def test_serialization():
model, old = ufed_model()
pipe = io.StringIO()
ufedmm.serialize(old, pipe)
pipe.seek(0)
new = ufedmm.deserialize(pipe)
assert new.__repr__() == old.__repr__()
for var1, var2 in zip(old.variables, new.variables):
assert var1.__repr__() == var2.__repr__()
dt = 2 * unit.femtoseconds
nsteps = 1000000
mass = 30 * unit.dalton * (unit.nanometer / unit.radians)**2
Ks = 1000 * unit.kilojoules_per_mole / unit.radians**2
Ts = 1500 * unit.kelvin
limit = 180 * unit.degrees
sigma = 18 * unit.degrees
height = 2.0 * unit.kilojoules_per_mole
deposition_period = 200
phi = ufedmm.CollectiveVariable('phi', model.phi, -limit, limit, mass, Ks, Ts,
sigma)
psi = ufedmm.CollectiveVariable('psi', model.psi, -limit, limit, mass, Ks, Ts,
sigma)
ufed = ufedmm.UnifiedFreeEnergyDynamics([phi, psi], temp, height,
deposition_period)
ufedmm.serialize(ufed, 'ufed_object.yml')
integrator = ufedmm.GeodesicBAOABIntegrator(temp, gamma, dt)
integrator.setRandomNumberSeed(seed)
platform = openmm.Platform.getPlatformByName(args.platform)
simulation = ufed.simulation(model.topology, model.system, integrator,
platform)
ufed.set_positions(simulation, model.positions)
ufed.set_random_velocities(simulation, seed)
output = ufedmm.MultipleFiles(stdout, 'output.csv')
reporter = ufedmm.StateDataReporter(output,
100,
ufed.driving_force,
step=True,
speed=True)
simulation.reporters.append(reporter)
simulation.step(nsteps)