HOOMD-blue v3.0.0-beta.8 release

[Joshua Anderson]

HOOMD-blue v3.0.0-beta.8 is now available. Thanks to all who contributed!

Documentation: https://hoomd-blue.readthedocs.io/
Release: https://github.com/glotzerlab/hoomd-blue/releases/tag/v3.0.0-beta.8
Report issues: https://github.com/glotzerlab/hoomd-blue/issues
Contribute: https://github.com/glotzerlab/hoomd-blue/pulls

There are a number of breaking changes in this release. Please bear with us while we incrementally improve the API so that the final stable 3.0 API will be as clean as possible.

v3.0-beta is nearly feature complete: https://github.com/glotzerlab/hoomd-blue/projects/3

v3.0.0-beta.8 (2021-08-03)
^^^^^^^^^^^^^^^^^^^^^^^^^^

*Added*

- Consistent documentation of parameter dimensions and units reference documentation.
- ``md.update.ReversePerturbationFlow`` - implementation of ``mueller_plathe_flow`` from v2.
- ``md.pair.ExpandedMie`` - Mie potential where ``r`` is replaced with ``r - delta``.
- ``md.pair.Table`` - Pair potential evaluated using the given tabulated values.
- ``md.constrain.Distance`` - fix distances between pairs of particles.
- ``hpmc.compute.SDF`` - compute the pressure of convex hard particle systems.
- ``Snapshot.wrap()`` - wrap snapshot particles back into the box.
- Support gcc11.
- ``md.bond.Tether`` - A bond with minimum and maximum lengths.
- ``State.get_snapshot`` and ``State.set_snapshot`` - methods to access the global snapshot.
- ``State.set_box`` set a new simulation box without modifying particle properties.
- ``md.long_range.pppm.make_pppm_coulomb_forces`` - Long range electrostatics evaluated by PPPM.
- ``md.long_range.pppm.Coulomb`` - The reciprocal part of PPPM electrostatics.
- ``md.force.ActiveOnManifold`` - Active forces constrained to manifolds.

*Changed*

- Improved documentation.
- [breaking] Constructor arguments that set a default value per type or pair of types now have
default in their name (e.g. ``r_cut`` to ``default_r_cut`` for pair potentials and ``a`` to
``default_a`` for HPMC integrators).
- [developer] Support git worktree checkouts.
- [breaking] Rename ``nrank`` to ``ranks_per_partition`` in ``Communicator``.
- rowan is now an optional dependency when running unit tests.
- ``Snapshot`` and ``Box`` methods that make in-place modifications return the object.

*Fixed*

- Bug where ``ThermdynamicQuantities.volume`` returned 0 in 2D simulations.
- Update neighbor list exclusions after the number of particles changes.
- Test failures with the CMake option ``BUILD_MD=off``.
- ``write.Table`` can now display MD pressures.

*Deprecated*

- ``State.snapshot`` - use ``get_snapshot`` and ``set_snapshot``.
- The ability to set boxes with the property ``State.box`` - use ``set_box``.

*Removed*

- [breaking] ``Simulation.write_debug_data``.
- [breaking] ``shared_msg_file`` option to ``Device``. ``msg_file`` now has the same behavior as
``shared_msg_file``.
- [developers] C++ and Python implementations of ``constraint_ellipsoid``, from ``hoomd.md.update``
and ``sphere`` and ``oneD`` from ``hoomd.md.constrain``.
- [developers] Doxygen configuration files.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan