Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 119, Issue 15
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
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Sent: Wednesday, January 09, 2013 11:00 AM
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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@barc.gov.in)
----------------------------------------------------------------------
Message: 1
Date: Tue, 8 Jan 2013 16:07:28 -0600
From: Matt Newville
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@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@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@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@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
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@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@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@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 3 Date: Wed, 9 Jan 2013 10:28:17 +0530 From: sumitk@barc.gov.in To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] self absorption correction Message-ID: <335f18a7175b0c8a9d74662ec1c2dfe7.squirrel@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). ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 119, Issue 15 ****************************************
On Wednesday, January 09, 2013 07:43:34 PM Monson, Todd wrote:
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.
Todd, Whitespace barely matters. I'd recommend using spaces rather than tabs (but, in truth, I don't recall off the top of my head how Feff deals with tabs). Put Feff keywords in uppercase. Make sure the file ends in a new line. Other wise order of keywords doesn't matter. Atoms puts all keywords above the POTENTIALS list and the POTENTIALS list above the ATOMS list, but even that ordering doesn't matter. The best way to determine if a feff.inp file will work with feff is to point feff at it. If it finds something it doesn't like, it will give you some sort of error message. Good luck, B -- Bruce Ravel ------------------------------------ bravel@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
Todd, Bruce,
On Wed, Jan 9, 2013 at 2:05 PM, Bruce Ravel
On Wednesday, January 09, 2013 07:43:34 PM Monson, Todd wrote:
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.
Todd,
Whitespace barely matters. I'd recommend using spaces rather than tabs (but, in truth, I don't recall off the top of my head how Feff deals with tabs). Put Feff keywords in uppercase. Make sure the file ends in a new line. Other wise order of keywords doesn't matter.
For Feff6L (the one that comes with ifeffit), tabs (and most other non-printable ASCII characters other than newline and carriage-return) are replaced by spaces before parsing, so tabs and spaces can be mixed without trouble. I can't say how Feff8 or Feff9 handles tabs. Keywords do need to be in upper case. You know, to make it look more Fortran-y and like we're doing REAL WORK HERE. Cheers, --Matt
participants (3)
-
Bruce Ravel -
Matt Newville -
Monson, Todd