def initialise(
number_of_particles,
temperature,
box_length,
init_conf,
timestep_length=1e-14,
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
):
"""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.
mass: float (optional)
The mass of the particles being simulated.
constants: float, array_like (optional)
The values of the constants for the forcefield used.
forcefield: function (optional)
The particular forcefield to be used to find the energy and forces.
Returns
-------
System
System information.
"""
from pylj import util
system = util.System(
number_of_particles,
temperature,
box_length,
constants,
forcefield,
mass,
init_conf=init_conf,
timestep_length=timestep_length,
)
v = np.random.rand(system.particles.size, 2, 12)
v = np.sum(v, axis=2) - 6.0
mass_kg = mass * 1.6605e-27
v = v * np.sqrt(1.3806e-23 * system.init_temp / mass_kg)
v = v - np.average(v)
system.particles["xvelocity"] = v[:, 0]
system.particles["yvelocity"] = v[:, 1]
return system
def initialise(number_of_particles, temperature, box_length, init_conf):
"""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'
Returns
-------
System
System information.
"""
system = util.System(number_of_particles,
temperature,
box_length,
init_conf=init_conf)
system.particles['xvelocity'] = 0
system.particles['yvelocity'] = 0
return system
def test_system_too_small(self):
with self.assertRaises(AttributeError) as context:
util.System(
2,
300,
2,
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
)
self.assertTrue(
"With a box length of 2 the cell is too small to "
"really hold more than one particle." in str(context.exception))
def test_system_too_big(self):
with self.assertRaises(AttributeError) as context:
util.System(
2,
300,
1000,
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
)
self.assertTrue("With a box length of 1000 the particles are probably "
"too small to be seen in the viewer. Try something "
"(much) less than 600." in str(context.exception))
def initialise(
number_of_particles,
temperature,
box_length,
init_conf,
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
):
"""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'
mass: float (optional)
The mass of the particles being simulated.
constants: float, array_like (optional)
The values of the constants for the forcefield used.
forcefield: function (optional)
The particular forcefield to be used to find the energy and forces.
Returns
-------
System
System information.
"""
from pylj import util
system = util.System(
number_of_particles,
temperature,
box_length,
constants,
forcefield,
mass,
init_conf=init_conf,
)
system.particles["xvelocity"] = 0
system.particles["yvelocity"] = 0
return system
def test_system_init_conf(self):
with self.assertRaises(NotImplementedError) as context:
util.System(
2,
300,
100,
init_conf="horseradish",
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
)
self.assertTrue("The initial configuration type horseradish is not "
"recognised. Available options are: square or "
"random" in str(context.exception))
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
def test_system_square(self):
a = util.System(
2,
300,
8,
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
)
assert_equal(a.number_of_particles, 2)
assert_equal(a.init_temp, 300)
assert_almost_equal(a.box_length * 1e10, 8)
assert_almost_equal(a.timestep_length, 1e-14)
assert_almost_equal(a.particles["xposition"] * 1e10, [2, 2])
assert_almost_equal(a.particles["yposition"] * 1e10, [2, 6])
assert_almost_equal(a.initial_particles["xposition"] * 1e10, [2, 2])
assert_almost_equal(a.initial_particles["yposition"] * 1e10, [2, 6])
assert_almost_equal(a.cut_off * 1e10, 4.0)
assert_equal(a.distances.size, 1)
assert_equal(a.forces.size, 1)
assert_equal(a.energies.size, 1)
def test_system_random(self):
a = util.System(
2,
300,
8,
init_conf="random",
mass=39.948,
constants=[1.363e-134, 9.273e-78],
forcefield=ff.lennard_jones,
)
assert_equal(a.number_of_particles, 2)
assert_equal(a.init_temp, 300)
assert_almost_equal(a.box_length * 1e10, 8)
assert_almost_equal(a.timestep_length, 1e-14)
self.assertTrue(0 <= a.particles["xposition"][0] * 1e10 <= 8)
self.assertTrue(0 <= a.particles["yposition"][0] * 1e10 <= 8)
self.assertTrue(0 <= a.particles["xposition"][1] * 1e10 <= 8)
self.assertTrue(0 <= a.particles["yposition"][1] * 1e10 <= 8)
assert_almost_equal(a.cut_off * 1e10, 4.0)
assert_equal(a.distances.size, 1)
assert_equal(a.forces.size, 1)
assert_equal(a.energies.size, 1)