[SciPy-User] Trajectory Integration via scipy.integrate or PyDSTool?

Sara Gallian sara2411@gmail....
Mon May 14 13:03:28 CDT 2012


Dear Rob,

thank you for the quick reply.
Unfortunately - I must say I'm  a bit ashamed of that - I have troubles with installing PyDSTool! :(
I'm using a Mac with Lion version 10.7.3 installed.
I copied the unzipped folder and changed the permission.
than added the path to my .profle file

PYTHONPATH="/usr/local/PyDSTool:${PYTHONPATH}"
export PYTHONPATH

The python version I'm using though, is the Enthough Distribution (EPD-7.1-2) , which path
PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PATH}"
export PATH
So I can't set the variable PYTHON to /sw/bin/python2.6..

Is there a conflict with EPD version I have installed? Or am I just getting it totally wrong?
Thank you!

Sara

On May 14, 2012, at 7:22 PM, Rob Clewley wrote:

> Hi Sara,
> 
> I think you should use a tool that's appropriate for the task. With an
> hour of work and help on this list or the PyDSTool forum at
> http://sourceforge.net/projects/pydstool/forums/forum/472291 you
> should be able to get your problem working quickly with PyDSTool. I
> expect your problem is easy to solve in PyDSTool, and difficult to do
> with odeint.
> 
> You can still use scipy's VODE in PyDSTool and you won't need any
> fancy installation. Check out the file vode_event_test1.py in the
> tests directory. Writing the vector field is simple, but in case you
> have specific problems setting up yours then you should send me your
> code on list so that I can help. I'd be interested to see what the
> equations look like.
> 
> It's very simple to define a terminal event, just copy and adapt the
> code in the file. You can write a loop so that whenever integration
> has stopped because of an event, you reverse the velocity IC and
> restart.
> 
> -Rob
> 
> On Mon, May 14, 2012 at 12:59 PM, Sara Gallian <sara2411@gmail.com> wrote:
>> Hi all,
>> I'm trying to integrate particle trajectories in a finite domain, and I need to make them "reflect" at the boundaries (i.e. reverse the velocity perpendicular to the plane they collided with). I started by using  scipy.integrate.odeint , but since the integration steps are variable, simply checking the position and reversing the velocity won't work!
>> Can anyone suggest the quickest way to obtain this? would Vode be able to handle this, or should I try to learn to use  PyDSTool?
>> I'm running pretty late on a deadline, so any suggestion is more than appreciated :)
>> Thanks!
>> Sara
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> 
> 
> 
> -- 
> Robert Clewley, Ph.D.
> Assistant Professor
> Neuroscience Institute and
> Department of Mathematics and Statistics
> Georgia State University
> PO Box 5030
> Atlanta, GA 30302, USA
> 
> tel: 404-413-6420 fax: 404-413-5446
> http://www2.gsu.edu/~matrhc
> http://neuroscience.gsu.edu/rclewley.html
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