New colloid shapes

Rigid bodies

Hoobas uses similar internal structure for rigid bodies as HOOMD-blue. Effectively, this means that inertia moments are defined in the proper body frame (diagonal tensor) and an orientation is defined for every rigid body in the simulation. For objects to be importable into HOOMD-blue, a method named self.relative_positions should be defined, as done for hoobas.Colloid.Colloid.

Quaternions are used to represent orientation. For objects to be importable into HOOMD-blue, the orientation should also be written to the first bead of the CompositeObject. Rotations should be handled by quaternion products, as done in hoobas.Colloid.Colloid.rotate(). Hoobas uses a body value to track whether a CompositeObject is rigid. For non-rigid bodies, this value is set to -1. A rigid body may have non-rigid sections, and beads of those sections should have a -1 value for their body value.

More shapes for Colloids

Colloid shapes are defined by hoobas.GenShape.Shape. Geometric shapes, such as spheres, cubes, tetrahedrons are considered normalized as they can simply be scaled by a size factor. These are opposed to complex shapes, which could be, for instance, proteins. The prototype code for a simple geometric shape is

class GeometricShape(hoobas.Shape):
    def __init__(self, Num):
        self.flags['normalized'] = True
        self.flags['simple_I_tensor'] = True
        self.flags['volume'] = V
        self.flags['surface'] = S
        self.table = np.array()

Where self.table is a 3 x N array defining a shape of volume V and area S. This is the normalized shape, i.e., what a size of 1.0 object should look like with approximately Num points on its surface. Very complicated and unique shapes such as proteins will generally require a specialized implementation.