September 2010 - Ifeffit - millenia.cars.aps.anl.gov

Help with Artemis fit
by Han Sen Soo 19 Sep '10

19 Sep '10

Hello, I'm a post-doc at LBL and I recently attended the XAFS Summer School at IIT. I just started trying to fit some data on titanium sites embedded in amorphous silica and I was hoping to get some advice on how to improve my fit. My first objective is to get an idea of the coordination number of Ti, and I'm trying to do this in Artemis by using the parameter N as my S0^2 and letting the amplitude of S0^2 vary. I'm not sure if this is appropriate? A problem I am encountering is that the physically reasonable fits look visually unacceptable. I am just trying to fit the first Ti-O shell initially and plan to work on the 2nd shell subsequently. The R space fit for the first shell has 2 peaks that are about 0.3 Å apart at 1.2 and 1.5 Å (uncorrected). With only 1 shell of O atoms at a distance I found for similar materials, a reasonable fit was found (including background fitting) but the amplitude of the fit at the 1.5 Å peak is too high while the amplitude at the 1.2 Å peak is too low. I naively tried to improve the fit by adding a 2nd shell at a shorter distance and tried different combinations of distances 0.02 Å apart, but I consistently find that the sigma^2 values for one or both shells become negative. I also realized that the resolution of the data may not be sufficient to distinguish shells that are less than 0.2 Å apart, which is what I am expecting based on data on similar materials. I have attached a pdf image of one of the bad fits. My question then is, should I not try to improve the fit and accept the 1 shell fit, or am I mis-interpreting the fit and are there ways I can introduce the 2nd shell without having an unphysical model (the main problem being the negative sigma^2)? Thanks for reading and any suggestions! han sen

2 1

Re: [Ifeffit] XasPerlBundle problems
by Joshua Kas 18 Sep '10

18 Sep '10

Hi Matt, Thanks for the quick response. I did run the command from within the horae install directory, and the file XasPerlBundle.pm is in the Bundle directory, i.e., verrocchio.phys #] pwd /tmp/horae-070 verrocchio.phys #] ls . Bundle INSTALL aug build_private libperlxray .. CPAN INSTALL_not_root build horae verrocchio.phys #] ls Bundle/ . .. XasPerlBundle.pm verrocchio.phys #] perl -MCPAN -e'install Bundle::XasPerlBundle' CPAN: Storable loaded ok Going to read /CPAN/Metadata Database was generated on Fri, 17 Sep 2010 18:28:36 GMT CPAN: LWP::UserAgent loaded ok Fetching with LWP: http://www.perl.com/CPAN/authors/01mailrc.txt.gz Going to read /CPAN/source/authors/01mailrc.txt.gz Fetching with LWP: http://www.perl.com/CPAN/modules/02packages.details.txt.gz Going to read /CPAN/source/modules/02packages.details.txt.gz Database was generated on Sat, 18 Sep 2010 17:59:57 GMT There's a new CPAN.pm version (v1.9402) available! [Current version is v1.7602] You might want to try install Bundle::CPAN reload cpan without quitting the current session. It should be a seamless upgrade while we are running... Fetching with LWP: http://www.perl.com/CPAN/modules/03modlist.data.gz Going to read /CPAN/source/modules/03modlist.data.gz Going to write /CPAN/Metadata Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. Try the command i /Bundle::XasPerlBundle/ to find objects with matching identifiers. Could there be something wrong with my installation of CPAN that would cause this behavior? Cheers, Josh Kas On Sat, Sep 18, 2010 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: XasPerlBundle problems (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Sep 2010 16:32:53 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XasPerlBundle problems > Message-ID: > <AANLkTi=tDjqnmBT8nhWZ0VtAMrvyZTSdvHLPePmR0iYu(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Josh, > > That cpan command should be done from the horae install directory. Saying > > perl -MCPAN -e 'install Bundle::XXX' > > is looking for the file named XXX.pm (which simply contains a list of > Perl modules) > in the directory Bundle/. I think that if it can't find that, then > it goes to look on-line. > > Cheers, > > --Matt > > > On Fri, Sep 17, 2010 at 3:24 PM, Joshua Kas <joshua.j.kas(a)gmail.com> > wrote: > > Hi, > > I'm trying to install horae on RHEL5 and I'm having trouble getting the > > prerequisites from CPAN. IFEFFIT installed fine, but when I try to > install > > ARTEMIS/ATHENA I have the following problem: > > > > verrocchio.phys #] perl -MCPAN -e 'install Bundle::XasPerlBundle' > > CPAN: Storable loaded ok > > Going to read /CPAN/Metadata > > ? Database was generated on Fri, 17 Sep 2010 18:28:36 GMT > > Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. > > Try the command > > > > ??? i /Bundle::XasPerlBundle/ > > > > to find objects with matching identifiers. > > > > This was after becoming root, then copying the CPAN/MyConfig.pm file to > > ~/.cpan/CPAN/. > > I am using the mose recent version of the horae tarball, i.e., horae-070. > > I'm out of ideas for now. > > Thanks very much for any help. > > Josh Kas > > > > On Fri, Sep 17, 2010 at 10:00 AM, > > <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > >> > >> Send Ifeffit mailing list submissions to > >> ? ? ? ?ifeffit(a)millenia.cars.aps.anl.gov > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> ? ? ? ?http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> or, via email, send a message with subject or body 'help' to > >> ? ? ? ?ifeffit-request(a)millenia.cars.aps.anl.gov > >> > >> You can reach the person managing the list at > >> ? ? ? ?ifeffit-owner(a)millenia.cars.aps.anl.gov > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of Ifeffit digest..." > >> > >> > >> Today's Topics: > >> > >> ? 1. Re: Bkg removal problem (Alfred Hummer) > >> ? 2. Mathematical expressions for the path parameters in ? ? ? Fitting > >> ? ? ?(sumitk(a)barc.gov.in) > >> ? 3. Re: Mathematical expressions for the path parameters in > >> ? ? ?Fitting (Shelly Kelly) > >> ? 4. Re: Mathematical expressions for the path parameters in > >> ? ? ?Fitting (Brandon Reese) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 16 Sep 2010 19:58:53 +0200 > >> From: Alfred Hummer <alfred.hummer(a)univie.ac.at> > >> To: ifeffit(a)millenia.cars.aps.anl.gov > >> Subject: Re: [Ifeffit] Bkg removal problem > >> Message-ID: <4C925ADD.90306(a)univie.ac.at> > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >> > >> > >> Thx for the detailed answer. Helped me a lot. > >> Also tested it with other programs using smoothed splines, leading to > >> similar results. > >> > >> And you are right, I don't expect a peak at about 1A in the FT. The > >> first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N > >> atoms at about 2A distance. > >> > >> best regards Alfred > >> > >> > >> Am 15.09.2010 19:00, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > >> > Send Ifeffit mailing list submissions to > >> > ? ? ? ifeffit(a)millenia.cars.aps.anl.gov > >> > > >> > To subscribe or unsubscribe via the World Wide Web, visit > >> > ? ? ? http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > or, via email, send a message with subject or body 'help' to > >> > ? ? ? ifeffit-request(a)millenia.cars.aps.anl.gov > >> > > >> > You can reach the person managing the list at > >> > ? ? ? ifeffit-owner(a)millenia.cars.aps.anl.gov > >> > > >> > When replying, please edit your Subject line so it is more specific > >> > than "Re: Contents of Ifeffit digest..." > >> > > >> > > >> > Today's Topics: > >> > > >> > ? ? 1. Re: Bkg removal problem (Bruce Ravel) > >> > > >> > > >> > ---------------------------------------------------------------------- > >> > > >> > Message: 1 > >> > Date: Tue, 14 Sep 2010 14:07:55 -0400 > >> > From: Bruce Ravel<bravel(a)bnl.gov> > >> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > >> > Subject: Re: [Ifeffit] Bkg removal problem > >> > Message-ID:<201009141407.55193.bravel(a)bnl.gov> > >> > Content-Type: Text/Plain; ?charset="iso-8859-1" > >> > > >> > > >> > Alfred, > >> > > >> > I certainly encourage you to look at Shelly's book chapter. It's very > >> > useful. > >> > > >> > The question you ask is one that we hear frequently on this mailing > >> > list. ?I don't mean anything bad by saying that -- in fact, it's an > >> > excellent question that every practitioner of XAS needs to come to > >> > terms with early on in his or her XAS career. ?Indeed, I am pleased > >> > that you are insightful enough to recognize your confusion and wise > >> > enough to ask for help. > >> > > >> > That said, I am a bit weary of answering questions about Rbkg on the > >> > mailing list. ?Yours ain't the first! ;-) > >> > > >> > Rather than answering here, I decided to write up a wiki page on the > >> > topic. ?That way, I'll have something to point to the next time > >> > someone asks about Rbkg. > >> > > >> > Here it is: > >> > ? ?http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk > >> > > >> > Hope it helps, > >> > B > >> > > >> > > >> > On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote: > >> >> Hi Alfred: > >> >> > >> >> You should take a look at my book chapter. I go through a lot of > >> >> details on how to remove the background. If you want a copy just send > >> >> me an email directly and I'll send you a pdf. > >> >> > >> >> Cheers, > >> >> Shelly > >> >> exafs(a)netzero.com > >> >> > >> >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer > >> >> > >> >> <alfred.hummer(a)univie.ac.at> ?wrote: > >> >>> Hello, > >> >>> > >> >>> Currently I am working on a Ga XAS spectrum. > >> >>> I'm trying to extract the EXAFS data but I'm not sure if the > >> >>> background > >> >>> function is right, or how to set the right values. > >> >>> > >> >>> I played around with different setting for kmin and Rbkg. > >> >>> So far I know that Rbkg defines the cutoff for the bkg frequencies > in > >> >>> the > >> >>> FT optimization and setting it to high leads to loss in information, > >> >>> as > >> >>> more high frequencies are included in the bkg. > >> >>> > >> >>> I also read that it is advisable to exclude strong white lines from > >> >>> the > >> >>> spline range (increasing kmin?). Would this a strategy in my case? > >> >>> > >> >>> I attached the project file. > >> >>> > >> >>> Maybe someone has a clue. The more I tried the bigger my > uncertainty. > >> >>> > >> >>> best regards > >> >>> > >> >>> Alfred > >> >>> > >> >>> > >> >>> _______________________________________________ > >> >>> Ifeffit mailing list > >> >>> Ifeffit(a)millenia.cars.aps.anl.gov > >> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> >> > >> >> _______________________________________________ > >> >> Ifeffit mailing list > >> >> Ifeffit(a)millenia.cars.aps.anl.gov > >> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> >> > >> > > >> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Fri, 17 Sep 2010 11:31:34 +0530 > >> From: sumitk(a)barc.gov.in > >> To: ifeffit(a)millenia.cars.aps.anl.gov > >> Subject: [Ifeffit] Mathematical expressions for the path parameters in > >> ? ? ? ?Fitting > >> Message-ID: > >> ? ? ? ?<edb6390523394cc867a1b7e12aa03d81.squirrel(a)bts.barc.gov.in> > >> Content-Type: text/plain;charset=UTF-8 > >> > >> Hello, > >> In EXAFS data modeling carried out by fitting excercise, we develop > >> mathematical expressions for ?different path parametrs as functions of a > >> smaller set of fitting parameters that can be adjusted to achieve to > best > >> fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > >> different environmentally relevent mineral oxides. In conection of this > i > >> also analysed some reference standard compounds. In developing > expression > >> for different path parameters, though i developed the expressions using > my > >> own ?understanding and taking help from one of Shelly's tutorial > regarding > >> SnO2 case, i am not confident. Basically SS2, and deltaE expressions > >> puzzle me. > >> Could someone help me in understanding basic approach in developing > their > >> expressions(for reference Eu2O3 structure could be taken). > >> Regards, > >> Sumit > >> > >> > >> > >> > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Fri, 17 Sep 2010 10:40:14 -0500 > >> From: Shelly Kelly <dr.sdkelly(a)gmail.com> > >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >> Subject: Re: [Ifeffit] Mathematical expressions for the path > >> ? ? ? ?parameters in ? Fitting > >> Message-ID: > >> ? ? ? ?<AANLkTim40RLMwFRFm1JN0becDx7MM7Lthqmw_xu=Jsk-(a)mail.gmail.com> > >> Content-Type: text/plain; charset=ISO-8859-1 > >> > >> Hi Sumit: > >> > >> There are a lot of different ways to constrain the EXAFS parameters in > >> a fitting model. Mostly they are determined by physically meaningful > >> relationships or through trial and error of "what works". I just sent > >> you my book chapter and you will find detailed discussion on many of > >> the common constraints in there. Another good place to look is in the > >> literature to find out what people have done for systems similar to > >> yours. > >> > >> HTH, > >> Shelly > >> > >> On Fri, Sep 17, 2010 at 1:01 AM, ?<sumitk(a)barc.gov.in> wrote: > >> > Hello, > >> > In EXAFS data modeling carried out by fitting excercise, we develop > >> > mathematical expressions for ?different path parametrs as functions of > a > >> > smaller set of fitting parameters that can be adjusted to achieve to > >> > best > >> > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > >> > different environmentally relevent mineral oxides. In conection of > this > >> > i > >> > also analysed some reference standard compounds. In developing > >> > expression > >> > for different path parameters, though i developed the expressions > using > >> > my > >> > own ?understanding and taking help from one of Shelly's tutorial > >> > regarding > >> > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > >> > puzzle me. > >> > Could someone help me in understanding basic approach in developing > >> > their > >> > expressions(for reference Eu2O3 structure could be taken). > >> > Regards, > >> > Sumit > >> > > >> > > >> > > >> > _______________________________________________ > >> > Ifeffit mailing list > >> > Ifeffit(a)millenia.cars.aps.anl.gov > >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > >> > >> > >> > >> ------------------------------ > >> > >> Message: 4 > >> Date: Fri, 17 Sep 2010 10:54:21 -0600 > >> From: Brandon Reese <bjreese(a)gmail.com> > >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >> Subject: Re: [Ifeffit] Mathematical expressions for the path > >> ? ? ? ?parameters in ? Fitting > >> Message-ID: > >> ? ? ? ?<AANLkTikQG0L=-QWp_EX51XSuOYvN7_JZvESh5o9LSDp6(a)mail.gmail.com> > >> Content-Type: text/plain; charset="iso-8859-1" > >> > >> Hi Shelly, > >> > >> I am also looking into different ways to constrain my EXAFS fits. ?If > you > >> wouldn't mind, I would also be very interested in a copy of your book > >> chapter. > >> > >> Thanks, > >> Brandon > >> > >> On Fri, Sep 17, 2010 at 9:40 AM, Shelly Kelly <dr.sdkelly(a)gmail.com> > >> wrote: > >> > >> > Hi Sumit: > >> > > >> > There are a lot of different ways to constrain the EXAFS parameters in > >> > a fitting model. Mostly they are determined by physically meaningful > >> > relationships or through trial and error of "what works". I just sent > >> > you my book chapter and you will find detailed discussion on many of > >> > the common constraints in there. Another good place to look is in the > >> > literature to find out what people have done for systems similar to > >> > yours. > >> > > >> > HTH, > >> > Shelly > >> > > >> > On Fri, Sep 17, 2010 at 1:01 AM, ?<sumitk(a)barc.gov.in> wrote: > >> > > Hello, > >> > > In EXAFS data modeling carried out by fitting excercise, we develop > >> > > mathematical expressions for ?different path parametrs as functions > of > >> > > a > >> > > smaller set of fitting parameters that can be adjusted to achieve to > >> > > best > >> > > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed > on > >> > > different environmentally relevent mineral oxides. In conection of > >> > > this i > >> > > also analysed some reference standard compounds. In developing > >> > > expression > >> > > for different path parameters, though i developed the expressions > >> > > using > >> > my > >> > > own ?understanding and taking help from one of Shelly's tutorial > >> > regarding > >> > > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > >> > > puzzle me. > >> > > Could someone help me in understanding basic approach in developing > >> > > their > >> > > expressions(for reference Eu2O3 structure could be taken). > >> > > Regards, > >> > > Sumit > >> > > > >> > > > >> > > > >> > > _______________________________________________ > >> > > Ifeffit mailing list > >> > > Ifeffit(a)millenia.cars.aps.anl.gov > >> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > >> > > >> > _______________________________________________ > >> > Ifeffit mailing list > >> > Ifeffit(a)millenia.cars.aps.anl.gov > >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > >>

1 0

XasPerlBundle problems
by Joshua Kas 17 Sep '10

17 Sep '10

Hi, I'm trying to install horae on RHEL5 and I'm having trouble getting the prerequisites from CPAN. IFEFFIT installed fine, but when I try to install ARTEMIS/ATHENA I have the following problem: verrocchio.phys #] perl -MCPAN -e 'install Bundle::XasPerlBundle' CPAN: Storable loaded ok Going to read /CPAN/Metadata Database was generated on Fri, 17 Sep 2010 18:28:36 GMT Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. Try the command i /Bundle::XasPerlBundle/ to find objects with matching identifiers. This was after becoming root, then copying the CPAN/MyConfig.pm file to ~/.cpan/CPAN/. I am using the mose recent version of the horae tarball, i.e., horae-070. I'm out of ideas for now. Thanks very much for any help. Josh Kas On Fri, Sep 17, 2010 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Bkg removal problem (Alfred Hummer) > 2. Mathematical expressions for the path parameters in Fitting > (sumitk(a)barc.gov.in) > 3. Re: Mathematical expressions for the path parameters in > Fitting (Shelly Kelly) > 4. Re: Mathematical expressions for the path parameters in > Fitting (Brandon Reese) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Sep 2010 19:58:53 +0200 > From: Alfred Hummer <alfred.hummer(a)univie.ac.at> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Bkg removal problem > Message-ID: <4C925ADD.90306(a)univie.ac.at> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Thx for the detailed answer. Helped me a lot. > Also tested it with other programs using smoothed splines, leading to > similar results. > > And you are right, I don't expect a peak at about 1A in the FT. The > first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N > atoms at about 2A distance. > > best regards Alfred > > > Am 15.09.2010 19:00, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > > Send Ifeffit mailing list submissions to > > ifeffit(a)millenia.cars.aps.anl.gov > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > or, via email, send a message with subject or body 'help' to > > ifeffit-request(a)millenia.cars.aps.anl.gov > > > > You can reach the person managing the list at > > ifeffit-owner(a)millenia.cars.aps.anl.gov > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Ifeffit digest..." > > > > > > Today's Topics: > > > > 1. Re: Bkg removal problem (Bruce Ravel) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 14 Sep 2010 14:07:55 -0400 > > From: Bruce Ravel<bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Bkg removal problem > > Message-ID:<201009141407.55193.bravel(a)bnl.gov> > > Content-Type: Text/Plain; charset="iso-8859-1" > > > > > > Alfred, > > > > I certainly encourage you to look at Shelly's book chapter. It's very > > useful. > > > > The question you ask is one that we hear frequently on this mailing > > list. I don't mean anything bad by saying that -- in fact, it's an > > excellent question that every practitioner of XAS needs to come to > > terms with early on in his or her XAS career. Indeed, I am pleased > > that you are insightful enough to recognize your confusion and wise > > enough to ask for help. > > > > That said, I am a bit weary of answering questions about Rbkg on the > > mailing list. Yours ain't the first! ;-) > > > > Rather than answering here, I decided to write up a wiki page on the > > topic. That way, I'll have something to point to the next time > > someone asks about Rbkg. > > > > Here it is: > > http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk > > > > Hope it helps, > > B > > > > > > On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote: > >> Hi Alfred: > >> > >> You should take a look at my book chapter. I go through a lot of > >> details on how to remove the background. If you want a copy just send > >> me an email directly and I'll send you a pdf. > >> > >> Cheers, > >> Shelly > >> exafs(a)netzero.com > >> > >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer > >> > >> <alfred.hummer(a)univie.ac.at> wrote: > >>> Hello, > >>> > >>> Currently I am working on a Ga XAS spectrum. > >>> I'm trying to extract the EXAFS data but I'm not sure if the background > >>> function is right, or how to set the right values. > >>> > >>> I played around with different setting for kmin and Rbkg. > >>> So far I know that Rbkg defines the cutoff for the bkg frequencies in > the > >>> FT optimization and setting it to high leads to loss in information, as > >>> more high frequencies are included in the bkg. > >>> > >>> I also read that it is advisable to exclude strong white lines from the > >>> spline range (increasing kmin?). Would this a strategy in my case? > >>> > >>> I attached the project file. > >>> > >>> Maybe someone has a clue. The more I tried the bigger my uncertainty. > >>> > >>> best regards > >>> > >>> Alfred > >>> > >>> > >>> _______________________________________________ > >>> Ifeffit mailing list > >>> Ifeffit(a)millenia.cars.aps.anl.gov > >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Sep 2010 11:31:34 +0530 > From: sumitk(a)barc.gov.in > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Mathematical expressions for the path parameters in > Fitting > Message-ID: > <edb6390523394cc867a1b7e12aa03d81.squirrel(a)bts.barc.gov.in> > Content-Type: text/plain;charset=UTF-8 > > Hello, > In EXAFS data modeling carried out by fitting excercise, we develop > mathematical expressions for different path parametrs as functions of a > smaller set of fitting parameters that can be adjusted to achieve to best > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > different environmentally relevent mineral oxides. In conection of this i > also analysed some reference standard compounds. In developing expression > for different path parameters, though i developed the expressions using my > own understanding and taking help from one of Shelly's tutorial regarding > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > puzzle me. > Could someone help me in understanding basic approach in developing their > expressions(for reference Eu2O3 structure could be taken). > Regards, > Sumit > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 17 Sep 2010 10:40:14 -0500 > From: Shelly Kelly <dr.sdkelly(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Mathematical expressions for the path > parameters in Fitting > Message-ID: > <AANLkTim40RLMwFRFm1JN0becDx7MM7Lthqmw_xu=Jsk-(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Sumit: > > There are a lot of different ways to constrain the EXAFS parameters in > a fitting model. Mostly they are determined by physically meaningful > relationships or through trial and error of "what works". I just sent > you my book chapter and you will find detailed discussion on many of > the common constraints in there. Another good place to look is in the > literature to find out what people have done for systems similar to > yours. > > HTH, > Shelly > > On Fri, Sep 17, 2010 at 1:01 AM, <sumitk(a)barc.gov.in> wrote: > > Hello, > > In EXAFS data modeling carried out by fitting excercise, we develop > > mathematical expressions for ?different path parametrs as functions of a > > smaller set of fitting parameters that can be adjusted to achieve to best > > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > > different environmentally relevent mineral oxides. In conection of this i > > also analysed some reference standard compounds. In developing expression > > for different path parameters, though i developed the expressions using > my > > own ?understanding and taking help from one of Shelly's tutorial > regarding > > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > > puzzle me. > > Could someone help me in understanding basic approach in developing their > > expressions(for reference Eu2O3 structure could be taken). > > Regards, > > Sumit > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 17 Sep 2010 10:54:21 -0600 > From: Brandon Reese <bjreese(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Mathematical expressions for the path > parameters in Fitting > Message-ID: > <AANLkTikQG0L=-QWp_EX51XSuOYvN7_JZvESh5o9LSDp6(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Shelly, > > I am also looking into different ways to constrain my EXAFS fits. If you > wouldn't mind, I would also be very interested in a copy of your book > chapter. > > Thanks, > Brandon > > On Fri, Sep 17, 2010 at 9:40 AM, Shelly Kelly <dr.sdkelly(a)gmail.com> > wrote: > > > Hi Sumit: > > > > There are a lot of different ways to constrain the EXAFS parameters in > > a fitting model. Mostly they are determined by physically meaningful > > relationships or through trial and error of "what works". I just sent > > you my book chapter and you will find detailed discussion on many of > > the common constraints in there. Another good place to look is in the > > literature to find out what people have done for systems similar to > > yours. > > > > HTH, > > Shelly > > > > On Fri, Sep 17, 2010 at 1:01 AM, <sumitk(a)barc.gov.in> wrote: > > > Hello, > > > In EXAFS data modeling carried out by fitting excercise, we develop > > > mathematical expressions for different path parametrs as functions of > a > > > smaller set of fitting parameters that can be adjusted to achieve to > best > > > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > > > different environmentally relevent mineral oxides. In conection of this > i > > > also analysed some reference standard compounds. In developing > expression > > > for different path parameters, though i developed the expressions using > > my > > > own understanding and taking help from one of Shelly's tutorial > > regarding > > > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > > > puzzle me. > > > Could someone help me in understanding basic approach in developing > their > > > expressions(for reference Eu2O3 structure could be taken). > > > Regards, > > > Sumit > > > > > > > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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Mathematical expressions for the path parameters in Fitting
by sumitk＠barc.gov.in 17 Sep '10

17 Sep '10

Hello, In EXAFS data modeling carried out by fitting excercise, we develop mathematical expressions for different path parametrs as functions of a smaller set of fitting parameters that can be adjusted to achieve to best fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on different environmentally relevent mineral oxides. In conection of this i also analysed some reference standard compounds. In developing expression for different path parameters, though i developed the expressions using my own understanding and taking help from one of Shelly's tutorial regarding SnO2 case, i am not confident. Basically SS2, and deltaE expressions puzzle me. Could someone help me in understanding basic approach in developing their expressions(for reference Eu2O3 structure could be taken). Regards, Sumit

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Re: [Ifeffit] Bkg removal problem
by Alfred Hummer 16 Sep '10

16 Sep '10

Thx for the detailed answer. Helped me a lot. Also tested it with other programs using smoothed splines, leading to similar results. And you are right, I don't expect a peak at about 1A in the FT. The first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N atoms at about 2A distance. best regards Alfred Am 15.09.2010 19:00, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Bkg removal problem (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 Sep 2010 14:07:55 -0400 > From: Bruce Ravel<bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Bkg removal problem > Message-ID:<201009141407.55193.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > > Alfred, > > I certainly encourage you to look at Shelly's book chapter. It's very > useful. > > The question you ask is one that we hear frequently on this mailing > list. I don't mean anything bad by saying that -- in fact, it's an > excellent question that every practitioner of XAS needs to come to > terms with early on in his or her XAS career. Indeed, I am pleased > that you are insightful enough to recognize your confusion and wise > enough to ask for help. > > That said, I am a bit weary of answering questions about Rbkg on the > mailing list. Yours ain't the first! ;-) > > Rather than answering here, I decided to write up a wiki page on the > topic. That way, I'll have something to point to the next time > someone asks about Rbkg. > > Here it is: > http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk > > Hope it helps, > B > > > On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote: >> Hi Alfred: >> >> You should take a look at my book chapter. I go through a lot of >> details on how to remove the background. If you want a copy just send >> me an email directly and I'll send you a pdf. >> >> Cheers, >> Shelly >> exafs(a)netzero.com >> >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer >> >> <alfred.hummer(a)univie.ac.at> wrote: >>> Hello, >>> >>> Currently I am working on a Ga XAS spectrum. >>> I'm trying to extract the EXAFS data but I'm not sure if the background >>> function is right, or how to set the right values. >>> >>> I played around with different setting for kmin and Rbkg. >>> So far I know that Rbkg defines the cutoff for the bkg frequencies in the >>> FT optimization and setting it to high leads to loss in information, as >>> more high frequencies are included in the bkg. >>> >>> I also read that it is advisable to exclude strong white lines from the >>> spline range (increasing kmin?). Would this a strategy in my case? >>> >>> I attached the project file. >>> >>> Maybe someone has a clue. The more I tried the bigger my uncertainty. >>> >>> best regards >>> >>> Alfred >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

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Bkg removal problem
by Alfred Hummer 14 Sep '10

14 Sep '10

Hello, Currently I am working on a Ga XAS spectrum. I'm trying to extract the EXAFS data but I'm not sure if the background function is right, or how to set the right values. I played around with different setting for kmin and Rbkg. So far I know that Rbkg defines the cutoff for the bkg frequencies in the FT optimization and setting it to high leads to loss in information, as more high frequencies are included in the bkg. I also read that it is advisable to exclude strong white lines from the spline range (increasing kmin?). Would this a strategy in my case? I attached the project file. Maybe someone has a clue. The more I tried the bigger my uncertainty. best regards Alfred

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changing valence state
by JeongEunSuk 11 Sep '10

11 Sep '10

Hi all I want to change valence state for XANES calculation in FEFF , from Co2+ to Co3+ Is it possible in FEFF?

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(Reposted) K-space vs R-spce fitting
by Lezama Pacheco, Juan Salvador 11 Sep '10

11 Sep '10

Hi Matt: Thanks so much for your answer. Let's see if I can make it more clear this time. Should dk have an effect on the actual fit, if it is performed in k-space? As I said, I found out that by changing dk (in k space) (keeping (kmin,kmax) constant) values change around 15%, so that tells me the actual fitting range is (kmin-dk/2,kmax+dk/2) is that so? Juan

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Hi ! I am PHD student in Taiwan.
by clo 11 Sep '10

11 Sep '10

Dear joly: I am PHD student at deparment of physics of National Sun Yat-Sen University in Taiwan. I have some problems about DOS simulation by using Feff. 1.I want to compare the simulation result with the LDA+"U" calculation, Could you give some suggestions for presentation the "U" potential part by Feff? thank you for your help Chun Pin Wu

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K-space vs R-spce fitting
by Lezama Pacheco, Juan Salvador 11 Sep '10

11 Sep '10

Dear All: First of all, nicely done you guys! This is indeed a set great of tools the community really appreciates it and I have been putting into heavy use. I have and issue though that has been making me scratch my head from time to time. I've been trying to figure out the feature of k-space and R-space fitting "relationship" for Ifeffit. I usually work out my fits in k-space although I have to admit that R-space fitting in combined approach will definitely be valuable. Now, as I am trying to work some data for Uranium (namely uranyl acetate standard) I am a little bit confused on the real independency of k-space and R-space fitting. This comes from the fact that even if I specified the fitting range in k (fitting in k space), the dk value seems to have an effect in the current fit values (changing as large as 15%). I understand the issue if the actual fitting range is then (kmin-dk/2,kmax+dk/2) but is this the case? Then what is the real relationship-independency between k-space and R-space fitting? For q-space that is of course another story. For the record I am using ixafs 1.2 on Mac OS X 10.5.8. Perl distribution seems to crash "unexpectedly" every time I tried the new 3.0.2, but that is another story in another thread... Thanks so much again Juan S Lezama

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