CHANGELOG.md

Changelog

v5.7.0

Library

• Modified MatrixFreeOp library switch initialisation to use BOOST_PP (!1794)
• Fix memory-leak with LowEnergyBlock preconditioner for time-updated matrices (!1627)
• Fix Fourier expansion integration weights are related test (!1803)
• Separate MeshGraph input/output functions into a new class (!1778)
• Added checkpoint file writing start time in the fieldconvert filter (!1789)
• Fix fieldconvert filter incorrect boundary values (!1789)
• Fix numerical precision issues with filters OutputStartTime (!1789)
• Fix AdaptiveSFD for MPI (!1821)

IncNavierStokesSolver

• Fix initial and boundary conditions in the moving reference frame (!1692)
• Fix memory-leak for the Mixed_CG_Discontinuous projection when initializing the traceMep (!1806)
• Add synthetic turbulence generation for the incompressible solver (!1664)

ShallowWaterSolver

• Implement implicit time-discritization (!1784)

NekMesh

• Added revolve module (!1825) FieldConvert
• Add vortexinducedvelocity module to compute the vortex-induced velocity (!1824)

Miscellaneous

• Use std::stod instead of boost::lexical_cast (!1819)

Documentation

• Add initial documentation for the IncNavierStokesSolver (!1822)

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)
• Support for implicit sliding meshes (!1787)
• Fix compilation issue with OpenCASCADE 7.8.0 (!1799)
• Fix MPI communicator for Parallel-in-Time (!1801)
• Fix warnings issued by MSVC compiler in LibUtilities and StdRegions (!1740)
• Fix Parareal convergence monitoring (!1802)
• Avoid copying input/output to/from padded aligned arrays in MatrixFree operators(!1783)

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)
• Extend peralign module to all types of meshes (!1702)

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)

• Fix convergence error in Fixed-point Jacobi algorithm (!1561)

• Update parallel-in-time code base in fieldconvert (!1565)

• Tidy-up Basis and Points classes (!1568)

• Remove unused function GetKey in NekFactory (!1567)

• Add new functionality and code improvements for the local p-refinement (!1571)

• Fix v_Exscan compilation bug (!1566)

• Tidy-up of comm class (!1572)

• Tidy-up Nektar tolerances (!1570)

• Tidy-up UnsteadySystem (!1579)

• Fix StaticCond approach + GMRES when restarting (!1583)

• Tidy-up NekManager (!1587)

• Slightly reduce memory allocation in GMRES (!1586)

• Tidy-up Advection class (!1580)

• Tidy-up diffusion class and subclasses (!1581)

• Tidy-up NekNonlinSys and fix some issues (!1563)

• Avoid pre-allocating memory in GMRES (!1591)

• Added a local space version of GMRES and ConjugateGradient (!1575)

• Added a jacobi preconditioner building on diagonal impelemtation (!1575)

• Add a priori convergence and null-input check to GMRES (!1590)

• Some tidy-up in StdRegions (!1595)

• Tidy-up/removed unused Lapack function definition (!1573)

• Some Tidy-up in MatrixFreeOps (!1599)

• Accelerate interpolation for regular and straight-edge elements (!1283)

• Fix an indexing error in MatrixFreeOps (!1602)

• Update Session File for Parallel-in-Time (!1516)

• Partially fix hdf5 partition for Parareal (!1611)

• Update Collection for Parareal-in-Time (!1607)

• New version of CreateCollection using basisKey (!1603)

• Remove unused Domain.cpp and Domain.h file (!1609)

• Remove useless ReadExpressions and SubstituteExpressions function in sessionReader (!1608)

• Corrected workspace size in triangle BwdTrans (!1610)

• Reactivate Reactivate Movement_fixed_3D_stacked_cylinders_curved_hdf5_par test except on ARM MacOS (!1536)

• Updated the PETSc version to v3.19.3 for THIRDPARTY_USE_PETSC, enabled local PETSc version usage (!1618)

• Rename communicator in LinearAlgebra (!1612)

• Add IProductWRTDerivBase operator for 3DH1D problems (!1483)

• Full support of mixed-order elements in DG (!1606)

• Refactoring collections for allowing variable output size inside the collections' operators, introduced PhysInterp1DScaled in Collections (!1620)

• Use default keyword for destructor in Driver (!1624)

• Add additional test for SDC time-integration(!1621)

• Fix to compiler flags for MSVC (!1604)

• Correct bug in scotch initialisation for substructuring (!1634)

• Add ability to build up Movement objects programmatically (!1600)

• Write out movement data to XML files (!1600)

CompressibleFlowSolver

• Fix AUSM3 Riemann solver and add tests to the CI (!1537)
• Set initial condition check points files to zero (0) (!1535)
• Prevent file overwrite with restart for the Compressible flow solver (!1540)
• Register Projection and GJPStabilisation in SessionReader (!1542)
• Redesign of AUSM Riemann solver class (!1577)
• Redesign of the compressible flow solver. Removal of RinglebFlow and IsentropicVortex subclasses (!1584)
• Redesign of PreconCfs class (!1578)
• Fix virtual functions in ContField class (!1616)
• Tidy-up Compressible flow solver print status (!1615)
• Update of for parallel-in-time (!1589)
• Fix some memory bugs for implicit compressible flow solver with LDGNS (!1617)

IncNavierStokesSolver

• Add an option to mask variables for the linear stability problem (!1280)

ShallowWaterSolver

• Fix NonlinearPeregrine solver due to a change of API (!1637)

FieldConvert

• Add option to use .csv files in pointdatatofld module (!1545)
• Add a new module to output power spectral in a given area (!1271)
• Add a new module to do field averaging (!1271)

IncNavierStokesSolver

• Register SolverType in SessionReader (!1541)
• Prevent file overwrite with restart for the IsentropicVortex solver (!1543)
• Fix GJP stabilisation for curved 3D elements (!1593)
• Enable SVV and GJP stabilisation for unresolved scales in VCSImplicit (!1592)
• Fix tolerance in KovaFlow_m10_VCSImplicit_SVV (!1619)

Miscellaneous

• Fix compilation against TetGen 1.6 (!1547)
• Tidy-up Parareal initial condition output (!1534)
• Remove double entry in documentation and slightly tidy-up code (!1530)
• Fixed deadlock problem for the LowEnergyBlock preconditioner which appeared for specific combinations of meshes and boundary conditions (!1553)
• Add a check to avoid unnecessary copy in DoOdoProjecton function (!1582)
• Update user guide and developer guide (!1598)
• Some various tidy-up (!1585)
• Added support for performance tests (!1614)
• Integrated performance tests into the CI system and enabled a test (!1629)
• Added additional performance tests and updated test documentation (!1631)
• Fix VmathTimer compilation error (!1635)
• Fix SIMD compilation error (!1636)
• Update ShallowWaterSolver performance test (!1643)

NekMesh

• Changed CMake to set NEKTAR_USE_THREAD_SAFETY to ON when MeshGen is set to ON (!1546)
• Fix VarOpti Tolerances (!1569)
• Fixed a bug where MeshElement/Tetrahedron did not assign edge IDs in the constructor (!1596)
• Reduce VarOpti memory usage by removing the storage for GetFunctional in NodeOpti (!1633)

Documentation

• Fix missing Tikz external package requires for bookworm (!1638)

CI

• Add testing and packaging for Debian bookworm (!1638)
• Added a NekMesh docker image and added the image to the CI (!1641) NekPy
• Add bindings for Movement-related classes (!1600)
• Add bindings for various helpful methods in the SpatialDomains library (!1600)

v5.3.0

Library

• Fixed avx512 back-end for SimdLib (!1333)
• Remove unnecessary IterPerExp methods (!1366)
• Added float to scalar and avx2 back-end, disable avx512, sse2, sve (!1255)
• Updated the library to use m_phys and m_coeff as function arguments (!1412)
• Added float and restored SVE back-end for SimdLib (!1373)
• Fix VmathSIMD by adding optional mapping with # of lanes (!1388)
• Added float and restore avx512 back-end for SimdLib (!1387)
• Fix namespace pollution which causes boost 1.74+ errors (!1389)
• Fix missing copy assignment operator warnings in clang 13+ (!1391)
• Added checkpoint file writing start time in the checkpoint filter (!1401)
• Fix boost 1.77 compatibility errors (!1420)
• Replaced depricated "sprintf" with "std::to_string" (!1406)
• Add compatiblity patch to solve conflict between flex 2.6.3 and scotch 6.0.4 (!1410)
• Add Parareal Driver module (!1317)
• Maintenance for C++-17 compatibility: removed std::unaray_function base class due to removal from the std (!1419)
• Fixed the comment of function Vvtvvtp in VmathArray (!1408)
• Add a FieldConvert utility to compute the divergence of the velocity (!1413)
• Added new filter to calculate variables integral on composite mesh (!1409)
• Overload PhysEvaluate to give first derivatives using barycentric interpolation (!1323)
• Non-conformal interface support (!1323)
• Fix a I/O issue related to the IO_InfoSteps parameter (!1422)
• Fix a I/O issue related to the IO_CheckSteps parameter (!1423)
• Fix boost 1.77 compatibility errors (!1402)
• Replaced depricated "sprintf" with "std::to_string" (!1406)
• Add compatiblity patch to solve conflict between flex 2.6.3 and scotch 6.0.4 (!1410)
• Templating FieldUtils::Interpolator class (!1420)
• Fix virtual function overrides in StdRegions and LocalRegions classes (!1435)
• Disable -Werror by default (!1443)
• Add missing override keyword to virtual functions in FieldUtils (!1452)
• Add override keyword to virtual functions in GlobalMapping and MultiRegions (!1450)
• Add fmod and modulus operator to interpreter (!1089)
• Add command line option and environment variable to disable backup field files (!1154)
• Add override keyword to virtual functions in SpatialDomains (!1448)
• Add missing override keyword to virtual functions in Collections (!1453)
• Update tutorial submodule (!1511)
• Add missing override keyword to virtual functions in SolverUtils (!1451)
• Add missing override keyword to virtual functions in LibUtilities (!1459)
• Enable ARM macOS runner, fixes for SCOTCH allocation and PETSc detection on macOS (!1462)
• Add FieldConvert module and filter to project velocity into body-fitted coordinate system (!1467)
• Add Curl operator to ExpList (!1475)
• Changed LinearAdvectionDiffusionReactionSolve arguments to be equivalent to HelmSolve (!1475)
• Added detection for advection matrices in GlobalLinSysIterative with silent switch from CG to GMRES (!1475)
• Added non-symmetric laplacian matrices via varcoeffs (!1475)
• Added matrix-free operator for LinearAdvection (!1475)
• Fix uninitialized coordinates in the Bodyforcing (!1472)
• Fix body-fitted velocity filter and also record the max/min for density,pressure, and temperature field (!1490)
• Fix typos in Vmath and VDmath (!1480)
• Fix minor typo and removed unused functions in LibUtilities/TimeIntegration (!1476)
• Fix RK5 time integration scheme (!1482)
• Fix fld file import for SingleMode expansion (!1487)
• Fix ESDIRK time integration scheme (!1484)
• Fix IMXGear time-integration scheme for consistent second-order accuracy (!1489)
• Fix ESDIRK time integration scheme (!1484)
• Fix TimeIntegrationDemo.cpp and add ESDIRK tst files to the CI (!1485)
• Add DIRKOrder1, BDFImplicitOrder3, BDFImplicitOrder4, RungeKutta1, and RungeKutta3 schemes to the register (!1485)
• Use DIRK (instead of IMEXdirk) schemes for the start-up phase of high-order BDF and AM schemes (!1485).
• Fix IMEXdirk_1_2_2 and IMEXdirk_2_3_3 time-integration schemes (!1499)
• Add extrapolation time-integration scheme (!1488)
• Fix CNAB/MCNAB time-integration schemes (!1493)
• Slightly tidy-up time integration algorithms (!1496)
• Reduced memory usage in the FilterHistoryPoint (!1458)
• Remove redundant functor typedef (!1498)
• Add missing m_ prefix to member variables in FFTW (!1504)
• Make some virtual functions protected (!1506)
• Remove trailing CONDITIONS tag in xml files (!1510)
• Disable problematic Movement_fixed_3D_stacked_cylinders_curved_hdf5_par test (!1507)
• Fix I/O issue related to Hdf5 that was unable to open file and fixed similar issue in other IO classes in BasicUtils (!1512)
• Remove unused function SetUpXmlDoc (!1513)
• Add new interpolation function to FieldUtils (!1514)
• Generalize the use of the space communicator (!1518)
• Add parallel-in-time feature to FieldConvert (!1520)
• Add Spectral Deferred Correction (SDC) time integration schemes (!1481)
• Redesign of Spectral Deferred Correction (SDC) algorithm (!1523)
• Modify SessionReader to read restart/exact solution files parallel-in-time (!1521)
• Fix Polylib_test.cpp (!1524)
• Update to Parareal file output (!1517)
• Add convergence criteria to Parareal driver (!1457)
• Add time metadata to tecplot output (!1525)
• Fix segmentation fault when no time integration method specified for unsteady problem (!1526)
• Set adjacent elements for m_bndcondExpansions for both CG and DG (!1491)
• Fix inconsisten treatment of 1D and 2D/3D expansions in DisContField::v_GetBoundaryToElmtMap (!1491)
• Tidy-up parallel-in-time processing in FieldConvert (!1529)

Python

• Add wrappers for Interpreter and Equation classes (!1329)

CompressibleFlowSolver

• Added Laplacian (NonSmooth) AV to the explicit Navier Stokes solver (!1372)
• Added Physical AV to the implicit Navier Stokes solver (!1372)
• Fixed Segmentation Fault when using C0 Smoother with Shock Capturing (!1394)
• The Incomplete IP method was made the default method for the IP method (!1377).
• Add additional parameters for the Isentropic Vortex equation system (!1323)
• Improve performance of the perconditioner and diffusion operator (!1393)
• Re-add the SFD test with an updated restart file (!1399)
• Improve performance of the block diagonal operator of the preconditioner (!1404)
• ExtractSurface2DCSF utility is updated to use the boost program option (!1407)
• Fix a Wuninitialized-const-reference warning (!1449)
• New implementation of the Stagnation Inflow Boundary Condition (!1478)
• Remove m_root in PreconCfs to avoid possible future conflict with parallel-in-time driver (!1515)
• Update to Parareal file output (!1517)

CardiacEPSolver

• Fix a shadowed loop counter variable in the benchmark filter (!1436)
• Update functions in derived classes to be consistent with the base class and add override keyword to virtual functions (!1439)
• Add dummy projection to CardiacEPSolver (!1527)

IncNavierStokesSolver

• Replaced depricated "sprintf" with "std::to_string" (!1406)
• Extended Reynolds Stresses filter to passive scalars (!1430)
• Added Implicit Solver (!1475)
• Fixed Taylor-Hood expansion for VCSWeakPressure (!1444)
• Fix filename in LinearisedAdvection (!1479)
• Added scalar advection terms to AdjointSolver (!1466)
• Remove member variables as funtion parameters in LinearisedAdvection solver (!1522)

VortexWaveInteractionSolver

• Replaced depricated "sprintf" with "std::to_string" (!1406)

DummySolver

• Fix CWIPI test to use DirectFull for projection of received data (!1502)

NekMesh

• Replace VTK pointers with VTK smart-pointers to avoid memory leaking, when exporting in .vtu format (!1386)
• Preserve CAD face labels and save in to session file as a "NAME=" tag on the composites (!1396)
• Fix a header include which caused compilation errors on OCC versions newer than v7.4 (!1395)
• Add option to refine curves in the same manner as the line refinement functionality (!1298)
• Add refined curves and refined lines now prompt the octree to subdivide until the desired refined delta is reached (!1298)
• Fix a segmentation fault with WriteOctree due to missing 'order' parameter (!1418)
• Multi domain input/output for Nekpp and HDF5 file formats (!1323)
• Fix CADSurfOCE curvature bug where negative curvature values could be returned causing incorrect mesh spacing (!1442)
• Fix ProjectCAD bug with findAndProject where the projection was missing and variable was passed without reference (!1442)
• Fix 3d_bl_wing test case for STEP files where the wrong surfaces were selected for the BL (!1442)
• Fix error when setting BL progression to 1.0 due a division by 0 (!1455)
• Changed the BOOLPARAMETERS tag in InputMCF to allow disabling the high order surface optimisation with "DisableSurfaceOptimiser" (surface optimisation is still enabled by default) (!1455)
• Fix 3d_bl_wing test case for STEP files - updated to use an improved CAD definition for the NACA aerofoil (!1486)

FieldConvert

• Add vars and dirs options in the gradient module to specify fields and partial derivative directions (!1415)
• Fix range option so that it also works with hdf5 (!1414)
• Fix halfmodetofourier module with triangles (!1492)
• Fix the output field names of WSS module of FieldConvert, revert !1352 (!1528)

Miscellaneous

• Updated gitignore to be friendly with CLion IDE (!1405)
• Correct header section of .cpp, .hpp, and .h files (!1426)
• Linux format .cpp, .hpp, and .h files (!1432)
• Fix wsign compare warning (!1437)
• Fix some Woverloaded-virtual warning (!1439)
• Add missing override keyword to virtual functions in solvers (!1440)
• Fix some Wunused-variable (!1438)
• Fix unused parameter warnings in virtual functions (!1441)
• Fix a Wreorder warning (!1445)
• Fix some Wimplicit-fallthrough warnings (!1446)
• Switch to using pkg-config for finding PETSc (!1454)
• Use Nektar::LibUtilities::Timer for better accuracy (!1468)
• Make some virtual functions protected (!1469)
• Extend clang-format checks to solvers, utilities, tests and templates (!1434)
• Fix documentation for exponential scheme (!1519)

CI

• Enable packaging for Fedora 35, removed Fedora 33/34 from package builds. (!1424)
• Add header checking for *.cpp, *.hpp and *.h files to the CI (!1431)
• Enable packaging for Fedora 36. (!1429)
• Fix XML files indentation (!1428)
• Update solvers CMakeList.txt to fix some warnings detection issue (!1447)
• Remove -fpermissive from NektarCommon.cmake (!1460)
• Remove old distribution versions, added Fedora 35/36 testing to CI (!1461)
• Kill orphan Tester-g processes on Windows and remove source tree after build (!1471)
• Fixed path issue and warning in the nektar-workbook image (!1470)

v5.2.0

Library

• Add Arm SVE backend to SIMD library (!1282)
• Added support for manifold MatrixFree operators (2D in 3D space) (!1304)
• Put in place automatic selection of explicit operations using an opt file (!1304)
• Fixed the moving reference frame rotation (Solver Utils) (!1305)
• Revised FilterAeroForces to accout for the moving reference frame (!1305)
• Add MaxMinFields filter to record the max/min at each quadrature point and output the max/min fields. (!1256)
• Simplify the logic in the MPI pairwise trace exchange (!1307)
• Fix imaginary mode in HalfModeToFourier module (!1247)
• Added a dummy output module OutputStdOut for NekMesh utilities that don't require an output file (!1318)
• Fix compiler errors on ARCHER2 using PrgEnv-cray (!1315)
• Fix cmake SIMD enable/disable options based on architecture (!1320)
• Restrucutred the communicators to reduce direct dependence on session file communicator (!1337)
• Fixed SIMD mask test (!1324)
• Fix memory leak in Timer.cpp (!1330)
• Fix cmake CWIPI option to remove Fortran check (!1331)
• Fix excessive verbose output in GetBndElmtExpansions method (!1341)
• Timer class was updated with safety checks to avoid wrong measurements (!1347)
• Fix to adjust for warnings/errors from Monterey updated compiler (!1355)
• Update nektar and nektar-env packages to Debian Bullseye (!1356)
• Reformat code with clang-format (!1359)
• Remove unnecessary IterPerExp methods (!1366)
• Fix erronous call to FwdTrans from MR 1366 (!1374)
• Fixed avx512 back-end for SimdLib (!1333)
• Added float to scalar and avx2 back-end, disable avx512, sse2, sve (!1255)
• Change MPI initialisation to allow MPI_Init call outside Nektar++ (!1376)
• Fixed incorrect summary output for diffusion/reaction terms (!1383)

FieldConvert

• Add calculation of CFL number for the incompressilbe flow (!1332)
• Added conditional to select the eNearestNeighbour method for 3D interpolation (!1335)
• Fixed the output field names of WSS module of FieldConvert (!1352)
• Add VTU output using VTK library (high-order & multi-block options) (!1343)

IncNavierStokesSolver

• Added Boundary conditions for moving reference frame (!1305)
• Added the virtual functions overwriting the FluidInterface for moving reference frame (!1305)
• Add Gradient Jump Penalty (GJP) Stabilisation into the solver (!1290)
• Equation types are registered to the session reader (!1344)
• Added Block-Preconditioner for Full Matrix solve (!1350)
• Update to Parareal file output (!1517)

ADRSolver:

• Add Gradient Jump Penalty (GJP) Stabilisation into the Unsteady Advection and Unsteady Advection Diffusion solvers (!1290)

PulseWaveSolver

• Parallelised solver (!1337)

NekMesh

• Allow for one or more blank lines between sections in Tecplot ascii (.dat) files (!1322)
• Small bug-fix for Python API for unused configuration options (!1348)
• Fix bug in ProcessVarOpti/ElUtil for segfault on non-tri or tet meshes (!1381)

CompressibleFlowSolver

• Added physical AV, dilatation sensor, Ducros's and smoothing (!1180)
• Added timers around important functions using the Timer class. Timers are available by specifying IO_Timer_Level > -1 (!1347)
• Fixed bug in the calculation of the discontinuity penalty factor for the DiffusionIP implementation (!1368)

Documentation

• Fix images not being displayed in HTML documentation and tutorials (!1370)

CI

• Remove unused build options (!1360)
• Enable NEKTAR_USE_VTK across full builds and in docker image (!1358)
• Add XML linting and checking in CI pipeline (!1433)

Packaging

• Fix various issues with debian unstable and centos8 packaging (!1362)
• Fix missing texlive package dependency for centos packaging (!1382)

v5.1.1

Library

• Fix a boost headers incompatibility with boost-1.77 (!1297)
• Add RungeKutta4 as an alternate name for ClassicalRungeKutta4 for time integration method (!1294)

Python

• Fix initialisation warning when using HDF5 (!1299)
• Fix issue with implementation of Diffusion IP (!1303)
• Split Helmholtz MatrixFree operator to improve compile times (!1292)
• Fix Boost deprecated header warnings (!1302)
• Add command lines to set starting time and starting checkpoint number of a time-dependent simulation (!1309)
• Fix an index referencing error in the Collections PhysDeriv method for Hex (!1314)

Python

• Updates to workbook, fix bugs in StdExpansion and SessionReader with MPI communication being recreated. (!1296)

BuildSystem

• Updated third party Lapack version 3.7.1 (!1312)

CompressibleFlowSolver

• Fix non-dimensional Sutherland law (!1253)

v5.1.0

Library

• Restructure library to use local coefficient storage down to the GlobalLinSys level. Removed GlobalCoeffs functionality (!963, !1145)
• Corrected the use of communicator in AssemblyMapDG and AssemblyCommDG which was not using GetRowComm() (!1144)
• Add interior penalty method to DG framework (!1101)
• Add an error filter for the time-evolution of the L2 and Linf errors (!1147)
• Fix successiveRHS method (!1176)
• Add cachedId in GetExpIndex and use in Fieldconvert (!1167)
• Fix bug in PreconditionerLowEnergy (!1161)
• Fix intel c compiler error in AeroFilters (!1198)
• Fix compilation errors when CWIPI interface enabled (!1207)
• Fix distance in ContainsPoint and GetLocCoords (!1200)
• Fix compiler warning of maybe-uninitialized elType in InputStar (!1217)
• Extend vectoisation to include all elements and initialise collections on first call (!1162)
• Add vectorisation of most element on basix operations (!1158)
• Add constant coefficients to matrix-free Helmholtz operator (!1284)
• Limit MPI methods based on core count (!1208)
• Split out IProduct.cpp and IProductWRTDerivBase.cpp in order to avoid long time compilations (!1228)
• Refactored time integration code using factory pattern (!1034, !1103)
• Fix WriteStream with empty Array/vector (!1233)
• Add interpolation at arbitrary point in 3DH1 (!1233) level. Removed GlobalCoeffs functionality (!963, !1159)
• Add interior penalty method to DG framework (!1101)
• Add an error filter for the time-evolution of the L2 and Linf errors (!1147)
• Enable global systems to be generated when using different values of variable coefficients (!1159)

FieldConvert

• Refactored time integration code using factory pattern (!1034)
• Fix to preprocessor logic for boost with Visual Studio >= 2015 (!1115)
• Fix type consistency and real comparison in SharedArray.hpp, replaced num_elements with size() (!1127, !1137, !1141)
• Use base MPI functions instead of the GS library in the trace exchange for parallel DG simulations (!1112)
• Replace PhysIntegral with Integral (!1246)
• Change the way periodic boundary conditions in parallel is setup to reduce excessive memory usage (!1235) (!1289)
• Add exponential and fractional-in-time integration schemes (!1106, !1111, !1210)
• Add nonlinear and linear system solvers (!1196)
• Add ESDIRK3 and ESDIRK4 time integration schemes (!1196)
• Add a filter to calculate mean value of solution fields (!1211)
• Fix the time dependent absorption forcing (!1254)
• Enable very high order (>100) quadrature use (!1262)
• Add rotation and improve performance of MovingReferenceFrame forcing (!1185)
• Fix BODYFORCE defined by a file (!1215, !1264)
• Add multi-level partitioning strategy for HDF5 geometry (!1209)
• Fix the URL of ccmio library (!1288)

FieldConvert:

• Add phifile module to compute shape functions for the SPM solver (!1065)
• Fix mean and innerProduct modules in 3DH1D cases (!1157)
• Add Python interface (!1081)
• Fix wss module with nparts option and reading of parallel xml files when the root partition is missing(!1197)
• Fix a segment error in the gradient module when the number of fields is smaller than space dimension(!1216)
• Add output of wall normal data from a single point (!1237)
• Add QCriterion for 2D flow (!1243)
• Fix to interppointsdatatofld to allow for mpi processing of large files (!1191)
• Fix the logic of C0Projection:helmsmoothing (!1220)
• Fix extract module for boundaries with periodic boundary conditions (!1277)

IncNavierStokesSolver:

• Add MaxMinFields filter to record the max/min at each quadrature point and output the max/min fields. (!1256)
• Fix imaginary mode in HalfModeToFourier module (!1247)

CardiacEPSolver

• Added additional parameter sets to Fenton-Karma model (!1119)
• Fix electrogram calculation in 1D/2D domains (!1285)

IncNavierStokesSolver

• Add Smoothed Profile Method (SPM) for the formulation of immersed boundaries (!1065)
• Add new filter AeroForcesSPM to compute aerodynamic forces in immersed boundaries (!1065)
• Add mask function and more baseflow parameters for the linear stability problem (!1201)
• Fix dudt in high-order pressure boundary condition (!1190)
• Add flow rate forcing with a scalar (!1026)

CompressibleFlowSolver

• Added the selective frequency damping support for the implicit solver (!!1267)
• Added vectorisation of the Interior Penalty method (!!223)
• Added a simplified implicit solver with naive preconditioner (!!1196)
• Add BRJ preconditioner to the implicit solver (!!1212)
• Fix implicit solver for Euler system (!!1252)
• Updated WallAdiabatic/WallViscous BC to accept time-dependent perturbations on the ghost state (!1248)

PulseWaveSolver

• Added viscoelasticity (!1138)
• Added empirical and power laws (!1138)
• Code tidying (!1138)

Documentation:

• Updated Windows source build instructions in user guide (!1152)

Tester

• Added test metric to check if warnings appear in output and error stream (!1225)

NekMesh

• Improved boundary layer splitting and output to CADfix (!938)
• Improve .geo reader and support 3D geometries with voids (!1031)
• Added r-adaptation code (!1109)
• Added Python bindings, change NekMeshUtils to NekMesh (!1149)
• Added pyramid element for the Star-CCM mesh (!1229)
• Added option to use absolute tolerance in peralign (!1225)

BuildSystem

• Toggle build type (!1135)
• Updated minimum required CMake version to 3.5.1 (!1152)
• Updated third party Boost version 1.71 (!1152)
• Updated third party OCE version to 0.18.3 (!1234)

v5.0.3

CompressibleFlowSolver

• Fix repeated output of u,v,w for Euler system

FieldConvert

• Fix the Filters output files numbering (!1251, !1261)
• Fix the Filters output files numbering (!1251)
• Fix 2D surfDistance calculation (!1263)

NekMesh

• Fix VTK Output for 3D meshes and support XML format (!1258)

Documentation

• Fix documentation to note restrictions on use of coupled solver (!1268) Library
• Add robustness to the read expansions (!1239)

v5.0.2

Library

• Fix bug in StdHexExp FillMode (!1192)

Documentation

• Updated Documentation to include HDF5 Mesh Output (!1230)
• Removed Ubuntu Trusty (14.04) from CI and added Focal (20.04) (!1238)

CI

• Add Debian Bullseye to CI system (!1181)

BuildSystem

• Updated third party zlib version to 1.2.9 to resolve OCE source build issue (!1227)
• Adding SolverUtils as a core library that is built by default (!1240)

v5.0.1

Library

• Fix incorrect coordinate dimension used in history point filter (!1118)
• Fix compile errors with GCC 9.x (!1108)
• Correct the Energy/Enstropy integral for the 3DH1 flow (!1132)
• Added IsRealEqual method to compare real numbers with relative tolerance. Started using it in SharedArray and in NekMesh to fix peralign-extrude tool chain (!1134)
• Fix performance of GetExp(coord) by using octree lookup (!1165)
• Fix Collection unit tests (!1160)
• Fix periodic boundary conditions with HDF5 input file (!1163)
• Fix DESTDIR issues for MacPorts (!1179)
• Fix Bodyforcing and history point filter bounds issue (!1184)

IncNavierStokesSolver

• Change the baseflow time in the Adjoint advection (!1133)

FieldConvert

• Fix OutputTecplot skipping final plane in 3DH1D (!1016)
• Fix Interppoints in 3DH1D (!1140)