News

HOOMD-blue v1.0.1 release

Added by joaander 9 days ago

Bug fixes
  1. Fixed bug where error messages were truncated and HOOMD exited with a segmentation fault instead (e.g. on Blue Waters)
  2. Fixed bug where plug-ins did not load on Blue Waters
  3. Fixed compile error with gcc4.4 and cuda5.0
  4. Fixed syntax error in read_snapshot()
  5. Fixed a bug where init.read_xml throwing an error (or any other command outside of run()) would hang in MPI runs
  6. Search the install path for hoomd_script - enable the hoomd executable to be outside of the install tree (useful with cray aprun)
  7. Fixed CMake 3.0 warnings
  8. Removed dependancy on tr1/random
  9. Fixed a bug where analyze.msd ignored images in the r0_file
  10. Fixed typos in pair.gauss documentation
  11. Fixed compile errors on Ubuntu 12.10
  12. Fix failure of integrate.nvt to reach target temperature in analyze.log. The fix is a new symplectic MTK integrate.nvt integrator. Simulation results in hoomd v1.0.0 are correct, just the temperature and velocity outputs are off slightly.
  13. Remove MPI from Mac OS X dmg build.
  14. Enable import hoomd_script as ...
Other changes
  1. Added default compile flag -march=native
  2. Support CUDA 6.5
  3. Binary builds for CentOS/RHEL 6, Fedora 20, Ubuntu 14.04 LTS, and Ubuntu 12.04 LTS.

Download the new version from the HOOMD-blue web page

HOOMD-blue v1.0.0 release

Added by joaander 5 months ago

New features

  • Support for python 3
  • New NPT integrator capable of flexible coupling schemes
  • Triclinic unit cell support
  • MPI domain decomposition
  • Snapshot save/restore
  • Autotune block sizes at run time
  • Improve performance in small simulation boxes
  • Improve performance with smaller numbers of particles per GPU
  • Full double precision computations on the GPU (compile time option must be enabled, binary builds provided on the download page are single precision)
  • Tabulated bond potential bond.table
  • Tabulated angle potential angle.table
  • Tabulated dihedral potental dihedral.table
  • update.box_resize now accepts period=None to trigger an immediate update of the box without creating a periodic updater
  • update.box_resize now replaces None arguments with the current box parameters
  • init.create_random and init.create_random_polymers can now create random configurations in triclinc and 2D boxes
  • init.create_empty can now create triclinic boxes
  • particle, bond, angle, dihedral, and impropers types can now be named in init.create_empty
  • system.replicate command replicates the simulation box

Download the new version from the HOOMD-blue web page

HOOMD-blue 0.10.1 release

Added by joaander over 2 years ago

  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

HOOMD-blue 0.10.0 release

Added by joaander almost 3 years ago

New features
  1. 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.
  2. Additional example scripts are now present in the documentation. The example scripts are cross-linked to the commands that are used in them.
  3. Most dump commands now accept the form: dump.ext(filename="filename.ext") which immediately writes out filename.ext.
  4. 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")
    
  5. Specify rigid bodies in XML input files
  6. 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
  7. Energy minimization of rigid bodies (integrate.mode_minimize_rigid_fire)
  8. Existing commands are now rigid-body aware
    • update.rescale_temp
    • update.box_resize
    • update.enforce2d
    • update.zero_momentum
  9. NVT integration using the Berendsen thermostat (integrate.berendsen)
  10. Bonds, angles, dihedrals, and impropers can now be created and deleted with the python data access API.
  11. Attribution clauses added to the HOOMD-blue license
Changes that may break existing job scripts
  1. 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.

HOOMD-blue 0.10.0 is available for download under an open source license. Check out the quick start tutorial to get started, or check out the full documentation to see everything it can do.

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