def setUpClass(cls):
box_l = 20.0
# start with a small box
cls.system.box_l = np.array([box_l, box_l, box_l])
cls.system.cell_system.set_n_square(use_verlet_lists=False)
fene = FeneBond(k=30, d_r_max=2)
cls.system.bonded_inter.add(fene)
positions = polymer.positions(n_polymers=cls.num_poly,
bond_length=0.9,
beads_per_chain=cls.num_mono,
seed=42)
for p in positions:
for ndx, m in enumerate(p):
part_id = len(cls.system.part)
cls.system.part.add(id=part_id, pos=m)
if ndx > 0:
cls.system.part[part_id].add_bond((fene, part_id - 1))
# bring two polymers to opposite corners:
# far in cell centre, but mirror images are close
head_id = 0
tail_id = head_id + cls.num_mono
cm = np.mean(cls.system.part[head_id:tail_id].pos, axis=0)
cls.system.part[head_id:tail_id].pos = cls.system.part[
head_id:tail_id].pos - cm + cls.system.box_l
head_id = cls.num_mono + 1
tail_id = head_id + cls.num_mono
cm = np.mean(cls.system.part[head_id:tail_id].pos, axis=0)
cls.system.part[head_id:tail_id].pos -= cm
def setUpClass(self):
box_l = 20.0
# start with a small bo
self.system.box_l = np.array([box_l, box_l, box_l])
self.system.cell_system.set_n_square(use_verlet_lists=False)
fene = FeneBond(k=30, d_r_max=2)
self.fene = fene
self.system.bonded_inter.add(fene)
def test_fene(self):
# system parameters
box_l = 10.0
system.box_l = [box_l, box_l, box_l]
skin = 0.4
time_step = 0.01
system.time_step = time_step
# thermostat and cell system
system.cell_system.skin = skin
system.periodicity = [1, 1, 1]
# particles and bond
system.part.add(
id=0, pos=[9.9, 9.75, 9.9], type=0, mol_id=0, fix=[1, 1, 1])
system.part.add(
id=1, pos=[9.9, 10.25, 9.9], type=0, mol_id=0, fix=[1, 1, 1])
k = 1e4
d_r_max = 1.5
r_0 = 0.1
fene = FeneBond(k=k, d_r_max=d_r_max, r_0=r_0)
system.bonded_inter.add(fene)
system.part[0].add_bond((fene, 1))
system.integrator.run(steps=0)
sim_stress_bonded = system.analysis.stress_tensor()['bonded']
sim_stress_fene = system.analysis.stress_tensor()[
'bonded', len(system.bonded_inter) - 1]
total_bonded_stresses = np.zeros([3, 3])
for i in range(len(system.bonded_inter)):
total_bonded_stresses = np.add(
total_bonded_stresses, system.analysis.stress_tensor()['bonded', i])
anal_stress_fene = self.get_anal_stress_fene(
system.part[0].pos, system.part[1].pos, k, d_r_max, r_0)
self.assertTrue(np.max(np.abs(sim_stress_bonded - anal_stress_fene))
< tol, 'bonded stress does not match analytical result')
self.assertTrue(np.max(np.abs(sim_stress_fene - anal_stress_fene))
< tol, 'bonded stress for fene does not match analytical result')
self.assertTrue(np.max(np.abs(sim_stress_bonded - total_bonded_stresses))
< tol, 'bonded stresses do not sum up to the total value')
sim_pressure_fene = system.analysis.pressure()[
'bonded', len(system.bonded_inter) - 1]
anal_pressure_fene = np.einsum("ii", anal_stress_fene) / 3.0
self.assertTrue(np.max(np.abs(sim_pressure_fene - anal_pressure_fene))
< tol, 'bonded pressure for fene does not match analytical result')
# Compare stress tensor observable to stress tensor from analysis
np.testing.assert_allclose(
StressTensor().calculate(),
system.analysis.stress_tensor()["total"].reshape(9),
atol=1E-10)
system.part.clear()
def test(self):
system = espressomd.System(box_l=[15.0, 15.0, 15.0])
system.cell_system.skin = 1
# Initial state. Skin does not influence cutoffs as long as there are
# no interactions
self.assertEqual(system.cell_system.max_cut_nonbonded, -1)
self.assertEqual(system.cell_system.max_cut_bonded, -1)
self.assertEqual(system.cell_system.interaction_range, -1)
# Bonded interaction
fene = FeneBond(r_0=1, d_r_max=2, k=1)
system.bonded_inter.add(fene)
self.assertEqual(system.cell_system.max_cut_bonded, 3)
n_nodes = np.product(system.cell_system.node_grid)
if n_nodes == 1:
# Bonds don't influence interaction range
self.assertEqual(system.cell_system.interaction_range, -1)
else:
self.assertEqual(
system.cell_system.interaction_range,
system.cell_system.max_cut_bonded + system.cell_system.skin)
system.bonded_inter.remove(fene._bond_id)
self.assertEqual(system.cell_system.max_cut_bonded, -1)
self.assertEqual(system.cell_system.interaction_range, -1)
if espressomd.has_features("LENNARD_JONES"):
lj_off_params = system.non_bonded_inter[
0, 0].lennard_jones.get_params()
system.non_bonded_inter[0,
0].lennard_jones.set_params(sigma=1,
epsilon=1,
cutoff=2.5,
shift="auto")
self.assertEqual(system.cell_system.max_cut_nonbonded, 2.5)
self.assertEqual(
system.cell_system.interaction_range,
system.cell_system.max_cut_nonbonded + system.cell_system.skin)
system.non_bonded_inter[0, 0].lennard_jones.set_params(
**lj_off_params)
self.assertEqual(system.cell_system.max_cut_nonbonded, -1)
self.assertEqual(system.cell_system.interaction_range, -1)
def setUpClass(self):
box_l = 20.0
# start with a small bo
self.system.box_l = np.array([box_l, box_l, box_l])
self.system.cell_system.set_n_square(use_verlet_lists=False)
fene = FeneBond(k=30, d_r_max=2)
self.system.bonded_inter.add(fene)
polymer.create_polymer(N_P=self.num_poly,
bond_length=0.9,
MPC=self.num_mono,
bond=fene)
# bring two polymers to opposite corners:
# far in centre cell, but mirror images are close
head_id = 0
tail_id = head_id + self.num_mono
cm = np.mean(self.system.part[head_id:tail_id].pos, axis=0)
self.system.part[head_id:tail_id].pos = self.system.part[
head_id:tail_id].pos - cm + self.system.box_l
head_id = self.num_mono + 1
tail_id = head_id + self.num_mono
cm = np.mean(self.system.part[head_id:tail_id].pos, axis=0)
self.system.part[head_id:tail_id].pos -= cm
def test_bonds(self):
"""Tests bond addition and removal."""
p1 = self.system.part[self.pid]
p2 = self.system.part.add(pos=p1.pos)
inactive_bond = FeneBond(k=1, d_r_max=2)
p2.add_bond([self.f1, p1])
with self.assertRaisesRegex(RuntimeError, "already exists on particle"):
p2.add_bond([self.f1, p1.id])
with self.assertRaisesRegex(RuntimeError, "already exists on particle"):
p2.add_bond((self.f1, p1))
with self.assertRaisesRegex(Exception, "1st element of Bond has to be of type BondedInteraction or int"):
p2.add_bond(('self.f1', p1))
with self.assertRaisesRegex(ValueError, "Bond partners have to be of type integer or ParticleHandle"):
p2.add_bond((self.f1, '1'))
with self.assertRaisesRegex(ValueError, r"Bond FeneBond\(.+?\) needs 1 partner"):
p2.add_bond((self.f1, p1, p2))
with self.assertRaisesRegex(Exception, "The bonded interaction has not yet been added to the list of active bonds in ESPResSo"):
p2.add_bond((inactive_bond, p1))
p2.delete_bond([self.f1, p1])
with self.assertRaisesRegex(RuntimeError, "doesn't exist on particle"):
p2.delete_bond([self.f1, p1])
with self.assertRaisesRegex(ValueError, "Bond partners have to be of type integer or ParticleHandle"):
p2.delete_bond((self.f1, 'p1'))
class PairCriteria(ut.TestCase):
"""Tests interface and implementation of pair criteria"""
es = espressomd.System(box_l=[1., 1., 1.])
f1 = FeneBond(k=1, d_r_max=0.05)
es.bonded_inter.add(f1)
f2 = FeneBond(k=1, d_r_max=0.05)
es.bonded_inter.add(f2)
es.part.add(id=0, pos=(0, 0, 0))
es.part.add(id=1, pos=(0.91, 0, 0))
p1 = es.part[0]
p2 = es.part[1]
epsilon = 1E-8
def test_distance_crit_periodic(self):
dc = pair_criteria.DistanceCriterion(cut_off=0.1)
# Interface
self.assertEqual(list(dc.get_params().keys()), ["cut_off", ])
self.assertTrue(abs(dc.get_params()["cut_off"] - 0.1) < self.epsilon)
# Decisions
# Periodic system. Particles in range via minimum image convention
self.es.periodicity = (1, 1, 1)
self.assertTrue(dc.decide(self.p1, self.p2))
self.assertTrue(dc.decide(self.p1.id, self.p2.id))
@utx.skipIfMissingFeatures("PARTIAL_PERIODIC")
def test_distance_crit_non_periodic(self):
dc = pair_criteria.DistanceCriterion(cut_off=0.1)
# Non-periodic system. Particles out of range
self.es.periodicity = (0, 0, 0)
self.assertTrue(not dc.decide(self.p1, self.p2))
self.assertTrue(not dc.decide(self.p1.id, self.p2.id))
@utx.skipIfMissingFeatures("LENNARD_JONES")
def test_energy_crit(self):
# Setup purely repulsive lj
self.es.non_bonded_inter[0, 0].lennard_jones.set_params(
sigma=0.11, epsilon=1, cutoff=2**(1. / 6.) * 0.11, shift="auto")
ec = pair_criteria.EnergyCriterion(cut_off=0.001)
# Interface
self.assertEqual(list(ec.get_params().keys()), ["cut_off", ])
self.assertTrue(abs(ec.get_params()["cut_off"] - 0.001) < self.epsilon)
# Decisions
# Periodic system. Particles in range via minimum image convention
self.es.periodicity = (1, 1, 1)
self.assertTrue(ec.decide(self.p1, self.p2))
self.assertTrue(ec.decide(self.p1.id, self.p2.id))
@utx.skipIfMissingFeatures(["LENNARD_JONES", "PARTIAL_PERIODIC"])
def test_energy_crit_non_periodic(self):
# Setup purely repulsive lj
self.es.non_bonded_inter[0, 0].lennard_jones.set_params(
sigma=0.11, epsilon=1, cutoff=2**(1. / 6.) * 0.11, shift="auto")
ec = pair_criteria.EnergyCriterion(cut_off=0.001)
# Interface
self.assertEqual(list(ec.get_params().keys()), ["cut_off", ])
self.assertTrue(abs(ec.get_params()["cut_off"] - 0.001) < self.epsilon)
# Non-periodic system. Particles out of range
self.es.periodicity = (0, 0, 0)
self.assertTrue(not ec.decide(self.p1, self.p2))
self.assertTrue(not ec.decide(self.p1.id, self.p2.id))
def test_bond_crit(self):
bc = pair_criteria.BondCriterion(bond_type=0)
# Interface
self.assertEqual(list(bc.get_params().keys()), ["bond_type", ])
self.assertEqual(bc.get_params()["bond_type"], 0)
# Decisions
# No bond yet. Should return false
self.assertTrue(not bc.decide(self.p1, self.p2))
self.assertTrue(not bc.decide(self.p1.id, self.p2.id))
# Add bond. Then the criterion should match
self.es.part[0].bonds = ((0, 1),)
self.assertTrue(bc.decide(self.p1, self.p2))
self.assertTrue(bc.decide(self.p1.id, self.p2.id))
# Place bond on the 2nd particle. The criterion should still match
self.es.part[0].bonds = ()
self.es.part[1].bonds = ((0, 0),)
self.assertTrue(bc.decide(self.p1, self.p2))
self.assertTrue(bc.decide(self.p1.id, self.p2.id))
class ParticleProperties(ut.TestCase):
# Particle id to work on
pid = 17
# Error tolerance when comparing arrays/tuples...
tol = 1E-9
# Handle for espresso system
system = espressomd.System(box_l=[100.0, 100.0, 100.0])
system.cell_system.skin = 0
system.time_step = 0.01
f1 = FeneBond(k=1, d_r_max=2)
system.bonded_inter.add(f1)
f2 = FeneBond(k=1, d_r_max=2)
system.bonded_inter.add(f2)
def setUp(self):
if not self.system.part.exists(self.pid):
self.system.part.add(id=self.pid, pos=(0, 0, 0))
def tearDown(self):
self.system.part.clear()
def generateTestForVectorProperty(_propName, _value):
"""Generates test cases for vectorial particle properties such as
position, velocity...
1st arg: name of the property (e.g., "pos"),
2nd array: value to be used for testing. Has to be numpy.array of floats
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.system.part[self.pid], propName, value)
np.testing.assert_allclose(
np.array(getattr(self.system.part[self.pid], propName)),
value,
err_msg=propName + ": value set and value gotten back differ.",
atol=self.tol)
return func
def generateTestForScalarProperty(_propName, _value):
"""Generates test cases for scalar particle properties such as
type, mass, charge...
1st arg: name of the property (e.g., "type"),
2nd array: value to be used for testing. int or float
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.system.part[self.pid], propName, value)
self.assertEqual(
getattr(self.system.part[self.pid], propName), value,
propName + ": value set and value gotten back differ.")
return func
test_pos = generateTestForVectorProperty("pos", np.array([0.1, 0.2, 0.3]))
test_v = generateTestForVectorProperty("v", np.array([0.2, 0.3, 0.4]))
test_f = generateTestForVectorProperty("f", np.array([0.2, 0.3, 0.7]))
test_type = generateTestForScalarProperty("type", int(3))
test_mol_id = generateTestForScalarProperty("mol_id", int(3))
test_bonds_property = generateTestForScalarProperty(
"bonds", ((f1, 1), (f2, 2)))
if espressomd.has_features(["MASS"]):
test_mass = generateTestForScalarProperty("mass", 1.3)
if espressomd.has_features(["ROTATION"]):
for x in 0, 1:
for y in 0, 1:
for z in 0, 1:
test_rotation = generateTestForVectorProperty(
"rotation", np.array([x, y, z], dtype=int))
test_omega_lab = generateTestForVectorProperty("omega_lab",
np.array([4., 2., 1.]))
test_omega_body = generateTestForVectorProperty(
"omega_body", np.array([4., 72., 1.]))
test_torque_lab = generateTestForVectorProperty(
"torque_lab", np.array([4., 72., 3.7]))
# The tested value has to be normalized!
test_quat = generateTestForVectorProperty(
"quat", np.array([0.5, 0.5, 0.5, 0.5]))
if espressomd.has_features(["LANGEVIN_PER_PARTICLE"]):
if espressomd.has_features(["PARTICLE_ANISOTROPY"]):
test_gamma = generateTestForVectorProperty(
"gamma", np.array([2., 9., 0.23]))
def test_gamma_single(self):
self.system.part[self.pid].gamma = 17.4
np.testing.assert_array_equal(
np.copy(self.system.part[self.pid].gamma),
np.array([17.4, 17.4, 17.4]),
"gamma: value set and value gotten back differ.")
else:
test_gamma = generateTestForScalarProperty("gamma", 17.3)
if espressomd.has_features(["PARTICLE_ANISOTROPY"]):
test_gamma_rot = generateTestForVectorProperty(
"gamma_rot", np.array([5., 10., 0.33]))
def test_gamma_rot_single(self):
self.system.part[self.pid].gamma_rot = 15.4
np.testing.assert_array_equal(
np.copy(self.system.part[self.pid].gamma_rot),
np.array([15.4, 15.4, 15.4]),
"gamma_rot: value set and value gotten back differ.")
else:
test_gamma_rot = generateTestForScalarProperty(
"gamma_rot", 14.23)
# test_director=generateTestForVectorProperty("director",
# np.array([0.5,0.4,0.3]))
if espressomd.has_features(["ELECTROSTATICS"]):
test_charge = generateTestForScalarProperty("q", -19.7)
if espressomd.has_features(["EXTERNAL_FORCES"]):
test_ext_force = generateTestForVectorProperty("ext_force",
[0.1, 0.2, 0.3])
test_fix = generateTestForVectorProperty("fix", [True, False, True])
if espressomd.has_features(["EXTERNAL_FORCES", "ROTATION"]):
test_ext_torque = generateTestForVectorProperty(
"ext_torque", [.4, .5, .6])
if espressomd.has_features(["DIPOLES"]):
test_dip = generateTestForVectorProperty("dip",
np.array([0.5, -0.5, 3]))
test_dipm = generateTestForScalarProperty("dipm", -9.7)
if espressomd.has_features(["VIRTUAL_SITES"]):
test_virtual = generateTestForScalarProperty("virtual", 1)
if espressomd.has_features(["VIRTUAL_SITES_RELATIVE"]):
def test_yy_vs_relative(self):
self.system.part.add(id=0, pos=(0, 0, 0))
self.system.part.add(id=1, pos=(0, 0, 0))
self.system.part[1].vs_relative = (0, 5.0, (0.5, -0.5, -0.5, -0.5))
self.system.part[1].vs_quat = [1, 2, 3, 4]
np.testing.assert_array_equal(self.system.part[1].vs_quat,
[1, 2, 3, 4])
res = self.system.part[1].vs_relative
self.assertEqual(res[0], 0, "vs_relative: " + res.__str__())
self.assertEqual(res[1], 5.0, "vs_relative: " + res.__str__())
np.testing.assert_allclose(res[2],
np.array((0.5, -0.5, -0.5, -0.5)),
err_msg="vs_relative: " + res.__str__(),
atol=self.tol)
@utx.skipIfMissingFeatures("DIPOLES")
def test_contradicting_properties_dip_dipm(self):
with self.assertRaises(ValueError):
self.system.part.add(pos=[0, 0, 0], dip=[1, 1, 1], dipm=1.0)
@utx.skipIfMissingFeatures(["DIPOLES", "ROTATION"])
def test_contradicting_properties_dip_quat(self):
with self.assertRaises(ValueError):
self.system.part.add(pos=[0, 0, 0],
dip=[1, 1, 1],
quat=[1.0, 1.0, 1.0, 1.0])
@utx.skipIfMissingFeatures("ELECTROSTATICS")
def test_particle_selection(self):
s = self.system
s.part.clear()
positions = ((0.2, 0.3, 0.4), (0.4, 0.2, 0.3), (0.7, 0.7, 0.7))
charges = [0, 1E-6, -1, 1]
# Place particles
i = 0
for pos in positions:
for q in charges:
s.part.add(pos=pos, q=q, id=i)
i += 1
# Scalar property
res = s.part.select(q=0)
self.assertEqual(len(res.id), len(positions))
for p in res:
self.assertAlmostEqual(p.q, 0, places=13)
# Vectorial property
res = s.part.select(pos=(0.2, 0.3, 0.4))
self.assertEqual(len(res.id), len(charges))
for p in res:
np.testing.assert_allclose((0.2, 0.3, 0.4),
np.copy(p.pos),
atol=1E-12)
# Two criteria
res = s.part.select(pos=(0.2, 0.3, 0.4), q=0)
self.assertEqual(tuple(res.id), (0, ))
# Empty result
res = s.part.select(q=17)
self.assertEqual(tuple(res.id), ())
# User-specified criterion
res = s.part.select(lambda p: p.pos[0] < 0.5)
self.assertEqual(tuple(sorted(res.id)), (0, 1, 2, 3, 4, 5, 6, 7))
def test_image_box(self):
s = self.system
s.part.clear()
pos = 1.5 * s.box_l
s.part.add(pos=pos)
np.testing.assert_equal(np.copy(s.part[0].image_box), [1, 1, 1])
def test_accessing_invalid_id_raises(self):
self.system.part.clear()
handle_to_non_existing_particle = self.system.part[42]
with self.assertRaises(RuntimeError):
handle_to_non_existing_particle.id
def test_parallel_property_setters(self):
s = self.system
s.part.clear()
s.part.add(pos=s.box_l * np.random.random((100, 3)))
# Copy individual properties of particle 0
print(
"If this test hangs, there is an mpi deadlock in a particle property setter."
)
for p in espressomd.particle_data.particle_attributes:
# Uncomment to identify guilty property
# print( p)
if not hasattr(s.part[0], p):
raise Exception(
"Inconsistency between ParticleHandle and particle_data.particle_attributes"
)
try:
setattr(s.part[:], p, getattr(s.part[0], p))
except AttributeError:
print("Skipping read-only", p)
# Cause a different mpi callback to uncover deadlock immediately
x = getattr(s.part[:], p)
def test_zz_remove_all(self):
for id in self.system.part[:].id:
self.system.part[id].remove()
self.system.part.add(pos=np.random.random(
(100, 3)) * self.system.box_l,
id=np.arange(100, dtype=int))
ids = self.system.part[:].id
np.random.shuffle(ids)
for id in ids:
self.system.part[id].remove()
with self.assertRaises(Exception):
self.system.part[17].remove()
def test_coord_fold_corner_cases(self):
system = self.system
system.time_step = .5
system.cell_system.set_domain_decomposition(use_verlet_lists=False)
system.cell_system.skin = 0
system.min_global_cut = 3
system.part.clear()
p1 = system.part.add(pos=3 * [np.nextafter(0., -1.)],
v=system.box_l / 3)
print(p1.pos)
p2 = system.part.add(pos=np.nextafter(system.box_l, 2 * system.box_l),
v=system.box_l / 3)
print(p2.pos)
p3 = system.part.add(pos=np.nextafter(system.box_l, (0, 0, 0)),
v=system.box_l / 3)
print(p3.pos)
p4 = system.part.add(pos=3 * [np.nextafter(0., 1.)],
v=system.box_l / 3)
print(p4.pos)
system.integrator.run(3)
for p in system.part:
for i in range(3):
self.assertGreaterEqual(p.pos_folded[i], 0)
self.assertLess(p.pos_folded[i], system.box_l[i])
# Force resort
system.part.add(pos=(0, 0, 0))
system.integrator.run(9)
for p in system.part:
for i in range(3):
self.assertGreaterEqual(p.pos_folded[i], 0)
self.assertLess(p.pos_folded[i], system.box_l[i])
class ClusterAnalysis(ut.TestCase):
"""Tests the cluster analysis"""
es = espressomd.System(box_l=(1, 1, 1))
f = FeneBond(k=1, d_r_max=0.05)
es.bonded_inter.add(f)
# Firt cluster
es.part.add(id=0, pos=(0, 0, 0))
es.part.add(id=1, pos=(0.91, 0, 0), bonds=((0, 0), ))
es.part.add(id=2, pos=(0, 0.2, 0))
es.part.add(id=3, pos=(0, 0.1, 0))
# 2nd cluster
es.part.add(id=4, pos=(0.5, 0.5, 0.5))
es.part.add(id=5, pos=(0.55, 0.5, 0.5))
cs = ClusterStructure()
np.random.seed(1)
# Setup check
handle_errors("")
def test_00_fails_without_criterion_set(self):
with (self.assertRaises(Exception)):
self.cs.run_for_all_pairs()
def test_set_criterion(self):
# Test setters/getters for criteria
dc = DistanceCriterion(cut_off=0.11)
self.cs.set_params(pair_criterion=dc)
# Do we get back the right criterion
dc_ret = self.cs.get_params()["pair_criterion"]
# Note: This work around the fact that the script interface does not
# yet assign the correct derived class when returning an object
self.assertEqual(dc_ret.name(), "PairCriteria::DistanceCriterion")
self.assertAlmostEqual(dc_ret.get_params()["cut_off"], 0.11, places=7)
# Is the cluster structure empty before being used
def test_analysis_for_all_pairs(self):
# Run cluster analysis
self.cs.set_params(pair_criterion=DistanceCriterion(cut_off=0.12))
self.cs.run_for_all_pairs()
# Number of clusters
self.assertEqual(len(self.cs.clusters), 2)
cids = self.cs.cluster_ids()
# Sizes of individual clusters
l2 = self.cs.clusters[cids[1]].size()
l1 = len(self.cs.clusters[cids[0]].particle_ids())
# Clusters should contain 2 and 4 particles
self.assertEqual(min(l1, l2), 2)
self.assertEqual(max(l1, l2), 4)
# Verify particle ids
smaller_cluster = None
bigger_cluster = None
if l1 < l2:
smaller_cluster = self.cs.clusters[cids[0]]
bigger_cluster = self.cs.clusters[cids[1]]
else:
smaller_cluster = self.cs.clusters[cids[1]]
bigger_cluster = self.cs.clusters[cids[0]]
self.assertEqual(bigger_cluster.particle_ids(), [0, 1, 2, 3])
self.assertEqual(smaller_cluster.particle_ids(), [4, 5])
# Test obtaining a ParticleSlice for a cluster
pids = bigger_cluster.particle_ids()
particles = bigger_cluster.particles()
# Do the number of entries match
self.assertEqual(len(pids), len(particles.id_selection))
# Compare ids of particles in the slice
self.assertEqual(all(particles.id_selection), all(pids))
# Test iteration over clusters
visited_sizes = []
for c in self.cs.clusters:
visited_sizes.append(c[1].size())
visited_sizes = sorted(visited_sizes)
self.assertEqual(visited_sizes, [2, 4])
def test_zz_single_cluster_analysis(self):
self.es.part.clear()
# Place particles on a line (crossing periodic boundaries)
for x in np.arange(-0.2, 0.21, 0.01):
self.es.part.add(pos=(x, 1.1 * x, 1.2 * x))
self.cs.pair_criterion = DistanceCriterion(cut_off=0.13)
self.cs.run_for_all_pairs()
self.assertEqual(len(self.cs.clusters), 1)
for c in self.cs.clusters:
# Discard cluster id
c = c[1]
# Center of mass should be at origin
self.assertTrue(
np.sqrt(np.sum(np.array(c.center_of_mass())**2)) <= 1E-8)
# Longest distance
self.assertTrue(
abs(c.longest_distance() -
self.es.distance(self.es.part[0], self.es.part[
len(self.es.part) - 1])) <= 1E-8)
# Radius of gyration
rg = 0.
com_particle = self.es.part[len(self.es.part) / 2]
for p in c.particles():
rg += self.es.distance(p, com_particle)**2
rg /= len(self.es.part)
rg = np.sqrt(rg)
self.assertTrue(abs(c.radius_of_gyration() - rg) <= 1E-6)
# Fractal dimension calc require gsl
if not espressomd.has_features("GSL"):
print("Skipping fractal dimension tests for lack of GSL")
return
# The fractal dimension of a line should be 1
dr = 0.
self.assertAlmostEqual(c.fractal_dimension(dr=dr)[0],
1,
delta=0.05)
# Fractal dimension of a disk should be close to 2
self.es.part.clear()
center = np.array((0.1, .02, 0.15))
for i in range(3000):
r_inv, phi = np.random.random(2) * np.array((0.2, 2 * np.pi))
r = 1 / r_inv
self.es.part.add(pos=center +
r * np.array((np.sin(phi), np.cos(phi), 0)))
self.cs.clear()
self.cs.run_for_all_pairs()
cid = self.cs.cluster_ids()[0]
df = self.cs.clusters[cid].fractal_dimension(dr=0.001)
self.assertAlmostEqual(df[0], 2, delta=0.08)
def test_analysis_for_bonded_particles(self):
# Run cluster analysis
self.cs.set_params(pair_criterion=BondCriterion(bond_type=0))
self.cs.run_for_bonded_particles()
# There should be one cluster containing particles 0 and 1
self.assertEqual(len(self.cs.clusters), 1)
self.assertEqual(
self.cs.clusters[self.cs.cluster_ids()[0]].particle_ids(), [0, 1])
# Check particle to cluster id mapping, once by ParticleHandle, once by id
self.assertEqual(self.cs.cid_for_particle(self.es.part[0]),
self.cs.cluster_ids()[0])
self.assertEqual(self.cs.cid_for_particle(1), self.cs.cluster_ids()[0])
def setUp(self):
self.es.part[self.pid].pos = 0, 0, 0
self.es.bondedInter[0] = FeneBond(k=1, d_r_max=5)
self.es.bondedInter[1] = FeneBond(k=1, d_r_max=5)
class ParticleProperties(ut.TestCase):
# Particle id to work on
pid = 17
# Error tolerance when comparing arrays/tuples...
tol = 1E-9
# Handle for espresso system
es = espressomd.System()
f1 = FeneBond(k=1, d_r_max=5)
es.bonded_inter.add(f1)
f2 = FeneBond(k=1, d_r_max=5)
es.bonded_inter.add(f2)
def arraysNearlyEqual(self, a, b):
"""Test, if the magnitude of the difference between two arrays is smaller than the tolerance"""
# Check length
if len(a) != len(b):
return False
# We have to use a loop, since we can't be sure, we're getting numpy
# arrays
sum = 0.
for i in range(len(a)):
sum += abs(a[i] - b[i])
if sum > self.tol:
return False
return True
def setUp(self):
if not self.es.part.exists(self.pid):
self.es.part.add(id=self.pid, pos=(0, 0, 0))
def generateTestForVectorProperty(_propName, _value):
"""Generates test cases for vectorial particle properties such as
position, velocity...
1st arg: name of the property (e.g., "pos"),
2nd array: value to be used for testing. Has to be numpy.array of floats
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.es.part[self.pid], propName, value)
self.assertTrue(
self.arraysNearlyEqual(
getattr(self.es.part[self.pid], propName), value),
propName + ": value set and value gotten back differ.")
return func
def generateTestForScalarProperty(_propName, _value):
"""Generates test cases for scalar particle properties such as
type, mass, charge...
1st arg: name of the property (e.g., "type"),
2nd array: value to be used for testing. int or float
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.es.part[self.pid], propName, value)
self.assertTrue(
getattr(self.es.part[self.pid], propName) == value,
propName + ": value set and value gotten back differ.")
return func
test_pos = generateTestForVectorProperty("pos", np.array([0.1, 0.2, 0.3]))
test_v = generateTestForVectorProperty("v", np.array([0.2, 0.3, 0.4]))
test_f = generateTestForVectorProperty("f", np.array([0.2, 0.3, 0.7]))
test_type = generateTestForScalarProperty("type", int(3))
test_bonds_property = generateTestForScalarProperty(
"bonds", ((f1, 1), (f2, 2)))
if "MASS" in espressomd.features():
test_mass = generateTestForScalarProperty("mass", 1.3)
if "ROTATION" in espressomd.features():
test_omega_lab = generateTestForVectorProperty("omega_lab",
np.array([4., 2., 1.]))
test_omega_body = generateTestForVectorProperty(
"omega_body", np.array([4., 72., 1.]))
test_torque_lab = generateTestForVectorProperty(
"torque_lab", np.array([4., 72., 3.7]))
# The tested value has to be normalized!
test_quat = generateTestForVectorProperty(
"quat", np.array([0.5, 0.5, 0.5, 0.5]))
if "ROTATIONAL_INERTIA" in espressomd.features():
test_gamma_rot = generateTestForVectorProperty(
"gamma_rot", np.array([5., 10., 0.33]))
else:
test_gamma_rot = generateTestForScalarProperty("gamma_rot", 14.23)
# test_director=generateTestForVectorProperty("director",np.array([0.5,0.4,0.3]))
if "ELECTROSTATICS" in espressomd.features():
test_charge = generateTestForScalarProperty("q", -19.7)
if "DIPOLES" in espressomd.features():
test_dip = generateTestForVectorProperty("dip",
np.array([0.5, -0.5, 3]))
test_dipm = generateTestForScalarProperty("dipm", -9.7)
if "VIRTUAL_SITES" in espressomd.features():
test_virtual = generateTestForScalarProperty("virtual", 1)
if "VIRTUAL_SITES_RELATIVE" in espressomd.features():
def test_zz_vs_relative(self):
self.es.part.add(id=0, pos=(0, 0, 0))
self.es.part.add(id=1, pos=(0, 0, 0))
self.es.part[1].vs_relative = (0, 5.0, (0.5, -0.5, -0.5, -0.5))
res = self.es.part[1].vs_relative
self.assertTrue(
res[0] == 0 and res[1] == 5.0 and self.arraysNearlyEqual(
res[2], np.array((0.5, -0.5, -0.5, -0.5))),
"vs_relative: " + res.__str__())
def test_fene(self):
# system parameters
system.box_l = 3 * [10.0]
skin = 0.4
time_step = 0.01
system.time_step = time_step
# thermostat and cell system
system.cell_system.skin = skin
system.periodicity = [1, 1, 1]
# particles and bond
p0 = system.part.add(pos=[9.9, 9.75, 9.9],
type=0,
mol_id=0,
fix=[1, 1, 1])
p1 = system.part.add(pos=[9.9, 10.25, 9.9],
type=0,
mol_id=0,
fix=[1, 1, 1])
k = 1e4
d_r_max = 1.5
r_0 = 0.1
fene = FeneBond(k=k, d_r_max=d_r_max, r_0=r_0)
system.bonded_inter.add(fene)
p0.add_bond((fene, p1))
system.integrator.run(steps=0)
sim_pressure_tensor = system.analysis.pressure_tensor()
sim_pressure_tensor_bonded = sim_pressure_tensor['bonded']
sim_pressure_tensor_fene = sim_pressure_tensor[
'bonded', len(system.bonded_inter) - 1]
total_bonded_pressure_tensor = np.zeros([3, 3])
for i in range(len(system.bonded_inter)):
total_bonded_pressure_tensor += sim_pressure_tensor['bonded', i]
anal_pressure_tensor_fene = self.get_anal_pressure_tensor_fene(
p0.pos, p1.pos, k, d_r_max, r_0)
np.testing.assert_allclose(
sim_pressure_tensor_bonded,
anal_pressure_tensor_fene,
atol=tol,
err_msg='bonded pressure tensor does not match analytical result')
np.testing.assert_allclose(
sim_pressure_tensor_fene,
anal_pressure_tensor_fene,
atol=tol,
err_msg=
'bonded pressure tensor for fene does not match analytical result')
np.testing.assert_allclose(
sim_pressure_tensor_bonded,
total_bonded_pressure_tensor,
atol=tol,
err_msg='bonded pressure tensor do not sum up to the total value')
sim_pressure = system.analysis.pressure()
sim_pressure_fene = sim_pressure['bonded',
len(system.bonded_inter) - 1]
anal_pressure_fene = np.einsum("ii", anal_pressure_tensor_fene) / 3.0
np.testing.assert_allclose(
sim_pressure_fene,
anal_pressure_fene,
atol=tol,
err_msg='bonded pressure for fene does not match analytical result'
)
# Compare pressure observables to pressure from analysis
np.testing.assert_allclose(PressureTensor().calculate(),
sim_pressure_tensor["total"],
rtol=0,
atol=1E-10)
self.assertAlmostEqual(Pressure().calculate(),
sim_pressure["total"],
delta=tol)
class ParticleProperties(ut.TestCase):
# Particle id to work on
pid = 17
# Error tolerance when comparing arrays/tuples...
tol = 1E-9
# Handle for espresso system
system = espressomd.System(box_l=[100.0, 100.0, 100.0])
system.cell_system.skin = 0
system.time_step = 0.01
f1 = FeneBond(k=1, d_r_max=2)
system.bonded_inter.add(f1)
f2 = FeneBond(k=1, d_r_max=2)
system.bonded_inter.add(f2)
def setUp(self):
if not self.system.part.exists(self.pid):
self.system.part.add(id=self.pid, pos=(0, 0, 0))
def tearDown(self):
self.system.part.clear()
def generateTestForVectorProperty(_propName, _value):
"""Generates test cases for vectorial particle properties such as
position, velocity...
1st arg: name of the property (e.g., "pos"),
2nd array: value to be used for testing. Has to be numpy.array of floats
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.system.part[self.pid], propName, value)
np.testing.assert_allclose(
np.array(getattr(self.system.part[self.pid], propName)), value,
err_msg=propName + ": value set and value gotten back differ.",
atol=self.tol)
return func
def generateTestForScalarProperty(_propName, _value):
"""Generates test cases for scalar particle properties such as
type, mass, charge...
1st arg: name of the property (e.g., "type"),
2nd array: value to be used for testing. int or float
"""
# This is executed, when generateTestForVectorProperty() is called
propName = _propName
value = _value
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
setattr(self.system.part[self.pid], propName, value)
self.assertEqual(getattr(self.system.part[self.pid], propName),
value, propName + ": value set and value gotten back differ.")
return func
test_pos = generateTestForVectorProperty("pos", np.array([0.1, 0.2, 0.3]))
test_v = generateTestForVectorProperty("v", np.array([0.2, 0.3, 0.4]))
test_f = generateTestForVectorProperty("f", np.array([0.2, 0.3, 0.7]))
test_type = generateTestForScalarProperty("type", int(3))
test_mol_id = generateTestForScalarProperty("mol_id", int(3))
test_bonds_property = generateTestForScalarProperty(
"bonds", ((f1, 1), (f2, 2)))
if espressomd.has_features(["MASS"]):
test_mass = generateTestForScalarProperty("mass", 1.3)
if espressomd.has_features(["ROTATION"]):
for x in 0, 1:
for y in 0, 1:
for z in 0, 1:
test_rotation = generateTestForVectorProperty(
"rotation", np.array([x, y, z], dtype=int))
test_omega_lab = generateTestForVectorProperty(
"omega_lab", np.array([4., 2., 1.]))
test_omega_body = generateTestForVectorProperty(
"omega_body", np.array([4., 72., 1.]))
test_torque_lab = generateTestForVectorProperty(
"torque_lab", np.array([4., 72., 3.7]))
# The tested value has to be normalized!
test_quat = generateTestForVectorProperty(
"quat", np.array([0.5, 0.5, 0.5, 0.5]))
def test_director(self):
"""
Test `director`. When set, it should get normalized.
"""
sample_vector = np.array([0.5, -0.4, 1.3])
sample_vector_normalized = sample_vector / \
np.linalg.norm(sample_vector)
setattr(self.system.part[self.pid], "director", sample_vector)
np.testing.assert_allclose(
np.array(getattr(self.system.part[self.pid], "director")),
sample_vector_normalized
)
if espressomd.has_features(["THERMOSTAT_PER_PARTICLE"]):
if espressomd.has_features(["PARTICLE_ANISOTROPY"]):
test_gamma = generateTestForVectorProperty(
"gamma", np.array([2., 9., 0.23]))
def test_gamma_single(self):
self.system.part[self.pid].gamma = 17.4
np.testing.assert_array_equal(
np.copy(self.system.part[self.pid].gamma),
np.array([17.4, 17.4, 17.4]),
"gamma: value set and value gotten back differ.")
else:
test_gamma = generateTestForScalarProperty("gamma", 17.3)
if espressomd.has_features(["PARTICLE_ANISOTROPY"]):
test_gamma_rot = generateTestForVectorProperty(
"gamma_rot", np.array([5., 10., 0.33]))
def test_gamma_rot_single(self):
self.system.part[self.pid].gamma_rot = 15.4
np.testing.assert_array_equal(
np.copy(self.system.part[self.pid].gamma_rot),
np.array([15.4, 15.4, 15.4]),
"gamma_rot: value set and value gotten back differ.")
else:
test_gamma_rot = generateTestForScalarProperty(
"gamma_rot", 14.23)
if espressomd.has_features(["ELECTROSTATICS"]):
test_charge = generateTestForScalarProperty("q", -19.7)
if espressomd.has_features(["EXTERNAL_FORCES"]):
test_ext_force = generateTestForVectorProperty(
"ext_force", [0.1, 0.2, 0.3])
test_fix = generateTestForVectorProperty("fix", [True, False, True])
if espressomd.has_features(["EXTERNAL_FORCES", "ROTATION"]):
test_ext_torque = generateTestForVectorProperty(
"ext_torque", [.4, .5, .6])
if espressomd.has_features(["DIPOLES"]):
test_dip = generateTestForVectorProperty(
"dip", np.array([0.5, -0.5, 3]))
test_dipm = generateTestForScalarProperty("dipm", -9.7)
if espressomd.has_features(["VIRTUAL_SITES"]):
test_virtual = generateTestForScalarProperty("virtual", 1)
if espressomd.has_features(["VIRTUAL_SITES_RELATIVE"]):
def test_yy_vs_relative(self):
self.system.part.add(id=0, pos=(0, 0, 0))
self.system.part.add(id=1, pos=(0, 0, 0))
self.system.part[1].vs_relative = (0, 5.0, (0.5, -0.5, -0.5, -0.5))
self.system.part[1].vs_quat = [1, 2, 3, 4]
np.testing.assert_array_equal(
self.system.part[1].vs_quat, [1, 2, 3, 4])
res = self.system.part[1].vs_relative
self.assertEqual(res[0], 0, "vs_relative: " + res.__str__())
self.assertEqual(res[1], 5.0, "vs_relative: " + res.__str__())
np.testing.assert_allclose(
res[2], np.array((0.5, -0.5, -0.5, -0.5)),
err_msg="vs_relative: " + res.__str__(), atol=self.tol)
# check exceptions
with self.assertRaisesRegex(ValueError, "needs input in the form"):
self.system.part[1].vs_relative = (0, 5.0)
with self.assertRaisesRegex(ValueError, "particle id has to be given as an int"):
self.system.part[1].vs_relative = ('0', 5.0, (1, 0, 0, 0))
with self.assertRaisesRegex(ValueError, "distance has to be given as a float"):
self.system.part[1].vs_relative = (0, '5', (1, 0, 0, 0))
with self.assertRaisesRegex(ValueError, "quaternion has to be given as a tuple of 4 floats"):
self.system.part[1].vs_relative = (0, 5.0, (1, 0, 0))
@utx.skipIfMissingFeatures("DIPOLES")
def test_contradicting_properties_dip_dipm(self):
with self.assertRaises(ValueError):
self.system.part.add(pos=[0, 0, 0], dip=[1, 1, 1], dipm=1.0)
@utx.skipIfMissingFeatures(["DIPOLES", "ROTATION"])
def test_contradicting_properties_dip_quat(self):
with self.assertRaises(ValueError):
self.system.part.add(pos=[0, 0, 0], dip=[1, 1, 1],
quat=[1.0, 1.0, 1.0, 1.0])
@utx.skipIfMissingFeatures("ELECTROSTATICS")
def test_particle_selection(self):
s = self.system
s.part.clear()
positions = ((0.2, 0.3, 0.4), (0.4, 0.2, 0.3), (0.7, 0.7, 0.7))
charges = [0, 1E-6, -1, 1]
# Place particles
i = 0
for pos in positions:
for q in charges:
s.part.add(pos=pos, q=q, id=i)
i += 2
# Scalar property
res = s.part.select(q=0)
self.assertEqual(len(res.id), len(positions))
for p in res:
self.assertAlmostEqual(p.q, 0, places=13)
# Vectorial property
res = s.part.select(pos=(0.2, 0.3, 0.4))
self.assertEqual(len(res.id), len(charges))
for p in res:
np.testing.assert_allclose(
(0.2, 0.3, 0.4), np.copy(p.pos), atol=1E-12)
# Two criteria
res = s.part.select(pos=(0.2, 0.3, 0.4), q=0)
self.assertEqual(tuple(res.id), (0,))
# Empty result
res = s.part.select(q=17)
self.assertEqual(tuple(res.id), ())
# User-specified criterion
res = s.part.select(lambda p: p.pos[0] < 0.5)
np.testing.assert_equal(sorted(res.id), np.arange(0, 16, 2, dtype=int))
def test_image_box(self):
s = self.system
s.part.clear()
pos = 1.5 * s.box_l
s.part.add(pos=pos)
np.testing.assert_equal(np.copy(s.part[0].image_box), [1, 1, 1])
def test_accessing_invalid_id_raises(self):
self.system.part.clear()
handle_to_non_existing_particle = self.system.part[42]
with self.assertRaises(RuntimeError):
handle_to_non_existing_particle.id
def test_parallel_property_setters(self):
s = self.system
s.part.clear()
s.part.add(pos=s.box_l * np.random.random((100, 3)))
# Copy individual properties of particle 0
print(
"If this test hangs, there is an mpi deadlock in a particle property setter.")
for p in espressomd.particle_data.particle_attributes:
# Uncomment to identify guilty property
# print( p)
if not hasattr(s.part[0], p):
raise Exception(
"Inconsistency between ParticleHandle and particle_data.particle_attributes")
try:
setattr(s.part[:], p, getattr(s.part[0], p))
except AttributeError:
print("Skipping read-only", p)
# Cause a different mpi callback to uncover deadlock immediately
_ = getattr(s.part[:], p)
def test_remove_particle(self):
"""Tests that if a particle is removed,
it no longer exists and bonds to the removed particle are
also removed."""
p1 = self.system.part[self.pid]
p2 = self.system.part.add(pos=p1.pos, bonds=[(self.f1, p1.id)])
p1.remove()
self.assertFalse(self.system.part.exists(self.pid))
self.assertEqual(len(p2.bonds), 0)
def test_bonds(self):
"""Tests bond addition and removal."""
p1 = self.system.part[self.pid]
p2 = self.system.part.add(pos=p1.pos)
inactive_bond = FeneBond(k=1, d_r_max=2)
p2.add_bond([self.f1, p1])
with self.assertRaisesRegex(RuntimeError, "already exists on particle"):
p2.add_bond([self.f1, p1.id])
with self.assertRaisesRegex(RuntimeError, "already exists on particle"):
p2.add_bond((self.f1, p1))
with self.assertRaisesRegex(Exception, "1st element of Bond has to be of type BondedInteraction or int"):
p2.add_bond(('self.f1', p1))
with self.assertRaisesRegex(ValueError, "Bond partners have to be of type integer or ParticleHandle"):
p2.add_bond((self.f1, '1'))
with self.assertRaisesRegex(ValueError, r"Bond FeneBond\(.+?\) needs 1 partner"):
p2.add_bond((self.f1, p1, p2))
with self.assertRaisesRegex(Exception, "The bonded interaction has not yet been added to the list of active bonds in ESPResSo"):
p2.add_bond((inactive_bond, p1))
p2.delete_bond([self.f1, p1])
with self.assertRaisesRegex(RuntimeError, "doesn't exist on particle"):
p2.delete_bond([self.f1, p1])
with self.assertRaisesRegex(ValueError, "Bond partners have to be of type integer or ParticleHandle"):
p2.delete_bond((self.f1, 'p1'))
def test_zz_remove_all(self):
for id in self.system.part[:].id:
self.system.part[id].remove()
self.system.part.add(
pos=np.random.random((100, 3)) * self.system.box_l,
id=np.arange(100, dtype=int))
ids = self.system.part[:].id
np.random.shuffle(ids)
for id in ids:
self.system.part[id].remove()
with self.assertRaises(Exception):
self.system.part[17].remove()
def test_coord_fold_corner_cases(self):
system = self.system
system.time_step = .5
system.cell_system.set_domain_decomposition(use_verlet_lists=False)
system.cell_system.skin = 0
system.min_global_cut = 3
system.part.clear()
p1 = system.part.add(
pos=3 * [np.nextafter(0., -1.)], v=system.box_l / 3)
print(p1.pos)
p2 = system.part.add(
pos=np.nextafter(system.box_l, 2 * system.box_l), v=system.box_l / 3)
print(p2.pos)
p3 = system.part.add(
pos=np.nextafter(system.box_l, (0, 0, 0)), v=system.box_l / 3)
print(p3.pos)
p4 = system.part.add(
pos=3 * [np.nextafter(0., 1.)], v=system.box_l / 3)
print(p4.pos)
system.integrator.run(3)
for p in system.part:
for i in range(3):
self.assertGreaterEqual(p.pos_folded[i], 0)
self.assertLess(p.pos_folded[i], system.box_l[i])
# Force resort
system.part.add(pos=(0, 0, 0))
system.integrator.run(9)
for p in system.part:
for i in range(3):
self.assertGreaterEqual(p.pos_folded[i], 0)
self.assertLess(p.pos_folded[i], system.box_l[i])
def test_particle_slice(self):
"""Tests operations on slices of particles"""
system = self.system
# Empty slice
system.part.clear()
self.assertEqual(len(system.part[:]), 0)
self.assertEqual(len(system.part[:].pos), 0)
self.assertEqual(len(system.part[:].id), 0)
with self.assertRaises(AttributeError):
system.part[:].pos = ((1, 2, 3,),)
# Slice containing particles
ids = [1, 4, 6, 3, 8, 9]
pos = np.random.random((len(ids), 3))
system.part.add(id=ids, pos=pos)
# All particles
self.assertEqual(len(system.part[:]), len(ids))
np.testing.assert_equal(system.part[:].id, sorted(ids))
np.testing.assert_equal(system.part[:].pos, pos[np.argsort(ids)])
# Access via slicing
np.testing.assert_equal(system.part[4:9].id,
[i for i in sorted(ids) if i >= 4 and i < 9])
np.testing.assert_equal(system.part[9:4:-1].id,
[i for i in sorted(ids, key=lambda i:-i) if i > 4 and i <= 9])
# Check that negative start and end on slices are not accepted
with self.assertRaises(IndexError):
system.part[-1:]
with self.assertRaises(IndexError):
system.part[:-1]
# Setting particle properties on a slice
system.part[:5].pos = 0, 0, 0
np.testing.assert_equal(system.part[:].pos,
[pos[i] if ids[i] >= 5 else [0, 0, 0] for i in np.argsort(ids)])
# Slice access via explicit list of ids
np.testing.assert_equal(system.part[ids[1:4]].id, ids[1:4])
# Check that ids passed in an explicit list must exist
with self.assertRaises(IndexError):
system.part[99, 3]
# Check that wrong types are not accepted
with self.assertRaises(TypeError):
system.part[[ids[0], 1.2]]
def test_to_dict(self):
self.system.part.clear()
p = self.system.part.add(
pos=np.random.uniform(size=(10, 3)) * self.system.box_l)
pp = str(p)
pdict = p.to_dict()
p.remove()
self.system.part.add(pdict)
self.assertEqual(str(self.system.part.select()), pp)