def test_stress_non_minimized_periodic_general(self, dim, dtype, coords):
key = random.PRNGKey(0)
N = 64
box = quantity.box_size_at_number_density(N, 0.8, dim)
displacement_fn, _ = space.periodic_general(box,
coords == 'fractional')
pos = random.uniform(key, (N, dim))
pos = pos if coords == 'fractional' else pos * box
energy_fn = energy.soft_sphere_pair(displacement_fn)
def exact_stress(R):
dR = space.map_product(displacement_fn)(R, R)
dr = space.distance(dR)
g = jnp.vectorize(grad(energy.soft_sphere), signature='()->()')
V = quantity.volume(dim, box)
dUdr = 0.5 * g(dr)[:, :, None, None]
dr = (dr + jnp.eye(N))[:, :, None, None]
return -jnp.sum(dUdr * dR[:, :, None, :] * dR[:, :, :, None] /
(V * dr),
axis=(0, 1))
exact_stress = exact_stress(pos)
ad_stress = quantity.stress(energy_fn, pos, box)
tol = 1e-7 if dtype is f64 else 2e-5
self.assertAllClose(exact_stress, ad_stress, atol=tol, rtol=tol)
def test_stress_lammps_periodic_general(self, dim, dtype):
key = random.PRNGKey(0)
N = 64
(box, R, V), (E, C) = test_util.load_lammps_stress_data(dtype)
displacement_fn, _ = space.periodic_general(box)
energy_fn = smap.pair(
lambda dr, **kwargs: jnp.where(dr < f32(2.5),
energy.lennard_jones(dr), f32(0.0)),
space.canonicalize_displacement_or_metric(displacement_fn))
ad_stress = quantity.stress(energy_fn, R, box, velocity=V)
tol = 5e-5
self.assertAllClose(energy_fn(R) / len(R), E, atol=tol, rtol=tol)
self.assertAllClose(C, ad_stress, atol=tol, rtol=tol)
