUse[0];
2089            break;          case ContactElementsZero:
2090     case(ReducedDegreesOfFreedom):          case ReducedContactElementsZero:
2091            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case ContactElementsOne:
2092            break;          case ReducedContactElementsOne:
2093     case(Elements):              return &mesh->ContactElements->tagsInUse[0];
2094     case(ReducedElements):          default:
2095            tags=mesh->Elements->tagsInUse;              stringstream temp;
2096            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2097     case(FaceElements):              throw FinleyAdapterException(temp.str());
2098     case(ReducedFaceElements):      }
2099            tags=mesh->FaceElements->tagsInUse;      return NULL;
2100            break;  }
2101     case(Points):  
2102            tags=mesh->Points->tagsInUse;  
2103            break;  bool MeshAdapter::canTag(int functionSpaceCode) const
2104     case(ContactElementsZero):  {
2105     case(ReducedContactElementsZero):      switch(functionSpaceCode) {
2106     case(ContactElementsOne):          case Nodes:
2107     case(ReducedContactElementsOne):          case Elements:
2108            tags=mesh->ContactElements->tagsInUse;          case ReducedElements:
2109            break;          case FaceElements:
2110     default:          case ReducedFaceElements:
2111        stringstream temp;          case Points:
2112        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;          case ContactElementsZero:
2113        throw FinleyAdapterException(temp.str());          case ReducedContactElementsZero:
2114    }          case ContactElementsOne:
2115    return tags;          case ReducedContactElementsOne:
2116                return true;
2117            default:
2118                return false;
2119        }
2120    }
2121    
2122    escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2123    {
2124        Mesh* mesh=m_finleyMesh.get();
2125        return mesh->getStatus();
2126    }
2127    
2128    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2129    {
2130        Mesh* mesh=m_finleyMesh.get();
2131        int order =-1;
2132        switch(functionSpaceCode) {
2133            case Nodes:
2134            case DegreesOfFreedom:
2135                order=mesh->approximationOrder;
2136                break;
2137            case ReducedNodes:
2138            case ReducedDegreesOfFreedom:
2139                order=mesh->reducedApproximationOrder;
2140                break;
2141            case Elements:
2142            case FaceElements:
2143            case Points:
2144            case ContactElementsZero:
2145            case ContactElementsOne:
2146                order=mesh->integrationOrder;
2147                break;
2148            case ReducedElements:
2149            case ReducedFaceElements:
2150            case ReducedContactElementsZero:
2151            case ReducedContactElementsOne:
2152                order=mesh->reducedIntegrationOrder;
2153                break;
2154            default:
2155                stringstream temp;
2156                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2157                throw FinleyAdapterException(temp.str());
2158        }
2159        return order;
2160    }
2161    
2162    bool MeshAdapter::supportsContactElements() const
2163    {
2164        return true;
2165    }
2166    
2167    escript::Data MeshAdapter::randomFill(const escript::DataTypes::ShapeType& shape,
2168           const escript::FunctionSpace& what, long seed, const boost::python::tuple& filter) const
2169    {
2170        escript::Data towipe(0, shape, what, true);
2171        // since we just made this object, no sharing is possible and we don't need to check for
2172        // exlusive write
2173        escript::DataTypes::ValueType& dv=towipe.getExpandedVectorReference();
2174        const size_t dvsize=dv.size();
2175        esysUtils::randomFillArray(seed, &(dv[0]), dvsize);
2176        return towipe;  
2177    }
2178    
2179    
2180    void MeshAdapter::addDiracPoints(const vector<double>& points,
2181                                     const vector<int>& tags) const
2182    {
2183        // points will be flattened
2184        const int dim = getDim();
2185        int numPoints=points.size()/dim;
2186        int numTags=tags.size();
2187        Mesh* mesh=m_finleyMesh.get();
2188    
2189        if ( points.size() % dim != 0 ) {
2190            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2191        }
2192    
2193        if ((numTags > 0) && (numPoints != numTags))
2194            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2195    
2196        mesh->addPoints(numPoints, &points[0], &tags[0]);
2197        checkFinleyError();
2198    }
2199    
2200    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2201    // {
2202    //       const int dim = getDim();
2203    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2204    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2205    //       Mesh* mesh=m_finleyMesh.get();
2206    //
2207    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2208    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2209    //
2210    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2211    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2212    //
2213    //       for (int i=0;i<numPoints;++i) {
2214    //         int tag_id=-1;
2215    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2216    //         if  ( numComps !=   dim ) {
2217    //                stringstream temp;
2218    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2219    //                throw FinleyAdapterException(temp.str());
2220    //         }
2221    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2222    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2223    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2224    //
2225    //         if ( numTags > 0) {
2226    //                boost::python::extract<string> ex_str(tags[i]);
2227    //                if  ( ex_str.check() ) {
2228    //                    tag_id=getTag( ex_str());
2229    //                } else {
2230    //                     boost::python::extract<int> ex_int(tags[i]);
2231    //                     if ( ex_int.check() ) {
2232    //                         tag_id=ex_int();
2233    //                     } else {
2234    //                          stringstream temp;
2235    //                          temp << "Error - unable to extract tag for point " << i;
2236    //                          throw FinleyAdapterException(temp.str());
2237    //                    }
2238    //                }
2239    //         }
2240    //            tags_ptr[i]=tag_id;
2241    //       }
2242    //
2243    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2244    //       checkPasoError();
2245    //
2246    //       TMPMEMFREE(points_ptr);
2247    //       TMPMEMFREE(tags_ptr);
2248    // }
2249    
2250    /*
2251    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2252    {
2253        boost::python::list points =  boost::python::list();
2254        boost::python::list tags =  boost::python::list();
2255        points.append(point);
2256        tags.append(tag);
2257        addDiracPoints(points, tags);
2258    }
2259    */
2260    
2261    /*
2262    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2263    {
2264        boost::python::list points =   boost::python::list();
2265        boost::python::list tags =   boost::python::list();
2266        points.append(point);
2267        tags.append(tag);
2268        addDiracPoints(points, tags);
2269  }  }
2270    */
   
2271  }  // end of namespace  }  // end of namespace
2272    

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