CHANGELOG.md

Changelog
=========

v5.3.0
------
**Library**
- 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)
- 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)
- 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 fmod and modulus operator to interpreter (!1089)

**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).
- Improve performance of the perconditioner and diffusion operator (!1393)
- Re-add the SFD test with an updated restart file (!1399)
- ExtractSurface2DCSF utility is updated to use the boost program option (!1407)
- Fix a Wuninitialized-const-reference warning (!1449)

**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)

**IncNavierStokesSolver**
- Replaced depricated "sprintf" with "std::to_string" (!1406)
- Extended Reynolds Stresses filter to passive scalars (!1430)

**VortexWaveInteractionSolver**
- Replaced depricated "sprintf" with "std::to_string" (!1406)

**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)
- 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)

**FieldConvert**
- Add vars and dirs options in the gradient module to specify fields and partial derivative directions (!1415)

**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 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)

**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)

**FieldConvert**
- Fix range option so that it also works with hdf5 (!1414)

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)

**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)