[Numpy-discussion] problems with numdifftools

Nicolai Heitz nicolaiheitz@gmx...
Tue Oct 26 16:24:39 CDT 2010


Am 26.10.2010 12:38, schrieb josef.pktd@gmail.com:

>  On Tue, Oct 26, 2010 at 3:28 PM, Pauli Virtanen<pav@iki.fi>   wrote:
>>  Tue, 26 Oct 2010 12:16:53 -0700, Nicolai Heitz wrote:
>>>  I am not sure if you are the right persons to contact but if not I would
>>>  appreciate a short notice and maybe an address where I can find help. I
>>>  already posted this this message in an other python mailing list and
>>>  they forwarded me to this list and told me that I might find help here.
>>  Some comments:
>>
>>  1) General advice: When doing numerics, it's generally a good idea to use
>>  units natural for the problem, and not SI ones. The numbers the computer
>>  sees should be of order 1. Not all numerical algorithms are scale
>>  invariant.
>  I also think it will be difficult to get good numbers by numerical
>  differenttiation with this scaling.
>
I knew before that the scaling might causes some problems but I didn't
expect them to arise on that level. I thought numdifftools should be
robust in those typical physical units/scales. I can transform it into
natural units but this is not the best solution and I still hope for
somebody to come up with a solution for SI units.
>>  2) The scipy-user list might be even more appropriate:
>>
>>  http://mail.scipy.org/mailman/listinfo/scipy-user
I contacted them already but they didn't responded so far and I was
forwarded to that list which was supposed to be more appropriated.
>>  3) The numdifftools authors might be more knowledgeable about their
>>  software:
>>
>>  http://code.google.com/p/numdifftools/
>>
>>  If you are sure it's a bug in numdifftools, click the issues tab and
>>  write a report. Be sure to include simple test case (like the one you
>>  attached).
>  Per might be reading this or scipy-user.
>
>  My guess would be that it is not a bug but numerical precision
>  problems in a difficult use case. The question is however useful,
>  because I haven't seen much discussion yet about a robust use of
>  numdifftools.
>
>  Josef
>
I am not sure if it is a bug either. I mean for most of the numbers I
tested the code (not having a magnitude of e-28) like 2.5, 1, 1e-10
numdifftools works all fine. My question is more like

1) Can I make it run/fix it, so that it is also going to work for the SI
scaling?
2) How can I be sure that increasing the number of ions or adding a
somehow more complicated term to the potential energy is not causing the
same problems even in natural units?
3) In which range is numdifftools working properly.

Nicolai
>>  --
>>  Pauli Virtanen
>>
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