Automatic initialization of an allosteric network

Begin with a few package imports:

from IPython.display import HTML

import numpy as np
import matplotlib.pyplot as plt

from packing_utils import *
from allosteric_utils import *
from plot_imports import *

Network generation

Generate a random contact network from a disk packing simulation to use as the elastic network:

n = 128 # number of disks/nodes
seed = 0
dim = 2

net = Packing(n, dim=dim, rfac=0.8, seed=seed)
net.params['contact'] = 0.05 # reduce the default contact repulsion
net.generate()

progress: 100%|########################################################| 1000.00/1000.00 [00:06<00:00]

Use the network graph to initialize an Allosteric Class object. Initially, the network has no sources or targets specified.

%matplotlib notebook

allo = Allosteric(net.graph, dim=dim)
allo.plot()

Source and target specification

There are a number of ways we can automatically add sources or targets. A call to allo.add_sources() or allo.add_targets() places one source or target, respectively, at random in the network, and the edge joining the node pair is removed. Sources will be colored blue, and targets red. Here we also include a random seed for reproducibility.

allo.add_sources(seed=12)

Suppose we’d like to place a target somewhere on the boundary. We can do so by specifying boundary=True. This will attempt to place a target (or source) on the boundary satisfying a minimum number of bonds per node.

allo.add_targets(boundary=True)

Let’s add four more targets by specifying 4 as the first argument. The selection algorithm tries to keep the sources and targets well-separated by maximizing the shortest distance to any current source or target pair.

allo.add_targets(4)

We can save the initialized network to a file:

allo.save('allo_auto_{:d}.txt'.format(n))