visuMapVtk.cpp

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/*
 * visuMapVtk.cpp
 * this tool will take a source file, target file (h5m) and a map file in nc format,
 *
 * example of usage:
 * ./mbvisumap -s source.h5m -t target.h5m -m map.nc -b startSourceID -e endSourceID -c startTargetID -f endTargetID
 * will associate row i in map with a partial mesh
 * will associate row j in map with a partial mesh
 *
 * can be built only if netcdf and hdf5 and eigen3 are available
 *
 *
 */
#include "moab/MOABConfig.h"
 
#ifndef MOAB_HAVE_EIGEN3
#error compareMaps tool requires eigen3 configuration
#endif
 
#include "moab/ProgOptions.hpp"
#include "moab/Core.hpp"
#include "moab/Range.hpp"
 
#include "netcdf.h"
#include <cmath>
#include <sstream>
#include <map>
#include <Eigen/Sparse>
 
#define ERR_NC( e ) \
 { \
 printf( "Error: %s\n", nc_strerror( e ) ); \
 exit( 2 ); \
 }
 
// copy from ReadNCDF.cpp some useful macros for reading from a netcdf file (exodus?)
// ncFile is an integer initialized when opening the nc file in read mode
 
int ncFile1;
 
#define GET_DIM1( ncdim, name, val ) \
 { \
 int gdfail = nc_inq_dimid( ncFile1, name, &( ncdim ) ); \
 if( NC_NOERR == gdfail ) \
 { \
 size_t tmp_val; \
 gdfail = nc_inq_dimlen( ncFile1, ncdim, &tmp_val ); \
 if( NC_NOERR != gdfail ) \
 { \
 ERR_NC( gdfail ) \
 } \
 else \
 ( val ) = tmp_val; \
 } \
 else \
 ( val ) = 0; \
 }
 
#define GET_VAR1( name, id, dims ) \
 { \
 ( id ) = -1; \
 int gvfail = nc_inq_varid( ncFile1, name, &( id ) ); \
 if( NC_NOERR == gvfail ) \
 { \
 int ndims; \
 gvfail = nc_inq_varndims( ncFile1, id, &ndims ); \
 if( NC_NOERR == gvfail ) \
 { \
 ( dims ).resize( ndims ); \
 gvfail = nc_inq_vardimid( ncFile1, id, &( dims )[0] ); \
 if( NC_NOERR != gvfail ) \
 { \
 ERR_NC( gvfail ) \
 } \
 } \
 } \
 }
 
#define GET_1D_INT_VAR1( name, id, vals ) \
 { \
 GET_VAR1( name, id, vals ); \
 if( -1 != ( id ) ) \
 { \
 size_t ntmp; \
 int ivfail = nc_inq_dimlen( ncFile1, ( vals )[0], &ntmp ); \
 if( NC_NOERR != ivfail ) \
 { \
 ERR_NC( ivfail ) \
 } \
 ( vals ).resize( ntmp ); \
 size_t ntmp1 = 0; \
 ivfail = nc_get_vara_int( ncFile1, id, &ntmp1, &ntmp, &( vals )[0] ); \
 if( NC_NOERR != ivfail ) \
 { \
 ERR_NC( ivfail ) \
 } \
 } \
 }
 
#define GET_1D_DBL_VAR1( name, id, vals ) \
 { \
 std::vector< int > dum_dims; \
 GET_VAR1( name, id, dum_dims ); \
 if( -1 != ( id ) ) \
 { \
 size_t ntmp; \
 int dvfail = nc_inq_dimlen( ncFile1, dum_dims[0], &ntmp ); \
 if( NC_NOERR != dvfail ) \
 { \
 ERR_NC( dvfail ) \
 } \
 ( vals ).resize( ntmp ); \
 size_t ntmp1 = 0; \
 dvfail = nc_get_vara_double( ncFile1, id, &ntmp1, &ntmp, &( vals )[0] ); \
 if( NC_NOERR != dvfail ) \
 { \
 ERR_NC( dvfail ) \
 } \
 } \
 }
 
using namespace moab;
using namespace std;
 
int main( int argc, char* argv[] )
{
 
 ProgOptions opts;
 int dimSource = 2; // for FV meshes is 2; for SE meshes, use fine mesh, dim will be 0
 int dimTarget = 2; //
 int otype = 0;
 
 std::string inputfile1, inputSource, inputTarget;
 opts.addOpt< std::string >( "map,m", "input map ", &inputfile1 );
 opts.addOpt< std::string >( "source,s", "source mesh", &inputSource );
 opts.addOpt< std::string >( "target,t", "target mesh", &inputTarget );
 opts.addOpt< int >( "dimSource,d", "dimension of source ", &dimSource );
 opts.addOpt< int >( "dimTarget,g", "dimension of target ", &dimTarget );
 opts.addOpt< int >( "typeOutput,o", " output type vtk(0), h5m(1)", &otype );
 
 int startSourceID = -1, endSourceID = -1, startTargetID = -1, endTargetID = -1;
 opts.addOpt< int >( "startSourceID,b", "start source id ", &startSourceID );
 opts.addOpt< int >( "endSourceID,e", "end source id ", &endSourceID );
 opts.addOpt< int >( "startTargetID,c", "start target id ", &startTargetID );
 opts.addOpt< int >( "endTargetID,f", "end target id ", &endTargetID );
 // -b startSourceID -e endSourceID -c startTargetID -f endTargetID
 
 opts.parseCommandLine( argc, argv );
 
 std::string extension = ".vtk";
 if( 1 == otype ) extension = ".h5m";
 // Open netcdf/exodus file
 int fail = nc_open( inputfile1.c_str(), 0, &ncFile1 );
 if( NC_NOWRITE != fail )
 {
 ERR_NC( fail )
 }
 
 std::cout << " opened " << inputfile1 << " for map 1 \n";
 
 int temp_dim;
 int na1, nb1, ns1;
 GET_DIM1( temp_dim, "n_a", na1 );
 GET_DIM1( temp_dim, "n_b", nb1 );
 GET_DIM1( temp_dim, "n_s", ns1 );
 std::cout << " n_a, n_b, n_s : " << na1 << ", " << nb1 << ", " << ns1 << " for map 1 \n";
 std::vector< int > col1( ns1 ), row1( ns1 );
 std::vector< double > val1( ns1 );
 int idrow1, idcol1, ids1;
 GET_1D_INT_VAR1( "row", idrow1, row1 );
 GET_1D_INT_VAR1( "col", idcol1, col1 );
 GET_1D_DBL_VAR1( "S", ids1, val1 );
 // first matrix
 typedef Eigen::Triplet< double > Triplet;
 std::vector< Triplet > tripletList;
 tripletList.reserve( ns1 );
 for( int iv = 0; iv < ns1; iv++ )
 {
 // all row and column indices are 1-based in the map file.
 // inside Eigen3, we will use 0-based; then we will have to add back 1 when
 // we dump out the files
 tripletList.push_back( Triplet( row1[iv] - 1, col1[iv] - 1, val1[iv] ) );
 }
 Eigen::SparseMatrix< double > weight1( nb1, na1 );
 
 weight1.setFromTriplets( tripletList.begin(), tripletList.end() );
 weight1.makeCompressed();
 // we read the matrix; now read moab source and target
 Core core;
 Interface* mb = &core;
 ErrorCode rval;
 Tag gtag = mb->globalId_tag();
 EntityHandle sourceSet, targetSet;
 // those are the maps from global ids to the moab entity handles corresponding to those global ids
 // which are corresponding to the global DOFs
 map< int, EntityHandle > sourceHandles;
 map< int, EntityHandle > targetHandles;
 rval = mb->create_meshset( MESHSET_SET, sourceSet );MB_CHK_SET_ERR( rval, "can't create source mesh set" );
 rval = mb->create_meshset( MESHSET_SET, targetSet );MB_CHK_SET_ERR( rval, "can't create target mesh set" );
 const char* readopts = "";
 rval = mb->load_file( inputSource.c_str(), &sourceSet, readopts );MB_CHK_SET_ERR( rval, "Failed to read" );
 rval = mb->load_file( inputTarget.c_str(), &targetSet, readopts );MB_CHK_SET_ERR( rval, "Failed to read" );
 Range sRange;
 rval = mb->get_entities_by_dimension( sourceSet, dimSource, sRange );MB_CHK_SET_ERR( rval, "Failed to get sRange" );
 vector< int > sids;
 sids.resize( sRange.size() );
 rval = mb->tag_get_data( gtag, sRange, &sids[0] );MB_CHK_SET_ERR( rval, "Failed to get ids for srange" );
 // all global ids are 1 based in the source file, and they correspond to the dofs in the map file
 for( size_t i = 0; i < sids.size(); i++ )
 {
 EntityHandle eh = sRange[i];
 int gid = sids[i];
 sourceHandles[gid] = eh;
 }
 Range tRange;
 rval = mb->get_entities_by_dimension( targetSet, dimTarget, tRange );MB_CHK_SET_ERR( rval, "Failed to get tRange" );
 vector< int > tids;
 tids.resize( tRange.size() );
 rval = mb->tag_get_data( gtag, tRange, &tids[0] );MB_CHK_SET_ERR( rval, "Failed to get ids for trange" );
 // all global ids are 1 based in the target file, and they correspond to the dofs in the map file
 for( size_t i = 0; i < tids.size(); i++ )
 {
 EntityHandle eh = tRange[i];
 int gid = tids[i];
 targetHandles[gid] = eh;
 }
 // a dense tag for weights
 Tag wtag;
 double defVal = 0;
 
 std::string name_map = inputfile1;
 // strip last 3 chars (.nc extension)
 name_map.erase( name_map.begin() + name_map.length() - 3, name_map.end() );
 // if path , remove from name
 size_t pos = name_map.rfind( '/', name_map.length() );
 if( pos != std::string::npos ) name_map = name_map.erase( 0, pos + 1 );
 
 rval = mb->tag_get_handle( "weight", 1, MB_TYPE_DOUBLE, wtag, MB_TAG_CREAT | MB_TAG_DENSE, &defVal );MB_CHK_SET_ERR( rval, "Failed to create weight" );
 EntityHandle partialSet;
 rval = mb->create_meshset( MESHSET_SET, partialSet );MB_CHK_SET_ERR( rval, "can't create partial set" );
 // how to get a complete row in sparse matrix? Or a complete column ?
 for( int col = startSourceID - 1; col <= endSourceID - 1; col++ )
 {
 Range targetEnts; // will find entries for column col-1 in sparse matrix weight1, and its entries
 // will assign a dense tag with values, and write out the file
 if( col < 0 ) continue;
 Eigen::SparseVector< double > colVect = weight1.col( col );
 // the row indices correspond to target cells
 for( Eigen::SparseVector< double >::InnerIterator it( colVect ); it; ++it )
 {
 double weight = it.value(); // == vec[ it.index() ]
 // we add back the 1 that we subtract
 int globalIdRow = it.index() + 1;
 EntityHandle th = targetHandles[globalIdRow];
 targetEnts.insert( th );
 rval = mb->tag_set_data( wtag, &th, 1, &weight );MB_CHK_SET_ERR( rval, "Failed to set weight tag on target" );
 }
 
 if( dimTarget == 0 )
 {
 Range adjCells;
 rval = mb->get_adjacencies( targetEnts, 2, false, adjCells, Interface::UNION );MB_CHK_SET_ERR( rval, " can't get adj cells " );
 targetEnts.merge( adjCells );
 }
 
 rval = mb->add_entities( partialSet, targetEnts );MB_CHK_SET_ERR( rval, "Failed to add target entities to partial set" );
 // write now the set in a numbered file
 std::stringstream fff;
 fff << name_map << "_column" << col + 1 << extension;
 rval = mb->write_mesh( fff.str().c_str(), &partialSet, 1 );MB_CHK_ERR( rval );
 // remove from partial set the entities it has
 rval = mb->clear_meshset( &partialSet, 1 );MB_CHK_SET_ERR( rval, "Failed to empty partial set" );
 }
 
 // how to get a complete row in sparse matrix?
 for( int row = startTargetID - 1; row <= endTargetID - 1; row++ )
 {
 Range sourceEnts; // will find entries for row in sparse matrix weight1, and its entries
 // will assign a dense tag with values, and write out the file
 if( row < 0 ) continue;
 Eigen::SparseVector< double > rowVect = weight1.row( row );
 // the row indices correspond to target cells
 for( Eigen::SparseVector< double >::InnerIterator it( rowVect ); it; ++it )
 {
 double weight = it.value(); // == vec[ it.index() ]
 int globalIdCol = it.index() + 1;
 EntityHandle sh = sourceHandles[globalIdCol];
 sourceEnts.insert( sh );
 rval = mb->tag_set_data( wtag, &sh, 1, &weight );MB_CHK_SET_ERR( rval, "Failed to set weight tag on source" );
 }
 if( dimSource == 0 )
 {
 Range adjCells;
 rval = mb->get_adjacencies( sourceEnts, 2, false, adjCells, Interface::UNION );MB_CHK_SET_ERR( rval, " can't get adj cells " );
 sourceEnts.merge( adjCells );
 }
 rval = mb->add_entities( partialSet, sourceEnts );MB_CHK_SET_ERR( rval, "Failed to add source entities" );
 // write now the set in a numbered file
 std::stringstream fff;
 fff << name_map << "_row" << row + 1 << extension;
 rval = mb->write_mesh( fff.str().c_str(), &partialSet, 1 );MB_CHK_ERR( rval );
 rval = mb->clear_meshset( &partialSet, 1 );MB_CHK_SET_ERR( rval, "Failed to empty partial set" );
 }
 return 0;
}