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 pbc():
number_of_particles = 1
temperature = 100
box_length = 30
number_of_steps = 10000
sample_frequency = 25
# Initialise the system
system = md.initialise(number_of_particles, temperature, box_length,
'square')
system.particles['xvelocity'] = (np.random.randn() - 0.5) * 14
system.particles['yvelocity'] = (np.random.randn() - 0.5) * 14
# This sets the sampling class
sample_system = sample.JustCell(system)
# Start at time 0
system.time = 0
# Begin the molecular dynamics loop
for i in range(0, number_of_steps):
# At each step, calculate the forces on each particle and get
# acceleration
system.compute_force()
# Run the equations of motion integrator algorithm
system.integrate(md.velocity_verlet)
# Sample the thermodynamic and structural parameters of the system
system.md_sample()
# Allow the system to interact with a heat bath
system.heat_bath(temperature)
# Iterate the time
system.time += system.timestep_length
system.step += 1
# At a given frequency sample the positions and plot the RDF
if system.step % sample_frequency == 0:
sample_system.update(system)
def simulation(temperature):
"""
Runs a molecular dynamics simulation in suing the pylj molecular dynamics engine.
Parameters
----------
number_of_particles: int
The number of particles in the simulation
temperature: float
The temperature for the initialisation and thermostating
box_length: float
The length of the simulation square
number_of_steps: int
The number of molecular dynamics steps to run
sample_frequency:
How regularly the visualisation should be updated
Returns
-------
pylj.util.System
The complete system information from pylj
"""
# Initialise the system
system = md.initialise(20, temperature, 20, 'square')
# This sets the sampling class
sample_system = sample.JustCell(system)
# Start at time 0
system.time = 0
# Begin the molecular dynamics loop
for i in range(0, 1000):
# Run the equations of motion integrator algorithm, this
# includes the force calculation
system.integrate(md.velocity_verlet)
# Sample the thermodynamic and structural parameters of the system
system.md_sample()
# Allow the system to interact with a heat bath
system.heat_bath(temperature)
# Iterate the time
system.time += system.timestep_length
system.step += 1
# At a given frequency sample the positions and plot the RDF
if system.step % 10 == 0:
sample_system.update(system)
return system
def simulation(temperature):
"""
Runs a molecular dynamics simulation in suing the pylj molecular dynamics engine.
Parameters
----------
temperature: float
The temperature for the initialisation and thermostating
Returns
-------
pylj.util.System
The complete system information from pylj
"""
# Initialise the system
system = md.initialise(2,
temperature,
10,
'square',
constants=[440.5, 1.522e-10],
forcefield=bond)
system.cut_off = 30
system.particles['xposition'] = [5e-10, 6e-10]
system.particles['yposition'] = [5e-10, 6e-10]
# This sets the sampling class
sample_system = sample.JustCell(system, scale=2)
# Start at time 0
system.time = 0
# Begin the molecular dynamics loop
for i in range(0, 4000):
# Run the equations of motion integrator algorithm, this
# includes the force calculation
system.integrate(md.velocity_verlet)
# Sample the thermodynamic and structural parameters of the system
system.md_sample()
# Allow the system to interact with a heat bath
system.heat_bath(temperature)
# Iterate the time
system.time += system.timestep_length
system.step += 1
# At a given frequency sample the positions and plot the RDF
if system.step % 10 == 0:
sample_system.update(system)
return system