def agents_factory(rng, dim, aligned_flag,
n=None, rho_0=None,
chi=None, onesided_flag=None,
tumble_flag=None, p_0=None, tumble_chemo_flag=None,
rotation_flag=None, Dr_0=None, rotation_chemo_flag=None,
temporal_chemo_flag=None, dt_mem=None, t_mem=None, time=None,
spatial_flag=None, v_0=None,
periodic_flag=None, L=None, origin_flags=None, obstructor=None,
c_field_flag=None, c_field=None):
if rho_0 is not None:
try:
volume_free = obstructor.volume_free
except AttributeError:
volume_free = np.product(L)
n = int(round(rho_0 * volume_free))
ds = directions_factory(n, dim, aligned_flag=aligned_flag,
rng=rng)
ps = positions_factory(spatial_flag, periodic_flag, n, dim, L,
origin_flags, rng, obstructor)
rudder_sets = rudder_set_factory(temporal_chemo_flag,
ds,
ps, v_0, dt_mem, t_mem, time,
c_field_flag, c_field,
onesided_flag, chi,
tumble_flag, p_0, tumble_chemo_flag,
rotation_flag, Dr_0, dim, rotation_chemo_flag)
swims = swimmers_factory(spatial_flag, v_0, ds)
return Agents(ds, ps, rudder_sets, swims)
def test_partial_infinite_boundaries(self):
L = np.array([np.inf, 1.7])
ps = positions.positions_factory(spatial_flag=True,
periodic_flag=True,
n=self.n, L=L, rng=self.rng)
dr = self.rng.uniform(-1.0, 1.0, size=ps.r.shape)
ps.displace(dr)
r_naive = ps.r_0[:, 0] + dr[:, 0]
# Check no wrapping along infinite axis
self.assertTrue(np.allclose(r_naive, ps.r_w[:, 0]))
self.assertTrue(np.allclose(r_naive, ps.r[:, 0]))
# Check done wrapping along finite axis
self.assertTrue(np.all(np.abs(ps.r_w[:, 1]) < L[1] / 2.0))
def setUp(self):
super(TestPeriodicPositions1D, self).setUp()
self.ps = positions.positions_factory(spatial_flag=True,
periodic_flag=True,
n=self.n, L=self.L,
rng=self.rng)
