CHANGELOG.md

Changelog

v4.5.0

NekMesh:

• Add periodic boundary condition meshing in 2D (!733)
• Adjust boundary layer thickness in corners in 2D (!739)

Library

• Added in sum factorisation version for pyramid expansions and orthogonal expansion in pyramids (!750)

Documentation:

• Added the developer-guide repository as a submodule (!751)

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)

FieldConvert:

• Fix issue with field ordering in the interppointdatatofld module (!754)
• Fix issue with FieldConvert when range flag used (!761)

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)

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)
• 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).