def test_modify_velocity(self):
part = particles.PointParticles(4)
part.v = self.four_by3
assert_equals(part.n, 4)
sttr = lambda v: part.__setattr__("v", v)
assert_raises(ValueError, sttr, self.three_by3)
np.testing.assert_array_equal(part.v, self.four_by3)
def test_modify_force(self):
part = particles.PointParticles(4)
part.f = self.four_by3
assert_equals(part.n, 4)
sttr = lambda f: part.__setattr__("f", f)
assert_raises(ValueError, sttr, self.three_by3)
np.testing.assert_array_equal(part.f, self.four_by3)
def test_modify_position(self): part = particles.PointParticles(4) me = self.four_by3.copy() part.x = self.four_by3 np.testing.assert_array_equal(part.x, self.four_by3) part.x[0, 0] = 1000 np.testing.assert_array_equal(me, self.four_by3)
def test_modify_position(self):
part = particles.PointParticles(4)
part.x = self.four_by3
assert_equals(part.n, 4)
sttr = lambda x: part.__setattr__("x", x)
assert_raises(ValueError, sttr, self.three_by3)
np.testing.assert_array_equal(part.x, self.four_by3)
def test_modify_mass(self):
part = particles.PointParticles(4)
part.mass = np.array([1.0, 1.0, 2.0, 2.0], dtype=np.float32)
assert_equals(part.n, 4)
part.mass = 1.0
np.testing.assert_array_equal(part.mass, np.array([1, 1, 1, 1], dtype=np.float32))
sttr = lambda mass: part.__setattr__("mass", mass)
assert_raises(ValueError, sttr, np.array([1.0, 1.0, 1.0]))
def test_modify_type(self):
part = particles.PointParticles(4)
part.t = np.array([1, 1, 2, 2], dtype=np.int32)
np.testing.assert_array_equal(part.t, np.array([1, 1, 2, 2]))
part.t = 1
np.testing.assert_array_equal(part.t, np.array([1, 1, 1, 1], dtype=np.int32))
sttr = lambda t: part.__setattr__("t", t)
assert_raises(ValueError, sttr, np.array([1, 1, 1]))
from pexmd import particles, box, integrator, interaction
import numpy as np
import matplotlib.pyplot as plt
# Weird way to initialize the particles (see #2)
positions = np.array([[-0.6, -0.6, 0.0], [0.6, -0.5, 0.0], [-0.6, 0.6, 0.0],
[0.6, 0.6, 0.0]])
part = particles.PointParticles(len(positions))
part.x = positions
part.t = 1
part.mass = np.array([3.0, 3.0, 2.0, 3.0])
dt = 0.005
evol = integrator.Andersen(dt, 100, 0.5)
# We should initalize this in a much better way (see #3)
x0 = np.array([-0.7] * 3)
xf = np.array([0.7] * 3)
b = box.Box(x0, xf, t='Fixed')
#lj = interaction.LennardJones([1, 1], 5.4, 1.0, 1.0, "None")
lj = interaction.Morse([1, 1], 5.4, 1.0, 1.0, "None")
pp = []
kk = []
tt = []
for t in np.arange(0, 2, dt):
part.x, part.v = evol.first_step(part.x, part.v, part.a)
part.x, part.v = b.wrap_boundary(part.x, part.v)
part.f, e = lj.forces(part.x, part.v, part.t)
part.x, part.v = evol.last_step(part.x, part.v, part.a)
tt.append(t)
def test_calculate_acceleration(self):
part = particles.PointParticles(4)
part.f = self.four_by3
part.mass = 2.0
np.testing.assert_array_equal(part.a, self.four_by3 / 2)
def test_create_point_particles(self):
part = particles.PointParticles(3)
np.testing.assert_array_equal(part.idx, np.arange(3))
nparticles = 80
dt = 0.1
t_end = 20
temperature_ini = 100.0
scale = 100.
# Initializing particles:
positions_ini = np.random.rand(nparticles, 3)
positions_ini = scale * 10000 * positions_ini
velocities_ini = np.random.normal(0.,
math.sqrt(temperature_ini),
size=(nparticles, 3))
#velocities_ini = np.zeros((nparticles, 3), dtype=np.float32)
masses_ini = np.full((nparticles), 1.)
part = particles.PointParticles(nparticles)
part.x = positions_ini
part.v = velocities_ini
part.t = 1
part.mass = masses_ini
evol = integrator.Andersen(dt, temperature_ini, 10.)
# We should initalize this in a much better way (see #3)
x0 = np.array([-scale] * 3)
xf = np.array([scale] * 3)
b = box.Box(x0, xf, t='Periodic')
#lj = interaction.LennardJones([1, 1], 5.4, 1.0, 1.0, "Displace")
lj = interaction.Morse([1, 1], 5.4, 1.0, 1.0, 1.0, "Displace")
def test_set_position_wrong_size(self):
part = particles.PointParticles(4)
sttr = lambda x: part.__setattr__("x", x)
assert_raises(ValueError, sttr, self.three_by3)
def test_set_position_from_list(self): part = particles.PointParticles(4) part.x = self.lfour_by3 assert_equals(part.n, 4) assert_equals(type(part.x), np.ndarray)
def test_set_position_from_array(self): part = particles.PointParticles(4) part.x = self.four_by3 assert_equals(part.n, 4)