[SciPy-user] scipy.odeint args question

Luke hazelnusse@gmail....
Tue Jun 5 21:19:26 CDT 2007


I'm trying to write a tool that needs to be able to integrate
n-dimensional systems of 1st order differential equations.  I need to
be able to basically plug various dynamical systems, along with their
Jacobians, and any associated parameters that occur on the RHS of the
ODE's that may need to be varied.  My issue is with how scipy.odeint
handles extra function arguments.

My differential equations are of the form:

def f(x,t,param):
  ...
  return dxdt

def J(x,t,param):
  ...
  return dfdx

The param argument would be a rank 1 array (or list), that gets used
in the function definitions of the RHS.  For example, the Lorenz
equations have three parameters, sigma, r, and b, but other systems
have other numbers of parameters, so it makes sense to just pass this
as a vector (or list).  If it is not done in this fashion, then
systems with different numbers of parameters have to be hard-coded...
really annoying.

I would like to be able to call scipy.odeint something like:

y = scipy.odeint(f, x0, t, args = param, Dfun = J)
or
y = scipy.odeint(f, x0, t, args = (param), Dfun = J)

This is where I can't get things to work -- odeint needs a tuple for
the args argument, and I can't figure out how to make it work.  The
following works, but is way to restrictive for what I need because I
want to be able to make my code modular enough to be able to integrate
*any* dynamical system that has an arbritrary number of parameters.
Here is what works, for a system with three parameters, a, b, and c;

def f(x,t,a,b,c):
  ...
  return dxdt

def J(x,t,a,b,c):
  ...
  return dfdx

y = scipy.odeint(f, x0, t, args = (a,b,c), Dfun = J)

This above works fine, but again, if you need to evaluate f anywhere,
then you have to know how many parameters it takes and call the
function in a fashion that explicitly lays out how each parameter gets
passed.


Am I overlooking something really simple here that would make this
work?  I know in matlab's ode45 you can just pass scalars or arrays or
matrices of additional parameters and it doesn't really matter -- you
just pass them through.

Thanks,
~Luke


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