def test_velocity_verlet(self):
a = md.initialise(2, 300, 8, "square")
a.particles, a.distances, a.forces, a.energies = md.velocity_verlet(
a.particles, 1, a.box_length, a.cut_off, a.constants, a.forcefield,
a.mass)
assert_almost_equal(a.particles["xprevious_position"] * 1e10, [2, 2])
assert_almost_equal(a.particles["yprevious_position"] * 1e10, [2, 6])
def test_initialise_square(self):
a = md.initialise(2, 300, 8, "square")
assert_equal(a.number_of_particles, 2)
assert_almost_equal(a.box_length, 8e-10)
assert_almost_equal(a.init_temp, 300)
assert_almost_equal(a.particles["xposition"] * 1e10, [2, 2])
assert_almost_equal(a.particles["yposition"] * 1e10, [2, 6])
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 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 test_calculate_temperature(self):
a = md.initialise(1, 300, 8, "square")
a.particles["xvelocity"] = [1e-10]
a.particles["yvelocity"] = [1e-10]
a.particles["xacceleration"] = [1e4]
a.particles["yacceleration"] = [1e4]
b = md.calculate_temperature(a.particles, mass=39.948)
assert_almost_equal(b * 1e23, 4.8048103702737945)
def test_update_velocities(self):
a = md.initialise(2, 300, 8, 'square')
a.particles['xvelocity'] = 1e-10
a.particles['yvelocity'] = 1e-10
a.particles['xacceleration'] = 1e4
a.particles['yacceleration'] = 1e4
xacceleration_new = 2e4
yacceleration_new = 2e4
b = md.update_velocities(
[a.particles['xvelocity'], a.particles['yvelocity']],
[xacceleration_new, yacceleration_new],
[a.particles['xacceleration'], a.particles['yacceleration']],
a.timestep_length)
assert_almost_equal(b[0][0] * 1e10, 2.5)
assert_almost_equal(b[1][0] * 1e10, 2.5)
assert_almost_equal(b[0][1] * 1e10, 2.5)
assert_almost_equal(b[1][1] * 1e10, 2.5)
def test_update_positions(self):
a = md.initialise(2, 300, 8, 'square')
a.particles['xvelocity'] = 1e4
a.particles['yvelocity'] = 1e4
a.particles['xacceleration'] = 1e4
a.particles['yacceleration'] = 1e4
b, c = md.update_positions(
[a.particles['xposition'], a.particles['yposition']], [
a.particles['xprevious_position'],
a.particles['yprevious_position']
], [a.particles['xvelocity'], a.particles['yvelocity']],
[a.particles['xacceleration'], a.particles['yacceleration']],
a.timestep_length, a.box_length)
assert_almost_equal(b[0][0] * 1e10, 3)
assert_almost_equal(b[1][0] * 1e10, 3)
assert_almost_equal(b[0][1] * 1e10, 3)
assert_almost_equal(b[1][1] * 1e10, 7)
def md_simulation(
number_of_particles, temperature, box_length, number_of_steps
):
system = md.initialise(
number_of_particles, temperature, box_length, "square"
)
sample_system = sample.Energy(system)
system.time = 0
for i in range(0, number_of_steps):
system.integrate(md.velocity_verlet)
system.md_sample()
system.heat_bath(temperature)
system.time += system.timestep_length
system.step += 1
if system.step % 10 == 0:
sample_system.update(system)
return system
def test_update_velocities(self):
a = md.initialise(2, 300, 8, "square")
a.particles["xvelocity"] = 1e-10
a.particles["yvelocity"] = 1e-10
a.particles["xacceleration"] = 1e4
a.particles["yacceleration"] = 1e4
xacceleration_new = 2e4
yacceleration_new = 2e4
b = md.update_velocities(
[a.particles["xvelocity"], a.particles["yvelocity"]],
[xacceleration_new, yacceleration_new],
[a.particles["xacceleration"], a.particles["yacceleration"]],
a.timestep_length,
)
assert_almost_equal(b[0][0] * 1e10, 2.5)
assert_almost_equal(b[1][0] * 1e10, 2.5)
assert_almost_equal(b[0][1] * 1e10, 2.5)
assert_almost_equal(b[1][1] * 1e10, 2.5)
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
def test_update_positions(self):
a = md.initialise(2, 300, 8, "square")
a.particles["xvelocity"] = 1e4
a.particles["yvelocity"] = 1e4
a.particles["xacceleration"] = 1e4
a.particles["yacceleration"] = 1e4
b, c = md.update_positions(
[a.particles["xposition"], a.particles["yposition"]],
[
a.particles["xprevious_position"],
a.particles["yprevious_position"]
],
[a.particles["xvelocity"], a.particles["yvelocity"]],
[a.particles["xacceleration"], a.particles["yacceleration"]],
a.timestep_length,
a.box_length,
)
assert_almost_equal(b[0][0] * 1e10, 3)
assert_almost_equal(b[1][0] * 1e10, 3)
assert_almost_equal(b[0][1] * 1e10, 3)
assert_almost_equal(b[1][1] * 1e10, 7)
def test_calculate_msd_large(self):
a = md.initialise(2, 300, 8, "square")
a.particles["xposition"] = [7e-10, 3e-10]
a.particles["yposition"] = [7e-10, 7e-10]
b = md.calculate_msd(a.particles, a.initial_particles, a.box_length)
assert_almost_equal(b, 10e-20)
def test_calculate_msd(self):
a = md.initialise(2, 300, 8, 'square')
a.particles['xposition'] = [3e-10, 3e-10]
a.particles['yposition'] = [3e-10, 7e-10]
b = md.calculate_msd(a.particles, a.initial_particles, a.box_length)
assert_almost_equal(b, 2e-20)
