HOOMD-blue¶

HOOMD-blue is a general purpose particle simulation toolkit. It performs hard particle Monte Carlo simulations of a variety of shape classes, and molecular dynamics simulations of particles with a range of pair, bond, angle, and other potentials. HOOMD-blue runs fast on NVIDIA GPUs, and can scale across thousands of nodes. For more information, see the HOOMD-blue website.

Resources¶

GitHub Repository: Source code and issue tracker.
Installation Guide: Instructions for installing and compiling HOOMD-blue.
hoomd-users Google Group: Ask questions to the HOOMD-blue community.
HOOMD-blue Tutorial: Beginner’s guide, code examples, and sample scripts.
HOOMD-blue website: Additional information, benchmarks, and publications.

Job scripts¶

HOOMD-blue job scripts are Python scripts. You can control system initialization, run protocols, analyze simulation data, or develop complex workflows all with Python code in your job.

Here is a simple example:

import hoomd
from hoomd import md
hoomd.context.initialize()

# Create a 10x10x10 simple cubic lattice of particles with type name A
hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0, type_name='A'), n=10)

# Specify Lennard-Jones interactions between particle pairs
nl = md.nlist.cell()
lj = md.pair.lj(r_cut=3.0, nlist=nl)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)

# Integrate at constant temperature
md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.langevin(group=hoomd.group.all(), kT=1.2, seed=4)

# Run for 10,000 time steps
hoomd.run(10e3)

Save this script as lj.py and run it with python lj.py (or singularity exec software.simg python3 lj.py if using Singularity containers).

Getting started

Additional Python packages

Reference