Dear Bruce and Matt,

I really appreciate for your patience and answers.
I always knew that all messages on the mailing list have been archived and I've tried to check in the archives for an answer, but I can't proceed with it because it seems that the link to the old discussions was broken on IFEFFIT site at that time!


Anyway, I thank you guys again!



Danilo OLIVEIRA DE SOUZA (PhD student)
Université de Sciences et Technologies de Lille (Université Lille 1)
UCCS - Unité de Catalise et Chimie du Solid, Bat. C3, Bureau 110.
Cité Scientifique, 59655, VIlleneuve d'Ascq CEDEX.

danilo.olsouza@gmail.com
d.oliveira-de-souza@ed.univ-lille1.fr
tel: +33 06.63.55.86.12


2014/1/22 <ifeffit-request@millenia.cars.aps.anl.gov>
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Today's Topics:

   1. "Save marked groups as..." command (Danilo Oliveira de Souza)
   2. Re: "Save marked groups as..." command (Bruce Ravel)
   3. Re: "Save marked groups as..." command (Matt Newville)


----------------------------------------------------------------------

Message: 1
Date: Wed, 22 Jan 2014 16:40:56 +0100
From: Danilo Oliveira de Souza <danilo.olsouza@gmail.com>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] "Save marked groups as..." command
Message-ID:
        <CANbKcaVUm4ZQVq+zWeiOfMhU3APEcFCn0t+Uz6SeHiQyM05xTw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear list,

I have a big collection of data from a catalytic reaction.
I tried to export all the spectra (about 200) to a unique file containing
the normalized ones. I used the "File>Save marked groups as>norm(E)" option.
Unfortunately, Athena (Demeter 0.9.18) is not able to make one unique file
(it crashes and I have to initialize it again), instead I had to creat 4
different files of 45 spectra each (the maximum group I could gather on a
file). Is there any bug on it or some kind of limitation to creat these
kind of files?

Best regards,


*Danilo OLIVEIRA DE SOUZA* (PhD)
Universit? de Sciences et Technologies de Lille (Universit? Lille 1)
UCCS - Unit? de Catalise et Chimie du Solid, Bat. C3, 110.
Cit? Scientifique, 59655, VIlleneuve d'Ascq CEDEX, France.

danilo.olsouza@gmail.com
d.oliveira-de-souza@ed.univ-lille1.fr
tel: +33 06.63.55.86.12
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Message: 2
Date: Wed, 22 Jan 2014 11:03:10 -0500
From: Bruce Ravel <bravel@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] "Save marked groups as..." command
Message-ID: <52DFEBBE.9050906@bnl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 01/22/2014 10:40 AM, Danilo Oliveira de Souza wrote:
> Dear list,
>
> I have a big collection of data from a catalytic reaction.
> I tried to export all the spectra (about 200) to a unique file
> containing the normalized ones. I used the "File>Save marked groups
> as>norm(E)" option.
> Unfortunately, Athena (Demeter 0.9.18) is not able to make one unique
> file (it crashes and I have to initialize it again), instead I had to
> creat 4 different files of 45 spectra each (the maximum group I could
> gather on a file). Is there any bug on it or some kind of limitation to
> creat these kind of files?

The fact that Ifeffit, written in Fortran, has hard-wired limits on
things has been discussed dozens of times on this mailing list.  The
advice to partition your data into groups of about 50 has been given on
this mailing list dozens of times.  Y'know, this mailing list has been
archived since the beginning and can be searched.

A quick skim of the Ifeffit source code (another thing anyone can do)
suggests that the hard-wired limit for the maximum number of columns in
an output data file is 99.

I will try to preempt Matt's response and say that Larch addresses most
of these limitations.  A version of Athena which can talk to Larch
(replacing Ifeffit as the computational backend) will be available soon.

B





--
  Bruce Ravel  ------------------------------------ bravel@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:    http://xafs.org/BruceRavel
  Software:    https://github.com/bruceravel


------------------------------

Message: 3
Date: Wed, 22 Jan 2014 10:03:24 -0600
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] "Save marked groups as..." command
Message-ID:
        <CA+7ESbpCC17PX0qf30dikjWhXLL1jc=hV1r_wwYoQ7cSordzQw@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Danilo,

On Wed, Jan 22, 2014 at 9:40 AM, Danilo Oliveira de Souza
<danilo.olsouza@gmail.com> wrote:
> Dear list,
>
> I have a big collection of data from a catalytic reaction.
> I tried to export all the spectra (about 200) to a unique file containing
> the normalized ones. I used the "File>Save marked groups as>norm(E)" option.
> Unfortunately, Athena (Demeter 0.9.18) is not able to make one unique file
> (it crashes and I have to initialize it again), instead I had to creat 4
> different files of 45 spectra each (the maximum group I could gather on a
> file). Is there any bug on it or some kind of limitation to creat these kind
> of files?
>
> Best regards,
>
>
> Danilo OLIVEIRA DE SOUZA (PhD)
> Universit? de Sciences et Technologies de Lille (Universit? Lille 1)
> UCCS - Unit? de Catalise et Chimie du Solid, Bat. C3, 110.
> Cit? Scientifique, 59655, VIlleneuve d'Ascq CEDEX, France.
>
> danilo.olsouza@gmail.com
> d.oliveira-de-souza@ed.univ-lille1.fr
> tel: +33 06.63.55.86.12
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>

This is sort of "known problem".  That is, we know that there will be
some threshold where the underlying ifeffit engine will run out of
memory, way before any reasonable laptop being used today would
actually be short of memory.   I can't say that we know that 200
spectra will never work, or that 45 will always work, it depends on
the size of the arrays and how much processing  you've done on the
data.

The problem is effectively removed with Larch, the next generation of
the Ifeffit engine.  I know Bruce is working on (and making progress
on!) having Athena use Larch, which will be particularly useful for
handling large data sets.

For now, I think you're sort of stuck with having to grup the data as
you are doing.   As always, any help on Larch and Demeter would be
greatly welcome.

--
--Matt



------------------------------

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End of Ifeffit Digest, Vol 131, Issue 26
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