Reference documentation for deal.II version Git 3f75665 2017-01-19 16:58:38 -0500
Changes between Version 7.2 and 7.3

This is the list of changes made between the deal.II releases listed above. All entries are signed with the names of the author.

### Incompatibilities

Following are a few modifications to the library that unfortunately are incompatible with previous versions of the library, but which we deem necessary for the future maintainability of the library. Unfortunately, some of these changes will require modifications to application programs. We apologize for the inconvenience this causes.

1. Changed: There are various changes to PETScWrappers::MPI::Vector to minimize usage errors and to make the behavior similar to Trilinos: objects with ghost elements are now read-only, the function update_ghost_values() is no longer required (but called automatically if needed). This requires some changes in user code.
(Timo Heister, 2013/02/16)

2. Changed: Over the past few years, deal.II has accumulated a number of things that we would like to change but that would introduce incompatibility. Examples are inconsistent naming of functions or types, or things put into the wrong namespace. In reality, while there are about 100 examples of things we'd like to get rid of, most of them are rather obscure to begin with and will not affect most user code. Nevertheless, as a developer community, we are very careful in making such incompatible changes.

All this said, it is sometimes necessary. We plan to create an incompatible release 8.0 at a later time. To give users a chance to already see which functions need to be changed, we have introduced markers into the deal.II header files that identify which functions, classes or symbols are now deprecated. If your compiler supports this, it will then warn if you are using any of these. The documentation for each of these symbols discusses the recommended alternative, which are in all cases already in place. In other words, you can already change your code in such a way that it compiles both with the current 7.3 release as well as with the future 8.0 release in which these symbols will have been removed.
(Matthias Maier, Timo Heister, Wolfgang Bangerth, 2013/1/5)

3. Changed: deal.II previously had two separate classes, DoFHandler and MGDoFHandler, for standard and multilevel discretizations, respectively. There were also corresponding accessor hierarchies for the cell and face iterators. This turned out to be an obstacle for future developments. Consequently, the functionality of the MGDoFHandler class has been merged into the standard DoFHandler (which already was a base class of MGDoFHandler; moving the functions down in the class hierarchy therefore does not significantly affect how these classes are used). The MGDoFHandler class still exists for now, but is deprecated and will be removed in deal.II 8.0. Use the DoFHandler class instead which has obtained all the functionality of the old MGDoFHandler class.

From a user perspective, there is only one significant change: The old MGDoFHandler::distribute_dofs() function called DoFHandler::distribute_dofs() and then distributed degrees of freedom on all levels of the multilevel hierarchy. In the new scheme, this is now achieved using the function DoFHandler::distribute_mg_dofs(). In other words, where you previously used the class MGDoFHandler and called MGDoFHandler::distribute_dofs(), you should now use the class DoFHandler and call first DoFHandler::distribute_dofs() and then DoFHandler::distribute_mg_dofs().
(Markus Bürg, Timo Heister, Guido Kanschat, 2013/01/03)

4. Removed: The Triangulation and DoFHandler classes had a great number of functions that allowed to get the first and last iterators to cells, faces, lines, quads and hexes overall and on each level of the mesh hierarchy individually. While conceptually a nice idea to offer such a rich set of functions, there are two factors that led us to drastically reduce this set of functions: (i) A large interface makes it more difficult to fully document what every function is doing and more difficult to find what one is looking for. (ii) A large interface makes it incredibly difficult to evolve the data structures on which these functions operate. We felt that the many functions we have impeded our ability to make changes to the internal storage of data. A survey of the deal.II code base as well as some larger applications also shows that most of these functions are rarely used, if at all.
Consequently, most of these functions have been removed. The only functions that remain are the following (for each of the Triangulation and the various DoFHandler classes):


cell_iterator        begin       (const unsigned int level = 0) const;
active_cell_iterator begin_active(const unsigned int level = 0) const;
cell_iterator        end         () const;
cell_iterator        end         (const unsigned int level) const;
active_cell_iterator end_active  (const unsigned int level) const;



Codes that have previously used functions like begin_active_line etc. to loop over the lines or quads of a triangulation need to be changed to loop over cells, and on each cell loop over the lines or quads of this cell. In most cases we have encountered (in deal.II or its testsuite) this was a rather trivial modification. A case to watch out for is that the old loop over all lines encountered all lines only once whereas one may encounter it multiple times when looping over all cells and then the lines of each cell. This case is easily avoided by flagging each treated line using the user flags associated with lines, quads, and cells.
(Wolfgang Bangerth, 2012/09/22)

5. New: In the past, deal.II used a std::vector of bools in many places to denote component masks (see GlossComponentMask) as well as for block masks (see GlossBlockMask). This was neither descriptive (the data type does not indicate what it is supposed to represent, nor whether the proper size for such an argument would be equal to the number of degrees of freedom per cell, the number of vector components of the finite element, or the number of degrees of freedom in total).
There are now new class types ComponentMask and BlockMask that are used in these places. They are used both descriptively (as a return type of the function FiniteElement::get_nonzero_components indicating the vector components within which a given shape function is nonzero) as well as prescriptively (as input arguments to functions such as those listed in the glossary entry linked to above).
While the descriptive places are not backward compatible (they return a ComponentMask which is not convertible to the std::vector of bools returned before), most of the prescriptive places are in fact backward compatible (because the std::vector of bool that was passed previously can implicitly be converted to an object of type ComponentMask. The sole exception is the function DoFTools::extract_dofs (and its multigrid equivalent DoFTools::extract_level_dofs) that previously could interpret its argument as either a component or a block mask, depending on a boolean flag. This function now exists in two different versions, one that takes a ComponentMask and one that takes a BlockMask. Call sites need to be adjusted.
(Wolfgang Bangerth, 2012/09/22)

6. Removed: the optional argument offset got removed from DoFHandler and MGDoFHandler::distribute_dofs() because it was never working correctly and it is not used.
(Timo Heister, 2012/09/03)

### General

1. Changed: parallel sparse matrices now also require the use of compress(VectorOperation) like vectors do. See the glossary for details. Old functions are now deprecated.
(Timo Heister, 2013/02/25)

2. New: step-49 demonstrates advanced techniques for mesh creation and manipulation.
(Timo Heister, 2013/02/19)

3. Fixed: Many places in the documentation have been made to consistently use doxygen markup that indicates that this is code, so that doxygen will cross-link the piece of code to class and function names. Many typos have also been fixed.
(Felix Gruber, 2013/02/15)

4. Fixed: Starting in release 7.1, we first built the deal.II shared libraries in the local /tmp or similar directory rather than the final location because linking becomes very slow over remotely mounted file systems. Unfortunately, this schemes turns out not to work under Cygwin on Windows systems: executables cannot link with libraries that have been moved/renamed after linking. If we are running on Cygwin, we therefore revert to the old scheme.
(Wolfgang Bangerth, 2013/02/11)

5. New: finite element FE_Q_DG0 that implements polynomials of order k with an additional discontinuous constant function.
(Daniel Arndt, Timo Heister, 2013/01/07)

6. step-6 now uses ConstraintMatrix::distribute_local_to_global() instead of condense(), which is the preferred way to use a ConstraintMatrix (and the only sensible way in parallel).
(Timo Heister, 2012/11/02)

7. Simplifications of the internal structures of Triangulation and DoFHandler, in particular removal of specializations.
(Guido Kanschat, 2012/09/13)

### Specific improvements

1. Fixed: The ArpackSolver interface to the ARPACK eigenvalue solver could not be compiled with newer C++ compilers. This is now fixed.
(Juan Carlos Araujo Cabarcas, Wolfgang Bangerth, 2013/02/20)

2. New: PETScWrappers::MPI::BlockVector now has a constructor and reinit that takes a std::vector<IndexSet> (same interface as in Trilinos).
(Timo Heister, 2013/02/19)

3. New: PETScWrappers::*Matrix::add(other, factor) to add a scaled other matrix to the current matrix.
(Jose Javier Munoz Criollo, 2013/02/19)

4. New: GridGenerator::extrude_triangulation() allows you to extrude a 2d mesh to turn it into a 3d mesh.
(Timo Heister, 2013/02/16)

5. PETScWrappers::Vector::operator= and PETScWrappers::MPI::Vector::operator= now call update_ghost_values() automatically if necessary. This means that update_ghost_values() does not need to be called from user code at all any more.
(Timo Heister, 2013/02/14)

6. Fixed: VectorTools::interpolate did not work properly in 1d if boundary indicators had been set to anything but the default (i.e., zero at the left and one at the right end of the domain). This was a hold-over from the past when these were the only possible values. This is now fixed.
(Kevin Dugan, Wolfgang Bangerth, 2013/02/14)

7. Improved: The iterator class of the deal.II SparseMatrix class and SparsityPattern have been revised for performance. Iterating over a row of the matrix and querying the column index and the value is now similarly fast as iterating over a vector.
(Martin Kronbichler, 2013/02/12)

8. New: A new overload of BlockMatrixBase::add allows to add one block matrix to another, with a scaling factor.
(Jean-Paul Pelteret, 2013/02/05)

9. Fixed: The FEValues machinery silently accepted the case when the mapped cell (or the cell geometry) were distorted. An assertion has been added to the computation of the Jacobian determinants for the volume element that aborts whenever the Jacobian determinant in a quadrature point becomes too small or negative.
(Martin Kronbichler, 2013/01/18)

10. Improved: SLEPcWrappers:: The interface to SLEPc has an improved handle on SolverControl and solver data can now be extracted at run time. An example usage has been added to step-36.
(Toby D. Young, 2013/01/18)

11. Fixed: Various variants of the TrilinosWrappers::SparseMatrix::reinit functions take a parameter drop_tolerance that allows to remove small values from the matrix and replace them by zero instead. This was not enforced for values on the diagonal of the matrix but only for off-diagonal ones. This is now fixed.
(Wolfgang Bangerth, 2013/01/17)

12. New: All vector classes should now have a in_local_range() function indicating whether a given index is locally stored or not.
(Daniel Arndt, 2013/01/14)

13. Fixed: The one-argument version of ConstraintMatrix::condense was not prepared to deal with parallel vectors. This is now fixed.
(Daniel Arndt, Wolfgang Bangerth, 2013/1/9)

14. New: Utilities::int_to_string can now deal with any 32-bit integer, not just those with up to 6 digits.
(Wolfgang Bangerth, 2013/1/5)

15. New: The PETScWrappers::MatrixBase::write_ascii() now takes a (defaulted) argument allowing to select the PETSc Viewer style.

16. New: The PETScWrappers::MPI::Vector::print() function overloads the function of same name in the base class to ensure that the output generated by a parallel vector makes sense.

17. New: The PETScWrappers::VectorBase class now has a function PETScWrappers::VectorBase::write_ascii() that allows writing the vector's data to the default output stream.

18. Fixed: PETScWrappers::SparseDirectMUMPS forgot to release its memory upon destruction. This is now fixed.
(Alexander Grayver, 2012/12/12)

19. Fixed: Using the copy constructor of FESystem led to trouble down the road because some pointers were freed by the copy while still in use by the original object. This is now fixed.
(Timo Heister, Wolfgang Bangerth, 2012/12/03)

20. Improved: GridTools::make_periodicity_constraints substantially: The low level interface now allows to specify a face orientation that will be used when matching and constraining DoFs for periodic boundary conditions. With that, the high level interface will work correctly on (mainly 3d) grids that have cells in non standard orientation.
(Matthias Maier, 2012/12/01)

21. Fixed: Fix GeometryInfo<2>::child_cell_on_face to respect face_flip
(Matthias Maier, 2012/12/01)

22. New: There is now a version of DoFTools::make_zero_boundary_constraints() that accepts a boundary indicator as argument.
(Wolfgang Bangerth, 2012/11/25)

23. Fixed: The DoFTools::make_flux_sparsity_pattern() function had a bug that triggered in 1d whenever there were neighboring cells that differed in refinement level by more than one. This is now fixed.
(Wolfgang Bangerth, 2012/11/20)

24. Improved: The inner product, norm, and mean value computation of deal.II's own Vector class are now parallelized by threads. The parallelization does not change the order in which the additions take place, ensuring exact reproducibility from one run to the next.
(Martin Kronbichler, 2012/11/18)

25. New: The TrilinosWrappers::PreconditionBase class now has a function TrilinosWrappers::PreconditionBase::Tvmult that allows applying the transpose preconditioner.
(Guido Kanschat, 2012/11/04)

26. New: The parallel::distributed::Triangulation::n_global_levels() function returns the maximal refinement level over all involved processors.
(Timo Heister, 2012/11/04)

27. New: In addition to the regular subdomain ids (see GlossSubdomainId) there is now a second set of flags called "level subdomain ids" that also assigns a subdomain to every cell in a multigrid hierarchy.
(Timo Heister, 2012/11/04)

28. Changed: GridOut::write_xfig has been improved in a number of ways. In particular, one can now color cells based on a number of different criteria that can be set in GridOutFlags::XFig.
(Guido Kanschat, 2012/11/04)

29. The class Utilities::MPI::MPI_InitFinalize now also initializes PETSc, when PETSc is installed.
(Timo Heister, 2012/11/02)

30. Fixed: DoFTools::make_flux_sparsity_pattern wasn't prepared to deal with adaptively refined meshes in 1d.
(Wolfgang Bangerth, 2012/10/30)

31. New: Added PETScWrappers::PreconditionParaSails and PETScWrappers::PreconditionNone. PETScWrappers::PreconditionParaSails implements the interface to use the ParaSails sparse approximate inverse preconditioner from the HYPRE suite. ParaSails supports parallel distributed computations and can handle nonsymmetric and also indefinite problems. PETScWrappers::PreconditionNone implements non-preconditioning in PETSc which can be of use together with the PETScWrappers::MatrixFree class.
(Martin Steigemann, 2012/10/26)

32. New: The PETScWrappers::SparseDirectMUMPS class now allows to exploit symmetry of the matrix, using the PETScWrappers::SparseDirectMUMPS::set_symmetric_mode() function.
(Alexander Grayver, 2012/10/23)

33. Fixed: Several static const member variables of the Accessor classes were not properly instantiated. This only rarely created trouble because they are typically only used as template arguments and the compiler substituted them. However, one would get linker errors when passing around a reference to them. This is now fixed.
(Wolfgang Bangerth, Guido Kanschat, 2012/10/11)

34. Fixed: Handle lucky breakdowns in GMRES/FGMRES.
(Bärbel Janssen, Timo Heister, 2012/10/09)

35. Fixed: GridTools::find_cells_adjacent_to_vertex got into trouble with anisotropically refined meshes. This is now fixed.
(Abner Salgado, Tobias Leicht, Wolfgang Bangerth, 2012/10/08)

36. Fixed: FESystem can now deal with n_elements==0 for a block.
(Timo Heister, 2012/09/28)

37. Fixed: ParameterHandler::print_parameters, when using ParameterHandler::OutputStyle::LaTeX would always print a list of parameters in each section as a latex itemized environment. However, if there are none, we end up with an empty list which latex does not like. This is now fixed.
(Wolfgang Bangerth, 2012/09/27)

38. New: Added SparsityTools::distribute_sparsity_pattern() for BlockCompressedSimpleSparsityPattern. This allows parallel computations with distributed::Triangulation and PETScWrappers::MPI::BlockSparseMatrix.
(Timo Heister, 2012/09/25)

(Timo Heister, 2012/09/25)

40. New: There is now a function hp::FECollection::n_blocks() in analogy to the existing function hp::FECollection::n_components().
(Wolfgang Bangerth, 2012/09/20)

41. Changed: step-8 now outputs data in VTK format, rather than GMV. GMV has long been dead.
(Wolfgang Bangerth, 2012/09/19)

42. Fixed: One can compile deal.II with MPI support but run programs that aren't intended to use parallel communications and that, in fact, do not call MPI_Init at all. They are nevertheless supposed to work but previously the TimerOutput would crash under these conditions. This is now fixed.
(Timo Heister, Wolfgang Bangerth, 2012/09/18)

43. Fixed: If you pipe content into the deallog object and there is no end-line or flush after this content, and if a file stream is associated to this object, and if that happens at the end of the lifetime of the program, then the program would crash. This is now fixed.
(Timo Heister, Wolfgang Bangerth, 2012/09/17)

44. Fixed: The use of TableHandler::set_precision affected not only the precision with which elements of a table were printed, but also the precision carried by the output stream after writing the table was finished. It thus affected the precision with which later output was produced. This is now fixed.
(Timo Heister, 2012/09/16)

45. Fixed: Output of super-columns in TableHandler::write_text() was inconsistent. This is now fixed.
(Timo Heister, 2012/09/16)

46. Changed: Due to incompatibilties with some hdf5 packages installed from repositories we disable auto-detection of hdf5. Use –with-hdf if you need it.
(Timo Heister, 2012/09/14)

47. New MeshWorker::LocalIntegrator and integration_loop() provide a less confusing interface to MeshWorker loops.
(Guido Kanschat, 2012/09/13)

48. New: TableHandler TextOutputFormat::simple_table_with_separate_column_description that skips aligning the columns for increased performance.
(Timo Heister, 2012/09/10)

49. Fixed: The Clang C++ compiler had some trouble dealing with obtaining the return value of a Threads::Task object, due to a compiler bug in dealing with friend declarations. This is now fixed.
(Wolfgang Bangerth, 2012/09/04)

50. Fixed: When applying a ConstraintMatrix to a block matrix where the last few rows are empty, we ran into an unrelated assertion. This is now fixed.
(Jason Sheldon, Wolfgang Bangerth, 2012/09/04)