bring your own forcefield

Although pylj was originally designed to use only the Lennard-Jones potential model, hence pyLennard-Jones. Following the release of pylj-1.1.0, it is now possible to pass custom forcefields to the simulation. As of pylj-1.5.0, these have become class-based.

A rough piece of advice for the particle sizing is that 10 looks normal, and is the fixed size in Buckingham and Square Well potentials, but this can be set as a function of the constants as in the Lennard-Jones forcefield. As for mixing rules, these are usually either geometric or arithmetic means of the two constants.

Writing your own forcefield and passing it to the pylj engine is very simple, firstly the forcefield should have the following form,

class forcefield(object):

    def __init__(self, constants)
        # Define constants
        # For instance:
        self.a = constants[0]
        self.b = constants[1]

        # Define sizing, this could be equal to 10 or some function of the constants
        # For instance:
        self.point_size = self.a**2

    def energy(self, dr):
        self.energy = func(dr, self.a, self.b)
        return energy

    def force(self, dr):
        self.force = other_func(dr, self.a, self.b)
        return force

    def mixing(self, constants2):
        a2 = constants2[0]
        b2 = constants2[1]

        self.a = mixing_func(self.a, a2)
        self.b = other_mixing_func(self.b, b2)

An example of this for the Lennard-Jones forcefield (which is the default for pylj) and be found in the pylj.forcefields module.

It is necessary to pass this forcefield to the pylj engine. This can be achieved during the initialisation of the System class object, by passing the defined class as the variable forcefield. This can be seen for the Lennard-Jones forcefield in the System class definition in the pylj.util module.