HOOMD-blue 0.10.0 release

Added by joaander over 2 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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