BOUT++ v4.3.0

4.3.0 is a big feature release:

• Fields are now "tagged" with their "y-direction": that is, whether
  they are in field-aligned space or not. This allows us to perform
  more internal checking, for example, that only field-aligned
  Field3Ds are passed to fromFieldAligned and that calculations
  are done in the correct y-direction space. Users may need to call
  f.setDirectionY(YDirectionType::Aligned) for a Field3D f to set
  the direction tag
• Add toFieldAligned and fromFieldAligned free functions
• bout::utils::is_Field and variants provide simpler methods of
  checking that input types are Fields in templated code
• Many, many more functions and operators support staggering. We're
  now also much more consistent about checking function arguments have
  compatible staggered locations
• New emptyFrom(f) and zeroFrom(f) helper functions for creating
  Fields either allocated but not initialised, or allocated and
  initialised to 0.0 respectively, while ensuring the result is
  compatible with the Field f (same mesh, same staggering, etc.)
• Expressions used in input files now have support for unicode,
  escaping characters and implicit multiplication. See
  #1333 for more
  details.
• Internationalisation support, including translations for French,
  German, Spanish, and Simplified and Traditional Chinese
• Keyword arguments for boundaries in input files, e.g. dirichlet(1, width=3)
• File-level attributes in output files
• Write more things to output files, including processor indices and
  parallel transform information
• Complete overhaul of the derivative operators:
  • derivative operators can now use native vectorisation where
    possible, as well parallelisation via OpenMP.
  • users can register their own derivative operators and choose
    them at runtime
  • more consistent handling of staggering in all directions and for
    all Field types
  • better handling of field-aligned Fields
• Various bug fixes for parallel derivative inversions
• Introduced zstart and zend, in preparation for introducing
  guard cells in the z-direction
• Options has several new features:
  • it can now store Fields. This uses an implementation
    of C++17's std::variant backported to work with
    C++11. Unfortunately, there are some compilers which have
    problems (see installation issues for help)
  • Options::isSection gained the ability to check whether an
    input argument is a subsection or not
  • now records the type of the option when used
  • gained the .doc method which allows documentation to be added
    as an attribute, which can be recorded in the BOUT.settings
    file post-run
• FFTW is now an optional dependency
• A non-Fourier implementation of Delp2
• A generic linear operator inversion class (see
  #1439)
• Array, Matrix and Tensor all gained a reallocate
  method. This allows dynamic resizing of those objects, but
  invalidates the existing data
• FieldFactory now has separate parsing and generating stages, so
  functions can be parsed once and evaluated multiple times (e.g. for
  time-dependent functions)
• Enable communications for simulations with no core, only divertor
  legs
• Coordinates on staggered grids can now be read from grid files
• New FDDX_U2 implementation
• Support for SUNDIALS versions 2.6 to 4.1.0
• BoutInitialise has been pulled apart into separate utility
  functions under the bout::experimental namespace so that they can
  be used individually
• LaplaceCyclic now accepts C1 and C2 coefficients which may be
  different
• LaplaceNaulin may use the DC parts of C for faster convergence
• LaplaceNaulin also gained an under-relaxation factor, which may
  improve convergence and robustness
• The Laplace solvers gained a uses3DCoefs method. This returns
  true if the solver can make use of Field3D coefficients rather
  than using the DC component of them
• A new time Solver: Runge-Kutta-Legendre stabilised explicit
  method, splitrk. See
  #1673 for more
  details
• Experimental support for CMake
• Added HeatFluxSNB which calculates heat flux using the
  Shurtz-Nicolai-Busquet (SNB) model. Nonlocal (kinetic) corrections
  to the Spitzer-Harm collisional heat flux, which become important
  when the mean free path becomes a small (~1%) fraction of the
  temperature scale length
• The new BOUT_SCOREP_REGION("name") will automatically instrument a
  scope with Score-P if BOUT++ was compiled with Score-P
  support (see the documentation for more information)
• NYPE may be given instead of NXPE in input files for decomposing
  the mesh in (x, y)
• Many fixes and improvements for Hypnotoad:
  • Use centred differencing to compute dx from psi instead of
    forward differencing
  • Fix for when the separatrix is exactly on a grid point
  • Fix for when the separatrix is very close to the X-point
  • Fix computation of ShiftAngle
  • Add a checkbox to the 'Output' tab, which if selected outputs
    metrics for orthogonal coordinates (i.e. using ShiftedMetric)
  • We now check what coordinate system was used to generate grid
    files in Hypnotoad when reading them in BOUT++
  • Lots of fixes for non-orthogonal grids (see
    #1593,
    #1596, and
    #1636)
  • Use double precision everywhere
  • Add option to write y-boundary guard cells
  • See here for a complete
    list
• Many, many more tests! Unit test coverage since v4.2.0 has doubled
• We have begun to move parts of the codebase into a bout::
  namespace. This should help ensure we play nice with other
  libraries, as well as logically group related things across parts of
  the codebase

Deprecations:

• invert_laplace: create an instance of a Laplacian via
  Laplacian::create and use the setCoef* and solve methods
• Karniadakis time Solver: the current implementation is very slow
  and will be removed in 5.0
• MsgStack::setPoint: use MsgStack::push("")
• The following Mesh methods were experimental, low-level
  communication routines that turned out to not be so useful:
  • sendToProc
  • receiveFromProc
  • UpXSplitIndex
  • DownXSplitIndex
  • sendYOutIndest
  • sendYOutOutdest
  • sendYInIndest
  • sendYInOutdest
  • irecvYOutIndest
  • irecvYOutOutdest
  • irecvYInIndest
  • irecvYInOutdest
• Mesh::XGLOBAL and Mesh::YGLOBAL: use Mesh::getGlobalXIndex and
  either Mesh::getGlobalYIndexNoBoundaries or
  Mesh::getGlobalYIndex instead. The former (NoBoundaries) is a
  direct replacement for YGLOBAL, whereas the latter includes the
  boundaries and so is consistent with XGLOBAL which does too
• Laplacian::setFlags: use Laplacian::setGlobalFlags,
  Laplacian::setInnerBoundaryFlags and
  Laplacian::setOuterBoundaryFlags instead
• The staggered parallel differential operators that end CtoL or
  LtoC (e.g. Div_par_CtoL, Grad_par_LtoC): the corresponding
  versions without the suffix now support staggering. For example,
  instead of Div_par_CtoL(f) use Div_par(f, CELL_YLOW) instead

Removed:

• The serial implementation of parderiv. The cyclic version
  works both serially and in parallel
• comm_group: not used internally and too low-level to be useful
• Support for the scipy and scientific netCDF libraries in
  boututils has been dropped. These were very slow and scientific
  is no longer available
• Laplace3D: use Laplacian instead

BOUT++ v4.2.3

This is a bugfix release:

• Add counters to Timers to avoid double-counting sections #1817 (ZedThree)
• Bugfix: cyclic parallel derivative inversion done in wrong space #1807 (ZedThree)
• Add instructions for Ubuntu 16.04 #1690 (dschwoerer)
• Allow relative paths to be followed when making #1670 (johnomotani)
• Update examples/staggered_grid for v4.2 #1645 (johnomotani)
• Add EXTRA_LIBS to LIBS when searching for libraries #1632 (ZedThree)
• Recent fixes/improvements for Travis into master #1627 (ZedThree)
• Bug in calculation of ShiftAngle (qloop) #1626 (bendudson)

See CHANGELOG.md for more details

Note: if you download the source code tarball from GitHub, please download the file BOUT++-v4.2.3.tar.gz rather than the GitHub generated tarballs. This is because the GitHub tarball does not include the submodules.

BOUT++ v4.2.2

This is a bugfix release:

• Fix a couple of bugs when updating Coordinates objects on the mesh
• Fix a bug in FCI: missed the last point in Z for corner
  displacements
• Fix location not being set correctly in LaplaceXZ
• Fix some bugs in finite volume methods:
  • Wrong region used in loop
  • Metric component indexed at wrong location
  • Use field-aligned field if necessary
• Fix wall-time limit not triggering on all processes
• Link against libdl if needed for backtrace
• Provide version numbering for Hypnotoad
• Small improvements to testing frameworks
• Various warning fixes

BOUT++ v4.2.1

This is a bugfix release, fixing a small number of issues:

• Try to provide some thread safety to msg_stack
• Fix listing available derivative methods
• Initialize Coordinates objects in BoutMesh::load()
• Use localmesh for d2x and d2y, and interpolate them to location
• Several Hypnotoad fixes
• Silence remaining warnings on master
• Fix bugs in boututils.calculus.deriv2D
• Fix failure of collect() with integer slice argument
• Fix setCoefs in InvertPar
• Support BoutOutputs caching option in boutcore fromBoutOutputs
• Check for nullptr in NcFormat::get/setAttribute
• Set location in LaplaceCyclic::solve() and DC()

See CHANGELOG.md for more details

Note: if you download the source code tarball from GitHub, please download the file BOUT++-v4.2.1.tar.gz rather than the GitHub generated tarballs. This is because the GitHub tarball does not include the submodules.

BOUT++ v4.2.0

BOUT++ v4.2.0 is a big feature release:

• Large number of optimisations (as much as 140% faster than v4.1.2!)
• OpenMP in many more places, enables parallelisation in Z (as well as X for FCI)
• Better support for OpenMP, including in Python tools
• Much more versatile region system, allowing arbitrary regions (can e.g. mask certain parts of the domain for most common operations)
• Specialised macro for looping over Fields, handles arbitrary regions, OpenMP parallelisation, while also supporting native vectorisation
• Add support for new region system to many functions
• Better support for staggered grids: many bugfixes and many more functions support setting the location
• Coordinates objects can be created at different locations, through the Mesh::getCoordinates and Field::getCoordinates methods
• Support for compiling as a shared library
• Experimental Python API via Cython module
• Arithmetic operators on fields are now generated using Jinja2
• Improved PETSc compatibility (better support out of the box, supports up to 3.9, drops support for versions before 3.4)
• New support classes for 2D/3D arrays (Matrix/Tensor)
• New interface for Options
• Divergence operators for FCI
• Support for attributes in NetCDF files
• Default Laplacian changed to cyclic
• Many C++ modernisation fixes
• New monotonic Hermite spline interpolator
• Better configure experience
• Zoidberg can produce curvilinear grids in all three directions (enables e.g. stellarator geometry. Current version of BOUT++ can't actually handle this yet -- upcoming version!)
• Many more tests, and a better testing framework for the integrated tests
• Some potential memory leaks and null pointer dereferences fixed

Deprecations

• DataIterator is deprecated in favour of the new Region and Ind2D/3D/Perp family. This should not affect user code -- if it does, replacing DataIterator with auto should do the right thing in most cases
• DataFile::writeVar: use DataFile::addOnce
• Field::setName and Field::getName: just use Field::name directly instead
• Field::error and bout_error: use BoutException instead
• rvector/rmatrix/rtensor families of functions: use Matrix/Tensor instead
• operator^(Vector2D/Vector3D): use cross() instead
• The derivative function overloads with this order of arguments: DD?(..., DIFF_METHOD, CELL_LOC, REGION). Instead, use DD?(..., CELL_LOC, DIFF_METHOD, REGION)
• Vector derivative function overloads with three separate outloc_[xyz] arguments: use the versions with a single outloc argument instead
• CyclicReduce::setCoefs and solve overloads that take T[] or T**: use the version that takes Array<T> instead
• The FCI class constructors that take a bool yperiodic argument: this is no longer supported
• Mesh::coordinates is deprecated in favour of the more consistently-named Mesh::getCoordinates. There is also now Field::getCoordinates which may be more convenient

Removed functions

• PhysicsModel::addToRestart and Solver::addToRestart: use restart.add directly instead
• Solver::addMonitor(MonitorFunc): use the Monitor* overloads instead
• The get/set array/data methods in the Field classes: these methods are no longer supported

BOUT++ v4.1.2

This is a bug-fix release, fixing the following issues in BOUT++:

• Updates to the documentation
• Added missing __setitem__ and keys functions to python Datafile
• Fixed INVERT_KX_ZERO in serial_tri Laplace solver
• Fixed incorrect number of guard cells in serial_tri Laplace solver
• Fixed Laplacexy examples
• Fixed bug in calculation of non-uniform correction
• Disabled plotting of test-fci-slab when running the integrated tests
• Fixed bug during configure if NetCDF not found
• Fixed typo in bout-runners example input file

BOUT++ v4.1.1

This a bug-fix release for BOUT++ that fixes the following:

• Automatically checkout GoogleTest submodule if necessary
• Fix memory leak in multigrid solver
• Don't pause on showing plot for FCI test by default
• Fix broken integrated tests that aren't run in the test suite
• Initialise some uninitialised variables
• Cleanup all Array instances at end of simulation
• Set boundaries correctly in Delp2
• Set PYTHONPATH when running tests
• Fix some segfaults caused by Field3D move constructors
• Fix some errant newlines when specifying -q on the command line
• Fix some segfaults in ConditionalOutput
• Fix broken links and code blocks in the documentation

BOUT++ v4.1.0

BOUT++ v4.1.0 is a feature release, containing some interesting new features, including:

• A way to cleanly stop simulations either through a stop-file, or via a KILL
  signal
• User-defined multiple monitors with different frequencies
• Four new boundary iterators for the inner and outer boundaries in
  double null configurations
• Better handling of 1D/2D Fields
• Dumping the actual settings used during a simulation to a file
• Colour output to highlight warnings/errors, along with options to
  increase/decrease verbosity
• Configure-time options to enable profiling with Score-P and coverage
  checking with gcov
• Removal of various functions deprecated in v4.0.0
• An overhauled testing framework with unit tests using GoogleTest

This release also represents a major tidy up of the codebase, fixing several hundred warnings, removing unused and unnecessary code, and implementing a better, more comprehensive testing suite.

For a more comprehensive changelog, please see CHANGELOG.md

BOUT++ v4.0.1

4.0.1 is purely a bug-fix release, with various fixes to some of the python tools, patching several memory leaks, and some important fixes for Intel compilers.

BOUT++ 4.0.0

Merge pull request #461 from boutproject/v4.0.0-RC

Release v4.0.0