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tests: Check serialization of particle properties
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@jngrad
jngrad committed Dec 21, 2022
1 parent 25a9b97 commit 6abe23c
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32 changes: 32 additions & 0 deletions testsuite/python/save_checkpoint.py
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Expand Up @@ -372,6 +372,38 @@
lbf_cpt_path = path_cpt_root / "lb.cpt"
lbf.save_checkpoint(str(lbf_cpt_path), lbf_cpt_mode)

# set various properties
p8 = system.part.add(id=8, pos=[2.0] * 3 + system.box_l)
p4.v = [-1., 2., -4.]
p8.lees_edwards_offset = 0.2
if espressomd.has_features('MASS'):
p3.mass = 1.5
if espressomd.has_features('ROTATION'):
p3.quat = [1., 2., 3., 4.]
p4.director = [3., 2., 1.]
p4.omega_body = [0.3, 0.5, 0.7]
p3.rotation = [True, False, True]
if espressomd.has_features('EXTERNAL_FORCES'):
p3.fix = [False, True, False]
p3.ext_force = [-0.6, 0.1, 0.2]
if espressomd.has_features(['EXTERNAL_FORCES', 'ROTATION']):
p3.ext_torque = [0.3, 0.5, 0.7]
if espressomd.has_features('ROTATIONAL_INERTIA'):
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.])
p4.gamma = gamma
if espressomd.has_features('ROTATION'):
p3.gamma_rot = 2. * gamma
if espressomd.has_features('ENGINE'):
p3.swimming = {"f_swim": 0.03}
if espressomd.has_features('ENGINE') and lbf_actor:
p4.swimming = {"v_swim": 0.02, "mode": "puller", "dipole_length": 1.}
if espressomd.has_features('LB_ELECTROHYDRODYNAMICS') and lbf_actor:
p8.mu_E = [-0.1, 0.2, -0.3]

# save checkpoint file
checkpoint.save(0)

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76 changes: 74 additions & 2 deletions testsuite/python/test_checkpoint.py
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Expand Up @@ -157,12 +157,84 @@ def test_lees_edwards(self):
self.assertAlmostEqual(protocol.time_0, 0.2, delta=1e-10)
self.assertAlmostEqual(protocol.shear_velocity, 1.2, delta=1e-10)

def test_part(self):
p1, p2 = system.part.by_ids([0, 1])
def test_particle_properties(self):
p1, p2, p3, p4, p8 = system.part.by_ids([0, 1, 3, 4, 8])
np.testing.assert_allclose(np.copy(p1.pos), np.array([1.0, 2.0, 3.0]))
np.testing.assert_allclose(np.copy(p2.pos), np.array([1.0, 1.0, 2.0]))
np.testing.assert_allclose(np.copy(p1.f), particle_force0)
np.testing.assert_allclose(np.copy(p2.f), particle_force1)
self.assertEqual(p1.type, 0)
self.assertEqual(p2.type, 0)
self.assertEqual(p3.type, 1)
self.assertEqual(p4.type, 1)
np.testing.assert_allclose(np.copy(p3.v), [0., 0., 0.])
np.testing.assert_allclose(np.copy(p4.v), [-1., 2., -4.])
np.testing.assert_allclose(p8.lees_edwards_offset, 0.2)
np.testing.assert_equal(np.copy(p1.image_box), [0, 0, 0])
np.testing.assert_equal(np.copy(p8.image_box), [0, 0, 0]
if 'THERM.SDM' in modes else [1, 1, 1])
self.assertEqual(p8.lees_edwards_flag, 0)
if espressomd.has_features('MASS'):
np.testing.assert_allclose(p3.mass, 1.5)
np.testing.assert_allclose(p4.mass, 1.)
if espressomd.has_features('ROTATIONAL_INERTIA'):
np.testing.assert_allclose(np.copy(p3.rinertia), [2., 3., 4.])
np.testing.assert_allclose(np.copy(p4.rinertia), [1., 1., 1.])
if espressomd.has_features('ELECTROSTATICS'):
np.testing.assert_allclose(p1.q, 1.)
if espressomd.has_features(
['MASS', 'ROTATION']) and 'THERM.LB' not in modes:
p5 = system.part.by_id(5)
np.testing.assert_allclose(p2.q, +0.118, atol=1e-3)
np.testing.assert_allclose(p5.q, -1.118, atol=1e-3)
else:
np.testing.assert_allclose(p2.q, -1.)
np.testing.assert_allclose(p3.q, 0.)
np.testing.assert_allclose(p4.q, 0.)
if espressomd.has_features('DIPOLES'):
np.testing.assert_allclose(np.copy(p1.dip), [1.3, 2.1, -6.])
if espressomd.has_features('ROTATION'):
np.testing.assert_allclose(np.copy(p3.quat), [1., 2., 3., 4.])
np.testing.assert_allclose(np.copy(p4.director) * np.sqrt(14.),
[3., 2., 1.])
np.testing.assert_allclose(np.copy(p3.omega_body), [0., 0., 0.])
np.testing.assert_allclose(np.copy(p4.omega_body), [0.3, 0.5, 0.7])
np.testing.assert_equal(np.copy(p3.rotation), [True, False, True])
if espressomd.has_features('EXTERNAL_FORCES'):
np.testing.assert_equal(np.copy(p3.fix), [False, True, False])
np.testing.assert_allclose(np.copy(p3.ext_force), [-0.6, 0.1, 0.2])
if espressomd.has_features(['EXTERNAL_FORCES', 'ROTATION']):
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.])
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)
if espressomd.has_features('ROTATION'):
np.testing.assert_allclose(p3.gamma_rot, 2. * gamma)
if espressomd.has_features('ENGINE'):
self.assertEqual(p3.swimming, {"f_swim": 0.03, "mode": "N/A",
"v_swim": 0., "dipole_length": 0.})
if espressomd.has_features('ENGINE') and has_lb_mode:
self.assertEqual(p4.swimming, {"v_swim": 0.02, "mode": "puller",
"f_swim": 0., "dipole_length": 1.})
if espressomd.has_features('LB_ELECTROHYDRODYNAMICS') and has_lb_mode:
np.testing.assert_allclose(np.copy(p8.mu_E), [-0.1, 0.2, -0.3])
if espressomd.has_features('VIRTUAL_SITES_RELATIVE'):
from scipy.spatial.transform import Rotation as R
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
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])
self.assertEqual(vs_id, p1.id)
np.testing.assert_allclose(vs_dist, np.sqrt(2.))
np.testing.assert_allclose(q[q_ind], r.as_quat(), atol=1e-10)
np.testing.assert_allclose(np.copy(p2.vs_quat), [1., 0., 0., 0.])

def test_part_slice(self):
np.testing.assert_allclose(np.copy(p_slice.id), [4, 1])
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