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

how to manage Demeter with a newer FEFF version ?
by fred.mosselmans＠diamond.ac.uk 10 Jun '15

10 Jun '15

Dear Janeth, Feff8.5L (and presumably 8.4) works in some fashion in Demeter version 18.2 , in later versions it doesnt. : It runs through atoms and gives fits that seems sensible for transuranic elements in the times I and some of my collaborators have used it. Thus in the short term if you want to use something higher than FEFF6 in your exafs calculations and want to use Demeter that's your option, If you need to use FeFF9 and want to use Demeter: I think your best option is to have a go at persuading some of the software guys at your facility to collaborate with Bruce and Matt in adding a FEFF9 option to larch and in turn then Demeter. Best wishes Fred ---------------------------------------------------------------------- Message: 1 Date: Mon, 08 Jun 2015 11:13:33 +0200 From: "M. Janeth LOZANO RODRIGUEZ" <janeth.lozano-rodriguez(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? Message-ID: <55755CBD.6010007(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 148, Issue 10 ****************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 10
by Guanghui Zhang 08 Jun '15

08 Jun '15

Janeth, As far as I know, Bruce is working on integraton of FEFF 8.5 into Demeter. I also experienced reviewers asking for newer version of FEFF in the data analysis. Below was a summary of our response. Feff 6 does not understand valence, and FEFF 8 uses a self-consistency loop to transfer charge between the atom types, resulting in something that can be related to formal valence in some situations. In the regime in which the EXAFS fit is evaluated, the photoelectron has large kinetic energy and is not particularly sensitive to the details of the potential surface. In almost all situations, FEFF 8 is a modest improvement at best over FEFF 6 for EXAFS analysis. There are some demonstrated cases where FEFF 8 is slightly better than FEFF 6 at modeling EXAFS. The most notable cases are when H is in the input file – FEFF 6 is terrible at this. I got those information from previous discussion on the Ifeffit, see: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg03381.ht… I am not an expert, and I hope someone can help correct me if I am wrong. Thanks Guanghui 2015-06-08 Guanghui 发件人：ifeffit-request(a)millenia.cars.aps.anl.gov 发送时间：2015-06-08 12:00 主题：Ifeffit Digest, Vol 148, Issue 10 收件人："ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> 抄送： 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. how to manage Demeter with a newer FEFF version ? (M. Janeth LOZANO RODRIGUEZ) ---------------------------------------------------------------------- Message: 1 Date: Mon, 08 Jun 2015 11:13:33 +0200 From: "M. Janeth LOZANO RODRIGUEZ" <janeth.lozano-rodriguez(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? Message-ID: <55755CBD.6010007(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 148, Issue 10 ****************************************

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how to manage Demeter with a newer FEFF version ?
by M. Janeth LOZANO RODRIGUEZ 08 Jun '15

08 Jun '15

Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 02 Jun '15

02 Jun '15

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 6
by Nidhi Tiwari 02 Jun '15

02 Jun '15

congratulations :) Give your Best *Nidhi Tiwari*, Junior Research Fellow, Atomic and Molecular Physics Division, Bhabha Atomic Research Center, Mumbai- 400085 On Mon, Jun 1, 2015 at 10:30 PM, <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: Create Atoms input with just coordinates (M Ferrier) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Jun 2015 18:04:40 +0200 > From: M Ferrier <mferrier(a)hotmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Create Atoms input with just coordinates > Message-ID: <DUB118-W1424A6BB66DA7BFA91C7C2DFB60(a)phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > Thank you very much. It worked except that the feff calculation created > ipot 0 and 1 for the same atom (core atom) I just had to change the ipot > values in the text before running feff. But once done it did calculation > correctly I think. > > Maryline > > From: scalvin(a)sarahlawrence.edu > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Mon, 1 Jun 2015 10:53:36 -0400 > Subject: Re: [Ifeffit] Create Atoms input with just coordinates > > Hi Maryline, > Use a = b = c = 10, with alpha = beta = gamma = 90. Now enter the > coordinates from your simulation in units of angstroms/10 (which happens to > be nm). > ?Scott CalvinSarah Lawrence College > On Jun 1, 2015, at 10:43 AM, M Ferrier <mferrier(a)hotmail.com> wrote:Hi, > > I am trying to create an Atoms input file for actinium. Since not a lot is > known about this element we run some DT calculations. One molecule of Ac > acetate in a box surrounded by water. > I have the coordinate of each elements. I was told the symmetry was P1 (I > guess for the box) but unfortunately their is no symmetry in liquid and > thus we cannot input the cell parameters (distances a, b, c and angles > alpha, beta, gamma). I was wondering if their were a way to make Atoms run > to obtain the Feff calculations. Or we should use a different model with a > known solid? > > Thank you for your help > > Maryline Ferrier _______________________________________________Ifeffit > mailing listIfeffit@millenia.cars.aps.anl.govhttp:// > 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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Create Atoms input with just coordinates
by M Ferrier 01 Jun '15

01 Jun '15

Hi, I am trying to create an Atoms input file for actinium. Since not a lot is known about this element we run some DT calculations. One molecule of Ac acetate in a box surrounded by water. I have the coordinate of each elements. I was told the symmetry was P1 (I guess for the box) but unfortunately their is no symmetry in liquid and thus we cannot input the cell parameters (distances a, b, c and angles alpha, beta, gamma). I was wondering if their were a way to make Atoms run to obtain the Feff calculations. Or we should use a different model with a known solid? Thank you for your help Maryline Ferrier

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low and negative ss2 and bug in the log file of fit history
by Raj kumar 01 Jun '15

01 Jun '15

Dear All, I am trying to fit the first shell FT of bulk YbVO4 (measured in dispersive EXAFS) with the reference YbVO4. The resultant SS2 value for the first shell is found to be low for wide k-range selection, whereas approaching negative for the relatively short k-range window. While approaching negative value (of ss2), i have tried to constraint the ss2 value using expression abs(ss). In that case, ss2 value is found to take value 0. Please help me to figure out the problem. Further i have found a small bug in the fit history window. After each fit, earlier data set in the log file of fit history is found to overwritten with the latest fitting parameters (like k range, dk, etc..). Here in my log file window, all fit data set contain the same data set value as like the last fit (fit9). Regards, Raj

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by fred.mosselmans＠diamond.ac.uk 01 Jun '15

01 Jun '15

Dear Kug-Seung Your main initial problem is you didn't understand the structure of Mn3O4. It is a spinel with two Mn sites one octahedral and one tetrahedral. You need to consider both sites to have a chance of fitting, and set multiplication factors on the relative amps in the ratio. It has 1/3 tetrahedral sites and 2/3 octahedral. You need to do the feff calculation twice with each site as the core atom. In the attached project I have done this. You then end up with a lot of paths so to try to restrict the no of variables I have made several of sigma squared to be the same. I am sure this model could be improved upon but I wanted to show you how to get going in fitting the structure. In theory as the Mn tetrahedral site and octahedral sites are different oxidations states they might (should) have different E0s as well but with a limited data range this gets hard to test properly. Best wishes Fred Mosselmans Message: 1 Date: Mon, 01 Jun 2015 15:59:40 +0900 From: ??? <lks3006(a)postech.ac.kr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Mn3O4 EXAFS fitting Message-ID: <1433141980110.23146.postech(a)postech.ac.kr> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150601/4ec…>

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Re: [Ifeffit] _Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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