diff --git a/testsuite/python/brownian_dynamics.py b/testsuite/python/brownian_dynamics.py index 223340e15..f99d94018 100644 --- a/testsuite/python/brownian_dynamics.py +++ b/testsuite/python/brownian_dynamics.py @@ -161,5 +161,5 @@ class BrownianThermostat(ut.TestCase): system.integrator.run(3) np.testing.assert_allclose( - part.omega_lab, [0, 0, 1.3 / 1.5], atol=1e-14) + np.copy(part.omega_lab), [0, 0, 1.3 / 1.5], atol=1e-14) # noise only @@ -168,5 +168,5 @@ class BrownianThermostat(ut.TestCase): kT=1, gamma=1, gamma_rotation=1.5, act_on_virtual=False, seed=41) system.integrator.run(3) - self.assertGreater(np.linalg.norm(part.omega_lab), 0.) + self.assertGreater(np.linalg.norm(np.copy(part.omega_lab)), 0.) diff --git a/testsuite/python/lees_edwards.py b/testsuite/python/lees_edwards.py index 002340bd2..4539f1af5 100644 --- a/testsuite/python/lees_edwards.py +++ b/testsuite/python/lees_edwards.py @@ -397,5 +397,5 @@ class LeesEdwards(ut.TestCase): a=k_non_bonded / 2, n=-2, cutoff=r_cut) system.integrator.run(0) - r_12 = system.distance_vec(p1, p2) + r_12 = np.copy(system.distance_vec(p1, p2)) np.testing.assert_allclose( @@ -405,5 +405,5 @@ class LeesEdwards(ut.TestCase): np.testing.assert_allclose( np.copy(system.analysis.pressure_tensor()["non_bonded"]), - np.outer(r_12, p2.f) / system.volume()) + np.outer(r_12, np.copy(p2.f)) / system.volume()) np.testing.assert_almost_equal( @@ -438,5 +438,5 @@ class LeesEdwards(ut.TestCase): shear_direction="x", shear_plane_normal="y", protocol=lin_protocol) # Test position and velocity of VS with Le shift - old_p3_pos = p3.pos + old_p3_pos = np.copy(p3.pos) expected_p3_pos = old_p3_pos - \ np.array((get_lin_pos_offset(system.time, **params_lin), 0, 0)) @@ -444,5 +444,5 @@ class LeesEdwards(ut.TestCase): np.testing.assert_allclose(np.copy(p3.pos_folded), expected_p3_pos) np.testing.assert_allclose( - p3.v, p1.v + np.array((params_lin["shear_velocity"], 0, 0))) + np.copy(p3.v), np.copy(p1.v) + np.array((params_lin["shear_velocity"], 0, 0))) # Check distances diff --git a/testsuite/python/test_checkpoint.py b/testsuite/python/test_checkpoint.py index f295cec44..4b30aaefb 100644 --- a/testsuite/python/test_checkpoint.py +++ b/testsuite/python/test_checkpoint.py @@ -217,12 +217,12 @@ class CheckpointTest(ut.TestCase): np.testing.assert_allclose(np.copy(p3.ext_torque), [0.3, 0.5, 0.7]) if espressomd.has_features('ROTATIONAL_INERTIA'): - np.testing.assert_allclose(p3.rinertia, [2., 3., 4.]) + np.testing.assert_allclose(np.copy(p3.rinertia), [2., 3., 4.]) if espressomd.has_features('THERMOSTAT_PER_PARTICLE'): gamma = 2. if espressomd.has_features('PARTICLE_ANISOTROPY'): gamma = np.array([2., 3., 4.]) - np.testing.assert_allclose(p4.gamma, gamma) + np.testing.assert_allclose(np.copy(p4.gamma), gamma) if espressomd.has_features('ROTATION'): - np.testing.assert_allclose(p3.gamma_rot, 2. * gamma) + np.testing.assert_allclose(np.copy(p3.gamma_rot), 2. * gamma) if espressomd.has_features('ENGINE'): self.assertEqual(p3.swimming, {"f_swim": 0.03, "mode": "N/A", @@ -237,9 +237,11 @@ class CheckpointTest(ut.TestCase): q_ind = ([1, 2, 3, 0],) # convert from scalar-first to scalar-last vs_id, vs_dist, vs_quat = p2.vs_relative - d = p2.pos - p1.pos + d = np.copy(p2.pos - p1.pos) + vs_quat = np.copy(vs_quat) + p_quat = np.copy(p1.quat) theta = np.arccos(d[2] / np.linalg.norm(d)) assert abs(theta - 3. * np.pi / 4.) < 1e-8 q = np.array([0., 0., np.sin(theta / 2.), -np.cos(theta / 2.)]) - r = R.from_quat(p1.quat[q_ind]) * R.from_quat(vs_quat[q_ind]) + r = R.from_quat(p_quat[q_ind]) * R.from_quat(vs_quat[q_ind]) self.assertEqual(vs_id, p1.id) np.testing.assert_allclose(vs_dist, np.sqrt(2.)) @@ -500,5 +502,5 @@ class CheckpointTest(ut.TestCase): self.assertEqual(p_virt.vs_relative[1], np.sqrt(2.)) np.testing.assert_allclose( - p_real.vs_relative[2], [1., 0., 0., 0.], atol=1e-10) + np.copy(p_real.vs_relative[2]), [1., 0., 0., 0.], atol=1e-10) def test_mean_variance_calculator(self): @@ -785,6 +787,6 @@ class CheckpointTest(ut.TestCase): p2 = system.part.add(pos=[system.box_l[0] - 1., 1.6, 0.], type=6) system.integrator.run(0, recalc_forces=True) - np.testing.assert_allclose(p1.f, [0., 1e8, 0.], atol=1e-3) - np.testing.assert_allclose(p2.f, [0., 1e8, 0.], atol=1e-3) + np.testing.assert_allclose(np.copy(p1.f), [0., 1e8, 0.], atol=1e-3) + np.testing.assert_allclose(np.copy(p2.f), [0., 1e8, 0.], atol=1e-3) p1.remove() p2.remove()