HOOMd-blue v3.0.0-beta.9 release

[Joshua Anderson]

HOOMD-blue v3.0.0-beta.9 is now available. Thanks to all who tested, submitted bug reports, and contributed code!

Documentation: https://hoomd-blue.readthedocs.io/
Release: https://github.com/glotzerlab/hoomd-blue/releases/tag/v3.0.0-beta.9
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.9 is nearly feature complete: https://github.com/glotzerlab/hoomd-blue/projects/3

*Added*

- `Communicator.num_partitions` - the number of partitions in the
communicator.
- `domain_decomposition` argument to `State` factory methods - set the
parameters of the MPI domain decomposition
- `State.domain_decomposition` - number of domains in the x, y, and z
directions in the domain decomposition.
- `State.domain_decomposition_split_fractions` - the fractional
positions of the split planes in the domain decomposition.
- `hoomd.update.FilterUpdater` - an updater that evaluates the
particles associated with a
[hoomd.filter.ParticleFilter]{.title-ref} instance.
- `hoomd.update.RemoveDrift` - Remove the average drift from a system
restrained on a lattice.
- Developer documentation for HOOMD-blue\'s Python object data model
in `ARCHITECTURE.md`.
- Autocomplete support for interactive notebooks.
- `hoomd.md.methods.OverdampedViscous` - Overdamped integrator with a
drag force but no random force .
- `MutabilityError` exception when setting read-only operation
parameters.

*Changed*

- Improved documentation.
- \[breaking\] Moved `manifold_constrant` to separate integration
method classes in `hoomd.md.methods.rattle`.
- \[breaking\] Moved `trigger` to first argument position in
[hoomd.update.BoxResize]{.title-ref}, [hoomd.write.DCD]{.title-ref},
and [hoomd.write.GSD]{.title-ref}.
- \[breaking\] `hoomd.data.LocalSnapshot` particle data API now
matches `Snapshot`. Changes to angular momentum, moment of intertia,
and rigid body id attributes.
- `hoomd.write.CustomWriter` now exposes action through the `writer`
attribute.
- \[breaking\] Active force rotational diffusion is managed by
`hoomd.md.update.ActiveRotationalDiffusion`.

*Fixed*

- `TypeParameter` can set multiple parameters after calling
`hoomd.Simulation.run`.
- `tune.LoadBalancer` can be used in a simulation.
- `hoomd.md.pair.Pair` `r_cut` type parameter can be set to 0.
- MD integration methods can be removed from the integrator\'s method
list.
- Neighborlist exclusions update when the number of bonds change.
- Errors related to equality checks between HOOMD operations.
- The integrator can be removed from a simulation after running.
- `hoomd.md.constrain.Rigid.create_bodies` method correctly assigns
the body attribute.
- Setting rigid attribute of a MD integrator to `None` is allowed.

*Removed*

- `Snapshot.exists` - use `snapshot.communicator.rank == 0`
- `State.snapshot` - use `get_snapshot` and `set_snapshot`
- The `State.box` property setter - use `State.set_box`

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

[Joshua Anderson]

All,

The v3.0.0 final release will be made when it is done. I do not know exactly when that will be. You can monitor our progress and contribute on the GitHub project page: https://github.com/glotzerlab/hoomd-blue/projects/3

The latest betas are very stable, actively used in research by many groups, and almost feature complete with v2.9. The only major features missing in 3.0.0-beta.9 are MD walls, HPMC walls, HPMC external potentials, and HPMC user defined potentials.

P.S. This is a reply to a message that Google Groups marked as spam and will not let me approve for unknown reasons.

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