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311 | /*
* 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 INS_ID( stringvar, prefix, id ) sprintf( stringvar, prefix, id )
#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_DIMB1( ncdim, name, varname, id, val ) \
INS_ID( name, varname, id ); \
GET_DIM1( ncdim, name, val );
#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;
}
|