CHANGELOG.md 29.5 KB
Newer Older
Dave Moxey's avatar
Dave Moxey committed
1 2 3
Changelog
=========

Spencer Sherwin's avatar
Spencer Sherwin committed
4
v5.0.0
5
------
Dave Moxey's avatar
Dave Moxey committed
6 7 8
**Library**
- Added in sum factorisation version for pyramid expansions and orthogonal
  expansion in pyramids (!750)
Dave Moxey's avatar
Dave Moxey committed
9
- Significant overhaul of CMake infrastructure (!770, !804)
Michael Turner's avatar
Michael Turner committed
10
- Fix ThridpartyCCM options (!802)
Julian Marcon's avatar
Julian Marcon committed
11
- Fix Windows CRLF tokens in GEO reader and improve comment handling (!805)
Douglas Serson's avatar
Douglas Serson committed
12
- Use chrono in Timer (!807)
Kilian Lackhove's avatar
Kilian Lackhove committed
13 14
- Fix caching of FUNCTION tags that read from file and provide the same
  functionality in FUNCTIONs defined for forcings (!759)
Michael Turner's avatar
Michael Turner committed
15
- Add patch to tinyxml to fix size_t vs int bug (!820)
Michael Turner's avatar
Michael Turner committed
16
- Add ARPACK thirdparty build capabilities (!828)
Kilian Lackhove's avatar
Kilian Lackhove committed
17
- Added native support for csv files in addititon to pts (!760 !835)
Kilian Lackhove's avatar
Kilian Lackhove committed
18
- Utilize LAPACK_DIR env variable to find the native blas/lapack install (!827)
19
- Remove StdExpansion use from MultiRegion (use Expansions instead). (!831)
Douglas Serson's avatar
Douglas Serson committed
20
- Simplify RawType typedefs (!840)
Douglas Serson's avatar
Douglas Serson committed
21 22
- Remove unused files from BasicUtils (!841)
- Remove checks for old boost versions which are no longer supported (!841)
Dave Moxey's avatar
Dave Moxey committed
23
- Refactor ParseUtils to be more consistent (!843)
Kilian Lackhove's avatar
Kilian Lackhove committed
24 25
- Added support for using the distance to a specific region (e.g. outlet) in the
  function definitions for the Absorption Forcing (!769)
26

27
**NekMesh**:
28
- Add feature to read basic 2D geo files as CAD (!731)
29
- Add periodic boundary condition meshing in 2D (!733)
30
- Adjust boundary layer thickness in corners in 2D (!739)
Julian Marcon's avatar
Julian Marcon committed
31
- Add non-O BL meshing in 2D (!757)
Michael Turner's avatar
Michael Turner committed
32
- Add ability to compile CCIO library but tar file is not yet openly
Spencer Sherwin's avatar
Spencer Sherwin committed
33
  available whist we seek permission from Simens (!799)
Michael Turner's avatar
Michael Turner committed
34
- Fix issue with reading CCM files due to definition of default arrays
Spencer Sherwin's avatar
Spencer Sherwin committed
35
  rather than a vector (!797)
Michael Turner's avatar
Michael Turner committed
36
- Fix inverted triangles and small memory issue in surface meshing (!798)
Michael Turner's avatar
Michael Turner committed
37
- Update for the CAD system, more advance self-healing and analysis (!822)
Julian Marcon's avatar
Julian Marcon committed
38
- Additional curve types in GEO reader: BSpline, Circle, Ellipse (!800)
Michael Turner's avatar
Michael Turner committed
39
- Fix default command line argument value (!823)
40

Dave Moxey's avatar
Dave Moxey committed
41 42
**FieldConvert**:
- Add input module for Semtex field files (!777)
Kilian Lackhove's avatar
Kilian Lackhove committed
43
- Fixed interppoints module (!760)
Douglas Serson's avatar
Douglas Serson committed
44
- Move StreamFunction utility to a FieldConvert module (!809)
Douglas Serson's avatar
Douglas Serson committed
45
- Extend wss module to compressible flows (!810)
Douglas Serson's avatar
Douglas Serson committed
46
- Allow explicitly setting bool options of FieldConvert modules as false (!811)
Douglas Serson's avatar
Douglas Serson committed
47
- Enable output to multiple files (!844)
Douglas Serson's avatar
Douglas Serson committed
48
- Allow using xml file without expansion tag in FieldConvert (!849)
49

Chris Cantwell's avatar
Chris Cantwell committed
50 51 52
**Documentation**:
- Added the developer-guide repository as a submodule (!751)

Dave Moxey's avatar
Dave Moxey committed
53 54
v4.4.1
------
Michael Turner's avatar
Michael Turner committed
55
**Library**
Michael Turner's avatar
Michael Turner committed
56
- Remove m_offset_elmt_id and GetOffsetElmtId which fixed problems in 2D when
57
  quad elements are listed before tri elements (!758)
Michael Turner's avatar
Michael Turner committed
58
- Remove the duplicate output of errorutil (!756)
Dave Moxey's avatar
Dave Moxey committed
59
- Fix BLAS CMake dependencies (!763)
Dave Moxey's avatar
Dave Moxey committed
60
- Fix interpolation issue with Lagrange basis functions (!768)
61 62
- Fix issue with average fields not working with different polynomial order
  fields (!776)
Douglas Serson's avatar
Douglas Serson committed
63
- Fix rounding of integer parameters (!774)
Douglas Serson's avatar
Douglas Serson committed
64
- Fix Hdf5 output in FilterFieldConvert (!781)
Kilian Lackhove's avatar
Kilian Lackhove committed
65 66
- Fixed extreme memory consumption of Interpolator when interpolating from pts
  to fld or between different meshes (!783)
Dave Moxey's avatar
Dave Moxey committed
67
- Fix deadlock with HDF5 input (!786)
Dave Moxey's avatar
Dave Moxey committed
68
- Fix missing entriess in LibUtilities::kPointsTypeStr (!792)
Dave Moxey's avatar
Dave Moxey committed
69
- Fix compiler warnings with CommDataType (!793)
70 71 72 73 74
- 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)
75
- Fix available classes being listed multiple times (!817)
Chris Cantwell's avatar
Chris Cantwell committed
76
- Fix Intel compiler warnings (!837)
Kilian Lackhove's avatar
Kilian Lackhove committed
77
- Fix overwriting and backup of chk/fld files on slow file systes (!741)
Douglas Serson's avatar
Douglas Serson committed
78
- Fix DriverAdaptive with second order IMEX (!850)
79 80 81
- 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)
Chris Cantwell's avatar
Chris Cantwell committed
82
- Fix bug due to subtractive cancellation in polylib routines (!778)
Michael Turner's avatar
Michael Turner committed
83

84 85
**FieldConvert:**
- Fix issue with field ordering in the interppointdatatofld module (!754)
Dave Moxey's avatar
Dave Moxey committed
86
- Fix issue with FieldConvert when range flag used (!761)
87
- Fix issue when using output-points combined with noequispaced (!775)
Douglas Serson's avatar
Douglas Serson committed
88
- Fix equispacedoutput for 3DH1D with triangles (!787)
Michael Turner's avatar
Michael Turner committed
89

Dave Moxey's avatar
Dave Moxey committed
90
**NekMesh**:
Dave Moxey's avatar
Dave Moxey committed
91
- Fix memory consumption issue with Gmsh output (!747, !762)
92 93 94
- 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)
Dave Moxey's avatar
Dave Moxey committed
95
- Fix issue with older rea input files (!765)
Dave Moxey's avatar
Dave Moxey committed
96
- Fix memory leak in variational optimiser, add small optimisations (!785)
97
- Check the dimensionality of the CAD system before running the 2D generator (!780)
98
- Fix uninitialised memory bug in Nek5000 input module (!801)
Dave Moxey's avatar
Dave Moxey committed
99

Spencer Sherwin's avatar
Spencer Sherwin committed
100 101
**IncNavierStokesSolver**
- Fix an initialisation issue when using an additional advective field (!779)
102
- Fix MovingBody boundary condition (!852)
Spencer Sherwin's avatar
Spencer Sherwin committed
103

104 105 106
**Utilities**
- Fix vtkToFld missing dependency which prevented compiling with VTK 7.1 (!808)

Chris Cantwell's avatar
Chris Cantwell committed
107 108 109 110
**Documentation**
- Added missing details on artificial viscosity and dealising to compressible
  flow solver user guide (!846)

Chris Cantwell's avatar
Chris Cantwell committed
111 112 113
**Packaging**
- Added missing package for FieldUtils library (!755)

Douglas Serson's avatar
Douglas Serson committed
114 115 116
**ADRSolver:**
- Fix UnsteadyAdvectionDiffusion with DG (!855)

Dave Moxey's avatar
Dave Moxey committed
117 118
v4.4.0
------
Dave Moxey's avatar
Dave Moxey committed
119
**Library**:
Dave Moxey's avatar
Dave Moxey committed
120 121
- Add support for variable polynomial order for 3D simulations with continuous
  Galerkin discretisation (!604)
Dave Moxey's avatar
Dave Moxey committed
122 123
- Bump version of gsmpi to suppress autotuning output unless `--verbose` is
  specified (!652)
Dave Moxey's avatar
Dave Moxey committed
124 125
- Add support for variable polynomial order with periodic boundary conditions
  (!658)
Dave Moxey's avatar
Dave Moxey committed
126 127
- Statistics are now printed for lowest level of multi-level static condensation
  (!656)
128 129
- Sped up interpolataion from pts files and fixed parallel pts import (!584)
- Increased required boost version to 1.56.0 (!584)
Dave Moxey's avatar
Dave Moxey committed
130 131
- New FieldUtils library allows support for most `FieldConvert` post-processing
  operations during simulation using a new filter (!589)
Dave Moxey's avatar
Dave Moxey committed
132
- Adjust CMake dependencies to reduce compile time (!671)
Dave Moxey's avatar
Dave Moxey committed
133
- Homogeneous1D dealiasing improvements (!622)
134 135 136
- 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)
Chris Cantwell's avatar
Chris Cantwell committed
137 138
- Allow expansions to be loaded directly from field file (!617)
- New options for load balancing (DOF or BOUNDARY) in mesh partitioner (!617)
Dave Moxey's avatar
Dave Moxey committed
139
- Rework nodal utilities to support nodal prismatic elements (!660)
Kilian Lackhove's avatar
Kilian Lackhove committed
140
- Update Body/Field forces at each timestep (!665)
141 142
- Update nodalutil to include quad and hex elements and introduce SPI nodal
  points (!696)
Dave Moxey's avatar
Dave Moxey committed
143 144
- Add ability to restart time-averaging and Reynolds stresses from checkpoint
  file (!678)
Dave Moxey's avatar
Dave Moxey committed
145 146
- Extend ExtractDataToCoeffs to support interpolation between basis types for
  quads and hexahedra (!682)
Kilian Lackhove's avatar
Kilian Lackhove committed
147 148 149
- 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)
Douglas Serson's avatar
Douglas Serson committed
150 151
- Fix bug in `Vmath::FillWhiteNoise` which caused `ForcingNoise` to have
  a repeated pattern (!718)
Chris Cantwell's avatar
Chris Cantwell committed
152
- Fix bug in the calculation of the RHS magnitude in CG solver (!721)
Dave Moxey's avatar
Dave Moxey committed
153
- Fix bug in MPI detection for recent CMake on OS X (!725)
Dave Moxey's avatar
Dave Moxey committed
154
- Fix bug in CMake Homebrew and MacPorts detection for OS X (!729)
Douglas Serson's avatar
Douglas Serson committed
155
- Fix bug in FieldUtils when using half mode expansions (!734)
156
- Do not read the same fld/pts files again for every variable (!670)
Dave Moxey's avatar
Dave Moxey committed
157
- Fix bug in CMake PETSc detection for Ubuntu 16.04/Debian 9 (!735)
Dave Moxey's avatar
Dave Moxey committed
158
- Fix warnings with Intel compiler (!742)
Dave Moxey's avatar
Dave Moxey committed
159

Dave Moxey's avatar
Dave Moxey committed
160 161 162
**ADRSolver:**
- Add a projection equation system for C^0 projections (!675)

163 164 165 166
**APESolver:**
- Use a continuous basefield projection and revert to constant c formulation (!664)
- Added ability to compute CFL number (!664)
- Output Sourceterm (!664)
Kilian Lackhove's avatar
Kilian Lackhove committed
167
- Use the Forcing framework to define source terms (!665)
Dave Moxey's avatar
Dave Moxey committed
168

Dave Moxey's avatar
Dave Moxey committed
169 170
**IncNavierStokesSolver:**
- Add ability to simulate additional scalar fields (!624)
Dave Moxey's avatar
Dave Moxey committed
171
- Improve performance when using homogeneous dealiasing (!622)
Douglas Serson's avatar
Douglas Serson committed
172
- Fix linearised advection for full 3D cases (!708)
173 174
- Added a weak pressure formulation following Guermond & Shen (!713)
- Added a convective like outflow boundary condition from Dong (!713)
Spencer Sherwin's avatar
Spencer Sherwin committed
175
- Added the ability to specifiy Womersley boundary conditions for pulsatile flow (!472)
Dave Moxey's avatar
Dave Moxey committed
176

Chris Cantwell's avatar
Chris Cantwell committed
177 178
**CardiacEPSolver:**
- Added a Python translator utility to generate cell models from CellML (!723)
Dave Moxey's avatar
Dave Moxey committed
179

Dave Moxey's avatar
Dave Moxey committed
180 181
**FieldConvert:**
- Allow equi-spaced output for 1D and 2DH1D fields (!613)
182
- Update quality metric to include scaled Jacobian output (!695)
Chris Cantwell's avatar
Chris Cantwell committed
183
- Allow multiple XML files to be specified in InterpField module (!705)
Dave Moxey's avatar
Dave Moxey committed
184
- Fix issues with isocontour module (!719)
Spencer Sherwin's avatar
Spencer Sherwin committed
185
- Fix issue with interpolator routine (!746)
Dave Moxey's avatar
Dave Moxey committed
186

187 188
**NekMesh:**
- Modify curve module to allow for spline input (!628)
189
- Add STL surface writer module (!668)
190 191
- New module for inserting an alternate high-order surface into the working
  mesh (!669)
Dave Moxey's avatar
Dave Moxey committed
192
- Add curve projection routines to CAD system (!697)
Michael Turner's avatar
Michael Turner committed
193 194
- Extensive clean-up of NekMeshUtils/MeshElements and extension of makeorder to
  consider CAD information (!698)
Dave Moxey's avatar
Dave Moxey committed
195
- Improvements to mesh linearisation module (!659)
Dave Moxey's avatar
Dave Moxey committed
196
- Add support for Gmsh high-order output (!679)
Dave Moxey's avatar
Dave Moxey committed
197
- Move CAD classes to factory format (!676)
Michael Turner's avatar
Michael Turner committed
198 199
- Add module to check topology of the mesh along with boundary connectivity
  to detect problems such as hanging nodes (!691)
Dave Moxey's avatar
Dave Moxey committed
200
- Add option to `linearise` module to linearise only prisms (!688)
Dave Moxey's avatar
Dave Moxey committed
201
- Add reader for Nek5000 mesh files (!680)
202
- Add option to `linearise` to use element quality (!690)
Michael Turner's avatar
Michael Turner committed
203 204
- Add flag to `insertsurface` process for non-conforming geometries (!700)
- Bug fix to get two meshgen regression tests working (!700)
205
- Remove libANN in deference to boost::geometry (!703)
Dave Moxey's avatar
Dave Moxey committed
206
- Refactor library to use NekMesh modules for CAD generation (!704)
Michael Turner's avatar
Michael Turner committed
207
- Add `varopti` process module to optimise meshes (!711)
Michael Turner's avatar
Michael Turner committed
208 209 210
- Add a mesh extract option to the linearise module to visualise the result
  (!712)
- 2D to 3D mesh extrusion module (!715)
Julian Marcon's avatar
Julian Marcon committed
211
- Add new two-dimensional mesher from NACA code or step file (!720)
Dave Moxey's avatar
Dave Moxey committed
212
- Add basic gmsh cad (.geo) reader to the meshing system (!731)
Michael Turner's avatar
Michael Turner committed
213
- Fix inverted boundary layer in 2D (!736)
Julian Marcon's avatar
Tidy.  
Julian Marcon committed
214
- More sensible element sizing with boundary layers in 2D (!736)
Michael Turner's avatar
Michael Turner committed
215 216 217
- 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)
Michael Turner's avatar
Michael Turner committed
218
- Replace LAPACK Eigenvalue calculation with handwritten function in
Jan Eichstaedt's avatar
Jan Eichstaedt committed
219
  varopti (!738)
Michael Turner's avatar
Michael Turner committed
220
- Improved node-colouring algorithm for better load-balancing
Jan Eichstaedt's avatar
Jan Eichstaedt committed
221 222 223
  in varopti (!738)
- Simplified calculation of the energy functional in varopti for improved
  performance (!738)
224

Dave Moxey's avatar
Dave Moxey committed
225
**FieldConvert:**
Dave Moxey's avatar
Dave Moxey committed
226 227
- Move all modules to a new library, FieldUtils, to support post-processing
  during simulations (!589)
Dave Moxey's avatar
Dave Moxey committed
228
- Add module to stretch homogeneous direction (!609)
Dave Moxey's avatar
Dave Moxey committed
229
- Add module to add composite ID of elements as a field (!674)
Dave Moxey's avatar
Dave Moxey committed
230
- Add reader for Nek5000 field files (!680)
Dave Moxey's avatar
Dave Moxey committed
231

Chris Cantwell's avatar
Chris Cantwell committed
232 233
**Tester:**
- Fix output not displayed on segfault or system error (!745)
Dave Moxey's avatar
Dave Moxey committed
234

Chris Cantwell's avatar
Chris Cantwell committed
235 236
v4.3.5
------
Douglas Serson's avatar
Douglas Serson committed
237
**Library:**
Douglas Serson's avatar
Douglas Serson committed
238
- Fix bug in DG with hybrid meshes (!694)
Douglas Serson's avatar
Douglas Serson committed
239
- Fix issue with parallel output (!699)
Dave Moxey's avatar
Dave Moxey committed
240
- Fix performance issue with iterative full solver (!693)
Chris Cantwell's avatar
Chris Cantwell committed
241
- Enforced precision on history point output (!706)
Douglas Serson's avatar
Douglas Serson committed
242

Chris Cantwell's avatar
Chris Cantwell committed
243 244 245
**Documentation**
- Update build instructions in user guide for Windows (!692)

Chris Cantwell's avatar
Chris Cantwell committed
246 247 248
**Tester**
- Fix bug in tester when no parameters specified for test executable (!701)

Dave Moxey's avatar
Dave Moxey committed
249 250 251
v4.3.4
------
**Library:**
Chris Cantwell's avatar
Chris Cantwell committed
252 253
- Fix performance issue with `v_ExtractDataToCoeffs` for post-processing of
  large simulations (!672)
Chris Cantwell's avatar
Chris Cantwell committed
254 255
- Added additional assertions to ensure homogeneous simulations have an even
  number of planes per process (!666)
Douglas Serson's avatar
Douglas Serson committed
256
- Fix compilation with NEKTAR_USE_MESHGEN option
Chris Cantwell's avatar
Chris Cantwell committed
257
- Fix IterativeFull solver in parallel (!685)
Douglas Serson's avatar
Douglas Serson committed
258
- Fix error message for missing fld file (!689)
Dave Moxey's avatar
Dave Moxey committed
259

Douglas Serson's avatar
Douglas Serson committed
260 261 262
**IncNavierStokesSolver:**
- Fix 2nd order time-integration for VCSMapping (!687)

263 264 265 266 267 268
v4.3.4
------
**Library:**
- Fix performance issue with `v_ExtractDataToCoeffs` for post-processing of large
  simulations (!672)

Douglas Serson's avatar
Douglas Serson committed
269 270
v4.3.3
------
Dave Moxey's avatar
Dave Moxey committed
271
**Library**:
Kilian Lackhove's avatar
Kilian Lackhove committed
272
- Auto-detect a shared filesystem and removed --shared-filesystem option (!654)
Dave Moxey's avatar
Dave Moxey committed
273 274
- Fix filters when using adaptive driver to avoid output being overwritten after
  each adaptive update (!588)
Dave Moxey's avatar
Dave Moxey committed
275
- Minor fix to suppress Xxt output unless `--verbose` is specified (!642)
Michael Turner's avatar
Michael Turner committed
276
- Fix of DirectFull solver in case where only Neumann boundary conditions
Martin Vymazal's avatar
Martin Vymazal committed
277
  are imposed. (!655)
Dave Moxey's avatar
Dave Moxey committed
278

Dave Moxey's avatar
Dave Moxey committed
279 280
**FieldConvert**:
- Fix to avoid repeated import of field file (!649)
Dave Moxey's avatar
Dave Moxey committed
281
- Fix issue with C^0 projection (!644)
Chris Cantwell's avatar
Chris Cantwell committed
282
- Fix verbose output when using --procid (!648)
Dave Moxey's avatar
Dave Moxey committed
283

Dave Moxey's avatar
Dave Moxey committed
284 285
**NekMesh:**
- Fix namespace issue in Star-CCM+ input header in NekMesh (!661)
Dave Moxey's avatar
Dave Moxey committed
286

Dave Moxey's avatar
Dave Moxey committed
287 288
**CompressibleFlowSolver**:
- Fix issue with residual output (!647)
289
- Issues with 1D Euler solver fixed (!565)
Dave Moxey's avatar
Dave Moxey committed
290
- Fix deadlocking issue with boundary conditions (!657)
Dave Moxey's avatar
Dave Moxey committed
291

Douglas Serson's avatar
Douglas Serson committed
292 293
**Packaging**:
- Fix NekMesh dependencies for DEB package (!650)
294
- Fix PETSc build on newer linux distributions (!646)
Douglas Serson's avatar
Douglas Serson committed
295

Chris Cantwell's avatar
Chris Cantwell committed
296 297 298
v4.3.2
------
**Library**:
Dave Moxey's avatar
Dave Moxey committed
299
- Add small optimisation for DriverAdaptive (!618)
Chris Cantwell's avatar
Chris Cantwell committed
300
- Updated FFTW build to use the compiler used for building Nektar++ (!629)
Chris Cantwell's avatar
Chris Cantwell committed
301
- Fix numbering bug in periodic boundary conditions (!631)
Douglas Serson's avatar
Douglas Serson committed
302
- Print error message for invalid equation also in release version (!634)
Chris Cantwell's avatar
Chris Cantwell committed
303 304
- HistoryPoints filter now uses closest plane to requested z-coordinate and
  output is produced in physical space (!621).
Dave Moxey's avatar
Dave Moxey committed
305 306
- Fix minor performance issue with time integration schemes (!632)
- Fix FilterCheckpoint filter to be consistent with `IO_CheckSteps` (!633)
Chris Cantwell's avatar
Chris Cantwell committed
307
- Fix CMake configuration for building on Windows 10 with VS 2015 (!641)
Dave Moxey's avatar
Dave Moxey committed
308
- Fix `IO_CheckSteps` to avoid missing first checkpoint (!639)
309 310
- Fix bug in iterative solver where only root process would ASSERT when
  exceeding the maximum number of iterations (!636)
Chris Cantwell's avatar
Chris Cantwell committed
311

Chris Cantwell's avatar
Chris Cantwell committed
312 313
**FieldConvert**:
- Fix appearence of duplicate messages when running in parallel (!626)
Dave Moxey's avatar
Dave Moxey committed
314
- Fix issue with efficiency when using large number of 3DH1D planes (!627)
Dave Moxey's avatar
Dave Moxey committed
315
- Add module for combining average fields (!620)
Chris Cantwell's avatar
Chris Cantwell committed
316
- Fix wall shear stress processing module for parallel execution (!635)
Chris Cantwell's avatar
Chris Cantwell committed
317

Dave Moxey's avatar
Dave Moxey committed
318 319 320
**Packaging**:
- Fixes for DEB package dependencies (!630)

Dave Moxey's avatar
Dave Moxey committed
321 322 323 324 325
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)
326
- Fixed a number of documentation issues (!586, !593, !596)
Chris Cantwell's avatar
Chris Cantwell committed
327
- Fix Homogeneous transform when unshuffling is not used. (!599)
Chris Cantwell's avatar
Chris Cantwell committed
328
- Fix namespace pollution in library header files. (!601)
Dave Moxey's avatar
Dave Moxey committed
329
- Fix issue with METIS compilation on clang 7.3 (!603)
Dave Moxey's avatar
Dave Moxey committed
330
- Fix issue with heterogeneous quadrilaterals (!607)
Chris Cantwell's avatar
Chris Cantwell committed
331 332
- Fix bug in modified Arnoldi algorithm causing convergence to be reported when
  number of vectors is less than `nvec` (!608)
Chris Cantwell's avatar
Chris Cantwell committed
333
- Fix uninitialised array bug in AssemblyMap (!598)
Dave Moxey's avatar
Dave Moxey committed
334
- Fix issue with LAPACK call in eigenvalue calculation (!610)
Dave Moxey's avatar
Dave Moxey committed
335
- Fix FieldConvert processing of partitions in serial (!612)
Dave Moxey's avatar
Dave Moxey committed
336 337
- Fix use of multi-level static condensation in parallel with periodic
  boundary conditions (!614)
Chris Cantwell's avatar
Chris Cantwell committed
338
- Fix NaN detection to work in parallel (!605)
Chris Cantwell's avatar
Chris Cantwell committed
339 340
- Add additional constructor to ContField3DHomogeneous1D for FieldConvert
  extract module. (!590)
Dave Moxey's avatar
Dave Moxey committed
341

Chris Cantwell's avatar
Chris Cantwell committed
342 343 344
**NekMesh**:
- Fix incorrect link directory on CCMIO library.

Chris Cantwell's avatar
Chris Cantwell committed
345 346 347 348
**FieldConvert**:
- Fix to FLD input to update the field definitions always, not just when a range
  is specified. (!611)

Chris Cantwell's avatar
Chris Cantwell committed
349 350 351 352
**Tester**:
- Remove requirement for executable to be specified in .tst file if it is
  overridden on the command-line (!595)

Chris Cantwell's avatar
Chris Cantwell committed
353 354 355
**Packaging**:
- Fix dependency resolution on generation of DEB packages. (!616)

Dave Moxey's avatar
Dave Moxey committed
356 357
v4.3.0
------
358
**Library:**
Dave Moxey's avatar
Dave Moxey committed
359
- Changed default XML format to compress mesh data (!533, !547)
360
- Various fixes for 3D homogeneous post-processing (!531, !529, !528, !526, !521)
Chris Cantwell's avatar
Chris Cantwell committed
361
- Fix boundary condition imposition for 3D homogeneous 2D HelmSolve (!545)
362
- Fix range with variable p option (!522)
363
- Fix bug with hexahedra of heterogeneous order (!520) and reading files (!522)
364 365
- Fix history point output formatting (!518)
- Fix for OS X 10.11 (!512)
366
- Fix `HexGeom::v_GetDir` to support heterogeneous basis functions (!520)
367 368 369
- Added new `NekMeshUtils` library to support new `NekMesh` executable and
  associated CAD routines. Old CAD wrappers in LibUtilities now moved to
  `NekMeshUtils` (!527)
370 371 372
- 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)
Dave Moxey's avatar
Dave Moxey committed
373 374
- Add support for PETSc matrix shell to use Nektar++ operations/preconditioners
  (!537)
Douglas Serson's avatar
Douglas Serson committed
375
- Fix bug with initial conditions of CG simulations using variable P (!543)
Douglas Serson's avatar
Douglas Serson committed
376
- Fix bug in 3DH2D with non-zero Dirichlet boundary conditions (!545)
Michael Turner's avatar
Michael Turner committed
377
- Added in a method to convert equispaced interpolated points back to
378
  coefficients which requires the introduction of a new StdRegions matrix.(!561)
Chris Cantwell's avatar
Chris Cantwell committed
379
- Empty XML tags which would override non-empty XML tags are now ignored (!581)
380
- Add contribution guide (!551)
Douglas Serson's avatar
Douglas Serson committed
381
- Add a filter to calculate exponential moving averages (!566)
382 383 384

**APESolver:**
- Fix restarting from checkpoint file (!517)
Dave Moxey's avatar
Dave Moxey committed
385

Chris Cantwell's avatar
Chris Cantwell committed
386 387
**IncNavierStokesSolver**
- Fix floquet stability analysis for HalfMode case (!536)
Douglas Serson's avatar
Douglas Serson committed
388
- Add a filter to calculate Reynolds stresses (!566)
Chris Cantwell's avatar
Chris Cantwell committed
389

390
**FieldConvert:**
Dave Moxey's avatar
Dave Moxey committed
391
- Extended surface distance module to support hexahedra and quads (!524)
392
- Small fixes in interpolation routine (!515)
393 394
- Add support for surface extraction in 3DH1D case (!521)
- Add support for isocontour extraction for 3DH1D (!525)
395
- Add process module to calculate high-order mesh quality metric (!527).
Douglas Serson's avatar
Douglas Serson committed
396
- Add module to extract one of the planes of 3DH1D (!542)
397 398 399
- 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)
400
- Add module to project set of points to a fld file(!561)
401 402
- 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)
Chris Cantwell's avatar
Chris Cantwell committed
403
- Add option to output equi-spaced points in VTU format (!550)
Spencer Sherwin's avatar
Spencer Sherwin committed
404
- Add module innerproduct (!568)
405
- Add command line option of `--part-only` and `--part-only-overlapping` (!569)
406

Dave Moxey's avatar
Dave Moxey committed
407 408 409
**NekMesh:**
- `MeshConvert` is now renamed to `NekMesh` to reflect new mesh generation
  functionality (!527).
410 411 412
- Enable face curvature inside core MeshConvert objects (!511)
- Add linearise processing module to remove all curvature from high order
  elements (!509)
Dave Moxey's avatar
Dave Moxey committed
413

414 415 416
**Documentation:**
- Added git submodule for including Nektar++ tutorials in the source tree (!507)

Dave Moxey's avatar
Dave Moxey committed
417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
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:**
436 437
- A range of fixes for the coupled stability solver, which now works in parallel
  (!508)
Dave Moxey's avatar
Dave Moxey committed
438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523

**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
------

524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564
**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)
Dave Moxey's avatar
Dave Moxey committed
565

566 567 568 569 570 571 572 573 574
**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)
Dave Moxey's avatar
Dave Moxey committed
575 576 577 578

v4.0.0
------

579 580 581 582 583 584 585 586 587 588 589 590 591
**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)
Dave Moxey's avatar
Dave Moxey committed
592

593 594 595 596 597 598
**FieldConvert:**
- Fixes for parallel operation and interpolation of points (!351)

**IncNavierStokesSolver:**
- Fixes for sponge layer (!272)
- Fix setting of initial conditions (!298)
Dave Moxey's avatar
Dave Moxey committed
599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707

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).