using scipy.integrate.odeint with dictionary [Python]

Question

I'm trying to solve decay equations using scipy.integrate.odeint. I'm trying to have initial values from a dictionary, but it isn't working and I'm not sure if it can work. Here is the code I'm working with:

from scipy.integrate import odeint
import numpy as np
import matplotlib.pyplot as plt

def decay(init,t):
    f0 = - init['a']/.5
    f1 = init['a']/.5 - init['b']/.2
    f2 = init['b']/.2
    return [f0,f1,f2]

if __name__ == '__main__':
    init = {'a':5, 'b':0, 'c':0}
    time = np.linspace(0, 10, 101)
    soln  = odeint(decay, init ,time)
    a = soln[:,0]
    b = soln[:,1]
    c = soln[:,2]
    print a
    print b
    print c
    plt.plot(time, a, color = 'g')
    plt.plot(time, b, color = 'r')
    plt.plot(time, c, color = 'b')
    plt.show()

It works as expected if instead of a dictionary I use a list like this:

from scipy.integrate import odeint
import numpy as np
import matplotlib.pyplot as plt

def decay(init,t):
    a,b,c = init
    f0 = - a/.5
    f1 = a/.5 - b/.2
    f2 = b/.2
    return [f0,f1,f2]

if __name__ == '__main__':
    init = [5,0,0]
    time = np.linspace(0, 10, 101)
    soln  = odeint(decay, init ,time)
    a = soln[:,0]
    b = soln[:,1]
    c = soln[:,2]
    print a
    print b
    print c
    plt.plot(time, a, color = 'g')
    plt.plot(time, b, color = 'r')
    plt.plot(time, c, color = 'b')
    plt.show()

However, I need to be using a dictionary for my purposes. Is there a way to use a dictionary to call the initial values?

According to the docs, the second parameter is supposed to be an array -- numpy converts list to array just fine, but it won't convert a dict to an array ... So what you're asking for probably isn't possible... — mgilson
– mgilson, Commented Jun 9, 2016 at 22:16

mgilson · Accepted Answer · 2016-06-09 23:17:09Z

1

If this works:

init = [5,0,0]
time = np.linspace(0, 10, 101)
soln  = odeint(decay, init ,time)

then this should as well:

adict = {'a':5, 'b':0, 'c':0}
init = [adict['a'],adict['b'],adict['c']]
time = np.linspace(0, 10, 101)
soln  = odeint(decay, init ,time)

In other words, regardless of where you are getting this dictionary from, you need to convert its values to a list.

init = adict.values() (or list(adict.values()) in Py3) won't work since a dictionary orders the keys in its own way:

In [306]: list({'a':5, 'b':0, 'c':0}.values())
Out[306]: [0, 0, 5]

or for a longer list of keys, this might be simpler:

In [307]: adict = {'a':5, 'b':0, 'c':0}
In [308]: init = [adict[k] for k in ['a','b','c']]
In [309]: init
Out[309]: [5, 0, 0]

edited Jun 9, 2016 at 23:17

mgilson

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answered Jun 9, 2016 at 22:28

hpaulj

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