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)
• Fix AdaptiveSFD for MPI (!1821)

IncNavierStokesSolver

• Fix initial and boundary conditions in the moving reference frame (!1692, !1820)
• 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)