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update RubberBand to add biasing feature

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Pim Nelissen
2025-10-27 15:40:31 +01:00
parent ef95114fe8
commit 11ae29dea8
1 changed files with 21 additions and 12 deletions
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33
RubberBand.py
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@ -4,39 +4,48 @@ from Link import Link
class RubberBand: class RubberBand:
# class attributes # class attributes
k_B = 1
def __init__(self, N, a=1., kBT=1., biased=False, force=0.):
def __init__(self, N, a=1., T=1.):
""" """
RubberBand is a class that can simulate a rubber band with N RubberBand is a class that can simulate a rubber band with N
incompressible links of length a. incompressible links of length a.
Parameters: Parameters
N (int) The number of links. ----------
a (float) The fixed length of links. N : int
T (float) Temperature of the system. The number of links.
a : float, optional
The fixed length of the links. The default is 1..
kBT : float, optional
Temperature of the system (arb. units). The default is 1..
force : float, optional
Force applied to the RubberBand.
The default is 0, which is an unbiased RubberBand.
""" """
self.N = N self.N = N
self.a = a self.a = a
self.T = T self.kBT = kBT
self.links = self.__sample_links() self.links = self.__sample_links(force=force)
def w(self, f, l): def w(self, f, l):
beta = (self.k_B*self.T)**(-1) beta = (self.kBT)**(-1)
return np.exp(beta*f*l) return np.exp(beta*f*l)
@property @property
def length(self): def length(self):
return self.a * np.sum([l.direction for l in self.links]) return self.a * np.sum([l.direction for l in self.links])
def __sample_links(self): def __sample_links(self, force):
""" """
Sample N Link objects with a random direction. Sample N Link objects with a random direction.
""" """
samples = np.random.random_sample((self.N,)) samples = np.random.random_sample((self.N,))
directions = np.ones(samples.shape) directions = np.ones(samples.shape)
directions[samples < 0.5] = -1.
p_negative = 1 - 0.5*(1 + np.tanh(force*self.a/self.kBT))
directions[samples < p_negative] = -1.
directions = directions.astype(int) directions = directions.astype(int)
return [Link(d) for d in directions] return [Link(d) for d in directions]