HOOMD-blue

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Official Binaries

Official binaries of HOOMD-blue are available via conda through the glotzer channel. Conda is a python-centric packaging system targeted at computational researchers. The default package database includes many useful packages such as scipy, ipython and scikit-learn. Many more user-provided packages are available through channels on anaconda.org.

To install HOOMD-blue, first download and install miniconda following conda's instructions. Then add the glotzer channel and install HOOMD-blue:

$ conda config --add channels glotzer
$ conda install hoomd

If you have already installed hoomd in conda, you can upgrade to the latest version:

$ conda update --all

If you find HOOMD-blue useful in your research, please cite it. See the citation page for instructions.

Requirements

  • On Linux (64-bit):
    • A recent linux distribution (such as CentOS/RHEL 6, ubuntu 14.04, or newer)
    • [optional] NVIDIA drivers 375.26 or newer
    • [optional] CUDA capable NVIDIA GPU, compute 3.0 or newer.
  • On Mac:
    • OSX 10.8 or newer
    • Note: Mac builds are not MPI or GPU enabled.

Source

Use git to clone from HOOMD-blue's bitbucket repository, or download from this website (see links below).

See the user manual for system requirements and build instructions.

Change Log

v2.3.0

Released 2018/04/25

Download HOOMD-blue v2.3.0

New features

  • General:

    • Store BUILD_* CMake variables in the hoomd cmake cache for use in external plugins.
    • init.read_gsd and data.gsd_snapshot now accept negative frame indices to index from the end of the trajectory.
    • Faster reinitialization from snapshots when done frequently.
    • New command line option --single-mpi allows non-mpi builds of hoomd to launch within mpirun (i.e. for use with mpi4py managed pools of jobs)
    • For users of the University of Michigan Flux system: A --mode option is no longer required to run hoomd.

  • MD:

    • Improve performance with md.constrain.rigid in multi-GPU simulations.
    • New command integrator.randomize_velocities() sets a particle group's linear and angular velocities to random values consistent with a given kinetic temperature.
    • md.force.constant() now supports setting the force per particle and inside a callback

  • HPMC:

    • Enabled simulations involving spherical walls and convex spheropolyhedral particle shapes.
    • Support patchy energetic interactions between particles (CPU only)
    • New command hpmc.update.clusters() supports geometric cluster moves with anisotropic particles and/or depletants and/or patch potentials. Supported move types: pivot and line reflection (geometric), and AB type swap.

  • JIT:

    • Add new experimental jit module that uses LLVM to compile and execute user provided C++ code at runtime. (CPU only)
    • Add jit.patch.user: Compute arbitrary patch energy between particles in HPMC (CPU only)
    • Add jit.patch.user_union: Compute arbitrary patch energy between rigid unions of points in HPMC (CPU only)
    • Patch energies operate with implicit depletant and normal HPMC integration modes.
    • jit.patch.user_union operates efficiently with additive contributions to the cutoff.

  • MPCD:

    • The mpcd component adds support for simulating hydrodynamics using the multiparticle collision dynamics method.

Beta feature

  • Node local parallelism (optional, build with ENABLE_TBB=on):
    • The Intel TBB library is required to enable this feature.
    • The command line option --nthreads limits the number of threads HOOMD will use. The default is all CPU cores in the system.
    • Only the following methods in HOOMD will take advantage of multiple threads:
      • hpmc.update.clusters()
      • HPMC integrators with implicit depletants enabled
      • jit.patch.user_union

Node local parallelism is still under development. It is not enabled in builds by default and only a few methods utilize multiple threads. In future versions, additional methods in HOOMD may support multiple threads.

To ensure future workflow compatibility as future versions enable threading in more components, explicitly set --nthreads=1.

Bug fixes

  • Fixed a problem with periodic boundary conditions and implicit depletants when depletant_mode=circumsphere
  • Fixed a rare segmentation fault with hpmc.integrate.*_union() and hpmc.integrate.polyhedron
  • md.force.active and md.force.dipole now record metadata properly.
  • Fixed a bug where HPMC restore state did not set ignore flags properly.
  • hpmc_boxmc_ln_volume_acceptance is now available for logging.

Other changes

  • Eigen is now provided as a submodule. Plugins that use Eigen headers need to update include paths.
  • HOOMD now builds with pybind 2.2. Minor changes to source and cmake scripts in plugins may be necessary. See the updated example plugin.
  • HOOMD now builds without compiler warnings on modern compilers (gcc6, gcc7, clang5, clang6).
  • HOOMD now uses pybind11 for numpy arrays instead of num_util.
  • HOOMD versions v2.3.x will be the last available on the anaconda channel glotzer.

v2.2.5

Released 2018/04/20

Download HOOMD-blue v2.2.5

Bug fixes

  • Pin cuda compatible version in conda package to resolve libcu*.so not found errors in conda installations.

v2.2.4

Released 2018/03/05

Download HOOMD-blue v2.2.4

Bug fixes

  • Fix a rare error in md.nlist.tree when particles are very close to each other.
  • Fix deadlock when init.read_getar is given different file names on different ranks.
  • Sample from the correct uniform distribution of depletants in a sphere cap with depletant_mode='overlap_regions' on the CPU
  • Fix a bug where ternary (or higher order) mixtures of small and large particles were not correctly handled with depletant_mode='overlap_regions' on the CPU
  • Improve acceptance rate in depletant simulations with depletant_mode='overlap_regions'

v2.2.3

Released 2018/01/25

Download HOOMD-blue v2.2.3

Bug fixes

  • Write default values to gsd frames when non-default values are present in frame 0.
  • md.wall.force_shifted_lj now works.
  • Fix a bug in HPMC where run() would not start after restore_state unless shape parameters were also set from python.
  • Fix a bug in HPMC Box MC updater where moves were attempted with zero weight.
  • dump.gsd() now writes hpmc shape state correctly when there are multiple particle types.
  • hpmc.integrate.polyhedron() now produces correct results on the GPU.
  • Fix binary compatibility across python minor versions.

v2.2.2

Released 2017/12/04

Download HOOMD-blue v2.2.2

Bug fixes

  • md.dihedral.table.set_from_file now works.
  • Fix a critical bug where forces in MPI simulations with rigid bodies or anisotropic particles were incorrectly calculated
  • Ensure that ghost particles are updated after load balancing.
  • meta.dump_metadata no longer reports an error when used with md.constrain.rigid
  • Miscellaneous documentation fixes
  • dump.gsd can now write GSD files with 0 particles in a frame
  • Explicitly report MPI synchronization delays due to load imbalance with profile=True
  • Correctly compute net torque of rigid bodies with anisotropic constituent particles in MPI execution on multiple ranks
  • Fix PotentialPairDPDThermoGPU.h for use in external plugins
  • Use correct ghost region with constrain.rigid in MPI execution on multiple ranks
  • hpmc.update.muvt() now works with depletant_mode='overlap_regions'
  • Fix the sampling of configurations with in hpmc.update.muvt with depletants
  • Fix simulation crash after modifying a snapshot and re-initializing from it
  • The pressure in simulations with rigid bodies (md.constrain.rigid()) and MPI on multiple ranks is now computed correctly

v2.2.1

Released 2017/10/04

Download HOOMD-blue v2.2.1

Bug fixes

  • Add special pair headers to install target
  • Fix a bug where hpmc.integrate.convex_polyhedron, hpmc.integrate.convex_spheropolyhedron, hpmc.integrate.polyedron, hpmc.integrate.faceted_sphere, hpmc.integrate.sphere_union and hpmc.integrate.convex_polyhedron_union produced spurious overlaps on the GPU

v2.2.0

Released 2017/09/08

Download HOOMD-blue v2.2.0

New features

  • General:

    • Add hoomd.hdf5.log to log quantities in hdf5 format. Matrix quantities can be logged.
    • dump.gsd can now save internal state to gsd files. Call dump_state(object) to save the state for a particular object. The following objects are supported:
      • HPMC integrators save shape and trial move size state.
    • Add dynamic argument to hoomd.dump.gsd to specify which quantity categories should be written every frame.
    • HOOMD now inter-operates with other python libraries that set the active CUDA device.
    • Add generic capability for bidirectional ghost communication, enabling multi body potentials in MPI simulation.

  • MD:

    • Added support for a 3 body potential that is harmonic in the local density.
    • force.constant and force.active can now apply torques.
    • quiet option to nlist.tune to quiet the output of the embedded run() commands.
    • Add special pairs as exclusions from neighbor lists.
    • Add cosine squared angle potential md.angle.cosinesq.
    • Add md.pair.DLVO() for evaluation of colloidal dispersion and electrostatic forces.
    • Add Lennard-Jones 12-8 pair potential.
    • Add Buckingham (exp-6) pair potential.
    • Add Coulomb 1-4 special_pair potential.
    • Check that composite body dimensions are consistent with minimum image convention and generate an error if they are not.
    • md.integrate.mode.minimize_fire() now supports anisotropic particles (i.e. composite bodies)
    • md.integrate.mode.minimize_fire() now supports flexible specification of integration methods
    • md.integrate.npt()/md.integrate.nph() now accept a friction parameter (gamma) for damping out box fluctuations during minimization runs
    • Add new command integrate.mode_standard.reset_methods() to clear NVT and NPT integrator variables

  • HPMC:

    • hpmc.integrate.sphere_union() takes new capacity parameter to optimize performance for different shape sizes
    • hpmc.integrate.polyhedron() takes new capacity parameter to optimize performance for different shape sizes
    • hpmc.integrate.convex_polyhedron and convex_spheropolyhedron now support arbitrary numbers of vertices, subject only to memory limitations (max_verts is now ignored).
    • HPMC integrators restore state from a gsd file read by init.read_gsd when the option restore_state is True.
    • Deterministic HPMC integration on the GPU (optional): mc.set_params(deterministic=True).
    • New hpmc.update.boxmc.ln_volume() move allows logarithmic volume moves for fast equilibration.
    • New shape: hpmc.integrate.convex_polyhedron_union performs simulations of unions of convex polyhedra.
    • hpmc.field.callback() now enables MC energy evaluation in a python function
    • The option depletant_mode='overlap_regions' for hpmc.integrate.* allows the selection of a new depletion algorithm that restores the diffusivity of dilute colloids in dense depletant baths

Deprecated

  • HPMC: hpmc.integrate.sphere_union() no longer needs the max_members parameter.
  • HPMC: hpmc.integrate.convex_polyhedron and convex_spheropolyhedron no longer needs the max_verts parameter.
  • The static argument to hoomd.dump.gsd should no longer be used. Use dynamic instead.

Bug fixes

  • HPMC:

    • hpmc.integrate.sphere_union() and hpmc.integrate.polyhedron() missed overlaps.
    • Fix alignment error when running implicit depletants on GPU with ntrial > 0.
    • HPMC integrators now behave correctly when the user provides different RNG seeds on different ranks.
    • Fix a bug where overlapping configurations were produced with hpmc.integrate.faceted_sphere()

  • MD:

    • charge.pppm() with order=7 now gives correct results
    • The PPPM energy for particles excluded as part of rigid bodies now correctly takes into account the periodic boundary conditions

  • EAM:

    • metal.pair.eam now produces correct results.

Other changes

  • Optimized performance of HPMC sphere union overlap check and polyhedron shape
  • Improved performance of rigid bodies in MPI simulations
  • Support triclinic boxes with rigid bodies
  • Raise an error when an updater is given a period of 0
  • Revised compilation instructions
  • Misc documentation improvements
  • Fully document constrain.rigid
  • -march=native is no longer set by default (this is now a suggestion in the documentation)
  • Compiler flags now default to CMake defaults
  • ENABLE_CUDA and ENABLE_MPI CMake options default OFF. User must explicitly choose to enable optional dependencies.
  • HOOMD now builds on powerpc+CUDA platforms (tested on summitdev)
  • Improve performance of GPU PPPM force calculation
  • Use sphere tree to further improve performance of hpmc.integrate.sphere_union()

v2.1.9

Released 2017/08/22

Download HOOMD-blue v2.1.9

Bug fixes

  • Fix a bug where the log quantity momentum was incorrectly reported in MPI simulations.
  • Raise an error when the user provides inconsistent charge or diameter lists to md.constrain.rigid.
  • Fix a bug where pair.compute_energy() did not report correct results in MPI parallel simulations.
  • Fix a bug where make rigid bodies with anisotropic constituent particles did not work on the GPU.
  • Fix hoomd compilation after the rebase in the cub repository.
  • deprecated.dump.xml() now writes correct results when particles have been added or deleted from the simulation.
  • Fix a critical bug where charge.pppm() calculated invalid forces on the GPU

v2.1.8

Released 2017/07/19

Download HOOMD-blue v2.1.8

Bug fixes

  • init.read_getar now correctly restores static quantities when given a particular frame.
  • Fix bug where many short calls to run() caused incorrect results when using md.integrate.langevin.
  • Fix a bug in the Saru pseudo-random number generator that caused some double-precision values to be drawn outside the valid range [0,1) by a small amount. Both floats and doubles are now drawn on [0,1).
  • Fix a bug where coefficients for multi-character unicode type names failed to process in Python 2.

Other changes

  • The Saru generator has been moved into hoomd/Saru.h, and plugins depending on Saru or SaruGPU will need to update their includes. The SaruGPU class has been removed. Use hoomd::detail::Saru instead for both CPU and GPU plugins.

v2.1.7

Released 2017/05/11

Download HOOMD-blue v2.1.7

Bug fixes

  • Fix PPM exclusion handling on the CPU
  • Handle r_cut for special pairs correctly
  • Fix tauP reference in NPH documentation
  • Fixed constrain.rigid on compute 5.x.
  • Fixed random seg faults when using sqlite getar archives with LZ4 compression
  • Fixed XZ coupling with hoomd.md.integrate.npt integration
  • Fixed aspect ratio with non-cubic boxes in hoomd.hpmc.update.boxmc

v2.1.6

Released 2017/04/12

Download HOOMD-blue v2.1.6

Bug fixes

  • Document hpmc.util.tune_npt
  • Fix dump.getar.writeJSON usage with MPI execution
  • Fix a bug where integrate.langevin and integrate.brownian correlated RNGs between ranks in multiple CPU execution
  • Bump CUB to version 1.6.4 for improved performance on Pascal architectures. CUB is now embedded using a git submodule. Users upgrading existing git repositories should reinitialize their git submodules with git submodule update --init
  • CMake no longer complains when it finds a partial MKL installation.

v2.1.5

Released 2017/03/09

Download HOOMD-blue v2.1.5

Bug fixes

  • Fixed a compile error on Mac

v2.1.4

Released 2017/03/09

Download HOOMD-blue v2.1.4

Bug fixes

  • Fixed a bug re-enabling disabled integration methods
  • Fixed a bug where adding particle types to the system failed for anisotropic pair potentials
  • scipy is no longer required to execute DEM component unit tests
  • Issue a warning when a subsequent call to context.initialize is given different arguments
  • DPD now uses the seed from rank 0 to avoid incorrect simulations when users provide different seeds on different ranks
  • Miscellaneous documentation updates
  • Defer initialization message until context.initialize
  • Fixed a problem where a momentary dip in TPS would cause walltime limited jobs to exit prematurely
  • HPMC and DEM components now correctly print citation notices

v2.1.3

Released 2017/02/07

Download HOOMD-blue v2.1.3

Bug fixes

  • Fixed a bug where the WalltimeLimitReached was ignored

v2.1.2

Released 2017/01/11

Download HOOMD-blue v2.1.2

Bug fixes

  • (HPMC) Implicit depletants with spheres and faceted spheres now produces correct ensembles
  • (HPMC) Implicit depletants with ntrial > 0 now produces correct ensembles
  • (HPMC) NPT ensemble in HPMC (hpmc.update.boxmc) now produces correct ensembles
  • Fix a bug where multiple nvt/npt integrators caused warnings from analyze.log.
  • update.balance() is properly ignored when only one rank is available
  • Add missing headers to plugin install build
  • Fix a bug where charge.pppm calculated an incorrect pressure

Other changes

  • Drop support for compute 2.0 GPU devices
  • Support cusolver with CUDA 8.0

v2.1.1

Released 2016/10/23

Download HOOMD-blue v2.1.1

Bug fixes

  • Fix force.active memory allocation bug
  • Quiet Python.h warnigns when building (python 2.7)
  • Allow multi-character particle types in HPMC (python 2.7)
  • Enable dump.getar.writeJSON in MPI
  • Allow the flow to change directions in md.update.mueller_plathe_flow
  • Fix critical bug in MPI communication when using HPMC integrators

v2.1.0

Released 2016/10/04

Download HOOMD-blue v2.1.0

New features

  • enable/disable overlap checks between pairs of constituent particles for hpmc.integrate.sphere_union()
  • Support for non-additive mixtures in HPMC, overlap checks can now be enabled/disabled per type-pair
  • Add md.constrain.oned to constrain particles to move in one dimension
  • hpmc.integrate.sphere_union() now takes max_members as an optional argument, allowing to use GPU memory more efficiently
  • Add md.special_pair.lj() to support scaled 1-4 (or other) exclusions in all-atom force fields
  • md.update.mueller_plathe_flow(): Method to create shear flows in MD simulations
  • use_charge option for md.pair.reaction_field
  • md.charge.pppm() takes a Debye screening length as an optional parameter
  • md.charge.pppm() now computes the rigid body correction to the PPPM energy

Deprecated

  • HPMC: the ignore_overlaps flag is replaced by hpmc.integrate.interaction_matrix

Other changes

  • Optimized MPI simulations of mixed systems with rigid and non-rigid bodies
  • Removed dependency on all boost libraries. Boost is no longer needed to build hoomd
  • Intel compiler builds are no longer supported due to c++11 bugs
  • Shorter compile time for HPMC GPU kernels
  • Include symlinked external components in the build process
  • Add template for external components
  • Optimized dense depletant simulations with HPMC on CPU

Bug fixes

  • fix invalid mesh energy in non-neutral systems with md.charge.pppm()
  • Fix invalid forces in simulations with many bond types (on GPU)
  • fix rare cases where analyze.log() would report a wrong pressure
  • fix possible illegal memory access when using md.constrain.rigid() in GPU MPI simulations
  • fix a bug where the potential energy is misreported on the first step with md.constrain.rigid()
  • Fix a bug where the potential energy is misreported in MPI simulations with md.constrain.rigid()
  • Fix a bug where the potential energy is misreported on the first step with md.constrain.rigid()
  • md.charge.pppm() computed invalid forces
  • Fix a bug where PPPM interactions on CPU where not computed correctly
  • Match logged quantitites between MPI and non-MPI runs on first time step
  • Fix md.pair.dpd and md.pair.dpdlj set_params
  • Fix diameter handling in DEM shifted WCA potential
  • Correctly handle particle type names in lattice.unitcell
  • Validate md.group.tag_list is consistent across MPI ranks

Older versions

Older change log entries are available in the source file ChangeLog.md.