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NEWS
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NEWS
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1.6.2 -> 1.7.0
* Benchmarking support
- Add benchmark_example() macro, $LIBMESH_BENCHMARK env
- Add CLI overrides, comments, performance logging, and benchmark parameters to many examples
* BoundaryInfo
- Apply zero-D nodeset names in gmsh_IO
- Act on id to name maps in BoundaryInfo::regenerate_id_sets
- Selectively remove boundary information after mesh stitching
- Add nodes into nodesets in build_cube
- Add set names from other mesh when stitching
- MeshBase reference member in BoundaryInfo changed to pointer
* Docs
- Mention "make uninstall" in README.md
- Update Elem documentation with reference coordinate intervals.
- Update DenseMatrix docs
- Add more verbose documentation for InfFE constraints
- Improve comments on AMR with InfElem.
- Update documentation for intro_ex3, ex4
* Elem
- Fix Elem::is_child_on_edge()
- Add Elem::center_node_on_side()
- Add Elem::true_centroid(), Elem::vertex_average(), deprecate Elem::centroid()
- Add optimized Elem::true_centroid() overrides for some Elems
- Use displacement vectors for relative_fuzzy_equals() in has_affine_map() tests
- Don't connect interior_parents in other meshes
- Handle interior_parents in connect_families()
- Assert interior_parent() AMR consistency
- Use hack_p_level inside set_p_level
- Sync p refinement flags along with p levels
- Add Elem::hack_p_level_and_refinement_flag and use in Elem unpack
- Add Elem::n_permutations(), Elem::permute()
- Add Elem::swap*nodes helper functions
- Add Elem::is_singular_node()
- Deprecate the SideEdge class
- Use non-allocating build_edge_ptr where possible
- Add "fill" overload for build_edge_ptr
- Stop using SideEdge proxies
- Add const version of build_edge_ptr
- Add Elem::simple_build_edge_ptr implementation
- Deprecate the Side class
- Deprecate attempts to build proxy Side objects
- Stop building proxy sides by default
- Set subdomain_id+p_level in all side/edge elems
- Add Elem::has_invertible_map() and overrides for some elements
* ExodusIO
- Support empty sidesets + nodesets in ExodusII
- Update contrib ExodusII to version 8.11
- Get exodusII.h include out of our headers
- Add and use ExodusII_IO_Helper::update()
- inquire() function signature change, move to anonymous namespace
- Undef multiple guard macros for Exodus+Nemesis
- Fix Exodus extra integers unit tests
- Fix extra_integers read in ExodusII_IO
- Add support for writing components of CONSTANT MONOMIAL_VEC variables
- Add ExodusII_IO::get_elem_num_map() and get_node_num_map() APIs
- Add ExodusII_IO::write_nodeset_data() API
- Add unit test of writing nodeset data to Exodus file
- Exodus_II_IO::copy_*_solution(DistMesh) fixes
- Make ExodusII_IO_Helper::nodal_var_values a map
- Handle incomplete node and elem var maps
- Add number of nodes per Elem sanity check
* FE
- Fix FE side unit tests with --enable-complex
- Allow second order L2_LAGRANGE on first order elements
- Allow arbitrary order L2_HIERARCHIC with arbitrary order elements
- Change max order for L2 families
- Rotate FE test meshes after permuting elements
- Add a cubic to fe_test analytic functions
- Fix p>2 SIDE_HIERARCHIC second derivatives
- Permuting edges fixes p=2 SIDE_HIERARCHIC HEX27
- Disable higher order SIDE_HIERARCHIC on HEX27
- Add warnings to permute_elements doc
- Test all FE except HERMITE with permuted elements
- Add test_permute unit test
- Non-templated FEMap instantiate shim
- Add missing PYRAMID14 master point
- Add Unit tests for SIDE_HIERARCHIC FE
- Support SIDE_DISCONTINUOUS in projections
- Add SIDE_HIERARCHIC FE and related enums
- Add shape functions for NEDELEC_ONE FEs on TET10 mesh elements
* FEMContext
- Use vars vectors in GenericProjector functors
- Use _active_vars in FEMContext calculations
- Sort FEMContext::_active_vars
- Optional active_vars in all FEMContext::FEMContext
- Add active_vars member, accessor to FEMContext
- Use delegating constructor idiom for FEMContext
- Raw ALE variables should be protected
- Fix docs that referred to old example
* InfFE
- Disable misc ex15 with --enable-node-constraints
- Don't test InfFE AMR with ENABLE_NODE_CONSTRAINTS
- Fix compilation with node constraints + InfFE
- Update documentation
- add further virtual_for_inffe-statements
- add dimension-parameter for decay_deriv
- correct computation of derivatives for non-affine mapped base
- correct base_point function for non-affine base
- add test for inf side
- add new InfElem test: numerical derivatives
- change in InfFE::reinit(elem, pts):
- Add support for InfFE::reinit(side)
- Adapted tests for infinite elements; added further test-calculations.
- fix inverse_map in InfFE: for nonaffine base, the intersection was wrong
- Update misc_ex1, ex14 to new InfFE APIs
- Change 'child_side' to 'child_base' to reduce confusion.
- Add test-calc. for infinite elem + AMR
- Add html documentation for new example
- Ran bootstrap for the new example
- Add new example: miscellaneous 15
- Enable AMR with infinite elements
* Isogeometric Analysis (IGA)
- Rational function shapes_need_reinit is true!
- Test inverse_map on less trivial master points
- Fix manifold-vs-nodeelem checks
- testMasterCenters() in IGA unit tests
- Use gzipped bxt meshes in unit tests
- Support zipped files with DynaIO
- Add testProjectionRegression to Dyna unit tests
- Move BERNSTEIN HEX27 interior DoFs to node
- DynaIO unit tests on more meshes.
- Do some regression testing on IGA projections
- Process constraints when DynaIO adds them
- Do *not* sync done_saving_ids across processors
- Deprecate SparsityPattern::Build direct access
- solve_for_constrained_dofs for IGA project_vector
- Added System::solve_for_unconstrained_dofs
- Allow belated System::add_matrix()
- DofMap::process_mesh_constraint_rows
- Don't store zero entries in IGA constraint rows
- DofMap::constrained_sparsity_construction() option
- Comment on math in solve_for_unconstrained_dofs()
- Omit add_spline_constraints call in fem_system_ex5
- Don't call add_spline_constraints in Dyna tests
- Move spline constraint work from DynaIO to DofMap
- Use MeshBase constraint_rows in DynaIO
- Store constraint_rows with a MeshBase
- Allow renumbering and distributing on IGA meshes
- delete_remote_elements support for constraint_rows
- Beginning gather(constraint_rows) work
- Don't try to redistribute() constraint_rows
- Remove deleted nodes from Mesh constraint_rows
- Store mesh constraint_rows by pointer
- Store elem ids in MeshBase::constraint_rows
- Default to non-SECOND approximations again
- Run reduced_basis_ex5 twice, once with .bext mesh
- Don't try to reserialize a distributed IGA mesh
- Fix delete_remote_elements constraint erasure
- Add Twisted_Beam bext file
- Allow reduced_basis_ex5 to read mesh files
- Support 1D/2D calculations in reduced_basis_ex5
- Do not skip NodeElems with constrained DoFs!
- Use new L2System features in calculator app
- Support null L2System::input_system
- Support multi-dimensional meshes in L2system
- Add subdomains_list to apps L2system
* Mesh
- Include unpartitioned elements in MeshBase::subdomain_ids
- Allow Elem, Node re-insert in ReplicatedMesh
- Move MeshCommunication::*gather to MeshBase
- Implement mesh move constructors in terms of MeshBase::assign() function
- Add more verbose output to MeshBase::get_info()
- Add API to tell mesh it is not prepared
- Deprecate public MeshBase::boundary_info member
- Add global data structures for mesh subdomain and boundary ids
* MeshFunction
- Add MeshFunction copy constructor; implement MeshFunction clone() in terms of this
- MeshFunction::set_point_locator_tolerance(): set both PointLocator tolerances
- MeshFunction: use unique_ptr to manage PointLocator
- Add non-const accessor for underlying PointLocator
* Misc. bugfixes and improvements
- Ghost periodic point neighbors in GhostPointNeighbors
- Add MeshInput::is_parallel_format() accessor
- Update contrib version of Eigen to 3.3.9
- Update contrib version of lcov to 1.15
- Upgrade TIMPI to 1.7.0_bootstrapped
- Update MetaPhysicL to 1.1.0_bootstrapped
- Add TypeVector overloads for std::norm and friends for Eigen::Matrix
- Add support for exchanging adjoint physics
- System: store unique_ptrs in _vectors map
- Add copy assignment+constructor for ParsedFunction and unit tests
- Move basic matrix storage and create virtual matrix APIs in System
- Add InterMeshProjection class to handle arbitrary projections between meshes
- PointLocatorTree: use std::shared_ptr to manage tree
- Add new PointLocator derived class based on Nanoflann
- Don't try to autodetect headers for tecio in system locations
- Add nodal quadrature rules for Pyramids
- Add MeshModification::permute_elements()
- Officially deprecate UniquePtr
- Improve performance of BoundingBox::contains_point() by inlining it
- Add chunked_mapvector, a variant of mapvector that tries to improve performance
- Mimic STL and boost constructors in our allocators
- DofMap: add const DofConstraints accessor
- Fix --disable-amr builds
- Fix --enable-all-static builds
- fparser: update deprecated throw specifications
- Fix BC issue in systems_of_equations_ex8
- Create multi_evaluable predicate
- Add Elem::affine_tol and use in has_affine_map comparison tests
- Disable HDF5 file locking unless the user insists
- Set next unique id in copy_nodes_and_elements
- PointLocatorTree: avoid Elem::contains_point() warning when using custom tolerances
- Updates to C++11/14/17 configure tests
- Fix compilation with both CAPNP and GLPK enabled
- Turn off gdb backtraces by default
- Add and test Dense{Vector,Matrix} std::initializer_list constructors
- Add configure test for C++11 <initializer_list> header
- Avoid allocating sparse matrix when using JFNK
- Fix leak in merge_ghost_functor_outputs
- Detect if PETSc has strumpack
- Add local_singular_node to Elem for catching singular nodes in inverse_map
- Add bounding box scaling
- Remove potential deadlock with Singletons and RemoteElem
- DofMap::distribute_dofs() now returns the total number of DOFs across all procs
- Drop SHA1 lib, use std::hash instead
- Add EDGE4 case to get_refspace_nodes
- Use RAII to clean up some PETSc objects with WrappedPetsc<T>
- Don't potentially throw from 'exceptionless' error macros
- Make ReferenceCounter::increment_{de,con}structor_count() noexcept
- Re-enable check_dirichlet_bcid_consistency
- Move linear_solver member from LinearImplicitSystem to ImplicitSystem
- ImplicitSystem::get_linear_solver() now throws an error
- UnsteadySolver: old_local_nonlinear_solution is now a std::shared_ptr
- PeriodicBoundaries now stores unique_ptrs instead of dumb ptrs
- Fix scatter for node constraints
- Add some vector CompareTypes
- Fix possible overflow in PeriodicBoundaries::neighbor
- Ignore remote elems coming from pbcs in DefaultCoupling
- ParsedFEMFunction: change "parsers" to a vector of unique_ptrs
- Generalize default constructors for TypeTensor and TypeVector
* NemesisIO
- Support Nemesis writes of complex-valued elem data
- Unit tests for Nemesis::copy_elemental_solution
- Add Nemesis copy_nodal_solution unit tests
- Allow testing Exodus copy_*_solution distributed
- Test Exodus+Nemesis both replicated+distributed
- Factor Exodus/Nemesis into separate unit tests
- NemesisIO::copy_nodal_solution
- Use NemesisIO::read even on one processor
- Manually set unique_id in NemesisIO
- Keep internal node_num_map one-based in Nemesis_IO
- Nemesis_IO::get_nodal_var_names()
- Unit test for NemesisIO write_equation_systems
- Handle empty node intersections
- Write Nemesis cmaps even if they're empty
- NemesisIO::assert_symmetric_cmaps() refactoring
- NemesisIO::write_nodal_solution subparametric case
- Implement NemesisIO(ReplicatedMesh&)
- Test Nemesis read for arbitrary MeshType
- Add testNemesisRead() unit test
- Fix off-by-one errors in Nemesis_IO
- Remove Nemesis_IO_Helper::put_n_coord
- Remove Nemesis_IO_Helper::create
- Fixes for --disable-nemesis builds
- Fix NemesisIO Hex27 output issue
* NumericVector
- Add virtual NumericVector::max_allowed_id() API.
- Generalize multi-vector operations to always use global forms
- NumericVector: Make indexing add/set operations toggle _is_closed
- DistributedVector GHOSTED in serial can be SERIAL
- Read/write numeric vector projection/type info
* Partitioner
- Use Partitioner::build with command line override
- Add/use Partitioner::build(PartitionerType) with command line override
- Add PartitionerType enum
- Fix SFC Partitioner on distributed meshes
* Reduced Basis
- Enable plotting of EIM functions
- Updates to RBConstruction truth solve outputs
- RBConstruction: Handle exceptions thrown during assembly
- Add observation values to EIM
- Update rb_data.capnp and serialization/deserialization support for EIM observation values
- Add _preserve_rb_eim_solutions flag to RBEIMEvaluation
- Made eim_solutions_for_training_set private with getters in RBEIMEvaluation
- Cleanup of RBEIMConstruction
- Skip reinit when there are no DOFs on Elem
- Enable eim-best-fit with lookup table
- Add set_EIM_rhs_vec() to RBEIMEvaluation
* SparseMatrix
- Fix memory issue for matrix_matrix_mult and add option for reusing matrix
- Add PetscMatrix::create_submatrix_nosort()
- Add PetscMatrix::add_sparse_matrix()
- Fix PetscMatrix::matrix_matrix_mult()
- Fix PetscMatrix::print_personal()
- Add LumpedMassMatrix
* SparsityPattern
- Add comments to SparsityPattern::Build methods
- default+delete SparsityPattern::Build functions
- Use SparsityPattern for n_nz in SparseMatrix
- Make DofMap::build_sparsity() public
- DofMap::get_sparsity_pattern() accessor
- Keep n_nz and n_oz in SparsityPattern::Build
- Use new SparsityPatternBuild accessors in DofMap
- More SparsityPattern::Build methods
- Add SparsityPattern::build accessors, reorganize
- Remove SparsityPattern::Build::mesh
- Remove non-unique DOF ids in Build::sorted_connected_dofs()
1.6.1 -> 1.6.2
* Mimic stl and boost constructors in our allocators
* Weaken partitioner_test for SFC on 8+ processors
* Fix for deprecated warning in SLEPc not-quite-3.15
* fix typo in type_to_n_nodes_map
* amended solver_types
* set constant 0 to float
* Fix example doc and combine if-statements
* Fix docs that referred to old example
* Update docs for named boundary (side, edge, node) sets.
* Make RadialBasisInterpolation quiet
* misc_ex13: fix doc string
* Prerequest nothing on side FE in RB ex2
* libmesh_cast_ptr -> cast_ptr in example
* Fix deprecated warnings in SLEPc 3.15
* Add missing PYRAMID14 master point
* Don't try to autodetect headers for tecio in system
* Wrap Petsc include for dmimpl.h in ignore and restore warnings.
* undef MAJOR_VERSION and MINOR_VERSION before including petsc.h in config tests
* Fix for --enable-petsc-required
* Fix nodes_on_edge for 2nd order InfCell cases
* Fix Elem::is_child_on_edge
* Fix asserts in PetscMatrix::add_sparse_matrix()
* Fix residual history vector pointer constness in newer PETSc versions
1.6.0 -> 1.6.1
* Do *not* sync done_saving_ids across processors
* Fix compilation with both CAPNP and GLPK enabled
* Re-reserve non-zero pattern after Eigen::setZero
* Generalize default constructors for TypeTensor and TypeVector
* Make ReferenceCounter::increment_{de,con}structor_count() noexcept
* Work around warnings in system xdr/rpc headers
* Don't try to cast ostream to bool
* Remove potential deadlock with Singletons and RemoteElem
* Fix NemesisIO Hex27 output issue
* Fix SFC Partitioner on distributed meshes
* Don't apply a regex to the string "All Tests"
* Remove non-unique DOF ids in Build::sorted_connected_dofs()
* Initialize next_unpartitioned_unique_id
* Eliminate leak in merge_ghost_functor_outputs
* The SHAPE and SKEW metrics for Quad elements should have similar bounds.
* Turn off gdb backtraces by default
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
1.5.2 -> 1.5.3
* Fix standalone header bug introduced in 1.5.2
1.5.1 -> 1.5.2
* Cherry-pick following commit from 1.6.0 branch and fix merge conflicts
d25f5ad57 Combination of MoveInsertable fixes (#2170)
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.
1.4.1 -> 1.4.2
* Cherry-pick following commit from 1.6.0 branch and fix merge conflicts
d25f5ad57 Combination of MoveInsertable fixes (#2170)
* Cherry-pick b3e1c10d6 to fix compilation with recent versions of PETSc
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