def test_computeForces():
""""""
box = md.Box(0., 0., 5. * md.hcp.uc_centered_a, 0.5 * md.hcp.uc_centered_b)
atoms = md.MD(box, cutoff=2.5)
if __plot:
cmn.figure()
cmn.plotBox(box)
cmn.plotAtoms(atoms.x, atoms.y, radius=atoms.radius)
cmn.plt.show()
atoms.buildVerletLists()
print(atoms.vl)
cpp.computeForces(
atoms.x,
atoms.y # atom positions
,
atoms.vl.vl_size,
atoms.vl.vl_list # linearized verlet list data structure
,
atoms.ax,
atoms.ay # atom forces
)
print(f'ax={atoms.ax}')
print(f'ay={atoms.ay}')
r = md.hcp.uc_centered_a
r01sq = r**2
r02sq = (2 * r)**2
fx01 = lj.force_factor(r01sq) * r
fx02 = lj.force_factor(r02sq) * 2 * r
expected = np.array([fx01, fx01, fx01, fx01, 0.00]) \
+ np.array([fx02, fx02, fx02, 0.00, 0.00]) \
- np.array([0.00, fx01, fx01, fx01, fx01]) \
- np.array([0.00, 0.00, fx02, fx02, fx02])
assert np.all(atoms.ax == expected)
assert np.all(atoms.ay == np.zeros((atoms.n_atoms, ), dtype=float))
def test_force_is_derivative_of_potential():
n = 1000
# Generate n random numbers in ]0,5*R0]
# np.random.random generate numbers in [
rij = (5*R0)*(1.0 - np.random.random(n))
fij = lj.force_factor(rij**2)*rij
d = 1e-10
rij0 = rij - d
vij0 = lj.potential(rij0**2)
rij1 = rij + d
vij1 = lj.potential(rij1**2)
dvij = (vij1 - vij0)/(2*d)
for i in range(n):
print(f'{i} {fij[i]} == {dvij[i]} {np.abs(fij[i]-dvij[i])}')
assert fij[i] == pytest.approx(dvij[i],1e-4)
def test_computeForces():
""""""
box = md.Box(0., 0., 5. * md.hcp.uc_centered_a, 0.5 * md.hcp.uc_centered_b)
atoms = md.MD(box, cutoff=2.5)
if __plot:
cmn.figure()
cmn.plotBox(box)
cmn.plotAtoms(atoms.x, atoms.y, radius=atoms.radius)
cmn.plt.show()
atoms.buildVerletLists()
print(atoms.vl)
energy = atoms.computeForces()
r = md.hcp.uc_centered_a
r01sq = r**2
r02sq = (2 * r)**2
fx01 = lj.force_factor(r01sq) * r
fx02 = lj.force_factor(r02sq) * 2 * r
expected = np.array([fx01, fx01, fx01, fx01, 0.00]) \
+ np.array([fx02, fx02, fx02, 0.00, 0.00]) \
- np.array([0.00, fx01, fx01, fx01, fx01]) \
- np.array([0.00, 0.00, fx02, fx02, fx02])
assert np.all(atoms.ax == expected)
print(atoms.ay)
assert np.all(atoms.ay == np.zeros((atoms.n_atoms, ), dtype=float))
def test_zero_force_R0():
"""verify that the force magnitude is zero at R0."""
rij2 = R0**2
fij = lj.force_factor(rij2)
# account for round-off error R0**6 is not exactly 5, although R0 is defined as 2**1/6
assert fij == pytest.approx(0.0, 5e-16)