HOOMD-blue

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Official Binaries

Official binaries of HOOMD-blue are available via conda through the glotzer channel. Conda is a python-centric packaging system targeted at computational researchers. The default package database includes many useful packages such as scipy, ipython and scikit-learn. Many more user-provided packages are available through channels on anaconda.org.

To install HOOMD-blue, first download and install miniconda following conda's instructions. Then add the glotzer channel and install HOOMD-blue:

$ conda config --add channels glotzer
$ conda install hoomd

If you have already installed hoomd in conda, you can upgrade to the latest version:

$ conda update --all

If you find HOOMD-blue useful in your research, please cite it. See the citation page for instructions.

Requirements

  • On Linux (64-bit):
    • CPU with AVX capabilities (2011 or newer)
    • A recent linux distribution (such as CentOS/RHEL 6, ubuntu 14.04, or newer)
    • [optional] NVIDIA drivers 352.55 or newer
    • [optional] CUDA capable NVIDIA GPU, compute 2.0 or newer.
  • On Mac:
    • CPU with AVX capabilities (2011 or newer)
    • OSX 10.8 or newer
    • Note: Mac builds are not MPI or GPU enabled.

User supported binaries

A HOOMD-blue user maintains an Arch Linux (AUR) package.

Source

Use git to clone from HOOMD-blue's bitbucket repository.

See the user manual for system requirements and build instructions.

Change Log

v2.0.3

Released 2016/08/30

  • hpmc.util.tune now works with particle types as documented
  • Fix pressure computation with pair.dpd() on the GPU
  • Fix a bug where dump.dcd corrupted files on job restart
  • Fix a bug where HPMC walls did not work correctly with MPI
  • Fix a bug where stdout/stderr did not appear in MPI execution
  • HOOMD will now report an human readable error when users forget context.initialize()
  • Fix syntax errors in frenkel ladd field

v2.0.2

Released 2016/08/09

  • Support CUDA Toolkit 8.0
  • group.rigid()/nonrigid() did not work in MPI simulations
  • Fix builds with ENABLE_DOXYGEN=on
  • Always add -std=c++11 to the compiler command line arguments
  • Fix rare infinite loops when using hpmc.integrate.faceted_sphere
  • Fix hpmc.util.tune to work with more than one tunable
  • Fix a bug where dump.gsd() would write invalid data in simulations with changing number of particles
  • replicate() sometimes did not work when restarting a simulation

v2.0.1

Released 2016/07/15

Bug fixes

  • Fix acceptance criterion in mu-V-T simulations with implicit depletants (HPMC).
  • References to disabled analyzers, computes, updaters, etc. are properly freed from the simulation context.
  • Fix a bug where init.read_gsd ignored the restart argument.
  • Report an error when HPMC kernels run out of memory.
  • Fix ghost layer when using rigid constraints in MPI runs.
  • Clarify definition of the dihedral angle.

v2.0.0

Released 2016/06/22

HOOMD-blue v2.0 is released under a clean BSD 3-clause license.

New packages

  • dem - simulate faceted shapes with dynamics
  • hpmc - hard particle Monte Carlo of a variety of shape classes.

Bug fixes

  • Angles, dihedrals, and impropers no longer initialize with one default type.
  • Fixed a bug where integrate.brownian gave the same x,y, and z velocity components.
  • Data proxies verify input types and vector lengths.
  • dump.dcd no longer generates excessive metadata traffic on lustre file systems

New features

  • Distance constraints constrain.distance - constrain pairs of particles to a fixed separation distance
  • Rigid body constraints constrain.rigid - rigid bodies now have central particles, and support MPI and replication
  • Multi-GPU electrostatics charge.pppm - the long range electrostatic forces are now supported in MPI runs
  • context.initialize() can now be called multiple times - useful in jupyter notebooks
  • Manage multiple simulations in a single job script with SimulationContext as a python context manager.
  • util.quiet_status() / util.unquiet_status() allow users to control if line status messages are output.
  • Support executing hoomd in Jupyter (ipython) notebooks. Notice, warning, and error messages now show up in the notebook output blocks.
  • analyze.log can now register python callback functions as sources for logged quantities.
  • The GSD file format (http://gsd.readthedocs.io) is fully implemented in hoomd
    • dump.gsd writes GSD trajectories and restart files (use truncate=true for restarts).
    • init.read_gsd reads GSD file and initializes the system, and can start the simulation from any frame in the GSD file.
    • data.gsd_snapshot reads a GSD file into a snapshot which can be modified before system initialization with init.read_snapshot.
    • The GSD file format is capable of storing all particle and topology data fields in hoomd, either static at frame 0, or varying over the course of the trajectory. The number of particles, types, bonds, etc. can also vary over the trajectory.
  • force.active applies an active force (optionally with rotational diffusion) to a group of particles
  • update.constrain_ellipsoid constrains particles to an ellipsoid
  • integrate.langevin and integrate.brownian now apply rotational noise and damping to anisotropic particles
  • Support dynamically updating groups. group.force_update() forces the group to rebuild according to the original selection criteria. For example, this can be used to periodically update a cuboid group to include particles only in the specified region.
  • pair.reaction_field implements a pair force for a screened electrostatic interaction of a charge pair in a dielectric medium.
  • force.get_energy allows querying the potential energy of a particle group for a specific force
  • init.create_lattice initializes particles on a lattice.
    • lattice.unitcell provides a generic unit cell definition for create_lattice
    • Convenience functions for common lattices: sq, hex, sc, bcc, fcc.
  • Dump and initialize commands for the GTAR file format (http://libgetar.readthedocs.io).
    • GTAR can store trajectory data in zip, tar, sqlite, or bare directories
    • The current version stores system properties, later versions will be able to capture log, metadata, and other output to reduce the number of files that a job script produces.
  • integrate.npt can now apply a constant stress tensor to the simulation box.
  • Faceted shapes can now be simulated through the dem component.

Changes that require job script modifications

  • context.initialize() is now required before any other hoomd script command.
  • init.reset() no longer exists. Use context.initialize() or activate a SimulationContext.
  • Any scripts that relied on undocumented members of the globals module will fail. These variables have been moved to the context module and members of the currently active SimulationContext.
  • bonds, angles, dihedrals, and impropers no longer use the set_coeff syntax. Use bond_coeff.set, angle_coeff.set, dihedral_coeff.set, and improper_coeff.set instead.
  • hoomd_script no longer exists, python commands are now spread across hoomd, hoomd.md, and other sub packages.
  • integrate.\*_rigid() no longer exists. Use a standard integrator on group.rigid_center(), and define rigid bodies using constrain.rigid()
  • All neighbor lists must be explicitly created using nlist.\*, and each pair potential must be attached explicitly to a neighbor list. A default global neighbor list is no longer created.
  • Moved cgcmm into its own package.
  • Moved eam into the metal package.
  • Integrators now take kT arguments for temperature instead of T to avoid confusion on the units of temperature.
  • phase defaults to 0 for updaters and analyzers so that restartable jobs are more easily enabled by default.
  • dump.xml (deprecated) requires a particle group, and can dump subsets of particles.

Other changes

  • CMake minimum version is now 2.8
  • Convert particle type names to str to allow unicode type name input
  • __version__ is now available in the top level package
  • boost::iostreams is no longer a build dependency
  • boost::filesystem is no longer a build dependency
  • New concepts page explaining the different styles of neighbor lists
  • Default neighbor list buffer radius is more clearly shown to be r_buff = 0.4
  • Memory usage of nlist.stencil is significantly reduced
  • A C++11 compliant compiler is now required to build HOOMD-blue

Removed

  • Removed integrate.bdnvt: use integrate.langevin
  • Removed mtk=False option from integrate.nvt - The MTK NVT integrator is now the only implementation.
  • Removed integrate.\*_rigid(): rigid body functionality is now contained in the standard integration methods
  • Removed the global neighbor list, and thin wrappers to the neighbor list in nlist.
  • Removed PDB and MOL2 dump writers.
  • Removed init.create_empty

Deprecated

  • Deprecated analyze.msd.
  • Deprecated dump.xml.
  • Deprecated dump.pos.
  • Deprecated init.read_xml.
  • Deprecated init.create_random.
  • Deprecated init.create_random_polymers.

Older versions

Older change log entries are available in the source file ChangeLog.md.