HOOMD-blue

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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

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).

Additional Python packages