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