def setup(self):
pes = toys.HarmonicOscillator(A=[1.0], omega=[1.0], x0=[0.0])
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 100000,
'n_steps_per_frame': 2
}
self.engine = toys.Engine(options=options, topology=topology)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine)
cv = paths.FunctionCV("Id", lambda snap : snap.coordinates[0][0])
self.cv = cv
self.center = paths.CVDefinedVolume(cv, -0.2, 0.2)
self.interface = paths.CVDefinedVolume(cv, -0.3, 0.3)
self.outside = paths.CVDefinedVolume(cv, 0.6, 0.9)
self.extra = paths.CVDefinedVolume(cv, -1.5, -0.9)
self.flux_pairs = [(self.center, self.interface)]
self.sim = DirectSimulation(storage=None,
engine=self.engine,
states=[self.center, self.outside],
flux_pairs=self.flux_pairs,
initial_snapshot=self.snap0)
def setup_module():
# set up globals
global gaussian, linear, outer, harmonic
gaussian = toy.Gaussian(6.0, [2.5, 40.0], [0.8, 0.5])
outer = toy.OuterWalls([1.12, 2.0], [0.2, -0.25])
linear = toy.LinearSlope([1.5, 0.75], 0.5)
harmonic = toy.HarmonicOscillator([1.5, 2.0], [0.5, 3.0], [0.25, 0.75])
global init_pos, init_vel, sys_mass
init_pos = np.array([0.7, 0.65])
init_vel = np.array([0.6, 0.5])
sys_mass = np.array([1.5, 1.5])