CHANGELOG.md

Ferrite.jl changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

• DofHandler now supports fields on subdomains and mixed grids. (#667)
• Support for embedded elements in CellValues. (#651)
• Support for vectorized interpolations with dimension different from the spatial dimension in CellValues. (#651)
• All keyword arguments supported by WriteVTK.jl can be given to vtk_grid (only compress earlier) (#687)

Removed

• BREAKING: MixedDofHandler has been renamed to DofHandler. Update by replacing MixedDofHandler to DofHandler. (#667)

Other improvements

• BREAKING: All CellValues have a finer granularity on the different types of dimensions used. Custom CellValues and dispatches on their type parameters must be updated to respect the new type. (#651)

0.3.14 - 2023-04-03

Added

• Support reordering dofs of a MixedDofHandler by the built-in orderings FieldWise and ComponentWise. This includes support for reordering dofs of fields on subdomains. (#645)
• Support specifying the coupling between fields in a MixedDofHandler when creating the sparsity pattern. (#650)
• Support Metis dof reordering with coupling information for MixedDofHandler. (#650)
• Pretty printing for MixedDofHandler and L2Projector. (#465)

Other improvements

• The MixedDofHandler have gone through a performance review (see #629) and now performs the same as DofHandler. This was part of the push to merge the two DoF handlers. Since MixedDofHandler is strictly more flexible, and now equally performant, it will replace DofHandler in the next breaking release. (#637, #639, #642, #643, #656, #660)

Internal changes

Changes listed here should not affect regular usage, but listed here in case you have been poking into Ferrite internals:

• Ferrite.ndim(dh, fieldname) has been removed, use Ferrite.getfielddim(dh, fieldname) instead. (#658)
• Ferrite.nfields(dh) has been removed, use length(Ferrite.getfieldnames(dh)) instead. (#444, #653)
• getfielddims(::FieldHandler) and getfieldinterpolations(::FieldHandler) have been removed (#647, #659)

0.3.13 - 2023-03-23

Added

• Support for classical trilinear and triquadratic wedge elements. (#581)
• Symmetric quadrature rules up to order 10 for prismatic elements. (#581)
• Finer granulation of dof distribution, allowing to distribute different amounts of dofs per entity. (#581)

Fixed

• Dof distribution for embedded elements. (#581)
• Improve numerical accuracy in shape function evaluation for the Lagrange{2,Tetrahedron,(3|4|5)} interpolations. (#582, #633)

Other improvements

• Documentation:
  • New "Developer documentation" section in the manual for documenting Ferrite.jl internals and developer tools. (#611)
  • Fix a bug in constraint computation in Stoke's flow example. (#614)
• Performance:
  • Benchmarking infrastructure to help tracking performance changes. (#388)
  • Performance improvements for various accessor functions for MixedDofHandler. (#621)

Internal changes

• To clarify the dof management vertices(ip), edges(ip) and faces(ip) has been deprecated in favor of vertexdof_indices(ip), edgedof_indices(ip) and facedof_indices(ip). (#581)
• Duplicate grid representation has been removed from the MixedDofHandler. (#577)

0.3.12 - 2023-02-28

Added

• Added a basic show method for assemblers. (#598)

Fixed

• Fix an issue in constraint application of Symmetric-wrapped sparse matrices (i.e. obtained from create_symmatric_sparsity_pattern). In particular, apply!(K::Symmetric, f, ch) would incorrectly modify f if any of the constraints were inhomogeneous. (#592)
• Properly disable the Metis extension on Julia 1.9 instead of causing precompilation errors. (#588)
• Fix adding Dirichlet boundary conditions on nodes when using MixedDofHandler. (#593, #594)
• Fix accidentally slow implementation of show for Grids. (#599)
• Fixes to topology functionality. (#453, #518, #455)
• Fix grid coloring for cell sets with 0 or 1 cells. (#600)

Other improvements

• Documentation improvements:
  • Simplications and clarifications to hyperelasticity example. (#591)
  • Remove duplicate docstring entry for vtk_point_data. (#602)
  • Update documentation about initial conditions. (#601, #604)

0.3.11 - 2023-01-17

Added

• Metis.jl extension for fill-reducing DoF permutation. This uses Julias new package extension mechanism (requires Julia 1.10) to support a new DoF renumbering order DofOrder.Ext{Metis}() that can be passed to renumber! to renumber DoFs using the Metis.jl library. (#393, #549)
• BlockArrays.jl extension for creating a globally blocked system matrix. create_sparsity_pattern(BlockMatrix, dh, ch; kwargs...) return a matrix that is blocked by field (requires DoFs to be (re)numbered by field, i.e. renumber!(dh, DofOrder.FieldWise())). For custom blocking it is possible to pass an uninitialized BlockMatrix with the correct block sizes (see BlockArrays.jl docs). This functionality is useful for e.g. special solvers where individual blocks need to be extracted. Requires Julia version 1.9 or above. (#567)
• New function apply_analytical! for setting the values of the degrees of freedom for a specific field according to a spatial function f(x). (#532)
• New cache struct CellCache to be used when iterating over the cells in a grid or DoF handler. CellCache caches nodes, coordinates, and DoFs, for the cell. The cache cc can be re-initialized for a new cell index ci by calling reinit!(cc, ci). This can be used as an alternative to CellIterator when more control over which element to loop over is needed. See documentation for CellCache for more information. (#546)
• It is now possible to create the sparsity pattern without constrained entries (they will be zeroed out later anyway) by passing keep_constrained=false to create_sparsity_pattern. This naturally only works together with local condensation of constraints since there won't be space allocated in the global matrix for the full (i.e. "non-condensed") element matrix. Creating the matrix without constrained entries reduces the memory footprint, but unless a significant amount of DoFs are constrained (e.g. high mesh resolution at a boundary) the savings are negligible. (#539)

Changed

• ConstraintHandler: update! is now called implicitly in close!. This was easy to miss, and somewhat of a strange requirement when solving problems without time stepping. (#459)
• The function for computing the inhomogeneity in a Dirichlet constraint can now be specified as either f(x) or f(x, t), where x is the spatial coordinate and t the time. (#459)
• The elements of a CellIterator are now CellCache instead of the iterator itself, which was confusing in some cases. This change does not affect typical user code. (#546)

Deprecated

• Adding fields to a DoF handler with push!(dh, ...) has been deprecated in favor of add!(dh, ...). This is to make it consistent with how constraints are added to a constraint handler. (#578)

Fixed

• Fix shape_value for the linear, discontinuous Lagrange interpolation. (#553)
• Fix reference_coordinate dispatch for discontinuous Lagrange interpolations. (#559)
• Fix show(::Grid) for custom cell types. (#570)
• Fix apply_zero!(Δa, ch) when using inhomogeneous affine constraints (#575)

Other improvements

• Internal changes defining a new global matrix/vector "interface". These changes make it easy to enable more array types (e.g. BlockMatrix support added in this release) and solvers in the future. (#562, #571)
• Performance improvements:
  • Reduced time and memory allocations for global sparse matrix creation (Julia >= 1.10). (#563)
• Documentation improvements:
  • Added an overview of the Examples section. (#531)
  • Added an example showing topology optimization. (#531)
  • Various typo fixes. (#574)
  • Fix broken links. (#583)

0.3.10 - 2022-12-11

Added

• New functions apply_local! and apply_assemble! for applying constraints locally on the element level before assembling to the global system. (#528)
• New functionality to renumber DoFs by fields or by components. This is useful when you need the global matrix to be blocked. (#378, #545)
• Functionality to renumber DoFs in DofHandler and ConstraintHandler simultaneously: renumber!(dh::DofHandler, ch::ConstraintHandler, order). Previously renumbering had to be done before creating the ConstraintHandler since otherwise DoF numbers would be inconsistent. However, this was inconvenient in cases where the constraints impact the new DoF order permutation. (#542)
• The coupling between fields can now be specified when creating the global matrix with create_sparsity_pattern by passing a Matrix{Bool}. For example, in a problem with unknowns (u, p) and corresponding test functions (v, q), if there is no coupling between p and q it is unnecessary to allocate entries in the global matrix corresponding to these DoFs. This can now be communicated to create_sparsity_pattern by passing the coupling matrix [true true; true false] in the keyword argument coupling. (#544)

Changed

• Runtime and allocations for application of boundary conditions in apply! and apply_zero! have been improved. As a result, the strategy keyword argument is obsolete and thus ignored. (#489)
• The internal representation of Dirichlet boundary conditions and AffineConstraints in the ConstraintHandler have been unified. As a result, conflicting constraints on DoFs are handled more consistently: the constraint added last to the ConstraintHandler now always override any previous constraints. Conflicting constraints could previously cause problems when a DoF where prescribed by both Dirichlet and AffineConstraint. (#529)
• Entries in local matrix/vector are now ignored in the assembly procedure. This allows, for example, using a dense local matrix [a b; c d] even if no entries exist in the global matrix for the d block, i.e. in [A B; C D] the D block is zero, and these global entries might not exist in the sparse matrix. (Such sparsity patterns can now be created by create_sparsity_pattern, see #544.) (#543)

Fixed

• Fix affine constraints with prescribed DoFs in the right-hand-side. In particular, DoFs that are prescribed by just an inhomogeneity are now handled correctly, and nested affine constraints now give an error instead of silently giving the wrong result. (#530, #535)
• Fixed internal inconsistency in edge ordering for 2nd order RefTetrahedron and RefCube. (#520, #523)

Other improvements

• Performance improvements:
  • Reduced time and memory allocations in DoF distribution for MixedDofHandler. (#533)
  • Reduced time and memory allocations reductions in getcoordinates!. (#536)
  • Reduced time and memory allocations in affine constraint condensation. (#537, #541, #550)
• Documentation improvements:
  • Use :static scheduling for threaded for-loop (#534)
  • Remove use of @inbounds (#547)
• Unification of create_sparsity_pattern methods to remove code duplication between DofHandler and MixedDofHandler. (#538, #540)

0.3.9 - 2022-10-19

Added

• New higher order function interpolations for triangles (Lagrange{2,RefTetrahedron,3}, Lagrange{2,RefTetrahedron,4}, and Lagrange{2,RefTetrahedron,5}). (#482, #512)
• New Gaussian quadrature formula for triangles up to order 15. (#514)
• Add debug mode for working with Ferrite internals. (#524)

Changed

• The default components to constrain in Dirichlet and PeriodicDirichlet have changed from component 1 to all components of the field. For scalar problems this has no effect. (#506, #509)

0.3.8 - 2022-10-05

Added

• Ferrite.jl now has a logo! (#464)
• New keyword argument search_nneighbors::Int in PointEvalHandler for specifying how many neighboring elements to consider in the kNN search. The default is still 3 (usually sufficient). (#466)
• The IJV-assembler now support assembling non-square matrices. (#471)
• Periodic boundary conditions have been reworked and generalized. It now supports arbitrary relations between the mirror and image boundaries (e.g. not only translations in x/y/z direction). (#478, #481, #496, #501)

Fixed

• Fix PointEvalHandler when the first point is missing. (#466)
• Fix the ordering of nodes on the face for (Quadratic)Tetrahedron cells. (#475)

Other improvements

• Many improvements to the documentation. (#467, #473, #487, #494, #500)
• Improved error messages in reinit! when number of geometric base functions and number of element coordinates mismatch. (#469)
• Remove some unnecessary function parametrizations. (#503)
• Remove some unnecessary allocations in grid coloring. (#505)
• More efficient way of creating the sparsity pattern when using AffineConstraints and/or PeriodicDirichlet. (#436)

0.3.7 - 2022-07-05

Fixed

• Fix tests for newer version of WriteVTK (no functional change). (#462)

Other improvements

• Various improvements to the heat equation example and the hyperelasticity example in the documentation. (#460, #461)

0.3.6 - 2022-06-30

Fixed

• Fix a bug with L2Projection of mixed grid. (#456)

Other improvements

• Expanded manual section of Dirichlet BCs. (#458)

0.3.5 - 2022-05-30

Added

• Functionality for querying information about the grid topology (e.g. neighboring cells, boundaries, ...). (#363)

Fixed

• Fix application of boundary conditions when combining RHSData and affine constraints. (#431)

0.3.4 - 2022-02-25

Added

• Affine (linear) constraints between degrees-of-freedom. (#401)
• Periodic Dirichlet boundary conditions. (#418)
• Evaluation of arbitrary quantities in FE space. (#425)

Changed

• Interpolation(s) and the quadrature rule are now stored as part of the CellValues structs (cv.func_interp, cv.geo_interp, and cv.qr). (#428)

0.3.3 - 2022-02-04

Changed

• Verify user input in various functions to eliminate possible out-of-bounds accesses. (#407, #411)

0.3.2 - 2022-01-18

Added

• Support for new interpolation types: DiscontinuousLagrange, BubbleEnrichedLagrange, and CrouzeixRaviart. (#352, #392)

Changed

• Julia version 1.0 is no longer supported for Ferrite versions >= 0.3.2. Use Julia version

  = 1.6. (#385)

• Quadrature data for L2 projection can now be given as a matrix of size "number of elements" x "number of quadrature points per element". (#386)
• Projected values from L2 projection can now be exported directly to VTK. (#390)
• Grid coloring can now act on a subset of cells. (#402)
• Various functions related to cell values now use traits to make it easier to extend and reuse functionality in external code. (#404)

Fixed

• Exporting tensors to VTK now use correct names for the components. (#406)