need help with ODE solver from scipy

[Robert Kern]

T.Crane wrote:
> Hi,
> 
> OK, I'm trying to figure out how to use the ODE solver
> (scipy.integrate.ode.ode). 

You will get more help from the scipy-user list than you will here.

  http://www.scipy.org/Mailing_Lists

> Here's what I'm doing (in iPython)
> 
> y0 = [0,1,1]
> dt = 0.01
> tEnd = 12
> t0 = 0
> Y = zeros([tEnd/dt, 3])
> 
> As an aside, I've used this assignment for Y in the past and it
> worked.  When I tried it this morning I got a TypeError and a message
> saying I needed to use an integer.  

Well, the current behavior is correct. When you give us a float instead of an
int for a dimension, we shouldn't guess what you want. Particularly, in this
case, truncating is incorrect. I ran your code and eventually wound up with an
IndexError because your iteration ran past the end of Y and T.

> So, instead...
> 
> Y = zeros([int(tEnd/dt), 3])
> T = zero([int(tEnd/dt)])

Also, a better way to do this is simply to leave these as lists and simply
append to them. That way, you don't have to manage indices.

> index = 0
> def foo(t,y):
>     dy = zeros([3])
>     dy[0] = y[1]*y[2]
>     dy[1] = -y[0]*y[2]
>     dy[2] = -0.51*y[0]*y[1]
>     return dy
> 
> r = ode(foo).set_integrator('vode').set_initial_value(y0,t0)
> while r.successful() and r.t < tEnd:
>     r.integrate(r.t+dt)
>     Y[index] = r.y
>     T[index] = r.t
>     index += 1
> 
> As a further aside, this system of three coupled linear ODE's is from
> an example in MATLAB's documentation on their function ode45, so I
> know what I 'should' get.  The while loop and call to ode is adapted
> from scipy's (very limited) documentation on scipy.integrate.ode.ode.
> 
> At the end of this while loop I've gotten a few different results
> depending on what I have no idea.  This morning another TypeError
> exception was thrown, saying:
> 
> TypeError:  Array can not be safely cast to required type.
> 
> Although, to be fair this is after the output from one iteration:
> 
> array([0.01, 1. , 1.  ])
> 
> So, clearly this isn't working right.  Does anyone have any experience
> using this function or anything they can contribute?

I tried your example and it worked for me (after fixing the IndexError). Could
you come to scipy-user with the complete code that you ran (the one above isn't
the one you ran; there is at least one typo), and the full traceback of the error?

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco