BOUT++ Project

BOUT++ v4.3.3 released!

Thu, 29 Jul 2021 00:00:00 +0000

Another version of BOUT++ out the door! 4.3.3 is a bugfix release:

Better documentation and tests
Fix shiftOutput for aligned fields
Some improvements to the Python API, including support for Python’s exponentiation operator **, and MPI-aware logging
Fix an uninitialised variable in Delp2
Bump the version of jinja2 from 2.10 to 2.11
Fix for some Solvers not always using user preconditioner/Jacobian
Some minor fixes to the build systems

You can download this version from here: https://github.com/boutproject/BOUT-dev/releases/tag/v4.3.3 and you can reference this version using the following DOI: 10.5281/zenodo.5142504.

BOUT++ v4.3.2 released!

Wed, 21 Oct 2020 00:00:00 +0000

I’m happy to announce the release of BOUT++ v4.3.2, which fixes several bugs in the library code, examples and the project infrastructure:

Make downloading the submodules a bit nicer, including an option for using non-bundled versions when using configure
Make dz in the Python API a property
Make Div_par_K_Grad_par check the staggered location of its inputs
Enable split-flux derivatives on staggered fields
Fix Grad2_par2 implementation in InvertParCR
Fix an issue writing FieldPerps
Make it easier to compile the examples with different versions of BOUT++, plus fixes for the tokamak-2fluid example
Fix Div_par when using more than one y-guard cell
Fix an issue with text attributes in HDF5 files

You can download this version from here: https://github.com/boutproject/BOUT-dev/releases/tag/v4.3.2 and you can reference this version using the following DOI: 10.5281/zenodo.4046792.

Thanks to everybody who contributed bugfixes and testing for this version, particularly Ben Dudson, Brendan Shanahan, David Schwörer, and John Omotani!

BOUT++ v4.3.1 released!

Fri, 27 Mar 2020 00:00:00 +0000

These are strange times, but there is a little light: a BOUT++ bugfix release!

4.3.1 is a bugfix release, with a few minor fixes to library code, notably:

Fix the creation of the RGN_OUTER_X region
Several small bugs in the Python API
Preserve restart files if there’s a crash during initialisation
Fix some segfaults in the PvodeSolver
Fix some issues with Hypnotoad (see #1783 (friva000))

Other changes are mostly housekeeping changes for the BOUT++ project.

Get a tarball and a citation reference from: https://zenodo.org/record/3727089

Roadmap for v5.0

Wed, 06 Nov 2019 00:00:00 +0000

BOUT++ has grown organically over the years, and now we want to tidy things up, smooth off rough edges and redesign some important components. Some of these changes will necessarily be backwards-incompatible, and unfortunately may require changes to physics models. Where that is the case, we hope to be able to provide tools to make the changes as easy as possible.

This is a non-exhaustive list of features and changes we would like to implement in the next major release (v5) of BOUT++. We’ve separated the out into “smaller” and “larger”. Smaller changes are those we think should be orthogonal to other items, or won’t require much in the way of designing. Larger changes likely affect many separate parts of the framework, and will require some effort to design them correctly.

Smaller

Integrate {fmt} and spdlog
Namespacing and header moving
- Renaming/project layout
Replace FieldData, FieldGroup functionality
Investigate how much Vector2D/3D require base-class
Timer features and options for default Monitor
Remove non-PhysicsModel based solving
Remove (deprecated) invert_laplace
Standardise all factory methods
Improving the Python wrapper
- Using Pybind11?
Mesh initialisation
Coordinates lazy computation of Christoffel symbols

Larger:

Solver, PhysicsModel, Problem – ownership and interrelatedness
- Separate PhysicsModel virtual for dumping?
- Fields take the DataFile and handle writing itself?
- How to handle dumping both local variables and evolving variables
Mesh rewrite
- Simpler API
- Fewer assumptions
- More flexible domains
- New way of specifying branch cuts alongside existing system
- Non-logically-rectangular meshes
- Higher-level topology API
- What is the sufficient abstraction?
Coordinates rewrite
- Output/convert to real space for visualisation/field line mapping etc.
- Real space mapping inside BOUT++
- New input format for geometry specification
Boundaries rewrite
- Regions and operators
File I/O rewrite

BOUT++ v4.3.0 released!

Fri, 25 Oct 2019 00:00:00 +0000

I am very happy to announce the release of BOUT++ v4.3.0! This is a feature release and is backwards compatible with v4.2. The headline features are:

New derivatives machinery allows native vectorisation where possible, as well as OpenMP parallelisation
We now handle both staggered and field-aligned Fields more consistently, with more checking that operations make sense and are done in the correct space or at the correct location
Multiple parallel slices (the new name for “yup” and “ydown”) re-enables 4th-order central differencing in the y-direction
Up to 10% faster over v4.2.2!

We have removed a few deprecated features, which you can read in the change summary below.

You can read a summary of all the changes and download a tarball here: https://github.com/boutproject/BOUT-dev/releases/tag/v4.3.0

You can cite this version using this DOI: https://zenodo.org/record/3518905

Many thanks for all the people who contributed to this version, including those who submitted bug reports!

The plan now for BOUT++ is to start a new major version, with the opportunity to redesign some parts of the library in a potentially backwards incompatible way. We intend to support v4 at least until the release of v5.0, backporting new features where possible, and providing a route for upgrading to the next version. With that in mind, I would like to strongly recommend sticking to v4.3 for production simulations, and only using the “next” branch for development work.

BOUT++ v4.2.3 released!

Wed, 23 Oct 2019 00:00:00 +0000

I’m happy to announce the release of v4.2.3, a small bugfix release:

Fix Timers double-counting sections
Fix cyclic parallel derivative inversion done in wrong space
Fix calculation of ShiftAngle (qloop) in Hypnotoad
Fix relative paths in makefiles
Fix an issue when searching for libraries in configure

You can download a tarball of this release from: https://github.com/boutproject/BOUT-dev/releases/tag/v4.2.3

You can cite this release with the following DOI: https://doi.org/10.5281/zenodo.3242507

BOUT++ v4.2.2 released!

Fri, 01 Mar 2019 00:00:00 +0000

Following hot on the heels of v4.2.1 is the latest release, 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

See CHANGELOG.md for more details. You can download the source tarball from https://github.com/boutproject/BOUT-dev/releases/tag/v4.2.2

Note: if you download the source code tarball from GitHub, please download the file BOUT++-v4.2.2.tar.gz rather than the GitHub generated tarballs. This is because the GitHub tarball does not include the submodules.

Google Summer of Code Ideas

Wed, 06 Feb 2019 00:00:00 +0000

The BOUT++ Project is participating in the Google Summer of Code (GSoC) 2019. GSoC is open to University students aged 18 or over.

If you are interested, see https://summerofcode.withgoogle.com/ for more information.

Ideas for Projects with BOUT++

Here is a non-exhaustive list for suggested projects. We are of course open to ideas for projects not on this list!

Make xarray work with BOUT++. A proof-of-concept exists, but the majority of the BOUT++ post-processing library needs porting over.
Improving the Python wrapper to the C++ API by using e.g. pybind11 or similar.
Calling Python from BOUT++. This could use much of the same code (bindings, type conversion) as calling BOUT++ from Python. It would allow input files or physics models to use python expressions to extend the code.
Improve user extensibility of the library, by making all factories use the generic factory class. This would allow users to easily add things like solvers and boundary conditions in their physics models, without needing to modify the core library.
Self-describing data output format. Make the output data files easier to interpret for generic tools, by including more metadata in a standardised way. This would make the data easier to manipulate and work with. This complements, maybe is part of, the work on xarray.

BOUT++ v4.2.1 released!

Wed, 23 Jan 2019 00:00:00 +0000

I’m happy to announce a new release of 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. You can download the source tarball from https://github.com/boutproject/BOUT-dev/releases/tag/v4.2.1

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 released!

Wed, 17 Oct 2018 00:00:00 +0000

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

See CHANGELOG.md for more details. You can download the source tarball from https://github.com/boutproject/BOUT-dev/releases/tag/v4.2.0