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 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 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])
import openpathsampling.engines.toy as toys
import numpy as np
import argparse
def make_parser():
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]