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NEWS
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1.5.1 -> 1.6.0
* Exodus/Nemesis
- Add MappedOutputVector/MappedInputVector classes for single-precision I/O
- Add support for reading edgesets
- Improve ElementMaps and reduce copy/paste bolierplate
- Call newer exII::ex_put_concat_all_blocks(), ex_get_block(), ex_get_ids(), etc. APIs
- Avoid unnecessary localize in Nemesis write_nodal_data()
- Better error message when invalid node id is found in nodeset
- Handle complex variables in write_element_data_from_discontinuous_nodal_data()
- Make writing the complex modulus optional
- Add capability to load elemental variables into element IDs
- Add ExodusII_IO::read_header() and unit test
- Respect empty output names in NemesisIO
- Fixes for appending to Nemesis files
- Preserve ordering of nodal variables in NemesisIO
- Explicitly delete copy/move assignment operators in ExodusII_IO_Helper
- Add support for reading nodeset variables
* Add DiagonalMatrix, a SparseMatrix which uses a NumericVector for storage
* FEMap
- Put mapping methods into mapping classes
- Move MappingType out of Elem
- Add first rational mapping unit test
- Respect non-LAGRANGE maps with C1 elements
* FE
- Remove some explicit instantiations and related macros
- Refactor/optimize 1D Lagrange shape(), shape_deriv(), shape_second_deriv() calls
- Add second derivatives for Bernstein FEs
- Add some FE tests at fourth order
- Allow GenericProjector to work with vector finite elements
- InfFE: Add new shape()-API; Change API for shape_ptr and its derivs
- Skip redundant resize in init_shape_functions
- Add FE::shape_derivs(), shapes(), all_shapes() APIs
- Extend FEMap optimizations to 0D+1D+2D
- Explicitly use FEAbstract::get_nothing() to avoid all FE computations
- Add 'extra_checks' parameter to FEMap::inverse_map()
- Add dual shape functions (dual_phi, dual_dphi, and dual_d2phi) in FEBase
- Add new FEInterface::n_dofs() APIs taking Elem pointers
- Add new FEInterface::n_dofs_at_node() APIs taking Elem pointers
- Add new FEInterface::n_dofs_per_elem() APIs taking Elem pointers
- Add new FEInterface::n_shape_functions() APIs taking Elem pointers
- Add new FEInterface::shape() APIs taking Elem pointers
- Add new FEInterface::ifem_ APIs taking Elem pointers
* Add unit tests for !contains_point()
* Add/use libmesh_map_find() macro
* Add/use libmesh_vector_at() macro
* DynaIO
- Add mesh reader for BEXT files
- Add unit test of reading 25-element patch file
- Add DynaIO::add_spline_constraints() and unit test
* Add/set SNES divergence tolerance
* Separate headers string_to_enum.h and enum_to_string.h
* Reduced Basis
- Added an option to use the energy inner-product
- Updates for reduced_basis_ex7
- Uncomment RBConstruction::compute_residual_dual_norm_slow() for debugging
- Added extra error checking in rb_data_deserialization.C
- RBConstruction: Add post processing callbacks
- Skip enrichment if RHS norm is exactly 0
- Add support for POD training in RBConstruction
- Update RBConstructionBase<Base>::generate_training_parameters_deterministic()
- Update TransientRBConstruction to not use lapack calls directly
- RBEIMConstruction: Move FE getter calls outside elem loop
- Skip NODEELEMs in assembly
- Add RBEIMConstruction::init_context() override
- Update to post_process_elem_matrix_and_vector() in RBConstruction
- RBConstruction update to store an untransformed basis
- Optionally pre-evalaute theta functions for efficiency
- Fix wrong function call syntax in rb_data_deserialization.C
- Evaluate theta functions at multiple parameters simultaneously
- Early return when there are no training samples
- Major refresh of the EIM framework
- Add support for defining RBParametrizedFunctions based on a look-up table
- Deprecate {RBParameters,RBParametrized}::get_parameter_names()
* Xdr
- Efficiency improvments: restrict iteration, handle ids while parsing
- Reset stream precision after writing an integral value
- Add unit test of Xdr::data(vector)
- Fix access past end of vector in data_stream() implementations
* Update Tetgen to version 1.5.1
* Mesh
- Additional options for adding extra integers+data
- Merge extra integers during copies+submeshes
- Add MeshBase::add_elem(std::unique_ptr<Elem>)
- Add MeshRefinement::add_elem(unique_ptr)
- Add MeshBase::insert_elem(std::unique_ptr<Elem>)
- Add MeshBase::add_node(std::unique_ptr<Node>)
- Add MeshBase::insert_node(std::unique_ptr<Node>)
- Add MeshBase::remove_orphaned_nodes()
- Unit tests for MeshTools::Generation::build_cube()
- Reset ReplicatedMesh::_n_* during clear()
- Many DistributedMesh unique id fixes
- MeshGeneration::build_sphere() DistributedMesh fixes and unit tests
- Use max_node_id to size vectors indexed by node id
- Updates to allow_find_neighbors(true) in prepare_for_use(), find_neighbors()
- allgather() before falling back on Metis
- Preserve extra ints and mapping data in flatten(), all_second_order(), create_submesh(), etc.
* AbaqusIO
- Read .inp files with *Surface sections referring to element sets
- Add string_to_num(), strip_ws() helper functions
- Add support for "MASS" elements and "NODE" sidesets
* TIMPI
- Move parallel* files into contrib/TIMPI submodule
- Use push_parallel_packed_range() in scatter_constraints
- Use TIMPI::communicator to merge LibMeshInit APIs
- Use Communicator::duplicate() correctly
* Allow adaptivity_ex3 to run with more variables
* Misc. bugfixes
- Fixes for compilation with PETSc enabled, MPI disabled
- Copy point locator tolerance in MeshFunction::clone()
- Threading: OverlappingCouplingFunctor, MeshFunction, Clough-Tocher, etc.
- Sync nodes after all_second_order if not replicated
- Add missing PYRAMID cases to l2_lagrange_n_dofs()
- Fixes for --disable-second and other less common build configurations
- Fix all_second_order() for DistributedMesh
- Don't try to enable ParMETIS without METIS
- Add check for nearly coincident nodes when stitching
- Call enforce_constraints_on_residual() using local solution
- Do GHOSTED localizes to ghosted vectors
- Split scraping of PETSc configure and testing the PETSc installation for viability
- Fixes for DistributedMesh unique_id generation
- Fix reverse iterator usage bug in adjoint AMR constraints
- DofMap::add_constraint_row(): assert there is no diagonal entry
- Fix parallel_ghost_sync.h for N->M operations
- Switch boost includes from -I to -isystem to ignore warnings
- Fix valgrind issue with VecSetDM
- Non-proxy sides now have same p_level() as Elem they are built from
- Use std::stable_sort in CentroidPartitioner
- parmetis.m4: Fix potential uninitialized variable
- Avoid calling DofObject::id() when id can be invalid
- Bugfix for sparse QoI constraint cases
- Associate a mesh when adding GhostingFunctor to DofMap
- PeriodicBoundaries fixes for "sharktooth" meshes
- Disambiguating Node constructor should be marked explicit
- Fix subdomain expansion with element DoFs
- Fix indexing in EquationSystems::get_vars_active_subdomains()
- ParsedFunction and ParsedFEMFunction no longer store vectors of
FunctionParserADBase<T> since that class is not MoveInsertible
- Ignore remote elems coming from pbcs in DefaultCoupling
- Rational function shapes_need_reinit is true!
- Delete MeshBase and derived class' move constructors
- Fixes for unit tests in non-standard configurations
- Fix "make install" issue where it was possible to get interactive mv questions
- Move BERNSTEIN HEX27 interior DoFs to node
* pkgconfig
- Remove extra flags from pkgconfig Cflags
- Conditionally add libmesh-*.pc files based on METHODS
* VTK
- Fix mesh reference in VTKIO write
- Try linking to VTK CommonExecutionModel too
- Set data mode to binary when _compress is true
* BoundaryInfo
- Add BoundaryInfo::remove_node(node, id)
- Fix outdated docs
- Add BoundaryInfo::erase_if() helper function
- Add BoundaryInfo::NodeBCTuple typedef
- Control sorting method used in build_node_list(), build_side_list()
- add_elements(): Add flag controlling setting of parent side ids
- Copy name maps in BoundaryInfo::operator=
- Clear BoundaryInfo set names during clear()
- Add methods to synchronize side boundary ids on the fly
* PETSc/SLEPc
- Add support for shell matrices in SLEPc eigenvalue solver
- Use MAT_INPLACE_MATRIX in newer PETSc versions
- Remove support for PETSc < 3.5.x
- Additional PETSc install variant detection
- Allow third-party non-PETSc METIS
- PetscSolverException: use specific error message if available
- Updates to support PETSC 3.13
- Add API to retrieve only eigenvalue when eigenvector is not needed
- Add support for shell preconditioning matrix in EigenSystem
- Add sparse matrix-matrix multiplication and addition
- Check whether nonlinear residual vector and base vector pointers are equal
- Improve EigenSolver initial guess setup
* Add ExactSolution::set_excluded_subdomains() API
* C++ modernization
- Add configure test for and use std::make_shared in library
- Replace more calls to "new" with std::make_shared, libmesh_make_unique
- IntRange helper functions: index_range(), make_range()
- Use range-based for-loops wherever possible
- Add/use vectormap::emplace()
- Add configure tests for std container emplace functions
- Prefer emplace() to insert() for std containers
- Add configure tests for std container emplace_hint()
- Use std::reference_wrapper in several examples
* Use lower-order quadrature in JumpErrorEstimator
* Tree::find_elements() optimizations
* FParser
- Refactor and make JIT code modular
- Update diagnostic pragmas
- eval_mixed_derivatives, eval_at_point skip_context
- Fix JIT disabling
- Disable derivative caching
- Refactor compiled function pointer and pImmed update
- Fix value return in JIT function
* PointLocator: Add tolerance for finding elements
* Add ParallelType to ImplicitSystem::add_matrix() API
* Add fem_system_ex5 demonstrating IGA
* DenseMatrix: Use helper struct to determine whether to use blas_lapack
* Elem
- Copy Elem interior parents during copy construction
- Add Elem::local_side_node()
- Add Elem::local_edge_node()
- Add edge to side map for all Cell-derived types
- Make Edge3::volume() calculation more robust and add unit tests
- Add Quad::quality(TWIST) unit test
- Add Tri::quality(SHAPE) metric
- Elem::simple_build_side_ptr() returning unique_ptr
- Quad4::build_side_ptr() should call simple_build_side_ptr()
- Optimize Elem::find_point_neighbors()
- Add geometric constants for Edge-derived elems
* Add SparseMatrix::clone(), zero_clone() and derived class implementations
* PointLocator: fix BoundingBox intersection test for QuadTree
* Add FileSolutionHistory and test in existing example
* Add DirichletBoundary copy assignment operator
* Add multi-file support to meshtool app
* QGaussLobatto: add fallback on regular Gauss quadrature
* Move some m4 files into an autoconf-submodule for sharing between different projects
* Make "NumericVector localize()" scalable when possible
* Add Lagrange-specific code path to ConstrainDirichlet
* Clean up of deprecated code, support for --disable-deprecated builds
* Clean up strip_dup_libs.pl script which sorts/modifies the list of linker libraries
* TwoStepTimeSolver: add adjoint support
* Add/use libmesh_error_msg_if() macro
* Inline a more efficient implementation of BoundingBox::intersects()
* Add html documentation for several of the newer examples
* Fixes for node balancing algorithms during partitioning
* GhostPointNeighbors optimizations
1.5.0 -> 1.5.1
* Fix compilation with --enable-petsc --disable-mpi
* Fix multithreading bugs in MeshFunction, GenericProjector, tests
* Fix configure summary CPPFLAGS output
* Fix consistency of --enable-curl with NetCDF
* Fix bug in Triangle interface
1.4.1 -> 1.5.0
* Write Exodus files in netCDF-4 format when HDF5 is available.
* Add left multiply (by vector) method to type_tensor
* Update bundled netCDF from version 4.4.1.1 to 4.6.2, remove netCDF-3 source.
* Handle different combinations of METIS/ParMETIS in PETSc.
* Add --enable-capnp-required configure option.
* Add surface-terms and gradients to misc_ex14.
* Infinite elements fixes
-Dimension of the local_transform object corrected
-Allow infinite elements in System::point_gradient()
-Fixed diagonal in InfHex::contains_point()
-Reorganisation in InfFE::init_face_shape_functions()
-Fix memory leak in inf_fe_boundary.C
-Replace unrolled loops in legendre_eval() and jacobi_eval().
* Add _extra_parameters map to RBParameters.
* Add support for PETSc GMG (Boris Boutkov).
-Support complex numbers.
-Unit test coverage.
* ReplicatedMesh::add_elem(): fix missing unique id update.
* Add ability to skip "non-critical" partitioning when updating mesh.
* configure:
-match PETSc 64/32-bit index sizes when possible instead of throwing an error.
-Support SLEPC installed by PETSc.
* Bug fix: Close residual/vector before applying constraints.
* Run fem_sys_ex1 with GMG+FS options.
* Add is_zero() to TypeVector and TypeTensor.
* Bug fix: FEInterface::get_continuity() should take a const reference.
* Add DofMap::swap_dof_constraints() API.
* Add subdomain iteration range objects
-active_subdomain_set_elements_ptr_range
-active_subdomain_elements_ptr_range
-active_local_subdomain_elements_ptr_range
* GmshIO:
-Add support for reading gmsh-4 files.
-Enable reading of meshes with a mix of 1, 2, and 3D elements.
* Drop VecScatterCreateWithData() workaround. This PETSc rename did not happen.
* Add non-blocking exchange (NBX) for pushing/pulling data.
* DenseMatrix:
-Add support for DualNumber.
-Add DenseMatrix::sub_matrix().
* Add outer product for TypeVectors.
* Fix remote_elem copying in UnstructuredMesh.
* Add OverlappingCoupling GhostingFunctor, unit tests.
* Fix 2006 bug with refinement within ES::reinit().
* Bug fix: Don't constrain hanging nodes at variable boundary.
* Rewrite GenericProjector
-Add Lagrange interpolation optimization.
-Fix threading.
-Add unit tests.
* Add "extra integers" support.
-MeshBase::get_*_integer_index API
-MeshBase::add_elem_integer() API
-MeshBase::add_node_integer() API
-Add Systems with extra integers.
-Unit tests
-CheckpointIO support
* Bug fix: Improve NodeElem support in ReplicatedMesh::stitch_meshes().
* Add FEMContext::interior_rate_gradient().
* Drop long-deprecated Elem APIs.
-Elem::node()
-Elem::get_node()
-Elem::neighbor()
-Elem::side()
-Elem::build_side()
-Elem::build_edge()
-Elem::child()
* Bug fix: DofMap::local_variable_indices().
* Several contrib/metaphysicl submodule updates (latest is 0.6.0)
* ExodusII_IO:
-Fix indexing issue in read_elemental_var_values().
-Improve support for scalar variables.
-Read/write all nodesets simultaneously.
-Use nodal map when reading nodal variables.
-Add read_sideset_data()
-Add write_sideset_data()
* Bug fix: avoid NaNs in block restricted vector variables when using PETSc 3.8.3
* Improve diagnostic message when cpr header can't be opened.
* Add Communicator::split_by_type(), unit tests.
* Add support for PETSc-3.11.x.
* Quadrature:
-Don't pass p_level and type as parameters, use class members.
-Use get_order() everywhere instead of passing p_level.
-Add QNodal quadrature class.
-Fix const correctness issue in QJacobi.
-Fix some hard-coded long double precision literals.
-More digits for SEVENTH-order quadrature on TRIs.
* Always add block size for petsc matrix.
* Bug fix: Explicitly call SubFunctor::join() in SortAndCopy::join().
* Re-enable misc ex9 on non-PETSc builds.
* Switch signs of on-diagonal and off-diagonal entries for constraints.
* Ignore -Wstack-protector warnings in 3rd party code.
* Add LOG_SCOPE_WITH macro, supports use of custom PerfLogs.
* Bug fix: Clear old SLEPc solver before solving again.
* Bug fix: PointLocatorTree had bad definition of is_planar_xy
* PetscMatrix:
-Add local_m()
-Add local_n()
-Add get_local_size()
-Add reset_preallocation()
-Make mallocs uniformly an error.
* NumericVector: Add component-wise multiplication operator *=
* TriangleIO improvements:
-Add functions with a unit test for creating a hole from a mesh
-Regions support, toggle Triangle prints
-Add boundary marker capability
-Support disconnected enclosures
* Bug fix: Elem::second_order_equivalent_type().
* Generalize subdomain comparison for var groups.
* Add FEMContext::set_jacobian_tolerance().
* Bug fix: Avoid dangling reference in SparsityPattern::Build
* Bug fix: In FEMap, set 'failing' back to false after print_info().
* Add libmesh_cppunit.h file with unit test boilerplate to unit tests directory.
* Add/improve support for Real == float128 via boost::multiprecision.
* Add MONOMIAL_VEC fe type and associated example.
* Add DofObject::get/set_extra_datum(), non-integer DofObject data.
* If we build METIS ourselves, then install metis.h.
* Bug fix: Set the correct MPI communicator in VTKIO.
* Pedantic debugging flags are now *disabled* by default, use
--enable-glibcxx-debugging to turn them back on.
* Big header file refactoring, reduce header dependencies as much as possible.
* Bug fix: FEXYZ::shape_deriv() of phi_1 in 1D was wrong.
* Add RATIONAL_BERNSTEIN FEType.
* Allow TRI3SUBDIVISION elements in more quadrature rules.
1.4.0 -> 1.4.1
* This is a bugfix release for 1.4.0.
* Correctly identify automake 1.15 as too old
* Close residual/vector before applying constraints
* Capture iterations from PETSc in DiffSolver
* Fix 2006 bug with refinement within ES::reinit()
* Fix remote_elem copying in UnstructuredMesh
* Fix issue with subdomain-restricted variables and hanging nodes (#2099)
* Drop VecScatterCreateWithData() workaround. This did not end up making
it into a release version of PETSc.
* Fix doco in DenseMatrix::right_multiply.
* FEInterface::get_continuity() should take a const reference.
* Fix complex-enabled bug in unit test.
* Fixes for mesh stitching when NodeElems are involved.
* Remove deprecated Elem API calls from misc_ex6.
* Assert consistent ErrorVector values for flagging.
* Restrict adaptivity ex3 max_r_steps.
1.3.1 -> 1.4.0
* BoundaryInfo:
- BoundaryInfo::build_foo_list(): sort vector before returning.
- Warn if user tries to add a boundary id for a non-existent node.
- Add std::tuple-enabled versions of various BoundaryInfo functions
(originals are now deprecated).
* BoundingBox:
- Add BoundingBox::signed_distance().
- Add "fuzzy" BoundingBox::intersects() function.
* C++11 updates.
- Prefer vector::data() to &v[0].
- Use C++11 iterator-returning erase member functions when possible
- Test for and use C++11 std::iota
- Add configure test for std containers with iterating-returning erase.
- Require and test for C++11 std::begin/end support for C arrays.
- C++11 decltype support is now required.
- Default/delete copy/move constructors and assignment operators
in various classes; add unit tests.
- Switch all enumerations to "fixed type" enums with underlying type int.
- Drop usage of libmesh_nullptr, libmesh_final, libmesh_override etc. from library.
* Compiler support:
- Fix trailing return type issue affecting GCC 7.1
- Fix Intel warnings
- Fix warnings discovered in GCC 8.1 and clang 6.1.
- Fix ptrdiff_t/ std::ptrdiff_t incompatibility issue.
* configure tests:
- Many updates to m4 tests including use of standardized autoconf
macros like AS_IF, AS_CASE, etc.
- Fix bug in Trilinos DTK configure test.
- Fix cppunit test, cppunit-config is no longer distributed with cppunit.
- Apply -march/mtune flag when profiling as well.
- Add configure option for turning on/off -Werror.
- Add configure option --enable-paranoid-warnings.
- Add --disable-deprecated configure flag and remove deprecated code.
- Update docs for processor_id_type, the default size is now 4 bytes.
- 1D/2D-only fixes
- Disable HDF5 detection by default.
- Improve support for PGI compiler
- Add support for --enable-march and --with-gcc-arch.
- configure: detect when PETSc is built with support for different partitioners
- Remove --enable-default-comm-world configure option.
- threads.m4: Only error if user requested TBB and it wasn't available.
* DofMap:
- eval_old_dofs needs var, not var_component
- Fix local_variable_indices numbering assumption and add unit test.
- Different constraint enforcement for hanging nodes
- Avoid calling set_dof_coupling() with an empty/non-nullptr CouplingMatrix.
- Add unit test for DofCoupling with variable groups.
- Add optimized DofObject::dof_number() overload.
- Fix copy/paste bug in DofMap::add_neighbors_to_send_list().
- Allow linear transformations between boundaries for periodic BCs with vector variables.
- Support adjacent/overlapping periodic boundary conditions.
- Optimizations/fixes to SparsityPattern::Build::parallel_sync().
- Fix adaptivity bug in which Elements w/o neighbors were treated as unrefined islands.
* FE:
- Add const accessor methods for psi map second derivatives.
- Add const accessor methods for dpsi_maps in FEMap.
- Allow user-defined tolerance for negative Jacobian failures.
- Fix FEInterface bug in which wrong FEType was passed to
shape()/shape_deriv() calls.
- Combine HIERARCHIC/L2_HIERARCHIC and LAGRANGE/L2_LAGRANGE shape
function implementations.
- Enable base-side in InfFE::reinit(elem, side)
- Add unit test demonstrating DGFEMContext assembly.
* for loops:
- Add index_range() helper function for vector loops.
- Convert many traditional for-loops into range-based for loops.
- Remove many lines of iterator boilerplate.
- Cache n_processors() rather than calling it every loop iteration.
* GhostingFunctors
- Add ability to disable default GhostingFunctors.
- Drop one more over-zealous assert when removing GhostingFunctors.
- Miscellaneous GhostingFunctor iteration optimizations.
- Use unordered_set in GhostPointNeighbors functor.
- Don't assert GhostingFunctor presence before removing.
* Elem:
- Add "filling" overloads for side_ptr(), build_side_ptr().
- Add unit tests for Elem::simple_side_ptr().
- Add non-const returning versions of Elem::family_tree_ functions.
- Mark methods final in Elem subclass superclasses.
- Mark new side_ptr functions override to avoid warnings.
- Use stack arrays in Elem::operator==,key() instead of heap vectors.
- Simplify loose_bounding_box for 'bi/tri/linear' elements.
- Add Elem::nodes_on_side() utility function
* Mesh:
- Use only one search in DistributedMesh::add_point()
- Replace buggy "binary search" algorithm with nanoflann-based
algorithm in ReplicatedMesh::stitching_helper().
- Fix failure to sync nodes in some AMR cases
- Fix for --disable-amr builds.
- Move UnstructuredMesh::all_{first,second}_order() functions to correct C file.
- Add version of MeshTools::build_nodes_to_elem_map() that builds a std::unordered_map.
- LaplaceMeshSmoother: restrict smoothing to specified subdomains.
- MeshTools::find_boundary_nodes: Add overload that builds a std::set.
- Fix bug in Evaluable multi-predicate.
- Fix overzealous assertion in UnstructuredMesh::copy_nodes_and_elements()
by wrapping proc ids.
- Add asserts to various MeshTools utilities for DistributedMesh use cases.
* Mesh I/O:
- Acquire BC lists outside the CheckPointIO id loop (optimization).
- ExodusII_IO: Add ability to write more general discontinuous data.
- ExodusII_IO: Fix issue where hide_output() flag was not respected.
- AbaqusIO: support more element type strings.
- NemesisIO: various fixes for writing/reading communication maps (cmaps).
- NemesisIO: add ability to plot ErrorVector.
- Fix bug when writing discontinuous ExodusII files with subdomain-restricted variables.
- Add support for elemental variable writing in Nemeis.
- Fix indexing bug in Nemesis variable hiding code.
- ExodusII_IO: skip writing elemental variables on inactive blocks.
- Fixed bug in discontinuous plotting with Exodus format.
- Fix Exodus solution writing for meshes with node numbering gaps.
- XdrIO::write meshes with discontiguous node ids.
- Improve/generalize configure test for XDR headers.
* MetaPhysicL
- MetaPhysicL is now a git submodule in libmesh. If you configure libmesh
with --enable-metaphysicl, use the submodule version of metaphysicl for
best results.
- Add --enable-metaphysicl-required configure option.
* Partitioners:
- Fix LinearPartitioner on small distributed meshes
- Fix buffer overrun in Hilbert SFC Partitioner.
- Add Partitioner unit tests.
- Add support for different node partitioning strategies
- Allow partitioners to refer to the "original" based on the new local ordering.
- Generalizations to ParmetisPartitioner required for idaholab/moose#11629.
- Factor out Node::choose_processor_id heuristic.
- Tweaks to the way that newly created nodes are partitioned.
- Define USE_GKRAND when building Metis. This is consistent with PETSc's METIS.
- Don't use LIBMESH_TLS in contrib/metis. This is consistent with PETSc's METIS.
* Numerics:
- Laspack fixes
- Move TypeVector::unit into the header.
- Fix issue with constness in LaspackMatrix::add().
- SparseMatrix::add() ref should be const
- Add new PetscNonlinearSolver interface: set_snesmf_reuse_base().
- Make SparseMatrix::add() const correct.
- Add DualNumber to libMesh::CompareTypes
- Avoid modifying solution vector in TaoOptimizationSolver callbacks.
- Add LibMeshVecScatterCreate macro, maintain compatibility with PETSc master.
- PetscMatrix: Add support for MATHYPRE, MatHYPRESetPreallocation.
- Avoid use of MATHYPRE when Hypre is not available or PETSc is too old.
- Disable Trilinos when configured with --with-dof-id-bytes=8
- Add typedef'd index_type in TypeVector, TypeTensor, TypeNTensor.
- Change return type of TypeTensor::operator*
- TypeVector/TypeTensor: make default constructors public.
- TypeTensor: Add operator*=(TypeTenosr&).
- Fix bug with --enable-petsc-hypre-required when PETSc is not found.
- Add PetscDMWrapper for eventual geometric multigrid support.
- Add --require-petsc-hypre configure option.
- NumericVector::operator/= argument is now const reference.
* Parallel:
- Fix bug in Parallel::minloc/maxloc.
- The libmesh_call_mpi() macro now includes #ifdef LIBMESH_HAVE_MPI checks.
- Add PostWaitDereferenceSharedPtr/nonblocking_receive_packed_range().
- Fix MPI Datatype leaks (again).
- Use parallel_sync in Parallel::Sort.
- Add support for StandardType<Tuple>.
- Add PostWaitDereferenceTag class and reference counting for MessageTags.
- Replace old "round-robin" communication algorithm with parallel_sync.
- Use MessageTag in parallel_sync probe calls.
- Split include/parallel headers into several files.
- Drop (attempted) MPI-1 support that was apparently long broken anyway.
* Examples:
- Add new example, systems_of_equations_ex9, demonstrating linear
elasticity with periodic constraints.
- Run examples in the order: "dbg, devel, oprof, opt"
* Miscellaneous:
- GenericProjector: pre-request JxW to fix issue with certain FEs.
- reduced_basis: Fix output data format in legacy SCM writes.
- Homepage: mention Github issues and pull requests
- Utility::hashword is now compatible with both std::array and std::vector.
1.2.1 -> 1.3.0
* Weaken copy_node_and_elements partition assertion.
* Switch to "diagnostic push/pop" calls for GCC to ignore warnings.
* Fix performance issue and bugs in CouplingMatrix row iterators.
* Add --with-thread-model=openmp option, default to pthreads instead of TBB.
* Cache dof indices when computing sparsity (optimization).
* Temporarily skip running fem_system_ex2 due to changes in 3b4b2fb.
* Install the gzstream.h header along with the rest of libmesh.
* Update to latest nanoflann (pre-1.3.0).
* PetscNonlinearSolver:
- Allow user to provid separate fd and mffd evaluation functions.
- Use MatSNESMFSetReuseBase() API.
* Remove libmesh_experimental() from dg_fem_context.C.
* Make nested Parameters::Value public to allow use of the begin()/end() API.
* Remove update() call from FEMSystem::assembly(), call beforehand as necessary.
* Update LICENSE.txt file distributed with Metis.
* Add new shape quality metrics for QUAD4 elements.
* Remove many libmesh_error_msg("We'll never get here.") sections.
* Deprecate raw memory returning Preconditioner::build().
* Drop support for older compilers from DETERMINE_CXX_BRAND.
* JumpErrorEstimator fix for non-zero-norm SCALAR.
* Make LinearPartitioner DistributedMesh-compatible.
* Add System::projection_matrix() which uses MetaPhysicL.
* Add MetaPhysicL 0.2.0 to contrib.
* Avoid repeated function calls in old_dof_indices().
* Add support for detecting Intel 18.
* Break EquationSystems::reinit() into solutions and systems parts.
* Fix check in PetscVector<Complex>::localize_to_one().
* TypeNTensor:
- Add add_scaled() method.
- Add _coords data member.
* Add FEInterface::n_dofs_at_node_function().
* Add the as_range() utility for working with std:: multi containers.
* Fix unit test of writing vector and scalar variables in parallel.
* Infinite Elements:
- Enable second order infinite elements.
- Optimize contains_point() by avoiding inverse_map() calls.
- Change type of "current frequency" to Number.
- Add support for System::point_value().
- DistributedMesh fixes.
- Add miscellaneous_ex14 demonstrating infinite element use with complex frequencies.
* Use node_ref_range(), neighbor_ptr_range(), side_index_range(), etc. in loops.
* EigenSolver: don't always close() matrix before solve.
* Add --disable-deprecated configure option.
* Add support for SHELL8 elements, which are basically treated as QUAD8s.
* Avoid n_children() calls in for-loop bodies, use range-based loops.
* Add potential early return from refine_and_coarsen_elements().
* Add SparseMatrix::flux() API.
* Fix bug with XDR output of 64-bit int, long.
* Move libmesh library PATH to beginning of 'libmesh-config --libs'.
* Fix many documentation typos, spelling errors, etc.
* Add backward-compatible support for [[fallthrough]] attribute.
* Add Parallel::allgather(vector<string>) overload.
* TetGenIO: Update code for reading .ele files.
* Use the base class version of greedy_termination_test in RBEIMConstruction.
* Pass sanitizer flags when both compiling and linking.
* DofMap:
- Add dof_owner() search.
- Add semilocal_index().
- Add check for cyclic constraints.
* Disable dlopen(), getpwuid() when doing all-static linking.
* Mesh:
- Add is_serial_on_zero().
- Add set_distributed().
- Optimizations/bug fixes in stitch_meshes().
- Add various element_ptr_range(), node_ptr_range() to facilitate range-based for-loops.
- Fix constructor bug where _count_lower_dim_elems_in_point_locator was uninitialized.
* Add constructor to FEMContext for specifying extra_quadrature_order.
* Build system changes for compiling on Windows with MSys2.
* Write version to reduced basis Xdr headers.
* Avoid redundant init of old, older System vectors.
* Make SparseMatrix::close() non-const, avoid calling it on const objects.
* Set LIBMESH_HAVE_EXTERNAL_BOOST if an external boost is found.
* PerfLog:
- Add getter for underlying PerfLog data structure.
- Use const char * instead of std::string for speed.
- Add PerfData::pause_for().
* Fixes for coarsening of adaptively-refined DistributedMeshes.
* Add DenseVector(N, value) constructor.
* Improvements to src/apps/meshdiff.C
* Doxygen:
- Use \deprecated and \returns flags in documentation.
- Add client-side search boxes on Doxygen pages.
* Disallow renumbering when plotting ErrorVector.
* Fixes to AdjointRefinementErrorEstimator in FEMSystem with lift function.
* Add adjoints_ex6.
* Fixes in UnstructuredMesh::find_neighbors().
* Use new APIs in fem_system_ex1.
* Fparser
- Add support for "erf" in parsed function strings.
- Avoid race condition on asynchronous networked filesystems.
- Close file descriptors returned by mkstemp.
- Add registered derivatives to hash.
* Miscellaneous fixes for non-standard configurations.
- --disable-exodus
- --disable-amr
- --disable-fparser
- --disable-mpi
- --disable-optional
- --disable-exceptions
* C++11:
- LibMesh now requires a C++11-conforming compiler.
- The last C++03 commit is 613c152f0, tag:cpp03_final.
- Add configure test for std::erf().
- Add test for noexcept keyword.
- LIBMESH_BEST_UNORDERED_XYZ macros now required to be std::unordered_map,set etc.
- No space between nested closing template angle brackets.
- Replace UniquePtr with std::unique_ptr everywhere.
- Use libmesh_make_unique instead of 'new' where possible.
- Use containers of std::unique_ptrs where possible.
* Add StreamRedirector class to handle stream resetting with RAII, use in WhichNodeAmITest.
* Make build_cube() use ordered element ids for DistributedMesh.
* Fix BoundaryMesh unit test in parallel.
* Fix ReferenceCountedObject::operator=().
* Add ifdef'd move constructor to ReferenceCounter.
* Remove old, unused scripts from contrib/bin.
* Respect subdomains_relative_to set in BoundaryInfo::sync().
* Store string passed to libmesh_error_msg inside exception object.
* Disallow remote element removal during Mesh copy.
* Remove -Wunused-parameter from our CFLAGS list.
* Add optional Exodus file output to adjoints_ex*
* PetscDiffSolver: enforce constraints on current_local_solution to avoid PETSc locking issue.
* BoundingBox
- Add union_with(Point).
- MeshTools::create_nodal_bounding_box().
- Add MeshTools::create_local_bounding_box().
- Use nodal bounding box for Hilbert transformations.
* ExodusII_IO:
- Fix single-precision bug in write_timestep().
- Batch writing of subdomain, block, and sideset data to file.
- Fix copy_elemental_solution() in parallel.
- Add write_timestep_discontinuous().
- Turn off verbose output by default in debug mode.
- Add read_elemental_variable(), read_global_variable() interfaces.
- Add optional system_names arguments to write_timestep() methods.
* CheckpointIO:
- DistributedMesh fixes and additonal unit testing.
- Fix remote_elem child link handling.
- More robust extra_ghost_elem handling.
- The splitter unit tests require XDR.
- Put sideset/nodeset names in header.
- Fix read_remote_elem() in N->M case.
- Store integer data type in CheckpointIO files.
- Support changing the number of ghosted layers in Splitter.
- Changes to CheckpointIO filenaming scheme.
- Refactor mesh splitter app into a function.
* AbaqusIO: support more element types, optionally skip sideset generation.
* Elem:
- Add more total_family_tree_* methods.
- Add remove_links_to_me().
- Add which_node_am_i().
- Add raw_child_ptr() accessor.
* Fix assert in reduced_basis_ex4.
1.2.0 -> 1.2.1
* Bugfix/compatibility release.
* Update bundled NetCDF from 4.3.1 -> 4.4.1.1.
* Fix for upcoming MatGetSubMatrix name change.
* 64-bit indices fix in src/apps/amr.C.
* Add empty LIBMESH_PARALLEL_FLOAT_OPS macro for --disable-mpi case.
1.1.0 -> 1.2.0
* 1.2.0 is the last release that does not require a C++11 compiler.
* Add Eigen optimizations for DenseVector::l2_norm(), l1_norm(), linfty_norm(), dot().
* Add clang-specific vectorization pragmas in DenseVector.
* Fix BoundaryInfo::operator=
* Add EquationSystems flag to skip internal refine/coarsen calls.
* Add MeshBase::is_replicated() function.
* AbaqusIO: Support reading elements of type 'S3'.
* AbaqusIO: Support generated elsets and nsets.
* ImplicitSystem: Allow users to control if the matrix and RHS should be zeroed out.
* Fix issue where delete_remote_elements() was called inappropriately.
* Remove PetscMatrix::update_preallocation_and_zero().
* Deprecate old Elem and Mesh interfaces and constructors.
* Officially remove long-deprecated MeshData class.
* Fix unsigned int/size_t mismatch in for loops.
* Move BoundingBox to its own header, deprecate old usage.
* Add Elem::loose_bounding_box() implementations.
* GmshIO: Allow multiple lower-dimensional elements for BCs.
* Add BoundaryInfo::regenerate_id_sets().
* Use *parallel* max_elem_id in assert code.
* Fix DistributedMesh build_node_list_from_side_list().
* Support for VTK-7.1.
* Misc. VTK improvements from @acbauer (avoid memory leaks, etc.).
* Fix issues with mesh extrusion when using DistributedMesh.
* Add MappedSubdomainPartitioner, maps subdomains to processor ids.
* Add Distributed-compatible BoundaryInfo unit tests.
* FEMSystem: Add solvers for second-order in time problems.
* Add missing Pyramid sidesets in ExodusII_IO.
* Add SubdomainPartitioner, partitions "chunks" of subdomains.
* Fix issues with vectormap::find().
* Add evaluable_nodes iterators.
* CheckPointIO format can now be used to pre-split meshes.
* Fix several issues in CheckPointIO.
* Misc. Doxygen updates, fix issue with missing libmesh_final classes.
* int -> PetscBLASInt in BLAS/LAPACK routines.
* AdjointRefinement ghosted adjoint compatibility.
* Fixes for multisystem XDA reads.
* Fix gmsh numbering and node ordering for PRISM15.
* PointLocator fixes and updates for "truss-like" meshes.
* Add extra package search paths in trilinos.m4.
* inverse_map() fixes for infinite elements.
* Update AutoPtr unit test to test UniquePtr.
* Adjust tolerance in Edge3::volume().
* Update fix for errno.h inclusion in a namespace.
* Reorder paths starting with /lib to the end of the linking list.
* Fix misc. documentation typos and wording in geom, quadrature, partitioning.
* Use the -fno-limit-debug-info flag in dbg/devel mode for clang.
* Use the '-Wunused -Wunused-parameter' flags for clang in all modes.
* Avoid printing unprintable [unsigned] char Parameters.
* Only serialize the Mesh to processor 0 for Exodus.
* Add a barrier() to ~LibMeshInit to avoid missing potential error messages.
* Misc. DistributedMesh fixes.
* Fixes for MeshTools::n*levels().
* Various source code formatting improvements.
* Optionally skip find_neighbors in MeshBase::read().
* SLEPc: Add option to set initial guess.
* SLEPc: Add 'target' spectrum positions.
* SLEPc: detect major, minor, subminor version numbers during configure.
* Add SLEPC_VERSION_LESS_THAN macro.
* Fix binary writing of GMV files.
* Fix bug when merging NULL+non-null CouplingMatrix.
* Mange the lifetimes of various protected members with UniquePtrs.
* Add PointNeighborCoupling class and unit test.
* Fix bugs in MeshTools::all_tri().
* Deprecate ImplicitSystem::get_linear_solver().
* Use os_unfair_lock() for Mac OS X Sierra compatibility.
* Allow virtual methods for edge_fe_reinit() and elem_fe_reinit().
* Enable 1D Hermite elements of arbitrary p.
* Prefix libMesh Parallel:: macros with LIBMESH_.
* Fix GetPot off-by-1 bug.
* Add support for --redirect-output command line option.
* Move serial->replicated_mesh.h, parallel->distributed_mesh.h headers.
* Add GetPot::get_subsection_names() and unit tests.
* Various Trilinos ifdef fixes.
* Add PointLocatorBase::locate_node() and unit tests.
* Various Doxygen fixes, update docs at libmesh.github.io.
* Bugfix for FEMContext::pre_fe_reinit SCALAR case
* Add historic authorship information for various classes.
* Add libmesh_isinf() helper function.
* Optionally skip lower dimensional element counting in TreeNode.
* More robust caching with Clough-Tocher elements.
* Add MeshTools::paranoid_n_levels().
* Add MeshCommunication::send_coarse_ghosts().
* Fixes for MeshTools::n*levels on empty meshes.
* Ignore TBB placement-new warnings in GCC6.
* Fix bug in Tri3::contains_point() implementation affecting small triangles.
* Fix issue with missing incrementing copy constructor to ReferenceCounter class.
* Add compiler.m4 support for Intel 2017 compilers.
* Fix for ExodusII_IO::write_timestep() in single precision case.
* Fix issue with accessing read-only solution vector in PetscDiffSolver.
* Include CITATION file with distributed tarballs.
* Disallow remote element removal during Mesh copy.
* Fix ExodusII_IO::copy_* on distributed meshes.
1.0.0 -> 1.1.0
* Add interface for passing the transpose nullspace to PETSc.
* Fixes for MPI implementations not quite compatible with MPI-2.
* Generalize/modernize systems_of_equations_ex2,3.
* Fix/document issues with DirichletBoundary variable ordering.
* Add new GhostingFunctor interfaces for generalizing which dofs are ghosted.
* Correctly use MPI_UNSIGNED_LONG_LONG to wrap unsigned long long types.
* Add TransientSystem<EigenSystem> typedef.
* Add gather(), allgather() overloads for std::string.
* Fix pack_range bug.
* Misc. NemesisIO fixes including writing node/sideset ids and names.
* Abaqus reader now tolerates whitespace before commas in *NODE sections.
* Add BoundaryVolumeSolutionTransfer class.
* Fix FParser AD data file race in parallel.
* Add --drop-cerr command line argument.
* Fix warnings by avoiding the possibility of throwing from destructors.
* Fix multi-dimensional mesh partitioning bug in Metis.
* Add vector<vector> scatter implementation.
* Update bundled Eigen from 3.2.5 to 3.2.9.
* Fix detection of VTK 6.0 (we skipped straight to 6.1 for some reason)
* Add QUADSHELL4/TRISHELL3 support to Exodus reader, FE, and Mesh classes.
* Update bundled boost subset from 1.55 to 1.61.
* Minimum boost version required for building libmesh bumped to 1.57.
* Remove deprecated Mesh IO classes (DivaIO, LegacyXdrIO, MGF).
* Fix deprecated header warnings caused by CPPUnit.
* Misc. infinite elements fixes from Hubert Weissmann.
* Enhance MeshFunction/PointLocator to work with discontinuous FEM on faces.
* Enhance System::point_value() interface to make it harder to call incorrectly.
* Implement DenseMatrix::svd() for --enable-complex builds.
* Avoid double call to KSPSetFromOptions.
* Throw exception from TypeTensor::solve() on zero determinant.
* Handle exceptions thrown by TypeTensor::solve() in FE::inverse_map().
* Remove previously-deprecated PointLocatorList class.
* Fix Hypre detection for PETSc 3.6.x+ builds.
* Use n_active_elem() instead of n_elem() when flagging by elem fraction.
* Guard Trilinos header includes with ignore/restore warnings headers.
* Fix issue where the PointLocator _initialized flag was not reset by clear().
* Add get_array() capability to PetscVector and use internally.
* Enhance DenseMatrix::evd() interface to also compute left and right eigenvalues.
* Add MPI_Scatter wrappers to Parallel:: interface.
* Add --enable-petsc-required configure option.
* Add extensive unit tests of various FE/Elem combinations.
* Fix caching bugs in FEXYZ and CLOUGH element types.
* Fix bugs and add unit tests of reading unique ids.
* Use PetscViewerPushFormat in PetscMatrix and PetscVector.
* Miscellaneous --enable-single (single precision) bug fixes.
* Keep boundary IDs consistent on DistributedMesh.
* Avoid writing trailing whitespace to XDA files.
* Add --enable-cxx11-required configure option.
* Add all_first_order option to meshtool.
* Optimize stitch_meshes() algorithm by avoiding unnecessary PointLocator calls.
* Add configure test for std::make_unique() and libmesh_make_unique() workaround.
* Add MeshBase::active_semilocal_elements_begin()/end() accessors.
* Handle NULL elements in EquationSystems::get_solution().
* Fix const-correctness issues in Elem interface, deprecate old interfaces.
* Add configure test of C++11 noexcept.
* Remove object-oriented C from misc_ex7.
* Restrict several examples to only run with specific linear solver packages.
* Slight optimizations to Tri6, Hex8::volume().
* Add optimized specialization of Elem::contains_point() for Tet4.
* Add TypeTensor::solve() and replace inverse/multiply in a few places.
* Add unit test for FParser automatic differentiation optimization.
* Don't use WRITE_PARALLEL_FILES for Xdr files unless requested.
* Update systems_of_equations_ex8 to use EDGE2 elements for connecting contact nodes.
* Add unit tests for EulerSolver, Euler2Solver, and NewmarkSolver.
* Don't assume interior_parents() are always part of the same Mesh.
* Add vectormap::find() const and non-const versions.
* Avoid repeatedly destroying/creating vector in compute_affine_map().
* Add reinit_func() to NewmarkSolver, setters for beta, gamma.
* Better documentation for FEMContext::<elem,side,edge>_reinit.
* Call connect_children() in MeshCommunication.
* Use write_discontinuous_exodusII() to plot stress in systems_of_equations_ex6.
* FEInterface::map() now handles infinite elements.
* Replace a few remaining deprecated uses of TypeVector::size() with norm().
* Only call ex_update() on Exodus files that are open for writing.
* Fix logic bug in ParameterVector::clear().
* Add DofMap::gather_constraints() helper function, use in allgather_constraints().
* Fix for writing NodeElems in ExodusII_IO_Helper::write_elements().
* Add ability to set user-defined flags when calling TetgenMeshInterface functions.
* Move ReplicatedMesh->replicated_mesh.h, DistributedMesh->distributed_mesh.h
0.9.5 -> 1.0.0
* Add parallel I/O for Nemesis format, solution vector is no longer broadcast.
* Elem: add node_ref(), node_ptr(), node_id().
* Mesh: add node_ref(), elem_ref(), elem_ptr().
* Deprecate DivaIO, Xdr{MESH,MGF,SOLN,MHEAD,SHEAD,HEAD}, LegacyXdrIO classes.
* Improve HDF5 configure tests, link against -lhdf5_cpp when available.
* Use PETSc's METIS, if available and PETSc is enabled.
* Add RAII-based performance logging macro, LOG_SCOPE.
* VTKIO is a "parallel" I/O format, it is now marked as such.
* Optimize FEMap calculations, standardize get_foo() usage.
* Configure with --enable-unique-ptr by default.
* CondensedEigenSystem: condense out constrained dofs to avoid spurious eigenvalues.
* Add OrderWrapper shim class, we are no longer limited by Order enum.
* Free communicators created by a split().
* Add --with-thread-model configure flag, split threads.h into separate files.
* Make adaptivity_ex3 use HIERARCHIC elements by default, test p and hp refinement.
* hp-adaptivity/coarsening fixes for ParallelMesh.
* Fixes for infinite elements in misc_ex1, ExodusII_IO.
* Add C++03/11 appropriate locking to PetscVector::_get_array().
* FEMContext: Don't increment hardest_fe_type order for SCALARs.
* Add SPARSELU SolverType for Eigen.
* Add misc_ex12 demonstrating the MITC4 element.
* Bugfix for DofMap::constrain_element_matrix().
* Add Type{Vector,Tensor}::norm(), norm_sq() replacing size(), size_sq().
* Allow KSP tolerances to be set from the command line.
* Remove PETSc < 2.3.3 code paths.
* Add triple_product(a,b,c) for TypeVectors.
* Fix EIM truth_solve on hybrid meshes.
* Optimize EIM by storing inner_product * basis functions
* Add method to plot EIM parameterized functions.
* Add notion of time-dependence to FunctionBase.
* Replace NULL usage with backwards-compatible libmesh_nullptr.
* Optimized memory usage in EIM construction.
* Add optimized Elem::volume() implementations for all Elem types.
* Refactor EnsightIO object to use C++ I/O and string handling.
* Mulitple re-optimizations of new GenericProjector codepath.
* Mark various leaf classes as "libmesh_final".
* Redesign Parallel packed_range functions.
* Add GMRES support to EigenSparseLinearSolver.
* MeshBase::spatial_dimension() is no longer simply LIBMESH_DIM.
* Add unit test of refining a slit mesh.
* NewmarkSolver: fix cache w/o restore bug.
* Fix dimension==0 issue in MeshTools::Generation::build_sphere() after clearing mesh.
* Add EigenSparseMatrix::l1_norm(), linfty_norm().
* Fix memory leak in vector_fe_ex{2,3,4}.
* Generalize build_cube() Gauss-Lobatto grid using redistribute().
* PointLocatorList class deprecated.
* Set preprocessor tokens when PETSc has SuperLU_dist and/or MUMPS support.
* Make System::calculate_norm() work on mixed-dimension meshes.
* Add support for writing NodeElems in Exodus using "SPHERE" elements.
* MeshTools::Modification::all_tri() generalized to work with Prisms, Hexes.
* Use unique_ids to disambiguate Hilbert orderings with overlapping nodes.
* Fixes for unique_ids with ParallelMesh.
* Unify spacing around pointer/reference declarations, establish coding convention.
* Many configure tests added for C++11 features. Test regardless of --enable/--disable-cxx11.
* Fix for writing Exodus files with non-contiguous node numberings.
* Add BounaryInfo::remove_id().
* Fix misc. Doxygen warnings, simplify examples documentation generation.
* Misc. updates/fixes to FParser AD and JIT capabilities.
* Check for consistency between libMesh and PETSc scalar and index types.
* Add DenseMatrix::svd_solve().
* Fix DenseMatrix::svd(sigma, U, VT) in rectangular case.
* Refactor Elem::side() functions to use existing "sides_node_map" arrays.
* Add Elem::key() interface, consistent with Elem::key(side) on lower-dimensional elements.
* PETSc/TAO interface updates for PETSc 3.7.0.
* Detect and workaround TRI3 numbering inconsistency in Cubit 14 and 15.
* Update bundled automake from 1.12.5 -> 1.15.
* Update bundled libtool from 2.4.2 -> 2.4.6.
* Make header/forward declaration fixes suggested by cppclean.
* Deprecate BoundaryInfo::add_{side,node,edge}() which returned result by value.
* Replace deprecated BoundaryInfo functions with versions taking a vector by reference.
* Refactor/update the UCDIO class.
0.9.4 -> 0.9.5
* Add interface to SLEPc's solver for generalized indefinite Hermitian eigenvalue problems (GHIEP).
* Refactor NumericVector::insert(), add PetscVector<T>::insert() specializations.
* Refactor NumericVector::add_vector().
* Add DiffContext::elem_solution_rate.
* Add systems_of_equations_ex7, solves large deformation elasticity.
* Add hand-coded TypeTensor<T>::inverse().
* Add static Elem::invalid_subdomain_id value.
* Bugfix in PatchRecoveryErrorEstimator.
* Miscellaneous improvements to FParser/FPOptimizer/JIT/AD code.
* Add/enhance unit tests for many classes.
* Add Elem::build(NODEELEM).
* Add CompositeFunction and CompositeFEMFunction.
* Add NameBasedIO, refactor UnstructuredMesh::read().
* Add 2D Grundmann-Moller quadrature rules for triangles.
* Improve OpenMP configure test.
* Return "invalid" ids from MeshBase::get_id_by_name(), BoundaryInfo::get_id_by_name() rather than erroring.
* Generalize the concept of "dimension" in Mesh with elem_dimensions std::set.
* Add the ParameterAccessor, ParameterMultiPointer class hierarchies.
* Fix bug in adjoints_ex3.
* Allow custom gdb command, enabling/disabling of gdb backtraces.
* Add mixed dimension mesh support to PointLocator.
* Add post-init() EquationSystems::add_system().
* Fix PointLocator bug in 2D case where elements aren't in x-y plane.
* Update AutoPtr to UniquePtr, add build support for Howard Hinnant's C++03 unique_ptr implementation.
* Miscellaneous bugfixes to support configuring with --with-dof-id-bytes=8.
* Add TopologyMap class, use to look up new nodes during refinement.
* Merge METIS/ParMETIS upstream patches from PETSc repo.
* Make METIS IDXTYPEWIDTH and REALTYPEWIDTH match dof_id_type and Real, respectively.
* Add MeshBase::{bnd,bid}_nodes_{begin,end}.
* Add systems_of_equations_ex8, solves linear elasticity with contact.
* Add GenericProjector, use to refactor FEM projection code.
* Add support for linking against VTK 6.2+.
* Add ErrorEstimatorType enum.
* Correctly compute second derivatives on non-affine elements.
* Tetgen is no longer enabled unless libmesh is configured with --disable-strict-lgpl.
* Miscellaneous bugfixes in RBEIMConstruction.
* Adding Optimization{Solver,System} classes, examples with nlopt and TAO instantiations.
* Add configure test for dlopen() and friends.
* Add embedding matrix for Prism15.
* Add EigenSparseLinearSolver::get_converged_reason().
* Add support for 1D elements in MeshTools::find_nodal_neighbors().