[Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15
Monson, Todd
tmonson at sandia.gov
Wed Jan 9 13:43:34 CST 2013
When making my own feff input file, how should the data be delimited. When looking at existing feff input files I see a mixture of different spaces and tabs and am unsure how I should separate coordinates, ipots, tags, etc.
Thanks,
Todd
-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request at millenia.cars.aps.anl.gov
Sent: Wednesday, January 09, 2013 11:00 AM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15
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Today's Topics:
1. Re: Larch 0.9.17 available for download and testing
(Matt Newville)
2. Re: Larch 0.9.17 available for download and testing
(Yu-Sheng Chen)
3. self absorption correction (sumitk at barc.gov.in)
----------------------------------------------------------------------
Message: 1
Date: Tue, 8 Jan 2013 16:07:28 -0600
From: Matt Newville <newville at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing
Message-ID:
<CA+7ESbq8w5MOAFu-rRJUi71WpVDjoNXG6VOpmiD_xryztVFQdQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Bruce,
Again, sorry (ever so slightly -- the skiing was great!!) for the
delay. I think (not 100% sure) I understand have solved the trouble
with wxmplot on ubuntu.
On an ubuntu 12.04 system (that had been upgraded a few times, and is begging to be updated to 12.10), I saw that importing wxmplot raised an error because maplotlib requires wx version 2.8 or greater but a regular old "import wx" was using the antique wx 2.6 series. I would be tempted to say that ubuntu is acting strangely by assuming "import wx" means "oldest possible version of a library", but I'm sure fixing at my end is easier than fixing all installed Ubuntu systems.
I've updated wxmplot to version 0.9.11, which now correctly requires wx 2.8 or higher. You should be able to now do easy_install or install with 'python setup.py install' from the wxmplot-0.9.11 source kit linked at http://newville.github.com/wxmplot/installation.html
I also had to make sure that larch was insisting that wx 2.8 or higher was being used. These changes are now pushed into the github distribution.
With these changes, I could successfully install wxmplot and larch on
an Ubuntu. I think that must be the same problem you were seeing,
but I'd be happy to hear your experience.
--Matt
On Wed, Jan 2, 2013 at 1:51 PM, Bruce Ravel <bravel at bnl.gov> wrote:
>
> Matt,
>
> I am having some troubles getting Larch installed on one of my Ubuntu
> machines. "sudo python setup.py install" complains about wxmplot
> being missing. OK, I did
>
> bruce at lachesis [xraylarch] > sudo -E easy_install wxmplot
> sudo: unable to resolve host lachesis.bnl.gov
> Searching for wxmplot
> Best match: wxmplot 0.9.10
> Processing wxmplot-0.9.10-py2.7.egg
> wxmplot 0.9.10 is already the active version in easy-install.pth
>
> Using /usr/local/lib/python2.7/dist-packages/wxmplot-0.9.10-py2.7.egg
> Processing dependencies for wxmplot
> Finished processing dependencies for wxmplot
>
> and tried again.
>
> bruce at lachesis [xraylarch] > sudo python setup.py install
> sudo: unable to resolve host lachesis.bnl.gov
> Checking dependencies....
> == Cannot Install Larch: Required Modules are Missing ==
> wxmplot is REQUIRED
>
> Please read INSTALL for further information.
>
> OK. I cloned a copy of wxmplot from your github repo and installed it
> by hand with no problem. However, same result when trying to setup
> xraylarch.
>
> Any advice?
>
> Thx,
> B
>
> --
>
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology Synchrotron Methods
> Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY,
> 11973
>
> Homepage: http://xafs.org/BruceRavel
> Software: https://github.com/bruceravel
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
------------------------------
Message: 2
Date: Tue, 8 Jan 2013 23:21:54 +0000
From: Yu-Sheng Chen <yschen at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing
Message-ID:
<63D4F9008F0BD04FAC515D20F0CC6A46437D035A at CARSMAIL2.CARS.APS.ANL.GOV>
Content-Type: text/plain; charset="us-ascii"
Hello Mark.
I think you got 3 shifts this coming run.
Yu-Sheng
****************************************
Yu-Sheng Chen, Ph.D.
Center for Advanced Radiation Sources
The University of Chicago c/o APS/ANL
9700 S. Cass Ave.
Bldg. 434 D
Argonne, IL 60439
USA
Tel: +1 630-252-0471
Fax: +1 630-252-0460
EMail: yschen at cars.uchicago.edu
-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Matt Newville
Sent: Tuesday, January 08, 2013 4:07 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Larch 0.9.17 available for download and testing
Hi Bruce,
Again, sorry (ever so slightly -- the skiing was great!!) for the
delay. I think (not 100% sure) I understand have solved the trouble
with wxmplot on ubuntu.
On an ubuntu 12.04 system (that had been upgraded a few times, and is begging to be updated to 12.10), I saw that importing wxmplot raised an error because maplotlib requires wx version 2.8 or greater but a regular old "import wx" was using the antique wx 2.6 series. I would be tempted to say that ubuntu is acting strangely by assuming "import wx" means "oldest possible version of a library", but I'm sure fixing at my end is easier than fixing all installed Ubuntu systems.
I've updated wxmplot to version 0.9.11, which now correctly requires wx 2.8 or higher. You should be able to now do easy_install or install with 'python setup.py install' from the wxmplot-0.9.11 source kit linked at http://newville.github.com/wxmplot/installation.html
I also had to make sure that larch was insisting that wx 2.8 or higher was being used. These changes are now pushed into the github distribution.
With these changes, I could successfully install wxmplot and larch on
an Ubuntu. I think that must be the same problem you were seeing,
but I'd be happy to hear your experience.
--Matt
On Wed, Jan 2, 2013 at 1:51 PM, Bruce Ravel <bravel at bnl.gov> wrote:
>
> Matt,
>
> I am having some troubles getting Larch installed on one of my Ubuntu
> machines. "sudo python setup.py install" complains about wxmplot
> being missing. OK, I did
>
> bruce at lachesis [xraylarch] > sudo -E easy_install wxmplot
> sudo: unable to resolve host lachesis.bnl.gov
> Searching for wxmplot
> Best match: wxmplot 0.9.10
> Processing wxmplot-0.9.10-py2.7.egg
> wxmplot 0.9.10 is already the active version in easy-install.pth
>
> Using /usr/local/lib/python2.7/dist-packages/wxmplot-0.9.10-py2.7.egg
> Processing dependencies for wxmplot
> Finished processing dependencies for wxmplot
>
> and tried again.
>
> bruce at lachesis [xraylarch] > sudo python setup.py install
> sudo: unable to resolve host lachesis.bnl.gov
> Checking dependencies....
> == Cannot Install Larch: Required Modules are Missing ==
> wxmplot is REQUIRED
>
> Please read INSTALL for further information.
>
> OK. I cloned a copy of wxmplot from your github repo and installed it
> by hand with no problem. However, same result when trying to setup
> xraylarch.
>
> Any advice?
>
> Thx,
> B
>
> --
>
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology Synchrotron Methods
> Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY,
> 11973
>
> Homepage: http://xafs.org/BruceRavel
> Software: https://github.com/bruceravel
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
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------------------------------
Message: 3
Date: Wed, 9 Jan 2013 10:28:17 +0530
From: sumitk at barc.gov.in
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] self absorption correction
Message-ID:
<335f18a7175b0c8a9d74662ec1c2dfe7.squirrel at bts.barc.gov.in>
Content-Type: text/plain;charset=UTF-8
Thanks Bruce. Till the time i look into the suggested works, here is the missing informations.
Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data.
The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04.
Material: Eu(III) sorbed on silica.
Sumit
--
Sumit Kumar
Scientific Officer(E)
Radioanalytical Chemistry Division
Bhabha Atomic Research Centre
Mumbai, India-400 085.
Phone: +91-22-2559 4093/0644 (O).
------------------------------
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