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.

v3.0.1

Fixed:

• Display status of trunk-patch branch in the GitHub actions badge.
• Add EvaluatorPairTable.h to installation directory.
• Add hoomd.filter.Rigid to the documentation.
• Prevent TypeError: 'bool' object is not iterable errors when
  comparing Tag filters with different lengths arrays.
• Simulation.tps and Simulation.walltime update every step of the
  run.

v3.0.0

Overview

HOOMD-blue v3.0.0 is the first production release with the new API that
has been developed and implemented over more than 2 years. Those still
using v2.x will need to make changes to their scripts to use v3. See the
[migrating]{.title-ref} page for an overview and individual class and
method documentation for more information. To summarize, the new API is
object oriented, allows HOOMD-blue to work effectively as a Python
package, and provides more hooks for Python code to directly interface
with the simulation.

New features in v3 since v2.9.7:

• Zero-copy data access through numpy and cupy.
• Triggers determine what timesteps operations execute on.
• User-defined operations, triggers, particle filters, variants, and
  forces.
• Logging subsystem supports array quantities.
• Implicit depletants for 2D shapes in HPMC.
• Harmonically mapped averaging for MD thermodynamic quantities of
  crystals.
• TWF and OPP pair potentials.
• Tether bond potential.
• Manifold constraints for MD integration methods (using RATTLE) and
  active forces.
• Document code architecture in ARCHITECTURE.md.
• Overdamped viscous MD integration method.
• User-defined pair potentials work with HPMC on the GPU.
• Long range tail correction for Lennard-Jones potential.
• Anisotropic Lennard-Jones-like pair potential for polyhedra and
  ellipsoids.
• Newtownian event chain Monte Carlo for spheres and convex polyhedra.

See the full change log below for all v3 beta releases.

Changes from v3.0.0-beta.14:

Added

• hoomd.hpmc.tune.BoxMCMoveSize - Tune BoxMC move sizes to meet
  target acceptance ratios.
• hoomd.hpmc.nec.integrate.Sphere - Newtonian event chain Monte
  Carlo for hard spheres.
• hoomd.hpmc.nec.integrate.ConvexPolyhedron - Newtonian event chain
  Monte Carlo for hard convex polyhedra.
• hoomd.hpmc.nec.tune.ChainTime - Tune chain times in newtonian
  event chain Monte Carlo method.

Changed

• Improve documentation.
• [breaking] Renamed the hoomd.md.bond.Table energy parameter from
  V to U.
• [breaking] Renamed the hoomd.md.pair.Table energy parameter from
  V to U.
• [breaking] Renamed the hoomd.md.angle.Table energy parameter
  from V to U.
• [breaking] Renamed the hoomd.md.dihedral.Table energy parameter
  from V to U.
• [breaking] Renamed hoomd.md.nlist.Nlist to
  hoomd.md.nlist.NeighborList.
• [developer] Updater and Analyzer in C++ have a m_trigger
  member now.
• [developer] _TriggeredOperation has been moved to
  TriggeredOperation and custom trigger setting and getting logic
  removed.

Fixed

• FIRE.converged may be queried before calling Simulation.run.
• Bug where using __iadd__ to certain attributes would fail with an
  exception.
• Bug where hoomd.md.pair.LJ.additional_energy is NaN when
  tail_correction is enabled and some pairs have r_cut=0.
• Compile error with CUDA 11.7.
• Compile errors on native ubuntu 20.04 systems.
• Compile errors with ENABLE_GPU=on and clang as a host compiler.

Removed

• [developers] Removed IntegratorData class. It is replaced by
  structs that are defined in the integrator classes.
• get_ordered_vertices from hoomd.md.pair.aniso.ALJ.
• Removed optional coxeter dependency.
• The limit parameter from hoomd.md.methods.NVE.
• The limit parameter from hoomd.md.methods.rattle.NVE.
• The diameter_shift parameter from hoomd.md.nlist.NeighborList.
• The max_diameter parameter from hoomd.md.nlist.NeighborList.

v3.0.0-beta.14

Added

• hoomd.hpmc.external.field.Harmonic - harmonic potential of
  particles to specific sites in the simulation box and orientations.
• Support cereal 1.3.1
• Guide on how to model molecular systems.
• version.floating_point_precision - Floating point width in bits
  for the particle properties and local calculations.
• hoomd.md.pair.LJ.tail_correction - Option to enable the isotropic
  integrated long range tail correction.
• hoomd.md.Integrator.linear_momentum - Compute the total system
  linear momentum. Loggable.
• hoomd.md.bond.Table - Tabulated bond potential.
• hoomd.md.angle.Table - Tabulated angle potential.
• hoomd.md.dihedral.Table - Tabulated dihedral potential.
• hoomd.md.improper.Harmonic - Compute the harmonic improper
  potential and forces.
• Tutorial on Organizing and executing simulations.
• C++ and build system overview in ARCHITECTURE.md.
• hoomd.hpmc.external.wall - Overlap checks between particles and
  wall surfaces.
• hoomd.md.pair.ansio.ALJ - an anisotropic Lennard-Jones-like pair
  potential for polyhedra and ellipsoids.
• New optional dependency: coxeter, needed for some ALJ methods.

Changed

• Support variant translational and rotational spring constants in
  hoomd.hpmc.external.field.Harmonic.
• [breaking] Renamed hoomd.md.angle.Cosinesq to
  hoomd.md.angle.CosineSquared.
• [breaking] hoomd.Box no longer has a matrix property use
  to_matrix and from_matrix.

Fixed

• Compilation errors on FreeBSD.
• TypeError when instantiating special pair forces.
• Inconsistent state when using the walls setter of a
  hoomd.md.external.wall.WallPotential.

Removed

• [breaking] Removed hoomd.md.pair.SLJ potential and wall. Use
  hoomd.md.pair.ExpandedLJ.
• [breaking] hoomd.Box.lattice_vectors property no longer exists.