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).

v4.2.1

Fixed

• hoomd.write.Table correctly displays floating point values that are exactly 0.0 (#1625).
• hoomd.write.HDF5Log defaults to "f8" formatting except when the value is an [int]{.title-ref}, or a [numpy.number]{.title-ref} (#1620).
• Attempt to workaround PMI_Init returned 1 error on OLCF Frontier (#1629).
• Apple clang 15 compiles HOOMD-blue without errors (#1626).

v4.2.0

Fixed

• Make HDF5Log example more visible (#1602).
• Access valid GPU memory in hoomd.hpmc.update.Clusters (#1607).
• Test suite passes on the ROCm GPU platform (#1607).
• Provide an error message when using md.external.field.Periodic in 2D (#1603).
• hoomd.write.GSD reports "File exists" in the exception description when using the 'xb' mode and the file exists (#1609).
• Write small numbers correctly in hoomd.write.Table (#1617).
• Make examples in hoomd.md.methods.NVE and hoomd.md.methods.DisplacementCapped more visible (#1601).

Added

• Documentation page: "How to apply arbitrary forces in MD" (#1610).
• Documentation page: "How to prevent particles from moving" (#1611).
• Documentation page: "How to minimize the potential energy of a system" (#1614).
• Documentation page: "How to continuously vary potential parameters" (#1612).
• Documentation page: "How to determine the most efficient device" (#1616).
• Documentation page: "How to choose the neighbor list buffer distance" (#1615).
• Documentation page: "How to compute the free energy of solids" (#1613).
• MPCD particle data is now available included in Snapshot (#1580).
• Add variable parameters to hpmc.external.user.CPPExternalPotential (#1608).

Changed

• Removed the unused ExternalFieldComposite.h and all the related ExternalFieldComposite* (#1604).

v4.1.0

Fixed

• Improved documentation (#1585).
• Update mesh documentation (#1587).
• Follow detailed balance in hoomd.hpmc.update.Shape (#1595).
• pre-commit environment installs correctly on macos-arm64 (#1597).
• Install all HPMC headers for use by plugins (#1573).
• Bond potentials can now be implemented via external plugins (#1591).

Added

• Tested example code snippets in select modules (#1574) (#1586).
• hoomd.util.make_example_simulation - create an example Simulation object (#1574) (#1586).
• hoomd.write.Burst now has a __len__ method (#1575).
• Support clang 15 and 16 on Linux (#1593).
• hoomd.write.HDF5Logger - write log quantities to HDF5 files (#1588).
• default_gamma and default_gamma_r arguments to hoomd.md.methods.rattle.Brownian hoomd.md.methods.rattle.Langevin, and hoomd.md.methods.rattle.OverdampedViscous (#1589).

v4.0.1

Fixed

• Prevent ValueError: signal only works in main thread of the main interpreter when importing hoomd in a non-main thread (#1576).
• The recommended conda install commands find the documented version (#1578).
• CMake completes without error when HOOMD_GPU_PLATFORM=HIP (#1579).
• Tests pass with GSD 3.0.0 installed (#1577).
• Provide full CUDA error message when possible (#1581).
• Notice level 4 gives additional GPU initialization details (#1581).
• Show particle out of bounds error messages in exception description (#1581).

Changed

• Package source in hoomd-x.y.z.tar.gz (previously hoomd-vx.y.z.tar.gz) (#1572).