CHANGELOG.md

Changelog
=========

v5.6.0
------
**Library**
- Clean-up Set_Rhs_Magnitude function in NekLinSysIter (!1729)
- Consistently use template parameters in VmathArray (!1748)
- Fix issue with CMake and zlib versions >= 1.3.0 (!1744)
- Add 1D demo and test of h-type convergence for a CG projection. (!1738)
- Add 2D projection demo and tests following 1D added in MR !1738. (!1762)
- Tidy up tolerance in NekLinSystIter and NekNonlinSysIter solvers (!1722)
- Enable varcoeffs for Collections (!1701)
- Fix misplaced " in Nektar++Config.cmake (!1742)
- Further tidy-up in linear solver (!1761)
- Use FwdTrans in UnsteadySystem when using Parareal (!1785)
- Automate deployment of README.md to dockerhub (!1786)
- Fix memory leak with Block preconditioner for time-updated matrices (!1737)

**CompressibleFlowSolver**
- Complete second Frechet derivative implementation (!1761)
- Add conditional updating of elemental Mass and Laplacian matrices for LinearADR matrices (!1766)
- Added routine to order expansion in an optimal manner for MatrixFree/Collection ops (!1770)
- Fix PFASST I/O and pre-initialize coarse preconditioner for Parareal (!1749)
- Remove collection offset arrays since no longer required (!1771)
- Fix summary output (!1779)
- Update Docker images to use bookworm (!1775)
- Update `clang-tidy` and `clang-format` to v16 (!1777)
- Add coverage metric capturing (!1776)

**ShallowWaterSolver**
- Refractoring to reduce code duplication (!1782)

**NekPy**
- Add binding to NekPy to check of geometry elements are valid (!1755)
- Update NekPy to more modern packaging (!1747)
- Add wrapper for selected SolverUtils classes, particularly Filter (!1379)
- Add VTK support for OutputVtk module (!1379)
- Add bindings for SolverUtils::EquationSystem and UnsteadySystem (!1752)
- Return native Python types when getting session variables and parameters (!1380)

**NekMesh**
- Fix optiKind flags in VarOpti for freenodes that are on more than a single curve / surface (!1597)
- Fix VarOpti Surface Node Sliding on the CAD in 2D  (!1569)
- Add feature for r-adaption on user-defined CAD curves (!1349)
- Add feature for r-adaption on user-defined CAD curves (!1349)
- Add unit testing infrustructure and initial example (!1753)
- Added a custom cmake cache file to load defaults for building only NekMesh without the solvers (!1641)


**IncNavierStokesSolver**
- Matrix-Free LinearADR operator for VCSImplicit and others (!1627)
- Make substepping normal velocity evaluation more efficient (!1795)

**FieldConvert**
- Add range function as an option in Xml Input, align python usage and start depracation of -r option (!1791) 

v5.5.0
------
**Library**
- Fix Nektar++Config.cmake to use MPI_CXX (!1224)
- Redesign of Parareal and PFASST driver (!1613)
- Update default global system solver parameters for paralell-in-time (!1649)
- Add member function in MPI communicator to check if time-parallel is enable (!1647)
- Fixed FilterError for homogeneous expansions (!1640)
- Fix ForcingAbsorption for homogeneous expansions (!1650)
- Update AssemblyMap to reduce verbosity when using parallel-in-time (!1651)
- Tidy-up of Collection library (!1622)
- Tidy-up of I/O in BasicUtils (!1623)
- Fix local implementation of CG with Null preconditioner (!1658)
- Update to use C++17 nested namespaces (!1556, !1670)
- Fix a minor bug in ProcessWallNormalData (!1663)
- Fix Explist::v_GetNormals and GetElmtNormalLength (!1625)
- Replace `boost::random` with `std::random` (!1673)
- Add a new feature of Lagrangian points tracking in parallel (!1666)
- Add Robin BC to xxt full solver (!1679)
- Update Parareal file output and tidy-up Parareal/PFASST interpolation (!1678)
- Move from `boost::filesystem` to `std::filesystem` (!1674)
- Use `[[deprecated]]` attribute (!1682)
- Fix QuadExp::v_ComputeTraceNormals(!1685)
- Replace `boost::thread` with `std::thread` (!1687)
- Replace `boost::math::tgamma` by `std::tgamma`(!1686)
- Remove `#include <boost/math/special_functions/fpclassify.hpp>` header (!1686)
- Replace `boost::regex` with `std::regex` (!1676)
- Update SDC scheme for implicit PFASST (!1659)
- Pre-allocate memory for GMRES (!1668)
- Update hdf5 read to only read in selected elements to reduce memory overhead (!1351)
- Remove arbitrary factor in  `GlobalLinSysIterative.cpp` (!1694)
- Some tidy-up in LinearAlgebra (!1699)
- Some further tidy-up in LinearAlgebra (!1700)
- Updated hdf5 to 1.12.3 (!1696)
- Remove redundant tolerance limiter in GMRES (!1707)
- Remove unused tolerance parameter in NekSys class and subclasses (1708)
- Avoid repeatly operator assignment in NekNonlinSysNewton class (!1709)
- Add an exact solution for GetLocCoords of straight-edge quad elements (!1704)
- Add sliding mesh capability (!1605)
- Remove MaxIterations parameter from AssemblyMap (!1710)
- Consistently use relative tolerance for GMRES (!1706)
- Fix use of absolute tolerance for iterative solvers (!1711)
- Move solver info loading form NekSys (and its derived classes) to the callers (!1716)
- Tidy physderiv and helmholtz in MatrixFreeOps (!1653)
- Remove time estimation for Parareal and PFASST drivers (!1691)
- Tidy and clarify implementation of Dirichlet boundary condition in GlobalLinSys (!1724)
- Remove unused file NekLinAlgAlgorithms.hpp (!1728)

**ADRSolver**
- Add support for spatially-constant, but variable direction, diffusion to
  ADRSolver. (!1669)
- Inline Vmath library (!1667)
- Refactor UnsteadyReactionDiffusion as a subclass of UnsteadyDiffusion (!1713)
- Tidy-up ADRSolver (!1715)
- Refactor UnsteadyAdvectionDiffusion as a subclass of UnsteadyAdvection (!1720)
- Update UnsteadyReactionDiffusion solver for explicit time-stepping (!1731)
- Refactor UnsteadyViscousBurgers as a subclass of UnsteadyInviscidBurgers solver (!1718)

**CardiacEPSolver**
- Fix cell model history point filter output after base class change (!1342)
- Add const qualifier to SetUniversalUniqueMap (!1644)
- Add safety check for FinTime parameter for parallel-in-time (!1652)

**IncNavierStokesSolver**
- Save BndElmtExpansion and avoid re-building (!1648)
- Add Simo-advection and a switch for Simo-/Dong-advection to VCSImplicit (!1630)
- Add a new feature of elasticaly mounted object using the moving reference frame (!1495)
- Some tidy-up (!1693)
- Fix memory leak in VCSImplicit due to matrix updating (!1688)
- Rename Simo-/Dong-advection to Extrapolated/Updated respectively for VCSImplicit (!1717)
- Update test for SuccessiveRHS parameter (!1727)
- Fix segmentation error in IncNavierStokesSolver when AeroForces filter is used (!1726)
- Added Examples in solvers/IncNavierStokesSolver/Examples, matching with the user-guide (!1723)
- Extend support for IO timer levels to IncNavierStokesSolver (!1732)
- Fixed issue with substepping when using mixed BCs (!1639)

**CompressibleFlowSolver**
- Add three subsonic inflow boundary conditions: EnforceEntropyPresure, EnforceEntropyVelocity, and EnforceEntropyTotalEnthalpy (!1398)
- Update implicit solver for implicit PFASST (!1659)
- Some tidy-up in the compressible flow solver (!1698)
- Fix ESDIRK scheme for compressible flow solver (!1690)
- Some further tidy-up in compressible flow solver (!1700)

**Documentation**
- Update instructions for VS2022 (!1714)
- Update ADRSolver user guide (!1730)

**ShallowWaterSolver**
- Reduce memory footprint of the Peregrine solver(!1680)
- Fix Peregrine solver for Parareal output(!1689)

**FieldConvert**
- Fix typo in user-guide and fix but for parallel-in-time FieldConvert (!1645)
- Fixed FieldConvert -m addfld (!1500)
- Add a new FieldConvert module to zero a plane in wavespace (!1632)
- Fix tecplot output for line and plane points (!1497)

**CI**
- Disable macOS Intel runner (!1655)
- Upgrade Win10 runners (!1656)
- Add `clang-tidy` support to CI for static analysis (!1556)
- Remove some uncompiled files and add quality step to check (!1672)
- Add `clang-15` tester (!1671)
- Update performance tests to use minimum execution time (!1733)
- Fix missing dependencies for clang-tidy and uncompiled-files jobs (!1736)

**NekMesh**
- Replace deprecated boost::filesystem functions (!1654)
- Remove deprecated AddTraceIntegral interface from ExpList.h (!1646)

**Packaging**
- Remove unnecessary Boost dependencies after C++17 migration (!1734)

**Miscellaneous**
- Add a particle tracker utilitiy using equation system infrastructure (!1310)
- Remove deprecated fs::copy_directory function call (!1662)
- Added a sample python script for wallnormaldata module (!1663)
- Replace boost::lexical_cast with std::to_string for integer variable (!1677)
- Use `[[maybe_unused]]` attribute in solvers (!1683)
- Use `[[maybe_unused]]` attribute in library (!1684)
- Fix sse2 SIMD bug (!1559)
- Improved the Incompressible NS section of User-guide (!1719)

v5.4.0
------
**Library**
- Add unit tests for Polylib (!1533)
- Add the absolution tolerance for the iterative linear system solver (!1549)
- Redesign of Parareal driver (!1509) 
- Add PFASST driver (!1501)
- Add local p-refinement functionality (!1508)
- Tidy-up SDC schemes (!1550)
- Add min/max and fmin/fmax function to the interpretor registry (!1552)
- Fix a _m128d to _m128i conversion bug in sse2.hpp (!1551)
- Register TimeIntegrationMethod to SessionReader (!1539)
- Remove unecessary for loop in NekLinSysIterGMRES (!1554)
- Generalize the use of size_t in TimeIntegration (!1555)
- Fix convergence error in Fixed-point Jacobi algorithm (!1561)
- Tidy-up NekLinSys (!1562)
- Tidy-up TimeIntegration (!1505)
- Fix Adams-Bashforth time integration scheme (!1558)
- Remove unused Kernel directory (!1560)
- Remove unused files in BasicUtils (!1564)