def make_mstis_engine():
pes = (
toys.OuterWalls([1.0, 1.0], [0.0, 0.0])
+ toys.Gaussian(-0.7, [12.0, 12.0], [0.0, 0.4])
+ toys.Gaussian(-0.7, [12.0, 12.0], [-0.5, -0.5])
+ toys.Gaussian(-0.7, [12.0, 12.0], [0.5, -0.5])
)
topology=toys.Topology(
n_spatial=2,
masses=[1.0, 1.0],
pes=pes
)
integ = toys.LangevinBAOABIntegrator(dt=0.02, temperature=0.1, gamma=2.5)
options={
'integ': integ,
'n_frames_max': 5000,
'n_steps_per_frame': 1
}
toy_eng = toys.Engine(
options=options,
topology=topology
).named('toy_engine')
template = toys.Snapshot(
coordinates=np.array([[-0.5, -0.5]]),
velocities=np.array([[0.0,0.0]]),
engine=toy_eng
)
toy_eng.current_snapshot = template
return toy_eng
def make_mistis_engine():
pes = (
toys.OuterWalls([1.0, 1.0], [0.0, 0.0])
+ toys.Gaussian(-1.0, [12.0, 12.0], [-0.5, 0.5])
+ toys.Gaussian(-1.0, [12.0, 12.0], [-0.5, -0.5])
+ toys.Gaussian(-1.0, [12.0, 12.0], [0.5, -0.5])
)
topology=toys.Topology(n_spatial=2,
masses=[1.0, 1.0],
pes=pes)
integ = toys.LangevinBAOABIntegrator(dt=0.02, temperature=0.1, gamma=2.5)
options = {
'integ': integ,
'n_frames_max': 5000,
'n_steps_per_frame': 1
}
toy_eng = toys.Engine(
options=options,
topology=topology
).named('engine')
return toy_eng
def setUp(self):
pes = linear
integ = toy.LangevinBAOABIntegrator(dt=0.002, temperature=0.5,
gamma=1.0)
topology=toy.Topology(
n_spatial = 2,
masses = sys_mass,
pes = pes
)
options={
'integ' : integ,
'n_frames_max' : 5}
sim = toy.Engine(options=options,
topology=topology
)
template = toy.Snapshot(
coordinates=init_pos.copy(),
velocities=init_pos.copy(),
engine=sim
)
sim.positions = init_pos.copy()
sim.velocities = init_vel.copy()
sim.n_steps_per_frame = 10
self.sim = sim
def setup(self):
integ = toys.LangevinBAOABIntegrator(dt=0.002,
temperature=1.0,
gamma=2.5)
options = {'integ': integ, 'n_frames_max': 5}
topology_2D = toys.Topology(n_spatial=2, masses=[1.0], pes=None)
engine_2D = toys.Engine(options=options, topology=topology_2D)
self.snap_2D = toys.Snapshot(coordinates=np.array([[0.0, 0.0]]),
velocities=np.array([[2.0, 4.0]]),
engine=engine_2D)
topology_6D = toys.Topology(n_spatial=3,
n_atoms=2,
masses=[1.0, 2.0],
pes=None)
engine_6D = toys.Engine(options=options, topology=topology_6D)
self.snap_6D = toys.Snapshot(coordinates=np.array([[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0]]),
velocities=np.array([[1.0, 0.0, 0.0],
[1.0, 0.0, 0.0]]),
engine=engine_6D)
parser = argparse.ArgumentParser()
parser.add_argument('--nsteps', type=int, default=10000)
return parser
parser = make_parser()
opts = parser.parse_args()
n_steps = opts.nsteps
pes = (toys.OuterWalls([1.0,1.0], [0.0,0.0])
+ toys.Gaussian(-0.7, [30.0, 0.5], [-0.6, 0.0])
+ toys.Gaussian(-0.7, [30.0, 0.5], [0.6, 0.0])
+ toys.Gaussian(0.5, [85.0, 70.0], [0.1, 0.0]))
topology = toys.Topology(n_spatial=2, masses=[1.0, 1.0], pes=pes)
engine = toys.Engine(
{'integ': toys.LangevinBAOABIntegrator(dt=0.02,
temperature=0.1,
gamma=2.5),
'n_frames_max': 5000,
'n_steps_per_frame': 10}, topology)
template = toys.Snapshot(coordinates=np.array([[0.0, 0.0]]),
velocities=np.array([[0.0, 0.0]]),
engine=engine)
def val(snapshot, index):
return snapshot.xyz[0][index]
cv_x = paths.FunctionCV("xval", val, index=0)
cv_y = paths.FunctionCV("yval", val, index=1)
stateA = paths.CVDefinedVolume(cv_x, float("-inf"), -0.6).named("A")
stateB = paths.CVDefinedVolume(cv_x, 0.6, float("inf")).named("B")