v7.0.1

Fixed

• Fixed external component builds with Eigen 5.x (#2272).

v7.0.0

HOOMD-blue 7.0 writes GSD schema 2.0 files. Update your other software for compatibility:

• gsd >= 5.0
• Ovito >= 3.15.2
• gsd-vmd >= 0.6.0

HOOMD-blue 7.0 also changes the definition of the 3D rotation trial move size a (2D rotation moves are not changed). You will need to retune any hard-coded or saved values. Here are the distributions of the trial move rotation angles in HOOMD-blue 2.0--6.x and in 7.0+ for comparison:

Added

• hoomd.hpmc.integrate.HPMCIntegrator.translate_move_dimensions: Sets the dimensionality of HPMC translation moves, enabling interfacial confinement (xy) in 3D simulations (#2265).
• create_state_from_gsd can now read GSD schema 2.0 files (#2249).
• write.GSD and write.Burst can now write double precision values to GSD files. Set precision="double" to enable. The default value is "single", consistent with previous releases (#2249).

Changed

• Use tabs in binary installation documentation (#2246).
• Improve the sampling of 3D rotation trial moves (#2264).

Fixed

• Fixed Helfrich equation in the docs (#2242)
• Build with Eigen 5.x (#2261)

v6.1.1

Fixed

• Divide by zero with MPCD if rigid body has constituent with zero mass (#2228).
• Ensure that GSD files are always flushed on exit (#2236).
• Code examples in md.nlist, md.angle, md.bond, md.special_pair, md.compute, md.dihedral, md.force, md.integrate, and md.update now execute without errors (#2185).

v6.1.0

Added

• Support 2D simulations in hoomd.md.pair.friction (#2184).

Removed

• SIGTERM handler (#2209).

Fixed

• Table writer no longer errors on NaN scalar values (#2189).
• Table writer no longer errors on Inf scalar values (#2196).
• Fixed vertex neighbor check in dynamical bonding code (#2202).
• Fixed Helfrich energy calculation for logging (#2215)

v6.0.0

Added

• Implemented rigid body compatibility with MPCD without MPI (#2136).
• Add thermodynamically consistent frictional contact forces: hoomd.md.pair.friction (#2116).
• create_bodies method takes optional masses argument to set masses (#2169).

Fixed

• Use the provided alpha parameter in make_pppm_coulomb_forces (#2153).
• Add a unit test to verify that the export name of hoomd.hpmc.compute.FreeVolume, and resolved the existing export name conflicts (#2163).
• Scale move sizes correctly when the acceptance rate is 0 (#2174).

Changed

• Setting two tuples of type parameters like this lj.r_cut[('A', 'B'), ('C', 'D')] = ... now sets the parameters A-B and C-D. This is consistent with the behavior when setting more than two parameters. For example: lj.r_cut[('A', 'B'), ('C', 'D'), ('E', 'F')] = ... sets parameters for A-B, C-D, and E-F. In previous HOOMD-blue releases, the two-tuple code path was different (it would set A-C, A-D, B-C, and B-D). Update your scripts accordingly. (#2157)

v5.4.0

Added

• The Zetterling MD pair potential: hoomd.md.pair.Zetterling (#2086).
• The YLZ anisotropic MD pair potential: hoomd.md.pair.aniso.YLZ (#2110).
• Dynamic bond topologies with mesh potentials: hoomd.md.update.MeshDynamicalBonding (#2093).

Fixed

• Display vector math symbol correctly in the documentation (#2109).
• Display equations correctly in the documentation (#2118).

v5.3.1

Fixed

• Ensure that GPU devices have concurrent unified memory capabilities (#2099).
• Fix segfault when attaching nlists with meshes (#2089).
• Install cuh headers (#2091).
• Reduce the time needed to generate mesh bonds (#2097).
• Equations displayed in hoomd.hpmc.compute.SDF documentation (#2096).
• Support CUDA 12.9 (#2102).

v5.3.0

Added

• The Zetterling pair potential: hoomd.hpmc.pair.Zetterling (#2057).
• hoomd.write.GSD now automatically flushes on frame writes 10 seconds or longer since the previous flush. Configure this time with auto_flush_period. The flush does not occur on a timer -- it is only called after a normally scheduled frame write (#2085).

Changed

• The GSD write buffer size now defaults to 1 MiB. Files will thus grow in size more continuiously (the previous default was 64 MiB). File size changes are subject to additional buffering by the OS and may or may not be predictable. At the same time, new frames will no longer be available for reading until after the file is flushed (which occurs on write after 10 seconds by default) or closed (#2085).

Fixed

• The formulas in the docs for variant.box.Interpolate are now consistent (#2060).
• Do not increment z image in 2D simulation boxes (#2071).
• Code block example in hoomd.md.pair.DPDConservative (#2084).
• Equations displayed in hoomd.md.methods.thermostats.Bussi documentation (#2081).
• Do not issue "Cannot acquire access to array in use" error when using FIRE on the GPU with integrate_rotational_dof=True (#2082).

v5.2.0

Added

• Set constituent particle velocities for rigid bodies (#2024).
• Mesh tutorial (hoomd-examples#160).

Changed

• Use KaTeX to render math equations in the documentation (#2053).
• The "Organizing and Executing Simulations" tutorial now demonstrates the use of row (hoomd-examples#155).

Fixed

• The documentation builds without warnings in Python 3.13 environments (#2049).
• Remove the error message that NEC prints when one particle simultaneously collides with two others (#2029).
• Compile without errors with recent versions of clang (#2042).

v5.1.1

Fixed

• Prevent warnings about forces that provide torques (or not) (#2015).
• Compile without errors or warnings with CUDA 12.8 (#2019).
• force.Active applies torques correctly when the filter is not All (#2020).
• MD integrators no longer integrate the z degree of freedom in 2D simulation boxes (#2021).
• HPMC integrators no longer miss pairwise interactions when updaters, such as RemoveDrift move particles (#2022).