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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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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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// create a copy of the filename to overcome the non-constness of call |
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// to Finley_Mesh_read |
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// Win32 refactor |
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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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|
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printf("ksteube finley::loadMesh %s\n", fName); |
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|
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double blocktimer_start = blocktimer_time(); |
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Finley_resetError(); |
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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 - loadMesh:: Could not read NetCDF file."); |
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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, "mpi_size"); |
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int mpi_rank = NetCDF_Get_Int_Attribute(&dataFile, fName, "mpi_rank"); |
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int numDim = NetCDF_Get_Int_Attribute(&dataFile, fName, "numDim"); |
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int order = NetCDF_Get_Int_Attribute(&dataFile, fName, "order"); |
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int reduced_order = NetCDF_Get_Int_Attribute(&dataFile, fName, "reduced_order"); |
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int numNodes = NetCDF_Get_Int_Attribute(&dataFile, fName, "numNodes"); |
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int num_Elements = NetCDF_Get_Int_Attribute(&dataFile, fName, "num_Elements"); |
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int num_FaceElements = NetCDF_Get_Int_Attribute(&dataFile, fName, "num_FaceElements"); |
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int num_ContactElements = NetCDF_Get_Int_Attribute(&dataFile, fName, "num_ContactElements"); |
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int num_Points = NetCDF_Get_Int_Attribute(&dataFile, fName, "num_Points"); |
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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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free(&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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// printf("ksteube Nodes_Id: "); for (int i=0; i<numNodes; i++) { printf(" %d", mesh_p->Nodes->Id[i]); } printf("\n"); |
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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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free(&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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free(&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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free(&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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free(&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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free(&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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free(&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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free(&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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|
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#if 0 /* Not yet...finish the above first */ |
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/* read elements */ |
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if (Finley_noError()) { |
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mesh_p->Elements=Finley_ElementFile_alloc(typeID,mesh_p->order, mesh_p->reduced_order, mpi_info); |
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if (Finley_noError()) { |
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Finley_ElementFile_allocTable(mesh_p->Elements, numEle); |
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mesh_p->Elements->minColor=0; |
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mesh_p->Elements->maxColor=numEle-1; |
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if (Finley_noError()) { |
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} |
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} |
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} |
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#endif |
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|
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/* get the face elements */ |
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|
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/* get the Contact face element */ |
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|
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/* get the nodal element */ |
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|
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/* get the name tags */ |
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|
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} /* Finley_noError() after Finley_Mesh_alloc() */ |
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|
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#if 0 /* Not yet...finish the above first */ |
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if (Finley_noError()) Finley_Mesh_resolveNodeIds(mesh_p); |
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if (Finley_noError()) Finley_Mesh_prepare(mesh_p, optimize); |
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#endif |
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|
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checkFinleyError(); |
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temp=new MeshAdapter(mesh_p); |
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|
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if (! Finley_noError()) { |
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Finley_Mesh_free(mesh_p); |
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} |
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/* win32 refactor */ |
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TMPMEMFREE(fName); |
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|
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blocktimer_increment("LoadMesh()", blocktimer_start); |
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return temp; |
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#else |
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throw DataException("Error - loadMesh: is not compiled with NetCFD. Please contact your installation manager."); |
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#endif /* USE_NETCDF */ |
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} |
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|
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AbstractContinuousDomain* readMesh(const std::string& fileName, |
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int integrationOrder, |
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int reducedIntegrationOrder, |
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int optimize) |
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{ |
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// |
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// create a copy of the filename to overcome the non-constness of call |
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// to Finley_Mesh_read |
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Finley_Mesh* fMesh=0; |
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// Win32 refactor |
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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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double blocktimer_start = blocktimer_time(); |
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|
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fMesh=Finley_Mesh_read(fName,integrationOrder, reducedIntegrationOrder, (optimize ? TRUE : FALSE)); |
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checkFinleyError(); |
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AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
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|
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/* win32 refactor */ |
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TMPMEMFREE(fName); |
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|
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blocktimer_increment("ReadMesh()", blocktimer_start); |
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return temp; |
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} |
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|
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AbstractContinuousDomain* readGmsh(const std::string& fileName, |
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int numDim, |
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int integrationOrder, |
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int reducedIntegrationOrder, |
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int optimize) |
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{ |
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// |
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// create a copy of the filename to overcome the non-constness of call |
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// to Finley_Mesh_read |
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Finley_Mesh* fMesh=0; |
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// Win32 refactor |
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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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double blocktimer_start = blocktimer_time(); |
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|
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fMesh=Finley_Mesh_readGmsh(fName, numDim, integrationOrder, reducedIntegrationOrder, (optimize ? TRUE : FALSE)); |
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checkFinleyError(); |
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AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
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|
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/* win32 refactor */ |
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TMPMEMFREE(fName); |
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|
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blocktimer_increment("ReadGmsh()", blocktimer_start); |
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return temp; |
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} |
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|
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AbstractContinuousDomain* brick(int n0,int n1,int n2,int order, |
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double l0,double l1,double l2, |
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int periodic0,int periodic1, |
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int periodic2, |
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int integrationOrder, |
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int reducedIntegrationOrder, |
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int useElementsOnFace, |
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int useFullElementOrder, |
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int optimize) |
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{ |
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int numElements[]={n0,n1,n2}; |
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double length[]={l0,l1,l2}; |
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int periodic[]={periodic0, periodic1, periodic2}; |
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|
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// |
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// linearInterpolation |
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Finley_Mesh* fMesh=NULL; |
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|
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if (order==1) { |
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fMesh=Finley_RectangularMesh_Hex8(numElements,length,periodic,integrationOrder,reducedIntegrationOrder, |
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useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)) ; |
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} |
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else if (order==2) { |
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fMesh=Finley_RectangularMesh_Hex20(numElements,length,periodic,integrationOrder,reducedIntegrationOrder, |
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useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)) ; |
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} else { |
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stringstream temp; |
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temp << "Illegal interpolation order: " << order; |
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setFinleyError(VALUE_ERROR,temp.str().c_str()); |
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} |
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// |
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// Convert any finley errors into a C++ exception |
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checkFinleyError(); |
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AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
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return temp; |
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} |
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AbstractContinuousDomain* rectangle(int n0,int n1,int order, |
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double l0, double l1, |
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int periodic0,int periodic1, |
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int integrationOrder, |
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int reducedIntegrationOrder, |
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int useElementsOnFace, |
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int useFullElementOrder, |
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int optimize) |
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{ |
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int numElements[]={n0,n1}; |
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double length[]={l0,l1}; |
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int periodic[]={periodic0, periodic1}; |
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|
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Finley_Mesh* fMesh=0; |
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if (order==1) { |
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fMesh=Finley_RectangularMesh_Rec4(numElements, length,periodic,integrationOrder,reducedIntegrationOrder, |
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useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)); |
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} |
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else if (order==2) { |
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fMesh=Finley_RectangularMesh_Rec8(numElements,length,periodic,integrationOrder,reducedIntegrationOrder, |
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useElementsOnFace,useFullElementOrder,(optimize ? TRUE : FALSE)); |
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} |
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else { |
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stringstream temp; |
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temp << "Illegal interpolation order: " << order; |
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setFinleyError(VALUE_ERROR,temp.str().c_str()); |
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} |
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// |
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// Convert any finley errors into a C++ exception |
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checkFinleyError(); |
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AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
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return temp; |
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} |
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|
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AbstractContinuousDomain* meshMerge(const boost::python::list& meshList) |
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{ |
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Finley_Mesh* fMesh=0; |
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// |
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// extract the meshes from meshList |
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int numMsh=boost::python::extract<int>(meshList.attr("__len__")()); |
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Finley_Mesh **mshes = (numMsh) ? TMPMEMALLOC(numMsh,Finley_Mesh*) : (Finley_Mesh**)NULL; |
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for (int i=0;i<numMsh;++i) { |
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AbstractContinuousDomain& meshListMember=boost::python::extract<AbstractContinuousDomain&>(meshList[i]); |
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const MeshAdapter* finley_meshListMember=static_cast<const MeshAdapter*>(&meshListMember); |
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mshes[i]=finley_meshListMember->getFinley_Mesh(); |
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} |
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// |
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// merge the meshes: |
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fMesh=Finley_Mesh_merge(numMsh,mshes); |
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TMPMEMFREE(mshes); |
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// |
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// Convert any finley errors into a C++ exception |
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checkFinleyError(); |
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AbstractContinuousDomain* temp=new MeshAdapter(fMesh); |
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|
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return temp; |
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} |
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AbstractContinuousDomain* glueFaces(const boost::python::list& meshList, |
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double safety_factor, |
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double tolerance, |
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int optimize) |
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{ |
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Finley_Mesh* fMesh=0; |
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// |
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// merge the meshes: |
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AbstractContinuousDomain* merged_meshes=meshMerge(meshList); |
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// |
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// glue the faces: |
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const MeshAdapter* merged_finley_meshes=static_cast<const MeshAdapter*>(merged_meshes); |
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fMesh=merged_finley_meshes->getFinley_Mesh(); |
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Finley_Mesh_glueFaces(fMesh,safety_factor,tolerance,(optimize ? TRUE : FALSE)); |
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|
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// |
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// Convert any finley errors into a C++ exception |
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checkFinleyError(); |
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return merged_meshes; |
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} |
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AbstractContinuousDomain* joinFaces(const boost::python::list& meshList, |
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double safety_factor, |
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double tolerance, |
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int optimize) |
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{ |
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Finley_Mesh* fMesh=0; |
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// |
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// merge the meshes: |
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AbstractContinuousDomain* merged_meshes=meshMerge(meshList); |
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// |
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// join the faces: |
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const MeshAdapter* merged_finley_meshes=static_cast<const MeshAdapter*>(merged_meshes); |
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fMesh=merged_finley_meshes->getFinley_Mesh(); |
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Finley_Mesh_joinFaces(fMesh,safety_factor,tolerance, (optimize ? TRUE : FALSE)); |
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// |
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// Convert any finley errors into a C++ exception |
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checkFinleyError(); |
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return merged_meshes; |
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} |
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|
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// end of namespace |
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|
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} |
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