int usermult(Mat A, Vec x, Vec y)
{
// Wrap PETSc Vec as dolfin::PETScVector
boost::shared_ptr<Vec> _x(&x, NoDeleter());
boost::shared_ptr<Vec> _y(&y, NoDeleter());
PETScVector __x(_x);
PETScVector __y(_y);
// Extract pointer to PETScLinearOperator
void* ctx = 0;
MatShellGetContext(A, &ctx);
PETScLinearOperator* _A = ((PETScLinearOperator*) ctx);
// Call user-defined mult function through wrapper
dolfin_assert(_A);
GenericLinearOperator* wrapper = _A->wrapper();
dolfin_assert(wrapper);
wrapper->mult(__x, __y);
return 0;
}
bool
readFreeFemFile( RegionMesh<LinearTriangle, MC> & mesh,
const std::string & fileName,
markerID_Type regionFlag, bool /*useless*/ = false)
{
MeshElementBareHandler<BareEdge> _be;
std::pair<BareEdge, bool> _edge;
typedef LinearTriangle GeoShape;
typename RegionMesh<GeoShape, MC>::point_Type * pp = 0;
typename RegionMesh<GeoShape, MC>::edge_Type * pe = 0;
typename RegionMesh<GeoShape, MC>::face_Type * pf = 0;
std::ifstream __is ( fileName.c_str() );
if( __is.fail() )
{
std::cerr << " Error in readFreeFemFile: File " << fileName
<< " not found or locked"
<< std::endl;
abort();
}
// first row: how many vertices, triangles, edges
UInt __nv, __nt, __ne, i1, i2, i3;
__is >> __nv >> __nt >> __ne;
#ifdef DEBUG
debugStream ( 8000 ) << "number of vertices: "<< __nv << "\n";
debugStream ( 8000 ) << "number of triangles: "<< __nt << "\n";
debugStream ( 8000 ) << "number of edges: "<< __ne << "\n";
#endif
// first section: read the list of vertices
// on each row find the two coordinates and the label for each node
std::vector<Real> __x(2*__nv);
std::vector<bool> __isonboundary(__nv);
std::vector<UInt> __whichboundary(__nv);
#ifdef DEBUG
debugStream ( 8000 ) << "reading "<< __nv << " nodes\n";
#endif
// count the number of nodes on the boundary
UInt __nbv( 0 );
// reading vertices
for ( UInt __i = 0; __i < __nv; ++ __i )
{
__is >> __x[ 2 * __i ] >> __x[ 2 * __i + 1 ] >> __whichboundary[ __i ];
__isonboundary[ __i ] = __whichboundary[ __i ];
__nbv += __isonboundary[ __i ];
}
// second section: read the list of triangles
// on each row find the three nodes and the label for each triangle
std::vector<int> __triangle_nodes( 3 * __nt );
std::vector<int> __triangle_label( __nt );
#ifdef DEBUG
debugStream ( 8000 ) << "reading "<< __nt << " triangles\n";
#endif
std::map<UInt,UInt> edge_to_firstAdjacentElementIdentity, edge_to_firstAdjacentElementPosition;
// reading vertices
for ( UInt __i = 0; __i < __nt; ++__i )
{
__is >> __triangle_nodes[ 3 * __i ]
>> __triangle_nodes[ 3 * __i + 1 ]
>> __triangle_nodes[ 3 * __i + 2 ]
>> __triangle_label[ __i ];
//from 1-based numbering to 0-based numbering
__triangle_nodes[3 * __i]--;
__triangle_nodes[3 * __i+1]--;
__triangle_nodes[3 * __i+2]--;
// dump first the existing edges, to maintain the correct numbering
// if everything is correct the numbering in the bareedge
// structure will reflect the actual edge numbering
std::pair<UInt, bool> _check;
i1 = __triangle_nodes[ 3 * __i ];
i2 = __triangle_nodes[ 3 * __i + 1 ];
i3 = __triangle_nodes[ 3 * __i + 2 ];
_edge = makeBareEdge( i1, i2 );
_check = _be.addIfNotThere( _edge.first );
edge_to_firstAdjacentElementIdentity[ _check.first ] = __i;
edge_to_firstAdjacentElementPosition[ _check.first ] = 0;
_edge = makeBareEdge( i2, i3 );
_check = _be.addIfNotThere( _edge.first );
edge_to_firstAdjacentElementIdentity[ _check.first ] = __i;
edge_to_firstAdjacentElementPosition[ _check.first ] = 1;
_edge = makeBareEdge( i3, i1 );
_check = _be.addIfNotThere( _edge.first );
edge_to_firstAdjacentElementIdentity[ _check.first ] = __i;
edge_to_firstAdjacentElementPosition[ _check.first ] = 2;
}
// ( __triangle[ 3 * i + 2] > __triangle[ 3 * i + 1 ] )
// third section: read the list of edges
// NOTE: only boundary edges are stored
// on each row find the two nodes and the label for each edge
std::vector<int> __edge_nodes( 2 * __ne );
std::vector<int> __edge_label( __ne );
// reading edges
for ( UInt __i = 0; __i < __ne; ++__i )
{
__is >> __edge_nodes[ 2 * __i ] >> __edge_nodes[ 2 * __i + 1 ] >> __edge_label[ __i ];
}
//from 1-based numbering to 0-based numbering
for(UInt i(0); i<__edge_nodes.size(); i++)
__edge_nodes[i]--;
// Set mesh properties
// Add Marker to list of Markers
mesh.setMarkerID( regionFlag );
// Till now I only have information about boundary edges - I don't know the MAX num of edges
// Euler formula: ne = nv + nt - 1
mesh.setMaxNumEdges ( _be.size() );
mesh.setMaxNumGlobalEdges( _be.size() );
// Here the REAL number of edges (all of them)
mesh.setNumEdges ( _be.size() );
mesh.setNumBEdges ( __ne );
mesh.setMaxNumFaces ( __nt );
mesh.setMaxNumGlobalFaces( __nt );
// Here the REAL number of edges (all of them)
mesh.setNumFaces ( __nt);
mesh.setMaxNumPoints ( __nv, true );
mesh.setMaxNumGlobalPoints( __nv );
mesh.setNumVertices ( __nv );
mesh.setNumGlobalVertices ( __nv );
mesh.numBVertices() = __nbv;
mesh.setNumBPoints( mesh.numBVertices() );
#ifdef DEBUG
debugStream ( 8000 ) << "number of points : " << mesh.numPoints() << "\n";
debugStream ( 8000 ) << "number of boundary points : " << mesh.numBPoints() << "\n";
debugStream ( 8000 ) << "number of vertices : " << mesh.numVertices() << "\n";
debugStream ( 8000 ) << "number of boundary vertices : " << mesh.numBVertices() << "\n";
#endif
for ( UInt __i = 0; __i < __nv; ++__i )
{
pp = &mesh.addPoint( __isonboundary[ __i ], true );
pp->setMarkerID( __whichboundary[ __i ] );
pp->x() = __x[ 2 * __i ];
pp->y() = __x[ 2 * __i + 1 ];
pp->z() = 0;
pp->setId( __i );
}
// add the edges to the mesh
for ( UInt __i = 0; __i < __ne; ++__i )
{
pe = &( mesh.addEdge( true ) );
pe->setMarkerID( markerID_Type( __edge_label[ __i ] ) );
pe->setPoint( 0, mesh.point( __edge_nodes[ 2 * __i ] ) );
pe->setPoint( 1, mesh.point( __edge_nodes[ 2 * __i + 1 ] ) );
pe->setId( __i );
_edge = makeBareEdge( __edge_nodes[ 2 * __i ], __edge_nodes[ 2 * __i + 1 ] );
UInt map_it( _be.id( _edge.first ) );
pe->firstAdjacentElementIdentity() = edge_to_firstAdjacentElementIdentity[ map_it ];
pe->firstAdjacentElementPosition() = edge_to_firstAdjacentElementPosition[ map_it ];
}
// add the triangles to the mesh
for ( UInt __i = 0; __i < __nt; ++__i )
{
pf = &( mesh.addFace(true) );
pf->setId( __i );
pf->setMarkerID( markerID_Type( __triangle_label[ __i ] ) );
pf->setPoint( 0, mesh.point( __triangle_nodes[ 3 * __i ] ) );
pf->setPoint( 1, mesh.point( __triangle_nodes[ 3 * __i + 1 ] ) );
pf->setPoint( 2, mesh.point( __triangle_nodes[ 3 * __i + 2 ] ) );
}
return true;
} // Function readFreeFemFile