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
scikit-learn. Many more user-provided packages are available through
channels on anaconda.org.
$ 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.
- 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.
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.
BUILD_*CMake variables in the hoomd cmake cache for use in external plugins.
data.gsd_snapshotnow accept negative frame indices to index from the end of the trajectory.
- Faster reinitialization from snapshots when done frequently.
- New command line option
--single-mpiallows 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
--modeoption is no longer required to run hoomd.
- Improve performance with
md.constrain.rigidin 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
- Improve performance with
- 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.
- Add new experimental
jitmodule that uses LLVM to compile and execute user provided C++ code at runtime. (CPU only)
jit.patch.user: Compute arbitrary patch energy between particles in HPMC (CPU only)
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_unionoperates efficiently with additive contributions to the cutoff.
- Add new experimental
mpcdcomponent adds support for simulating hydrodynamics using the multiparticle collision dynamics method.
- Node local parallelism (optional, build with
- The Intel TBB library is required to enable this feature.
- The command line option
--nthreadslimits 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 integrators with implicit depletants enabled
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.
- Fixed a problem with periodic boundary conditions and implicit depletants when
- Fixed a rare segmentation fault with
md.force.dipolenow record metadata properly.
- Fixed a bug where HPMC restore state did not set ignore flags properly.
hpmc_boxmc_ln_volume_acceptanceis now available for logging.
- 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
- HOOMD versions v2.3.x will be the last available on the anaconda channel
- Pin cuda compatible version in conda package to resolve
libcu*.sonot found errors in conda installations.
- Fix a rare error in
md.nlist.treewhen particles are very close to each other.
- Fix deadlock when
init.read_getaris 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
- Write default values to gsd frames when non-default values are present in frame 0.
- Fix a bug in HPMC where
run()would not start after
restore_stateunless shape parameters were also set from python.
- Fix a bug in HPMC Box MC updater where moves were attempted with zero weight.
hpmcshape 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.
- 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_metadatano longer reports an error when used with
- Miscellaneous documentation fixes
dump.gsdcan now write GSD files with 0 particles in a frame
- Explicitly report MPI synchronization delays due to load imbalance with
- Correctly compute net torque of rigid bodies with anisotropic constituent particles in MPI execution on multiple ranks
PotentialPairDPDThermoGPU.hfor use in external plugins
- Use correct ghost region with
constrain.rigidin MPI execution on multiple ranks
hpmc.update.muvt()now works with
- Fix the sampling of configurations with in
- 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
- Add special pair headers to install target
- Fix a bug where
hpmc.integrate.convex_polyhedron_unionproduced spurious overlaps on the GPU
hoomd.hdf5.logto log quantities in hdf5 format. Matrix quantities can be logged.
dump.gsdcan 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.gsdto 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.
- Added support for a 3 body potential that is harmonic in the local density.
force.activecan now apply torques.
nlist.tuneto quiet the output of the embedded
- Add special pairs as exclusions from neighbor lists.
- Add cosine squared angle potential
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.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
convex_spheropolyhedronnow support arbitrary numbers of vertices, subject only to memory limitations (
max_vertsis now ignored).
- HPMC integrators restore state from a gsd file read by
init.read_gsdwhen the option
- Deterministic HPMC integration on the GPU (optional):
hpmc.update.boxmc.ln_volume()move allows logarithmic volume moves for fast equilibration.
- New shape:
hpmc.integrate.convex_polyhedron_unionperforms simulations of unions of convex polyhedra.
hpmc.field.callback()now enables MC energy evaluation in a python function
- The option
hpmc.integrate.*allows the selection of a new depletion algorithm that restores the diffusivity of dilute colloids in dense depletant baths
hpmc.integrate.sphere_union()no longer needs the
convex_spheropolyhedronno longer needs the
- The static argument to
hoomd.dump.gsdshould no longer be used. Use dynamic instead.
- 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
order=7now gives correct results
- The PPPM energy for particles excluded as part of rigid bodies now correctly takes into account the periodic boundary conditions
metal.pair.eamnow produces correct results.
- 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
-march=nativeis no longer set by default (this is now a suggestion in the documentation)
- Compiler flags now default to CMake defaults
ENABLE_MPICMake 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
- Fix a bug where the log quantity
momentumwas incorrectly reported in MPI simulations.
- Raise an error when the user provides inconsistent
- 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
init.read_getarnow correctly restores static quantities when given a particular frame.
- Fix bug where many short calls to
run()caused incorrect results when using
- 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.
- The Saru generator has been moved into
hoomd/Saru.h, and plugins depending on Saru or SaruGPU will need to update their includes. The
SaruGPUclass has been removed. Use
hoomd::detail::Saruinstead for both CPU and GPU plugins.
- Fix PPM exclusion handling on the CPU
r_cutfor special pairs correctly
- Fix tauP reference in NPH documentation
constrain.rigidon compute 5.x.
- Fixed random seg faults when using sqlite getar archives with LZ4 compression
- Fixed XZ coupling with
- Fixed aspect ratio with non-cubic boxes in
- 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.
- Fixed a compile error on Mac
- 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
- Fixed a bug where the WalltimeLimitReached was ignored
- (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
- Drop support for compute 2.0 GPU devices
- Support cusolver with CUDA 8.0
force.activememory allocation bug
- Quiet Python.h warnigns when building (python 2.7)
- Allow multi-character particle types in HPMC (python 2.7)
- Allow the flow to change directions in
- Fix critical bug in MPI communication when using HPMC integrators
- enable/disable overlap checks between pairs of constituent particles for
- Support for non-additive mixtures in HPMC, overlap checks can now be enabled/disabled per type-pair
md.constrain.onedto 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
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
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
- HPMC: the
ignore_overlapsflag is replaced by
- 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
- fix invalid mesh energy in non-neutral systems with
- 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
- Fix a bug where the potential energy is misreported in MPI simulations with
- Fix a bug where the potential energy is misreported on the first step with
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 diameter handling in DEM shifted WCA potential
- Correctly handle particle type names in lattice.unitcell
md.group.tag_listis consistent across MPI ranks
Older change log entries are available in the source file ChangeLog.md.