v3.0.0-beta.1

Overview

v3 has a completely new Python API. See the tutorials, migration guide
and new API documentation learn about it. The API documentation serves
as the complete list of all features currently implemented in
v3.0.0-beta.1. Not all features in v2 have been ported in v3.0.0-beta.1.
Future beta releases will add additional functionality.

Added

• Zero-copy data access through numpy (CPU) and cupy (GPU).
• User-defined operations in Python.
• User-defined triggers determine what time steps operations execute
  on.
• New logging subsystem supports array quantities and binary log
  files.
• Implicit depletants are now supported by any hpmc integrator
  through mc.set_fugacity('type', fugacity).
• Enable implicit depletants for two-dimensional shapes in hpmc.
• jit.patch.user() and jit.patch.user_union() now support GPUs via
  NVRTC.
• Add harmonically mapped averaging.
• Add Visual Studio Code workspace

Changed

• The run method has minimal overhead
• All loggable quantities are directly accessible as object
  properties.
• Operation parameters are always synchronized.
• Operations can be instantiated without a device or MPI communicator.
• Writers write output for step+1 at the bottom of the run loop.
• HOOMD writes minimal output to stdout/stderr by default.
• CMake >=3.9, cereal, eigen, and pybind11 are required to
  compile HOOMD.
• Plugins must be updated to build against v3.
• By default, HOOMD installs to the site-packages directory
  associated with the python executable given, which may be inside a
  virtual environment.
• Refactored CMake code.
• git submodule update no longer runs when during CMake
  configuration.
• Use random123 library for implicit depletants in hpmc.
• HOOMD requires a GPU that supports concurrent managed memory access
  (Pascal or newer).

Bug fixes

• Improved accuracy of DLVO potential on the GPU.
• Improved performance of HPMC simulations on the CPU in non-cubic
  boxes.

Removed

• HOOMD-blue no longer parses command line options.
• Type swap moves in hpmc.update.muvt() are no longer supported
  (transfer_ratio option to muvt.set_params())
• The option implicit=True to hpmc.integrate.* is no longer
  available (use set_fugacity).
• static parameter in dump.gsd
• util.quiet_status and util.unquiet_status.
• deprecated.analyze.msd.
• deprecated.dump.xml.
• deprecated.dump.pos.
• deprecated.init.read_xml.
• deprecated.init.create_random.
• deprecated.init.create_random_polymers.
• hpmc ignore_overlaps parameter.
• hpmc sphere_union::max_members parameter.
• hpmc convex_polyhedron_union.
• hpmc setup_pos_writer method.
• hpmc depletant_mode='circumsphere'.
• hpmc max_verts parameter.
• hpmc depletant_mode parameter.
• hpmc ntrial parameter.
• hpmc implicit boolean parameter.
• group parameter to md.integrate.mode_minimize_fire
• cgcmm.angle.cgcmm
• cgcmm.pair.cgcmm
• COPY_HEADERS CMake option.
• Many other python modules have been removed or re-implemented with
  new names. See the migration guide and new API documentation for a
  complete list.

v2.9.3

Bug fixes

• Fix a compile error with CUDA 11

v2.9.2

Bug fixes

• Fix a bug where repeatedly using objects with period=None would
  use significant amounts of memory.
• Support CUDA 11.
• Reccomend citing the 2020 Computational Materials Science paper
  10.1016/j.commatsci.2019.109363.

v2.9.1

Bug fixes

• Fixed a minor bug where the variable period timestep would be off by
  one when the timestep got sufficiently large.
• Updated collections API to hide DeprecationWarning.
• Fix scaling of cutoff in Gay-Berne potential to scale the current
  maximum distance based on the orientations of the particles,
  ensuring ellipsoidal energy isocontours.
• Misc documentation fixes.

v2.9.0

New features

• General
  • Read and write GSD 2.0 files.
    • HOOMD >=2.9 can read and write GSD files created by HOOMD
      <= 2.8 or GSD 1.x. HOOMD <= 2.8 cannot read GSD files
      created by HOOMD >=2.9 or GSD >= 2.0.
    • OVITO >=3.0.0-dev652 reads GSD 2.0 files.
    • A future release of the gsd-vmd plugin will read GSD 2.0
      files.
• HPMC
  • User-settable parameters in jit.patch.
  • 2D system support in muVT updater.
  • Fix bug in HPMC where overlaps were not checked after adding new
    particle types.
• MD
  • The performance of nlist.tree has been drastically improved
    for a variety of systems.

v2.8.2

Tagging v2.8.2