def __init__(self, capital_lambda:float, nReplicas:int,
system=perturbed_system.perturbedSystem(temperature=300.0, lam=0.0,
potential=pot.OneD.linearCoupledPotentials(),
integrator=stochastic.metropolisMonteCarloIntegrator()), build=False):
'''
initialize Ensemble object
:param capital_lambda: state of ensemble, 0 <= capital_lambda < pi
:param num: number of replicas
:param system: a system1D instance
:param build: build memory?whconda
'''
assert 0.0 <= capital_lambda <= 2 * np.pi, "capital_lambda not allowed"
assert nReplicas >= 1, "At least one system is needed"
self.nReplicas = nReplicas
self.system = system
self.capital_lambda = capital_lambda
self.build = build #build
self.dis = 2.0 * np.pi / nReplicas
self.exchange_dimensions = {self._parameter_name: np.arange(0, 2*np.pi, self.dis )}
self._temperature_exchange = system.temperature
self.initialise()
self.exchange_information: pd.DataFrame = pd.DataFrame(columns=["Step", "capital_lambda","TotE", "biasE", "doAccept"])
self.system_trajs: dict = {}
def testTraj(self):
integrator = metropolisMonteCarloIntegrator()
ha = OneD.harmonicOscillatorPotential(x_shift=-5)
hb = OneD.harmonicOscillatorPotential(x_shift=5)
pot = OneD.linearCoupledPotentials(Va=ha, Vb=hb)
sys = perturbedSystem(temperature=300.0,
potential=pot,
sampler=integrator)
lam = 0.5
sys.lam = lam
ens = self.convBelt(0.0, 1, system=sys)
def __init__(self,
capital_lambda: float,
n_replicas: int,
system:systemCls =
perturbed_system.perturbedSystem(
temperature=300.0,
lam=0.0,
potential=pot.OneD.linearCoupledPotentials(
Va=pot.OneD.harmonicOscillatorPotential(k=1, x_shift=0),
Vb=pot.OneD.harmonicOscillatorPotential(k=2, x_shift=0)
),
sampler=stochastic.metropolisMonteCarloIntegrator()
),
build: bool = False):
"""
initialize Ensemble object
Parameters
----------
capital_lambda: float
state of ensemble, 0 <= capital_lambda < pi
n_replicas: int
number of replicas
system: systemCls, optional
a system1D instance
build:bool, optional
build memory?
"""
assert 0.0 <= capital_lambda <= 2 * np.pi, "capital_lambda not allowed"
assert n_replicas >= 1, "At least one system is needed"
super().__init__()
self.system = system
self.capital_lambda = capital_lambda
self.build = build # build
self.dis = 2.0 * np.pi / n_replicas
self.exchange_dimensions = {
self._parameter_name:
[
self.calculate_replica_lambda(self.capital_lambda, i)
for i in range(n_replicas)
]
}
self._temperature_exchange = system.temperature
self.initialise()
self.system_trajs: dict = {}
def test_run_step(self):
integrator = metropolisMonteCarloIntegrator()
ha = OneD.harmonicOscillatorPotential(x_shift=-5)
hb = OneD.harmonicOscillatorPotential(x_shift=5)
pot = OneD.linearCoupledPotentials(Va=ha, Vb=hb)
sys = perturbedSystem(temperature=300.0,
potential=pot,
sampler=integrator)
ens = self.convBelt(0.0, 1, system=sys)
ens.calculate_total_ensemble_energy()
ens.run()
ens.calculate_total_ensemble_energy()
ens.get_replicas_positions()
def interactive_conveyor_belt(conveyorBelt=None, numsys:int=8, nbins:int=100, steps:int=100):
#if none given build cvb
if(isinstance(conveyorBelt, type(None))):
import ensembler.potentials.OneD as pot
import ensembler.system.perturbed_system as system
import ensembler.ensemble.replicas_dynamic_parameters as cvb
import ensembler.integrator as integ
integrat = integ.stochastic.metropolisMonteCarloIntegrator()
potential = pot.linearCoupledPotentials(Va=pot.harmonicOscillator(k=1.0), Vb=pot.harmonicOscillator(k=2.0))
syst = system.perturbedSystem(potential=potential , integrator=integrat)
conveyorBelt=cvb.ConveyorBelt(0.0, 8, system=syst, build=False)
conveyorBelt.simulate(steps)
(cvb_traj, systrajs) = conveyorBelt.get_trajs()
if(len(cvb_traj)==0):
raise IOError("Could not find any conveyor belt simulation in conveyorbelt traj. Please simulate first.")
bins=np.zeros(nbins)
dhdlbins=np.zeros(nbins)
for i in systrajs:
for j in range(systrajs[i].shape[0]):
index=int(np.floor(systrajs[i].lam[j]*nbins))
if index == nbins:
index=nbins-1
bins[index]+=1
dhdlbins[index]+=systrajs[i].dhdlam[j]
dhdlbins/=bins
ene = np.cumsum(dhdlbins)/nbins
lam = np.linspace(0, 1, nbins)
nReps=conveyorBelt.nReplicas
def redraw(CapLam, M):
plotEnsembler(lam, ene, CapLam=np.deg2rad(CapLam), M=M)
#build layout and components
player = ipywidgets.Play(value=0, min=0, max=360, step=1,
description="rotate")
capLam_slider = ipywidgets.IntSlider(value=0, min=0, max=360, step=1,
orientation='vertical',
description="Capital Lambda",
continous_update=True)
nReplicas_slider = ipywidgets.IntSlider(value=8, min=2, max=20, step=1,
orientation='vertical',
description="number of Replicas")
ipywidgets.jslink((capLam_slider, 'value'), (player, 'value'))
interactive_plot = ipywidgets.interactive_output(redraw,
{'CapLam':capLam_slider,
'M':nReplicas_slider})
controls = ipywidgets.VBox([player, ipywidgets.HBox([capLam_slider, nReplicas_slider])])
app = ipywidgets.AppLayout(header=None,
left_sidebar=controls,
center=interactive_plot,
right_sidebar=None,
footer=None,
align_items="center")
display(app)
return app