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).

v4.0.0

Fixed

• Fix error with MPI_Allreduce on OLCF Frontier (#1547).
• Correct equations in virial pressure documentation (#1548).
• Work around cases where Python's garbage collector fails to collect Operation objects (#1457).
• Incorrect behavior with hpmc.external.user.CPPExternalPotential in MPI domain decomposition simulations (#1562).

Added

• hoomd.md.ConstantVolume integration method (#1419).
• hoomd.md.ConstantPressure integration method, implementing the Langevin piston barostat (#1419).
• Thermostats in hoomd.md.methods.thermostats that work with ConstantVolume and ConstantPressure, including the new Bussi-Donadio-Parrinello thermostat (#1419).
• hoomd.md.external.wall.Gaussian (#1499).
• hoomd.write.GSD.maximum_write_buffer_size - Set the maximum size of the GSD write buffer (#1541).
• hoomd.write.GSD.flush - flush the write buffer of an open GSD file (#1541).
• On importing hoomd, install a SIGTERM handler that calls sys.exit(1) (#1541).
• More descriptive error messages when calling Simulation.run (#1552).
• hoomd.Snapshot.from_gsd_frame - convert a gsd.hoomd.Frame object to hoomd.Snapshot (#1559).
• hoomd.device.NoticeFile - a file-like object that writes to hoomd.device.Device.notice (#1449).
• hoomd.write.Burst - selective high-frequency frame writing to GSD files (#1543).
• Support LLVM 16 (#1568).
• More detailed status message for found CUDA libraries (#1566).

Changed

• hoomd.md.constrain.Rigid no longer takes diameters or charges as keys in the body parameters. create_bodies method now takes an optional charges argument to set charges (#1350).
• Control the precision with the CMake options HOOMD_LONGREAL_SIZE (default: 64) and HOOMD_SHORTREAL_SIZE (default: 32) (#355).
• [developers] ShortReal and LongReal types enable mixed precision implementations (#355).
• hoomd.md.constrain.Rigid now updates constituent particle types each step (#1440).
• Moved hoomd.mesh.Mesh.triangles to hoomd.mesh.Mesh.triangulation (#1464).
• hoomd.write.GSD does not write particles/diameter by default (#1266).
• Updated tutorials to use HOOMD-blue v4 API, work with up to date releases of freud, gsd, and signac. Also make general improvements to the tutorials.
• Document changes needed to migrate from v3 to v4 in the migration guide.
• More descriptive error messages when calling Simulation.run (#1552).
• Increase performance of hoomd.write.GSD (#1538).
• Increase performance of hoomd.State.get_snapshot in serial (#1538).
• hoomd.write.GSD.dynamic now allows fine grained control over individual particle fields (#1538).
• No longer test with GCC 7-8, Python 3.6-3.7, or Clang 6-9) (#1544).
• Improved error messages with NVRTC compiled code (#1567).

Deprecated

• Scalar, Scalar2, Scalar3, and Scalar4 data types. Use LongReal[N] instead in new code (#355).
• hoomd.Snapshot.from_gsd_snapshot - use hoomd.Snapshot.from_gsd_frame (#1559).

Removed

• fix_cudart_rpath CMake macro (#1383).
• ENABLE_MPI_CUDA CMake option (#1401).
• Berendsen, NPH, NPT, NVE, NVT MD integration methods (#1419).
• hoomd.write.GSD.log (#1480).
• CMake option and compiler definition SINGLE_PRECISION (#355).
• charges key in hoomd.md.constrain.Rigid.body (#1496).
• diameter key in hoomd.md.constrain.Rigid.body. (#1496).
• hoomd.md.dihedral.Harmonic. (#1496).
• hoomd.device.GPU.memory_traceback parameter. (#1496).
• hoomd.md.pair.aniso.Dipole.mode parameter. (#1496).
• hoomd.md.pair.aniso.ALJ.mode parameter (#1496).
• hoomd.md.pair.Gauss (#1499).
• hoomd.md.external.wall.Gauss (#1499).
• msg_file property and argument in hoomd.device.Device. (#1499).
• The sdf attribute of hoomd.hpmc.compute.SDF - use sdf_compression (#1523).
• alpha parameter and attribute in Langevin, BD, and OverdampedViscous integration methods (#1266).
• needsDiameter and setDiameter API in C++ potential evaluators (#1266).

v3.11.0

Added:

• hoomd.md.Integrator.validate_groups verifies that MD integration methods are applied to distinct subsets of the system and that those subsets consist of integrable particles (automatically called when attached) (#1466).

Changed:

• hoomd.hpmc.compute.SDF computes pressures for systems of concave and non-monotonic patch interactions (#1391).
• Reorganize documentation contents to fit in the sidebar, including landing pages for tutorials and how-to guides (#1526).

Fixed:

• Improved readability of images in the documentation (#1521).
• hoomd.write.Table now raises a meaningful error when given incorrect logger categories (#1510).
• Correctly document the 1/2 scaling factor in the pairwise virial computation (#1525).
• thermalize_particle_momenta now sets 0 velocity and angular momentum for rigid constituent particles (#1472).
• Reduce likelihood of data corruption when writing GSD files (#1531).
• Clarify migration process for hoomd.md.pair.ExpandedLJ (#1501).

Deprecated:

• The sdf attribute of hoomd.hpmc.compute.SDF - use sdf_compression (#1391).

v3.10.0

Added:

• The message_filename property and argument to Device, CPU, and GPU to replace msg_file (#1497).
• hoomd.md.pair.Gaussian to replace hoomd.md.pair.Gauss (#1497).
• hoomd.md.pair.ExpandedGaussian - the expanded Gaussian pair force (#1493).
• Guide: How to apply arbitrary pair potentials in HPMC (#1505).

Changed:

• Use furo style for HTML documentation (#1498).

Fixed:

• The hoomd.md.pair potentials ExpandedLJ, ExpandedMie, LJGauss, and TWF now shift V(r_cut) to 0 properly when mode == 'shift' (#1504).
• Corrected errors in the pair potential documentation (#1504).
• Note that the 'body' exclusion should be used with hoomd.md.constrain.Rigid (#1465).
• Correctly identify the 'xyz' mode in hoomd.md.methods.NPH (#1509).

Deprecated:

• The msg_file property and argument to Device, CPU, and GPU.
• hoomd.md.pair.Gauss.

v3.9.0

Added:

• GPU code path for hoomd.update.BoxResize (#1462).
• logger keyword argument and property to hoomd.write.GSD (#1481).

Changed:

• Issue [FutureWarning]{.title-ref} warnings when using deprecated APIs (#1485).
• Reformat the list of deprecated features. (#1490).
• In simulations with rigid bodies, remove D degrees of freedom when the system is momentum conserving (#1467).

Fixed:

• Compile without errors using hipcc and ROCM 5.1.0 (#1478).
• Document that hoomd.md.force.Force can be added to Operations.computes (#1489).
• hoomd.md.constrain.Rigid.create_bodies completes without segmentation faults when particle body tags are not -1 (#1476).
• hoomd.hpmc.compute.FreeVolume computes the free area correctly in 2D simulations (#1473).

Deprecated:

• Deprecate write.GSD log keyword argument and property in favor of logger (#1481).

v3.8.1

Fixed:

• #1468:
  Conserve linear momentum in simulations using
  hoomd.md.constrain.Rigid on more than 1 MPI rank.

v3.8.0

Added

• Support Python 3.11.
• Support CUDA 11.8.
• Support CUDA 12.0.0 final.

Fixed

• Improve numerical stability of orientation quaternions when using
  hoomd.md.update.ActiveRotationalDiffusion
• Reduced memory usage and fix spurious failures in test_nlist.py.
• Avoid triggering TypeError("expected x and y to have same length")
  in hoomd.hpmc.compute.SDF.betaP.

Deprecated

• The following integration methods are deprecated. Starting in
  v4.0.0, the same functionalities will be available via
  hoomd.md.methods.ConstantVolume/
  hoomd.md.methods.ConstantPressure with an appropriately chosen
  thermostat argument.
  • hoomd.md.methods.NVE
  • hoomd.md.methods.NVT
  • hoomd.md.methods.Berendsen
  • hoomd.md.methods.NPH
  • hoomd.md.methods.NPT

Removed

• Support for CUDA 10.

v3.7.0

Added

• Neighborlist.r_cut sets the base cutoff radius for neighbor
  search - for use when the neighbor list is used for analysis or
  custom Python code.
• Neighborlist.cpu_local_nlist_arrays provides zero-copy access to
  the computed neighbor list.
• Neighborlist.gpu_local_nlist_arrays provides zero-copy access to
  the computed neighbor list.
• Neighborlist.local_pair_list provides the rank local pair list by
  index.
• Neighborlist.pair_list provides the global pair list by tag on
  rank 0.
• hoomd.md.dihedral.Periodic - a new name for the previous
  Harmonic potential.
• default_gamma and default_gamma_r arguments to the
  hoomd.md.methods: Brownian, Langevin, and OverdampedViscous.
• reservoir_energy loggable in hoomd.md.methods.Langevin.
• hoomd.md.force.Constant applies constant forces and torques to
  particles.

Changed

• [plugin developers] Refactored the LocalDataAccess C++ classes
  to add flexibility.

Fixed

• hoomd.hpmc.nec integrators compute non-infinite virial pressures
  for 2D simulations.
• Raise an exception when attempting to get the shape specification of
  shapes with 0 elements.
• Box conversion error message now names hoomd.Box.

Deprecated

• hoomd.md.dihedral.Harmonic - use the functionally equivalent
  hoomd.md.dihedral.Periodic.
• charges key in hoomd.md.constrain.Rigid.body.
• diameters key in hoomd.md.constrain.Rigid.body.