Dune 2.3.1

Download the Dune 2.3.1 module sources

DUNE 2.3.1 - Release Notes

  • All modules compile with GCC 4.9 and Clang 3.4.

Build system

  • Support for CMake 3.0

dune-common

  • Tab completion for dunecontrol
  • Use std::chrono::high_resolution_clock for the Timer class to improve scalability (see this bug).
  • Fix handling of ParMETIS flags.
  • Several fixes for PoolAllocator

dune-geometry

  • Fix evaluation of Jacobian at tip of pyramid (see this bug).

dune-grid

  • Several minor fixes and improvements if used with CMake.

dune-istl

  • Improve support for SCOTCH, a ParMETIS replacement.
  • Fix bug in block tridiag solver.

dune-localfunctions

No mentionable changes.

dune-grid-howto

No mentionable changes.

dune-grid-dev-howto

No mentionable changes.

DUNE 2.3.0 - Release Notes

  • All modules compile with g++ 4.7, 4.8 and Clang 3.1, 3.2, 3.3.

buildsystem

  • The deprecated build system macro DUNE_CHECK_ALL_M has been removed. Please use DUNE_CHECK_ALL instead.
  • As an experimental feature CMake is supported as a replacement for the current buildsystem based on autotools. It is still undecided when DUNE will switch, how long the transition period will be or whether this switch will happen at all (see this bug). dunecontrol enables CMake when the flag --use-cmake is set, everything is built in the module’s default build directory build-cmake.

dune-common

  • The file diagonalmatrix.hh containing the class of the same name has been moved from dune-istl to dune-common, since it is now used from the dune-geometry module.
  • There is a new file power.hh, which collects various compile-time power methods.
  • The files collectivecommunication.hh mpicollectivecommunication.hh mpiguard.hh mpihelper.hh mpitraits.hh have been moved to the directory dune/common/parallel (see this bug).
  • The macro DUNE_UNUSED_PARAMETER marks intentional unused function parameters to get rid of compiler warnings.
  • Hash support is provided by dune/common/hash.hh.
  • An adapter Dune::singleton to turn a class into a singleton was added.
  • The macro DUNE_CONSTEXPR is defined as constexpr, if supported by the compiler, and empty otherwise.
  • The semantics of Dune::PoolAllocator have changed. It now has an internal state (the pool) and thus is not fully usable for non C++11 containers.
  • There is a new communicator (VariableSizeCommunicator) for the parallel index sets. Its communication methods are more adapted to the communication interface of dune-grid. It is usable for implementing these methods by using the mapping of entities to local and global indices and the partition information.

Deprecated and removed features

  • FieldVector::size is now a method rather than an enum value. This makes FieldVector more compliant with the stl conventions for container classes. The configure flag --enable-fieldvector-size-is-method has been removed as its purpose was to ease the transition. If you need the container size as an enum value use FieldVector::dimension.
  • The class Power_m_p from the file misc.hh has been deprecated. Use the new class StaticPower from the new file power.hh instead.
  • The geometrytype.hh and geometrytypeindex.hh files, backward-compatibility headers for <dune/geometry/type.hh> and <dune/geometry/typeindex.hh>, have been removed. Please use type.hh and typeindex.hh directly.
  • The deprecated finitestack.hh file has been removed. Please use std::stack<Dune::ReservedVector> instead of the FiniteStack class.
  • The class SelectType (from typetraits.hh) has been deprecated. Please use the new class conditional instead, which does the same thing, but can be used like the corresponding one from the C++11 standard library.
  • Similarly, we have deprecated TypeTraits::isPointer, TypeTraits::isReference, TypeTraits::PointeeType, and TypeTraits::ReferredType. Please use is_pointer, is_lvalue_reference, remove_pointer, remove_reference, (respectively) instead.
  • The file misc.hh is deprecated. Most math-related stuff has moved to math.hh. The two methods hasPrefix and hasSuffix are now in the new header stringutility.hh. The methods SQR and genFilename disappear with no replacement.
  • Support for very old MPI implementations is now deprecated, specifically implementations without support for the MPI-2.1 standard. This should affect very few users because all common MPI packages have been compatible with that standard since 2009.

dune-geometry

  • The method ReferenceElement::geometry returns the (affine) embedding of subentities into the reference element. It uses an AffineGeometry to interpolate the vertex positions of the subentity.
  • AxisAlignedCubeGeometry, a new implementation of the Geometry interface has been added. As expected, it implements the geometry for axis-aligned hypercubes of arbitrary dimension and codimension. Since such hypercubes have a lot of structure, the implementation is very fast.
  • Similarly, AffineGeometry implements the Geometry interface for affine geometries. In affine geometries the Jacobian of the map to the reference element is constant. Using this can result in more efficient code (thanks to Martin Nolte).
  • A reimplementation of the generic geometries, named MultiLinearGeometry has been added. It comes without a complicated TMP and abandons the use of dynamic polymorphism in the case of multiple geometry types. Despite these simplifications, it shows slightly better performance.
  • A new class CompositeQuadratureRule allows to build composite quadrature rules by refining a reference element and using a given other quadrature rule for each subelement. Due to some limitations of the virtual refinement mechanism, this currently only works for simplex elements.
  • Virtual refinement moved from dune-grid to dune-geometry.
  • Gauss-Lobatto quadrature rules added without external dependencies.
  • The enumeration values Gauss, Jacobian_1_0, and Jacobian_2_0 used to denote 1d numerical quadrature rules have been replaced by the more informative names GaussLegendre, GaussJacobi_1_0, and GaussJacobian_2_0. For a transitional period, the old names are still available. Note: It is impossible to mark enum values as deprecated. After the next release the old names will disappear without a warning from the compiler.

Deprecated and removed features

  • The methods ReferenceElement::global have been deprecated; use ReferenceElement::geometry< codim>( i ).global instead. The non-interface method ReferenceElement::mapping, which is superceded by the global method, has been deprecated, too.
  • The classes GenericReferenceElement* are renamed as ReferenceElement*. The old names are deprecated and will be removed after Dune 2.3.
  • Many functions and constructors using topologyId as an argument were removed which were deprecated in Dune 2.2. In many cases a replacement, with Dune::GeometryType as an argument, has to be used.
  • The support for ALGLIB has been removed.
  • The method volumeOuterNormal on the ReferenceElement has been renamed to integrationOuterNormal. It has always actually returned the outer normal to a face whose length coincides with the integration element of the face. The old name is now deprecated and will be removed after Dune 2.3.
  • The class MockGeometry has been deprecated and will be removed in Dune 2.3. Use the new MultiLinearGeometry instead. In most cases, replacing MockGeometry by MultiLinearGeometry and adapting the includes will do.
  • The method initializeTopology of the class ReferenceElement has been deprecated and will disappear after the 2.3 release. There is no replacement, you are not supposed to call such a method at all.
  • The enumeration value Invalid_Rule, from the set of all possible one-dimensional rules, has been removed. There is no replacement.

dune-grid

  • The EntitySeed now has a default constructor (see this bug). A state of an EntitySeed can now be checked using the method isValid(). After default construction the state is not isValid().
  • As all other facades classes in the Dune grid interface. Grid implementors can access the mutable and const EntitySeed implementation via Grid::getRealImplementation (see this bug).
  • The type Jacobian exported by Geometry has been renamed to JacobianInverseTransposed. The old type is still there for backward compatibility.
  • The types JacobianTransposed and JacobianInverseTransposed are now set by the Geometry implementations. Previously they were hardwired to be FieldMatrices of the proper size. The change allows to use special purpose data types for, e.g., structured grids, resulting in quite a bit of speed-up. It means, though, that you cannot rely on the Jacobians to be FieldMatrices anymore. The precise interface requirements for these matrices is still being worked out.
  • GeometryGrid now uses the new MultiLinearGeometry instead of the generic geometry implementation.
  • There is a new class GmshWriter, which allows to write grids in the native format of the gmsh grid generator.
  • EntitySeed now has a default constructor, this is especially helpful if you want to store sets of EntitySeeds in an std::vector, or a similar container.
  • Grids have new methods leafGridView and levelGridView. These behave just like the corresponding leafView and levelView methods, respectively. Their advantage is that the names correspond to the method return types, which are LeafGridView and LevelGridView, respectively. The old methods will be deprecated eventually.
  • The persistent container interface was cleaned up, some methods are deprecated.
  • When the new flag --enable-extra-utils is set, the utility programs in src/ are built.

UGGrid

  • You need to have at least UG-3.9.1-patch9 now to use UGGrid.
  • If you have even UG-3.9.1-patch10 installed, UGGrid provides dynamic load-balancing for vertex data. Thanks to Bernd Flemisch.
  • UGGrid can do face and edge communication now. Thanks to Bernd Flemisch.
  • Parallel UGGrid implements edge ids now.

Deprecated and removed features

  • The transition headers for the headers moved to dune-geometry were removed. Mostly quadrature rules and the generic reference element are affected.
  • Virtual refinement moved to dune-geometry and is deprecated in dune-grid.
  • The classes ALUCubeGrid, ALUSimplexGrid, and ALUConformGrid have been marked deprecated. Use instead the new class ALUGrid and specialize it with cube or simplex and nonconforming or conforming from <dune/grid/alugrid/common/declaration.hh>. More details
  • The struct VTKOptions has been removed, it was alreadey deprecated in Dune 2.1. Use VTK::ascii, VTK::base64, VTK::appendedraw instead of VTKOptions::ascii, VTKOptions::binary, VTKOptions::binaryappended. Most of the issues will be resolved by executing

    for i in `find . -name \*.[ch][ch] | xargs grep VTKOption | cut --delimiter=":" -f 1`; do
     sed "s/VTKOptions/VTK/g" $i> tmp && mv tmp $i
    done
    for i in `find . -name \*.[ch][ch] | xargs grep binary | cut --delimiter=":" -f 1`; do
      sed "s/VTK::binary/VTK::base64/g" $i> tmp && mv tmp $i
    done
    for i in `find . -name \*.[ch][ch] | xargs grep binaryappended | cut --delimiter=":" -f 1`; do
     sed "s/VTK::binaryappended/VTK::appendedraw/g" $i> tmp && mv tmp $i
    done
             
  • The interface methods ilevelbegin/ilevelend and ileafbegin/ileafend on the Entity have been deprecated and will be removed after Dune 2.3. Use the methods ibegin/iend on the corresponding grid view to obtain the intersection iterators.

  • The classes HierarchicIterator, LeafIterator, LevelIterator, and their header files have been deprecated and will be removed after Dune 2.3. Use the EntityIterator interface instead.

  • The type ctype and the integer dimensionworld exported by the Entity facade class are deprecated now, and will be removed eventually. They give geometrical information, which is not supposed to be known to a topological object like the Entity. Please use Geometry::ctype and Geometry::coorddimension instead.

  • Two constructors of YaspGrid have been deprecated. These took the number of elements in a FieldVector<int> and the periodicity in a FieldVector<bool>. In their place, the corresponding constructors taking array<int> and std::bitset are to be used.

Changes for maintainers of grid implementations

  • There is now an interface class EntitySeed, which forward calls to an implementation specific engine class. From now on users of grids only get this interface class, and not the engine directly. This brings EntitySeed in conformance with the rest of the grid interface. Implementors of grids may need to tweak their implementations a little.

dune-istl

  • UMFPACK is a new linear solver backend. It is a direct solver which in some cases is faster up to factor of six compared to SuperLU.
  • BCRSMatrix has a new build mode called implicit. It may reduce memory usage and computation time. Some problematic but rare corner cases for setting up BCRS matrices are now forbitten for all build modes.
  • There is a new implementation of a sequential algebraic multigrid method (FastAMG), that better utilizes the memory bandwidth.
  • We have added a generalized conjugate gradient method (GeneralizedPCGSolver), that allows for using preconditioners whose behaviour might change from step to step.

Deprecated and removed features

  • All transition headers which included parallel headers were removed. The original headers were moved to dune/istl/parallel or dune-common in Dune 2.1, use these instead.
  • Matrix::transposedMult was removed, it was deprecated in Dune 2.2. Use Matrix::mtv instead.
  • The file diagonalmatrix.hh containing the class of the same name has been moved from dune-istl to dune-common, since it is now used from the dune-geometry module.

dune-localfunctions

  • Support for Lagrangian shape functions of arbitrary order on cubes of dimension 1, 2, and 3 has been added (thanks to Matthias Wohlmuth).
  • Support for first-order dual mortar basis functions for simplices and cubes of any dimension has been added (thanks to Jonathan Youett).
  • Rannacher-Turek elements in 3d have been implemented (thanks to Christoph Gersbacher).
  • Support for Brezzi-Douglas-Marini elements of first order in 3d for cubes and of second order in 2d for simplices and cubes have been added (thanks to Human Rezaijafari). The interpolation operator is not or not properly implemented for these elements.
  • Raviart-Thomas elements have a new and more convenient naming scheme. Use the new headers <dune/localfunctions/raviartthomas/raviartthomascube.hh>, <dune/localfunctions/raviartthomas/raviartthomassimplex.hh> and the new classes RaviartThomasCubeLocalFiniteElement and RaviartThomasSimplexLocalFiniteElement instead of the deprecated ones.

Deprecated and removed features

  • The header <dune/localfunctions/lagrange/q22d.hh>, deprecated in Dune 2.2, has been removed. Please use the more general <dune/localfunctions/lagrange/qk.hh> instead.
  • The header <dune/localfunctions/lagrange/q2.hh> has been deprecated. Again, please use the more general <dune/localfunctions/lagrange/qk.hh> instead.
  • The support for ALGLIB has been removed. Some of its features are provided by GMP. Some others, like Lobatto points for Lagrangian shape functions, are no longer provided.
  • The class RannacherTurek2DLocalFiniteElement<D, R> is deprecated and will be removed after Dune 2.3. Please use RannacherTurekLocalFiniteElement<D, R, 2> instead.

dune-grid-howto

dune-grid-dev-howto

  • The whole module is deprecated and will be removed. IdentityGrid will be moved to dune-grid until the next release.

Known Bugs

  • Our drop-in replacement of std::shared_ptr differs slightly from the official implementation. With Dune::shared_ptr only the destructor of the base class A will be called in the following example:
struct A{...};
struct B:public A{...};
void voo()
{
  shared_ptr<A> p = shared_ptr<A>(new B);
}

In contrast the shared_ptr in (std|std::tr1|boost) will call the destructor of B even if it is not virtual. We intend to resolve this issue only implicitly by eventually discarding our own reimplemention of shared_ptr: * The pseudo inverse used in the generic geometries might fail for nearly singular matrices. This is not really a problem unless the grid is nearly degenerate. * The parallel UGGrid may return wrong ids on very complex adaptively refined and load-balanced grids. The reason is that the Dune grid interface mandates that two entities on different levels have the same id if they are copies. Therefore the UGGrid id/subId methods look through the ancestry of a given entity to see if there are copies. However, UG does so-called vertical load-balancing, which means that the ancestry may be distributed across different processors. Since the current code does not take that into account, wrong ids will be returned in the presence of vertical load-balancing. This is a potentially severe issue, because users do not get error messages, only ids that are tacitly wrong. * PoolAllocator is a stateful allocator and therefore not usable with containers according to standard before C++11. * Building shared libraries with CMake might break if you are using external static libraries compiled without support for position independent code (g++ -fpic).

A list of all bugs can be found online in our bug-tracker http://www.dune-project.org/flyspray/.

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