Composite Design Pattern

Overview

Questions:

• How to compose objects into tree structures?

• How to define a common interface for branches and leaves within a tree?

Objectives:

• Understand the composite design pattern.

• Show an example of the composite design pattern relavant to the Computational Molecular Sciences domain.

Problem

Consider a Monte Carlo (MC) simulation of a strongly associating system. Conducting a ‘naive’ simulation on such systems using conventional MC algorithms would require prohibitively amounts of time, as the aggregate structures do not change sufficiently often during the course of a simulation (i.e. clusters are not created or destroyed frequently). To reproduce the correct statistics, it is necessary to design and use algorithms that more efficiently sample configurations of the ensemble of interest. Cluster moves are one tool to accelerate sampling of aggregate configurations.

In a typical cluster move, you might find two kinds of objects: particles and clusters. Particles are elements that tend to aggregate into clusters. For instance, a surfactant molecule that tend to aggregate into larger micellar structures. A cluster object usually contains one or more particles and thus is a composite object, while a particle is a simple object. Cluster and particles may have similar operations and attributes, such as center-of-mass translation or solid body rotation. It would be convenient treat both cluster and particle objects uniformly by defining a common interface.

A basic cluster algorithm would involve the following steps

1. Check for the formation of clusters

2. Select a cluster randomly

3. Make a random perturbation using the selected cluster, such as translation, rotation, removal or addition of particles to the selected cluster.

4. Accept or reject the new configuration.

In this example, we will imagine we are implementing functionality to address point 3. We would like to create objects for particles and clusters and provide them with methods for center-of-mass translation.

Solution: the composite design pattern

The composite design pattern allows you to create tree structures and handle their components (branches and leaves) uniformly. The composite pattern uses the following elements

1. Component. This is an abstract class that will serve as parent for the branch and leaf elements. In our example, a Component class would be an abstraction for patchy particles (leaves) and clusters (branches).

PYTHON

from abc import ABC, abstractmethod

class Component(ABC):

    '''Base class for a Component. This is the 'component'
    base class in the pattern.'''

    @abstractmethod
    def translate(self):
        pass

2. Leaf. These are objects that have no children. They implement methods described by the Component parent class. LJ particles, Gay Berne or any other type of particle might serve as leaf objects.

PYTHON

class Sphere(Component):

    '''A Sphere is a type of particle, for instance,
    point particles with Lennard-Jones potential.
    This is a leaf in the pattern.'''

    def translate(self):
        print('translating sphere')

class Gay_Berne(Component):

    '''A Gay Berne particle is an anisotropic model
    of the 12-6 Lennard-Jones potential. It is used
    exstensively to model liquid crystals. Another
    leaf in the pattern'''

    def translate(self):
        print('translating gay berne')

3. Branch. This element stores child components and implement methods defined by the component interface.

PYTHON

class Cluster(Component):

    '''A cluster is a collection of particles. It can
    be composed of spherical, anisotropic, patchy or 
    any other particle. This is a 'composite' in the
    Composite patern'''

    def __init__(self):
        self._particles = []

    def translate(self):
        for children in self._particles:
            children.translate()

    def add_particle(self, particle):
        self._particles.append(particle)

4. Client code. The code that manipulate objects in the hierarchy using the interface defined by Component.

PYTHON

def main():

    argon = Sphere()
    krypton = Sphere()
    liquid_crystal = Gay_Berne()
   
    cluster = Cluster()
    cluster.add_particle(argon)
    cluster.add_particle(krypton)
    cluster.add_particle(liquid_crystal)

    argon.translate()
    krypton.translate()
    cluster.translate()

if __name__ == "__main__":
    main()

Key Points

• The composite design pattern provides a way for manipulating a tree data structure