Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition

HOOMD-blue related news items now on the web

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  • News

Feb 1, 2010 | [ Back to top ]

Documentation for development version online

With recent improvements to the model used for hoomd development, the up to date development version (trunk/) available via subversion is consistently being kept as stable and bug free as a packaged release version. Users wishing to take advantage of the latest features and performance enhancements should now feel comfortable using the latest version in trunk/ for production simulations. For convenience, documentation compiled from trunk/ is now being updated to this web site on a regular basis.

Links of interest

Dec 21, 2009 | [ Back to top ]

HOOMD-blue 0.8.2 win64 build updated to python 2.6

Python 2.6 is the latest stable python in the 2.x series and is now the only 2.x version available for download. Correspondingly, the win64 build of hoomd on the download page has been updated to work with python 2.6.x.

Dec 9, 2009 | [ Back to top ]

HOOMD-blue 0.8.2 Released

The much-delayed HOOMD-blue 0.8.2 release is finally complete. The delays actually resulted in an extensive amount of testing and subsequent bug fixes making this a really solid release. We hope you enjoy it!

Major changes since 0.8.1:

  • Performance enhancements
  • Time varying quantities can now be given to various updaters (temperature and pressure, for example)
  • update.box_resize added to change the box size slowly over many time steps
  • run() commands can now be limited to a given wall-clock time (potentially useful on shared cluster with wall-clock time limits on jobs)
  • Angle, dihedral and improper forces can now be specified
  • Neighbor exclusions can now be changed to optionally include/exclude 1-2, 1-3, and 1-4 pairs.
  • New command line options for controlling how HOOMD-blue uses the GPU - see the documentation for details
  • Plus many bug fixes and other small improvements

See the change log for a more detailed list.

A big thanks goes to Axel Kohlmeyer, David LeBard, and Ben Levine from the ICMS group at Temple University for contributing many features to this release. Their biggest contribution is the angle, dihedral, and improper forces.

Known Issues for the current release are listed here. If you have a problem that is not listed, don't hesitate to contact us. Also contact us if you have any feature requests for future releases.

Sep 10, 2009 | [ Back to top ]

HOOMD is going blue!

HOOMD's lead developer has graduated and moved on to a position at the University of Michigan, and the center of HOOMD development is moving with him. Due to technical reasons regarding licensing, a name change must be part of the move. Thus HOOMD development will continue under the name HOOMD-blue! It stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition.

If you are familiar with the language used commonly in open source projects, this is technically a fork of the original HOOMD project. For all practical purposes, however, it actually is not a fork as we have the same developers continuing to work on the code as if nothing happened. No major changes to the roadmap are planned and, if anything, the development effort will only accelerate after this move. Our apologies for any confusions this might cause, but such changes are inevitable with young projects developed by graduate students.

The new web URL for HOOMD is at http://codeblue.umich.edu/hoomd-blue/ and the server combines that directly with Trac and SVN hosting for the project at http://codeblue.umich.edu/hoomd-blue/trac/ and https://codeblue.umich.edu/hoomd-blue/svn/ respectively. The old website and SVN will be left up for a few months for continuity before they are taken down.

A new feature we are proud to offer on this Trac web is the ability for users, not just developers, to register accounts with the system. To do this, go to the Trac web page, click the register link in the upper right and follow the onscreen instructions. After verifying your e-mail address with the system, you will be able to edit and add to the wiki, post new tickets and add comments to existing tickets.

Getting this new page operational has been the major blocker delaying the release of 0.8.2. Now that we are up and running, expect this next packaged release soon!

Aug 12, 2009 | [ Back to top ]

HOOMD 0.8.1 Released

HOOMD 0.8.1 is complete.

Major changes since 0.8.0:

  • Performance enhancements
  • Particles can be assigned a non-unit mass
  • init.reset() command for looping simulations
  • PDB dump file format
  • Shifted and smoothed pair potentials
  • Gaussian pair potential
  • Append options for analyze.* command output
  • Update and analyze commands can be given a non-linear period
  • Bug fixes

See the change log for a more detailed list.

Known Issues for the current release are listed here. If you have a problem that is not listed, don't hesitate to contact us. Also contact us if you have any feature requests for future releases.

March 24, 2009 | [ Back to top ]

Hotfix to HOOMD 0.8.0

A serious issue was discovered in the windows builds of HOOMD 0.8.0. Any use of dump.dcd would result in the hoomd executable crashing. This issue is fixed in hotfix binaries labeled version 0.8.0.1. Users compiling from the source tarball will need to apply the following diff: r1581.

Linux and Mac users are unaffected.

Jan 12, 2009 | [ Back to top ]

HOOMD 0.8.0 Released

HOOMD 0.8.0 is complete.

Major changes since 0.7.1:

  • Performance enhancements
  • Execution on multiple GPUs
  • Support for GTX 280 and Tesla 1000 series GPUs
  • Brownian dynamics integrator
  • NPT integrator
  • FENE bonds
  • Tracking of particle images for MSD analysis
  • Improved user documentation
  • Bug fixes

See the change log for a more detailed list.

Known Issues for the current release are listed here. If you have a problem that is not listed, don't hesitate to contact us. Also contact us if you have any feature requests for future releases.

Dec 22, 2008 | [ Back to top ]

hoomd-users mailing list created

A mailing list for users of HOOMD has been created. Subscribe to the list below or at the Contact page. After subscribing, feel free to send any support questions, feature requests, or bug reports to the list. It will also be used for announcing new releases of HOOMD.

The mailing list is hosted at Google Groups and the archives can be accessed at http://groups.google.ca/group/hoomd-users.

Subscribe to hoomd-users

Email:

Sep 23, 2008 | [ Back to top ]

HOOMD 0.7.1 Released

A critical bug that might cause incorrect results in simulations with tiny box sizes was just discovered. HOOMD 0.7.1 is being released to fix this issue. All users should upgrade immediately. Large simulations with 1000's of particles are not effected, only tiny simulations with a few 100 particles experience the bug.

Changes since 0.7.0

  • Fixed a bug where systems with box dimensions less than 3*(r_cut+r_buff) would run incorrectly and without producing an error.
  • Fixed a bug that prevented extremely low density systems from being run.

We are committed to providing an accurate, as well as fast, simulation software and have a stringent battery of automatic unit tests to verify the correct calculation of every force and integration step in HOOMD. This critical bug slipped through simply because none of those test cases was set in such a tiny box size.

  • Known Issues
  • Full change log

Sep 12, 2008 | [ Back to top ]

HOOMD 0.7.0 Released

HOOMD 0.7.0 is finally done!

The biggest change is the inclusion of the job scripting system. With it, configuring simulations in HOOMD is a snap. See the quick start tutorial for in introduction. HOOMD 0.7.0 has also been thoroughly tested for stability and accuracy. We have a 2-GPU machine that has been running research simulations 24/7 for weeks now without a single crash or other problem.

In other words, HOOMD is now ready to be used by anyone for serious research, download it now.

Changes since 0.6.0:

  • Job scripting system
  • User documentation
  • Stability improvements
  • Energy logging
  • File conversion scripts
  • GPU selection
  • Advanced initial configuration generator (for polymers)
  • Particle types named by strings
  • Bug fixes

... and much, much more. See the change log for a more detailed list.

This page lists the current known issues. If you have a problem that is not listed, don't hesitate to contact us. Also contact us if you have any feature requests.

Aug 13, 2008 | [ Back to top ]

HOOMD 0.6.1 Released

With a lot of recent interest in HOOMD, we thought it pertinent to release an updated version with the performance and stability bugs fixed. The benchmarks page has been updated to reflect the performance of 0.6.1.

Changes since 0.6.0

  • Compatibility improved with certain versions of Boost
  • Numerous performance and stability improvements
  • HOOMD should now compile on CUDA capable Mac OS X systems. We don't have such a system, so we cannot test this configuration

Major new features, such as the job scripting system are still on track for release in a few months with 0.7.0.

Download HOOMD | May 22, 2008 | [ Back to top ]

Progress update

We are making good progress toward HOOMD version 0.7. Major changes include a fix to the CUDA bug workaround that is present in 0.6.0. In the current development version, simulations are stable for runs longer than 150+ hours, with lj_liquid_bmark running at ~193 time steps per second on a Tesla C870.

Another major change is the inclusion of a simple scripting system for creating simulations. With the new scripting system, running simulations will be made much easier than in 0.6.0. For example, a simple Lennard-Jones liquid simulation will look something like this

# note: this is preliminary syntax, it may change in the final release
from hoomd_script import *
init.create_random(N=1000, phi_p=0.2, 'A')
integrate.nvt(T=1.2, tau=0.5, dt=0.005)

coeff = pair_coeff()
coeff.set(('A', 'A'), dict(epsilon=1.0, sigma=1.0))

lj = pair.lj(r_cut=3.0)
lj.pair_coeff(coeff)

run(1e6)

If this looks similar to LAMMPS scripts to you, that is no accident. HOOMD's scripting system has been designed to be that way so that LAMMPS users can use HOOMD with little or no learning curve.

It's hard to put an exact date on the release, but it should be coming within the next few months.

Detailed change log | May 14, 2008 | [ Back to top ]

HOOMD at the APS March Meeting 2008

We were at the American Physical Society (APS) march meeting in New Orleans and displayed a poster on our work "Molecular Dynamics of Polymer Systems on Graphics Processing Units (GPUs)".

Download poster | March 28, 2008 | [ Back to top ]

HOOMD 0.6.0 Released

HOOMD 0.6.0 is the first public release of HOOMD. It includes several benchmarks and demos to showcase the performance of the GPU. It is not intended for use with production simulations.

We are hard at work on the next release which will include an easy to use scripting system for setting up and running simulations

Download HOOMD | Feb 8, 2008 | [ Back to top ]

Paper accepted

Our paper has been accepted for publication in the Journal of Computational Physics, and should appear there soon. The preprint is available for download from this site.

About HOOMD | Download preprint | Feb 6, 2008 | [ Back to top ]

HOOMD source code now available

The source code for HOOMD is now available for download under a BSD-style license. It can be accessed through the subversion server http://svn2.assembla.com/svn/hoomd. An online source code browser is also available at the development page. For more information, see the documentation.

Any interested developers are welcome to download, browse and use the code. Users wishing to put HOOMD to work performing simulations should wait until HOOMD 0.6 is released, which will include executables to download.

HOOMD development home | Feb 4, 2008 | [ Back to top ]