def periodic_boundary(number_of_steps, temperature):
"""This is a piece of exemplary code to show a single particle traveling across the periodic boundary.
Parameters
----------
number_of_steps: int
Number of step in simulation.
temperature: float
Temperature of simulation.
"""
number_of_particles = 1
sample_freq = 10
system = md.initialise(number_of_particles, temperature, 50, 'square')
sampling = sample.JustCell(system)
system.time = 0
for i in range(0, number_of_steps):
system.particles, system.distances, system.forces = comp.compute_forces(system.particles,
system.distances,
system.forces, system.box_length)
system.particles = md.velocity_verlet(system.particles, system.timestep_length, system.box_length)
system = md.sample(system.particles, system.box_length, system.initial_particles, system)
system.particles = comp.heat_bath(system.particles, system.temperature_sample, temperature)
system.time += system.timestep_length
system.step += 1
if system.step % sample_freq == 0:
sampling.update(system)
def md_nve(number_of_particles, temperature, box_length, number_of_steps, sample_frequency):
"""This is an example NVE (constant number of particles, system volume and system energy) simulation.
Parameters
----------
number_of_particles: int
Number of particles to simulate.
temperature: float
Initial temperature of the particles, in Kelvin.
box_length: float
Length of a single dimension of the simulation square, in Angstrom.
number_of_steps: int
Number of integration steps to be performed.
sample_frequency: int
Frequency with which the visualisation environment is to be updated.
Returns
-------
System
System information.
"""
system = md.initialise(number_of_particles, temperature, box_length, 'square')
sample_system = sample.Interactions(system)
system.time = 0
for i in range(0, number_of_steps):
system.particles, system.distances, system.forces = comp.compute_forces(system.particles,
system.distances,
system.forces, system.box_length)
system.particles = md.velocity_verlet(system.particles, system.timestep_length, system.box_length)
system = md.sample(system.particles, system.box_length, system.initial_particles, system)
system.time += system.timestep_length
system.step += 1
if system.step % sample_frequency == 0:
sample_system.update(system)
return system
def initialise(number_of_particles,
temperature,
box_length,
init_conf,
timestep_length=1e-14):
"""Initialise the particle positions (this can be either as a square or random arrangement), velocities (based on
the temperature defined, and calculate the initial forces/accelerations.
Parameters
----------
number_of_particles: int
Number of particles to simulate.
temperature: float
Initial temperature of the particles, in Kelvin.
box_length: float
Length of a single dimension of the simulation square, in Angstrom.
init_conf: string, optional
The way that the particles are initially positioned. Should be one of:
- 'square'
- 'random'
timestep_length: float (optional)
Length for each Velocity-Verlet integration step, in seconds.
Returns
-------
System
System information.
"""
system = util.System(number_of_particles,
temperature,
box_length,
init_conf=init_conf,
timestep_length=timestep_length)
v = np.random.rand(system.particles.size, 2) - 0.5
v2sum = np.average(np.square(v))
v = (v - np.average(v)) * np.sqrt(2 * system.init_temp / (v2sum))
system.particles['xvelocity'] = v[:, 0]
system.particles['yvelocity'] = v[:, 1]
system.particles, system.distances, system.forces = comp.compute_forces(
system.particles, system.distances, system.forces, system.box_length)
return system