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

Mon May 14 17:56:04 EDT 2012

On Mon, May 14, 2012 at 4:47 PM, Sara Gallian <sara2411 at gmail.com> wrote:
> I have already set both paths in my .profile :
[SNIP]
> but I receive an error when I try to import the module.
> I don't understand why..

For purely installation issues you should post to the PyDSTool user
forum in any follow up questions you still have. I don't think the
scipy list wants to hear about this non-scipy issue!

Briefly, though, if you look at the installation notes, it also shows
how you should write and place a PyDSTool.pth file in python's
site-packages folder. That is quite possibly your remaining problem.

-Rob

> On 14.05.2012, at 22:28, Rob Clewley wrote:
>
>> Sara,
>>
>> Your Hamiltonian system really requires a symplectic integrator or
>> similar, as Lou mentions, that truly respects energy conservation. A
>> regular ODE integrator will create numerical error in the total
>> energy, as it is oblivious. In lieu of such a thing, at the very least
>> you can make a correction at those detected events in your loop to
>> restore the total energy.
>>
>> Anyway, regarding your installation. You should change your PATH to
>> point to whichever version of python you are using, i.e. the version
>> that has numpy, scipy etc. installed through EPD. It looks like you
>> are using a Mac, so if you've installed EPD you should point to that
>> version of python with your PATH. /sw/ is not a valid directory with
>> EPD. If EPD installs outside of the Mac Framework then you will need
>> to change the path, but if it uses the Framework python then there is
>> nothing to change.
>>
>> Also, and I haven't given this much thought, but in the absence of a
>> geometric integrator, you could possibly even solve the system more
>> accurately as a differential-algebraic system (DAE), using the energy
>> constant as the algebraic constraint. But there might be more
>> mathematical problems with that approach that I'm not seeing (I'm not
>> an expert). At least you could try setting such a thing with the Radau
>> integrator in PyDSTool, and there are DAE examples provided.
>>
>> Feel free to share your equations and code in more detail if you're
>> still struggling. With small integration steps you might be fine using
>> RK4 with the energy correction at boundaries.
>>
>> -Rob
>>
>> On Mon, May 14, 2012 at 2:12 PM, Sara Gallian <sara2411 at gmail.com> wrote:
>>> Dear Lou,
>>> I'm just moving a bunch of electrons in a static b field
>>> dv/dt = q/m v x B
>>> B depends on the position, in general
>>> They move in this field, without interacting, till they bounce off a wall,
>>> that specularly reflects them
>>> Yes, the dynamic is conservative.
>>> I could just write a RK4 and check the position at every ts, but I was
>>> hoping to be able to use a better tool
>>> Thanks
>>> Sara
>>>
>>> Sent from my iPhone
>>>
>>> On 14.05.2012, at 20:03, Lou Pecora <lou_boog2000 at yahoo.com> wrote:
>>>
>>> Hi, Sara,
>>>
>>> Can you give more information?
>>>
>>> Are the particles in a potential or is it free flight between hard wall
>>> collisions?  Do the particles interact?  I assume the dynamics are
>>> conservative (Hamiltonian). Is that correct?
>>>
>>> -- Lou Pecora, my views are my own.
>>> ________________________________
>>> From: Rob Clewley <rob.clewley at gmail.com>
>>> To: SciPy Users List <scipy-user at scipy.org>
>>> Sent: Monday, May 14, 2012 1:22 PM
>>> Subject: Re: [SciPy-User] Trajectory Integration via scipy.integrate or
>>> PyDSTool?
>>>
>>> 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 at 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
>>>> _______________________________________________
>>>> SciPy-User mailing list
>>>> SciPy-User at scipy.org
>>>> http://mail.scipy.org/mailman/listinfo/scipy-user
>>>
>>>
>>>
>>> --
>>> 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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>>>
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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
>> _______________________________________________
>> SciPy-User mailing list
>> SciPy-User at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-user
>
> _______________________________________________
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> SciPy-User at scipy.org
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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