[SciPy-user] (no subject)

Adrián López alopez at imim.es
Thu Feb 23 12:55:03 CST 2006


Hi people,

I use SciPy since a few months ago. I use it mainly to integrate a  
system of ODEs. Until now this piece of code was running nicely with  
the previous version of SciPy:


from Numeric import *

from scipy.integrate import odeint

def func(x, t, *args):

         xdot = [0.0, 5.0, 0.0, 15.0, 0.0, 0.0, 0.0]

         xdot[0] = + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0

         xdot[1] = - (x[1] * beta) + x[4] * beta

         xdot[2] = - (x[2] * beta) + x[5] * beta

         xdot[3] = + x[6] * beta - (x[3] * beta)

         xdot[4] = + alpha0 + (alpha + (x[3])**( n) * alpha1) / ((K)** 
( n) + (x[3])**( n)) - (k1 * x[4])

         xdot[5] = + alpha0 + (alpha + (x[1])**( n) * alpha1) / ((K)** 
( n) + (x[1])**( n)) - (k1 * x[5])

         xdot[6] = - (k1 * x[6]) + alpha0 + (alpha + (x[2])**( n) *  
alpha1) / ((K)**( n) + (x[2])**( n))

         g.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n'%(t, xdot[0], xdot 
[1], xdot[2], xdot[3], xdot[4], xdot[5], xdot[6]))

         return xdot

t = arange(0, 100.01, 0.01)

alpha0 = 0.0
alpha1 = 0.0
K = 1.0
beta = 5.0
n = 2.1
k1 = 1.0
alpha = 250.0
cell = 1.0

parameters = [alpha0, alpha1, K, beta, n, k1, alpha, cell]

x_0 = [0.0, 5.0, 0.0, 15.0, 0.0, 0.0, 0.0]

g = open('repressilator.veloc.out', 'w')

args = (parameters, g)

x = odeint(func, x_0, t, args)



But now, with the new version,  it is giving me the ugly error of

[alopez at thymus tmp]$ python file.py
Segmentation fault

on a linux machine and

Macintosh-3:~/work/tmp adrianlopez$ python test.py
Bus error

on a mac.

There is something wrong on my code? Is there some problem on odeint  
from scipy.integrate? Could be any trouble calling also Numeric?

I will appreciate any comment,

Thanks for your help,

--

Adrián López García de Lomana, Graduate Student

Computational Biochemistry and Biophysics Lab
Research Group on Biomedical Informatics (GRIB) - IMIM / UPF
c/ Dr. Aiguader, 80; 08003 Barcelona (Spain)
http://diana.imim.es




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