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).

v5.1.0

Added

• The WangFrenkel potential (#1970).
• mpcd.update.ReverseNonequilibriumShearFlow (#1983).
• Support rocm 6 (#2002).

Fixed

• Correctly reference TriggeredOperation in inherited documentation (#1990).

Removed

• Support for rocm5 (#2002).

v5.0.1

Fixed

• Prevent missing 1 required positional argument: 'kT' errors when using NEC integrators (#1965).
• Note the current version of CUDA in the micromamba installation instructions (#1972).
• Provide a navigation bar on the 404 not found page in the documentation (#1986).

v5.0.0

Fixed

• Ensure that users set unique seeds on all partitions when performing Gibbs ensemble simulations (#1925)
• Mesh potentials return only one volume or area when ignore_type == True (#1928)
• Ensure correct methods are used by hoomd.mpcd.fill.VirtualParticleFiller for certain geometries, improving performance on the GPU in these cases (#1934).
• Correctly apply HPMCIntegrator.external_potentials in hoomd.hpmc.update.MuVT (#1941).
• Ensure GPU autotuners for MPCD methods are included in hoomd.Operations.is_tuning_complete and hoomd.Operations.tune_kernel_parameters through hoomd.mpcd.Integrator (#1951).
• Read after write hazard in the GPU implementation of Dipole, ALJ, and all Patchy potentials in hoomd.md.pair.ansiso (#1944).
• Read after write hazard in the GPU implementation of hoomd.md.mesh.conservation.Volume (#1953).
• hoomd.hpmc.pair.Pair.energy now computes the correct energy when there are multiple pair potentials with different r_cut values (#1955).
• Initializing large numbers (~100+ million) of MPCD particles with domain decomposition no longer causes a segmentation fault (#1897).

Added

• mpcd.geometry.ConcentricCylinders (#1894).
• kT parameter to all HPMC integrators. All HPMC-related operations respect the set kT (#1869).
• P property of hoomd.hpmc.compute.SDF (#1869).
• MPCD supports non-cubic collision cells, including both orthorhombic and triclinic cell shapes. The cell size is controlled by the number of cells along each lattice vector that defines the simulation box (#1950).

Changed

• betaP is replaced by P in hoomd.hpmc.update.BoxMC (#1869)
• hoomd.update.Clusters is now hoomd.update.GCA (#1926)
• hoomd.hpmc.external.wall.WallPotential is now hoomd.hpmc.external.WallPotential and can be added to IntegratorHPMC.external_potentials (#1941)
• hoomd.hpmc.external.field.Harmonic is now hoomd.hpmc.external.Harmonic and can be added to IntegratorHPMC.external_potentials (#1941).
• Document one class per html page and show inherited members in class documentation (#1952).

Removed

• _InternalCustomUpdater.update. (#1699).
• _InternalCustomTuner.tune. (#1699).
• _InternalCustomWriter.write. (#1699).
• HDF5Log.write. (#1699).
• hoomd.util.GPUNotAvailableError (#1708).
• Snapshot.from_gsd_snapshot (#1888).
• box1, box2, and variant arguments to hoomd.update.BoxResize (#1888).
• hpmc.pair.user.CPPPotentialBase, hpmc.pair.user.CPPPotential, hpmc.pair.user.CPPPotentialUnion, and hpmc.integrate.HPMCIntegrator.pair_potential (#1888).
• hoomd.hpmc.external.user.CPPExternalPotential (#1888).
• Implicit depletants from HPMC. (#1931).
• Device.num_cpu_threads. (#1932).
• Device.gpu_ids and the single-process multi-GPU feature (#1936).
• [c++] GlobalArray and GlobalVector (#1938).
• IntegratorHPMC.external_potential (#1941).

v4.9.1

Fixed

• Correct compile errors with -DENABLE_GPU=on -DHOOMD_GPU_PLATFORM=HIP (#1920)

v4.9.0

Added

• Support Python 3.13 (#1915)
• Patchy potentials for MD simulations: hoomd.md.pair.aniso.PatchyExpandedGaussian, hoomd.md.pair.aniso.PatchyExpandedLJ, hoomd.md.pair.aniso.PatchyExpandedMie, hoomd.md.pair.aniso.PatchyGaussian, hoomd.md.pair.aniso.PatchyLJ, hoomd.md.pair.aniso.PatchyMie, and hoomd.md.pair.aniso.PatchyYukawa (#1412).
• Double-well potentials in HPMC: hoomd.hpmc.pair.LJGauss and hoomd.hpmc.pair.OPP (#1889).
• Mesh potentials: hoomd.md.mesh.bending.BendingRigidity, hoomd.md.mesh.bending.Helfrich, hoomd.md.mesh.conservation.Area, hoomd.md.mesh.conservation.TriangleArea, and hoomd.md.mesh.conservation.Volume (#1792, #1793, #1794, #1795).
• start and end arguments to hoomd.write.Burst.dump (#1870)
• hoomd.mpcd.geometry.CosineChannel for a serpentine (cosine) channel (#1836).
• hoomd.mpcd.geometry.CosineExpansionContraction for an expansion-contraction channel (#1836).

Fixed

• Errors in the documentation (#1830, #1861, #1872, #1884, #1896).
• Thermalize momenta of particles with floppy body tags (#1891).
• Spheropolyhedra with two vertices can now be saved as a valid gsd_shape_spec (#1898).

Changed

• Improved build instructions (#1909).

v4.8.2

Fixed:

• Correct citation to Langevin piston paper (#1849).
• External walls, external fields, and constrains can now be implemented via external plugins (#1849).
• Prevent compile errors with -DENABLE_GPU=on -DHOOMD_GPU_PLATFORM=HIP (#1851).
• Prevent /usr/lib64/slurm/auth_munge.so: undefined symbol: slurm_conf error on Purdue Anvil (#1850).