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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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#ifdef PASO_MPI |
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#include <mpi.h> |
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#endif |
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#ifdef USE_NETCDF |
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#include <netcdfcpp.h> |
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#endif |
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#include "MeshAdapterFactory.h" |
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#include "FinleyError.h" |
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extern "C" { |
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#include "escript/blocktimer.h" |
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} |
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|
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#include <boost/python/extract.hpp> |
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|
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#include <sstream> |
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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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#ifdef USE_NETCDF |
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// A convenience method to retrieve an integer attribute from a NetCDF file |
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int NetCDF_Get_Int_Attribute(NcFile *dataFile, char *fName, char *attr_name) { |
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NcAtt *attr; |
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char error_msg[LenErrorMsg_MAX]; |
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if (! (attr=dataFile->get_att(attr_name)) ) { |
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sprintf(error_msg,"Error retrieving integer attribute '%s' from NetCDF file '%s'", attr_name, fName); |
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throw DataException(error_msg); |
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} |
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int temp = attr->as_int(0); |
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delete attr; |
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return(temp); |
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} |
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#endif |
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|
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AbstractContinuousDomain* loadMesh(const std::string& fileName) |
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{ |
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#ifdef USE_NETCDF |
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bool optimize=FALSE; // Don't optimize since this would cause problems with Data().dump() |
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Paso_MPIInfo *mpi_info = Paso_MPIInfo_alloc( MPI_COMM_WORLD ); |
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AbstractContinuousDomain* temp; |
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Finley_Mesh *mesh_p=NULL; |
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char error_msg[LenErrorMsg_MAX]; |
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|
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char *fName = Paso_MPI_appendRankToFileName(fileName.c_str(), |
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mpi_info->size, |
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mpi_info->rank); |
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|
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double blocktimer_start = blocktimer_time(); |
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Finley_resetError(); |
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int *first_DofComponent, *first_NodeComponent; |
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|
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// Open NetCDF file for reading |
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NcAtt *attr; |
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NcVar *nc_var_temp; |
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// netCDF error handler |
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NcError err(NcError::silent_nonfatal); |
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// Create the NetCDF file. |
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NcFile dataFile(fName, NcFile::ReadOnly); |
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if (!dataFile.is_valid()) { |
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sprintf(error_msg,"loadMesh: Opening file NetCDF %s for reading failed.", fName); |
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Finley_setError(IO_ERROR,error_msg); |
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Paso_MPIInfo_free( mpi_info ); |
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throw DataException(error_msg); |
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} |
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|
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// Read NetCDF integer attributes |
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int mpi_size = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"mpi_size"); |
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int mpi_rank = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"mpi_rank"); |
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int numDim = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"numDim"); |
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int order = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"order"); |
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int reduced_order = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"reduced_order"); |
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int numNodes = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"numNodes"); |
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int num_Elements = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_Elements"); |
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int num_FaceElements = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_FaceElements"); |
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int num_ContactElements = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_ContactElements"); |
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int num_Points = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_Points"); |
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int num_Elements_numNodes = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_Elements_numNodes"); |
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int Elements_TypeId = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"Elements_TypeId"); |
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int num_FaceElements_numNodes = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_FaceElements_numNodes"); |
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int FaceElements_TypeId = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"FaceElements_TypeId"); |
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int num_ContactElements_numNodes = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_ContactElements_numNodes"); |
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int ContactElements_TypeId = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"ContactElements_TypeId"); |
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int Points_TypeId = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"Points_TypeId"); |
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int num_Tags = NetCDF_Get_Int_Attribute(&dataFile, fName, (char *)"num_Tags"); |
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|
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// Verify size and rank |
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if (mpi_info->size != mpi_size) { |
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sprintf(error_msg, "Error loadMesh - The NetCDF file '%s' can only be read on %d CPUs instead of %d", fName, mpi_size, mpi_info->size); |
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throw DataException(error_msg); |
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} |
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if (mpi_info->rank != mpi_rank) { |
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sprintf(error_msg, "Error loadMesh - The NetCDF file '%s' should be read on CPU #%d instead of %d", fName, mpi_rank, mpi_info->rank); |
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throw DataException(error_msg); |
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} |
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|
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// Read mesh name |
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if (! (attr=dataFile.get_att("Name")) ) { |
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sprintf(error_msg,"Error retrieving mesh name from NetCDF file '%s'", fName); |
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throw DataException(error_msg); |
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} |
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char *name = attr->as_string(0); |
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delete attr; |
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|
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/* allocate mesh */ |
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mesh_p = Finley_Mesh_alloc(name,numDim,order,reduced_order,mpi_info); |
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if (Finley_noError()) { |
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|
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/* read nodes */ |
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Finley_NodeFile_allocTable(mesh_p->Nodes, numNodes); |
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// Nodes_Id |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_Id")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_Id from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Nodes->Id[0], numNodes) ) { |
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TMPMEMFREE(mesh_p->Nodes->Id); |
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throw DataException("Error - loadMesh:: unable to recover Nodes_Id from NetCDF file: " + *fName); |
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} |
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// Nodes_Tag |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_Tag")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_Tag from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Nodes->Tag[0], numNodes) ) { |
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TMPMEMFREE(mesh_p->Nodes->Tag); |
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throw DataException("Error - loadMesh:: unable to recover Nodes_Tag from NetCDF file: " + *fName); |
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} |
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// Nodes_gDOF |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_gDOF")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_gDOF from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Nodes->globalDegreesOfFreedom[0], numNodes) ) { |
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TMPMEMFREE(mesh_p->Nodes->globalDegreesOfFreedom); |
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throw DataException("Error - loadMesh:: unable to recover Nodes_gDOF from NetCDF file: " + *fName); |
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} |
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// Nodes_gNI |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_gNI")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_gNI from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Nodes->globalNodesIndex[0], numNodes) ) { |
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TMPMEMFREE(mesh_p->Nodes->globalNodesIndex); |
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throw DataException("Error - loadMesh:: unable to recover Nodes_gNI from NetCDF file: " + *fName); |
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} |
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// Nodes_grDfI |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_grDfI")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_grDfI from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Nodes->globalReducedDOFIndex[0], numNodes) ) { |
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TMPMEMFREE(mesh_p->Nodes->globalReducedDOFIndex); |
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throw DataException("Error - loadMesh:: unable to recover Nodes_grDfI from NetCDF file: " + *fName); |
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} |
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// Nodes_grNI |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_grNI")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_grNI from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Nodes->globalReducedNodesIndex[0], numNodes) ) { |
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TMPMEMFREE(mesh_p->Nodes->globalReducedNodesIndex); |
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throw DataException("Error - loadMesh:: unable to recover Nodes_grNI from NetCDF file: " + *fName); |
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} |
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// Nodes_Coordinates |
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if (!(nc_var_temp = dataFile.get_var("Nodes_Coordinates"))) { |
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TMPMEMFREE(mesh_p->Nodes->Coordinates); |
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throw DataException("Error - loadMesh:: unable to read Nodes_Coordinates from netCDF file: " + *fName); |
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} |
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if (! nc_var_temp->get(&(mesh_p->Nodes->Coordinates[0]), numNodes, numDim) ) { |
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TMPMEMFREE(mesh_p->Nodes->Coordinates); |
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throw DataException("Error - load:: unable to recover Nodes_Coordinates from netCDF file: " + *fName); |
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} |
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// Nodes_DofDistribution |
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first_DofComponent = TMPMEMALLOC(mpi_size+1,index_t); |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_DofDistribution")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_DofDistribution from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&first_DofComponent[0], mpi_size+1) ) { |
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throw DataException("Error - loadMesh:: unable to recover Nodes_DofDistribution from NetCDF file: " + *fName); |
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} |
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|
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// Nodes_NodeDistribution |
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first_NodeComponent = TMPMEMALLOC(mpi_size+1,index_t); |
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if (! ( nc_var_temp = dataFile.get_var("Nodes_NodeDistribution")) ) |
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throw DataException("Error - loadMesh:: unable to read Nodes_NodeDistribution from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&first_NodeComponent[0], mpi_size+1) ) { |
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throw DataException("Error - loadMesh:: unable to recover Nodes_NodeDistribution from NetCDF file: " + *fName); |
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} |
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|
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/* read elements */ |
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if (Finley_noError()) { |
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mesh_p->Elements=Finley_ElementFile_alloc((ElementTypeId)Elements_TypeId,mesh_p->order, mesh_p->reduced_order, mpi_info); |
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if (Finley_noError()) Finley_ElementFile_allocTable(mesh_p->Elements, num_Elements); |
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mesh_p->Elements->minColor=0; |
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mesh_p->Elements->maxColor=num_Elements-1; |
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if (num_Elements>0) { |
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if (Finley_noError()) { |
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// Elements_Id |
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if (! ( nc_var_temp = dataFile.get_var("Elements_Id")) ) |
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throw DataException("Error - loadMesh:: unable to read Elements_Id from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Elements->Id[0], num_Elements) ) { |
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TMPMEMFREE(mesh_p->Elements->Id); |
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throw DataException("Error - loadMesh:: unable to recover Elements_Id from NetCDF file: " + *fName); |
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} |
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// Elements_Tag |
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if (! ( nc_var_temp = dataFile.get_var("Elements_Tag")) ) |
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throw DataException("Error - loadMesh:: unable to read Elements_Tag from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Elements->Tag[0], num_Elements) ) { |
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TMPMEMFREE(mesh_p->Elements->Tag); |
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throw DataException("Error - loadMesh:: unable to recover Elements_Tag from NetCDF file: " + *fName); |
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} |
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// Elements_Owner |
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if (! ( nc_var_temp = dataFile.get_var("Elements_Owner")) ) |
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throw DataException("Error - loadMesh:: unable to read Elements_Owner from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Elements->Owner[0], num_Elements) ) { |
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TMPMEMFREE(mesh_p->Elements->Owner); |
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throw DataException("Error - loadMesh:: unable to recover Elements_Owner from NetCDF file: " + *fName); |
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} |
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// Elements_Color |
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if (! ( nc_var_temp = dataFile.get_var("Elements_Color")) ) |
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throw DataException("Error - loadMesh:: unable to read Elements_Color from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->Elements->Color[0], num_Elements) ) { |
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TMPMEMFREE(mesh_p->Elements->Color); |
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throw DataException("Error - loadMesh:: unable to recover Elements_Color from NetCDF file: " + *fName); |
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} |
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// Elements_Nodes |
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int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int); |
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if (!(nc_var_temp = dataFile.get_var("Elements_Nodes"))) { |
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TMPMEMFREE(mesh_p->Elements->Nodes); |
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throw DataException("Error - loadMesh:: unable to read Elements_Nodes from netCDF file: " + *fName); |
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} |
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if (! nc_var_temp->get(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes) ) { |
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TMPMEMFREE(Elements_Nodes); |
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throw DataException("Error - load:: unable to recover Elements_Nodes from netCDF file: " + *fName); |
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} |
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// Copy temp array into mesh_p->Elements->Nodes |
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for (int i=0; i<num_Elements; i++) { |
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for (int j=0; j<num_Elements_numNodes; j++) { |
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mesh_p->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)] |
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= Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)]; |
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} |
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} |
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TMPMEMFREE(Elements_Nodes); |
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} |
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} /* num_Elements>0 */ |
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} |
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|
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/* get the face elements */ |
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if (Finley_noError()) { |
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mesh_p->FaceElements=Finley_ElementFile_alloc((ElementTypeId)FaceElements_TypeId,mesh_p->order, mesh_p->reduced_order, mpi_info); |
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if (Finley_noError()) Finley_ElementFile_allocTable(mesh_p->FaceElements, num_FaceElements); |
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mesh_p->FaceElements->minColor=0; |
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mesh_p->FaceElements->maxColor=num_FaceElements-1; |
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if (num_FaceElements>0) { |
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if (Finley_noError()) { |
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// FaceElements_Id |
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if (! ( nc_var_temp = dataFile.get_var("FaceElements_Id")) ) |
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throw DataException("Error - loadMesh:: unable to read FaceElements_Id from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->FaceElements->Id[0], num_FaceElements) ) { |
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TMPMEMFREE(mesh_p->FaceElements->Id); |
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throw DataException("Error - loadMesh:: unable to recover FaceElements_Id from NetCDF file: " + *fName); |
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} |
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// FaceElements_Tag |
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if (! ( nc_var_temp = dataFile.get_var("FaceElements_Tag")) ) |
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throw DataException("Error - loadMesh:: unable to read FaceElements_Tag from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->FaceElements->Tag[0], num_FaceElements) ) { |
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TMPMEMFREE(mesh_p->FaceElements->Tag); |
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throw DataException("Error - loadMesh:: unable to recover FaceElements_Tag from NetCDF file: " + *fName); |
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} |
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// FaceElements_Owner |
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if (! ( nc_var_temp = dataFile.get_var("FaceElements_Owner")) ) |
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throw DataException("Error - loadMesh:: unable to read FaceElements_Owner from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->FaceElements->Owner[0], num_FaceElements) ) { |
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TMPMEMFREE(mesh_p->FaceElements->Owner); |
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throw DataException("Error - loadMesh:: unable to recover FaceElements_Owner from NetCDF file: " + *fName); |
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} |
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// FaceElements_Color |
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if (! ( nc_var_temp = dataFile.get_var("FaceElements_Color")) ) |
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throw DataException("Error - loadMesh:: unable to read FaceElements_Color from netCDF file: " + *fName); |
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if (! nc_var_temp->get(&mesh_p->FaceElements->Color[0], num_FaceElements) ) { |
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TMPMEMFREE(mesh_p->FaceElements->Color); |
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throw DataException("Error - loadMesh:: unable to recover FaceElements_Color from NetCDF file: " + *fName); |
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} |
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// FaceElements_Nodes |
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int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int); |
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if (!(nc_var_temp = dataFile.get_var("FaceElements_Nodes"))) { |
| 291 |
TMPMEMFREE(mesh_p->FaceElements->Nodes); |
| 292 |
throw DataException("Error - loadMesh:: unable to read FaceElements_Nodes from netCDF file: " + *fName); |
| 293 |
} |
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if (! nc_var_temp->get(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes) ) { |
| 295 |
TMPMEMFREE(FaceElements_Nodes); |
| 296 |
throw DataException("Error - load:: unable to recover FaceElements_Nodes from netCDF file: " + *fName); |
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} |
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// Copy temp array into mesh_p->FaceElements->Nodes |
| 299 |
for (int i=0; i<num_FaceElements; i++) { |
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for (int j=0; j<num_FaceElements_numNodes; j++) { |
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mesh_p->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)] |
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= FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)]; |
| 303 |
} |
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} |
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TMPMEMFREE(FaceElements_Nodes); |
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} |
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} /* num_FaceElements>0 */ |
| 308 |
} |
| 309 |
|
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/* get the Contact elements */ |
| 311 |
if (Finley_noError()) { |
| 312 |
mesh_p->ContactElements=Finley_ElementFile_alloc((ElementTypeId)ContactElements_TypeId,mesh_p->order, mesh_p->reduced_order, mpi_info); |
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if (Finley_noError()) Finley_ElementFile_allocTable(mesh_p->ContactElements, num_ContactElements); |
| 314 |
mesh_p->ContactElements->minColor=0; |
| 315 |
mesh_p->ContactElements->maxColor=num_ContactElements-1; |
| 316 |
if (num_ContactElements>0) { |
| 317 |
if (Finley_noError()) { |
| 318 |
// ContactElements_Id |
| 319 |
if (! ( nc_var_temp = dataFile.get_var("ContactElements_Id")) ) |
| 320 |
throw DataException("Error - loadMesh:: unable to read ContactElements_Id from netCDF file: " + *fName); |
| 321 |
if (! nc_var_temp->get(&mesh_p->ContactElements->Id[0], num_ContactElements) ) { |
| 322 |
TMPMEMFREE(mesh_p->ContactElements->Id); |
| 323 |
throw DataException("Error - loadMesh:: unable to recover ContactElements_Id from NetCDF file: " + *fName); |
| 324 |
} |
| 325 |
// ContactElements_Tag |
| 326 |
if (! ( nc_var_temp = dataFile.get_var("ContactElements_Tag")) ) |
| 327 |
throw DataException("Error - loadMesh:: unable to read ContactElements_Tag from netCDF file: " + *fName); |
| 328 |
if (! nc_var_temp->get(&mesh_p->ContactElements->Tag[0], num_ContactElements) ) { |
| 329 |
TMPMEMFREE(mesh_p->ContactElements->Tag); |
| 330 |
throw DataException("Error - loadMesh:: unable to recover ContactElements_Tag from NetCDF file: " + *fName); |
| 331 |
} |
| 332 |
// ContactElements_Owner |
| 333 |
if (! ( nc_var_temp = dataFile.get_var("ContactElements_Owner")) ) |
| 334 |
throw DataException("Error - loadMesh:: unable to read ContactElements_Owner from netCDF file: " + *fName); |
| 335 |
if (! nc_var_temp->get(&mesh_p->ContactElements->Owner[0], num_ContactElements) ) { |
| 336 |
TMPMEMFREE(mesh_p->ContactElements->Owner); |
| 337 |
throw DataException("Error - loadMesh:: unable to recover ContactElements_Owner from NetCDF file: " + *fName); |
| 338 |
} |
| 339 |
// ContactElements_Color |
| 340 |
if (! ( nc_var_temp = dataFile.get_var("ContactElements_Color")) ) |
| 341 |
throw DataException("Error - loadMesh:: unable to read ContactElements_Color from netCDF file: " + *fName); |
| 342 |
if (! nc_var_temp->get(&mesh_p->ContactElements->Color[0], num_ContactElements) ) { |
| 343 |
TMPMEMFREE(mesh_p->ContactElements->Color); |
| 344 |
throw DataException("Error - loadMesh:: unable to recover ContactElements_Color from NetCDF file: " + *fName); |
| 345 |
} |
| 346 |
// ContactElements_Nodes |
| 347 |
int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int); |
| 348 |
if (!(nc_var_temp = dataFile.get_var("ContactElements_Nodes"))) { |
| 349 |
TMPMEMFREE(mesh_p->ContactElements->Nodes); |
| 350 |
throw DataException("Error - loadMesh:: unable to read ContactElements_Nodes from netCDF file: " + *fName); |
| 351 |
} |
| 352 |
if (! nc_var_temp->get(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes) ) { |
| 353 |
TMPMEMFREE(ContactElements_Nodes); |
| 354 |
throw DataException("Error - load:: unable to recover ContactElements_Nodes from netCDF file: " + *fName); |
| 355 |
} |
| 356 |
// Copy temp array into mesh_p->ContactElements->Nodes |
| 357 |
for (int i=0; i<num_ContactElements; i++) { |
| 358 |
for (int j=0; j<num_ContactElements_numNodes; j++) { |
| 359 |
mesh_p->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)] |
| 360 |
= ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)]; |
| 361 |
} |
| 362 |
} |
| 363 |
TMPMEMFREE(ContactElements_Nodes); |
| 364 |
} |
| 365 |
} /* num_ContactElements>0 */ |
| 366 |
} |
| 367 |
|
| 368 |
/* get the Points (nodal elements) */ |
| 369 |
if (Finley_noError()) { |
| 370 |
mesh_p->Points=Finley_ElementFile_alloc((ElementTypeId)Points_TypeId,mesh_p->order, mesh_p->reduced_order, mpi_info); |
| 371 |
if (Finley_noError()) Finley_ElementFile_allocTable(mesh_p->Points, num_Points); |
| 372 |
mesh_p->Points->minColor=0; |
| 373 |
mesh_p->Points->maxColor=num_Points-1; |
| 374 |
if (num_Points>0) { |
| 375 |
if (Finley_noError()) { |
| 376 |
// Points_Id |
| 377 |
if (! ( nc_var_temp = dataFile.get_var("Points_Id")) ) |
| 378 |
throw DataException("Error - loadMesh:: unable to read Points_Id from netCDF file: " + *fName); |
| 379 |
if (! nc_var_temp->get(&mesh_p->Points->Id[0], num_Points) ) { |
| 380 |
TMPMEMFREE(mesh_p->Points->Id); |
| 381 |
throw DataException("Error - loadMesh:: unable to recover Points_Id from NetCDF file: " + *fName); |
| 382 |
} |
| 383 |
// Points_Tag |
| 384 |
if (! ( nc_var_temp = dataFile.get_var("Points_Tag")) ) |
| 385 |
throw DataException("Error - loadMesh:: unable to read Points_Tag from netCDF file: " + *fName); |
| 386 |
if (! nc_var_temp->get(&mesh_p->Points->Tag[0], num_Points) ) { |
| 387 |
TMPMEMFREE(mesh_p->Points->Tag); |
| 388 |
throw DataException("Error - loadMesh:: unable to recover Points_Tag from NetCDF file: " + *fName); |
| 389 |
} |
| 390 |
// Points_Owner |
| 391 |
if (! ( nc_var_temp = dataFile.get_var("Points_Owner")) ) |
| 392 |
throw DataException("Error - loadMesh:: unable to read Points_Owner from netCDF file: " + *fName); |
| 393 |
if (! nc_var_temp->get(&mesh_p->Points->Owner[0], num_Points) ) { |
| 394 |
TMPMEMFREE(mesh_p->Points->Owner); |
| 395 |
throw DataException("Error - loadMesh:: unable to recover Points_Owner from NetCDF file: " + *fName); |
| 396 |
} |
| 397 |
// Points_Color |
| 398 |
if (! ( nc_var_temp = dataFile.get_var("Points_Color")) ) |
| 399 |
throw DataException("Error - loadMesh:: unable to read Points_Color from netCDF file: " + *fName); |
| 400 |
if (! nc_var_temp->get(&mesh_p->Points->Color[0], num_Points) ) { |
| 401 |
TMPMEMFREE(mesh_p->Points->Color); |
| 402 |
throw DataException("Error - loadMesh:: unable to recover Points_Color from NetCDF file: " + *fName); |
| 403 |
} |
| 404 |
// Points_Nodes |
| 405 |
int *Points_Nodes = TMPMEMALLOC(num_Points,int); |
| 406 |
if (!(nc_var_temp = dataFile.get_var("Points_Nodes"))) { |
| 407 |
TMPMEMFREE(mesh_p->Points->Nodes); |
| 408 |
throw DataException("Error - loadMesh:: unable to read Points_Nodes from netCDF file: " + *fName); |
| 409 |
} |
| 410 |
if (! nc_var_temp->get(&(Points_Nodes[0]), num_Points) ) { |
| 411 |
TMPMEMFREE(Points_Nodes); |
| 412 |
throw DataException("Error - load:: unable to recover Points_Nodes from netCDF file: " + *fName); |
| 413 |
} |
| 414 |
// Copy temp array into mesh_p->Points->Nodes |
| 415 |
for (int i=0; i<num_Points; i++) { |
| 416 |
mesh_p->Nodes->Id[mesh_p->Points->Nodes[INDEX2(0,i,1)]] = Points_Nodes[i]; |
| 417 |
} |
| 418 |
TMPMEMFREE(Points_Nodes); |
| 419 |
} |
| 420 |
} /* num_Points>0 */ |
| 421 |
} |
| 422 |
|
| 423 |
/* get the tags */ |
| 424 |
if (Finley_noError()) { |
| 425 |
if (num_Tags>0) { |
| 426 |
// Temp storage to gather node IDs |
| 427 |
int *Tags_keys = TMPMEMALLOC(num_Tags, int); |
| 428 |
char name_temp[4096]; |
| 429 |
int i; |
| 430 |
|
| 431 |
// Tags_keys |
| 432 |
if (! ( nc_var_temp = dataFile.get_var("Tags_keys")) ) |
| 433 |
throw DataException("Error - loadMesh:: unable to read Tags_keys from netCDF file: " + *fName); |
| 434 |
if (! nc_var_temp->get(&Tags_keys[0], num_Tags) ) { |
| 435 |
TMPMEMFREE(Tags_keys); |
| 436 |
throw DataException("Error - loadMesh:: unable to recover Tags_keys from NetCDF file: " + *fName); |
| 437 |
} |
| 438 |
for (i=0; i<num_Tags; i++) { |
| 439 |
// Retrieve tag name |
| 440 |
sprintf(name_temp, "Tags_name_%d", i); |
| 441 |
if (! (attr=dataFile.get_att(name_temp)) ) { |
| 442 |
sprintf(error_msg,"Error retrieving tag name from NetCDF file '%s'", fName); |
| 443 |
throw DataException(error_msg); |
| 444 |
} |
| 445 |
char *name = attr->as_string(0); |
| 446 |
delete attr; |
| 447 |
Finley_Mesh_addTagMap(mesh_p, name, Tags_keys[i]); |
| 448 |
} |
| 449 |
} |
| 450 |
} |
| 451 |
|
| 452 |
} /* Finley_noError() after Finley_Mesh_alloc() */ |
| 453 |
|
| 454 |
if (Finley_noError()) Finley_Mesh_createMappings(mesh_p, first_DofComponent, first_NodeComponent); |
| 455 |
TMPMEMFREE(first_DofComponent); |
| 456 |
TMPMEMFREE(first_NodeComponent); |
| 457 |
|
| 458 |
checkFinleyError(); |
| 459 |
temp=new MeshAdapter(mesh_p); |
| 460 |
|
| 461 |
if (! Finley_noError()) { |
| 462 |
Finley_Mesh_free(mesh_p); |
| 463 |
} |
| 464 |
|
| 465 |
/* win32 refactor */ |
| 466 |
TMPMEMFREE(fName); |
| 467 |
|
| 468 |
blocktimer_increment("LoadMesh()", blocktimer_start); |
| 469 |
return temp; |
| 470 |
#else |
| 471 |
throw DataException("Error - loadMesh: is not compiled with NetCFD. Please contact your installation manager."); |
| 472 |
#endif /* USE_NETCDF */ |
| 473 |
} |
| 474 |
|
| 475 |
AbstractContinuousDomain* readMesh(const std::string& fileName, |
| 476 |
int integrationOrder, |
| 477 |
int reducedIntegrationOrder, |
| 478 |
int optimize) |
| 479 |
{ |
| 480 |
// |
| 481 |
// create a copy of the filename to overcome the non-constness of call |
| 482 |
// to Finley_Mesh_read |
| 483 |
Finley_Mesh* fMesh=0; |
| 484 |
// Win32 refactor |
| 485 |
if( fileName.size() == 0 ) |
| 486 |
{ |
| 487 |
throw DataException("Null file name!"); |
| 488 |
} |
| 489 |
|
| 490 |
char *fName = TMPMEMALLOC(fileName.size()+1,char); |
| 491 |
|
| 492 |
strcpy(fName,fileName.c_str()); |
| 493 |
double blocktimer_start = blocktimer_time(); |
| 494 |
|
| 495 |
fMesh=Finley_Mesh_read_MPI(fName,integrationOrder, reducedIntegrationOrder, (optimize ? TRUE : FALSE)); |
| 496 |
checkFinleyError(); |
| 497 |
AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
| 498 |
|
| 499 |
/* win32 refactor */ |
| 500 |
TMPMEMFREE(fName); |
| 501 |
|
| 502 |
blocktimer_increment("ReadMesh()", blocktimer_start); |
| 503 |
return temp; |
| 504 |
} |
| 505 |
|
| 506 |
AbstractContinuousDomain* readGmsh(const std::string& fileName, |
| 507 |
int numDim, |
| 508 |
int integrationOrder, |
| 509 |
int reducedIntegrationOrder, |
| 510 |
int optimize) |
| 511 |
{ |
| 512 |
// |
| 513 |
// create a copy of the filename to overcome the non-constness of call |
| 514 |
// to Finley_Mesh_read |
| 515 |
Finley_Mesh* fMesh=0; |
| 516 |
// Win32 refactor |
| 517 |
if( fileName.size() == 0 ) |
| 518 |
{ |
| 519 |
throw DataException("Null file name!"); |
| 520 |
} |
| 521 |
|
| 522 |
char *fName = TMPMEMALLOC(fileName.size()+1,char); |
| 523 |
|
| 524 |
strcpy(fName,fileName.c_str()); |
| 525 |
double blocktimer_start = blocktimer_time(); |
| 526 |
|
| 527 |
fMesh=Finley_Mesh_readGmsh(fName, numDim, integrationOrder, reducedIntegrationOrder, (optimize ? TRUE : FALSE)); |
| 528 |
checkFinleyError(); |
| 529 |
AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
| 530 |
|
| 531 |
/* win32 refactor */ |
| 532 |
TMPMEMFREE(fName); |
| 533 |
|
| 534 |
blocktimer_increment("ReadGmsh()", blocktimer_start); |
| 535 |
return temp; |
| 536 |
} |
| 537 |
|
| 538 |
AbstractContinuousDomain* brick(int n0,int n1,int n2,int order, |
| 539 |
double l0,double l1,double l2, |
| 540 |
int periodic0,int periodic1, |
| 541 |
int periodic2, |
| 542 |
int integrationOrder, |
| 543 |
int reducedIntegrationOrder, |
| 544 |
int useElementsOnFace, |
| 545 |
int useFullElementOrder, |
| 546 |
int optimize) |
| 547 |
{ |
| 548 |
int numElements[]={n0,n1,n2}; |
| 549 |
double length[]={l0,l1,l2}; |
| 550 |
int periodic[]={periodic0, periodic1, periodic2}; |
| 551 |
|
| 552 |
// |
| 553 |
// linearInterpolation |
| 554 |
Finley_Mesh* fMesh=NULL; |
| 555 |
|
| 556 |
if (order==1) { |
| 557 |
fMesh=Finley_RectangularMesh_Hex8(numElements,length,periodic,integrationOrder,reducedIntegrationOrder, |
| 558 |
useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)) ; |
| 559 |
} |
| 560 |
else if (order==2) { |
| 561 |
fMesh=Finley_RectangularMesh_Hex20(numElements,length,periodic,integrationOrder,reducedIntegrationOrder, |
| 562 |
useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)) ; |
| 563 |
} else { |
| 564 |
stringstream temp; |
| 565 |
temp << "Illegal interpolation order: " << order; |
| 566 |
setFinleyError(VALUE_ERROR,temp.str().c_str()); |
| 567 |
} |
| 568 |
// |
| 569 |
// Convert any finley errors into a C++ exception |
| 570 |
checkFinleyError(); |
| 571 |
AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
| 572 |
return temp; |
| 573 |
} |
| 574 |
AbstractContinuousDomain* rectangle(int n0,int n1,int order, |
| 575 |
double l0, double l1, |
| 576 |
int periodic0,int periodic1, |
| 577 |
int integrationOrder, |
| 578 |
int reducedIntegrationOrder, |
| 579 |
int useElementsOnFace, |
| 580 |
int useFullElementOrder, |
| 581 |
int optimize) |
| 582 |
{ |
| 583 |
int numElements[]={n0,n1}; |
| 584 |
double length[]={l0,l1}; |
| 585 |
int periodic[]={periodic0, periodic1}; |
| 586 |
|
| 587 |
Finley_Mesh* fMesh=0; |
| 588 |
if (order==1) { |
| 589 |
fMesh=Finley_RectangularMesh_Rec4(numElements, length,periodic,integrationOrder,reducedIntegrationOrder, |
| 590 |
useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)); |
| 591 |
} |
| 592 |
else if (order==2) { |
| 593 |
fMesh=Finley_RectangularMesh_Rec8(numElements,length,periodic,integrationOrder,reducedIntegrationOrder, |
| 594 |
useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)); |
| 595 |
} |
| 596 |
else { |
| 597 |
stringstream temp; |
| 598 |
temp << "Illegal interpolation order: " << order; |
| 599 |
setFinleyError(VALUE_ERROR,temp.str().c_str()); |
| 600 |
} |
| 601 |
// |
| 602 |
// Convert any finley errors into a C++ exception |
| 603 |
checkFinleyError(); |
| 604 |
AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
| 605 |
return temp; |
| 606 |
} |
| 607 |
|
| 608 |
AbstractContinuousDomain* meshMerge(const boost::python::list& meshList) |
| 609 |
{ |
| 610 |
Finley_Mesh* fMesh=0; |
| 611 |
// |
| 612 |
// extract the meshes from meshList |
| 613 |
int numMsh=boost::python::extract<int>(meshList.attr("__len__")()); |
| 614 |
Finley_Mesh **mshes = (numMsh) ? TMPMEMALLOC(numMsh,Finley_Mesh*) : (Finley_Mesh**)NULL; |
| 615 |
for (int i=0;i<numMsh;++i) { |
| 616 |
AbstractContinuousDomain& meshListMember=boost::python::extract<AbstractContinuousDomain&>(meshList[i]); |
| 617 |
const MeshAdapter* finley_meshListMember=static_cast<const MeshAdapter*>(&meshListMember); |
| 618 |
mshes[i]=finley_meshListMember->getFinley_Mesh(); |
| 619 |
} |
| 620 |
// |
| 621 |
// merge the meshes: |
| 622 |
fMesh=Finley_Mesh_merge(numMsh,mshes); |
| 623 |
TMPMEMFREE(mshes); |
| 624 |
// |
| 625 |
// Convert any finley errors into a C++ exception |
| 626 |
checkFinleyError(); |
| 627 |
AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
| 628 |
|
| 629 |
return temp; |
| 630 |
} |
| 631 |
AbstractContinuousDomain* glueFaces(const boost::python::list& meshList, |
| 632 |
double safety_factor, |
| 633 |
double tolerance, |
| 634 |
int optimize) |
| 635 |
{ |
| 636 |
Finley_Mesh* fMesh=0; |
| 637 |
// |
| 638 |
// merge the meshes: |
| 639 |
AbstractContinuousDomain* merged_meshes=meshMerge(meshList); |
| 640 |
// |
| 641 |
// glue the faces: |
| 642 |
const MeshAdapter* merged_finley_meshes=static_cast<const MeshAdapter*>(merged_meshes); |
| 643 |
fMesh=merged_finley_meshes->getFinley_Mesh(); |
| 644 |
Finley_Mesh_glueFaces(fMesh,safety_factor,tolerance,(optimize ? TRUE : FALSE)); |
| 645 |
|
| 646 |
// |
| 647 |
// Convert any finley errors into a C++ exception |
| 648 |
checkFinleyError(); |
| 649 |
return merged_meshes; |
| 650 |
} |
| 651 |
AbstractContinuousDomain* joinFaces(const boost::python::list& meshList, |
| 652 |
double safety_factor, |
| 653 |
double tolerance, |
| 654 |
int optimize) |
| 655 |
{ |
| 656 |
Finley_Mesh* fMesh=0; |
| 657 |
// |
| 658 |
// merge the meshes: |
| 659 |
AbstractContinuousDomain* merged_meshes=meshMerge(meshList); |
| 660 |
// |
| 661 |
// join the faces: |
| 662 |
const MeshAdapter* merged_finley_meshes=static_cast<const MeshAdapter*>(merged_meshes); |
| 663 |
fMesh=merged_finley_meshes->getFinley_Mesh(); |
| 664 |
Finley_Mesh_joinFaces(fMesh,safety_factor,tolerance, (optimize ? TRUE : FALSE)); |
| 665 |
// |
| 666 |
// Convert any finley errors into a C++ exception |
| 667 |
checkFinleyError(); |
| 668 |
return merged_meshes; |
| 669 |
} |
| 670 |
|
| 671 |
// end of namespace |
| 672 |
|
| 673 |
} |
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