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.

v3.0.0-beta.13

Added

• md.pair.ExpandedLJ - A Lennard-Jones potential where r is
  replaced with r-delta.
• Support nested modification of operation parameters.
• wall - Define wall surfaces in the simulation box.
• md.external.wall - Pair interactions between particles and wall
  surfaces.
• Communicator.walltime - the wall clock time since creating the
  Communicator.
• hoomd.md.force.Custom - user defined forces in Python.

Changed

• Call update_group_dof implicitly in set_snapshot, when changing
  integrators or integration methods, and on steps where
  FilterUpdater acts on the system.
• [breaking] update_group_dof defers counting the degrees of
  freedom until the next timestep or the next call to
  Simulation.run.
• [breaking] Renamed md.bond.FENE to md.bond.FENEWCA.
• md.bond.FENEWCA takes a user provided delta parameter and
  ignores the particle diameters.
• [breaking] md.pair.DLVO takes user provided a1 and a2
  parameters and ignores the particle diameters.
• Removed invalid linker options when using gcc on Apple systems.
• Removed the r_on attribute and default_r_on constructor argument
  from pair potentials that do not use it.

Fixed

• Compile error with Apple clang clang-1300.0.29.30.
• Incorrect OPLS dihedral forces when compiled with
  Apple clang clang-1300.0.29.30.

Deprecated

• md.pair.SLJ - Replaced with md.pair.ExpandedLJ.

Removed

• Leftover state logging category.

v3.0.0-beta.12

Added

• Support simulations with arbitrarily large or small scales (within
  the limits of the floating point representation).

Changed

• Report full error details in the exception message.
• Improved documentation.
• [breaking]: buffer is now a required argument when constructing
  a neighbor list.
• [breaking]: force_tol, angmom_tol, and energy_tol are now
  required arguments to md.minimize.FIRE

Fixed

• Allow neighbor lists to store more than 2**32-1 total neighbors.
• Return expected parameter values instead of NaN when potential
  parameters are set to 0.

v3.0.0-beta.11

Added

• Support Python 3.10.
• Support clang 13.

Changed

• [developers] Place all all HOOMD C++ classes in the hoomd and
  nested namespaces.
• [developers] Use official pre-commit clang-format repository.

v3.0.0-beta.10

Added

• hoomd.md.minimize.FIRE - MD integrator that minimizes the
  system's potential energy.
• Include example AKMA and MD unit conversion factors in the
  documentation.
• BUILD_LLVM CMake option (defaults off) to enable features that
  require LLVM.
• hoomd.hpmc.pair.user.CPPPotential - user-defined pair potentials
  between particles in HPMC.
• hoomd.hpmc.pair.user.CPPPotentialUnion - user-defined site-site
  pair potentials between shapes in HPMC.
• hoomd.hpmc.external.user.CPPExternalPotential - user-defined
  external potentials in HPMC.
• Support user-defined pair potentials in HPMC on the GPU.

Changed

• Improved documentation.
• Improved error messages when setting operation parameters.
• Noted some dependencies of dependecies for building documentation.
• [devlopers] Removed m_comm from most classes. Use
  m_sysdef->isDomainDecomposed() instead.
• Add support for LLVM 12
• ENABLE_LLVM=on requires the clang development libraries.
• [breaking] Renamed the Integrator attribute aniso to
  integrate_rotational_dof and removed the 'auto' option. Users
  must now explicitly choose integrate_rotational_dof=True to
  integrate the rotational degrees of freedom in the system.

Fixed

• Calling hoomd.Operations.__len__ no longer raises a
  RecursionError.
• RATTLE integration methods execute on the GPU.
• Include EvaluatorPairDLVO.h in the installation for plugins.
• Bug in setting zero sized ManagedArrays.
• Kernel launch errors when one process uses different GPU devices.
• Race condition that lead to incorrect simulations with
  md.pair.Table.
• Bug where some particle filers would have 0 rotational degrees of
  freedom.

Removed

• The BUILD_JIT CMake option.
• Support for LLVM <= 9.

v3.0.0-beta.9

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.

Deprecated

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

v3.0.0-beta.8

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.

v2.9.7

Bug fixes

• Support CUDA 11.5. A bug in CUDA 11.4 may result in the error
  [__global__ function call is not configure]{.title-ref} when
  running HOOMD.