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

HOOMD-blue 0.10.0 release

New features

  • Added pair.dpdlj which uses the DPD thermostat and the Lennard-Jones potential. In previous versions, this could be accomplished by using two pair commands but at the cost of reduced performance.
  • Additional example scripts are now present in the documentation. The example scripts are cross-linked to the commands that are used in them.
  • Most dump commands now accept the form: dump.ext(filename="filename.ext") which immediately writes out filename.ext.
  • Added vis parameter to dump.xml which enables output options commonly used in files written for the purposes of visulization. dump.xml also now accepts parameters on the instantiation line. Combined with the previous feature, dump.xml(filename="file.xml", vis=True) is now a convenient short hand for what was previously 
xml = dump.xml()
xml.set_params(position = True, mass = True, diameter = True, \
                         type = True, bond = True, angle = True, \
                         dihedral = True, improper = True, charge = True)
xml.write(filename="file.xml")

  • Specify rigid bodies in XML input files
  • Simulations that contain rigid body constraints applied to groups of particles in BDNVT, NVE, NVT, and NPT ensembles.
    • integrate.bdnvt_rigid
    • integrate.nve_rigid
    • integrate.nvt_rigid
    • integrate.npt_rigid
  • Energy minimization of rigid bodies ( integrate.mode_minimize_rigid_fire )
  • Existing commands are now rigid-body aware
    • update.rescale_temp
    • update.box_resize
    • update.enforce2d
    • update.zero_momentum
  • NVT integration using the Berendsen thermostat ( integrate.berendsen )
  • Bonds, angles, dihedrals, and impropers can now be created and deleted with the python data access API.
  • Attribution clauses added to the HOOMD-blue license

Changes that may break existing job scripts

  • The wrap option to dump.dcd has been changed to unwrap_full and its meaning inverted. dump.dcd now offers two options for unwrapping particles, unwrap_full fully unwraps particles into their box image and unwrap_rigid unwraps particles in rigid bodies so that bodies are not broken up across a box boundary.

December 14, 2011 | [ Back to top ]

Git repository

HOOMD-blue source code is now hosted in a git repository at: https://codeblue.umich.edu/git/hoomd-blue. Issue tracking is now hosted in a codeblue.umich.edu redmine project

The old subversion repository and Trac page are no longer available.

November 07, 2011 | [ Back to top ]

RSS feed now available

An RSS feed is now available for this site. It is updated with every entry posted to the HOOMD-blue home page.

November 07, 2011 | [ Back to top ]

Simpatico: hybrid MC with HOOMD-blue

A new version of Simpatico has been released. It is capable of carrying out Markov Chain monte carlo simulations of coarse-grained polymer liquids. The hoomd-based hybrid MC integration on the GPU can be combined with CPU-based molecular Monte Carlo moves (e.g. configuration bias), or replica exchange on a cluster with a large number of GPUs. For more information, see the documentation or download it from the Simpatico homepage.

News courtesy of Jens Glaser

October 26, 2011 | [ Back to top ]

HOOMD-blue 0.10.0 release candidate

HOOMD-blue 0.10.0 includes support for simulations containing rigid bodies built of particles. The core algorithms are functional, and we are working hard to complete the polish and documentation that users expect of a hoomd release. Your input in the form of bug reports, questions, and requests is valuable to us as we prepare the final 0.10.0 and future releases. To that end, we are making the source code of the first 0.10.0 release candidate available for download now.

The documentation for the new rigid body functionality may be built from the source code in the usual manner. As a short introduction, the following steps are necessary to perform a simulation with rigid bodies. First, specify the body tag in your input XML file. Each particle is assigned an integer, -1 for particles that don't belong to rigid bodies and 0,1,2,3,...N_bodies-1 for particles that do. All particles with the same nonnegative index will be included in a single rigid body. Then, use one of the rigid body integration methods (i.e. integrate.nve_rigid) on the group containing the rigid bodies (group.rigid()).

Known issues in the first release candidate (0.9.2.3996_rigid)

  • One must set the "body" exclusion in simulations containing rigid bodies. nlist.reset_exclusions(exclusions=['body', 'bond'])
  • Computed pressures are incorrect when rigid bodies are present in the system.
  • And other minor issues

Download hoomd-rigid.0.9.2.3996 now.

June 16, 2011 | [ Back to top ]

Papers on DPD and rigid body dynamics accepted for publication

Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units
Trung Dac Nguyen, Carolyn L. Phillips, Joshua A. Anderson, and Sharon C. Glotzer
Computer Physics Communications, Accepted

Pseudo-Random Number Generation for Brownian Dynamics and Dissipative Particle Dynamics Simulations on GPU Devices
Carolyn L. Phillips, Joshua A. Anderson, and Sharon C. Glotzer
Journal of Computational Physics, Accepted

June 16, 2011 | [ Back to top ]

HOOMD-blue 0.9.2 Released

HOOMD-blue 0.9.2 is now available.

Major changes since 0.9.1:

  • Long-ranged electrostatics via PPPM
  • Support for CUDA 3.2 and 4.0
  • New neighbor list option to exclude by particle diameter (for pair.slj)
  • New syntax to specify multiple pair coefficients at once
  • Improved documentation
  • Significant performance boosts for small simulations
  • RPM and .deb packaging for CentOS, Fedora, and Ubuntu
  • Many bug fixes and other small improvements

See the change log for a more detailed list.

See the troubleshooting guide for known problems and solutions. 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.

April 04, 2011 | [ Back to top ]

Daily snapshots now being posted

Snapshots of the current development version of hoomd in trunk/ are now being built daily. These are available as RPM packages for Fedora 13, CentOS/RHEL 5.5, DEB packages for Ubuntu 10.04 and an app bundle for Mac OS X. Download the daily snapshots from here. Additional information regarding these builds is available on the downloads page and in the installation guide.

A live ebuild is now available in the sunrise overlay for Gentoo users.

Download and install current daily builds and utilize the latest features currently in development and take advantage of recent performance enhancements. Builds of trunk/ are relatively stable, but do be aware that recently added features may still be incomplete or contain bugs. Please contact us and report any issues you find with these builds.

Documentation for the current daily snapshot is available in the online trunk/ documentation.

Thank Eric Irrgang for the RPM packaging and Ross Smith for the DEB packaging, both new developers on the hoomd team at the University of Michigan.

March 18, 2011 | [ Back to top ]

HOOMD-blue 0.9.1 Released

HOOMD-blue 0.9.1 is now available.

Major changes since 0.9.0:

  • Particles can now be constrained to spheres
  • 10 to 50 percent faster performance
  • DPD (Dissipative Particle Dynamics) capability
  • EAM (Embedded Atom Method) capability
  • Removed limitation on number of exclusions
  • Support for compute 2.1 devices (such as the GTX 460)
  • Support for CUDA 3.1
  • Plus many bug fixes and other small improvements

See the change log for a more detailed list.

See the troubleshooting guide for known problems and solutions. 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.

October 08, 2010 | [ Back to top ]

HOOMD-blue 0.9.0 Released

HOOMD-blue 0.9.0 is now available.

Major changes since 0.8.2:

  • Support for Fermi generation GPUs
  • Performance enhancements
  • New pair potentials
  • Particle data is now accessible from hoomd scripts
  • Binary format dump files for simulation restarts
  • Numerous small enhancements to enable easily restartable jobs
  • 2D simulations are now possible
  • Integration methods can now be applied to specified groups of particles
  • All IMD commands issued by VMD are now understood
  • Plus many bug fixes and other small improvements

A few changes may cause scripts written for 0.8.x to fail

  • Integration routines have changed significantly to enable new use cases. Where scripts previously had commands like: 
    integrate.nve(dt=0.005)
    they now need 
    all = group.all()
integrate.mode_standard(dt=0.005)
integrate.nve(group=all)
  • sorter.set_params no longer takes the bin_width argument. It is replaced by a new grid argument.
  • conserved_quantity is no longer a quantity available for logging. Instead log the nvt reservoir energy and compute the total conserved quantity in post processing.

See the change log for a more detailed list.

See the troubleshooting guide for known problems and solutions. 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.

May 18, 2010 | [ Back to top ]

Archived announcements

Older announcements are archived here

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