def test_PBC2(self):
a = np.array([7.90146923, -13.72858524, 3.75326586], dtype=np.float32)
b = np.array([-1.36250901, 13.45423985, -0.36317623], dtype=np.float32)
box = np.array([5.5457325, 5.5457325, 5.5457325], dtype=np.float32)
def mindist(a, b, box):
x = a - b
return np.linalg.norm(x - np.rint(x / box) * box)
ref = mindist(a, b, box)
val = distance_array(np.array([a]), np.array([b]), box)[0, 0]
assert_allclose(val, ref, rtol=1e-6, atol=1e-6,
err_msg="Issue 151 not correct (PBC in distance array)")
def test_distance_array_parallel_pbc(self):
cython_parallel = distance_array(self.coord[0], self.coord[1], box=self.box)
assert_allclose(cython_parallel, self.ref_pbc, rtol=1e-6, atol=1e-6,
err_msg="Cython parallel distance matrix does not match C")
def test_distance_array_parallel_results(self):
result = np.empty((self.coord[0].shape[0], self.coord[0].shape[0])).astype(np.float32)
cython_parallel = distance_array(self.coord[0], self.coord[1], result=result)
assert_allclose(cython_parallel, self.ref, rtol=1e-6, atol=1e-6,
err_msg="Cython parallel distance matrix does not match C")
