Simulate rounded, faceted shapes in molecular dynamics.
The DEM component provides forces which apply short-range, purely repulsive interactions between contact points of two shapes. The resulting interaction is consistent with expanding the given polygon or polyhedron by a disk or sphere of a particular rounding radius.
The pair forces located in
hoomd.dem.pair behave like other
hoomd pair forces, computing forces and torques for each particle
based on its interactions with its neighbors. Also included are
geometric helper utilities in
When initializing systems, be sure to set the inertia tensor of DEM particles. Axes with an inertia tensor of 0 (the default) will not have their rotational degrees of freedom integrated. Because only the three principal components of inertia are given to hoomd, particle vertices should also be specified in the principal reference frame so that the inertia tensor is diagonal.
snap = hoomd.data.make_snapshot(512, box=hoomd.data.boxdim(L=10)) snap.particles.moment_inertia[:] = (10, 10, 10) system = hoomd.init.read_snapshot(snap)
To allow particles to rotate, use integrators which can update rotational degrees of freedom:
Note that the Nosé-Hoover thermostats used in
work by rescaling momenta and angular momenta. This can lead to
instabilities in the start of the simulation if particles are
initialized with 0 angular momentum and no neighbor interactions. Two
easy fixes for this problem are to initialize each particle with some
angular momentum or to first run for a few steps with
To store trajectories of DEM systems, use a format that knows about anisotropic particles, such as:
hoomd.dem is stable. When upgrading from version 2.x to 2.y (y > x),
existing job scripts that follow documented interfaces for functions and classes
will not require any modifications. Maintainer: Matthew Spellings.