CHANGELOG.md

Changelog

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)
• 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 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)
• 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)

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)

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)
• Add mask function and more baseflow parameters for the linear stability problem (!1201)

CompressibleFlowSolver

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

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)

NekMesh

• Fix compile errors when using intel cc (!1114)

Documentation

• Fix error in compilation of developer guide (!1136)

CI

• Added checked conversion from double to int in SessionReader (!1113)
• Switched to Gitlab CI (!1120, !1120, !1128, !1129, !1131, !1141)
• Updated bullseye build to remove UCX components (!1203)

v5.0.0

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)
• Significant overhaul of CMake infrastructure (!770, !804)
• Fix ThridpartyCCM options (!802)
• Fix Windows CRLF tokens in GEO reader and improve comment handling (!805)
• Use chrono in Timer (!807)
• Fix caching of FUNCTION tags that read from file and provide the same functionality in FUNCTIONs defined for forcings (!759)
• Transition to C++11 (!795, !847)
• Add patch to tinyxml to fix size_t vs int bug (!820, !1006)
• Add ARPACK thirdparty build capabilities (!828)
• Added native support for csv files in addititon to pts (!760, !835, !906)
• Utilize LAPACK_DIR env variable to find the native blas/lapack install (!827)
• Extend AeroForces filter to compressible flows (!815)
• Remove StdExpansion use from MultiRegion (use Expansions instead). (!831)
• Move steady state check and CFL output from solvers to SolverUtils (!832)
• Remove DG advection implementation from EquationSystem (!832)
• Simplify RawType typedefs (!840)
• Remove unused files from BasicUtils (!841)
• Remove checks for old boost versions which are no longer supported (!841)
• Refactor ParseUtils to be more consistent (!843, !896, !908)
• Added support for using the distance to a specific region (e.g. outlet) in the function definitions for the Absorption Forcing (!769)
• Improve performance of DisContField2D::v_ExtractTracePhys (!824)
• Fix small bug in Jacobian Energy (!857)
• fix variable name overriding in file functions (!870)
• Adds CFI CAD engine back-end (!864)
• Adds CFI Mesh IO support (!864)
• Cleanup of CAD system data structures (!864)
• Fix mac OSX on buildbots (!876)
• Fix error from (!826) (!876)
• Fix minor bug in ARPACK thirdparty build cmake (!874)
• 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)
• Switch MeshGraph to use factory pattern and add HDF5 geometry support (!900, !904, !941)
• Restructure the low energy preconditioner to handle pyramidic and variable p expansions (!920)
• Remove requirement for modmetis, switch to SCOTCH by default (!899)
• 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)
• Removed instance count from beginning of Array storage to improve memory alignment (!921)
• Fix naming issue of duplicate Unit tests (!924)
• 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)
• Added a coupling interface to exchange data between solvers at run time and a DummySolver to test the implementations (!853, !931, !950, !973, !1017)
• Fix compilation issue with newer Boost versions and clang (!940)
• If only NEKTAR_BUILD_LIBRARY is enabled, only libraries up to and including MultiRegions will be built by default (!945)
• Dont add doxygen documentation to the all target (!834)
• Fix missing metadata import from Hdf5 files (!971)
• Fix missing flags for periodic BC in DiffusionLDG (!985)
• Add the moving reference frame as a forcing (!987)
• 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)
• Added path prefixes to find packaged Scotch (!979, !1008)
• Add HDF5 geometry format (!977)
• Combine and generalise demo code in StdRegions and LocalRegions (!993)
• 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)
• 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 ContField3D.cpp (!1018)
• Fix bounding box for interpolation (!1033)
• Added IMEXOrder4, RK5 and AB4 time integration schemes (!1037)
• Fix TriExp.cpp orientation bug (!1048)
• Fix XML attributes in conditions.cpp to be unordered (!1015)
• Fix issue with HDF5 mesh input in serial (!1049)
• Add estimate of filters CPU time (!1044)
• Update CompressibleFlowSolver/Examples/Test_IsentropicVortex1.xml example (!1045)
• Add error if HDG used with periodic BCs (!1071)
• 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)
• Generalise ContainsPoint routine (!1078)
• Homogenized fallthrough to fix issues with gcc 7.4.0 (!1084)

NekMesh:

• Add feature to read basic 2D geo files as CAD (!731)
• Add periodic boundary condition meshing in 2D (!733)
• Adjust boundary layer thickness in corners in 2D (!739)
• Add non-O BL meshing in 2D (!757)
• Add ability to compile CCIO library but tar file is not yet openly available whist we seek permission from Simens (!799)
• Fix issue with reading CCM files due to definition of default arrays rather than a vector (!797)
• Fix inverted triangles and small memory issue in surface meshing (!798)
• Update for the CAD system, more advance self-healing and analysis (!822)
• Additional curve types in GEO reader: BSpline, Circle, Ellipse (!800)
• Fix default command line argument value (!823)
• Add projection meshing module which can curve linear meshes with CAD (!826)
• XML meshes now write with provenance information, including information about their source, for debugging purposes (!872)
• Force 3-node loops to avoid degenerate 1-triangle faces (!875)
• Smooth BL normals in 2D when normals intersect or cause invalid macro BL elements (!877)
• Revert triangle code to ThirdParty library (!883)
• Fix coinciding nodes issue with very fine meshes (!883)
• Skip CFI groups of bodies and non-numbered nodes (!891)
• Add ability to space out 2D BL nodes to better fit local target Delta (!890)
• Fix automatic peralign call in 2D periodic meshing (!888)
• Fix BL splitting call from MCF (!910)
• Support CFI combined lines (!917)
• Order nodes in Gmsh output (!912)
• Fix manifold face curvature nodes (!913)
• Fix writing 1D surfaces (!930)
• Fix surface string parsin in BL splitting (!937)
• Enable use of distributed packages for triangle and TetGen (!953)
• Fix issue with MLSC after Scotch conversion (!943)
• Add support for Gmsh 4.0 mesh file format (!964)
• Fix issue with extracting 1D curved surface from 2D file (!984)
• Fix surface extraction, added regression test (!994)
• Fix 2D meshing running out of memory due to missing else (!1012)
• Add support for .msh v4.1 file input (!1054)
• Added penalty term to LDG and LDGNS, slight generalization of LDG (!1080)

FieldConvert:

• Add input module for Semtex field files (!777)
• Fixed interppoints module (!760)
• Fix OutputTecplot in 2DH1D (!818)
• Move StreamFunction utility to a FieldConvert module (!809)
• Allow using expansion from session file with new --useSessionExpansion command line option (!842)
• Extend wss module to compressible flows (!810)
• Allow explicitly setting bool options of FieldConvert modules as false (!811)
• Enable output to multiple files (!844)
• Allow using xml file without expansion tag in FieldConvert (!849)
• Add Lambda 2 vortex detection criteria (!882)
• Add module for modifying/adding fields from expressions (!889, !903)
• Add module for evaluating the mean of variables on the domain (!894)
• Add module for counting the total number of DOF (!948)
• Fixed wss module for compressible flows (!958)
• Made Sutherland's law non-dimensional (!972)
• Add module for removing fields from .fld files (!978)
• Fixed nparts option in FieldConvert and automated Info.xml generation (!995)
• Added if statement to fix case of 1D/2D manifold interpolation in 1D/2D space, added check on dimensions for interpolation, fixed seg interp (!999)
• Fixed scaling for compressed xml, fixed error printout for mesh only (!1040)
• Add field conversion from Halfmode to SingleMode (!1032)
• Fix double precision output in .dat format (!1059)
• Add phase sampling feature in FilterFieldConvert (!1068)

IncNavierStokesSolver

• Replace steady-state check based on difference of norms by check based on norm of the difference, to be consistent with the compressible solver (!832)
• Updated SVV to allow for the DGKernel extension (!851)
• Pre-calculate Time invariant portion of Womersley Solution (!814)
• Fix for independent setting of SVV in Homogeneous direction (!936)
• Write flow field based on CFL threshold (!1025)
• Fix unsteady Stokes solver (!1074)

CompressibleFlowSolver

• Add 3D regression tests (!567)
• Introduce forcing for quasi-1D Euler simulations (!771)
• Allow performing axi-symmetric Euler and NS simulations (!771, !866)
• Add ability to use an exponential filtering for stabilization with seg, quad and hex elements (!771, !862)
• Fix compressible solver with NUMMODES=1 (!868)
• Introduce equations of state to account for real gas effects (!880)
• Made Sutherland's law non-dimensional (!972)
• Modified pressure outlet BCs to allow for the reference static pressure to be set from the VALUE fields (!981)
• hp scaling for Laplacian AV (!1013)
• Removed smooth AV (!1072)

AcousticSolver:

• Added two new boundary conditions to the APE system: RiemannInvariantBC and WhiteNoise (!782)
• Store base flow fields in a discontinuous projection (!918)
• Enabled 1D cases (!918)
• The APE system now uses u_i, c^2 and rho as base flow fields (!918)
• Added the Linearized Euler Equations (LEE) (!918)

ADRSolver:

• Fix forcing from file for Poisson solver (!1029)

APESolver:

• APESolver was replaced with AcousticSolver (!918)

PulseWaveSolver

• Added two new boundary conditions: AInflow and UInflow

CardiacEPSolver

• Converted FentonKarma model to dimensional form and added variants (!1011)

Documentation:

• Added an initial developer's guide (!1001)
• Updated user guide to reflect current implementation (!1051)
• Added manpages for key solvers and utilities (!1051)

Tester

• Fix build with boost 1.67 (!947)
• Various change to tests to decrease test time (!1053)
• Extend to support MPI tests with multiple executables (!1085)

Packaging:

• Add Dockerfiles and gitlab CI configuration for automatic builds (!1021, !1092, !1098)

v4.4.2

Library

• Fix evaluation of points (e.g. HistoryPoints, Interpolation to pts) close to the interface of two elements (!836)
• Fix deadlock in Hdf5 with homogeneous expansions (!858)
• Fix a few memory leaks in polylib (!863)
• Fix a crash when Interpolator is called on an empty field (!869)
• Fix petsc compile without MPI (!873)
• Fix calculation of BLPoints (!892)
• Fix deadlock in DiffusionLDG (!885)
• Fix uninitialised coefficients in DirectFull solver (!898)
• Updated PETSc to 3.7.7 (!916)
• Fix typecast to an integer which set Lz < 1 to zero when postprocess hdf5 output (!922)
• Fix program options errors on Windows in debug mode (!986)
• Fix potential clobbered output of ModArnoldi EVs when run in parallel (!983)

IncNavierStokesSolver

• Add a test for imaginary shift to be only used with Homogenous and SingleMode on. (!928)

NekMesh

• Fix missing periodic boundary meshing and boundary layer mesh adjustment configurations in 2D (!859)
• Fix 2D BL splitting where out-of-plane nodes would be created (!887)

Documentation:

• Fix sign of the viscous term in the velocity correction scheme equations in the user guide (!856)
• Fixed anonymous clone URL (!909)
• Add information on the limitations of Imaginary Shift for stability. (!928)

FieldConvert

• Allow passing input name with trailing separator (!879)
• Fix the interpcoord option of the interppointdatatofld module (!952)

Utilities

• Fix VtkToPng to account for deprecated VTK API for VTK version > 8.1 (!925)

v4.4.1

Library

• Remove m_offset_elmt_id and GetOffsetElmtId which fixed problems in 2D when quad elements are listed before tri elements (!758)
• Remove the duplicate output of errorutil (!756)
• Fix BLAS CMake dependencies (!763)
• Fix interpolation issue with Lagrange basis functions (!768)
• Fix issue with average fields not working with different polynomial order fields (!776)
• Fix rounding of integer parameters (!774)
• Fix Hdf5 output in FilterFieldConvert (!781)
• Fixed extreme memory consumption of Interpolator when interpolating from pts to fld or between different meshes (!783)
• Fix deadlock with HDF5 input (!786)
• Fix missing entriess in LibUtilities::kPointsTypeStr (!792)
• Fix compiler warnings with CommDataType (!793)
• Fix ability to set default implementation in Collections and added an option to set eNoCollections in FieldConvert as default (!789)
• Fix performance issue in ProcessIsoContour in relation to memory consumption (!821)
• Fix performance issue with ExtractPhysToBndElmt (!796)
• Fix available classes being listed multiple times (!817)
• Fix Intel compiler warnings (!837)
• Fix overwriting and backup of chk/fld files on slow file systes (!741)
• Fix DriverAdaptive with second order IMEX (!850)
• Fixed typo in eIMEXGear part (!854)
• Added regression tests for IMEXOrder1, IMEXOrder2, IMEXOrder3, MCNAB, IMEXGear, CNAB, 2nd order IMEX-DIRK, 3rd order IMEX-DIRK (!854)
• Fix bug due to subtractive cancellation in polylib routines (!778)

FieldConvert:

• Fix issue with field ordering in the interppointdatatofld module (!754)
• Fix issue with FieldConvert when range flag used (!761)
• Fix issue when using output-points combined with noequispaced (!775)
• Fix equispacedoutput for 3DH1D with triangles (!787)

NekMesh:

• Fix memory consumption issue with Gmsh output (!747, !762)
• Rework meshing control so that if possible viewable meshes will be dumped when some part of the system fails (!756)
• Add manifold meshing option (!756)
• Fix issue with older rea input files (!765)
• Fix memory leak in variational optimiser, add small optimisations (!785)
• Check the dimensionality of the CAD system before running the 2D generator (!780)
• Fix uninitialised memory bug in Nek5000 input module (!801)

IncNavierStokesSolver

• Fix an initialisation issue when using an additional advective field (!779)
• Fix MovingBody boundary condition (!852)

Utilities

• Fix vtkToFld missing dependency which prevented compiling with VTK 7.1 (!808)

Documentation

• Added missing details on artificial viscosity and dealising to compressible flow solver user guide (!846)

Packaging

• Added missing package for FieldUtils library (!755)

ADRSolver:

• Fix UnsteadyAdvectionDiffusion with DG (!855)

v4.4.0

Library:

• Add support for variable polynomial order for 3D simulations with continuous Galerkin discretisation (!604)
• Bump version of gsmpi to suppress autotuning output unless --verbose is specified (!652)
• Add support for variable polynomial order with periodic boundary conditions (!658)
• Statistics are now printed for lowest level of multi-level static condensation (!656)
• Sped up interpolataion from pts files and fixed parallel pts import (!584)
• Increased required boost version to 1.56.0 (!584)
• New FieldUtils library allows support for most FieldConvert post-processing operations during simulation using a new filter (!589)
• Adjust CMake dependencies to reduce compile time (!671)
• Homogeneous1D dealiasing improvements (!622)
• Add support for HDF5 as an alternative output to XML-based output, including refactoring of FieldIO, improvements to MPI interface and added communicators to boundary conditions (!615)
• Allow expansions to be loaded directly from field file (!617)
• New options for load balancing (DOF or BOUNDARY) in mesh partitioner (!617)
• Rework nodal utilities to support nodal prismatic elements (!660)
• Update Body/Field forces at each timestep (!665)
• Update nodalutil to include quad and hex elements and introduce SPI nodal points (!696)
• Add ability to restart time-averaging and Reynolds stresses from checkpoint file (!678)
• Extend ExtractDataToCoeffs to support interpolation between basis types for quads and hexahedra (!682)
• Enabled MUMPS support in PETSc if a Fortran compiler was found and added 3D support to the Helmholtz smoother used e.g. in FieldConverts C0Projection module (!714)
• Fix bug in Vmath::FillWhiteNoise which caused ForcingNoise to have a repeated pattern (!718)
• Fix bug in the calculation of the RHS magnitude in CG solver (!721)
• Fix bug in MPI detection for recent CMake on OS X (!725)
• Fix bug in CMake Homebrew and MacPorts detection for OS X (!729)
• Fix bug in FieldUtils when using half mode expansions (!734)
• Do not read the same fld/pts files again for every variable (!670)
• Fix bug in CMake PETSc detection for Ubuntu 16.04/Debian 9 (!735)
• Fix warnings with Intel compiler (!742)

ADRSolver:

• Add a projection equation system for C^0 projections (!675)

APESolver:

• Use a continuous basefield projection and revert to constant c formulation (!664)
• Added ability to compute CFL number (!664)
• Output Sourceterm (!664)
• Use the Forcing framework to define source terms (!665)

IncNavierStokesSolver:

• Add ability to simulate additional scalar fields (!624)
• Improve performance when using homogeneous dealiasing (!622)
• Fix linearised advection for full 3D cases (!708)
• Added a weak pressure formulation following Guermond & Shen (!713)
• Added a convective like outflow boundary condition from Dong (!713)
• Added the ability to specifiy Womersley boundary conditions for pulsatile flow (!472)

CardiacEPSolver:

• Added a Python translator utility to generate cell models from CellML (!723)

FieldConvert:

• Allow equi-spaced output for 1D and 2DH1D fields (!613)
• Update quality metric to include scaled Jacobian output (!695)
• Allow multiple XML files to be specified in InterpField module (!705)
• Fix issues with isocontour module (!719)
• Fix issue with interpolator routine (!746)

NekMesh:

• Modify curve module to allow for spline input (!628)
• Add STL surface writer module (!668)
• New module for inserting an alternate high-order surface into the working mesh (!669)
• Add curve projection routines to CAD system (!697)
• Extensive clean-up of NekMeshUtils/MeshElements and extension of makeorder to consider CAD information (!698)
• Improvements to mesh linearisation module (!659)
• Add support for Gmsh high-order output (!679)
• Move CAD classes to factory format (!676)
• Add module to check topology of the mesh along with boundary connectivity to detect problems such as hanging nodes (!691)
• Add option to linearise module to linearise only prisms (!688)
• Add reader for Nek5000 mesh files (!680)
• Add option to linearise to use element quality (!690)
• Add flag to insertsurface process for non-conforming geometries (!700)
• Bug fix to get two meshgen regression tests working (!700)
• Remove libANN in deference to boost::geometry (!703)
• Refactor library to use NekMesh modules for CAD generation (!704)
• Add varopti process module to optimise meshes (!711)
• Add a mesh extract option to the linearise module to visualise the result (!712)
• 2D to 3D mesh extrusion module (!715)
• Add new two-dimensional mesher from NACA code or step file (!720)
• Add basic gmsh cad (.geo) reader to the meshing system (!731)
• Fix inverted boundary layer in 2D (!736)
• More sensible element sizing with boundary layers in 2D (!736)
• Change variable names in mcf file to make more sense (!736)
• Fix issues in varopti module so that in can be compiled without meshgen on (!736)
• Replace LAPACK Eigenvalue calculation with handwritten function in varopti (!738)
• Improved node-colouring algorithm for better load-balancing in varopti (!738)
• Simplified calculation of the energy functional in varopti for improved performance (!738)

FieldConvert:

• Move all modules to a new library, FieldUtils, to support post-processing during simulations (!589)
• Add module to stretch homogeneous direction (!609)
• Add module to add composite ID of elements as a field (!674)
• Add reader for Nek5000 field files (!680)

Tester:

• Fix output not displayed on segfault or system error (!745)

v4.3.5

Library:

• Fix bug in DG with hybrid meshes (!694)
• Fix issue with parallel output (!699)
• Fix performance issue with iterative full solver (!693)
• Enforced precision on history point output (!706)

Documentation

• Update build instructions in user guide for Windows (!692)

Tester

• Fix bug in tester when no parameters specified for test executable (!701)

v4.3.4

Library:

• Fix performance issue with v_ExtractDataToCoeffs for post-processing of large simulations (!672)
• Added additional assertions to ensure homogeneous simulations have an even number of planes per process (!666)
• Fix compilation with NEKTAR_USE_MESHGEN option
• Fix IterativeFull solver in parallel (!685)
• Fix error message for missing fld file (!689)

IncNavierStokesSolver:

• Fix 2nd order time-integration for VCSMapping (!687)

v4.3.4

Library:

• Fix performance issue with v_ExtractDataToCoeffs for post-processing of large simulations (!672)

v4.3.3

Library:

• Auto-detect a shared filesystem and removed --shared-filesystem option (!654)
• Fix filters when using adaptive driver to avoid output being overwritten after each adaptive update (!588)
• Minor fix to suppress Xxt output unless --verbose is specified (!642)
• Fix of DirectFull solver in case where only Neumann boundary conditions are imposed. (!655)

FieldConvert:

• Fix to avoid repeated import of field file (!649)
• Fix issue with C^0 projection (!644)
• Fix verbose output when using --procid (!648)

NekMesh:

• Fix namespace issue in Star-CCM+ input header in NekMesh (!661)

CompressibleFlowSolver:

• Fix issue with residual output (!647)
• Issues with 1D Euler solver fixed (!565)
• Fix deadlocking issue with boundary conditions (!657)

Packaging:

• Fix NekMesh dependencies for DEB package (!650)
• Fix PETSc build on newer linux distributions (!646)

v4.3.2

Library:

• Add small optimisation for DriverAdaptive (!618)
• Updated FFTW build to use the compiler used for building Nektar++ (!629)
• Fix numbering bug in periodic boundary conditions (!631)
• Print error message for invalid equation also in release version (!634)
• HistoryPoints filter now uses closest plane to requested z-coordinate and output is produced in physical space (!621).
• Fix minor performance issue with time integration schemes (!632)
• Fix FilterCheckpoint filter to be consistent with IO_CheckSteps (!633)
• Fix CMake configuration for building on Windows 10 with VS 2015 (!641)
• Fix IO_CheckSteps to avoid missing first checkpoint (!639)
• Fix bug in iterative solver where only root process would ASSERT when exceeding the maximum number of iterations (!636)

FieldConvert:

• Fix appearence of duplicate messages when running in parallel (!626)
• Fix issue with efficiency when using large number of 3DH1D planes (!627)
• Add module for combining average fields (!620)
• Fix wall shear stress processing module for parallel execution (!635)

Packaging:

• Fixes for DEB package dependencies (!630)

v4.3.1

Library:

• Add THIRDPARTY_USE_SSL option to disable use of SSL on systems where CMake is not compiled with SSL support. (!602)
• Fixed a number of documentation issues (!586, !593, !596)
• Fix Homogeneous transform when unshuffling is not used. (!599)
• Fix namespace pollution in library header files. (!601)
• Fix issue with METIS compilation on clang 7.3 (!603)
• Fix issue with heterogeneous quadrilaterals (!607)
• Fix bug in modified Arnoldi algorithm causing convergence to be reported when number of vectors is less than nvec (!608)
• Fix uninitialised array bug in AssemblyMap (!598)
• Fix issue with LAPACK call in eigenvalue calculation (!610)
• Fix FieldConvert processing of partitions in serial (!612)
• Fix use of multi-level static condensation in parallel with periodic boundary conditions (!614)
• Fix NaN detection to work in parallel (!605)
• Add additional constructor to ContField3DHomogeneous1D for FieldConvert extract module. (!590)

NekMesh:

• Fix incorrect link directory on CCMIO library.

FieldConvert:

• Fix to FLD input to update the field definitions always, not just when a range is specified. (!611)

Tester:

• Remove requirement for executable to be specified in .tst file if it is overridden on the command-line (!595)

Packaging:

• Fix dependency resolution on generation of DEB packages. (!616)

v4.3.0

Library:

• Changed default XML format to compress mesh data (!533, !547)
• Various fixes for 3D homogeneous post-processing (!531, !529, !528, !526, !521)
• Fix boundary condition imposition for 3D homogeneous 2D HelmSolve (!545)
• Fix range with variable p option (!522)
• Fix bug with hexahedra of heterogeneous order (!520) and reading files (!522)
• Fix history point output formatting (!518)
• Fix for OS X 10.11 (!512)
• Fix HexGeom::v_GetDir to support heterogeneous basis functions (!520)
• Added new NekMeshUtils library to support new NekMesh executable and associated CAD routines. Old CAD wrappers in LibUtilities now moved to NekMeshUtils (!527)
• Fix initialisation bug in ExpList2DH1D and ExpListHomogeneous2D (!528, !529)
• Fix bug in ExpList1D which may lead to invalid .vtu files (!531)
• Make GetBoundaryToElmtMap consistent for 3DH1D (!526)
• Add support for PETSc matrix shell to use Nektar++ operations/preconditioners (!537)
• Fix bug with initial conditions of CG simulations using variable P (!543)
• Fix bug in 3DH2D with non-zero Dirichlet boundary conditions (!545)
• Added in a method to convert equispaced interpolated points back to coefficients which requires the introduction of a new StdRegions matrix.(!561)
• Empty XML tags which would override non-empty XML tags are now ignored (!581)
• Add contribution guide (!551)
• Add a filter to calculate exponential moving averages (!566)

APESolver:

• Fix restarting from checkpoint file (!517)

IncNavierStokesSolver

• Fix floquet stability analysis for HalfMode case (!536)
• Add a filter to calculate Reynolds stresses (!566)

FieldConvert:

• Extended surface distance module to support hexahedra and quads (!524)
• Small fixes in interpolation routine (!515)
• Add support for surface extraction in 3DH1D case (!521)
• Add support for isocontour extraction for 3DH1D (!525)
• Add process module to calculate high-order mesh quality metric (!527).
• Add module to extract one of the planes of 3DH1D (!542)
• Add module to enable mean mode of 3DH1D to be extracted (!530)
• Fix bug in C^0 projection (!541))
• Add command line option to set number of homogeneous planes (!540)
• Add module to project set of points to a fld file(!561)
• Add support for interpolating to a box of points and fix ability to run interppointstofld module in parallel when using a plane or box option (!561)
• Add option to output equi-spaced points in VTU format (!550)
• Add module innerproduct (!568)
• Add command line option of --part-only and --part-only-overlapping (!569)

NekMesh:

• MeshConvert is now renamed to NekMesh to reflect new mesh generation functionality (!527).
• Enable face curvature inside core MeshConvert objects (!511)
• Add linearise processing module to remove all curvature from high order elements (!509)

Documentation:

• Added git submodule for including Nektar++ tutorials in the source tree (!507)

v4.2.0

Library:

• Add Runge-Kutta SSP schemes for 2nd/3rd order using keys RungeKutta2_SSP and RungeKutta3_SSP. ClassicalRungeKutta4 is now called RungeKutta4. (!481)
• Add rudimentary support for 3D CAD models using OpenCascade - work in progress (!486)
• Allow filters to evaluate expressions in their parameter definitions (!489)
• Fix block preconditioner to work with periodic boundary conditions (!420)
• Dump a backtrace when crash occurs and Nektar++ is compiled in FullDebug mode (!495)
• Stop the execution of a time-dependent solver if NaN is detected in the solution field (!496)
• Fixes to improve robustness of interpolation routines (!499)
• Allow solvers to use multi-level static condensation with Xxt, most useful when running a 3DH1D simulation (!502)

IncNavierStokesSolver:

• A range of fixes for the coupled stability solver, which now works in parallel (!508)

MeshConvert:

• Add module to extract prismatic boundary layer elements from mixed prism-tet mesh (!493).

FieldConvert:

• Add a processing module to calculate height of an element connected to a surface, allowing for calculation of y plus values (!488)
• Fixes for equispaced output (!510)

v4.1.0

Library:

• Add support for interpolating point data from .pts files (!433)
• Fixes for curvilinear element normals (!443)
• Fix consistency issues between FFT and MVM approaches for homogeneous expansions (!444)
• Fix a bug in Tecplot output (!445)
• Fix a bug with PETSc and MPI_Finalize (!456)
• Fix bugs with mesh partitioning (!449, !480)
• Fix a bug with non-symmetric SVV parameters for curvilinear elements (!451)
• Fix detection of Intel MKL 2013/2015 (453)
• Fix linearised stability solver in parallel (!454)
• Add a filter for 1D energy spectra (!457)
• Add an incomplete developer guide containing most information from the wiki (!459)
• Change user defined boundary conditions to remove dependency on enumerator inside SpatialDomains (!460)
• Add a new collections library for optimised evaluation of operators (!461)
• Change minimum version of boost to 1.52.
• Add initial multithreading support (!463)
• Fix third-party boost compilation on OS X (!467)
• Disable some regression tests on 32-bit systems (!468)
• Fix memory issues inside collections (!473)
• Fix collections autotuning (!476)
• Fix VtkToPng utility (!477)
• Add PulseWaveSolver to packaging (!478)
• Fix bug in iterative static condensation solver (!483)
• Fix zlib install path on OS X (!484)
• Fix documentation HTML styling for user and developer guide (!485)
• Add fixes to support native Nektar++ extension in VisIt visulisation software (!490)
• Fix warnings on OS X (!491)

CardiacEPSolver:

• Fixes for stimuli (!442, !446), conductivity (!441), cell restarts (!458)
• Add a new filter for outputting cell states at specific points over time (!465)

Linear elastic solver (new):

• Add solver for linear elasticity equations (!400)

IncNavierStokesSolver:

• Add support for moving bodies (!344, !448)
• Fixes for modal energy filter (!427)
• Fix import of mesh file in the Adaptive SFD driver (!440) and other general fixes (!452)
• Documentation for high order pressure and outflow boundary conditions (!447)
• Update examples to use correct forcing terms (!470)
• Fixes for half-mode stability (!471)
• Fix static initialisation problem in extrapolation classes (!492)

CompressibleFlowSolver:

• Add support for sponge region (!396)
• Add support for adiabiatic walls (!430)
• Add utility to generate boundary layer from similarity solution (!438)

ShallowWaterSolver:

• Added a DG solver for the Boussinesq equations of Peregrine (!431)

APESolver:

• Add support for variable speed of sound (!438)

MeshConvert:

• Fix Star file input for highly stretched elements (!455)
• Add Star input from binary format (!474)
• Tidy up files to align with FieldConvert (!479)

FieldConvert:

• Major re-organisation of modules, most post-processing utilities now available within FieldConvert (!475)

v4.0.1

Library:

• Change hybrid parallelisation to use command line options (!368)
• Add support for multi-variable functions in expression evaluator: new functions include rad and ang for polar coordinates (!375)
• Add more documentation (!376, !383)
• Various OS X (!377, !378, !382, !425), compiler warning (!432), documentation (!434) Windows 7 (!391, !407), CMake (!392, !415), packaging (!435, !436) and Intel compiler (!414, !416) fixes
• Refactor of CG and DG assembly maps (!380)
• Fixes for PETSc running in serial (!381, !420)
• Fixes for running Arnoldi solver in parallel (!384)
• Enable MPI tests on Cray machines such as ARCHER (!386)
• Fix issues with extracting face physical values (!393)
• Fix threshold filter (!395)
• HDG can now use block preconditioner (!397)
• Fix issue with singular vertices in parallel (!398)
• Timing executables now use Timer class from LibUtilities (!402)
• Fix manifold history points again (!410)
• Fix time output inside energy filter (!412)
• Fix GetExpIndex function (!417)
• Fixes to external project compilation (!419)
• Fixes from CPC paper review (!422)
• Fixes for scotch partitioner tests (!423)
• Fixes for ACML BLAS libraries (!424)
• Allow prepartitioned meshes to be used (!426)
• Enable variable names to be remapped inside files to different names in XML functions (!428)

APESolver:

• Fixes for tests (!404)
• Add support for advection classes (!408)

CardiacEPSolver:

• Add benchmark (!411)
• Fix cardiac exmplaes (!418)

CompressibleFlowSolver:

• Add filter for kinetic energy/enstrophy calculation (!388)

FieldConvert:

• Support equi-spaced output for simplex elements to reduce storage (!421)

IncNavierStokesSolver:

• Unify advection classes with those in SolverUtils (!403, !408)

MeshConvert:

• Boundary layer refinement now supports hexahedra (!390)
• Improve support for Gmsh high order elements (!401)
• Many fixes for face-interior curvature (!401)
• Add rudimentary test suite (!401)
• New module for imposing curvature based on a scalar function (!401)

v4.0.0

Library:

• Update boost to 1.55 (!289)
• Fix parallel history points on manifold (!298)
• Add support for scotch partitioner (!311)
• Fixes for thirdparty builds (!319, !330, !353)
• Fix CMake >= 3.0.0 warnings (!320)
• Add support for PETSc library and tidy up global system classes (!322)
• Fixes for 1D Helmholtz solver (!326)
• Fixes for history points (!327) and solver output (!331)
• Fix issue with mesh IDs that do not start from zero (!354)

CardiacEPSolver:

• Simplify support for global conductiity (!295)

FieldConvert:

• Fixes for parallel operation and interpolation of points (!351)

IncNavierStokesSolver:

• Fixes for sponge layer (!272)
• Fix setting of initial conditions (!298)

v3.4.0

Library:

• New parallel output format. Parallel files are now stored in directories which contain partition information. (!100, !102, !236, !242, !249, !256).
• gzip-compressed XML mesh files are now supported with extension .xml.gz (!116, !140, !186).
• HDG solvers now run in parallel and have post-processing utilities (!188, !230).
• Partitioning can be done only on root process if shared filesystem is present with use of --shared-filesystem command line option (!220, !250).
• A variety of preconditioners are now supported, including linear space and low-energy preconditioning (!148).
• Many changes to geometric factors storage and interpolation (!99, !197).
• Improvements to identification of invalid elements (!208, !227).
• Removed elemental storage to reduce memory consumption by 30-50% for large problems (!240).
• Various performance and design improvements for discontinuous formulation (!134).
• Periodic boundary conditions are supported in 3D for both continuous and discontinuous formulations (!139, !150, !152, !155, !196).
• Utilities added to mesh converter to help identify pairs of periodic faces (!214).
• Preconditioner support for periodic boundary conditions (!231, !239).
• New radiation boundary condition type (!74).
• Some solvers (compressible flow solver, advection-diffusion-reaction solver) now support dealiasing options (!78, !146, !167).
• BLAS and vectorisation performance improvements for static-condensed iterative solver (!86, !109).
• New driver to improve steady state convergence and add parallel support (!91, !235).
• Updated to METIS v5.1.0 (!97, !142, !189).
• Iterative solvers now use previous timestep (when available) to improve convergence speed (!106).
• Added CPU timing for timestep loop (!156).
• Added provenance information (date, time, code version, git revision, etc) to field file output (!179).
• Disabled long-running regression tests by default (!183).
• Support for command line arguments without parameters (!187).
• Added support for reading boundary conditions from files, and appropriate utilities in MeshConvert to extract surfaces (!226).
• Updated XXt and Gs libraries to latest version (!232).
• Fix singularity check for Poisson equations (!74, !154).
• Fixes for 2D Gauss points (!73, !149, !157).
• Fixes to parallel I/O (!77, !218, !264).
• Fixes for parallel implementation (!93, !107, !121, !169, !217, !245, !246).
• Fixes for normal calculation (!94, !135).
• Improved compilation techniques, particularly when compiler includes MPI automatically (!80, !82, !84, !85, !113, !114, !131, !141, !166, !210, !241).
• Updated zlib to v1.2.7 (!115).
• Fix for boost 1.5.3 compilation (!120).
• Most compiler warnings silenced with clang/gcc (!81, !92, !103, !123, !201, !243).
• Attempts to improve mesh partitioning/load balancing (!160, !170, !175).
• Fixes for Newton iteration to interpolate inside deformed elements (!216, !251).
• Fixed curved tetrahedron and hexahedron issue (!219, !248).
• Fixed reading of field files for tetrahedron (!228).
• Fixed uninitialised variable inside SessionrReader (!233).
• Various improvements to support use of Nektar++ externally (!111, !260, !261).
• Fixed base flow reading (!112).

CardiacEPSolver:

• Cardiac electrophysiology solver improvements (!87, !95, !96, !108, !119, !165, !173, !174, !199, !222).

CompressibleFlowSolver:

• Compressible Navier-Stokes equations are now available for both DG and FR discretisations (!110, !125, !128).
• Meshes with spatially varying p in both 2D and 3D are now supported (!158).
• Homogeneous Fourier extension is now supported (!180).
• Various fixes (!90, !98, !147, !172).

DiffusionSolver (new):

• Added small solver to demonstrate usage of higher library levels outside of EquationSystem (!225).

IncNavierStokesSolver:

• Major refactoring of time-integration classes (!181, !184).
• Summary information now generated via callbacks (!182).
• Implemented new generic forcing function classes (!194).
• Current time now written out in field files (!198).
• Major refactoring of incompressible Navier-Stokes solver to improve readability and performance (212, !213).
• Spectral vanishing viscosity for stabilisation (!101, !104, !211, !263).
• Added filter to compute aerodynamic forces on surfaces (!168, !203, !204).
• Added filter to compute kinetic energy and enstrophy (!207, !257).

ShallowWaterSolver:

• Various improvements/modernisations to shallow water solver (!190).

Utilities:

• VTK to PNG converter (!122)
• Added scalar gradient utility (!129, !252).
• Added utility to calculate Q-criterion field (!153).
• Added support to XmlToVtk to write Jacobian field (!223).
• Added utility to calculate wall shear stress (!224).
• Fixed vorticity calculator (!138).

MeshConvert:

• Added face-interior quadrature and 2D/3D manifold support to spherigon code (!130).
• Fixes for boundary layer refinement and prism-to-tetrahedron splitting (!137, !202, !206, !244).

FieldConvert (new):

• Added new FieldConvert utility which will eventually encompass most existing utilities (!255).