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Changelog
=========

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v5.1.0
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**Library**
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- Restructure library to use local coefficient storage down to the GlobalLinSys
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  level. Removed GlobalCoeffs functionality (!963, !1145)
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- Corrected the use of communicator in AssemblyMapDG and AssemblyCommDG which
  was not using GetRowComm() (!1144)
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- Add interior penalty method to DG framework (!1101)
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- Add an error filter for the time-evolution of the L2 and Linf errors (!1147)
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- Fix successiveRHS method (!1176)
- Add cachedId in GetExpIndex and use in Fieldconvert (!1167)
- Fix bug in PreconditionerLowEnergy (!1161)
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- Fix intel c compiler error in AeroFilters (!1198)
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- Fix compilation errors when CWIPI interface enabled (!1207)
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- Fix distance in ContainsPoint and GetLocCoords (!1200)
- Fix compiler warning of maybe-uninitialized elType in InputStar (!1217)
- Add vectorisation of most element on basix operations (!1158)
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- Limit MPI methods based on core count (!1208)
- Split out IProduct.cpp and IProductWRTDerivBase.cpp in order to avoid long time compilations (!1228)

**FieldConvert**
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- Refactored time integration code using factory pattern (!1034)
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- Fix to preprocessor logic for boost with Visual Studio >= 2015 (!1115)
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- Fix type consistency and real comparison in SharedArray.hpp, replaced
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  num_elements with size() (!1127, !1137, !1141)
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- Use base MPI functions instead of the GS library in the trace exchange
  for parallel DG simulations (!1112)
  num_elements with size() (!1127, !1137, !1141)
- Fix to interppointsdatatofld to allow for mpi processing of large files (!1191)
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- Fix the logic of C0Projection:helmsmoothing (!1220)
- 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)
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- 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)
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**CardiacEPSolver**
- Added additional parameter sets to Fenton-Karma model (!1119)
**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)
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**PulseWaveSolver**
- Added viscoelasticity (!1138)
- Added empirical and power laws (!1138)
- Code tidying (!1138)

**Documentation**:
- Updated Windows source build instructions in user guide (!1152)

**NekMesh**
- Improved boundary layer splitting and output to CADfix (!938)
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- Improve .geo reader and support 3D geometries with voids (!1031)
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- Added r-adaptation code (!1109)
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- Added Python bindings, change NekMeshUtils to NekMesh (!1149)
**BuildSystem**
- Toggle build type (!1135)
- Updated minimum required CMake version to 3.5.1 (!1152)
- Updated third party Boost version 1.71 (!1152)
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v5.0.2
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**CI**
- Add Debian Bullseye to CI system (!1181)

v5.0.1
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**Library**
- Fix incorrect coordinate dimension used in history point filter (!1118)
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- 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)
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- Fix performance of GetExp(coord) by using octree lookup (!1165)
- Fix Collection unit tests (!1160)
- Fix periodic boundary conditions with HDF5 input file (!1163)
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- Fix DESTDIR issues for MacPorts (!1179)
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- Fix Bodyforcing and history point filter bounds issue (!1184)
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**IncNavierStokesSolver**
- Change the baseflow time in the Adjoint advection (!1133)

**FieldConvert**
- Fix OutputTecplot skipping final plane in 3DH1D (!1016)
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- Fix Interppoints in 3DH1D (!1140)
**NekMesh**
- Fix compile errors when using intel cc (!1114)

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**Documentation**
- Fix error in compilation of developer guide (!1136)
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**CI**
- Added checked conversion from double to int in SessionReader (!1113)
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- Switched to Gitlab CI (!1120, !1120, !1128, !1129, !1131, !1141)
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- Updated bullseye build to remove UCX components (!1203)
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v5.0.0
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**Library**
- Added in sum factorisation version for pyramid expansions and orthogonal
  expansion in pyramids (!750)
- Added detection of 'abort' file to cleanly terminate simulation early (!772)
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- Significant overhaul of CMake infrastructure (!770, !804)
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- Fix ThridpartyCCM options (!802)
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- Fix Windows CRLF tokens in GEO reader and improve comment handling (!805)
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- Use chrono in Timer (!807)
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- Fix caching of FUNCTION tags that read from file and provide the same
  functionality in FUNCTIONs defined for forcings (!759)
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- Transition to C++11 (!795, !847)
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- Add patch to tinyxml to fix size_t vs int bug (!820, !1006)
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- Add ARPACK thirdparty build capabilities (!828)
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- Added native support for csv files in addititon to pts (!760, !835, !906)
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- Utilize LAPACK_DIR env variable to find the native blas/lapack install (!827)
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- Extend AeroForces filter to compressible flows (!815)
- Remove StdExpansion use from MultiRegion (use Expansions instead). (!831)
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- Move steady state check and CFL output from solvers to SolverUtils (!832)
- Remove DG advection implementation from EquationSystem (!832)
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- Simplify RawType typedefs (!840)
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- Remove unused files from BasicUtils (!841)
- Remove checks for old boost versions which are no longer supported (!841)
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- Refactor ParseUtils to be more consistent (!843, !896, !908)
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- Added support for using the distance to a specific region (e.g. outlet) in the
  function definitions for the Absorption Forcing (!769)
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- Improve performance of DisContField2D::v_ExtractTracePhys (!824)
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- Fix small bug in Jacobian Energy (!857)
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- fix variable name overriding in file functions (!870)
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- Adds CFI CAD engine back-end (!864)
- Adds CFI Mesh IO support (!864)
- Cleanup of CAD system data structures (!864)
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- Fix mac OSX on buildbots (!876)
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- Fix error from (!826) (!876)
- Fix minor bug in ARPACK thirdparty build cmake (!874)
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- Added in sum factorisation version for pyramid expnasions and orthogonal
  expansion in pyramids (!750)
- Adjust boost third-party compilation to account for different toolset
  choices (!886)
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- Switch MeshGraph to use factory pattern and add HDF5 geometry support (!900,
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  !904, !941)
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- Restructure the low energy preconditioner to handle pyramidic and variable
  p expansions (!920)
- Remove requirement for modmetis, switch to SCOTCH by default (!899)
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- Switch MeshGraph to use factory pattern and add HDF5 geometry support
  (!900, !904)
- Fix bug in MeshPartition.cpp which caused incorrect array access when
  WeightPartitions was used in parallel (!923)
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- Removed instance count from beginning of Array storage to improve memory
  alignment (!921)
- Fix naming issue of duplicate Unit tests (!924)
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- Fix warnings about missing virtual destructors in abstract classes (!932)
- Fix ability to have periodic boundary conditions that are aligned by a
  rotation rather than just a translation (!933)
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- Added a coupling interface to exchange data between solvers at run time
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  and a DummySolver to test the implementations (!853, !931, !950, !973, !1017)
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- Fix compilation issue with newer Boost versions and clang (!940)
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- If only `NEKTAR_BUILD_LIBRARY` is enabled, only libraries up to and including
  `MultiRegions` will be built by default (!945)
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- Dont add doxygen documentation to the all target (!834)
- Fix missing metadata import from Hdf5 files (!971)
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- Fix missing flags for periodic BC in DiffusionLDG (!985)
- Add the moving reference frame as a forcing (!987)
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- Added rtree for element bounding box lookup to accelerate interpolation (!996,
  !1066)
- Fix integration weights on prisms and pyramids if not using the default
  integration rule (!998)
- Fix missing ContainsPoint in Pyramid expansion (!1000)
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- Added path prefixes to find packaged Scotch (!979, !1008)
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- Add HDF5 geometry format (!977)
- Combine and generalise demo code in StdRegions and LocalRegions (!993)
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- Fix for error output to allow for custom error streams (!944)
- Fixed bug in ReOrientQuadFacePhysMap (!1003)
- Add NekPy Python interface (!962, !990, !989, !1004, !1014, !1061, !1070)
- Fix edge case for ThirdPartyScotch and FindScoth (!1009)
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- Fix to populate m_elmtToExpId map if not already set up in GetExpIndex (!1019)
- Added flag to skip periodic BCs while filling Dirichlet BCs in
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  ContField3D.cpp (!1018)
- Fix bounding box for interpolation (!1033)
- Added IMEXOrder4, RK5 and AB4 time integration schemes (!1037)
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- Fix TriExp.cpp orientation bug (!1048)
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- Fix XML attributes in conditions.cpp to be unordered (!1015)
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- Fix issue with HDF5 mesh input in serial (!1049)
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- Add estimate of filters CPU time (!1044)
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- Update CompressibleFlowSolver/Examples/Test_IsentropicVortex1.xml example (!1045)
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- Add error if HDG used with periodic BCs (!1071)
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- Fix issues related to leading factors, arithmetic order and associativity of
  exponential operator in expression evaluator (!1066)
- Remove use of `using namespace std` in header files (!1066)
- Add error messages for use of ARPACK in serial (!1079)
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- Generalise ContainsPoint routine (!1078)
- Homogenized fallthrough to fix issues with gcc 7.4.0 (!1084)
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