/usr/include/dune/grid/alugrid/3d/alu3dgridfactory.cc is in libdune-grid-dev 2.4.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// vi: set et ts=4 sw=2 sts=2:
#ifndef DUNE_ALU3DGRID_FACTORY_CC
#define DUNE_ALU3DGRID_FACTORY_CC
#if COMPILE_ALUGRID_INLINE == 0
#include <config.h>
#endif
#include <algorithm>
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <iostream>
#include <fstream>
#include <dune/grid/alugrid/3d/alu3dgridfactory.hh>
#if HAVE_ALUGRID
#if COMPILE_ALUGRID_INLINE
#define alu_inline inline
#else
#define alu_inline
#endif
namespace Dune
{
template< class ALUGrid >
alu_inline
ALU3dGridFactory< ALUGrid > :: ~ALU3dGridFactory ()
{}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid > :: insertVertex ( const VertexType &pos )
{
if( ! allowGridGeneration_ )
DUNE_THROW( GridError, "ALU3dGridFactory allows insertion only for rank 0." );
vertices_.push_back( std::make_pair( pos, vertices_.size() ) );
}
template< class ALUGrid >
alu_inline
typename ALU3dGridFactory< ALUGrid >::VertexId
ALU3dGridFactory< ALUGrid >::insertVertex ( const VertexType &pos, const size_t globalId )
{
const VertexId vertexId = vertices_.size();
vertices_.push_back( std::make_pair( pos, globalId ) );
return vertexId;
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
:: insertElement ( const GeometryType &geometry,
const std::vector< VertexId > &vertices )
{
assertGeometryType( geometry );
if( geometry.dim() != dimension )
DUNE_THROW( GridError, "Only 3-dimensional elements can be inserted "
"into a 3-dimensional ALUGrid." );
if( vertices.size() != numCorners )
DUNE_THROW( GridError, "Wrong number of vertices." );
elements_.push_back( vertices );
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
:: insertBoundary ( const GeometryType &geometry,
const std::vector< VertexId > &vertices,
const int id )
{
assertGeometryType( geometry );
if( geometry.dim() != dimension-1 )
{
DUNE_THROW( GridError, "Only 2-dimensional boundaries can be inserted "
"into a 3-dimensional ALUGrid." );
}
if( vertices.size() != numFaceCorners )
DUNE_THROW( GridError, "Wrong number of vertices." );
BndPair boundaryId;
for( unsigned int i = 0; i < numFaceCorners; ++i )
{
const unsigned int j = FaceTopologyMappingType::dune2aluVertex( i );
boundaryId.first[ j ] = vertices[ i ];
}
boundaryId.second = id;
boundaryIds_.insert( boundaryId );
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
::insertBoundary ( const int element, const int face, const int id )
{
if( (element < 0) || (element >= (int)elements_.size()) )
DUNE_THROW( RangeError, "ALU3dGridFactory::insertBoundary: invalid element index given." );
BndPair boundaryId;
generateFace( elements_[ element ], face, boundaryId.first );
boundaryId.second = id;
boundaryIds_.insert( boundaryId );
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid > ::
insertBoundaryProjection( const DuneBoundaryProjectionType& bndProjection )
{
if( globalProjection_ )
DUNE_THROW(InvalidStateException,"You can only insert one globalProjection");
globalProjection_ = &bndProjection;
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid > ::
insertBoundaryProjection ( const GeometryType &type,
const std::vector< VertexId > &vertices,
const DuneBoundaryProjectionType *projection )
{
if( (int)type.dim() != dimension-1 )
DUNE_THROW( GridError, "Inserting boundary face of wrong dimension: " << type.dim() );
assert( type.isCube() || type.isSimplex() );
FaceType faceId;
copyAndSort( vertices, faceId );
if( vertices.size() != numFaceCorners )
DUNE_THROW( GridError, "Wrong number of face vertices passed: " << vertices.size() << "." );
if( boundaryProjections_.find( faceId ) != boundaryProjections_.end() )
DUNE_THROW( GridError, "Only one boundary projection can be attached to a face." );
boundaryProjections_[ faceId ] = projection;
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
::insertFaceTransformation ( const WorldMatrix &matrix, const WorldVector &shift )
{
faceTransformations_.push_back( Transformation( matrix, shift ) );
}
template< class ALUGrid >
alu_inline
ALUGrid *ALU3dGridFactory< ALUGrid >::createGrid ()
{
return createGrid( true, true, "" );
}
template< class ALUGrid >
alu_inline
ALUGrid *ALU3dGridFactory< ALUGrid >
::createGrid ( const bool addMissingBoundaries, const std::string dgfName )
{
return createGrid( addMissingBoundaries, true, dgfName );
}
template< class ALUGrid >
alu_inline
ALUGrid *ALU3dGridFactory< ALUGrid >
::createGrid ( const bool addMissingBoundaries, bool temporary, const std::string name )
{
typedef typename BoundaryIdMap :: iterator BoundaryIdIteratorType;
BoundaryProjectionVector* bndProjections = 0;
correctElementOrientation();
numFacesInserted_ = boundaryIds_.size();
if( addMissingBoundaries || ! faceTransformations_.empty() )
recreateBoundaryIds();
// if dump file should be written
if( allowGridGeneration_ && !temporary )
{
std::string filename ( name );
std::ofstream out( filename.c_str() );
out.setf( std::ios_base::scientific, std::ios_base::floatfield );
out.precision( 16 );
if( elementType == tetra )
out << "!Tetrahedra";
else
out << "!Hexahedra";
const unsigned int numVertices = vertices_.size();
// print information about vertices and elements
// to header to have an easy check
out << " ( noVertices = " << numVertices;
out << " | noElements = " << elements_.size() << " )" << std :: endl;
// now start writing grid
out << numVertices << std :: endl;
typedef typename VertexVector::iterator VertexIteratorType;
const VertexIteratorType endV = vertices_.end();
for( VertexIteratorType it = vertices_.begin(); it != endV; ++it )
{
const VertexType &vertex = it->first;
out << vertex[ 0 ];
for( unsigned int i = 1; i < dimensionworld; ++i )
out << " " << vertex[ i ];
out << std :: endl;
}
out << elements_.size() << std :: endl;
typedef typename ElementVector::iterator ElementIteratorType;
const ElementIteratorType endE = elements_.end();
for( ElementIteratorType it = elements_.begin(); it != endE; ++it )
{
array< unsigned int, numCorners > element;
for( unsigned int i = 0; i < numCorners; ++i )
{
const unsigned int j = ElementTopologyMappingType::dune2aluVertex( i );
element[ j ] = (*it)[ i ];
}
out << element[ 0 ];
for( unsigned int i = 1; i < numCorners; ++i )
out << " " << element[ i ];
out << std :: endl;
}
out << (boundaryIds_.size() + periodicBoundaries_.size()) << std :: endl;
const BoundaryIdIteratorType endB = boundaryIds_.end();
for( BoundaryIdIteratorType it = boundaryIds_.begin(); it != endB; ++it )
{
const std::pair< FaceType, int > &boundaryId = *it;
out << (-boundaryId.second) << " " << numFaceCorners;
for( unsigned int i = 0; i < numFaceCorners; ++i )
out << " " << boundaryId.first[ i ];
out << std::endl;
}
const typename PeriodicBoundaryVector::iterator endP = periodicBoundaries_.end();
for( typename PeriodicBoundaryVector::iterator it = periodicBoundaries_.begin(); it != endP; ++it )
{
typedef typename ALU3dBasicImplTraits< MPICommunicatorType >::HBndSegType HBndSegType;
const std::pair< BndPair, BndPair > &facePair = *it;
out << (-HBndSegType::periodic) << " " << (2*numFaceCorners);
for( unsigned int i = 0; i < numFaceCorners; ++i )
out << " " << facePair.first.first[ numFaceCorners == 3 ? (3 - i) % 3 : i ];
for( unsigned int i = 0; i < numFaceCorners; ++i )
out << " " << facePair.second.first[ numFaceCorners == 3 ? (3 - i) % 3 : i ];
out << std::endl;
}
// write global vertex ids
for( unsigned int i = 0; i < numVertices; ++i )
out << globalId( i ) << " -1" << std :: endl;
out.close();
}
const size_t boundarySegments = boundaryIds_.size();
const size_t bndProjectionSize = boundaryProjections_.size();
if( bndProjectionSize > 0 )
{
// the memory is freed by the grid on destruction
bndProjections = new BoundaryProjectionVector( boundarySegments,
(DuneBoundaryProjectionType*) 0 );
const BoundaryIdIteratorType endB = boundaryIds_.end();
int segmentIndex = 0;
for( BoundaryIdIteratorType it = boundaryIds_.begin(); it != endB; ++it, ++segmentIndex )
{
// generate boundary segment pointer
FaceType faceId ( (*it).first);
std::sort( faceId.begin(), faceId.end() );
const DuneBoundaryProjectionType* projection = boundaryProjections_[ faceId ];
// if no projection given we use global projection, otherwise identity
if( ! projection && globalProjection_ )
{
typedef BoundaryProjectionWrapper< dimensionworld > ProjectionWrapperType;
// we need to wrap the global projection because of
// delete in desctructor of ALUGrid
projection = new ProjectionWrapperType( *globalProjection_ );
assert( projection );
}
// copy pointer
(*bndProjections)[ segmentIndex ] = projection;
}
} // if( allowGridGeneration_ && !temporary )
// free memory
boundaryProjections_.clear();
// if we have a vector reset global projection
// because empty positions are filled with global projection anyway
if( bndProjections ) globalProjection_ = 0;
// ALUGrid is taking ownership of bndProjections
// and is going to delete this pointer
Grid* grid = createGridObj( bndProjections , name );
assert( grid );
// remove pointers
globalProjection_ = 0;
// is removed by grid instance
bndProjections = 0;
// insert grid using ALUGrid macro grid builder
if( !vertices_.empty() )
{
ALU3DSPACE MacroGridBuilder mgb ( grid->getBuilder()
#ifdef ALUGRID_VERTEX_PROJECTION
, grid->vertexProjection()
#endif
);
// now start inserting grid
const int vxSize = vertices_.size();
for( int vxIdx = 0; vxIdx < vxSize ; ++vxIdx )
{
// insert vertex
const VertexType &vertex = position( vxIdx );
mgb.InsertUniqueVertex( vertex[ 0 ], vertex[ 1 ], vertex[ 2 ], globalId( vxIdx ) );
}
typedef typename ElementVector::iterator ElementIteratorType;
const ElementIteratorType endE = elements_.end();
unsigned int elemIndex = 0;
for( ElementIteratorType it = elements_.begin(); it != endE; ++it, ++elemIndex )
{
if( elementType == hexa )
{
int element[ 8 ];
for( unsigned int i = 0; i < 8; ++i )
{
const unsigned int j = ElementTopologyMappingType::dune2aluVertex( i );
element[ j ] = globalId( (*it)[ i ] );
}
mgb.InsertUniqueHexa( element );
}
else if( elementType == tetra )
{
int element[ 4 ];
for( unsigned int i = 0; i < 4; ++i )
{
const unsigned int j = ElementTopologyMappingType::dune2aluVertex( i );
element[ j ] = globalId( (*it)[ i ] );
}
mgb.InsertUniqueTetra( element
#ifdef ALUGRID_3D_CONFORMING_REFINEMENT
, (elemIndex % 2)
#endif
);
}
else
DUNE_THROW( GridError, "Invalid element type");
}
const BoundaryIdIteratorType endB = boundaryIds_.end();
for( BoundaryIdIteratorType it = boundaryIds_.begin(); it != endB; ++it )
{
const BndPair &boundaryId = *it;
ALU3DSPACE Gitter::hbndseg::bnd_t bndType = (ALU3DSPACE Gitter::hbndseg::bnd_t ) boundaryId.second;
if( elementType == hexa )
{
int bndface[ 4 ];
for( unsigned int i = 0; i < numFaceCorners; ++i )
{
bndface[ i ] = globalId( boundaryId.first[ i ] );
}
mgb.InsertUniqueHbnd4( bndface, bndType );
}
else if( elementType == tetra )
{
int bndface[ 3 ];
for( unsigned int i = 0; i < numFaceCorners; ++i )
{
bndface[ i ] = globalId( boundaryId.first[ i ] );
}
mgb.InsertUniqueHbnd3( bndface, bndType );
}
else
DUNE_THROW( GridError, "Invalid element type");
}
const typename PeriodicBoundaryVector::iterator endP = periodicBoundaries_.end();
for( typename PeriodicBoundaryVector::iterator it = periodicBoundaries_.begin(); it != endP; ++it )
{
const std::pair< BndPair, BndPair > &facePair = *it;
if( elementType == hexa )
{
int perel[ 8 ];
for( unsigned int i = 0; i < numFaceCorners; ++i )
{
perel[ i+0 ] = globalId( facePair.first.first[ i ] );
perel[ i+4 ] = globalId( facePair.second.first[ i ] );
}
#ifdef ALUGRID_PERIODIC_BOUNDARY_PARALLEL
typedef typename ALU3DSPACE Gitter::hbndseg::bnd_t bnd_t ;
bnd_t bndId[ 2 ] = { bnd_t( facePair.first.second ),
bnd_t( facePair.second.second ) };
mgb.InsertUniquePeriodic4( perel, bndId );
#else
mgb.InsertUniquePeriodic4( perel );
#endif
}
else if( elementType == tetra )
{
int perel[ 6 ];
for( unsigned int i = 0; i < 3; ++i )
{
perel[ i+0 ] = globalId( facePair.first.first[ (3 - i) % 3 ] );
perel[ i+3 ] = globalId( facePair.second.first[ (3 - i) % 3 ] );
}
#ifdef ALUGRID_PERIODIC_BOUNDARY_PARALLEL
typedef typename ALU3DSPACE Gitter::hbndseg::bnd_t bnd_t ;
bnd_t bndId[ 2 ] = { bnd_t( facePair.first.second ),
bnd_t( facePair.second.second ) };
mgb.InsertUniquePeriodic3( perel, bndId );
#else
mgb.InsertUniquePeriodic3( perel );
#endif
}
else
DUNE_THROW( GridError, "Invalid element type" );
}
}
// clear vertices
vertices_ = VertexVector();
// clear elements
elements_ = ElementVector();
// free memory
boundaryIds_.clear();
#ifdef ALUGRID_EXPORT_MACROGRID_CHANGES
if( realGrid_ )
{
// make changes in macro grid known in every partition
grid->duneNotifyMacroGridChanges();
}
#else
if( grid->comm().size() > 1 )
DUNE_THROW(NotImplemented,"ALUGrid factory not working in parallel right now!");
#endif // #ifdef ALUGRID_EXPORT_MACROGRID_CHANGES
// reset wasRefined flags
grid->postAdapt();
// update additional information on grid
grid->calcExtras();
return grid;
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
::generateFace ( const ElementType &element, const int f, FaceType &face )
{
typedef ElementTopologyMapping< elementType > ElementTopologyMappingType;
const int falu = ElementTopologyMappingType :: generic2aluFace( f );
for( unsigned int i = 0; i < numFaceCorners; ++i )
{
const int j = ElementTopologyMappingType :: faceVertex( falu, i );
const int k = ElementTopologyMappingType :: alu2genericVertex( j );
face[ i ] = element[ k ];
}
}
template< class ALUGrid >
alu_inline
void
ALU3dGridFactory< ALUGrid >::correctElementOrientation ()
{
const typename ElementVector::iterator elementEnd = elements_.end();
for( typename ElementVector::iterator elementIt = elements_.begin();
elementIt != elementEnd; ++elementIt )
{
ElementType &element = *elementIt;
const VertexType &p0 = position( element[ 0 ] );
VertexType p1, p2, p3;
if( elementType == tetra )
{
p1 = position( element[ 1 ] );
p2 = position( element[ 2 ] );
p3 = position( element[ 3 ] );
}
else
{
p1 = position( element[ 1 ] );
p2 = position( element[ 2 ] );
p3 = position( element[ 4 ] );
}
p1 -= p0; p2 -= p0; p3 -= p0;
VertexType n;
n[ 0 ] = p1[ 1 ] * p2[ 2 ] - p2[ 1 ] * p1[ 2 ];
n[ 1 ] = p1[ 2 ] * p2[ 0 ] - p2[ 2 ] * p1[ 0 ];
n[ 2 ] = p1[ 0 ] * p2[ 1 ] - p2[ 0 ] * p1[ 1 ];
if( n * p3 > 0 )
continue;
if( elementType == hexa )
{
for( int i = 0; i < 4; ++i )
std::swap( element[ i ], element[ i+4 ] );
}
else
std::swap( element[ 2 ], element[ 3 ] );
} // end of loop over all elements
}
template< class ALUGrid >
alu_inline
bool ALU3dGridFactory< ALUGrid >
::identifyFaces ( const Transformation &transformation,
const FaceType &key1, const FaceType &key2,
const int defaultId )
{
WorldVector w = transformation.evaluate( position( key1[ 0 ] ) );
int org = -1;
for( unsigned int i = 0; i < numFaceCorners; ++i )
{
if( (w - position( key2[ i ] )).two_norm() < 1e-6 )
org = i;
}
if( org < 0 )
return false;
FaceType key0;
key0[ 0 ] = key2[ org ];
for( unsigned int i = 1; i < numFaceCorners; ++i )
{
w = transformation.evaluate( position( key1[ i ] ) );
const int j = ((org+numFaceCorners)-i) % numFaceCorners;
if( (w - position( key2[ j ] )).two_norm() >= 1e-6 )
return false;
key0[ i ] = key2[ j ];
}
int bndId[ 2 ] = { 20, 20 };
FaceType keys[ 2 ] = { key1, key2 };
for( int i=0; i<2; ++i )
{
typedef typename BoundaryIdMap :: iterator iterator ;
iterator pos = boundaryIds_.find( keys[ i ] );
if( pos != boundaryIds_.end() )
{
bndId[ i ] = (*pos).second ;
boundaryIds_.erase( pos );
}
}
BndPair bnd0 ( key0, bndId[ 0 ] );
BndPair bnd1 ( key1, bndId[ 1 ] );
periodicBoundaries_.push_back( std::make_pair( bnd0, bnd1 ) );
return true;
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
::searchPeriodicNeighbor ( FaceMap &faceMap, const typename FaceMap::iterator &pos,
const int defaultId )
{
typedef typename FaceTransformationVector::const_iterator TrafoIterator;
typedef typename FaceMap::iterator FaceMapIterator;
if( !faceTransformations_.empty() )
{
FaceType key1;
generateFace( pos->second, key1 );
const FaceMapIterator fend = faceMap.end();
for( FaceMapIterator fit = faceMap.begin(); fit != fend; ++fit )
{
FaceType key2;
generateFace( fit->second, key2 );
const TrafoIterator trend = faceTransformations_.end();
for( TrafoIterator trit = faceTransformations_.begin(); trit != trend; ++trit )
{
if( identifyFaces( *trit, key1, key2, defaultId) ||
identifyFaces( *trit, key2, key1, defaultId) )
{
faceMap.erase( fit );
faceMap.erase( pos );
return;
}
}
}
}
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
::reinsertBoundary ( const FaceMap &faceMap, const typename FaceMap::const_iterator &pos, const int id )
{
insertBoundary( pos->second.first, pos->second.second, id );
}
template< class ALUGrid >
alu_inline
void ALU3dGridFactory< ALUGrid >
::recreateBoundaryIds ( const int defaultId )
{
typedef typename FaceMap::iterator FaceIterator;
FaceMap faceMap;
const unsigned int numElements = elements_.size();
for( unsigned int n = 0; n < numElements; ++n )
{
for( unsigned int face = 0; face < numFaces; ++face )
{
FaceType key;
generateFace( elements_[ n ], face, key );
std::sort( key.begin(), key.end() );
const FaceIterator pos = faceMap.find( key );
if( pos != faceMap.end() )
faceMap.erase( key );
else
{
faceMap.insert( std::make_pair( key, SubEntity( n, face ) ) );
searchPeriodicNeighbor( faceMap, faceMap.find( key ), defaultId );
}
}
}
// swap current boundary ids with an empty vector
BoundaryIdMap boundaryIds;
boundaryIds_.swap( boundaryIds );
assert( boundaryIds_.size() == 0 );
// add all current boundary ids again (with their reordered keys)
typedef typename BoundaryIdMap::iterator BoundaryIterator;
const BoundaryIterator bndEnd = boundaryIds.end();
for( BoundaryIterator bndIt = boundaryIds.begin(); bndIt != bndEnd; ++bndIt )
{
FaceType key = bndIt->first;
std::sort( key.begin(), key.end() );
const FaceIterator pos = faceMap.find( key );
if( pos == faceMap.end() )
{
DUNE_THROW( GridError, "Inserted boundary segment is not part of the boundary." );
}
reinsertBoundary( faceMap, pos, bndIt->second );
faceMap.erase( pos );
}
// add all new boundaries (with defaultId)
const FaceIterator faceEnd = faceMap.end();
for( FaceIterator faceIt = faceMap.begin(); faceIt != faceEnd; ++faceIt )
reinsertBoundary( faceMap, faceIt, defaultId );
}
#if COMPILE_ALUGRID_LIB
template class ALU3dGridFactory< ALUGrid< 3, 3, cube, nonconforming > >;
template class ALU3dGridFactory< ALUGrid< 3, 3, simplex, nonconforming > >;
template class ALU3dGridFactory< ALUGrid< 3, 3, simplex, conforming > >;
#endif
}
#endif // end ENABLE_ALUGRID
#undef alu_inline
#endif // end DUNE_ALU3DGRID_FACTORY_CC
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