def test_pickling(simulation_factory, two_particle_snapshot_factory):
"""Test that RemoveDrift objects are picklable."""
sim = simulation_factory(two_particle_snapshot_factory())
remove_drift = hoomd.update.RemoveDrift(trigger=hoomd.trigger.Periodic(5),
reference_positions=[(0, 0, 1),
(-1, 0, 1)])
operation_pickling_check(remove_drift, sim)
def test_pickling(simulation_factory, two_particle_snapshot_factory):
"""Test pickling `hoomd.tune.ParticleSorter`."""
sim = simulation_factory(two_particle_snapshot_factory())
# need to remove tuner since operation_pickling_check adds operation to
# simulation
sorter = sim.operations.tuners.pop()
operation_pickling_check(sorter, sim)
def test_pickling(box_move, simulation_factory, two_particle_snapshot_factory):
boxmc = hoomd.hpmc.update.BoxMC(betaP=hoomd.variant.Constant(3))
setattr(boxmc, box_move['move'], box_move['params'])
sim = simulation_factory(two_particle_snapshot_factory())
mc = hoomd.hpmc.integrate.Sphere()
mc.shape['A'] = dict(diameter=1)
sim.operations.integrator = mc
operation_pickling_check(boxmc, sim)
def test_pickling(simulation_factory, two_particle_snapshot_factory):
"""Test that QuickCompress objects are picklable."""
qc = hoomd.hpmc.update.QuickCompress(trigger=hoomd.trigger.Periodic(10),
target_box=hoomd.Box.square(10.))
sim = simulation_factory(two_particle_snapshot_factory())
mc = hoomd.hpmc.integrate.Sphere(default_d=0.05)
mc.shape['A'] = dict(diameter=1)
sim.operations.integrator = mc
operation_pickling_check(qc, sim)
def test_pickling(simulation_factory, two_particle_snapshot_factory):
"""Test that Cluster objects are picklable."""
sim = simulation_factory(two_particle_snapshot_factory())
mc = hoomd.hpmc.integrate.Sphere(default_d=0.1, default_a=0.1)
mc.shape['A'] = dict(diameter=1.1)
mc.shape['B'] = dict(diameter=1.3)
sim.operations.integrator = mc
cl = hoomd.hpmc.update.Clusters(trigger=hoomd.trigger.Periodic(5),
pivot_move_probability=0.1)
operation_pickling_check(cl, sim)
def test_pickling(lattice_snapshot_factory, simulation_factory):
"""Assert the minimizer can be pickled when attached/unattached."""
snap = lattice_snapshot_factory(a=1.5, n=5)
sim = simulation_factory(snap)
nve = md.methods.NVE(hoomd.filter.All())
fire = md.minimize.FIRE(dt=0.0025,
force_tol=1e-1,
angmom_tol=1e-1,
energy_tol=1e-5,
methods=[nve])
operation_pickling_check(fire, sim)
def test_pickling(valid_args, simulation_factory,
two_particle_snapshot_factory):
integrator = valid_args[0]
args = valid_args[1]
# Need to unpack union integrators
if isinstance(integrator, tuple):
inner_integrator = integrator[0]
integrator = integrator[1]
inner_mc = inner_integrator()
for i in range(len(args["shapes"])):
# This will fill in default values for the inner shape objects
inner_mc.shape["A"] = args["shapes"][i]
args["shapes"][i] = inner_mc.shape["A"]
mc = integrator()
mc.shape["A"] = args
# L needs to be ridiculously large as to not be too small for the domain
# decomposition of some of the shapes definitions in valid_args which have
# shapes with large extent in at least one dimension.
sim = simulation_factory(two_particle_snapshot_factory(L=1000))
operation_pickling_check(mc, sim)
def test_pickling(self, move_size_tuner, simulation):
operation_pickling_check(move_size_tuner, simulation)
def test_pickling(simulation_factory, two_particle_snapshot_factory, logger):
sim = simulation_factory(two_particle_snapshot_factory())
table = hoomd.write.Table(1, logger)
operation_pickling_check(table, sim)
def test_pickling(simulation_factory, two_particle_snapshot_factory, tmp_path):
filename = tmp_path / "temporary_test_file.dcd"
sim = simulation_factory(two_particle_snapshot_factory())
dcd_dump = hoomd.write.DCD(filename, hoomd.trigger.Periodic(1))
operation_pickling_check(dcd_dump, sim)
def test_pickling(simulation_factory, two_particle_snapshot_factory,
box_resize):
sim = simulation_factory(two_particle_snapshot_factory())
operation_pickling_check(box_resize, sim)
def test_pickling(integrator_cls, integrator_args, shape, simulation_factory,
two_particle_snapshot_factory):
mc = integrator_cls(**integrator_args)
mc.shape["A"] = shape
sim = simulation_factory(two_particle_snapshot_factory(L=1000))
operation_pickling_check(mc, sim)
def test_pickling(simulation_factory, two_particle_snapshot_factory):
filter_ = hoomd.filter.All()
thermo = hoomd.md.compute.ThermodynamicQuantities(filter_)
sim = simulation_factory(two_particle_snapshot_factory())
operation_pickling_check(thermo, sim)
def test_pickling(self, boxmc_with_tuner, simulation):
_, move_size_tuner = boxmc_with_tuner
operation_pickling_check(move_size_tuner, simulation)
