Namespaces
namespace	Encoder

Classes
class	MeshFunction
class	AdaptiveLinearVariationalSolver
class	AdaptiveNonlinearVariationalSolver
class	ErrorControl
	(Goal-oriented) Error Control class. More...
class	Extrapolation
class	GenericAdaptiveVariationalSolver
class	GoalFunctional
class	TimeSeries
class	ALE
class	HarmonicSmoothing
class	MeshDisplacement
class	Array
class	ArrayView
class	Hierarchical
class	IndexSet
class	MPIInfo
class	MPI
class	NoDeleter
	NoDeleter is a customised deleter intended for use with smart pointers. More...
class	RangedIndexSet
class	Set
class	SubSystemsManager
class	Timer
class	UniqueIdGenerator
class	Variable
	Common base class for DOLFIN variables. More...
class	Assembler
class	AssemblerBase
	Provide some common functions used in assembler classes. More...
class	BasisFunction
	Represention of a finite element basis function. More...
class	DirichletBC
	Interface for setting (strong) Dirichlet boundary conditions. More...
class	DiscreteOperators
	Discrete gradient operators providing derivatives of functions. More...
class	DofMap
	Degree-of-freedom map. More...
class	DofMapBuilder
	Builds a DofMap on a Mesh. More...
class	Equation
class	FiniteElement
	This is a wrapper for a UFC finite element (ufc::finite_element). More...
class	Form
	Base class for UFC code generated by FFC for DOLFIN with option -l. More...
class	GenericDofMap
	This class provides a generic interface for dof maps. More...
class	LinearTimeDependentProblem
class	LinearVariationalProblem
class	LinearVariationalSolver
	This class implements a solver for linear variational problems. More...
class	LocalAssembler
class	LocalSolver
	Solve problems cell-wise. More...
class	MixedAssembler
class	MixedLinearVariationalProblem
class	MixedLinearVariationalSolver
	This class implements a solver for mixed linear variational problems. More...
class	MixedNonlinearVariationalProblem
class	MixedNonlinearVariationalSolver
	This class implements a solver for mixed nonlinear variational problems. More...
class	MultiMeshAssembler
class	MultiMeshDirichletBC
class	MultiMeshDofMap
class	MultiMeshForm
class	NonlinearVariationalProblem
class	NonlinearVariationalSolver
class	PETScDMCollection
class	PointSource
class	SparsityPatternBuilder
class	SystemAssembler
class	UFC
class	CoefficientAssigner
class	Constant
	This class represents a constant-valued expression. More...
class	Expression
class	Function
class	FunctionAssigner
class	FunctionAXPY
class	FunctionSpace
class	GenericFunction
class	LagrangeInterpolator
class	MultiMeshCoefficientAssigner
class	MultiMeshFunction
class	MultiMeshFunctionSpace
class	MultiMeshSubSpace
class	SpecialFacetFunction
class	MeshCoordinates
	This Function represents the mesh coordinates on a given mesh. More...
class	FacetArea
class	BoxMesh
class	IntervalMesh
class	RectangleMesh
class	SphericalShellMesh
class	UnitCubeMesh
class	UnitDiscMesh
	A unit disc mesh in 2D or 3D geometry. More...
class	UnitIntervalMesh
class	UnitSquareMesh
class	UnitTetrahedronMesh
class	UnitTriangleMesh
class	BoundingBoxTree
class	BoundingBoxTree1D
	Specialization of bounding box implementation to 1D. More...
class	BoundingBoxTree2D
	Specialization of bounding box implementation to 2D. More...
class	BoundingBoxTree3D
	Specialization of bounding box implementation to 3D. More...
class	CollisionPredicates
class	ConvexTriangulation
class	GenericBoundingBoxTree
class	GeometryDebugging
class	GeometryPredicates
class	GeometryTools
	This class provides useful tools (functions) for computational geometry. More...
class	IntersectionConstruction
class	MeshPointIntersection
class	Point
class	PredicateInitialization
class	SimplexQuadrature
	This class defines quadrature rules for simplices. More...
class	BoostGraphColoring
	This class colors a graph using the Boost Graph Library. More...
class	BoostGraphOrdering
	This class computes graph re-orderings. It uses Boost Graph. More...
class	CSRGraph
	Compressed Sparse Row graph. More...
class	GraphBuilder
	This class builds a Graph corresponding to various objects. More...
class	GraphColoring
	This class provides a common interface to graph coloring libraries. More...
class	ParMETIS
	This class provides an interface to ParMETIS. More...
class	SCOTCH
	This class provides an interface to SCOTCH-PT (parallel version). More...
class	ZoltanInterface
class	File
class	MeshValueCollection
class	GenericFile
	Base class for file I/O objects. More...
class	HDF5Attribute
class	HDF5File
class	HDF5Interface
class	HDF5Utility
class	RAWFile
	Output of data in raw binary format. More...
class	SVGFile
class	VTKFile
	Output of meshes and functions in VTK format. More...
class	VTKWriter
	Write VTK Mesh representation. More...
class	X3DFile
class	X3DOMParameters
	Class data to store X3DOM view parameters. More...
class	X3DOM
class	XDMFFile
	Read and write Mesh, Function, MeshFunction and other objects in XDMF. More...
class	XMLArray
	I/O of array data in XML format. More...
class	XMLFile
	I/O of DOLFIN objects in XML format. More...
class	XMLFunctionData
	I/O for XML representation of Function. More...
class	XMLMesh
	I/O of XML representation of a Mesh. More...
class	XMLMeshFunction
	I/O of XML representation of MeshFunction. More...
class	XMLMeshValueCollection
	I/O of XML representation of a MeshValueCollection. More...
class	XMLParameters
	I/O of Parameters in XML format. More...
class	XMLTable
	Output of XML representation of DOLFIN Table. More...
class	XMLVector
	I/O of XML representation of GenericVector. More...
class	XYZFile
	Simple and light file format for use with Xd3d. More...
class	Amesos2LUSolver
class	BelosKrylovSolver
class	BlockMatrix
	Block Matrix. More...
class	BlockVector
	Block vector. More...
class	CoordinateMatrix
	Coordinate sparse matrix. More...
class	DefaultFactory
	Default linear algebra factory based on global parameter "linear_algebra_backend". More...
class	EigenFactory
	Eigen linear algebra factory. More...
class	EigenKrylovSolver
class	EigenLUSolver
class	EigenMatrix
class	EigenVector
class	GenericLinearAlgebraFactory
	Base class for LinearAlgebra factories. More...
class	GenericLinearOperator
class	GenericLinearSolver
	This class provides a general solver for linear systems Ax = b. More...
class	GenericMatrix
	This class defines a common interface for matrices. More...
class	GenericTensor
	A common interface for arbitrary rank tensors. More...
class	GenericVector
	This class defines a common interface for vectors. More...
class	Ifpack2Preconditioner
	Implements preconditioners using Ifpack2 from Trilinos. More...
class	IndexMap
class	KrylovSolver
class	LinearAlgebraObject
class	LinearOperator
class	LinearSolver
	This class provides a general solver for linear systems Ax = b. More...
class	LUSolver
	LU solver for the built-in LA backends. More...
class	Matrix
class	MueluPreconditioner
	Implements Muelu preconditioner from Trilinos. More...
class	PETScBaseMatrix
class	PETScFactory
	PETSc linear algebra factory. More...
class	PETScKrylovSolver
class	PETScLinearOperator
	PETSc version of the GenericLinearOperator. More...
class	PETScLUSolver
class	PETScMatrix
class	PETScNestMatrix
class	PETScObject
class	PETScOptions
class	PETScPreconditioner
class	PETScVector
class	Scalar
class	SLEPcEigenSolver
class	SparsityPattern
class	SUNDIALSNVector
class	TensorLayout
class	TpetraFactory
	Tpetra linear algebra factory. More...
class	TpetraMatrix
class	TpetraVector
class	TrilinosParameters
class	TrilinosPreconditioner
	This class provides a common base for Trilinos preconditioners. More...
class	Vector
class	VectorSpaceBasis
class	Event
class	Logger
	Handling of error messages, logging and informational display. More...
class	LogManager
	Logger initialisation. More...
class	LogStream
class	Progress
class	Table
class	TableEntry
	This class represents an entry in a Table. More...
class	Lagrange
class	Legendre
	Interface for computing Legendre polynomials via Boost. More...
class	BoundaryComputation
	Provide a set of basic algorithms for the computation of boundaries. More...
class	BoundaryMesh
class	Cell
	A Cell is a MeshEntity of topological codimension 0. More...
class	CellType
class	DistributedMeshTools
class	DomainBoundary
class	DynamicMeshEditor
class	Edge
	An Edge is a MeshEntity of topological dimension 1. More...
class	Face
	A Face is a MeshEntity of topological dimension 2. More...
class	Facet
	A Facet is a MeshEntity of topological codimension 1. More...
class	FacetCell
class	HexahedronCell
	This class implements functionality for hexahedral cell meshes. More...
class	IntervalCell
	This class implements functionality for interval cell meshes. More...
class	LocalMeshData
	This class stores mesh data on a local processor corresponding to a portion of a (larger) global mesh. More...
class	LocalMeshValueCollection
class	Mesh
class	MeshColoring
class	MeshConnectivity
class	MeshData
class	MeshDomains
class	MeshEditor
class	MeshEntity
class	MeshEntityIterator
class	MeshEntityIteratorBase
	Base class for MeshEntityIterators. More...
class	MeshGeometry
	MeshGeometry stores the geometry imposed on a mesh. More...
class	MeshHierarchy
	Experimental implementation of a list of Meshes as a hierarchy. More...
class	MeshOrdering
class	MeshPartitioning
class	MeshQuality
	The class provides functions to quantify mesh quality. More...
class	MeshRelation
class	MeshRenumbering
	This class implements renumbering algorithms for meshes. More...
class	MeshSmoothing
	This class implements various mesh smoothing algorithms. More...
class	MeshTopology
class	MeshTransformation
class	MeshView
class	MultiMesh
class	PeriodicBoundaryComputation
	This class computes map from slave entity to master entity. More...
class	PointCell
	This class implements functionality for point cell meshes. More...
class	QuadrilateralCell
	This class implements functionality for quadrilaterial cells. More...
class	SubDomain
class	SubMesh
class	SubsetIterator
class	TetrahedronCell
	This class implements functionality for tetrahedral cell meshes. More...
class	TopologyComputation
class	TriangleCell
	This class implements functionality for triangular meshes. More...
class	Vertex
	A Vertex is a MeshEntity of topological dimension 0. More...
class	MultiStageScheme
	Place-holder for forms and solutions for a multi-stage Butcher tableau based method. More...
class	PointIntegralSolver
	This class is a time integrator for general Runge Kutta forms. More...
class	RKSolver
	This class is a time integrator for general Runge Kutta problems. More...
class	NewtonSolver
class	NonlinearProblem
class	OptimisationProblem
class	PETScSNESSolver
class	PETScTAOSolver
class	TAOLinearBoundSolver
class	GlobalParameters
	This class defines the global DOLFIN parameter database. More...
class	Parameter
	Base class for parameters. More...
class	Parameters
class	BisectionRefinement1D
	This class implements mesh refinement in 1D. More...
class	LocalMeshCoarsening
	This class implements local mesh coarsening for different mesh types. More...
class	ParallelRefinement
	Data structure and methods for refining meshes in parallel. More...
class	PlazaRefinementND
class	RegularCutRefinement
class	CVode
	Wrapper class to SUNDIALS CVODE. More...

Typedefs
typedef PetscInt	la_index
	Index type for compatibility with linear algebra backend(s).
typedef Form	TensorProductForm
	FIXME: Temporary fix.
typedef dolfin::Set< int >	graph_set_type
	Typedefs for simple graph data structures.
typedef std::vector< graph_set_type >	Graph
	Vector of unordered Sets.
typedef MeshEntityIteratorBase< Cell >	CellIterator
	A CellIterator is a MeshEntityIterator of topological codimension 0.
typedef MeshEntityIteratorBase< Edge >	EdgeIterator
	An EdgeIterator is a MeshEntityIterator of topological dimension 1.
typedef MeshEntityIteratorBase< Face >	FaceIterator
	A FaceIterator is a MeshEntityIterator of topological dimension 2.
typedef MeshEntityIteratorBase< Facet >	FacetIterator
typedef MeshEntityIteratorBase< Vertex >	VertexIterator
	A VertexIterator is a MeshEntityIterator of topological dimension 0.

Enumerations
enum class	TimingClear : bool { keep = false , clear = true }
enum class	TimingType : int { wall = 0 , user = 1 , system = 2 }
enum	LogLevel { CRITICAL = 50 , ERROR = 40 , WARNING = 30 , INFO = 20 , PROGRESS = 16 , TRACE = 13 , DBG = 10 }

Functions
std::shared_ptr< Mesh >	adapt (const Mesh &mesh)
std::shared_ptr< Mesh >	adapt (const Mesh &mesh, const MeshFunction< bool > &cell_markers)
std::shared_ptr< FunctionSpace >	adapt (const FunctionSpace &space)
std::shared_ptr< FunctionSpace >	adapt (const FunctionSpace &space, const MeshFunction< bool > &cell_markers)
std::shared_ptr< FunctionSpace >	adapt (const FunctionSpace &space, std::shared_ptr< const Mesh > adapted_mesh)
std::shared_ptr< Function >	adapt (const Function &function, std::shared_ptr< const Mesh > adapted_mesh, bool interpolate=true)
std::shared_ptr< GenericFunction >	adapt (std::shared_ptr< const GenericFunction > function, std::shared_ptr< const Mesh > adapted_mesh)
std::shared_ptr< MeshFunction< std::size_t > >	adapt (const MeshFunction< std::size_t > &mesh_function, std::shared_ptr< const Mesh > adapted_mesh)
	Refine mesh function<std::size_t> based on mesh.
std::shared_ptr< DirichletBC >	adapt (const DirichletBC &bc, std::shared_ptr< const Mesh > adapted_mesh, const FunctionSpace &S)
	Refine Dirichlet bc based on refined mesh.
void	adapt_markers (std::vector< std::size_t > &refined_markers, const Mesh &adapted_mesh, const std::vector< std::size_t > &markers, const Mesh &mesh)
	Helper function for refinement of boundary conditions.
std::shared_ptr< Form >	adapt (const Form &form, std::shared_ptr< const Mesh > adapted_mesh, bool adapt_coefficients=true)
std::shared_ptr< LinearVariationalProblem >	adapt (const LinearVariationalProblem &problem, std::shared_ptr< const Mesh > adapted_mesh)
	Refine linear variational problem based on mesh.
std::shared_ptr< NonlinearVariationalProblem >	adapt (const NonlinearVariationalProblem &problem, std::shared_ptr< const Mesh > adapted_mesh)
	Refine nonlinear variational problem based on mesh.
std::shared_ptr< ErrorControl >	adapt (const ErrorControl &ec, std::shared_ptr< const Mesh > adapted_mesh, bool adapt_coefficients=true)
void	solve (const Equation &equation, Function &u, const double tol, GoalFunctional &M)
void	solve (const Equation &equation, Function &u, const DirichletBC &bc, const double tol, GoalFunctional &M)
void	solve (const Equation &equation, Function &u, std::vector< const DirichletBC * > bcs, const double tol, GoalFunctional &M)
void	solve (const Equation &equation, Function &u, const Form &J, const double tol, GoalFunctional &M)
void	solve (const Equation &equation, Function &u, const DirichletBC &bc, const Form &J, const double tol, GoalFunctional &M)
void	solve (const Equation &equation, Function &u, std::vector< const DirichletBC * > bcs, const Form &J, const double tol, GoalFunctional &M)
void	mark (MeshFunction< bool > &markers, const dolfin::MeshFunction< double > &indicators, const std::string strategy, const double fraction)
void	dorfler_mark (MeshFunction< bool > &markers, const dolfin::MeshFunction< double > &indicators, const double fraction)
std::string	dolfin_version ()
	Return DOLFIN version string.
std::string	ufc_signature ()
	Return UFC signature string.
std::string	git_commit_hash ()
std::size_t	sizeof_la_index ()
	Return sizeof the dolfin::la_index type.
bool	has_debug ()
bool	has_openmp ()
	Return true if DOLFIN is compiled with OpenMP.
bool	has_mpi ()
	Return true if DOLFIN is compiled with MPI.
bool	has_petsc ()
	Return true if DOLFIN is compiled with PETSc.
bool	has_slepc ()
	Return true if DOLFIN is compiled with SLEPc.
bool	has_scotch ()
	Return true if DOLFIN is compiled with Scotch.
bool	has_sundials ()
	Return true if DOLFIN is compiled with SUNDIALS.
bool	has_umfpack ()
	Return true if DOLFIN is compiled with Umfpack.
bool	has_cholmod ()
	Return true if DOLFIN is compiled with Cholmod.
bool	has_parmetis ()
	Return true if DOLFIN is compiled with ParMETIS.
bool	has_zlib ()
	Return true if DOLFIN is compiled with ZLIB.
bool	has_hdf5 ()
	Return true if DOLFIN is compiled with HDF5.
bool	has_hdf5_parallel ()
	Return true if DOLFIN is compiled with Parallel HDF5.
void	init (int argc, char *argv[])
template<typename T>
std::shared_ptr< T >	reference_to_no_delete_pointer (T &r)
	Helper function to construct shared pointer with NoDeleter with cleaner syntax.
void	tic ()
	Start timing (should not be used internally in DOLFIN!).
double	toc ()
	Return elapsed wall time (should not be used internally in DOLFIN!).
double	time ()
	Return wall time elapsed since some implementation dependent epoch.
Table	timings (TimingClear clear, std::set< TimingType > type)
void	list_timings (TimingClear clear, std::set< TimingType > type)
void	dump_timings_to_xml (std::string filename, TimingClear clear)
std::tuple< std::size_t, double, double, double >	timing (std::string task, TimingClear clear)
std::string	indent (std::string block)
	Indent string block.
template<typename T>
std::string	container_to_string (const T &x, std::string delimiter, int precision, int linebreak=0)
std::string	to_string (const double *x, std::size_t n)
	Return string representation of given array.
template<class T>
std::size_t	hash_local (const T &x)
	Return a hash of a given object.
template<class T>
std::size_t	hash_global (const MPI_Comm mpi_comm, const T &x)
void	assemble (GenericTensor &A, const Form &a)
	Assemble tensor.
void	assemble_mixed (GenericTensor &A, const Form &a, bool add=false)
	Assemble tensor.
void	assemble_system (GenericMatrix &A, GenericVector &b, const Form &a, const Form &L, std::vector< std::shared_ptr< const DirichletBC > > bcs)
	Assemble system (A, b) and apply Dirichlet boundary conditions.
void	assemble_system (GenericMatrix &A, GenericVector &b, const Form &a, const Form &L, std::vector< std::shared_ptr< const DirichletBC > > bcs, const GenericVector &x0)
void	assemble_multimesh (GenericTensor &A, const MultiMeshForm &a)
	Assemble tensor from multimesh form.
double	assemble (const Form &a)
	Assemble scalar.
double	assemble_mixed (const Form &a, bool add=false)
	Assemble scalar.
double	assemble_multimesh (const MultiMeshForm &a)
	Assemble scalar from multimesh form.
void	assemble_local (Eigen::Matrix< double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor > &A_e, const Form &a, const Cell &cell)
	Assemble form to local tensor on a cell (Eigen version for pybind11).
void	assemble_local (const Form &a, const Cell &cell, std::vector< double > &tensor)
std::vector< std::size_t >	dof_to_vertex_map (const FunctionSpace &space)
std::vector< dolfin::la_index >	vertex_to_dof_map (const FunctionSpace &space)
void	set_coordinates (MeshGeometry &geometry, const Function &position)
void	get_coordinates (Function &position, const MeshGeometry &geometry)
Mesh	create_mesh (Function &coordinates)
void	solve (const Equation &equation, Function &u, Parameters parameters=empty_parameters)
void	solve (const Equation &equation, Function &u, const DirichletBC &bc, Parameters parameters=empty_parameters)
void	solve (const Equation &equation, Function &u, std::vector< const DirichletBC * > bcs, Parameters parameters=empty_parameters)
void	solve (const Equation &equation, Function &u, const Form &J, Parameters parameters=empty_parameters)
void	solve (const Equation &equation, Function &u, const DirichletBC &bc, const Form &J, Parameters parameters=empty_parameters)
void	solve (const Equation &equation, Function &u, std::vector< const DirichletBC * > bcs, const Form &J, Parameters parameters=empty_parameters)
void	assign (std::shared_ptr< Function > receiving_func, std::shared_ptr< const Function > assigning_func)
void	assign (std::shared_ptr< Function > receiving_func, std::vector< std::shared_ptr< const Function > > assigning_funcs)
void	assign (std::vector< std::shared_ptr< Function > > receiving_funcs, std::shared_ptr< const Function > assigning_func)
bool	check_cgal (bool result_dolfin, bool result_cgal, const std::string &function)
std::vector< Point >	cgal_intersection_check (const std::vector< Point > &dolfin_result, const std::vector< Point > &cgal_result, const std::string &function)
bool	cgal_collides_segment_point_2d (const Point &q0, const Point &q1, const Point &p, bool only_interior=false)
bool	cgal_collides_segment_point_3d (const Point &q0, const Point &q1, const Point &p, bool only_interior=false)
bool	cgal_collides_segment_segment_2d (const Point &p0, const Point &p1, const Point &q0, const Point &q1)
bool	cgal_collides_segment_segment_3d (const Point &p0, const Point &p1, const Point &q0, const Point &q1)
bool	cgal_collides_triangle_point_2d (const Point &p0, const Point &p1, const Point &p2, const Point &point)
bool	cgal_collides_triangle_point_3d (const Point &p0, const Point &p1, const Point &p2, const Point &point)
bool	cgal_collides_triangle_segment_2d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1)
bool	cgal_collides_triangle_segment_3d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1)
bool	cgal_collides_triangle_triangle_2d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1, const Point &q2)
bool	cgal_collides_triangle_triangle_3d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1, const Point &q2)
bool	cgal_collides_tetrahedron_point_3d (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0)
bool	cgal_collides_tetrahedron_segment_3d (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0, const Point &q1)
bool	cgal_collides_tetrahedron_triangle_3d (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0, const Point &q1, const Point &q2)
bool	cgal_collides_tetrahedron_tetrahedron_3d (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0, const Point &q1, const Point &q2, const Point &q3)
std::vector< Point >	cgal_intersection_segment_segment_2d (const Point &p0, const Point &p1, const Point &q0, const Point &q1)
std::vector< Point >	cgal_intersection_segment_segment_3d (const Point &p0, const Point &p1, const Point &q0, const Point &q1)
std::vector< Point >	cgal_triangulate_segment_segment_2d (const Point &p0, const Point &p1, const Point &q0, const Point &q1)
std::vector< Point >	cgal_triangulate_segment_segment_3d (const Point &p0, const Point &p1, const Point &q0, const Point &q1)
std::vector< Point >	cgal_intersection_triangle_segment_2d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1)
std::vector< Point >	cgal_intersection_triangle_segment_3d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1)
std::vector< Point >	cgal_triangulate_triangle_segment_2d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1)
std::vector< Point >	cgal_triangulate_triangle_segment_3d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1)
std::vector< Point >	cgal_intersection_triangle_triangle_2d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1, const Point &q2)
std::vector< Point >	cgal_intersection_triangle_triangle_3d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1, const Point &q2)
std::vector< std::vector< Point > >	cgal_triangulate_triangle_triangle_2d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1, const Point &q2)
std::vector< std::vector< Point > >	cgal_triangulate_triangle_triangle_3d (const Point &p0, const Point &p1, const Point &p2, const Point &q0, const Point &q1, const Point &q2)
std::vector< Point >	cgal_intersection_tetrahedron_triangle (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0, const Point &q1, const Point &q2)
std::vector< std::vector< Point > >	cgal_triangulate_tetrahedron_triangle (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0, const Point &q1, const Point &q2)
std::vector< Point >	cgal_intersection_tetrahedron_tetrahedron_3d (const Point &p0, const Point &p1, const Point &p2, const Point &p3, const Point &q0, const Point &q1, const Point &q2, const Point &q3)
bool	cgal_is_degenerate_2d (const std::vector< Point > &s)
bool	cgal_is_degenerate_3d (const std::vector< Point > &s)
double	cgal_polyhedron_volume (const std::vector< Point > &ch)
double	cgal_tet_volume (const std::vector< Point > &ch)
bool	cgal_tet_is_degenerate (const std::vector< Point > &t)
bool	cgal_triangulation_has_degenerate (std::vector< std::vector< Point > > triangulation)
bool	cgal_triangulation_overlap (std::vector< std::vector< Point > > triangulation)
std::shared_ptr< const MeshPointIntersection >	intersect (const Mesh &mesh, const Point &point)
Point	operator* (double a, const Point &p)
	Multiplication with scalar.
std::ostream &	operator<< (std::ostream &stream, const Point &point)
	Output of Point to stream.
void	exactinit ()
	Initialize tolerances for exact arithmetic.
double	orient1d (double a, double b, double x)
	Compute relative orientation of point x wrt segment [a, b].
double	_orient2d (const double a, const double b, const double *c)
double	orient2d (const Point &a, const Point &b, const Point &c)
	Convenience function using dolfin::Point.
double	_orient3d (const double a, const double b, const double c, const double d)
double	orient3d (const Point &a, const Point &b, const Point &c, const Point &d)
	Convenience function using dolfin::Point.
template<>
hid_t	HDF5Interface::hdf5_type< std::int64_t > ()
template<>
hid_t	HDF5Interface::hdf5_type< std::size_t > ()
template<typename Y, typename X>
Y &	as_type (X &x)
template<typename Y, typename X>
std::shared_ptr< Y >	as_type (std::shared_ptr< X > x)
template<typename Y, typename X>
bool	has_type (const X &x)
	Check whether the object matches a specific type.
int	usermult (Mat A, Vec x, Vec y)
	Callback function for PETSc mult function.
std::size_t	solve (const GenericLinearOperator &A, GenericVector &x, const GenericVector &b, std::string method="lu", std::string preconditioner="none")
	Solve linear system Ax = b.
void	list_linear_algebra_backends ()
	List available linear algebra backends.
void	list_linear_solver_methods ()
	List available solver methods for current linear algebra backend.
void	list_lu_solver_methods ()
	List available LU methods for current linear algebra backend.
void	list_krylov_solver_methods ()
	List available Krylov methods for current linear algebra backend.
void	list_krylov_solver_preconditioners ()
bool	has_linear_algebra_backend (std::string backend)
	Return true if a specific linear algebra backend is supported.
bool	has_lu_solver_method (std::string method)
bool	has_krylov_solver_method (std::string method)
bool	has_krylov_solver_preconditioner (std::string preconditioner)
std::map< std::string, std::string >	linear_algebra_backends ()
	Return available linear algebra backends.
std::map< std::string, std::string >	linear_solver_methods ()
std::map< std::string, std::string >	lu_solver_methods ()
std::map< std::string, std::string >	krylov_solver_methods ()
std::map< std::string, std::string >	krylov_solver_preconditioners ()
double	residual (const GenericLinearOperator &A, const GenericVector &x, const GenericVector &b)
	Compute residual \|\|Ax - b\|\|.
double	norm (const GenericVector &x, std::string norm_type="l2")
double	normalize (GenericVector &x, std::string normalization_type="average")
	Normalize vector according to given normalization type.
bool	in_nullspace (const GenericLinearOperator &A, const VectorSpaceBasis &x, std::string type="right")
void	info (std::string msg,...)
	Print message.
void	info (const Parameters &parameters, bool verbose=false)
	Print parameter (using output of str() method).
void	info (const Variable &variable, bool verbose=false)
	Print variable (using output of str() method).
void	info_stream (std::ostream &out, std::string msg)
	Print message to stream.
void	info_underline (std::string msg,...)
	Print underlined message.
void	warning (std::string msg,...)
	Print warning.
void	error (std::string msg,...)
void	dolfin_error (std::string location, std::string task, std::string reason,...)
void	deprecation (std::string feature, std::string version_deprecated, std::string message,...)
void	log (int debug_level, std::string msg,...)
	Print message at given debug level.
void	begin (std::string msg,...)
	Begin task (increase indentation level).
void	begin (int debug_level, std::string msg,...)
	Begin task (increase indentation level).
void	end ()
	End task (decrease indentation level).
void	set_log_active (bool active=true)
	Turn logging on or off.
void	set_log_level (int level)
	Set log level.
void	set_indentation_level (std::size_t indentation_level)
	Set indentation level.
void	set_output_stream (std::ostream &out)
	Set output stream.
int	get_log_level ()
	Get log level.
void	monitor_memory_usage ()
void	not_working_in_parallel (std::string what)
void	__debug (std::string file, unsigned long line, std::string function, std::string format,...)
void	__dolfin_assert (std::string file, unsigned long line, std::string function, std::string check)
std::size_t	ipow (std::size_t a, std::size_t n)
double	rand ()
void	seed (std::size_t s)
bool	near (double x, double x0, double eps=DOLFIN_EPS)
bool	between (double x, std::pair< double, double > range)
Mesh	refine (const Mesh &mesh, bool redistribute=true)
std::shared_ptr< const MeshHierarchy >	refine (const MeshHierarchy &hierarchy, const MeshFunction< bool > &markers)
	Refine a MeshHierarchy.
void	refine (Mesh &refined_mesh, const Mesh &mesh, bool redistribute=true)
Mesh	refine (const Mesh &mesh, const MeshFunction< bool > &cell_markers, bool redistribute=true)
void	refine (Mesh &refined_mesh, const Mesh &mesh, const MeshFunction< bool > &cell_markers, bool redistribute=true)
void	p_refine (Mesh &refined_mesh, const Mesh &mesh)
Mesh	p_refine (const Mesh &mesh)

Variables
Timer	__global_timer
Timer	__tic_timer
PredicateInitialization	predicate_initialization
	Initialize the predicate.
LogStream	cout
	dolfin::cout
LogStream	endl
	dolfin::endl;
bool	rand_seeded = false
GlobalParameters	parameters
	The global parameter database.
Parameters	empty_parameters ("empty")
	Default empty parameters.

Detailed Description

This comment in in timing.h but I think it is providing a doxygen docstring for the whole dolfin namespace... FIXME.

Typedef Documentation

◆ FacetIterator

typedef MeshEntityIteratorBase<Facet> dolfin::FacetIterator

A FacetIterator is a MeshEntityIterator of topological codimension 1.

◆ graph_set_type

typedef dolfin::Set<int> dolfin::graph_set_type

Typedefs for simple graph data structures.

DOLFIN container for graphs

Enumeration Type Documentation

◆ LogLevel

enum dolfin::LogLevel

These log levels match the levels in the Python 'logging' module (and adds trace/progress).

◆ TimingClear

enum class dolfin::TimingClear : bool

strong

Parameter specifying whether to clear timing(s):

TimingClear::keep
TimingClear::clear

◆ TimingType

enum class dolfin::TimingType : int

strong

Timing types:

TimingType::wall wall-clock time
TimingType::user user (cpu) time
TimingType::system system (kernel) time

Precision of wall is around 1 microsecond, user and system are around 10 millisecond (on Linux).

Function Documentation

◆ _orient2d()

double dolfin::_orient2d	(	const double *	a,
		const double *	b,
		const double *	c )

Compute relative orientation of points a, b, c. The orientation is such that orient2d(a, b, c) > 0 if a, b, c are ordered counter-clockwise.

◆ _orient3d()

double dolfin::_orient3d	(	const double *	a,
		const double *	b,
		const double *	c,
		const double *	d )

Compute relative orientation of points a, b, c, d. The orientation is such that orient3d(a, b, c, d) > 0 if a, b, c, d are oriented according to the left hand rule.

◆ adapt() [1/9]

std::shared_ptr< ErrorControl > dolfin::adapt	(	const ErrorControl &	ec,
		std::shared_ptr< const Mesh >	adapted_mesh,
		bool	adapt_coefficients = true )

Adapt error control object based on adapted mesh

Parameters

ec	(ErrorControl) The error control object to be adapted
adapted_mesh	(Mesh) The new mesh
adapt_coefficients	(bool) Optional argument, default is true. If false, any form coefficients are not explicitly adapted, but pre-adapted coefficients will be transferred.

Returns: ErrorControl The adapted error control object

◆ adapt() [2/9]

std::shared_ptr< Form > dolfin::adapt	(	const Form &	form,
		std::shared_ptr< const Mesh >	adapted_mesh,
		bool	adapt_coefficients = true )

Adapt form based on adapted mesh

Parameters

[in]	form	(Form) The form that should be adapted
[in]	adapted_mesh	(Mesh) The new mesh
[in]	adapt_coefficients	(bool) Optional argument, default is true. If false, the form coefficients are not explicitly adapted, but pre-adapted coefficients will be transferred.

Returns: Form The adapted form

◆ adapt() [3/9]

std::shared_ptr< Function > dolfin::adapt	(	const Function &	function,
		std::shared_ptr< const Mesh >	adapted_mesh,
		bool	interpolate = true )

Adapt Function based on adapted mesh

Parameters

[in]	function	(Function&) The function that should be adapted
[in]	adapted_mesh	(std::shared_ptr<const Mesh>) The new mesh
[in]	interpolate	(bool) Optional argument, default is true. If false, the function's function space is adapted, but the values are not interpolated.

Returns: Function The adapted function

◆ adapt() [4/9]

std::shared_ptr< FunctionSpace > dolfin::adapt ( const FunctionSpace & space )

Refine function space uniformly

Parameters

[in] space (FunctionSpace)

Returns: FunctionSpace

◆ adapt() [5/9]

std::shared_ptr< FunctionSpace > dolfin::adapt	(	const FunctionSpace &	space,
		const MeshFunction< bool > &	cell_markers )

Refine function space based on cell markers

Parameters

[in]	space	(FunctionSpace&)
[in]	cell_markers	(MehsFunction<bool>&)

Returns: FunctionSpace

◆ adapt() [6/9]

std::shared_ptr< FunctionSpace > dolfin::adapt	(	const FunctionSpace &	space,
		std::shared_ptr< const Mesh >	adapted_mesh )

Refine function space based on refined mesh

Parameters

[in]	space	(FunctionSpace&)
[in]	adapted_mesh	(std::sahred_ptr<const Mesh>)

Returns: FunctionSpace

◆ adapt() [7/9]

std::shared_ptr< Mesh > dolfin::adapt ( const Mesh & mesh )

Refine mesh uniformly

Parameters

[in] mesh (Mesh) Input mesh

Returns: std::shared_ptr<Mesh> adapted mesh

◆ adapt() [8/9]

std::shared_ptr< Mesh > dolfin::adapt	(	const Mesh &	mesh,
		const MeshFunction< bool > &	cell_markers )

Refine mesh based on cell markers

Parameters

[in]	mesh	(Mesh) Input mesh
[in]	cell_markers	(MeshFunction<bool>) Markers denoting cells to be refined

◆ adapt() [9/9]

std::shared_ptr< GenericFunction > dolfin::adapt	(	std::shared_ptr< const GenericFunction >	function,
		std::shared_ptr< const Mesh >	adapted_mesh )

Refine GenericFunction based on refined mesh

Parameters

[in]	function	(GeericFunction) The function that should be adapted
[in]	adapted_mesh	(Mehs) The new mesh

Returns: GenericFunction The adapted function

◆ as_type() [1/2]

template<typename Y, typename X>

std::shared_ptr< Y > dolfin::as_type ( std::shared_ptr< X > x )

Cast shared pointer object to its derived class, if possible. Caller must check for success (returns null if cast fails).

◆ as_type() [2/2]

template<typename Y, typename X>

Y & dolfin::as_type ( X & x )

Cast object to its derived class, if possible (non-const version). An error is thrown if the cast is unsuccessful.

◆ assemble_local()

void dolfin::assemble_local	(	const Form &	a,
		const Cell &	cell,
		std::vector< double > &	tensor )

Assemble form to local tensor on a cell (Legacy version for SWIG)

◆ assemble_system()

void dolfin::assemble_system	(	GenericMatrix &	A,
		GenericVector &	b,
		const Form &	a,
		const Form &	L,
		std::vector< std::shared_ptr< const DirichletBC > >	bcs,
		const GenericVector &	x0 )

Assemble system (A, b) on sub domains and apply Dirichlet boundary conditions

◆ assign() [1/3]

void dolfin::assign	(	std::shared_ptr< Function >	receiving_func,
		std::shared_ptr< const Function >	assigning_func )

Assign one function to another. The functions must reside in the same type of FunctionSpace. One or both functions can be sub functions.

Parameters

receiving_func	(std::shared_ptr<Function>) The receiving function
assigning_func	(std::shared_ptr<Function>) The assigning function

◆ assign() [2/3]

void dolfin::assign	(	std::shared_ptr< Function >	receiving_func,
		std::vector< std::shared_ptr< const Function > >	assigning_funcs )

Assign several functions to sub functions of a mixed receiving function. The number of receiving functions must sum up to the number of sub functions in the assigning mixed function. The sub spaces of the assigning mixed space must be of the same type ans size as the receiving spaces.

Parameters

receiving_func	(std::shared_ptr<Function>) The receiving function
assigning_funcs	(std::vector<std::shared_ptr<Function>>) The assigning functions

◆ assign() [3/3]

void dolfin::assign	(	std::vector< std::shared_ptr< Function > >	receiving_funcs,
		std::shared_ptr< const Function >	assigning_func )

Assign sub functions of a single mixed function to single receiving functions. The number of sub functions in the assigning mixed function must sum up to the number of receiving functions. The sub spaces of the receiving mixed space must be of the same type ans size as the assigning spaces.

Parameters

receiving_funcs	(std::vector<std::shared_ptr<Function>>) The receiving functions
assigning_func	(std::shared_ptr<Function>) The assigning function

◆ between()

bool dolfin::between	(	double	x,
		std::pair< double, double >	range )

Check whether x is between x0 and x1 (inclusive, to within DOLFIN_EPS)

Parameters

x	(double) Value to check
range	(std::pair<double, double>) Range to check

Returns: bool

◆ container_to_string()

template<typename T>

std::string dolfin::container_to_string	(	const T &	x,
		std::string	delimiter,
		int	precision,
		int	linebreak = 0 )

Return string representation of given container of ints, floats, etc.

◆ create_mesh()

Mesh dolfin::create_mesh ( Function & coordinates )

Creates mesh from coordinate function

Topology is given by underlying mesh of the function space and geometry is given by function values. Hence resulting mesh geometry has a degree of the function space degree. Geometry of function mesh is ignored.

Mesh connectivities d-0, d-1, ..., d-r are built on function mesh (where d is topological dimension of the mesh and r is maximal dimension of entity associated with any coordinate node). Consider clearing unneeded connectivities when finished.

Parameters

coordinates (Function) Vector Lagrange function of any degree

Returns: Mesh The mesh

◆ deprecation()

void dolfin::deprecation	(	std::string	feature,
		std::string	version_deprecated,
		std::string	message,
			... )

Issue deprecation warning for removed feature

Arguments feature (std::string) Name of the feature that has been removed. version_deprecated (std::string) Version number of the release in which the feature is deprecated. message (std::string) A format string explaining the deprecation.

◆ dof_to_vertex_map()

std::vector< std::size_t > dolfin::dof_to_vertex_map ( const FunctionSpace & space )

Return a map between dof indices and vertex indices

Only works for FunctionSpace with dofs exclusively on vertices. For mixed FunctionSpaces vertex index is offset with the number of dofs per vertex.

In parallel the returned map maps both owned and unowned dofs (using local indices) thus covering all the vertices. Hence the returned map is an inversion of vertex_to_dof_map.

Parameters

space (FunctionSpace) The FunctionSpace for what the dof to vertex map should be computed for

Returns: std::vector<std::size_t> The dof to vertex map

◆ dolfin_error()

void dolfin::dolfin_error	(	std::string	location,
		std::string	task,
		std::string	reason,
			... )

Print error message. Prefer this to the above generic error message.

Arguments location (std::string) Name of the file from which the error message was generated. task (std::string) Name of the task that failed. Note that this string should begin with lowercase. Note that this string should not be punctuated. reason (std::string) A format string explaining the reason for the failure. Note that this string should begin with uppercase. Note that this string should not be punctuated. Note that this string may contain printf style formatting. ... (primitive types like int, std::size_t, double, bool) Optional arguments for the format string.

Developers should read the file dolfin/log/README in the DOLFIN source tree for further notes about the use of this function.

◆ dorfler_mark()

void dolfin::dorfler_mark	(	dolfin::MeshFunction< bool > &	markers,
		const dolfin::MeshFunction< double > &	indicators,
		const double	fraction )

Mark cells using Dorfler marking

Parameters

markers	(MeshFunction<bool>) the cell markers (to be computed)
indicators	(MeshFunction<double>) error indicators (one per cell)
fraction	(double) the marking fraction

◆ dump_timings_to_xml()

void dolfin::dump_timings_to_xml	(	std::string	filename,
		TimingClear	clear )

Dump a summary of timings and tasks to XML file, optionally clearing stored timings. MPI_MAX, MPI_MIN and MPI_AVG reductions are stored. Collective on MPI_COMM_WORLD.

Arguments filename (std::string) output filename; must have .xml suffix; existing file is silently overwritten clear (TimingClear)

TimingClear::clear resets stored timings
TimingClear::keep leaves stored timings intact

◆ error()

void dolfin::error	(	std::string	msg,
			... )

Print error message and throw an exception. Note to developers: this function should not be used internally in DOLFIN. Use the more informative dolfin_error instead.

◆ get_coordinates()

void dolfin::get_coordinates	(	Function &	position,
		const MeshGeometry &	geometry )

Stores mesh coordinates into function

Mesh connectivities d-0, d-1, ..., d-r are built on function mesh (where d is topological dimension of the mesh and r is maximal dimension of entity associated with any coordinate node). Consider clearing unneeded connectivities when finished.

Parameters

position	(Function) Vectorial Lagrange function with matching degree and mesh
geometry	(MeshGeometry) Mesh geometry to be stored

◆ git_commit_hash()

std::string dolfin::git_commit_hash ( )

Return git changeset hash (returns "unknown" if changeset is not known)

◆ has_debug()

bool dolfin::has_debug ( )

Return true if DOLFIN is compiled in debugging mode, i.e., with assertions on

◆ has_krylov_solver_method()

bool dolfin::has_krylov_solver_method ( std::string method )

Return true if Krylov method for the current linear algebra backend is available

◆ has_krylov_solver_preconditioner()

bool dolfin::has_krylov_solver_preconditioner ( std::string preconditioner )

Return true if Preconditioner for the current linear algebra backend is available

◆ has_lu_solver_method()

bool dolfin::has_lu_solver_method ( std::string method )

Return true if LU method for the current linear algebra backend is available

◆ hash_global()

template<class T>

std::size_t dolfin::hash_global	(	const MPI_Comm	mpi_comm,
		const T &	x )

Return a hash for a distributed (MPI) object. A hash is computed on each process, and the hash of the std::vector of all local hash keys is returned. This function is collective.

◆ in_nullspace()

bool dolfin::in_nullspace	(	const GenericLinearOperator &	A,
		const VectorSpaceBasis &	x,
		std::string	type = "right" )

Check whether a vector space basis is in the nullspace of a given operator. The string option 'type' can be "right" for the right nullspace (Ax=0) or "left" for the left nullspace (A^Tx = 0). To test the left nullspace, A must also be of type GenericMatrix.

◆ info()

void dolfin::info	(	std::string	msg,
			... )

Print message.

The DOLFIN log system provides the following set of functions for uniform handling of log messages, warnings and errors. In addition, macros are provided for debug messages and dolfin_assertions.

Only messages with a debug level higher than or equal to the current log level are printed (the default being zero). Logging may also be turned off by calling set_log_active(false).

◆ init()

void dolfin::init	(	int	argc,
		char *	argv[] )

Initialize DOLFIN (and PETSc) with command-line arguments. This should not be needed in most cases since the initialization is otherwise handled automatically.

◆ intersect()

std::shared_ptr< const MeshPointIntersection > dolfin::intersect	(	const Mesh &	mesh,
		const Point &	point )

Compute and return intersection between Mesh and Point.

Arguments mesh (Mesh) The mesh to be intersected. point (Point) The point to be intersected.

Returns MeshPointIntersection The intersection data.

◆ ipow()

std::size_t dolfin::ipow	(	std::size_t	a,
		std::size_t	n )

Return a to the power n. NOTE: Overflow is not checked!

Parameters

a	(std::size_t) Value
n	(std::size_t) Power

Returns: std::size_t

◆ krylov_solver_methods()

std::map< std::string, std::string > dolfin::krylov_solver_methods ( )

Return a list of available Krylov methods for current linear algebra backend

◆ krylov_solver_preconditioners()

std::map< std::string, std::string > dolfin::krylov_solver_preconditioners ( )

Return a list of available preconditioners for current linear algebra backend

◆ linear_solver_methods()

std::map< std::string, std::string > dolfin::linear_solver_methods ( )

Return a list of available solver methods for current linear algebra backend

◆ list_krylov_solver_preconditioners()

void dolfin::list_krylov_solver_preconditioners ( )

List available preconditioners for current linear algebra backend

◆ list_timings()

void dolfin::list_timings	(	TimingClear	clear,
		std::set< TimingType >	type )

List a summary of timings and tasks, optionally clearing stored timings. MPI_AVG reduction is printed. Collective on MPI_COMM_WORLD.

Arguments clear (TimingClear)

TimingClear::clear resets stored timings
TimingClear::keep leaves stored timings intact type (std::set<TimingType>) subset of { TimingType::wall, TimingType::user, TimingType::system }

◆ lu_solver_methods()

std::map< std::string, std::string > dolfin::lu_solver_methods ( )

Return a list of available LU methods for current linear algebra backend

◆ mark()

void dolfin::mark	(	dolfin::MeshFunction< bool > &	markers,
		const dolfin::MeshFunction< double > &	indicators,
		const std::string	strategy,
		const double	fraction )

Mark cells based on indicators and given marking strategy

Parameters

markers	(MeshFunction<bool>) the cell markers (to be computed)
indicators	(MeshFunction<double>) error indicators (one per cell)
strategy	(std::string) the marking strategy
fraction	(double) the marking fraction

◆ monitor_memory_usage()

void dolfin::monitor_memory_usage ( )

Monitor memory usage. Call this function at the start of a program to continuously monitor the memory usage of the process.

◆ near()

bool dolfin::near	(	double	x,
		double	x0,
		double	eps = DOLFIN_EPS )

Check whether x is close to x0 (to within DOLFIN_EPS)

Parameters

x	(double) First value
x0	(double) Second value
eps	(double) Tolerance

Returns: bool

◆ norm()

double dolfin::norm	(	const GenericVector &	x,
		std::string	norm_type = "l2" )

Compute norm of vector. Valid norm types are "l2", "l1" and "linf".

◆ not_working_in_parallel()

void dolfin::not_working_in_parallel ( std::string what )

Report that functionality has not (yet) been implemented to work in parallel

◆ p_refine() [1/2]

dolfin::Mesh dolfin::p_refine ( const Mesh & mesh )

Return a p_refined mesh Increase the polynomial order of the mesh from 1 to 2, i.e. add points at the Edge midpoints, to make a quadratic mesh.

Parameters

mesh	(Mesh) The original linear mesh.

Returns: Mesh

◆ p_refine() [2/2]

void dolfin::p_refine	(	Mesh &	refined_mesh,
		const Mesh &	mesh )

Increase the polynomial order of the mesh from 1 to 2, i.e. add points at the Edge midpoints, to make a quadratic mesh.

Parameters

refined_mesh	(Mesh) The mesh that will be the quadratic mesh.
mesh	(Mesh) The original linear mesh.

◆ rand()

double dolfin::rand ( )

Return a random number, uniformly distributed between [0.0, 1.0)

Returns: double

◆ refine() [1/4]

dolfin::Mesh dolfin::refine	(	const Mesh &	mesh,
		bool	redistribute = true )

Create uniformly refined mesh

Parameters

mesh	(Mesh) The mesh to refine.
redistribute	(bool) Optional argument to redistribute the refined mesh if mesh is a distributed mesh.

Returns: Mesh The refined mesh.

mesh = refine(mesh);

dolfin::refine

Mesh refine(const Mesh &mesh, bool redistribute=true)

Definition refine.cpp:39

◆ refine() [2/4]

dolfin::Mesh dolfin::refine	(	const Mesh &	mesh,
		const MeshFunction< bool > &	cell_markers,
		bool	redistribute = true )

Create locally refined mesh

Parameters

mesh	(Mesh) The mesh to refine.
cell_markers	(MeshFunction<bool>) A mesh function over booleans specifying which cells that should be refined (and which should not).
redistribute	(bool) Optional argument to redistribute the refined mesh if mesh is a distributed mesh.

Returns: Mesh The locally refined mesh.

MeshFunction<bool> cell_markers(mesh, mesh->topology().dim());
cell_markers.set_all(false);
Point origin(0.0, 0.0, 0.0);
for (CellIterator cell(mesh); !cell.end(); ++cell)
{
    Point p = cell->midpoint();
    if (p.distance(origin) < 0.1)
        cell_markers[*cell] = true;
}
mesh = refine(mesh, cell_markers);

◆ refine() [3/4]

void dolfin::refine	(	Mesh &	refined_mesh,
		const Mesh &	mesh,
		bool	redistribute = true )

Create uniformly refined mesh

Parameters

refined_mesh	(Mesh) The mesh that will be the refined mesh.
mesh	(Mesh) The original mesh.
redistribute	(bool) Optional argument to redistribute the refined mesh if mesh is a distributed mesh.

◆ refine() [4/4]

void dolfin::refine	(	Mesh &	refined_mesh,
		const Mesh &	mesh,
		const MeshFunction< bool > &	cell_markers,
		bool	redistribute = true )

Create locally refined mesh

Parameters

refined_mesh	(Mesh) The mesh that will be the refined mesh.
mesh	(Mesh) The original mesh.
cell_markers	(MeshFunction<bool>) A mesh function over booleans specifying which cells that should be refined (and which should not).
redistribute	(bool) Optional argument to redistribute the refined mesh if mesh is a distributed mesh.

◆ seed()

void dolfin::seed ( std::size_t s )

Seed random number generator

Parameters

s	(std::size_t) Seed value

◆ set_coordinates()

void dolfin::set_coordinates	(	MeshGeometry &	geometry,
		const Function &	position )

Sets mesh coordinates from function

Mesh connectivities d-0, d-1, ..., d-r are built on function mesh (where d is topological dimension of the mesh and r is maximal dimension of entity associated with any coordinate node). Consider clearing unneeded connectivities when finished.

Parameters

geometry	(MeshGeometry) Mesh geometry to be set
position	(Function) Vectorial Lagrange function with matching degree and mesh

◆ solve() [1/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const DirichletBC &	bc,
		const double	tol,
		GoalFunctional &	M )

Solve linear variational problem a(u, v) == L(v) with single boundary condition

◆ solve() [2/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const DirichletBC &	bc,
		const Form &	J,
		const double	tol,
		GoalFunctional &	M )

Solve linear variational problem F(u; v) = 0 with single boundary condition

◆ solve() [3/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const DirichletBC &	bc,
		const Form &	J,
		Parameters	parameters = empty_parameters )

Solve nonlinear variational problem F(u; v) == 0 with a single boundary condition. The argument J should provide the Jacobian bilinear form J = dF/du.

Optional parameters can be passed to the LinearVariationalSolver or NonlinearVariationalSolver classes.

◆ solve() [4/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const DirichletBC &	bc,
		Parameters	parameters = empty_parameters )

Solve linear variational problem a(u, v) == L(v) or nonlinear variational problem F(u; v) = 0 with a single boundary condition.

Optional parameters can be passed to the LinearVariationalSolver or NonlinearVariationalSolver classes.

◆ solve() [5/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const double	tol,
		GoalFunctional &	M )

Solve linear variational problem a(u, v) == L(v) without essential boundary conditions

◆ solve() [6/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const Form &	J,
		const double	tol,
		GoalFunctional &	M )

Solve nonlinear variational problem F(u; v) = 0 without essential boundary conditions

◆ solve() [7/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		const Form &	J,
		Parameters	parameters = empty_parameters )

Solve nonlinear variational problem F(u; v) == 0 without boundary conditions. The argument J should provide the Jacobian bilinear form J = dF/du.

Optional parameters can be passed to the LinearVariationalSolver or NonlinearVariationalSolver classes.

◆ solve() [8/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		Parameters	parameters = empty_parameters )

Solve linear variational problem a(u, v) == L(v) or nonlinear variational problem F(u; v) = 0 without boundary conditions.

Optional parameters can be passed to the LinearVariationalSolver or NonlinearVariationalSolver classes.

◆ solve() [9/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		std::vector< const DirichletBC * >	bcs,
		const double	tol,
		GoalFunctional &	M )

Solve linear variational problem a(u, v) == L(v) with list of boundary conditions

◆ solve() [10/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		std::vector< const DirichletBC * >	bcs,
		const Form &	J,
		const double	tol,
		GoalFunctional &	M )

Solve linear variational problem F(u; v) = 0 with list of boundary conditions

◆ solve() [11/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		std::vector< const DirichletBC * >	bcs,
		const Form &	J,
		Parameters	parameters = empty_parameters )

Solve nonlinear variational problem F(u; v) == 0 with a list of boundary conditions. The argument J should provide the Jacobian bilinear form J = dF/du.

Optional parameters can be passed to the LinearVariationalSolver or NonlinearVariationalSolver classes.

◆ solve() [12/12]

void dolfin::solve	(	const Equation &	equation,
		Function &	u,
		std::vector< const DirichletBC * >	bcs,
		Parameters	parameters = empty_parameters )

Solve linear variational problem a(u, v) == L(v) or nonlinear variational problem F(u; v) = 0 with a list of boundary conditions.

Optional parameters can be passed to the LinearVariationalSolver or NonlinearVariationalSolver classes.

◆ timing()

std::tuple< std::size_t, double, double, double > dolfin::timing	(	std::string	task,
		TimingClear	clear )

Return timing (count, total wall time, total user time, total system time) for given task, optionally clearing all timings for the task

Arguments task (std::string) name of a task clear (TimingClear)

TimingClear::clear resets stored timings
TimingClear::keep leaves stored timings intact

Returns std::tuple<std::size_t, double, double, double> (count, total wall time, total user time, total system time)

◆ timings()

Table dolfin::timings	(	TimingClear	clear,
		std::set< TimingType >	type )

Return a summary of timings and tasks in a Table, optionally clearing stored timings

Arguments clear (TimingClear)

TimingClear::clear resets stored timings
TimingClear::keep leaves stored timings intact type (std::set<TimingType>) subset of { TimingType::wall, TimingType::user, TimingType::system }

Returns Table Table with timings

◆ vertex_to_dof_map()

std::vector< dolfin::la_index > dolfin::vertex_to_dof_map ( const FunctionSpace & space )

Return a map between vertex indices and dof indices

Only works for FunctionSpace with dofs exclusively on vertices. For mixed FunctionSpaces dof index is offset with the number of dofs per vertex.

Parameters

space (FunctionSpace) The FunctionSpace for what the vertex to dof map should be computed for

Returns: std::vector<dolfin::la_index> The vertex to dof map

Variable Documentation

◆ rand_seeded

bool dolfin::rand_seeded = false

Flag to determine whether to reseed dolfin::rand(). Normally on first call.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ FacetIterator

◆ graph_set_type

Enumeration Type Documentation

◆ LogLevel

◆ TimingClear

◆ TimingType

Function Documentation

◆ _orient2d()

◆ _orient3d()

◆ adapt() [1/9]

◆ adapt() [2/9]

◆ adapt() [3/9]

◆ adapt() [4/9]

◆ adapt() [5/9]

◆ adapt() [6/9]

◆ adapt() [7/9]

◆ adapt() [8/9]

◆ adapt() [9/9]

◆ as_type() [1/2]

◆ as_type() [2/2]

◆ assemble_local()

◆ assemble_system()

◆ assign() [1/3]

◆ assign() [2/3]

◆ assign() [3/3]

◆ between()

◆ container_to_string()

◆ create_mesh()

◆ deprecation()

◆ dof_to_vertex_map()

◆ dolfin_error()

◆ dorfler_mark()

◆ dump_timings_to_xml()

◆ error()

◆ get_coordinates()

◆ git_commit_hash()

◆ has_debug()

◆ has_krylov_solver_method()

◆ has_krylov_solver_preconditioner()

◆ has_lu_solver_method()

◆ hash_global()

◆ in_nullspace()

◆ info()

◆ init()

◆ intersect()

◆ ipow()

◆ krylov_solver_methods()

◆ krylov_solver_preconditioners()

◆ linear_solver_methods()

◆ list_krylov_solver_preconditioners()

◆ list_timings()

◆ lu_solver_methods()

◆ mark()

◆ monitor_memory_usage()

◆ near()

◆ norm()

◆ not_working_in_parallel()

◆ p_refine() [1/2]

◆ p_refine() [2/2]

◆ rand()

◆ refine() [1/4]

◆ refine() [2/4]

◆ refine() [3/4]

◆ refine() [4/4]

◆ seed()

◆ set_coordinates()

◆ solve() [1/12]

◆ solve() [2/12]

◆ solve() [3/12]

◆ solve() [4/12]

◆ solve() [5/12]

◆ solve() [6/12]