[Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
Carlo Segre
segre at iit.edu
Sun Feb 1 13:20:06 CST 2009
Hi Yordy:
I'm sorry. The xdp module is one that was written here by my group to
provide I/O for data files produced at our beamline. I have packaged it
for Debian but it is not out there for the general public yet. In the
program I sent you the xdp module is only used to write out the converted
data is a file format that we call SFF (Simple File Format).
The xdp module is not necessary if you simply write out the converted data
with a more normal set of commands.
Your email got me thinking though that I should finish the progrram and
make it useful to others. What I did, therefore, is to rewrite the
program without the use of xdp and making it a bit more user-friendly.
It now also handles both of the filetypes that Matt mentioned on a
previous post, and which are documented at
http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#head-e7e2389af58d378379f3bbe2a827c73a6df2a42e
The program now runs fine under Python 2.5 (I don't know about 2.6 but let
me know if it has problems!). It is used as a standard *nix filter, that
is, rename it to "lytle_convert" (or make a link to it) and make sure it
is executable and in the executing PATH so the system can find it.
The program is invoked from the command line as
$lytle_convert file0 [file1 file2 file3 ... fileN]
It does take wildcards so you can process a bunch of files at once. Since
all the Lytle database files are of the form "name.ext", the output file
name is made to be "name_ext.sff".
The program does its best to guess the steps per degree for the olert file
type which does not include that information in the header. The d-spacing
is assumed to be 1.92017. This may not work for all files (I have not
checked and I didn't have time to put in more intelligence right now) so
you might need to go in to modify the program to change these defaults. I
am thinking that I will add options to let the d-spacing and steps per
degree be set on the command line but that will have to wait for later.
Enjoy!
Carlo
On Sat, 31 Jan 2009, Yordy Licea Fonseca wrote:
> Hi Carlo,
>
> I´ve installed Python 2.6 for Windows XP to run your code. Latter I've
> installed a numpy 1.2.1 compiled for 2.6. I did neither find the
> *Numeric *module
> nor the *xdp* module you initialized first in the code. So I've intalled Py
> 2.4 version and again numpy, but didn not work.
> In 2.6 there is a *math* module that works similar to *Numeric*. As I did
> not find what *Numeric.zeros* does in line 32 I could not implement (if it
> were possible) with *math.*
> Could I use *xdrlib* module instead of *xdp?*
> **
> Would you send me or tell me please where to find those modules and which
> Python you recommend me to install?
>
> Best wishes, Yordy
>
>
>
>
> 2009/1/29 Carlo Segre <segre at iit.edu>
>
>> Ah, just premature sending...
>>
>> Carlo
>>
>> On Thu, 29 Jan 2009, Yordy Licea Fonseca wrote:
>>
>> Hi Carlo and Matt,
>>>
>>> Thank you very much for your help.
>>>
>>> Best wishes,
>>>
>>> Yordy
>>>
>>>
>>> On 29/01/2009, ifeffit-request at millenia.cars.aps.anl.gov <
>>> ifeffit-request at millenia.cars.aps.anl.gov> wrote:
>>>
>>>>
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>>>> When replying, please edit your Subject line so it is more specific
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>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Trouble with fitting with Artemis (Juraci A. Sampaio)
>>>> 2. Re: Trouble with fitting with Artemis (Richard Mayes)
>>>> 3. about Farrel Lytle data of Na2WO4.2H2O (Yordy Licea Fonseca)
>>>> 4. Re: about Farrel Lytle data of Na2WO4.2H2O (Matt Newville)
>>>> 5. uncertainty in linear combination analysis (Pushan Shah)
>>>> 6. Artemis parameters (abhijeet gaur)
>>>> 7. Energy shift (Eugenio Otal)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Wed, 28 Jan 2009 15:34:55 -0300
>>>> From: "Juraci A. Sampaio" <jasampaio at hotmail.com>
>>>> Subject: [Ifeffit] Trouble with fitting with Artemis
>>>> To: <ifeffit at millenia.cars.aps.anl.gov>
>>>> Message-ID: <COL107-W60310E438349CE1C72988AACC80 at phx.gbl>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>>
>>>> Hi there!I'm getting the following message when I try to fit my
>>>> data:WARNING. The following variables had no effect on the fit: !! >>
>>>> amp !! >>
>>>> enot !! >>
>>>> delr !! >> ss The
>>>> data
>>>> that I am trying to fit is the Cu metal example that come with the
>>>> iffefit
>>>> package. I am running Artemis on a Mac, OSX 10.4.11.I could run the
>>>> fitting
>>>> on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but
>>>> it
>>>> didn't work.I am wondering what could be wrong with my
>>>> machine/software?Thanks a lot.Juraci Sampaio
>>>> _________________________________________________________________
>>>> Confira v?deos com not?cias do NY Times, gols direto do Lance,
>>>> videocassetadas e muito mais no MSN Video!
>>>> http://video.msn.com/?mkt=pt-br
>>>> -------------- next part --------------
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>>>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/eb8f16cc/attachment-0001.html
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Wed, 28 Jan 2009 14:29:58 -0500
>>>> From: Richard Mayes <rtmayes at gmail.com>
>>>> Subject: Re: [Ifeffit] Trouble with fitting with Artemis
>>>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>>>> Message-ID:
>>>> <5a2a54820901281129n2b0d8fc4ib02a2ed2faeca8c5 at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Juraci,
>>>>
>>>> Can you please attach a project file so we can look at it and try to find
>>>> the problem. My first guess would be the parameters are not defined in
>>>> the
>>>> "guess,def,set" page like they are in the path list but without seeing
>>>> the
>>>> project file, it's hard to be specific.
>>>>
>>>> -Rich
>>>>
>>>> On Wed, Jan 28, 2009 at 1:34 PM, Juraci A. Sampaio <
>>>> jasampaio at hotmail.com
>>>>
>>>>> wrote:
>>>>>
>>>>
>>>> Hi there!
>>>>>
>>>>> I'm getting the following message when I try to fit my data:
>>>>> WARNING. The following variables had no effect on the fit:
>>>>> !! >> amp
>>>>> !! >> enot
>>>>> !! >> delr
>>>>> !! >> ss
>>>>>
>>>>> The data that I am trying to fit is the Cu metal example that come with
>>>>>
>>>> the
>>>>
>>>>> iffefit package. I am running Artemis on a Mac, OSX 10.4.11.
>>>>> I could run the fitting on a mac OSX 10.5 and it worked fine. I
>>>>> reinstall
>>>>> the IXAFS package but it didn't work.
>>>>>
>>>>> I am wondering what could be wrong with my machine/software?
>>>>>
>>>>> Thanks a lot.
>>>>>
>>>>>
>>>>> Juraci Sampaio
>>>>>
>>>>>
>>>>> ------------------------------
>>>>> Not?cias direto do New York Times, gols do Lance, videocassetadas e
>>>>>
>>>> muitos
>>>>
>>>>> outros v?deos no MSN Videos! Confira j?! <
>>>>>
>>>> http://video.msn.com/?mkt=pt-br>
>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Ifeffit mailing list
>>>>> Ifeffit at millenia.cars.aps.anl.gov
>>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>>>
>>>>>
>>>>> -------------- next part --------------
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>>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Wed, 28 Jan 2009 18:18:00 -0200
>>>> From: Yordy Licea Fonseca <yliceafonseca at gmail.com>
>>>> Subject: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
>>>> To: ifeffit at millenia.cars.aps.anl.gov
>>>> Message-ID:
>>>> <6bc7d27d0901281218t6eac4721o1922c155b95a1087 at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Hi,
>>>>
>>>> Sorry, I could not find enough information.
>>>> Would any of you tell me, please, how is the EXAFS data tabulated in
>>>> Farrel
>>>> Lytle data base?
>>>> The first column is the energy, what about others?
>>>> I would like to obtain the absorption coefficient vs energy from this
>>>> file:
>>>>
>>>> http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095
>>>>
>>>> Best wishes,
>>>>
>>>> --
>>>> Yordy E. Licea Fonseca
>>>> Departamento de F?sico-Qu?mica
>>>> Instituto de Qu?mica-IQ/UFRJ
>>>> Laborat?rio de Cat?lise Heterog?nea
>>>> Rio de Janeiro, RJ, CEP 21.949-909
>>>> Brasil
>>>> Email: yliceafonseca at gmail.com
>>>> -------------- next part --------------
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>>>>
>>>> ------------------------------
>>>>
>>>> Message: 4
>>>> Date: Wed, 28 Jan 2009 14:24:22 -0600
>>>> From: Matt Newville <newville at cars.uchicago.edu>
>>>> Subject: Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
>>>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>>>> Message-ID:
>>>> <b8522e3d0901281224v42f22a8cs6489a5792c4588f0 at mail.gmail.com>
>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>
>>>> Hi Yordy,
>>>>
>>>> The first column for that file is not energy, it is angular steps. See
>>>>
>>>>
>>>> http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#head-e7e2389af58d378379f3bbe2a827c73a6df2a42e
>>>>
>>>> and the other posts from earlier today for how to convert this data into
>>>> mu(E).
>>>>
>>>> --Matt
>>>>
>>>> On Wed, Jan 28, 2009 at 2:18 PM, Yordy Licea Fonseca
>>>> <yliceafonseca at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Sorry, I could not find enough information.
>>>>> Would any of you tell me, please, how is the EXAFS data tabulated in
>>>>>
>>>> Farrel
>>>>
>>>>> Lytle data base?
>>>>> The first column is the energy, what about others?
>>>>> I would like to obtain the absorption coefficient vs energy from this
>>>>> file:
>>>>>
>>>>> http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> --
>>>>> Yordy E. Licea Fonseca
>>>>> Departamento de F?sico-Qu?mica
>>>>> Instituto de Qu?mica-IQ/UFRJ
>>>>> Laborat?rio de Cat?lise Heterog?nea
>>>>> Rio de Janeiro, RJ, CEP 21.949-909
>>>>> Brasil
>>>>> Email: yliceafonseca at gmail.com
>>>>>
>>>>> _______________________________________________
>>>>> Ifeffit mailing list
>>>>> Ifeffit at millenia.cars.aps.anl.gov
>>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 5
>>>> Date: Thu, 29 Jan 2009 13:33:08 +1100
>>>> From: "Pushan Shah" <pshah at gse.mq.edu.au>
>>>> Subject: [Ifeffit] uncertainty in linear combination analysis
>>>> To: <ifeffit at millenia.cars.aps.anl.gov>
>>>> Message-ID: <4981B014.0BBD.0060.0 at gse.mq.edu.au>
>>>> Content-Type: text/plain; charset=US-ASCII
>>>>
>>>> Hello Everyone!
>>>>
>>>> How can I estimate an uncertainty in linear combination analysis and
>>>> calculate them in percentage error?
>>>>
>>>> Many thanks,
>>>> Pushan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 6
>>>> Date: Thu, 29 Jan 2009 15:41:55 +0530
>>>> From: abhijeet gaur <abhijeetgaur9 at gmail.com>
>>>> Subject: [Ifeffit] Artemis parameters
>>>> To: ifeffit at millenia.cars.aps.anl.gov
>>>> Message-ID:
>>>> <862a39070901290211s6a928d40yc902a09ff532f2a9 at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Hi
>>>> I am fitting a copper foil whose data is taken at room temperature. So
>>>> do I need to change the guess value of parameters enot, ss,amp, delr to
>>>> some
>>>> other value or I should take them as the default guess value. Also what
>>>> should be the ideal fitting range in R for the copper foil.
>>>>
>>>>
>>>> With thanks
>>>>
>>>> Abhijeet
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>>>> ------------------------------
>>>>
>>>> Message: 7
>>>> Date: Thu, 29 Jan 2009 11:00:32 -0200
>>>> From: Eugenio Otal <eugenioh at gmail.com>
>>>> Subject: [Ifeffit] Energy shift
>>>> To: ifeffit at millenia.cars.aps.anl.gov
>>>> Message-ID:
>>>> <da22ad30901290500s14de8d2dy4cbaf8ec693e6796 at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Hi Matt,
>>>> Thanks for your time, the shift is between calculated and experiment. I
>>>> attach two figures with and without correction, it matchs really good if
>>>> I
>>>> change 5.5eV the energy.
>>>> Thanks, euG
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>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> Ifeffit mailing list
>>>> Ifeffit at millenia.cars.aps.anl.gov
>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>>
>>>>
>>>> End of Ifeffit Digest, Vol 71, Issue 32
>>>> ***************************************
>>>>
>>>>
>>>
>>>
>>>
>>>
>> --
>> Carlo U. Segre -- Professor of Physics
>> Associate Dean for Special Projects, Graduate College
>> Illinois Institute of Technology
>> Voice: 312.567.3498 Fax: 312.567.3494
>> segre at iit.edu http://www.iit.edu/~segre segre at debian.org
>>
>
>
>
>
--
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498 Fax: 312.567.3494
segre at iit.edu http://www.iit.edu/~segre segre at debian.org
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