def test_lennard_jones_potential():
"""
Test the definition of lennard_jones_potential() function. It will pass when the calculated potential is equal to actual potential defined by lennard jones.
"""
coordinates = [np.array([0.0, 0.0, 0.0]), np.array([0.0, 0.0, 1.0])]
box_length = 10.0
box = mc_lj_potential.Box(box_length=box_length, coordinates=coordinates)
mcs = mc_lj_potential.MCState(box, cutoff=3.0)
expected_vaule = 224.0
calculated_value = mcs.lennard_jones_potential(0.5)
assert np.isclose(expected_vaule, calculated_value)
def test_get_particle_energy_equi():
"""
Test the get_paricle_energy() function when it is at the equilibrated point.
"""
coordinates = [np.array([0.0, 0.0, 0.0]), np.array([0.0, 0.0, 1.0])]
box_length = 10.0
box = mc_lj_potential.Box(box_length=box_length, coordinates=coordinates)
mcs = mc_lj_potential.MCState(box, cutoff=3.0)
expected_vaule = 0.0
calculated_value = mcs.get_particle_energy(0)
assert np.isclose(expected_vaule, calculated_value)
def test_get_particle_energy_cutoff():
"""
Test the get_particle_energy() function when the particle is exceed the cutoff.
"""
coordinates = [np.array([0.0, 0.0, 0.0]), np.array([0.0, 0.0, 4.0])]
box_length = 10.0
box = mc_lj_potential.Box(box_length=box_length, coordinates=coordinates)
mcs = mc_lj_potential.MCState(box, cutoff=3.0)
expected_vaule = 0.0
calculated_value = mcs.get_particle_energy(0)
assert np.isclose(expected_vaule, calculated_value)
def mcs():
"""
Set up the fixture to have a general MCState that can be callable for all tests of different energy functions.
"""
current_directory = os.path.dirname(os.path.abspath(__file__))
file_path = os.path.join(current_directory, "sample_config.xyz")
coordinates = mc_lj_potential.generate_initial_state(method = "file", file_name=file_path)
box_length = 10.0
cutoff = 3.0
box = mc_lj_potential.Box(box_length=box_length, coordinates=coordinates)
mcs = mc_lj_potential.MCState(box, cutoff = cutoff)
return mcs
import mc_lj_potential as mc
import numpy as np
np.random.seed(123)
num_particles = 100
box_length = 10.0
coordinates = mc.generate_initial_state(method='random',
num_particles=num_particles,
box_length=box_length)
#print(coordinates)
box = mc.Box(coordinates=coordinates, box_length=box_length)
#print(box.coordinates)
mcs = mc.MCState(box1=box, cutoff=3.0)
total_pair_energy = mcs.calculate_total_pair_energy()
#print(total_pair_energy)
#print(mcs.calculate_tail_correction())
#print(mcs.calculate_unit_energy())
#print(mcs.get_particle_energy(0))