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).

v4.8.1

Fixed:

• Prevent illegal instruction when accessing 0 length snapshot arrays (#1846)
• Fix MPCD compiler warning. (#1845)

v4.8.0

Added

• hoomd.mpcd reimplements the MPCD method for simulating hydrodynamic interactions. See the migrating page for an overview and individual class and method documentation for more information (#1784).
• MPCD tutorial.
• Support numpy 2.0 (#1797)
• hoomd.hpmc.external.External provides an abstract interface to external potentials (#1811).
• hoomd.hpmc.external.Linear computes the potential as a linear function of the distance from a point to a plane (#1811).
• HPMCIntegrator.external_potentials sets the list of external potentials applied to the system (#1811).
• hpmc.pair.ExpandedGaussian computes the expanded Gaussian pair potential in HPMC (#1817).

Changed

• Miscellaneous documentation improvements (#1786, #1800, #1820).
• Provide an error message for invalid Ellipsoid shape parameters (#1785).
• Provide the full CUDA error message when scanning devices (#1803).
• Test with gcc14, clang17, and clang18. No longer test with clang10, clang11, or clang12. (#1798, #1816).
• Ensure that Gaussian-type pair potentials have positive sigma values (#1810).
• Demonstrate Step and AngularStep in the tutorial "Modelling Patchy Particles".
• Fixed typographical errors in all tutorials.

Fixed

• Issue the proper error message when ALJ.shape is not set for all particle types (#1808).
• Correctly apply Brownian torque when elements of the inertia tensor are 0 (#1825).

Deprecated

• HPMCIntegrator.external_potential - use HPMCIntegrator.external_potentials (#1811).
• hoomd.hpmc.external.user.CPPExternalPotential - use hoomd.hpmc.external.Linear or write a custom component in C++ (#1811).

Removed

• Support for Python 3.8 (#1797).

v4.7.0

Fixed

• md.methods.rattle.Brownian executes without causing a segmentation fault on the CPU with domain decomposition (#1748).
• Compile BoxDim.h without warnings (#1756).
• Do not compute dipole-dipole interactions that are not necessary (#1758).
• Correctly define the units of gamma in md.methods.Langevin (#1771).
• Fix compile errors with external components that use the Expanded Mie potential (#1781).
• Allow HPMC pair potentials to be subclassed in external components (#1780).

Added

• "How to tune move sizes in multicomponent HPMC systems" documentation page (#1750).
• hoomd.box.from_basis_vectors - construct a box from arbitrary basis vectors (#1769).

Changed

• Make readthedocs builds more reproducible (#1758).

v4.6.0

Fixed

• create_state_from_gsd reads bond/angle/dihedral/improper/pair types when there are no corresponding groups (#1729).

Added

• hoomd.variant.box.BoxVariant - Describe boxes that change as a function of timestep (#1685).
• hoomd.variant.box.Constant - A constant box (#1685).
• hoomd.variant.box.Interpolate - Linearly interpolate between two boxes (#1685).
• hoomd.variant.box.InverseVolumeRamp - Linearly ramp the inverse volume of the system (#1685).
• hoomd.hpmc.update.QuickCompress now accepts a hoomd.variant.box.BoxVariant object for [target_box]{.title-ref} (#1736).
• box argument to hoomd.update.BoxResize that accepts a hoomd.variant.box.BoxVariant (#1740).
• hoomd.hpmc.pair.Union computes pair potentials between unions of points. Replaces CPPPotentialUnion (#1725).
• hoomd.hpmc.pair.Step - A step function potential (#1732).
• hoomd.hpmc.pair.AngularStep - Angular patches on particles with step function interactions (e.g. Kern-Frenkel) (#1728).

Changed

• Use FindPython on modern CMake installations. You may need to adjust build scripts in cases where the new behavior does not exactly match the old (i.e. use -DPython_EXECUTABLE in place of -DPYTHON_EXECUTABLE) (#1730).
• External components must switch from pybind11_add_module to hoomd_add_module (#1730).

Deprecated

• box1, box2, and variant arguments to hoomd.update.BoxResize (#1740).

v4.5.0

Fixed

• hoomd.hpmc.update.Shape properly restores shape alchemy parameters on rejected trial moves (#1696).
• hoomd.hpmc.update.Shape now functions with hoomd.device.GPU (#1696).
• hoomd.hpmc.update.MuVT applies external potentials (#1711).
• hoomd.hpmc.update.QuickCompress can now reshape boxes with tilt factors <= 0 (#1709).

Added

• Improve component build documentation and link to the hoomd-component-template repository (#1668).
• hoomd.md.improper.Periodic - CHARMM-like periodic improper potential (#1662).
• allow_unsafe_resize flag to hoomd.hpmc.update.QuickCompress (#1678).
• hoomd.error.GPUNotAvailableError (#1694).
• HPMC compile time pair potential framework (CPU only). Allows potential energy in HPMC simulations without CPPPotential.
  • hoomd.hpmc.pair.LennardJones - Evaluate Lennard Jones energy between particles (#1676).
  • HPMCIntegrator.pair_potentials - Set a list of pair potentials to evaluate (#1676).
  • HPMCIntegrator.pair_energy (loggable) - Total pair energy from all pair potentials. (#1676).

Deprecated

• _InternalCustomUpdater.update. (#1692).
• _InternalCustomTuner.tune. (#1692).
• _InternalCustomWriter.write. (#1692).
• HDF5Log.write. (#1692).
• hoomd.util.GPUNotAvailableError (#1694).
• hoomd.hpmc.pair.user.CPPPotentialBase (#1676).
• hoomd.hpmc.pair.user.CPPPotential - Use a built-in potential or compile your code in a component (#1676).
• hoomd.hpmc.pair.user.CPPPotentialUnion - Use a built-in potential or compile your code in a component (#1676).
• HPMCIntegrator.pair_potential - Use compiled potentials with pair_potentials (#1676).

Changed

• Refactored the C++ API for PatchEnergy potentials (#1676).
• Removed unused Operation._children methods (#1713).

v4.4.1

Fixed

• Correct net_virial values in local snapshots (#1672).
• Improve HPMC performance on the CPU when using a pair potential (#1679).
• Improve HPMC performance with 3D hard shapes (#1679).
• Improve HPMC performance on the CPU (#1687).

Changed

• Provide support via GitHub discussions (#1671).

v4.4.0

Added

• hoomd.md.external.field.Magnetic computes forces and torques on particles from an external magnetic field (#1637).
• Tutorial on placing barriers (hoomd-examples/#111).

Fixed

• Use mpirun specific local ranks to select GPUs before checking SLURM_LOCALID (#1647).
• Fix typographical errors in RevCross documentation (#1642).
• Use standards compliant thrust::get (#1660).

Changed

• Removed unused code (#1646).
• No longer issue a warning when hoomd.md.Integrator is used without an integration method (#1659).
• Increase performance of Force.forces, Force.torques, Force.energies, and Force.virials (#1654).

Deprecated

• num_cpu_threads > 1. Use num_cpu_threads = 1 (#1656).
• HPMCIntegrator.depletant_fugacity > 0 (#1657).

v4.3.0

Fixed

• md.alchemy.methods.NVT now evolves the elements provided in alchemical_dof (#1633).
• More consistent notice messages regarding MPI ranks used in GPU selection (#1635).
• hoomd.hpmc.compute.SDF computes correct pressures with patchy potentials. (#1636).

Added

• Support GCC 13 (#1634).
• Support Python 3.12 (#1634).
• tau parameter to hoomd.md.methods.thermostats.Bussi (#1619).

Changed

• Revise class documentation. (#1628).
• Add more code snippets to the class documentation (#1628).