v3.9.0

Added:

• GPU code path for hoomd.update.BoxResize (#1462).
• logger keyword argument and property to hoomd.write.GSD (#1481).

Changed:

• Issue [FutureWarning]{.title-ref} warnings when using deprecated APIs (#1485).
• Reformat the list of deprecated features. (#1490).
• In simulations with rigid bodies, remove D degrees of freedom when the system is momentum conserving (#1467).

Fixed:

• Compile without errors using hipcc and ROCM 5.1.0 (#1478).
• Document that hoomd.md.force.Force can be added to Operations.computes (#1489).
• hoomd.md.constrain.Rigid.create_bodies completes without segmentation faults when particle body tags are not -1 (#1476).
• hoomd.hpmc.compute.FreeVolume computes the free area correctly in 2D simulations (#1473).

Deprecated:

• Deprecate write.GSD log keyword argument and property in favor of logger (#1481).

v3.8.1

Fixed:

• #1468:
  Conserve linear momentum in simulations using
  hoomd.md.constrain.Rigid on more than 1 MPI rank.

v3.8.0

Added

• Support Python 3.11.
• Support CUDA 11.8.
• Support CUDA 12.0.0 final.

Fixed

• Improve numerical stability of orientation quaternions when using
  hoomd.md.update.ActiveRotationalDiffusion
• Reduced memory usage and fix spurious failures in test_nlist.py.
• Avoid triggering TypeError("expected x and y to have same length")
  in hoomd.hpmc.compute.SDF.betaP.

Deprecated

• The following integration methods are deprecated. Starting in
  v4.0.0, the same functionalities will be available via
  hoomd.md.methods.ConstantVolume/
  hoomd.md.methods.ConstantPressure with an appropriately chosen
  thermostat argument.
  • hoomd.md.methods.NVE
  • hoomd.md.methods.NVT
  • hoomd.md.methods.Berendsen
  • hoomd.md.methods.NPH
  • hoomd.md.methods.NPT

Removed

• Support for CUDA 10.

v3.7.0

Added

• Neighborlist.r_cut sets the base cutoff radius for neighbor
  search - for use when the neighbor list is used for analysis or
  custom Python code.
• Neighborlist.cpu_local_nlist_arrays provides zero-copy access to
  the computed neighbor list.
• Neighborlist.gpu_local_nlist_arrays provides zero-copy access to
  the computed neighbor list.
• Neighborlist.local_pair_list provides the rank local pair list by
  index.
• Neighborlist.pair_list provides the global pair list by tag on
  rank 0.
• hoomd.md.dihedral.Periodic - a new name for the previous
  Harmonic potential.
• default_gamma and default_gamma_r arguments to the
  hoomd.md.methods: Brownian, Langevin, and OverdampedViscous.
• reservoir_energy loggable in hoomd.md.methods.Langevin.
• hoomd.md.force.Constant applies constant forces and torques to
  particles.

Changed

• [plugin developers] Refactored the LocalDataAccess C++ classes
  to add flexibility.

Fixed

• hoomd.hpmc.nec integrators compute non-infinite virial pressures
  for 2D simulations.
• Raise an exception when attempting to get the shape specification of
  shapes with 0 elements.
• Box conversion error message now names hoomd.Box.

Deprecated

• hoomd.md.dihedral.Harmonic - use the functionally equivalent
  hoomd.md.dihedral.Periodic.
• charges key in hoomd.md.constrain.Rigid.body.
• diameters key in hoomd.md.constrain.Rigid.body.

v3.6.0

Changed

• In hoomd.md.pair.aniso.ALJ, shape.rounding_radii now defaults to
  (0.0, 0.0, 0.0).
• Revise hoomd.md.pair.aniso.ALJ documentation.
• hoomd.md.force.Force instances can now be added to the
  Operations list allowing users to compute force, torque, energy,
  and virials of forces that are not included in the dynamics of the
  system.
• [developers]: Removed internal methods _remove and _add from
  the data model.

Fixed

• Increase the performance of md.pair.Table on the CPU.
• Improve accuracy of hoomd.hpmc.update.BoxMC when used with patch
  potentials.
• Provide an accurate warning message when creating the state with
  many bond/angle/... types.
• Add missing documentation for hoomd.md.methods.Berendsen.
• CVE-2007-4559

v3.5.0

Added

• Example plugin that demonstrates how to add a MD pair potential.
• Support a large number of particle and bond types (subject to
  available GPU memory and user patience) for the Cell neighbor
  list, MD pair potentials, MD bond potentials, Brownian, and Langevin
  integration methods.

Changed

• Raise an error when initializing with duplicate types.
• hpmc.compute.SDF now computes pressures of systems with patch
  interactions.
• Raise descriptive error messages when the shared memory request
  exceeds that available on the GPU.

Fixed

• Include all Neighborlist attributes in the documentation.
• Memory allocation errors in C++ now result in MemoryError
  exceptions in Python.
• Add missing Autotuned.h header file.
• External components build correctly when ENABLE_MPI=on or
  ENABLE_GPU=on.
• Type parameter validation when items contain numpy.ndarray
  elements.
• Compile with CUDA 12.0.

Deprecated

• Device.memory_traceback attribute. This attribute has no effect.

v3.4.0

Added

• The new HOOMD-blue logo is now available in the documentation.
• hoomd.md.methods.DisplacementCapped class for relaxing
  configurations with overlaps.
• hoomd.md.methods.rattle.DisplacementCapped class for relaxing
  configurations with overlaps.
• hoomd.device.Device.notice - print user-defined messages to the
  configured message output stream.
• Tutorial: Modelling Rigid Bodies.
• AutotunedObject class that provides an interface to read and write
  tuned kernel parameters, query whether tuning is complete, and start
  tuning again at the object level.
• is_tuning_complete method to Operations. Check whether kernel
  parameter tuning is complete for all operations.
• tune_kernel_parameters methods to Operations and many other
  classes. Start tuning kernel parameters in all operations.
• hoomd.md.HalfStepHook - extensible hook class called between step
  1 and 2 of MD integration.
• hoomd.md.Integrator.half_step_hook - property to get/set the half
  step hook.

Fixed

• Active forces on manifolds now attach to the Simulation correctly.
• hoomd.update.FilterUpdater now accepts hoomd.filter.CustomFilter
  subclasses.
• Correct error message is given when a sequence like parameter is not
  given to a type parameter.
• Fix non-axis-aligned Cylinder walls in MD.
• hoomd.md.constrain.Constraint now has hoomd.md.force.Force as a
  base class.
• Provide a warning instead of an error when passing an out of range
  seed to the Simulation constructor.
• Compile with current versions of HIP and ROCm.
• Compilation errors with CUDA >=11.8.

v3.3.0

Added

• A decorator that modifies the namespace of operation and custom
  action classes hoomd.logging.modify_namespace.
• Tuner for the neighbor list buffer size
  hoomd.md.tune.NeighborListBuffer.
• Solver infrastructure for optimization problems.
• Simulation.initial_timestep: the timestep on which the last call
  to run started.
• variant_like, trigger_like, and filter_like typing objects for
  documentation.

Changed

• Removed "__main__" from some user custom action logging
  namespaces.

Fixed

• Improve documentation.
• Non-default loggables can now be explicitly specified with
  Logger.add.
• Iteration of Logger instances.
• The logging category of hoomd.md.Integrate.linear_momentum

v3.2.0

Added

• hoomd.md.nlist.Neighborlist.num_builds property - The number of
  neighbor list builds since the last call to Simulation.run.
• hoomd.md.nlist.Cell.dimensions property - The dimensions of the
  cell list.
• hoomd.md.nlist.Cell.allocated_particles_per_cell property - The
  number of particle slots allocated per cell.
• hoomd.mesh.Mesh - Triangular mesh data structure.
• hoomd.md.mesh.bond - Bond potentials on mesh edges.
• Support gcc 12.
• Support clang 14.
• Set ENABLE_LLVM=on in conda binary builds.

Fixed

• Clarify documentation.
• Box.dimension reports the correct value when reading in 2D boxes
  from GSD files generated in HOOMD v2.
• Improve performance of run time compiled HPMC potentials on the CPU.
• Pressing Ctrl-C or interrupting the kernel in Jupyter stops the run
  at the end of the current timestep.

v3.1.0

Added

• Support LLVM 13 when ENABLE_LLVM=on.
• hoomd.md.pair.LJGauss - Lennard-Jones-Gaussian pair potential.
• hoomd.md.alchemy.methods.NVT - Alchemical molecular dynamics
  integration method.
• hoomd.md.alchemy.pair.LJGauss - Lennard-Jones-Gaussian pair
  potential with alchemical degrees of freedom.
• hoomd.hpmc.update.Shape - Alchemical hard particle Monte Carlo
  through shape change moves.
• hoomd.hpmc.shape_move.Elastic - Shape move with elastic potential
  energy penalty.
• hoomd.hpmc.shape_move.ShapeSpace - Moves in a user defined shape
  space.
• hoomd.hpmc.shape_move.Vertex - Translate shape vertices.

Changed

• HPMC fugacity is now a per-type quantity.
• Improved documentation.
• [developers] Reduced the time needed for incremental builds.
• [developers] Reduced memory needed to compile HOOMD.

Fixed

• ALJ unit test passes in Debug builds.
• Add quotes to conda-forge gpu package installation example.
• hoomd.md.force.Custom zeroes forces, torques, energies, and
  virials before calling set_forces.
• Point tarball download link to
  https://github.com/glotzerlab/hoomd-blue/releases.