ctk3b / hoomd-blue

github mirror of hoomd-blue

HOOMD-blue

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

Prerequisites

• Required:
  • Python >= 2.6
  • boost >= 1.39.0
  • CMake >= 2.6.2
  • C++ Compiler (tested with gcc, clang, intel)
• Optional:
  • NVIDIA CUDA Toolkit >= 5.0
  • MPI (tested with OpenMPI, MVAPICH, impi)

Compiling HOOMD-blue

Use cmake to configure an out of source build and make to build hoomd.

mkdir build
cd build
cmake ../
make -j20

For more detailed instructions, see the documentationn.

Job scripts

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

Here is a simple example.

from hoomd_script import *
context.initialize()

# create 100 random particles of name A
init.create_random(N=100, phi_p=0.01, name='A')
# specify Lennard-Jones interactions between particle pairs
lj = pair.lj(r_cut=3.0)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
# integrate at constant temperature
all = group.all();
integrate.mode_standard(dt=0.005)
integrate.nvt(group=all, T=1.2, tau=0.5)
# run 10,000 time steps
run(10e3)

Save this as lj.py and run with hoomd lj.py.

Documentation

Documentation for the current stable release is available online: http://codeblue.umich.edu/hoomd-blue/doc/

Change log

See ChangeLog.md.