Code for Kuramoto in Python is available here or from code subpage.
Explanation on how to use it is on the bottom of this post.
Tiny introduction
Kuramoto^{[1, 2]} is probably one of the most popular and successful models for coupled oscillators. There is plenty of information about it, but in brief summary it models oscillators’ phases to be dependent on scaled phase differences for all pairs of oscillator.
A while ago I have actually wrote on a specific method that I used to find optimal parameters for a Kuramoto model given some observation. (See Bayesian Dynamic Inference here.)
Mathematically speaking this model is defined by a set of coupled ordinary differential equations (ODEs). Given N oscillators, dynamics for each oscillator’s phase is defined as is defined by , where the summation is over all others oscillators. Note that one can leave coupling with itself, because in such case , thus it doesn’t input anything into the final solution.
Quick note that Kuramoto coupling model can be used to reference model with coupling function that can be represented as a sum of harmonic functions. For example, second order means that we are including both and . In general Kuramoto model of order would describe .
Examples
Below are two examples. Both use the same core values with the exception that for the second system the coupling function defined by two harmonic terms. This naturally changes dynamics, but it shouldn’t change much average value, which is close to intrinsic frequency.
Exact values for the first experiment are presented in table below. Each row is a different oscillator with initial phase Φ_{0} and intrinsic frequency Ω. The following columns denote coupling strength between respective pairs of oscillators.
Φ_{0} | ω | k_{.1} | k_{.2} | k_{.3} | |
---|---|---|---|---|---|
1 | 0 | 28 | 0.2 | 1.1 | |
2 | π | 19 | 0.5 | -0.7 | |
3 | 0 | 11 | 0.3 | 0.9 |
Phase dynamics, i.e. time derivative of obtained phases, are presented in Fig. 1. One can see that all plots are centred on intrinsic frequency with some modulations.
Table below shows values used in the second simulation. Extra 3 columns denote scaling values used in second harmonic.
Φ_{0} | ω | k^{(1)}_{.1} | k^{(1)}_{.2} | k^{(1)}_{.3} | k^{(2)}_{.1} | k^{(2)}_{.2} | k^{(2)}_{.3} | |
---|---|---|---|---|---|---|---|---|
1 | 0 | 28 | 0.2 | 1.1 | -0.5 | 0.2 | ||
2 | π | 19 | 0.5 | -0.7 | -0.4 | 1.0 | ||
3 | 0 | 11 | 0.3 | 0.9 | 0.8 | 0.8 |
Again phase dynamics have been presented in a form of plot (Fig. 2). I think the difference is clear. Despite having similar mean values (approximately equal to intrinsic frequency), their modulations have change. Not only the frequency content of these modulations has changed, but also their amplitude.
Using code
Except for downloading code from either github or code subpage, one is expected to have SciPy module. Kuramoto uses it to solve differential equations.
Script below shows an example of how one can use the Kuramoto module. When you run this, make sure that kuramoto.py is either in your path. Note also that most of the code is to just defining initial parameters and plotting the results. Actual execution of the module are two lines. Fig. 1 is the expected output.
import numpy as np import pylab as plt from kuramoto import Kuramoto # Defining time array t0, t1, dt = 0, 40, 0.01 T = np.arange(t0, t1, dt) # Y0, W, K are initial phase, intrinsic freq and # coupling K matrix respectively Y0 = np.array([0, np.pi, 0]) W = np.array([28, 19, 11]) K1 = np.array([[ 0, 0.2, 1.1], [0.5, 0, -0.7], [0.3, 0.9, 0]]) K2 = np.array([[ 0, -0.5, 0.2], [-0.4, 0, 1.0], [ 0.8, 0.8, 0]]) K = np.dstack((K1, K2)).T # Passing parameters as a dictionary init_params = {'W':W, 'K':K, 'Y0':Y0} # Running Kuramoto model kuramoto = Kuramoto(init_params) odePhi = kuramoto.solve(T) # Computing phase dynamics phaseDynamics = np.diff(odePhi)/dt # Plotting response nOsc = len(W) for osc in range(nOsc): plt.subplot(nOsc, 1, 1+osc) plt.plot(T[:-1], phaseDynamics[osc]) plt.ylabel("$\dot\phi_{%i}$" %(osc+1)) plt.show()
[1] Y. Kuramoto, “Chemical Oscillations, Waves, and Turbulence,” 1984, doi: 10.1007/978-3-642-69689-3.
[2] Steven H. Strogatz, “From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators,” 2000, doi: 10.1016/S0167-2789(00)00094-4.
Dear Sir,
my name is Alessandro Scirè.
We recently published a Kuramoto-Based paper on PLOS ONE,
Self-organization in a diversity induced thermodynamics
Alessandro Scirè, Valerio Annovazzi-Lodi
Published: December 8, 2017https://doi.org/10.1371/journal.pone.0188753
visual results here: https://youtu.be/1pv-etX0-bE
We would be very interested in developing a python code for that problem, but we don’t know how to do it. Do you have any suggestion?
thank you
best regards
Alessandro Scirè PhD
alessandro.scire.jhgl@gmail.com
when I tried to run the script appears the next error: ValueError: x and y must have same first dimension, but have shapes (3999,) and (2,).
Hey Ramon,
Thanks for catching this. The error in unnecessary transposition of the `kuramoto.solve(T)` results (line 28). The code is fixed and tested so should be good. Please send me any questions you have. Sorry for the problem.
Dawid
Error is showing this:
Traceback (most recent call last):
File “k.py”, line 3, in
from kuramoto import kuramoto
ImportError: No module named kuramoto
Error :
Traceback (most recent call last):
File “k.py”, line 3, in
from kuramoto import Kuramoto
ImportError: No module named kuramoto
Getting an error:
from kuramoto import Kuramoto
ImportError: No module named kuramoto