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/* $Id$ */ |
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|
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/******************************************************* |
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* |
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* Copyright 2003-2007 by ACceSS MNRF |
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* Copyright 2007 by University of Queensland |
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* |
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* http://esscc.uq.edu.au |
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* Primary Business: Queensland, Australia |
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* Licensed under the Open Software License version 3.0 |
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* http://www.opensource.org/licenses/osl-3.0.php |
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* |
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*******************************************************/ |
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|
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#include "MeshAdapter.h" |
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#include "escript/Data.h" |
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#include "escript/DataFactory.h" |
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#ifdef USE_NETCDF |
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#include <netcdfcpp.h> |
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#endif |
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extern "C" { |
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#include "escript/blocktimer.h" |
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} |
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#include <vector> |
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|
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using namespace std; |
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using namespace escript; |
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|
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namespace finley { |
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|
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// |
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// define the static constants |
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MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames; |
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const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM; |
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const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM; |
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const int MeshAdapter::Nodes=FINLEY_NODES; |
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const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES; |
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const int MeshAdapter::Elements=FINLEY_ELEMENTS; |
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const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS; |
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const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS; |
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const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS; |
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const int MeshAdapter::Points=FINLEY_POINTS; |
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const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1; |
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const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1; |
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const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2; |
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const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2; |
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|
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MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh) |
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{ |
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setFunctionSpaceTypeNames(); |
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// |
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// need to use a null_deleter as Finley_Mesh_free deletes the pointer |
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// for us. |
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m_finleyMesh.reset(finleyMesh,null_deleter()); |
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} |
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|
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// |
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// The copy constructor should just increment the use count |
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MeshAdapter::MeshAdapter(const MeshAdapter& in): |
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m_finleyMesh(in.m_finleyMesh) |
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{ |
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setFunctionSpaceTypeNames(); |
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} |
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|
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MeshAdapter::~MeshAdapter() |
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{ |
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// |
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// I hope the case for the pointer being zero has been taken care of. |
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// cout << "In MeshAdapter destructor." << endl; |
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if (m_finleyMesh.unique()) { |
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Finley_Mesh_free(m_finleyMesh.get()); |
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} |
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} |
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|
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int MeshAdapter::getMPISize() const |
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{ |
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return m_finleyMesh.get()->MPIInfo->size; |
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} |
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int MeshAdapter::getMPIRank() const |
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{ |
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return m_finleyMesh.get()->MPIInfo->rank; |
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} |
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|
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|
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Finley_Mesh* MeshAdapter::getFinley_Mesh() const { |
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return m_finleyMesh.get(); |
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} |
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|
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void MeshAdapter::write(const std::string& fileName) const |
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{ |
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char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL; |
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strcpy(fName,fileName.c_str()); |
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Finley_Mesh_write(m_finleyMesh.get(),fName); |
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checkFinleyError(); |
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TMPMEMFREE(fName); |
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} |
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|
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void MeshAdapter::Print_Mesh_Info(const bool full=false) const |
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{ |
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Finley_PrintMesh_Info(m_finleyMesh.get(), full); |
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} |
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|
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void MeshAdapter::dump(const std::string& fileName) const |
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{ |
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#ifdef USE_NETCDF |
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const NcDim* ncdims[12]; |
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NcVar *ids, *data; |
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int *int_ptr; |
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Finley_Mesh *mesh = m_finleyMesh.get(); |
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Finley_TagMap* tag_map; |
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int num_Tags = 0; |
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int mpi_size = mesh->MPIInfo->size; |
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int mpi_rank = mesh->MPIInfo->rank; |
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int numDim = mesh->Nodes->numDim; |
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int numNodes = mesh->Nodes->numNodes; |
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int num_Elements = mesh->Elements->numElements; |
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int num_FaceElements = mesh->FaceElements->numElements; |
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int num_ContactElements = mesh->ContactElements->numElements; |
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int num_Points = mesh->Points->numElements; |
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int num_Elements_numNodes = mesh->Elements->numNodes; |
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int num_FaceElements_numNodes = mesh->FaceElements->numNodes; |
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int num_ContactElements_numNodes = mesh->ContactElements->numNodes; |
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char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank); |
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|
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/* Figure out how much storage is required for tags */ |
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tag_map = mesh->TagMap; |
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if (tag_map) { |
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while (tag_map) { |
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num_Tags++; |
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tag_map=tag_map->next; |
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} |
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} |
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|
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// NetCDF error handler |
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NcError err(NcError::verbose_nonfatal); |
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// Create the file. |
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NcFile dataFile(newFileName, NcFile::Replace); |
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// check if writing was successful |
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if (!dataFile.is_valid()) |
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throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName); |
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|
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// Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0) |
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if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName); |
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if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName); |
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if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName); |
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if (num_Elements>0) |
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if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName); |
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if (num_FaceElements>0) |
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if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName); |
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if (num_ContactElements>0) |
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if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName); |
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if (num_Points>0) |
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if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName); |
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if (num_Elements>0) |
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if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName); |
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if (num_FaceElements>0) |
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if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName); |
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if (num_ContactElements>0) |
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if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName); |
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if (num_Tags>0) |
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if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) ) |
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throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName); |
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|
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// Attributes: MPI size, MPI rank, Name, order, reduced_order |
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if (!dataFile.add_att("mpi_size", mpi_size) ) |
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throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("mpi_rank", mpi_rank) ) |
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throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("Name",mesh->Name) ) |
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throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("numDim",numDim) ) |
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throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("order",mesh->order) ) |
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throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("reduced_order",mesh->reduced_order) ) |
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throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("numNodes",numNodes) ) |
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throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_Elements",num_Elements) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_FaceElements",num_FaceElements) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_ContactElements",num_ContactElements) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_Points",num_Points) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) ) |
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throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) ) |
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throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) ) |
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throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) ) |
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throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName); |
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if (!dataFile.add_att("num_Tags", num_Tags) ) |
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throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName); |
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|
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// // // // // Nodes // // // // // |
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|
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// Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED) |
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if (numNodes>0) { |
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|
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// Nodes Id |
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if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->Id[0]; |
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if (! (ids->put(int_ptr, numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes Tag |
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if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->Tag[0]; |
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if (! (ids->put(int_ptr, numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes gDOF |
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if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0]; |
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if (! (ids->put(int_ptr, numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes global node index |
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if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->globalNodesIndex[0]; |
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if (! (ids->put(int_ptr, numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes grDof |
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if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->globalReducedDOFIndex[0]; |
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if (! (ids->put(int_ptr, numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes grNI |
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if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->globalReducedNodesIndex[0]; |
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if (! (ids->put(int_ptr, numNodes)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes Coordinates |
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if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName); |
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if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName); |
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|
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// Nodes degreesOfFreedomDistribution |
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if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0]; |
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if (! (ids->put(int_ptr, mpi_size+1)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName); |
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|
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} |
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|
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// // // // // Elements // // // // // |
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|
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if (num_Elements>0) { |
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|
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// Temp storage to gather node IDs |
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int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int); |
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|
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// Elements_Id |
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if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName); |
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int_ptr = &mesh->Elements->Id[0]; |
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if (! (ids->put(int_ptr, num_Elements)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName); |
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|
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// Elements_Tag |
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if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) ) |
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throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName); |
| 294 |
int_ptr = &mesh->Elements->Tag[0]; |
| 295 |
if (! (ids->put(int_ptr, num_Elements)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName); |
| 297 |
|
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// Elements_Owner |
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if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) ) |
| 300 |
throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName); |
| 301 |
int_ptr = &mesh->Elements->Owner[0]; |
| 302 |
if (! (ids->put(int_ptr, num_Elements)) ) |
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throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName); |
| 304 |
|
| 305 |
// Elements_Color |
| 306 |
if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) ) |
| 307 |
throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName); |
| 308 |
int_ptr = &mesh->Elements->Color[0]; |
| 309 |
if (! (ids->put(int_ptr, num_Elements)) ) |
| 310 |
throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName); |
| 311 |
|
| 312 |
// Elements_Nodes |
| 313 |
for (int i=0; i<num_Elements; i++) |
| 314 |
for (int j=0; j<num_Elements_numNodes; j++) |
| 315 |
Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]]; |
| 316 |
if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) ) |
| 317 |
throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName); |
| 318 |
if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) ) |
| 319 |
throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName); |
| 320 |
|
| 321 |
TMPMEMFREE(Elements_Nodes); |
| 322 |
|
| 323 |
} |
| 324 |
|
| 325 |
// // // // // Face_Elements // // // // // |
| 326 |
|
| 327 |
if (num_FaceElements>0) { |
| 328 |
|
| 329 |
// Temp storage to gather node IDs |
| 330 |
int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int); |
| 331 |
|
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// FaceElements_Id |
| 333 |
if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) ) |
| 334 |
throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName); |
| 335 |
int_ptr = &mesh->FaceElements->Id[0]; |
| 336 |
if (! (ids->put(int_ptr, num_FaceElements)) ) |
| 337 |
throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName); |
| 338 |
|
| 339 |
// FaceElements_Tag |
| 340 |
if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) ) |
| 341 |
throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName); |
| 342 |
int_ptr = &mesh->FaceElements->Tag[0]; |
| 343 |
if (! (ids->put(int_ptr, num_FaceElements)) ) |
| 344 |
throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName); |
| 345 |
|
| 346 |
// FaceElements_Owner |
| 347 |
if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) ) |
| 348 |
throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName); |
| 349 |
int_ptr = &mesh->FaceElements->Owner[0]; |
| 350 |
if (! (ids->put(int_ptr, num_FaceElements)) ) |
| 351 |
throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName); |
| 352 |
|
| 353 |
// FaceElements_Color |
| 354 |
if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) ) |
| 355 |
throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName); |
| 356 |
int_ptr = &mesh->FaceElements->Color[0]; |
| 357 |
if (! (ids->put(int_ptr, num_FaceElements)) ) |
| 358 |
throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName); |
| 359 |
|
| 360 |
// FaceElements_Nodes |
| 361 |
for (int i=0; i<num_FaceElements; i++) |
| 362 |
for (int j=0; j<num_FaceElements_numNodes; j++) |
| 363 |
FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]]; |
| 364 |
if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) ) |
| 365 |
throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName); |
| 366 |
if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) ) |
| 367 |
throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName); |
| 368 |
|
| 369 |
TMPMEMFREE(FaceElements_Nodes); |
| 370 |
|
| 371 |
} |
| 372 |
|
| 373 |
// // // // // Contact_Elements // // // // // |
| 374 |
|
| 375 |
if (num_ContactElements>0) { |
| 376 |
|
| 377 |
// Temp storage to gather node IDs |
| 378 |
int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int); |
| 379 |
|
| 380 |
// ContactElements_Id |
| 381 |
if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) ) |
| 382 |
throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName); |
| 383 |
int_ptr = &mesh->ContactElements->Id[0]; |
| 384 |
if (! (ids->put(int_ptr, num_ContactElements)) ) |
| 385 |
throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName); |
| 386 |
|
| 387 |
// ContactElements_Tag |
| 388 |
if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) ) |
| 389 |
throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName); |
| 390 |
int_ptr = &mesh->ContactElements->Tag[0]; |
| 391 |
if (! (ids->put(int_ptr, num_ContactElements)) ) |
| 392 |
throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName); |
| 393 |
|
| 394 |
// ContactElements_Owner |
| 395 |
if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) ) |
| 396 |
throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName); |
| 397 |
int_ptr = &mesh->ContactElements->Owner[0]; |
| 398 |
if (! (ids->put(int_ptr, num_ContactElements)) ) |
| 399 |
throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName); |
| 400 |
|
| 401 |
// ContactElements_Color |
| 402 |
if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) ) |
| 403 |
throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName); |
| 404 |
int_ptr = &mesh->ContactElements->Color[0]; |
| 405 |
if (! (ids->put(int_ptr, num_ContactElements)) ) |
| 406 |
throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName); |
| 407 |
|
| 408 |
// ContactElements_Nodes |
| 409 |
for (int i=0; i<num_ContactElements; i++) |
| 410 |
for (int j=0; j<num_ContactElements_numNodes; j++) |
| 411 |
ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]]; |
| 412 |
if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) ) |
| 413 |
throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName); |
| 414 |
if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) ) |
| 415 |
throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName); |
| 416 |
|
| 417 |
TMPMEMFREE(ContactElements_Nodes); |
| 418 |
|
| 419 |
} |
| 420 |
|
| 421 |
// // // // // Points // // // // // |
| 422 |
|
| 423 |
if (num_Points>0) { |
| 424 |
|
| 425 |
fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n"); |
| 426 |
|
| 427 |
// Temp storage to gather node IDs |
| 428 |
int *Points_Nodes = TMPMEMALLOC(num_Points,int); |
| 429 |
|
| 430 |
// Points_Id |
| 431 |
if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) ) |
| 432 |
throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName); |
| 433 |
int_ptr = &mesh->Points->Id[0]; |
| 434 |
if (! (ids->put(int_ptr, num_Points)) ) |
| 435 |
throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName); |
| 436 |
|
| 437 |
// Points_Tag |
| 438 |
if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) ) |
| 439 |
throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName); |
| 440 |
int_ptr = &mesh->Points->Tag[0]; |
| 441 |
if (! (ids->put(int_ptr, num_Points)) ) |
| 442 |
throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName); |
| 443 |
|
| 444 |
// Points_Owner |
| 445 |
if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) ) |
| 446 |
throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName); |
| 447 |
int_ptr = &mesh->Points->Owner[0]; |
| 448 |
if (! (ids->put(int_ptr, num_Points)) ) |
| 449 |
throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName); |
| 450 |
|
| 451 |
// Points_Color |
| 452 |
if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) ) |
| 453 |
throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName); |
| 454 |
int_ptr = &mesh->Points->Color[0]; |
| 455 |
if (! (ids->put(int_ptr, num_Points)) ) |
| 456 |
throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName); |
| 457 |
|
| 458 |
// Points_Nodes |
| 459 |
// mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]] |
| 460 |
for (int i=0; i<num_Points; i++) |
| 461 |
Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]; |
| 462 |
if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) ) |
| 463 |
throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName); |
| 464 |
if (! (ids->put(&(Points_Nodes[0]), num_Points)) ) |
| 465 |
throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName); |
| 466 |
|
| 467 |
TMPMEMFREE(Points_Nodes); |
| 468 |
|
| 469 |
} |
| 470 |
|
| 471 |
// // // // // TagMap // // // // // |
| 472 |
|
| 473 |
if (num_Tags>0) { |
| 474 |
|
| 475 |
// Temp storage to gather node IDs |
| 476 |
int *Tags_keys = TMPMEMALLOC(num_Tags, int); |
| 477 |
char name_temp[4096]; |
| 478 |
|
| 479 |
/* Copy tag data into temp arrays */ |
| 480 |
tag_map = mesh->TagMap; |
| 481 |
if (tag_map) { |
| 482 |
int i = 0; |
| 483 |
while (tag_map) { |
| 484 |
Tags_keys[i++] = tag_map->tag_key; |
| 485 |
tag_map=tag_map->next; |
| 486 |
} |
| 487 |
} |
| 488 |
|
| 489 |
// Tags_keys |
| 490 |
if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) ) |
| 491 |
throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName); |
| 492 |
int_ptr = &Tags_keys[0]; |
| 493 |
if (! (ids->put(int_ptr, num_Tags)) ) |
| 494 |
throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName); |
| 495 |
|
| 496 |
// Tags_names_* |
| 497 |
// This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string |
| 498 |
// because the NetCDF manual doesn't tell how to do an array of strings |
| 499 |
tag_map = mesh->TagMap; |
| 500 |
if (tag_map) { |
| 501 |
int i = 0; |
| 502 |
while (tag_map) { |
| 503 |
sprintf(name_temp, "Tags_name_%d", i); |
| 504 |
if (!dataFile.add_att(name_temp, tag_map->name) ) |
| 505 |
throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName); |
| 506 |
tag_map=tag_map->next; |
| 507 |
i++; |
| 508 |
} |
| 509 |
} |
| 510 |
|
| 511 |
TMPMEMFREE(Tags_keys); |
| 512 |
|
| 513 |
} |
| 514 |
|
| 515 |
|
| 516 |
// NetCDF file is closed by destructor of NcFile object |
| 517 |
#else |
| 518 |
Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager."); |
| 519 |
#endif /* USE_NETCDF */ |
| 520 |
checkFinleyError(); |
| 521 |
} |
| 522 |
|
| 523 |
string MeshAdapter::getDescription() const |
| 524 |
{ |
| 525 |
return "FinleyMesh"; |
| 526 |
} |
| 527 |
|
| 528 |
string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const |
| 529 |
{ |
| 530 |
FunctionSpaceNamesMapType::iterator loc; |
| 531 |
loc=m_functionSpaceTypeNames.find(functionSpaceType); |
| 532 |
if (loc==m_functionSpaceTypeNames.end()) { |
| 533 |
return "Invalid function space type code."; |
| 534 |
} else { |
| 535 |
return loc->second; |
| 536 |
} |
| 537 |
} |
| 538 |
|
| 539 |
bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const |
| 540 |
{ |
| 541 |
FunctionSpaceNamesMapType::iterator loc; |
| 542 |
loc=m_functionSpaceTypeNames.find(functionSpaceType); |
| 543 |
return (loc!=m_functionSpaceTypeNames.end()); |
| 544 |
} |
| 545 |
|
| 546 |
void MeshAdapter::setFunctionSpaceTypeNames() |
| 547 |
{ |
| 548 |
m_functionSpaceTypeNames.insert |
| 549 |
(FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom")); |
| 550 |
m_functionSpaceTypeNames.insert |
| 551 |
(FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom")); |
| 552 |
m_functionSpaceTypeNames.insert |
| 553 |
(FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes")); |
| 554 |
m_functionSpaceTypeNames.insert |
| 555 |
(FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes")); |
| 556 |
m_functionSpaceTypeNames.insert |
| 557 |
(FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements")); |
| 558 |
m_functionSpaceTypeNames.insert |
| 559 |
(FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements")); |
| 560 |
m_functionSpaceTypeNames.insert |
| 561 |
(FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements")); |
| 562 |
m_functionSpaceTypeNames.insert |
| 563 |
(FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements")); |
| 564 |
m_functionSpaceTypeNames.insert |
| 565 |
(FunctionSpaceNamesMapType::value_type(Points,"Finley_Points")); |
| 566 |
m_functionSpaceTypeNames.insert |
| 567 |
(FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0")); |
| 568 |
m_functionSpaceTypeNames.insert |
| 569 |
(FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0")); |
| 570 |
m_functionSpaceTypeNames.insert |
| 571 |
(FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1")); |
| 572 |
m_functionSpaceTypeNames.insert |
| 573 |
(FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1")); |
| 574 |
} |
| 575 |
|
| 576 |
int MeshAdapter::getContinuousFunctionCode() const |
| 577 |
{ |
| 578 |
return Nodes; |
| 579 |
} |
| 580 |
int MeshAdapter::getReducedContinuousFunctionCode() const |
| 581 |
{ |
| 582 |
return ReducedNodes; |
| 583 |
} |
| 584 |
|
| 585 |
int MeshAdapter::getFunctionCode() const |
| 586 |
{ |
| 587 |
return Elements; |
| 588 |
} |
| 589 |
int MeshAdapter::getReducedFunctionCode() const |
| 590 |
{ |
| 591 |
return ReducedElements; |
| 592 |
} |
| 593 |
|
| 594 |
int MeshAdapter::getFunctionOnBoundaryCode() const |
| 595 |
{ |
| 596 |
return FaceElements; |
| 597 |
} |
| 598 |
int MeshAdapter::getReducedFunctionOnBoundaryCode() const |
| 599 |
{ |
| 600 |
return ReducedFaceElements; |
| 601 |
} |
| 602 |
|
| 603 |
int MeshAdapter::getFunctionOnContactZeroCode() const |
| 604 |
{ |
| 605 |
return ContactElementsZero; |
| 606 |
} |
| 607 |
int MeshAdapter::getReducedFunctionOnContactZeroCode() const |
| 608 |
{ |
| 609 |
return ReducedContactElementsZero; |
| 610 |
} |
| 611 |
|
| 612 |
int MeshAdapter::getFunctionOnContactOneCode() const |
| 613 |
{ |
| 614 |
return ContactElementsOne; |
| 615 |
} |
| 616 |
int MeshAdapter::getReducedFunctionOnContactOneCode() const |
| 617 |
{ |
| 618 |
return ReducedContactElementsOne; |
| 619 |
} |
| 620 |
|
| 621 |
int MeshAdapter::getSolutionCode() const |
| 622 |
{ |
| 623 |
return DegreesOfFreedom; |
| 624 |
} |
| 625 |
|
| 626 |
int MeshAdapter::getReducedSolutionCode() const |
| 627 |
{ |
| 628 |
return ReducedDegreesOfFreedom; |
| 629 |
} |
| 630 |
|
| 631 |
int MeshAdapter::getDiracDeltaFunctionCode() const |
| 632 |
{ |
| 633 |
return Points; |
| 634 |
} |
| 635 |
|
| 636 |
// |
| 637 |
// return the spatial dimension of the Mesh: |
| 638 |
// |
| 639 |
int MeshAdapter::getDim() const |
| 640 |
{ |
| 641 |
int numDim=Finley_Mesh_getDim(m_finleyMesh.get()); |
| 642 |
checkFinleyError(); |
| 643 |
return numDim; |
| 644 |
} |
| 645 |
|
| 646 |
// |
| 647 |
// return the number of data points per sample and the number of samples |
| 648 |
// needed to represent data on a parts of the mesh. |
| 649 |
// |
| 650 |
pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const |
| 651 |
{ |
| 652 |
int numDataPointsPerSample=0; |
| 653 |
int numSamples=0; |
| 654 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 655 |
switch (functionSpaceCode) { |
| 656 |
case(Nodes): |
| 657 |
numDataPointsPerSample=1; |
| 658 |
numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes); |
| 659 |
break; |
| 660 |
case(ReducedNodes): |
| 661 |
numDataPointsPerSample=1; |
| 662 |
numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes); |
| 663 |
break; |
| 664 |
case(Elements): |
| 665 |
if (mesh->Elements!=NULL) { |
| 666 |
numSamples=mesh->Elements->numElements; |
| 667 |
numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes; |
| 668 |
} |
| 669 |
break; |
| 670 |
case(ReducedElements): |
| 671 |
if (mesh->Elements!=NULL) { |
| 672 |
numSamples=mesh->Elements->numElements; |
| 673 |
numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes; |
| 674 |
} |
| 675 |
break; |
| 676 |
case(FaceElements): |
| 677 |
if (mesh->FaceElements!=NULL) { |
| 678 |
numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes; |
| 679 |
numSamples=mesh->FaceElements->numElements; |
| 680 |
} |
| 681 |
break; |
| 682 |
case(ReducedFaceElements): |
| 683 |
if (mesh->FaceElements!=NULL) { |
| 684 |
numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes; |
| 685 |
numSamples=mesh->FaceElements->numElements; |
| 686 |
} |
| 687 |
break; |
| 688 |
case(Points): |
| 689 |
if (mesh->Points!=NULL) { |
| 690 |
numDataPointsPerSample=1; |
| 691 |
numSamples=mesh->Points->numElements; |
| 692 |
} |
| 693 |
break; |
| 694 |
case(ContactElementsZero): |
| 695 |
if (mesh->ContactElements!=NULL) { |
| 696 |
numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes; |
| 697 |
numSamples=mesh->ContactElements->numElements; |
| 698 |
} |
| 699 |
break; |
| 700 |
case(ReducedContactElementsZero): |
| 701 |
if (mesh->ContactElements!=NULL) { |
| 702 |
numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes; |
| 703 |
numSamples=mesh->ContactElements->numElements; |
| 704 |
} |
| 705 |
break; |
| 706 |
case(ContactElementsOne): |
| 707 |
if (mesh->ContactElements!=NULL) { |
| 708 |
numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes; |
| 709 |
numSamples=mesh->ContactElements->numElements; |
| 710 |
} |
| 711 |
break; |
| 712 |
case(ReducedContactElementsOne): |
| 713 |
if (mesh->ContactElements!=NULL) { |
| 714 |
numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes; |
| 715 |
numSamples=mesh->ContactElements->numElements; |
| 716 |
} |
| 717 |
break; |
| 718 |
case(DegreesOfFreedom): |
| 719 |
if (mesh->Nodes!=NULL) { |
| 720 |
numDataPointsPerSample=1; |
| 721 |
numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes); |
| 722 |
} |
| 723 |
break; |
| 724 |
case(ReducedDegreesOfFreedom): |
| 725 |
if (mesh->Nodes!=NULL) { |
| 726 |
numDataPointsPerSample=1; |
| 727 |
numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes); |
| 728 |
} |
| 729 |
break; |
| 730 |
default: |
| 731 |
stringstream temp; |
| 732 |
temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription(); |
| 733 |
throw FinleyAdapterException(temp.str()); |
| 734 |
break; |
| 735 |
} |
| 736 |
return pair<int,int>(numDataPointsPerSample,numSamples); |
| 737 |
} |
| 738 |
|
| 739 |
// |
| 740 |
// adds linear PDE of second order into a given stiffness matrix and right hand side: |
| 741 |
// |
| 742 |
void MeshAdapter::addPDEToSystem( |
| 743 |
SystemMatrixAdapter& 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, |
| 745 |
const escript::Data& d, const escript::Data& y, |
| 746 |
const escript::Data& d_contact,const escript::Data& y_contact) const |
| 747 |
{ |
| 748 |
escriptDataC _rhs=rhs.getDataC(); |
| 749 |
escriptDataC _A =A.getDataC(); |
| 750 |
escriptDataC _B=B.getDataC(); |
| 751 |
escriptDataC _C=C.getDataC(); |
| 752 |
escriptDataC _D=D.getDataC(); |
| 753 |
escriptDataC _X=X.getDataC(); |
| 754 |
escriptDataC _Y=Y.getDataC(); |
| 755 |
escriptDataC _d=d.getDataC(); |
| 756 |
escriptDataC _y=y.getDataC(); |
| 757 |
escriptDataC _d_contact=d_contact.getDataC(); |
| 758 |
escriptDataC _y_contact=y_contact.getDataC(); |
| 759 |
|
| 760 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 761 |
|
| 762 |
Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y ); |
| 763 |
checkFinleyError(); |
| 764 |
|
| 765 |
Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y ); |
| 766 |
checkFinleyError(); |
| 767 |
|
| 768 |
Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact ); |
| 769 |
checkFinleyError(); |
| 770 |
} |
| 771 |
|
| 772 |
void MeshAdapter::addPDEToLumpedSystem( |
| 773 |
escript::Data& mat, |
| 774 |
const escript::Data& D, |
| 775 |
const escript::Data& d) const |
| 776 |
{ |
| 777 |
escriptDataC _mat=mat.getDataC(); |
| 778 |
escriptDataC _D=D.getDataC(); |
| 779 |
escriptDataC _d=d.getDataC(); |
| 780 |
|
| 781 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 782 |
|
| 783 |
Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D); |
| 784 |
Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d); |
| 785 |
|
| 786 |
checkFinleyError(); |
| 787 |
} |
| 788 |
|
| 789 |
|
| 790 |
// |
| 791 |
// 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 |
| 794 |
{ |
| 795 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 796 |
|
| 797 |
escriptDataC _rhs=rhs.getDataC(); |
| 798 |
escriptDataC _X=X.getDataC(); |
| 799 |
escriptDataC _Y=Y.getDataC(); |
| 800 |
escriptDataC _y=y.getDataC(); |
| 801 |
escriptDataC _y_contact=y_contact.getDataC(); |
| 802 |
|
| 803 |
Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y ); |
| 804 |
checkFinleyError(); |
| 805 |
|
| 806 |
Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y ); |
| 807 |
checkFinleyError(); |
| 808 |
|
| 809 |
Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact ); |
| 810 |
checkFinleyError(); |
| 811 |
} |
| 812 |
// |
| 813 |
// adds PDE of second order into a transport problem |
| 814 |
// |
| 815 |
void MeshAdapter::addPDEToTransportProblem( |
| 816 |
TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M, |
| 817 |
const escript::Data& A, const escript::Data& B, const escript::Data& C,const escript::Data& D,const escript::Data& X,const escript::Data& Y, |
| 818 |
const escript::Data& d, const escript::Data& y, |
| 819 |
const escript::Data& d_contact,const escript::Data& y_contact) const |
| 820 |
{ |
| 821 |
DataArrayView::ShapeType shape; |
| 822 |
escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true); |
| 823 |
escriptDataC _source=source.getDataC(); |
| 824 |
escriptDataC _tmp=tmp.getDataC(); |
| 825 |
escriptDataC _M=M.getDataC(); |
| 826 |
escriptDataC _A=A.getDataC(); |
| 827 |
escriptDataC _B=B.getDataC(); |
| 828 |
escriptDataC _C=C.getDataC(); |
| 829 |
escriptDataC _D=D.getDataC(); |
| 830 |
escriptDataC _X=X.getDataC(); |
| 831 |
escriptDataC _Y=Y.getDataC(); |
| 832 |
escriptDataC _d=d.getDataC(); |
| 833 |
escriptDataC _y=y.getDataC(); |
| 834 |
escriptDataC _d_contact=d_contact.getDataC(); |
| 835 |
escriptDataC _y_contact=y_contact.getDataC(); |
| 836 |
|
| 837 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 838 |
Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem(); |
| 839 |
|
| 840 |
|
| 841 |
Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_tmp, &_M); |
| 842 |
checkFinleyError(); |
| 843 |
/* add mass matix to lumped mass matrix of transport problem */ |
| 844 |
double* tmp_prt=getSampleData(&_tmp,0); |
| 845 |
int i; |
| 846 |
int n=Paso_FCTransportProblem_getTotalNumRows(_tp); |
| 847 |
#pragma omp parallel for private(i) schedule(static) |
| 848 |
for (i=0;i<n ;++i) _tp->lumped_mass_matrix[i]+=tmp_prt[i]; |
| 849 |
|
| 850 |
Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, 0, 0, &_D, &_X, &_Y ); |
| 851 |
checkFinleyError(); |
| 852 |
|
| 853 |
Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->flux_matrix, &_source, 0, &_B, &_C, 0, 0, 0 ); |
| 854 |
checkFinleyError(); |
| 855 |
|
| 856 |
Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y ); |
| 857 |
checkFinleyError(); |
| 858 |
|
| 859 |
Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact ); |
| 860 |
checkFinleyError(); |
| 861 |
} |
| 862 |
|
| 863 |
// |
| 864 |
// interpolates data between different function spaces: |
| 865 |
// |
| 866 |
void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const |
| 867 |
{ |
| 868 |
const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain()); |
| 869 |
const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain()); |
| 870 |
if (inDomain!=*this) |
| 871 |
throw FinleyAdapterException("Error - Illegal domain of interpolant."); |
| 872 |
if (targetDomain!=*this) |
| 873 |
throw FinleyAdapterException("Error - Illegal domain of interpolation target."); |
| 874 |
|
| 875 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 876 |
escriptDataC _target=target.getDataC(); |
| 877 |
escriptDataC _in=in.getDataC(); |
| 878 |
switch(in.getFunctionSpace().getTypeCode()) { |
| 879 |
case(Nodes): |
| 880 |
switch(target.getFunctionSpace().getTypeCode()) { |
| 881 |
case(Nodes): |
| 882 |
case(ReducedNodes): |
| 883 |
case(DegreesOfFreedom): |
| 884 |
case(ReducedDegreesOfFreedom): |
| 885 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in); |
| 886 |
break; |
| 887 |
case(Elements): |
| 888 |
case(ReducedElements): |
| 889 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target); |
| 890 |
break; |
| 891 |
case(FaceElements): |
| 892 |
case(ReducedFaceElements): |
| 893 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target); |
| 894 |
break; |
| 895 |
case(Points): |
| 896 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target); |
| 897 |
break; |
| 898 |
case(ContactElementsZero): |
| 899 |
case(ReducedContactElementsZero): |
| 900 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target); |
| 901 |
break; |
| 902 |
case(ContactElementsOne): |
| 903 |
case(ReducedContactElementsOne): |
| 904 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target); |
| 905 |
break; |
| 906 |
default: |
| 907 |
stringstream temp; |
| 908 |
temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode(); |
| 909 |
throw FinleyAdapterException(temp.str()); |
| 910 |
break; |
| 911 |
} |
| 912 |
break; |
| 913 |
case(ReducedNodes): |
| 914 |
switch(target.getFunctionSpace().getTypeCode()) { |
| 915 |
case(Nodes): |
| 916 |
case(ReducedNodes): |
| 917 |
case(DegreesOfFreedom): |
| 918 |
case(ReducedDegreesOfFreedom): |
| 919 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in); |
| 920 |
break; |
| 921 |
case(Elements): |
| 922 |
case(ReducedElements): |
| 923 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target); |
| 924 |
break; |
| 925 |
case(FaceElements): |
| 926 |
case(ReducedFaceElements): |
| 927 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target); |
| 928 |
break; |
| 929 |
case(Points): |
| 930 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target); |
| 931 |
break; |
| 932 |
case(ContactElementsZero): |
| 933 |
case(ReducedContactElementsZero): |
| 934 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target); |
| 935 |
break; |
| 936 |
case(ContactElementsOne): |
| 937 |
case(ReducedContactElementsOne): |
| 938 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target); |
| 939 |
break; |
| 940 |
default: |
| 941 |
stringstream temp; |
| 942 |
temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode(); |
| 943 |
throw FinleyAdapterException(temp.str()); |
| 944 |
break; |
| 945 |
} |
| 946 |
break; |
| 947 |
case(Elements): |
| 948 |
if (target.getFunctionSpace().getTypeCode()==Elements) { |
| 949 |
Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in); |
| 950 |
} else if (target.getFunctionSpace().getTypeCode()==ReducedElements) { |
| 951 |
Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in); |
| 952 |
} else { |
| 953 |
throw FinleyAdapterException("Error - No interpolation with data on elements possible."); |
| 954 |
} |
| 955 |
break; |
| 956 |
case(ReducedElements): |
| 957 |
if (target.getFunctionSpace().getTypeCode()==ReducedElements) { |
| 958 |
Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in); |
| 959 |
} else { |
| 960 |
throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible."); |
| 961 |
} |
| 962 |
break; |
| 963 |
case(FaceElements): |
| 964 |
if (target.getFunctionSpace().getTypeCode()==FaceElements) { |
| 965 |
Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in); |
| 966 |
} else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) { |
| 967 |
Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in); |
| 968 |
} else { |
| 969 |
throw FinleyAdapterException("Error - No interpolation with data on face elements possible."); |
| 970 |
} |
| 971 |
break; |
| 972 |
case(ReducedFaceElements): |
| 973 |
cout << "A\n"; |
| 974 |
if (target.getFunctionSpace().getTypeCode()==FaceElements) { |
| 975 |
cout << "B\n"; |
| 976 |
Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in); |
| 977 |
cout << "C\n"; |
| 978 |
throw FinleyAdapterException("A"); |
| 979 |
} else { |
| 980 |
throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible."); |
| 981 |
} |
| 982 |
cout << "A\n"; |
| 983 |
break; |
| 984 |
case(Points): |
| 985 |
if (target.getFunctionSpace().getTypeCode()==Points) { |
| 986 |
Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in); |
| 987 |
} else { |
| 988 |
throw FinleyAdapterException("Error - No interpolation with data on points possible."); |
| 989 |
} |
| 990 |
break; |
| 991 |
case(ContactElementsZero): |
| 992 |
case(ContactElementsOne): |
| 993 |
if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) { |
| 994 |
Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in); |
| 995 |
} else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) { |
| 996 |
Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in); |
| 997 |
} else { |
| 998 |
throw FinleyAdapterException("Error - No interpolation with data on contact elements possible."); |
| 999 |
} |
| 1000 |
break; |
| 1001 |
case(ReducedContactElementsZero): |
| 1002 |
case(ReducedContactElementsOne): |
| 1003 |
if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) { |
| 1004 |
Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in); |
| 1005 |
} else { |
| 1006 |
throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible."); |
| 1007 |
} |
| 1008 |
break; |
| 1009 |
case(DegreesOfFreedom): |
| 1010 |
switch(target.getFunctionSpace().getTypeCode()) { |
| 1011 |
case(ReducedDegreesOfFreedom): |
| 1012 |
case(DegreesOfFreedom): |
| 1013 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in); |
| 1014 |
break; |
| 1015 |
|
| 1016 |
case(Nodes): |
| 1017 |
case(ReducedNodes): |
| 1018 |
if (getMPISize()>1) { |
| 1019 |
escript::Data temp=escript::Data(in); |
| 1020 |
temp.expand(); |
| 1021 |
escriptDataC _in2 = temp.getDataC(); |
| 1022 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2); |
| 1023 |
} else { |
| 1024 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in); |
| 1025 |
} |
| 1026 |
break; |
| 1027 |
case(Elements): |
| 1028 |
case(ReducedElements): |
| 1029 |
if (getMPISize()>1) { |
| 1030 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1031 |
escriptDataC _in2 = temp.getDataC(); |
| 1032 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target); |
| 1033 |
} else { |
| 1034 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target); |
| 1035 |
} |
| 1036 |
break; |
| 1037 |
case(FaceElements): |
| 1038 |
case(ReducedFaceElements): |
| 1039 |
if (getMPISize()>1) { |
| 1040 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1041 |
escriptDataC _in2 = temp.getDataC(); |
| 1042 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target); |
| 1043 |
|
| 1044 |
} else { |
| 1045 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target); |
| 1046 |
} |
| 1047 |
break; |
| 1048 |
case(Points): |
| 1049 |
if (getMPISize()>1) { |
| 1050 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1051 |
escriptDataC _in2 = temp.getDataC(); |
| 1052 |
} else { |
| 1053 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target); |
| 1054 |
} |
| 1055 |
break; |
| 1056 |
case(ContactElementsZero): |
| 1057 |
case(ContactElementsOne): |
| 1058 |
case(ReducedContactElementsZero): |
| 1059 |
case(ReducedContactElementsOne): |
| 1060 |
if (getMPISize()>1) { |
| 1061 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1062 |
escriptDataC _in2 = temp.getDataC(); |
| 1063 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target); |
| 1064 |
} else { |
| 1065 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target); |
| 1066 |
} |
| 1067 |
break; |
| 1068 |
default: |
| 1069 |
stringstream temp; |
| 1070 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode(); |
| 1071 |
throw FinleyAdapterException(temp.str()); |
| 1072 |
break; |
| 1073 |
} |
| 1074 |
break; |
| 1075 |
case(ReducedDegreesOfFreedom): |
| 1076 |
switch(target.getFunctionSpace().getTypeCode()) { |
| 1077 |
case(Nodes): |
| 1078 |
throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes."); |
| 1079 |
break; |
| 1080 |
case(ReducedNodes): |
| 1081 |
if (getMPISize()>1) { |
| 1082 |
escript::Data temp=escript::Data(in); |
| 1083 |
temp.expand(); |
| 1084 |
escriptDataC _in2 = temp.getDataC(); |
| 1085 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2); |
| 1086 |
} else { |
| 1087 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in); |
| 1088 |
} |
| 1089 |
break; |
| 1090 |
case(DegreesOfFreedom): |
| 1091 |
throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom"); |
| 1092 |
break; |
| 1093 |
case(ReducedDegreesOfFreedom): |
| 1094 |
Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in); |
| 1095 |
break; |
| 1096 |
case(Elements): |
| 1097 |
case(ReducedElements): |
| 1098 |
if (getMPISize()>1) { |
| 1099 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1100 |
escriptDataC _in2 = temp.getDataC(); |
| 1101 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target); |
| 1102 |
} else { |
| 1103 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target); |
| 1104 |
} |
| 1105 |
break; |
| 1106 |
case(FaceElements): |
| 1107 |
case(ReducedFaceElements): |
| 1108 |
if (getMPISize()>1) { |
| 1109 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1110 |
escriptDataC _in2 = temp.getDataC(); |
| 1111 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target); |
| 1112 |
} else { |
| 1113 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target); |
| 1114 |
} |
| 1115 |
break; |
| 1116 |
case(Points): |
| 1117 |
if (getMPISize()>1) { |
| 1118 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1119 |
escriptDataC _in2 = temp.getDataC(); |
| 1120 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target); |
| 1121 |
} else { |
| 1122 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target); |
| 1123 |
} |
| 1124 |
break; |
| 1125 |
case(ContactElementsZero): |
| 1126 |
case(ContactElementsOne): |
| 1127 |
case(ReducedContactElementsZero): |
| 1128 |
case(ReducedContactElementsOne): |
| 1129 |
if (getMPISize()>1) { |
| 1130 |
escript::Data temp=escript::Data( in, continuousFunction(asAbstractContinuousDomain()) ); |
| 1131 |
escriptDataC _in2 = temp.getDataC(); |
| 1132 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target); |
| 1133 |
} else { |
| 1134 |
Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target); |
| 1135 |
} |
| 1136 |
break; |
| 1137 |
default: |
| 1138 |
stringstream temp; |
| 1139 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode(); |
| 1140 |
throw FinleyAdapterException(temp.str()); |
| 1141 |
break; |
| 1142 |
} |
| 1143 |
break; |
| 1144 |
default: |
| 1145 |
stringstream temp; |
| 1146 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode(); |
| 1147 |
throw FinleyAdapterException(temp.str()); |
| 1148 |
break; |
| 1149 |
} |
| 1150 |
checkFinleyError(); |
| 1151 |
} |
| 1152 |
|
| 1153 |
// |
| 1154 |
// copies the locations of sample points into x: |
| 1155 |
// |
| 1156 |
void MeshAdapter::setToX(escript::Data& arg) const |
| 1157 |
{ |
| 1158 |
const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain()); |
| 1159 |
if (argDomain!=*this) |
| 1160 |
throw FinleyAdapterException("Error - Illegal domain of data point locations"); |
| 1161 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1162 |
// in case of values node coordinates we can do the job directly: |
| 1163 |
if (arg.getFunctionSpace().getTypeCode()==Nodes) { |
| 1164 |
escriptDataC _arg=arg.getDataC(); |
| 1165 |
Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg); |
| 1166 |
} else { |
| 1167 |
escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true); |
| 1168 |
escriptDataC _tmp_data=tmp_data.getDataC(); |
| 1169 |
Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data); |
| 1170 |
// this is then interpolated onto arg: |
| 1171 |
interpolateOnDomain(arg,tmp_data); |
| 1172 |
} |
| 1173 |
checkFinleyError(); |
| 1174 |
} |
| 1175 |
|
| 1176 |
// |
| 1177 |
// return the normal vectors at the location of data points as a Data object: |
| 1178 |
// |
| 1179 |
void MeshAdapter::setToNormal(escript::Data& normal) const |
| 1180 |
{ |
| 1181 |
const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain()); |
| 1182 |
if (normalDomain!=*this) |
| 1183 |
throw FinleyAdapterException("Error - Illegal domain of normal locations"); |
| 1184 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1185 |
escriptDataC _normal=normal.getDataC(); |
| 1186 |
switch(normal.getFunctionSpace().getTypeCode()) { |
| 1187 |
case(Nodes): |
| 1188 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes"); |
| 1189 |
break; |
| 1190 |
case(ReducedNodes): |
| 1191 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes"); |
| 1192 |
break; |
| 1193 |
case(Elements): |
| 1194 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements"); |
| 1195 |
break; |
| 1196 |
case(ReducedElements): |
| 1197 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order"); |
| 1198 |
break; |
| 1199 |
case (FaceElements): |
| 1200 |
Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal); |
| 1201 |
break; |
| 1202 |
case (ReducedFaceElements): |
| 1203 |
Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal); |
| 1204 |
break; |
| 1205 |
case(Points): |
| 1206 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements"); |
| 1207 |
break; |
| 1208 |
case (ContactElementsOne): |
| 1209 |
case (ContactElementsZero): |
| 1210 |
Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal); |
| 1211 |
break; |
| 1212 |
case (ReducedContactElementsOne): |
| 1213 |
case (ReducedContactElementsZero): |
| 1214 |
Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal); |
| 1215 |
break; |
| 1216 |
case(DegreesOfFreedom): |
| 1217 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom."); |
| 1218 |
break; |
| 1219 |
case(ReducedDegreesOfFreedom): |
| 1220 |
throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom."); |
| 1221 |
break; |
| 1222 |
default: |
| 1223 |
stringstream temp; |
| 1224 |
temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode(); |
| 1225 |
throw FinleyAdapterException(temp.str()); |
| 1226 |
break; |
| 1227 |
} |
| 1228 |
checkFinleyError(); |
| 1229 |
} |
| 1230 |
|
| 1231 |
// |
| 1232 |
// interpolates data to other domain: |
| 1233 |
// |
| 1234 |
void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const |
| 1235 |
{ |
| 1236 |
const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain()); |
| 1237 |
if (targetDomain!=*this) |
| 1238 |
throw FinleyAdapterException("Error - Illegal domain of interpolation target"); |
| 1239 |
|
| 1240 |
throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet."); |
| 1241 |
} |
| 1242 |
|
| 1243 |
// |
| 1244 |
// calculates the integral of a function defined of arg: |
| 1245 |
// |
| 1246 |
void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const |
| 1247 |
{ |
| 1248 |
const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain()); |
| 1249 |
if (argDomain!=*this) |
| 1250 |
throw FinleyAdapterException("Error - Illegal domain of integration kernel"); |
| 1251 |
|
| 1252 |
double blocktimer_start = blocktimer_time(); |
| 1253 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1254 |
escriptDataC _temp; |
| 1255 |
escript::Data temp; |
| 1256 |
escriptDataC _arg=arg.getDataC(); |
| 1257 |
switch(arg.getFunctionSpace().getTypeCode()) { |
| 1258 |
case(Nodes): |
| 1259 |
temp=escript::Data( arg, function(asAbstractContinuousDomain()) ); |
| 1260 |
_temp=temp.getDataC(); |
| 1261 |
Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]); |
| 1262 |
break; |
| 1263 |
case(ReducedNodes): |
| 1264 |
temp=escript::Data( arg, function(asAbstractContinuousDomain()) ); |
| 1265 |
_temp=temp.getDataC(); |
| 1266 |
Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]); |
| 1267 |
break; |
| 1268 |
case(Elements): |
| 1269 |
Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]); |
| 1270 |
break; |
| 1271 |
case(ReducedElements): |
| 1272 |
Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]); |
| 1273 |
break; |
| 1274 |
case(FaceElements): |
| 1275 |
Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]); |
| 1276 |
break; |
| 1277 |
case(ReducedFaceElements): |
| 1278 |
Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]); |
| 1279 |
break; |
| 1280 |
case(Points): |
| 1281 |
throw FinleyAdapterException("Error - Integral of data on points is not supported."); |
| 1282 |
break; |
| 1283 |
case(ContactElementsZero): |
| 1284 |
Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]); |
| 1285 |
break; |
| 1286 |
case(ReducedContactElementsZero): |
| 1287 |
Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]); |
| 1288 |
break; |
| 1289 |
case(ContactElementsOne): |
| 1290 |
Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]); |
| 1291 |
break; |
| 1292 |
case(ReducedContactElementsOne): |
| 1293 |
Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]); |
| 1294 |
break; |
| 1295 |
case(DegreesOfFreedom): |
| 1296 |
temp=escript::Data( arg, function(asAbstractContinuousDomain()) ); |
| 1297 |
_temp=temp.getDataC(); |
| 1298 |
Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]); |
| 1299 |
break; |
| 1300 |
case(ReducedDegreesOfFreedom): |
| 1301 |
temp=escript::Data( arg, function(asAbstractContinuousDomain()) ); |
| 1302 |
_temp=temp.getDataC(); |
| 1303 |
Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]); |
| 1304 |
break; |
| 1305 |
default: |
| 1306 |
stringstream temp; |
| 1307 |
temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode(); |
| 1308 |
throw FinleyAdapterException(temp.str()); |
| 1309 |
break; |
| 1310 |
} |
| 1311 |
checkFinleyError(); |
| 1312 |
blocktimer_increment("integrate()", blocktimer_start); |
| 1313 |
} |
| 1314 |
|
| 1315 |
// |
| 1316 |
// calculates the gradient of arg: |
| 1317 |
// |
| 1318 |
void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const |
| 1319 |
{ |
| 1320 |
const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain()); |
| 1321 |
if (argDomain!=*this) |
| 1322 |
throw FinleyAdapterException("Error - Illegal domain of gradient argument"); |
| 1323 |
const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain()); |
| 1324 |
if (gradDomain!=*this) |
| 1325 |
throw FinleyAdapterException("Error - Illegal domain of gradient"); |
| 1326 |
|
| 1327 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1328 |
escriptDataC _grad=grad.getDataC(); |
| 1329 |
escriptDataC nodeDataC; |
| 1330 |
escript::Data temp; |
| 1331 |
if (getMPISize()>1) { |
| 1332 |
if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) { |
| 1333 |
temp=escript::Data( arg, continuousFunction(asAbstractContinuousDomain()) ); |
| 1334 |
nodeDataC = temp.getDataC(); |
| 1335 |
} else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) { |
| 1336 |
temp=escript::Data( arg, reducedContinuousFunction(asAbstractContinuousDomain()) ); |
| 1337 |
nodeDataC = temp.getDataC(); |
| 1338 |
} else { |
| 1339 |
nodeDataC = arg.getDataC(); |
| 1340 |
} |
| 1341 |
} else { |
| 1342 |
nodeDataC = arg.getDataC(); |
| 1343 |
} |
| 1344 |
switch(grad.getFunctionSpace().getTypeCode()) { |
| 1345 |
case(Nodes): |
| 1346 |
throw FinleyAdapterException("Error - Gradient at nodes is not supported."); |
| 1347 |
break; |
| 1348 |
case(ReducedNodes): |
| 1349 |
throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported."); |
| 1350 |
break; |
| 1351 |
case(Elements): |
| 1352 |
Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC); |
| 1353 |
break; |
| 1354 |
case(ReducedElements): |
| 1355 |
Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC); |
| 1356 |
break; |
| 1357 |
case(FaceElements): |
| 1358 |
Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC); |
| 1359 |
break; |
| 1360 |
case(ReducedFaceElements): |
| 1361 |
Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC); |
| 1362 |
break; |
| 1363 |
case(Points): |
| 1364 |
throw FinleyAdapterException("Error - Gradient at points is not supported."); |
| 1365 |
break; |
| 1366 |
case(ContactElementsZero): |
| 1367 |
Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC); |
| 1368 |
break; |
| 1369 |
case(ReducedContactElementsZero): |
| 1370 |
Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC); |
| 1371 |
break; |
| 1372 |
case(ContactElementsOne): |
| 1373 |
Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC); |
| 1374 |
break; |
| 1375 |
case(ReducedContactElementsOne): |
| 1376 |
Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC); |
| 1377 |
break; |
| 1378 |
case(DegreesOfFreedom): |
| 1379 |
throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported."); |
| 1380 |
break; |
| 1381 |
case(ReducedDegreesOfFreedom): |
| 1382 |
throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported."); |
| 1383 |
break; |
| 1384 |
default: |
| 1385 |
stringstream temp; |
| 1386 |
temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode(); |
| 1387 |
throw FinleyAdapterException(temp.str()); |
| 1388 |
break; |
| 1389 |
} |
| 1390 |
checkFinleyError(); |
| 1391 |
} |
| 1392 |
|
| 1393 |
// |
| 1394 |
// returns the size of elements: |
| 1395 |
// |
| 1396 |
void MeshAdapter::setToSize(escript::Data& size) const |
| 1397 |
{ |
| 1398 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1399 |
escriptDataC tmp=size.getDataC(); |
| 1400 |
switch(size.getFunctionSpace().getTypeCode()) { |
| 1401 |
case(Nodes): |
| 1402 |
throw FinleyAdapterException("Error - Size of nodes is not supported."); |
| 1403 |
break; |
| 1404 |
case(ReducedNodes): |
| 1405 |
throw FinleyAdapterException("Error - Size of reduced nodes is not supported."); |
| 1406 |
break; |
| 1407 |
case(Elements): |
| 1408 |
Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp); |
| 1409 |
break; |
| 1410 |
case(ReducedElements): |
| 1411 |
Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp); |
| 1412 |
break; |
| 1413 |
case(FaceElements): |
| 1414 |
Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp); |
| 1415 |
break; |
| 1416 |
case(ReducedFaceElements): |
| 1417 |
Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp); |
| 1418 |
break; |
| 1419 |
case(Points): |
| 1420 |
throw FinleyAdapterException("Error - Size of point elements is not supported."); |
| 1421 |
break; |
| 1422 |
case(ContactElementsZero): |
| 1423 |
case(ContactElementsOne): |
| 1424 |
Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp); |
| 1425 |
break; |
| 1426 |
case(ReducedContactElementsZero): |
| 1427 |
case(ReducedContactElementsOne): |
| 1428 |
Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp); |
| 1429 |
break; |
| 1430 |
case(DegreesOfFreedom): |
| 1431 |
throw FinleyAdapterException("Error - Size of degrees of freedom is not supported."); |
| 1432 |
break; |
| 1433 |
case(ReducedDegreesOfFreedom): |
| 1434 |
throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported."); |
| 1435 |
break; |
| 1436 |
default: |
| 1437 |
stringstream temp; |
| 1438 |
temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode(); |
| 1439 |
throw FinleyAdapterException(temp.str()); |
| 1440 |
break; |
| 1441 |
} |
| 1442 |
checkFinleyError(); |
| 1443 |
} |
| 1444 |
|
| 1445 |
// sets the location of nodes: |
| 1446 |
void MeshAdapter::setNewX(const escript::Data& new_x) |
| 1447 |
{ |
| 1448 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1449 |
escriptDataC tmp; |
| 1450 |
const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain()); |
| 1451 |
if (newDomain!=*this) |
| 1452 |
throw FinleyAdapterException("Error - Illegal domain of new point locations"); |
| 1453 |
tmp = new_x.getDataC(); |
| 1454 |
Finley_Mesh_setCoordinates(mesh,&tmp); |
| 1455 |
checkFinleyError(); |
| 1456 |
} |
| 1457 |
|
| 1458 |
// saves a data array in openDX format: |
| 1459 |
void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const |
| 1460 |
{ |
| 1461 |
int MAX_namelength=256; |
| 1462 |
const int num_data=boost::python::extract<int>(arg.attr("__len__")()); |
| 1463 |
/* win32 refactor */ |
| 1464 |
char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL; |
| 1465 |
for(int i=0;i<num_data;i++) |
| 1466 |
{ |
| 1467 |
names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL; |
| 1468 |
} |
| 1469 |
|
| 1470 |
char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL; |
| 1471 |
escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL; |
| 1472 |
escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL; |
| 1473 |
|
| 1474 |
boost::python::list keys=arg.keys(); |
| 1475 |
for (int i=0;i<num_data;++i) { |
| 1476 |
std::string n=boost::python::extract<std::string>(keys[i]); |
| 1477 |
escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]); |
| 1478 |
if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this) |
| 1479 |
throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain"); |
| 1480 |
data[i]=d.getDataC(); |
| 1481 |
ptr_data[i]=&(data[i]); |
| 1482 |
c_names[i]=&(names[i][0]); |
| 1483 |
if (n.length()>MAX_namelength-1) { |
| 1484 |
strncpy(c_names[i],n.c_str(),MAX_namelength-1); |
| 1485 |
c_names[i][MAX_namelength-1]='\0'; |
| 1486 |
} else { |
| 1487 |
strcpy(c_names[i],n.c_str()); |
| 1488 |
} |
| 1489 |
} |
| 1490 |
Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data); |
| 1491 |
checkFinleyError(); |
| 1492 |
|
| 1493 |
/* win32 refactor */ |
| 1494 |
TMPMEMFREE(c_names); |
| 1495 |
TMPMEMFREE(data); |
| 1496 |
TMPMEMFREE(ptr_data); |
| 1497 |
for(int i=0;i<num_data;i++) |
| 1498 |
{ |
| 1499 |
TMPMEMFREE(names[i]); |
| 1500 |
} |
| 1501 |
TMPMEMFREE(names); |
| 1502 |
|
| 1503 |
return; |
| 1504 |
} |
| 1505 |
|
| 1506 |
// saves a data array in openVTK format: |
| 1507 |
void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const |
| 1508 |
{ |
| 1509 |
int MAX_namelength=256; |
| 1510 |
const int num_data=boost::python::extract<int>(arg.attr("__len__")()); |
| 1511 |
/* win32 refactor */ |
| 1512 |
char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL; |
| 1513 |
for(int i=0;i<num_data;i++) |
| 1514 |
{ |
| 1515 |
names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL; |
| 1516 |
} |
| 1517 |
|
| 1518 |
char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL; |
| 1519 |
escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL; |
| 1520 |
escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL; |
| 1521 |
|
| 1522 |
boost::python::list keys=arg.keys(); |
| 1523 |
for (int i=0;i<num_data;++i) { |
| 1524 |
std::string n=boost::python::extract<std::string>(keys[i]); |
| 1525 |
escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]); |
| 1526 |
if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this) |
| 1527 |
throw FinleyAdapterException("Error in saveVTK: Data must be defined on same Domain"); |
| 1528 |
data[i]=d.getDataC(); |
| 1529 |
ptr_data[i]=&(data[i]); |
| 1530 |
c_names[i]=&(names[i][0]); |
| 1531 |
if (n.length()>MAX_namelength-1) { |
| 1532 |
strncpy(c_names[i],n.c_str(),MAX_namelength-1); |
| 1533 |
c_names[i][MAX_namelength-1]='\0'; |
| 1534 |
} else { |
| 1535 |
strcpy(c_names[i],n.c_str()); |
| 1536 |
} |
| 1537 |
} |
| 1538 |
Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data); |
| 1539 |
|
| 1540 |
checkFinleyError(); |
| 1541 |
/* win32 refactor */ |
| 1542 |
TMPMEMFREE(c_names); |
| 1543 |
TMPMEMFREE(data); |
| 1544 |
TMPMEMFREE(ptr_data); |
| 1545 |
for(int i=0;i<num_data;i++) |
| 1546 |
{ |
| 1547 |
TMPMEMFREE(names[i]); |
| 1548 |
} |
| 1549 |
TMPMEMFREE(names); |
| 1550 |
|
| 1551 |
return; |
| 1552 |
} |
| 1553 |
|
| 1554 |
|
| 1555 |
// creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros: |
| 1556 |
SystemMatrixAdapter MeshAdapter::newSystemMatrix( |
| 1557 |
const int row_blocksize, |
| 1558 |
const escript::FunctionSpace& row_functionspace, |
| 1559 |
const int column_blocksize, |
| 1560 |
const escript::FunctionSpace& column_functionspace, |
| 1561 |
const int type) const |
| 1562 |
{ |
| 1563 |
int reduceRowOrder=0; |
| 1564 |
int reduceColOrder=0; |
| 1565 |
// is the domain right? |
| 1566 |
const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain()); |
| 1567 |
if (row_domain!=*this) |
| 1568 |
throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator."); |
| 1569 |
const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain()); |
| 1570 |
if (col_domain!=*this) |
| 1571 |
throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator."); |
| 1572 |
// is the function space type right |
| 1573 |
if (row_functionspace.getTypeCode()==DegreesOfFreedom) { |
| 1574 |
reduceRowOrder=0; |
| 1575 |
} else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) { |
| 1576 |
reduceRowOrder=1; |
| 1577 |
} else { |
| 1578 |
throw FinleyAdapterException("Error - illegal function space type for system matrix rows."); |
| 1579 |
} |
| 1580 |
if (column_functionspace.getTypeCode()==DegreesOfFreedom) { |
| 1581 |
reduceColOrder=0; |
| 1582 |
} else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) { |
| 1583 |
reduceColOrder=1; |
| 1584 |
} else { |
| 1585 |
throw FinleyAdapterException("Error - illegal function space type for system matrix columns."); |
| 1586 |
} |
| 1587 |
// generate matrix: |
| 1588 |
|
| 1589 |
Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder); |
| 1590 |
checkFinleyError(); |
| 1591 |
Paso_SystemMatrix* fsystemMatrix; |
| 1592 |
int trilinos = 0; |
| 1593 |
if (trilinos) { |
| 1594 |
#ifdef TRILINOS |
| 1595 |
/* Allocation Epetra_VrbMatrix here */ |
| 1596 |
#endif |
| 1597 |
} |
| 1598 |
else { |
| 1599 |
fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize); |
| 1600 |
} |
| 1601 |
checkPasoError(); |
| 1602 |
Paso_SystemMatrixPattern_free(fsystemMatrixPattern); |
| 1603 |
return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace); |
| 1604 |
} |
| 1605 |
// creates a TransportProblemAdapter |
| 1606 |
TransportProblemAdapter MeshAdapter::newTransportProblem( |
| 1607 |
const double theta, |
| 1608 |
const double dt_max, |
| 1609 |
const int blocksize, |
| 1610 |
const escript::FunctionSpace& functionspace, |
| 1611 |
const int type) const |
| 1612 |
{ |
| 1613 |
int reduceOrder=0; |
| 1614 |
// is the domain right? |
| 1615 |
const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain()); |
| 1616 |
if (domain!=*this) |
| 1617 |
throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator."); |
| 1618 |
// is the function space type right |
| 1619 |
if (functionspace.getTypeCode()==DegreesOfFreedom) { |
| 1620 |
reduceOrder=0; |
| 1621 |
} else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) { |
| 1622 |
reduceOrder=1; |
| 1623 |
} else { |
| 1624 |
throw FinleyAdapterException("Error - illegal function space type for system matrix rows."); |
| 1625 |
} |
| 1626 |
// generate matrix: |
| 1627 |
|
| 1628 |
Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder); |
| 1629 |
checkFinleyError(); |
| 1630 |
Paso_FCTransportProblem* transportProblem; |
| 1631 |
transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize); |
| 1632 |
checkPasoError(); |
| 1633 |
Paso_SystemMatrixPattern_free(fsystemMatrixPattern); |
| 1634 |
return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace); |
| 1635 |
} |
| 1636 |
|
| 1637 |
// |
| 1638 |
// vtkObject MeshAdapter::createVtkObject() const |
| 1639 |
// TODO: |
| 1640 |
// |
| 1641 |
|
| 1642 |
// |
| 1643 |
// returns true if data at the atom_type is considered as being cell centered: |
| 1644 |
bool MeshAdapter::isCellOriented(int functionSpaceCode) const |
| 1645 |
{ |
| 1646 |
switch(functionSpaceCode) { |
| 1647 |
case(Nodes): |
| 1648 |
case(DegreesOfFreedom): |
| 1649 |
case(ReducedDegreesOfFreedom): |
| 1650 |
return false; |
| 1651 |
break; |
| 1652 |
case(Elements): |
| 1653 |
case(FaceElements): |
| 1654 |
case(Points): |
| 1655 |
case(ContactElementsZero): |
| 1656 |
case(ContactElementsOne): |
| 1657 |
case(ReducedElements): |
| 1658 |
case(ReducedFaceElements): |
| 1659 |
case(ReducedContactElementsZero): |
| 1660 |
case(ReducedContactElementsOne): |
| 1661 |
return true; |
| 1662 |
break; |
| 1663 |
default: |
| 1664 |
stringstream temp; |
| 1665 |
temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode; |
| 1666 |
throw FinleyAdapterException(temp.str()); |
| 1667 |
break; |
| 1668 |
} |
| 1669 |
checkFinleyError(); |
| 1670 |
return false; |
| 1671 |
} |
| 1672 |
|
| 1673 |
bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const |
| 1674 |
{ |
| 1675 |
switch(functionSpaceType_source) { |
| 1676 |
case(Nodes): |
| 1677 |
switch(functionSpaceType_target) { |
| 1678 |
case(Nodes): |
| 1679 |
case(ReducedNodes): |
| 1680 |
case(ReducedDegreesOfFreedom): |
| 1681 |
case(DegreesOfFreedom): |
| 1682 |
case(Elements): |
| 1683 |
case(ReducedElements): |
| 1684 |
case(FaceElements): |
| 1685 |
case(ReducedFaceElements): |
| 1686 |
case(Points): |
| 1687 |
case(ContactElementsZero): |
| 1688 |
case(ReducedContactElementsZero): |
| 1689 |
case(ContactElementsOne): |
| 1690 |
case(ReducedContactElementsOne): |
| 1691 |
return true; |
| 1692 |
default: |
| 1693 |
stringstream temp; |
| 1694 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target; |
| 1695 |
throw FinleyAdapterException(temp.str()); |
| 1696 |
} |
| 1697 |
break; |
| 1698 |
case(ReducedNodes): |
| 1699 |
switch(functionSpaceType_target) { |
| 1700 |
case(ReducedNodes): |
| 1701 |
case(ReducedDegreesOfFreedom): |
| 1702 |
case(Elements): |
| 1703 |
case(ReducedElements): |
| 1704 |
case(FaceElements): |
| 1705 |
case(ReducedFaceElements): |
| 1706 |
case(Points): |
| 1707 |
case(ContactElementsZero): |
| 1708 |
case(ReducedContactElementsZero): |
| 1709 |
case(ContactElementsOne): |
| 1710 |
case(ReducedContactElementsOne): |
| 1711 |
return true; |
| 1712 |
case(Nodes): |
| 1713 |
case(DegreesOfFreedom): |
| 1714 |
return false; |
| 1715 |
default: |
| 1716 |
stringstream temp; |
| 1717 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target; |
| 1718 |
throw FinleyAdapterException(temp.str()); |
| 1719 |
} |
| 1720 |
break; |
| 1721 |
case(Elements): |
| 1722 |
if (functionSpaceType_target==Elements) { |
| 1723 |
return true; |
| 1724 |
} else if (functionSpaceType_target==ReducedElements) { |
| 1725 |
return true; |
| 1726 |
} else { |
| 1727 |
return false; |
| 1728 |
} |
| 1729 |
case(ReducedElements): |
| 1730 |
if (functionSpaceType_target==ReducedElements) { |
| 1731 |
return true; |
| 1732 |
} else { |
| 1733 |
return false; |
| 1734 |
} |
| 1735 |
case(FaceElements): |
| 1736 |
if (functionSpaceType_target==FaceElements) { |
| 1737 |
return true; |
| 1738 |
} else if (functionSpaceType_target==ReducedFaceElements) { |
| 1739 |
return true; |
| 1740 |
} else { |
| 1741 |
return false; |
| 1742 |
} |
| 1743 |
case(ReducedFaceElements): |
| 1744 |
if (functionSpaceType_target==ReducedFaceElements) { |
| 1745 |
return true; |
| 1746 |
} else { |
| 1747 |
return false; |
| 1748 |
} |
| 1749 |
case(Points): |
| 1750 |
if (functionSpaceType_target==Points) { |
| 1751 |
return true; |
| 1752 |
} else { |
| 1753 |
return false; |
| 1754 |
} |
| 1755 |
case(ContactElementsZero): |
| 1756 |
case(ContactElementsOne): |
| 1757 |
if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) { |
| 1758 |
return true; |
| 1759 |
} else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) { |
| 1760 |
return true; |
| 1761 |
} else { |
| 1762 |
return false; |
| 1763 |
} |
| 1764 |
case(ReducedContactElementsZero): |
| 1765 |
case(ReducedContactElementsOne): |
| 1766 |
if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) { |
| 1767 |
return true; |
| 1768 |
} else { |
| 1769 |
return false; |
| 1770 |
} |
| 1771 |
case(DegreesOfFreedom): |
| 1772 |
switch(functionSpaceType_target) { |
| 1773 |
case(ReducedDegreesOfFreedom): |
| 1774 |
case(DegreesOfFreedom): |
| 1775 |
case(Nodes): |
| 1776 |
case(ReducedNodes): |
| 1777 |
case(Elements): |
| 1778 |
case(ReducedElements): |
| 1779 |
case(Points): |
| 1780 |
case(FaceElements): |
| 1781 |
case(ReducedFaceElements): |
| 1782 |
case(ContactElementsZero): |
| 1783 |
case(ReducedContactElementsZero): |
| 1784 |
case(ContactElementsOne): |
| 1785 |
case(ReducedContactElementsOne): |
| 1786 |
return true; |
| 1787 |
default: |
| 1788 |
stringstream temp; |
| 1789 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target; |
| 1790 |
throw FinleyAdapterException(temp.str()); |
| 1791 |
} |
| 1792 |
break; |
| 1793 |
case(ReducedDegreesOfFreedom): |
| 1794 |
switch(functionSpaceType_target) { |
| 1795 |
case(ReducedDegreesOfFreedom): |
| 1796 |
case(ReducedNodes): |
| 1797 |
case(Elements): |
| 1798 |
case(ReducedElements): |
| 1799 |
case(FaceElements): |
| 1800 |
case(ReducedFaceElements): |
| 1801 |
case(Points): |
| 1802 |
case(ContactElementsZero): |
| 1803 |
case(ReducedContactElementsZero): |
| 1804 |
case(ContactElementsOne): |
| 1805 |
case(ReducedContactElementsOne): |
| 1806 |
return true; |
| 1807 |
case(Nodes): |
| 1808 |
case(DegreesOfFreedom): |
| 1809 |
return false; |
| 1810 |
default: |
| 1811 |
stringstream temp; |
| 1812 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target; |
| 1813 |
throw FinleyAdapterException(temp.str()); |
| 1814 |
} |
| 1815 |
break; |
| 1816 |
default: |
| 1817 |
stringstream temp; |
| 1818 |
temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source; |
| 1819 |
throw FinleyAdapterException(temp.str()); |
| 1820 |
break; |
| 1821 |
} |
| 1822 |
checkFinleyError(); |
| 1823 |
return false; |
| 1824 |
} |
| 1825 |
|
| 1826 |
bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const |
| 1827 |
{ |
| 1828 |
return false; |
| 1829 |
} |
| 1830 |
|
| 1831 |
bool MeshAdapter::operator==(const AbstractDomain& other) const |
| 1832 |
{ |
| 1833 |
const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other); |
| 1834 |
if (temp!=0) { |
| 1835 |
return (m_finleyMesh==temp->m_finleyMesh); |
| 1836 |
} else { |
| 1837 |
return false; |
| 1838 |
} |
| 1839 |
} |
| 1840 |
|
| 1841 |
bool MeshAdapter::operator!=(const AbstractDomain& other) const |
| 1842 |
{ |
| 1843 |
return !(operator==(other)); |
| 1844 |
} |
| 1845 |
|
| 1846 |
int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const |
| 1847 |
{ |
| 1848 |
int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0); |
| 1849 |
checkPasoError(); |
| 1850 |
return out; |
| 1851 |
} |
| 1852 |
|
| 1853 |
escript::Data MeshAdapter::getX() const |
| 1854 |
{ |
| 1855 |
return continuousFunction(asAbstractContinuousDomain()).getX(); |
| 1856 |
} |
| 1857 |
|
| 1858 |
escript::Data MeshAdapter::getNormal() const |
| 1859 |
{ |
| 1860 |
return functionOnBoundary(asAbstractContinuousDomain()).getNormal(); |
| 1861 |
} |
| 1862 |
|
| 1863 |
escript::Data MeshAdapter::getSize() const |
| 1864 |
{ |
| 1865 |
return function(asAbstractContinuousDomain()).getSize(); |
| 1866 |
} |
| 1867 |
|
| 1868 |
int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const |
| 1869 |
{ |
| 1870 |
int *out=0,i; |
| 1871 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1872 |
switch (functionSpaceType) { |
| 1873 |
case(Nodes): |
| 1874 |
out=mesh->Nodes->Id; |
| 1875 |
break; |
| 1876 |
case(ReducedNodes): |
| 1877 |
out=mesh->Nodes->reducedNodesId; |
| 1878 |
break; |
| 1879 |
case(Elements): |
| 1880 |
out=mesh->Elements->Id; |
| 1881 |
break; |
| 1882 |
case(ReducedElements): |
| 1883 |
out=mesh->Elements->Id; |
| 1884 |
break; |
| 1885 |
case(FaceElements): |
| 1886 |
out=mesh->FaceElements->Id; |
| 1887 |
break; |
| 1888 |
case(ReducedFaceElements): |
| 1889 |
out=mesh->FaceElements->Id; |
| 1890 |
break; |
| 1891 |
case(Points): |
| 1892 |
out=mesh->Points->Id; |
| 1893 |
break; |
| 1894 |
case(ContactElementsZero): |
| 1895 |
out=mesh->ContactElements->Id; |
| 1896 |
break; |
| 1897 |
case(ReducedContactElementsZero): |
| 1898 |
out=mesh->ContactElements->Id; |
| 1899 |
break; |
| 1900 |
case(ContactElementsOne): |
| 1901 |
out=mesh->ContactElements->Id; |
| 1902 |
break; |
| 1903 |
case(ReducedContactElementsOne): |
| 1904 |
out=mesh->ContactElements->Id; |
| 1905 |
break; |
| 1906 |
case(DegreesOfFreedom): |
| 1907 |
out=mesh->Nodes->degreesOfFreedomId; |
| 1908 |
break; |
| 1909 |
case(ReducedDegreesOfFreedom): |
| 1910 |
out=mesh->Nodes->reducedDegreesOfFreedomId; |
| 1911 |
break; |
| 1912 |
default: |
| 1913 |
stringstream temp; |
| 1914 |
temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription(); |
| 1915 |
throw FinleyAdapterException(temp.str()); |
| 1916 |
break; |
| 1917 |
} |
| 1918 |
return out; |
| 1919 |
} |
| 1920 |
int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const |
| 1921 |
{ |
| 1922 |
int out=0; |
| 1923 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1924 |
switch (functionSpaceType) { |
| 1925 |
case(Nodes): |
| 1926 |
out=mesh->Nodes->Tag[sampleNo]; |
| 1927 |
break; |
| 1928 |
case(ReducedNodes): |
| 1929 |
throw FinleyAdapterException(" Error - ReducedNodes does not support tags."); |
| 1930 |
break; |
| 1931 |
case(Elements): |
| 1932 |
out=mesh->Elements->Tag[sampleNo]; |
| 1933 |
break; |
| 1934 |
case(ReducedElements): |
| 1935 |
out=mesh->Elements->Tag[sampleNo]; |
| 1936 |
break; |
| 1937 |
case(FaceElements): |
| 1938 |
out=mesh->FaceElements->Tag[sampleNo]; |
| 1939 |
break; |
| 1940 |
case(ReducedFaceElements): |
| 1941 |
out=mesh->FaceElements->Tag[sampleNo]; |
| 1942 |
break; |
| 1943 |
case(Points): |
| 1944 |
out=mesh->Points->Tag[sampleNo]; |
| 1945 |
break; |
| 1946 |
case(ContactElementsZero): |
| 1947 |
out=mesh->ContactElements->Tag[sampleNo]; |
| 1948 |
break; |
| 1949 |
case(ReducedContactElementsZero): |
| 1950 |
out=mesh->ContactElements->Tag[sampleNo]; |
| 1951 |
break; |
| 1952 |
case(ContactElementsOne): |
| 1953 |
out=mesh->ContactElements->Tag[sampleNo]; |
| 1954 |
break; |
| 1955 |
case(ReducedContactElementsOne): |
| 1956 |
out=mesh->ContactElements->Tag[sampleNo]; |
| 1957 |
break; |
| 1958 |
case(DegreesOfFreedom): |
| 1959 |
throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags."); |
| 1960 |
break; |
| 1961 |
case(ReducedDegreesOfFreedom): |
| 1962 |
throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags."); |
| 1963 |
break; |
| 1964 |
default: |
| 1965 |
stringstream temp; |
| 1966 |
temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription(); |
| 1967 |
throw FinleyAdapterException(temp.str()); |
| 1968 |
break; |
| 1969 |
} |
| 1970 |
return out; |
| 1971 |
} |
| 1972 |
|
| 1973 |
|
| 1974 |
void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const |
| 1975 |
{ |
| 1976 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 1977 |
escriptDataC tmp=mask.getDataC(); |
| 1978 |
switch(functionSpaceType) { |
| 1979 |
case(Nodes): |
| 1980 |
Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp); |
| 1981 |
break; |
| 1982 |
case(ReducedNodes): |
| 1983 |
throw FinleyAdapterException("Error - ReducedNodes does not support tags"); |
| 1984 |
break; |
| 1985 |
case(DegreesOfFreedom): |
| 1986 |
throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags"); |
| 1987 |
break; |
| 1988 |
case(ReducedDegreesOfFreedom): |
| 1989 |
throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags"); |
| 1990 |
break; |
| 1991 |
case(Elements): |
| 1992 |
Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp); |
| 1993 |
break; |
| 1994 |
case(ReducedElements): |
| 1995 |
Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp); |
| 1996 |
break; |
| 1997 |
case(FaceElements): |
| 1998 |
Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp); |
| 1999 |
break; |
| 2000 |
case(ReducedFaceElements): |
| 2001 |
Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp); |
| 2002 |
break; |
| 2003 |
case(Points): |
| 2004 |
Finley_ElementFile_setTags(mesh->Points,newTag,&tmp); |
| 2005 |
break; |
| 2006 |
case(ContactElementsZero): |
| 2007 |
Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp); |
| 2008 |
break; |
| 2009 |
case(ReducedContactElementsZero): |
| 2010 |
Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp); |
| 2011 |
break; |
| 2012 |
case(ContactElementsOne): |
| 2013 |
Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp); |
| 2014 |
break; |
| 2015 |
case(ReducedContactElementsOne): |
| 2016 |
Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp); |
| 2017 |
break; |
| 2018 |
default: |
| 2019 |
stringstream temp; |
| 2020 |
temp << "Error - Finley does not know anything about function space type " << functionSpaceType; |
| 2021 |
throw FinleyAdapterException(temp.str()); |
| 2022 |
} |
| 2023 |
checkFinleyError(); |
| 2024 |
return; |
| 2025 |
} |
| 2026 |
|
| 2027 |
void MeshAdapter::setTagMap(const std::string& name, int tag) |
| 2028 |
{ |
| 2029 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 2030 |
Finley_Mesh_addTagMap(mesh, name.c_str(),tag); |
| 2031 |
checkPasoError(); |
| 2032 |
// throwStandardException("MeshAdapter::set TagMap is not implemented."); |
| 2033 |
} |
| 2034 |
|
| 2035 |
int MeshAdapter::getTag(const std::string& name) const |
| 2036 |
{ |
| 2037 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 2038 |
int tag=0; |
| 2039 |
tag=Finley_Mesh_getTag(mesh, name.c_str()); |
| 2040 |
checkPasoError(); |
| 2041 |
// throwStandardException("MeshAdapter::getTag is not implemented."); |
| 2042 |
return tag; |
| 2043 |
} |
| 2044 |
|
| 2045 |
bool MeshAdapter::isValidTagName(const std::string& name) const |
| 2046 |
{ |
| 2047 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 2048 |
return Finley_Mesh_isValidTagName(mesh,name.c_str()); |
| 2049 |
} |
| 2050 |
|
| 2051 |
std::string MeshAdapter::showTagNames() const |
| 2052 |
{ |
| 2053 |
stringstream temp; |
| 2054 |
Finley_Mesh* mesh=m_finleyMesh.get(); |
| 2055 |
Finley_TagMap* tag_map=mesh->TagMap; |
| 2056 |
while (tag_map) { |
| 2057 |
temp << tag_map->name; |
| 2058 |
tag_map=tag_map->next; |
| 2059 |
if (tag_map) temp << ", "; |
| 2060 |
} |
| 2061 |
return temp.str(); |
| 2062 |
} |
| 2063 |
|
| 2064 |
} // end of namespace |
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