def test_step(self):
potent = pot.OneD.harmonicOscillatorPotential()
integrator = self.integrator_class()
sys = system.system(potential=potent, sampler=integrator)
old_pos, oldForce = sys._currentPosition, sys._currentForce
newPos, _, posShift = integrator.step(system=sys)
self.assertNotEqual(old_pos, newPos, msg="Nothing happened here!")
def test_twoD_simulation_ana_plot(self):
# settings
sim_steps = 100
pot2D = harmonicOscillatorPotential2D()
sampler = metropolisMonteCarloIntegrator()
sys = system(potential=pot2D, sampler=sampler, start_position=[0, 0])
# simulate
cur_state = sys.simulate(sim_steps, withdraw_traj=True)
plotSimulations.twoD_simulation_analysis_plot(system=sys)
def test_integrate(self):
potent = pot.OneD.harmonicOscillatorPotential()
integrator = self.integrator_class()
steps = 42
sys = system.system(potential=potent, sampler=integrator)
old_pos, oldForce = sys._currentPosition, sys._currentForce
integrator.integrate(system=sys, steps=steps)
new_pos, new_Force = sys._currentPosition, sys._currentForce
self.assertEqual(steps + 1, len(sys.trajectory), msg="The simulation did not run or was too short!")
self.assertNotEqual(old_pos, new_pos, msg="Nothing happened here!")
self.assertNotEqual(oldForce, new_Force, msg="Nothing happened here!")
from ensembler.samplers.stochastic import langevinIntegrator
from ensembler.system import system
from ensembler.visualisation.plotSimulations import oneD_simulation_analysis_plot
##Simulation Setup
V = fourWellPotential(Vmax=4,
a=1.5,
b=4.0,
c=7.0,
d=9.0,
ah=2.,
bh=0.,
ch=0.5,
dh=1.)
sampler = langevinIntegrator(dt=0.1, gamma=10)
sys = system(potential=V, sampler=sampler, start_position=4, temperature=1)
##Simulate
sys.simulate(steps=1000)
##Visualize
positions = np.linspace(start=0, stop=10,
num=1000) #phase space to be visualized
oneD_simulation_analysis_plot(system=sys,
title="Langevin Simulation",
limits_coordinate_space=positions)
#Local elevation/metadynamics simulation:
##Imports
from ensembler.potentials.OneD import fourWellPotential, metadynamicsPotential
from ensembler.samplers.stochastic import langevinIntegrator
def test_1D_animation(self):
sim = system(potential=harmonicOscillatorPotential(),
sampler=metropolisMonteCarloIntegrator())
sim.simulate(100)
animationSimulation.animation_trajectory(simulated_system=sim)
def test_static_sim_plots(self):
sim = system(potential=harmonicOscillatorPotential(),
sampler=metropolisMonteCarloIntegrator())
sim.simulate(100)
plotSimulations.oneD_simulation_analysis_plot(sim)
