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

Updated daily builds available

New daily rpm/deb builds for are now available in the daily builds download area for Fedora 18, OpenSUSE 12.2, Ubuntu 12.04, and CentOS 6. These builds are MPI enabled using the OpenMPI package on each respective distribution. NVIDIA drivers 331.20 or newer must be installed to enable GPU execution. Let me know if you have any issues with these builds.

I plan to add Ubuntu 12.10 and Mac OS X (no MPI) builds soon.

January 27, 2014 | [ Back to top ]

Upcoming webinars on HOOMD-blue

The Virtual School for Computational Science and Engineering is supporting two upcoming webinars on HOOMD-blue.

Introduction to HOOMD-blue
December 10, 2013, 11:00 a.m. EST
Click here to register

Joshua A. Anderson, PhD
Research Area Specialist
Chemical Engineering
University of Michigan

HOOMD-blue is a general-purpose Molecular Dynamics simulation code accelerated on GPUs. This live interactive webinar will offer an introduction to HOOMD-blue, a description of what it does, how to download and install it as well as example simulations of the Lennard-Jones fluid. The target audience is all individuals interested in MD simulation, but prior knowledge is not required. Materials will be introductory, beginning with MD basics and moving into details of HOOMD-blue. A wide range of topics will be briefly covered, giving potential users an idea of how to do all the steps in a simulation, including defining parameters, executing the simulation and examining the output.

Using HOOMD-blue for Polymer Simulations and Big Systems
January 21, 2014, 11:00 a.m. EST
Click here to register

Dr. Jens Glaser
Research Fellow
Department of Chemical Engineering
University of Michigan

In this webinar, Dr. Glaser will demonstrate how real-world computational research in soft matter physics can be accelerated on a GPU-equipped desktop computer with the HOOMD-blue molecular dynamics software. A presentation of how to set up a simulation of a dense polymer liquid, and how to analyze and visualize the results is provided. There will be a demonstration of how self-assembled ordered structures of block copolymers emerge out of an initially disordered configuration. With external potentials, an artificially ordered phase can be produced as well. HOOMD-blue’s easy-to-use scripting interface and plug-ins are used to create a productive work-flow and extend its capabilities. As an advanced topic, there will be a discussion of how the upcoming version of HOOMD-blue can be used on compute clusters running on ten to hundreds of GPUs in parallel, to boost simulations of long polymer chains or large-scale systems.

November 27, 2013 | [ Back to top ]

HOOMD-blue 0.11.3 release

Bug fixes

  • Fixed a bug where charge.pppm could not be used after init.reset()
  • Data proxies can now set body angular momentum before the first run()
  • Fixed a bug where PPPM forces were incorrect on the GPU

April 10, 2013 | [ Back to top ]

Survey - feature requests

The HOOMD-blue developers would like to know what new features and capabilities that the user community is interested in, so we are conducting a quick survey this week. Any information you provide will be considered for future developments in HOOMD-blue. This form will only be available Feb 22 - March 1, 2013.

Follow the link to fill out the survey form: HOOMD-blue feature request survey

February 22, 2013 | [ Back to top ]

HOOMD-blue 0.11.2 release

New features

  • Block sizes tuned for K20

Bug fixes

  • Warn user that PPPM ignores rigid body exclusions
  • Document that proxy iterators need to be deleted before init.reset()
  • Fixed a bug where body angular momentum could not be set
  • Fixed a bug where analyze.log would report nan for the pressure tensor in nve and nvt simulations

December 19, 2012 | [ Back to top ]

HOOMD-blue 0.11.1 release

New features

  • Support for CUDA 5.0
  • Binary builds for Fedora 16 and OpenSUSE 12.1
  • Automatically specify /usr/bin/gcc to nvcc when the configured gcc is not supported

Bug fixes

  • Fixed a compile error with gcc 4.7
  • Fixed a bug where PPPM forces were incorrect with neighborlist exclusions
  • Fixed an issue where boost 1.50 and newer were not detected properly when BOOST_ROOT is set
  • Fixed a bug where accessing force data in python prevented init.reset() from working
  • Fixed a bug that prevented pair.external from logging energy
  • Fixed a unit test that failed randomly

November 02, 2012 | [ Back to top ]

HOOMD-blue 0.11.0 release

New features

  1. Support for Kepler GPUs (GTX 680)
  2. NPH integration (*integrate.nph*)
  3. Compute full pressure tensor
  4. Example plugin for new bond potentials
  5. New syntax for bond coefficients: bond.bond_coeff.set('type', params)
  6. New external potential: external.periodic applies a periodic potential along one direction (uses include inducing lamellar phases in copolymer systems)
  7. Significant performance increases when running analyze.log, analyze.msd, update.box_resize, update.rescale_temp, or update.zero_momentum with a small period
  8. Command line options may now be overwritten by scripts, ex: options.set_gpu(2)
  9. Added --user command line option to allow user defined options to be passed into job scripts, ex: --user="-N=5 -phi=0.56"
  10. Added table.set_from_file method to enable reading table based pair potentials from a file
  11. Added --notice-level command line option to control how much extra information is printed during a run. Set to 0 to disable, or any value up to 10. At 10, verbose debugging information is printed.
  12. Added --msg-file command line option which redirects the message output to a file
  13. New pair potential pair.force_shifted_lj : Implements http://dx.doi.org/10.1063/1.3558787

Bug fixes

  1. Fixed a bug where FENE bonds were sometimes computed incorrectly
  2. Fixed a bug where pressure was computed incorrectly when using pair.dpd or pair.dpdlj
  3. Fixed a bug where using OpenMP and CUDA at the same time caused invalid memory accesses
  4. Fixed a bug where RPM packages did not work on systems where the CUDA toolkit was not installed
  5. Fixed a bug where rigid body velocities were not set from python
  6. Disabled OpenMP builds on Mac OS X. HOOMD-blue w/ openmp enabled crashes due to bugs in Apple's OpenMP implementation.
  7. Fixed a bug that allowed users to provide invalid rigid body data and cause a seg fault.
  8. Fixed a bug where using PPPM resulted in error messages on program exit.

July 27, 2012 | [ Back to top ]

Optimal Filling of Shapes

HOOMD-blue users may find our recent publication in PRL interesting:

C. L. Phillips, J. A. Anderson, G. Huber, and S. C. Glotzer. Optimal Filling of Shapes Physical Review Letters 108(19): 1-5, May 2012. 10.1103/PhysRevLett.108.198304

Abstract:

We present filling as a type of spatial subdivision problem similar to covering and packing. Filling addresses the optimal placement of overlapping objects lying entirely inside an arbitrary shape so as to cover the most interior volume. In n-dimensional space, if the objects are polydisperse n-balls, we show that solutions correspond to sets of maximal n-balls. For polygons, we provide a heuristic for finding solutions of maximal disks. We consider the properties of ideal distributions of N disks as N goes to infinity. We note an analogy with energy landscapes.

HOOMD-blue is already well-suited to running simulations of filled shapes.

  • Use the particle diameter field to set the individual diameter of each particle.
  • Use pair.slj with a cutoff of 2**(1.0/6.0) for shifted WCA interactions.
  • Combine all particles in the shape together in a rigid body.

May 11, 2012 | [ Back to top ]

HOOMD-blue 0.10.1 release

v0.10.1 is a maintenance release. The following minor issues have been fixed:

  1. Add missing entries to credits page
  2. Add dist_check option to neighbor list. Can be used to force neighbor list builds at a specified frequency (useful in profiling runs with nvvp).
  3. Fix typos in ubuntu compile documentation
  4. Add missing header files to hoomd.h
  5. Add torque to the python particle data access API
  6. Support boost::filesystem API v3
  7. Expose name of executing gpu, n_cpu, hoomd version, git sha1, cuda version, and compiler version to python
  8. Fix a bug where multiple nvt_rigid or npt_rigid integrators didn't work correctly
  9. Fix missing pages in developer documentation

February 10, 2012 | [ Back to top ]

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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