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

EXAFS signal from dopant atoms
by Eugenio Paris 17 Sep '15

17 Sep '15

Dear all, I have a very general question about EXAFS analysis. Let's take as example a binary system AB in which i am substituting the atom B with another atom C so that we have AB(1-x)C(x). Let us imagine that we know the structure of binaries AB and AC with Rab and Rac atomic distances and we know that in AB(1-x)C(x) the substitutional site will be 100% the B-site. If I measure the EXAFS spectrum of atom C as a function of "x" what can I expect for the EXAFS oscillations? My idea is that when "x" is very small the EXAFS will be highly noisy and damped, while as "x" increases the oscillations will become more evident above the noise level. How to model this situation to get information on C-A bond? In Athena I can start with the .cif file of AC structure with full occupancy and obtain the distance and the DWF for the A-C bond but.. how to treat the signal-to-noise ratio? I mean, as "x" decreases I think there must be a leaking out of the EXAFS signal, should this effect be introduced in S0^2? Or can it affect the effective number of neighbors? Hope I explained myself, thank you! Eugenio Paris PhD student, University of Rome (Italy)

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ATOMS for XANES simulation by FEFF8.4
by María Elena Montero Cabrera 16 Sep '15

16 Sep '15

Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/

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[Resolved] Issues with Athena, first posted 2015-06-25 - Kaspersky antivirus caused the problems
by Nils Skoglund 16 Sep '15

16 Sep '15

Hi, I finally figured out what was causing the horrible performance of Athena on my system; as in all too many cases the antivirus policies of enforced by system managers was the culprit. Every time a change was made in Athena (e.g. using a drop-down menu) the shell would freeze for several seconds while the Kaspersky antivirus scanned whatever function was called, what Athena had stored in RAM and such before allowing the function call to proceed. The same was repeated for the renewing of plots in gnuplot, which is why I initially thought it was related to gnuplot. Once I managed to persuade our IT-staff that my user should have the permission to kill off that process, everything in Athena was working like a charm. In short, beware Kaspersky if you are not permitted to set exceptions for certain software due to local security policies at your university or institute. Best regards, Nils Skoglund -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 27 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 27 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: Ifeffit Digest, Vol 148, Issue 26 (Nils Skoglund) ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Jun 2015 09:59:01 +0200 From: "Nils Skoglund" <nils.skoglund(a)ltu.se> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 26 Message-ID: <005901d0b0af$220d5990$66280cb0$(a)ltu.se> Content-Type: text/plain; charset="us-ascii" Hello Everton, Matt and Pushkar, Thank you for your replies. I have tried both the 32-bit and 64-bit versions with uninstalling in between, to no avail. I'm curious if it is a priority issue between the dual GPU's on the laptop that gnuplot can't handle well; there's both a dedicated GPU and an integrated one. System temperatures look normal and none of the fans are revving up, so it shouldn't be heat-related. Other softwares handle plotting without issues so the suggestion about gnuplot being the culprit seems like the most reasonable one. If I narrow this issue down and find a way to work around it, I'll let you know. Until then I'll just find some other workstation for the evaluation work - thanks again! //Nils -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 26 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 26 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: Issues with Athena on high-performance systems (pushkar shejwalkar) 2. Re: Issues with Athena on high-performance systems (ebonturim(a)usp.br) ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Jun 2015 10:05:23 +0900 From: pushkar shejwalkar <pshejwalkar2004(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issues with Athena on high-performance systems Message-ID: <CAN0ZRcEm=2KRDeXO-=t60yDZHwT4Rp8Zzs6pwPSbt7ndiQBGCg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, I am not an expert in this. In fact , I am one of the very new user of athena. But have you tried uninstalling and then reinstalling the whole package again? ( I am sure you have but since you didnt mentioned just wondering?) Sometimes, that also helps. not sure why and how? but it did for me. Pushkar On Fri, Jun 26, 2015 at 5:00 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Nils, > > We run Athena on non-wimpy Windows 7 systems at our beamline computers > all the time, using both 64- and 32-bit Windows, and typically on > multi-core machines with at least 16 Gb RAM and multiple screens. > Like Robert, we don't see any real performance problems with a handful (<50) spectra. > Athena rarely makes a very big dent in the system resources (well, > comparable to a web browser, so a bit of a hog, but well under 1Gb RAM). > > Perhaps what you're seeing is related to the plotting with Gnuplot. > I'm not sure why that would be a problem... Any ideas? > > --Matt > > Hi, > > > > I?m curious if anyone else is experiencing issues with Athena in more > high-end systems running Windows 7? While I am used to having to wait > for the *first* plot to show up, the software is virtually unusable > to me now where any slight change (e.g. modifying range for the > spline) to already imported data takes up to over a minute to replot. > This didn?t use to be the case for me. The system is a laptop running > Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space > on the hard drives and a dedicated Intel HD 4600 graphics circuit. > > > > If anyone has a work-around for this problem or can suggest anything > to make Athena usable again, it would be most appreciated. Has anyone > noticed previous versions of Athena running more smoothly? > > > > Best regards, > > Nils > > > > *------------------------------------------------------------------* > > *Nils Skoglund, Ph.D.* > Post-doctoral researcher > > Energy Science > Department of Engineering Sciences and Mathematics Lule? University of > Technology > SE-971 87 Lule? > Sweden > > > > Cell : +46 (0)72 529 52 08 > > Web page: http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en > > Publications: http://www.researcherid.com/rid/D-3493-2011 > > *-------------------------------------------------------------------* > > > > _______________________________________________ > 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 > > -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

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Linear Combination Fitting problem
by Iuliia Mikulska 13 Sep '15

13 Sep '15

Hello, I'm using Demeter 0.9.21 on Windows 7 (32 bit). I encountering a few problems with Athena. So I wonder if it can be solved in future releases. 1. The names of my spectra are quite long (around 40 characters). The first problem is when I try to import data from Athena project file: appears "Import from Athena project file" window. In this window I can see the name of the spectra only partially and this window can not be resized. So my first question is if the "Import from Athena project file" window can be done resizable? 2. I'm using Athena to perform Linear Combination Fits of my spectra. As I said, the names of my spectra are quite long, so to see the full name in the Athena I need to resize the window. The resizing works fine, but if I change the "Main Window" to "Linear Combination Fitting" then the window of the program resizes back to the standard size and I need again to resize it to see the full name of the spectra. It happens each time when I'm using "Data menu" to access different data processing features. 3. When I performing Linear Combination fits, the results of the fits can not be saved into project. This option was perfectly working in old Athena. Here are steps how to reproduce this problem: 1. I chose the spectrum which I would like to fit with standards. 2. Then I chose a few Standards. 3. Then I press button "Fit this group". 4. Now in "Fit results" tab you can see the results of the fit. Up to this step everything works fine. Now I need to fit next spectra. So I choose next spectra in group list and then I repeat 2-4 aforementioned steps. I again get the proper fit. The problem comes when I would like to check the fit which I did for previous spectrum. So in group list I simply choose the previous spectrum, but "Fit results" tab is empty. "Standards" tab shows the standards used for fit of second spectrum. So you can access the results of the Linear Combination Fitting only immediately after fitting. As soon as you move to another spectrum, fit results for previous spectrum are lost. If you need more information, please let me know. Best regards, Iuliia Mikulska

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No plot window in Athena/Demeter on Mac OS X Yosemite
by Rémi BELISSONT 10 Sep '15

10 Sep '15

Hello, I’m currently using Athena using the iXAFS 3.0.3 application, which is – if I’ve well understood – an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads) So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/. I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. I runned the sudo port -v self update command Then sudo port install xorg-server demeter And port upgrade outdated to ensure everything is up to date Plus, I have XQuartz 2.7.7 installed. Here is my problem. Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I’m desperately trying to see via Plots/Save last plot as... I’ve seen a similar thread concerning such an issue in OS X Mavericks but couldn’t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html) I guess the issue comes from the DISPLAY environment but I don’t have any clue to solve that. Thank you in advance for your help, I think it may be useful for other users, Kind regards, Rémi

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Re: [Ifeffit] Deglitching
by Bruce Ravel 10 Sep '15

10 Sep '15

On 09/04/2015 01:37 PM, Robert Gordon wrote: > > I can confirm something funny is happening here. In 0.9.21, the deglitch > menu would not display > points. I upgraded to 0.9.22 today and deglitch now displays points, but > when I choose a point > in a test data file (As2O3) and double-click, the energy point removed > is 11804.228, regardless of where > I double-click. I reverted back to 0.9.21 and with the same dataset, > this did not occur. In 0.9.21, > double-click removed the closest point to where I clicked. > > I have win10pro x64 and installed the 64-bit versions of 0.9.21, .22 Can we *please* use the mailing list for these things. It is helpful to the next person who runs into these issues if a discoverable record is left behind. Using the preference tool, can you tell me what the value for gnuplot->terminal is? If it is something other than "wxt", try changing it to "wxt". The interaction with the cursor does not work correctly on some terminals. If that's not the problem, then I am at a loss. I don't see this behavior on any of my computers. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Error in running Artemis - Rmin too smaller than Rbkg
by M.F.Bertuzzo 08 Sep '15

08 Sep '15

Dear all, I am facing this error when I try to run a fit. The file in question required a larger than normal Rbkg value of 3.0. I have attatched the Athena file & the subsequent Artemis project file that I tried to fit so you can see the error I am facing. >From what I can understand, I need to reduce the Rbkg value in the Athena file to a lower number. But whenever I try to do this it causes the background function to mess up which then also causes problems for the fit in 'R' space. Is this problem because I have badly modeled the data badly in Athena to begin? I'm not really sure how to solve the problem so your help and advice is much appreciated! Many thanks, Marcus Bertuzzo, Postgraduate Researcher in Chemistry Functional Materials Group School of Physical Sciences University of Kent Canterbury Kent CT2 7NH

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Re: [Ifeffit] Deglitching
by Matt Newville 04 Sep '15

04 Sep '15

Hi Martina, On Sep 3, 2015 12:58 PM, "Martina Ralle" <rallem(a)ohsu.edu> wrote: > Hi Matt, > > > > I have a quick question. When I try to deglitch in Athena it won't let me > pick a point for deglitching. No matter where I double click it always > chooses 8990. > > > > Have others encountered this error? I am running athena on a Windows 7 64 > bit machine. The latest (not beta) version. > > > Sorry for the trouble. I haven't seen (or heard of) that myself, but I'll ask the ifeffit mailing list where maybe someone has a better idea what the trouble could be. > -martina > > > > Martina Ralle, Ph.D. > > Assistant Professor > > Department of Molecular and Medical Genetics > > Mail Code L103 > > OHSU > > 3181 SW Sam Jackson Pk Rd > > Portland, OR 97239 > > Phone 503 494-3225(o) 503 888-6128(m) > > >

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Spline range and FT range
by 이국승(에너지환경소재연구팀) 01 Sep '15

01 Sep '15

Hi everyone, While I was processing my data, I found that the FT features are changing as I change the spline range. I think the change is severe as my data contain a lot of noises at high-k regions (above 12k). The change is remarkable even when FT range is fixed and even when the spline range is far from the low and high limits of FT range. When data are imported into athena, the defalut values for spline ranges from 0 to the end of measured data and the high limit of FT range is set to a value of the high limit of spline range minus 2. There must be a relationship. Could anyone explain these things and general rules for setting the spline range? Thank you in advance. Best wishes, Kug-Seung Lee ________________________________ Kug-Seung Lee, Ph. D. Staff Scientist 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011 ________________________________

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Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster (Joshua Kas)
by Ganesh Subramanian 01 Sep '15

01 Sep '15

Dear Josh, Thanks for the altered input. It seems fine now as you mention. I ran the XANES calculations and compared with the existing literature of experimental XANES and it looks good. Thanks again, Ganesh On Sun, Aug 30, 2015 at 1:19 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: Error in Running XANES on FEFF8.4 for Cobalt based > cluster (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 30 Aug 2015 13:18:51 -0700 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: > < > CAHuhYRnxrcfiveDOkS7T2Lx5C3bEZg4LeNffOJeq0dZLYJpRcg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Ganesh, > It is common to see the > WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. > warning from feff when you have H atoms since the bonds tend to be very > short. However, these are not the ones that are causing the problem. These > warning can be ignored if the structure is reasonable. If the structure at > the bottom of this email is the input structure that you used, then there > is indeed an oxygen atom that is less than 0.1 angstrom from a carbon atom, > which is of course unphysical. That is probably what is causing the > problem, however, there are some other things that could be causing > problems as well. In particular, there are what I like to call "floating > atoms" in your file, i.e., single atoms or several atoms that are > disconnected from the rest of the cluster. I am sending a new input file > below that has fixed this problem. I deleted the O atom that was too close > to the C atom, and deleted all of the structure that wasn't connected to > the central atom by a string of bonds. You might worry about weather the C > or O atom is the one that should have been deleted in the structure, but > you can always test using both possibilities. I doubt that it will make > much difference since C and O look pretty similar, and the O atom is pretty > far from the Co. Also, the H atoms look a bit messed up, but I don't think > that will make much of a difference either. You can check by taking the H > atoms out and running and see if the results change much. > Cheers, > Josh Kas > > * Al K edge energy = 1559.0 eV > EDGE K > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 1 0 0 0 0 0 > > * *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 0 0 > CORRECTIONS 0 1 > > * *** Radius of small cluster for > * *** self-consistency calculation > * *** A sphere including 2 shells is > * *** a good choice > * *** l_scf = 0 for a solid, 1 for a molecule > * r_scf [ l_scf n_scf ca ] > SCF 5 0 > > * *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 8.0 > > * *** Radius of cluster for Full Multiple > * *** Scattering calculation > * *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 6 0 > * *** Energy grid over which to calculate > * *** DOS functions > * emin emax eimag > *LDOS -30 20 0.1 > > FOLP 3 0.8 > > POTENTIALS > 0 27 Co -1 -1 > 1 6 C -1 -1 > 2 15 P -1 -1 > 3 1 H -1 -1 > 4 7 N -1 -1 > 5 8 O -1 -1 > > ATOMS > 0.000000 0.000000 0.000000 0 Co > 0.000000 1 > -0.877000 -1.130000 1.209000 4 N > 1.872888 2 > 0.706000 0.763000 1.563000 4 N > 1.877119 3 > -0.886000 -0.853000 -1.472000 4 N > 1.918173 4 > 1.117000 1.157000 -1.052000 4 N > 1.921729 5 > 1.456000 -1.334000 -0.126000 1 C > 1.978729 6 > -1.601000 1.453000 -0.068000 4 N > 2.163107 7 > 1.122000 -2.209000 0.163000 3 H > 2.482969 8 > 1.765000 -1.394000 -1.054000 3 H > 2.483823 9 > 2.201000 -1.061000 0.448000 3 H > 2.484115 10 > -0.328000 -1.105000 2.581000 1 C > 2.826689 11 > 1.045000 1.233000 -2.389000 1 C > 2.884378 12 > 0.051000 0.367000 2.864000 1 C > 2.887869 13 > 1.756000 1.481000 1.751000 1 C > 2.888408 14 > -0.659000 -0.537000 -2.771000 1 C > 2.898464 15 > -1.715000 -2.120000 1.053000 1 C > 2.923086 16 > -1.810000 -1.877000 -1.395000 1 C > 2.957238 17 > 2.263000 1.829000 -0.603000 1 C > 2.971535 18 > -2.864000 1.125000 -0.216000 1 C > 3.084603 19 > 0.509000 -1.655000 2.598000 3 H > 3.122132 20 > -3.165000 0.225000 -0.264000 3 H > 3.183951 21 > -1.881000 -2.521000 -0.717000 3 H > 3.226095 22 > 0.212000 0.468000 -3.185000 1 C > 3.226173 23 > 0.260000 -3.225000 -0.293000 3 H > 3.248703 24 > -1.605000 2.854000 0.000000 1 C > 3.274346 25 > -1.931000 0.869000 2.513000 3 H > 3.286197 26 > 2.614000 1.957000 0.706000 1 C > 3.340850 27 > -2.232000 -2.499000 -0.241000 1 C > 3.359301 28 > -2.287000 -2.542000 0.830000 3 H > 3.518669 29 > -1.207000 1.214000 3.075000 1 C > 3.519413 30 > -1.019000 2.145000 2.831000 3 H > 3.695125 31 > 0.186000 -3.470000 1.287000 3 H > 3.705653 32 > -2.458000 -2.943000 -0.050000 1 C > 3.834777 33 > 0.288000 -3.903000 0.413000 1 C > 3.935343 34 > -1.387000 -1.820000 3.396000 1 C > 4.094995 35 > 2.553000 -0.694000 3.132000 3 H > 4.099862 36 > 1.198000 0.646000 3.906000 1 C > 4.136346 37 > 0.236000 0.648000 -4.119000 3 H > 4.176333 38 > 1.974000 1.827000 3.218000 1 C > 4.194059 39 > 1.979000 2.281000 -2.920000 1 C > 4.200691 40 > -1.954000 -2.872000 2.399000 1 C > 4.221576 41 > -1.356000 -1.474000 -3.722000 1 C > 4.226665 42 > 3.077000 2.276000 -1.823000 1 C > 4.239273 43 > -2.379000 -2.161000 -2.783000 1 C > 4.251429 44 > -3.699000 2.187000 -0.292000 4 N > 4.307068 45 > -2.114000 -1.164000 3.595000 3 H > 4.329886 46 > 4.151130 0.213470 -1.476130 3 H > 4.410942 47 > -3.398000 -2.805000 -0.293000 3 H > 4.415912 48 > -2.914000 3.318000 -0.141000 1 C > 4.418190 49 > -1.477000 1.171000 4.015000 3 H > 4.435425 50 > 0.084000 -2.932000 -3.384000 3 H > 4.478296 51 > -0.139000 -3.903000 2.219000 3 H > 4.491847 52 > 1.145000 -4.375000 0.380000 3 H > 4.538287 53 > 2.138000 -0.543000 4.017000 1 C > 4.582814 54 > 1.599000 -1.345000 4.232000 3 H > 4.719709 56 > 4.110000 1.128000 -2.086000 1 C > 4.745090 57 > 2.947000 1.705000 3.417000 3 H > 4.823663 58 > -3.841000 -0.653000 -2.863000 3 H > 4.834921 59 > 3.949000 2.548000 1.146000 1 C > 4.837377 60 > -3.203000 -3.637000 -0.340000 1 C > 4.858248 61 > -0.314000 -2.507000 -4.171000 1 C > 4.876565 62 > 2.363000 1.996000 -3.799000 3 H > 4.898998 63 > -1.074000 -4.151000 2.377000 1 C > 4.902490 64 > -2.168000 -4.410000 0.005000 1 C > 4.914097 65 > -2.368000 -3.147000 -2.947000 3 H > 4.918927 66 > 1.290000 3.658000 -3.054000 1 C > 4.936799 67 > -0.837000 -4.889000 0.206000 1 C > 4.964406 68 > 0.666000 3.369000 3.643000 3 H > 5.006512 69 > 1.635000 3.289000 3.463000 1 C > 5.048080 70 > -3.849000 -1.643000 -2.849000 1 C > 5.062712 71 > -4.475000 -1.815000 1.737000 3 H > 5.131961 72 > 0.388000 -2.058000 -4.689000 3 H > 5.135429 73 > -4.326000 -1.930000 -2.031000 3 H > 5.154041 74 > -1.382000 -4.745000 1.662000 3 H > 5.214134 75 > -4.736000 1.135000 1.925000 5 O > 5.236750 76 > -2.871000 -4.398000 0.183000 3 H > 5.255334 77 > -3.300000 -3.904000 -1.277000 3 H > 5.268961 78 > -4.074000 -3.355000 0.011000 3 H > 5.277653 79 > -1.914000 -0.761000 -4.955000 1 C > 5.366055 80 > 0.046000 3.646000 -3.941000 1 C > 5.369070 81 > -1.698000 -3.672000 -3.533000 3 H > 5.371115 82 > -2.633000 -0.152000 -4.682000 3 H > 5.373725 83 > -0.880000 -2.379000 4.741000 1 C > 5.376906 84 > -3.372000 -3.278000 2.760000 1 C > 5.452822 85 > 0.671000 1.054000 5.308000 1 C > 5.453074 86 > -0.293000 -1.712000 5.177000 3 H > 5.460597 87 > -4.181000 -1.407000 3.261000 3 H > 5.485848 88 > -1.200000 -0.248000 -5.388000 3 H > 5.525581 89 > 3.795000 3.637000 -1.723000 1 C > 5.531593 90 > 0.151000 1.882000 5.232000 3 H > 5.562243 91 > -5.154000 2.141000 -0.214000 1 C > 5.585105 92 > -0.348000 -3.198000 4.579000 3 H > 5.596030 93 > -4.430000 -2.157000 2.662000 1 C > 5.600339 94 > 0.099000 0.341000 5.663000 3 H > 5.674121 95 > -0.746000 -3.186000 -4.728000 3 H > 5.749878 96 > -1.148000 -4.612000 3.238000 3 H > 5.750921 97 > -5.597000 1.049000 -0.967000 5 O > 5.775976 98 > -4.998000 1.024000 2.714000 3 H > 5.778787 99 > -1.369000 -4.479000 -3.414000 4 N > 5.795774 100 > -3.647000 -4.018000 2.164000 3 H > 5.841903 101 > 4.578000 3.552000 -1.141000 3 H > 5.905647 102 > -1.672000 -4.987000 -2.760000 3 H > 5.939979 103 > 3.263000 -0.429000 5.058000 1 C > 6.034449 104 > -5.655000 1.939000 1.236000 1 C > 6.104625 105 > 5.047000 1.380000 -3.248000 1 C > 6.158418 106 > -6.144000 -0.550000 0.157000 3 H > 6.170566 107 > -3.372000 -3.628000 3.685000 3 H > 6.173491 108 > 1.428000 1.198000 5.912000 3 H > 6.198882 109 > -3.234000 -5.327000 -0.151000 1 C > 6.233658 110 > -0.566000 -6.250000 0.206000 1 C > 6.278956 111 > -5.537000 2.986000 -0.588000 3 H > 6.318252 112 > -0.435000 -4.923000 -4.197000 1 C > 6.483823 113 > -4.129000 -5.031000 -0.254000 3 H > 6.513380 114 > 4.649000 1.240000 -4.419000 5 O > 6.532868 115 > -4.629000 -2.157000 -4.093000 1 C > 6.544688 116 > -6.579000 0.277000 -0.201000 1 C > 6.587896 117 > 3.946000 0.575000 5.254000 5 O > 6.595912 118 > -2.062000 -2.707000 5.670000 1 C > 6.612760 119 > -0.029000 -4.281000 -5.051000 5 O > 6.621209 120 > -2.897000 -4.497000 3.921000 5 O > 6.632485 121 > -5.819000 2.808000 1.704000 3 H > 6.682009 122 > -4.241000 -1.749000 -4.909000 3 H > 6.718881 123 > 2.890000 -2.118000 5.767000 3 H > 6.789427 124 > -2.956000 -1.850000 5.836000 5 O > 6.798480 125 > 3.365000 -1.387000 5.883000 4 N > 6.917852 126 > -5.795000 -2.719000 3.077000 1 C > 7.102318 127 > 6.519000 1.843000 -2.135000 3 H > 7.102974 128 > -6.958000 1.182000 0.953000 1 C > 7.121734 129 > -5.572000 -1.864000 -4.025000 3 H > 7.121959 130 > 6.265000 1.753000 -2.972000 4 N > 7.152344 131 > -4.584000 -3.642000 -4.220000 1 C > 7.217037 132 > -6.768000 -0.507000 -2.663000 3 H > 7.290709 133 > -4.900000 -4.410000 -3.269000 5 O > 7.358292 134 > -6.097000 -1.290000 4.274000 3 H > 7.556758 135 > -2.049000 -3.867000 6.278000 4 N > 7.652802 136 > -7.386000 0.433000 2.084000 5 O > 7.686582 137 > -1.394000 -4.435000 6.126000 3 H > 7.690275 138 > -7.333000 -0.912000 -2.191000 5 O > 7.707471 139 > -6.196000 -3.784000 2.591000 5 O > 7.708590 140 > 3.913000 -1.320000 6.566000 3 H > 7.756695 141 > -7.697000 -0.106000 -1.106000 1 C > 7.776778 142 > -6.460000 -2.026000 3.953000 4 N > 7.839801 143 > -7.673000 1.820000 0.672000 3 H > 7.914475 144 > 6.835000 1.912000 -3.624000 3 H > 7.969087 145 > -4.202000 -4.117000 -5.391000 4 N > 7.979309 146 > -3.986000 -3.564000 -6.042000 3 H > 8.068213 147 > -8.116000 0.720000 -1.452000 3 H > 8.276241 148 > -6.953000 -4.513000 1.270000 5 O > 8.385957 149 > -2.691000 -4.077000 6.838000 3 H > 8.403669 150 > -8.380000 -0.585000 -0.571000 3 H > 8.419778 151 > -4.162000 -4.987000 -5.524000 3 H > 8.526839 152 > -8.821000 0.724000 2.726000 2 P > 9.260955 153 > -7.794000 -2.418000 4.430000 1 C > 9.285368 154 > -8.760000 -1.946000 2.636000 3 H > 9.352701 155 > -7.884000 -3.402000 4.375000 3 H > 9.636996 156 > -8.812000 -0.362000 3.897000 5 O > 9.642043 157 > -8.891000 -1.772000 3.614000 1 C > 9.759655 158 > -7.894000 -2.154000 5.378000 3 H > 9.791723 159 > -8.993000 2.042000 3.320000 5 O > 9.801337 160 > -9.840000 0.431000 1.688000 5 O > 9.993033 161 > -10.251000 -2.267000 4.070000 1 C > 11.259982 162 > -10.331000 -3.225000 3.886000 3 H > 11.499182 163 > -10.955000 -1.781000 3.591000 3 H > 11.665302 164 > -10.348000 -2.113000 5.035000 3 H > 11.700303 165 > END > > On Fri, Aug 28, 2015 at 2:03 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: Error in Running XANES on FEFF8.4 for Cobalt based > > cluster (Ganesh Subramanian) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 28 Aug 2015 14:03:16 -0700 > > From: Ganesh Subramanian <gunkanna(a)gmail.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: > > <CAAb9e-c_jTi=+KbQi6gPzYVNnSoikXAF= > > eYHtKkfSHWE+_y-kw(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Bruce, > > > > Thanks for the response and sorry for the delay in getting back to you. > > > > I retried the FEFF simulation using structural information from another > > article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): > > 3403-3413). The structural data from this article seems to be widely used > > by many others in simulating for optical absorption. But here with FEFF, > I > > still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple > > of other issues. With two different articles suggesting smaller bond > > distances for a few of their atoms, it seems like the distances are what > > they are. > > > > I have attached the log files and input file for this trial run. > > > > Is there any way to circumvent this error without altering the structure > ? > > > > Thanks, > > > > Ganesh > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > > based cluster > > > Message-ID: <55BA3978.4080801(a)bnl.gov> > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > > > 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > > > extending upto 18 A in radial distance from the central cobalt atom. > > But > > > > there are quite a few instances of Hydrogen atoms that are too > close. I > > > > tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to > > > > get a syntax type error, that i cant figure out. I checked the > crystal > > > > structure and the smallest hydrogen bond distance is 0.89 A. (I have > > > > attached the corresponding input and log file with suffix 'full > > cluster') > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > > when you have atoms that are separated by 1.75 Angstroms or less. That > > > message has nothing to do with the FOLP setting. > > > > > > > 2. *SCF for small cluster*: Since the problem with the hydrogen > > > > distances persisted, I decided to run the calculation for a smaller > > > > cluster (about 50 atoms). I used the conditions as prescribed for > small > > > > clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were > > too > > > > close (within this smaller cluster, there were about 3 of them, and > > none > > > > in the first or second shell of co-ordination) were removed manually. > > > > Now, I did not have the error on distances, did not require the FOLP > > > > card to be manually altered, but the log1 file seems to suggest that > > the > > > > SCF is not calculated. I cant figure why that is the case. (I have > > > > attached the corresponding input and log file with suffix 'small > > > cluster') > > > > > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > > > with these additional lines: > > > > > > Core-valence separation > > > WARNING: fatal error in subroutine corval. Try > > > to reduce ca1 in SCF card. If does not help, > > > SEND bug report to AUTHORS > > > CORVAL-1 > > > > > > I don't quite know what that means, but it gives some hints. The > source > > > code corval.f tells us that is "Finds the core-valence separation for > > > the cluster of atoms." I simply am not knowledgeable enough about the > > > details of Feff to know why your cluster triggered this warning. > > > > > > B > > > > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 535A > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ > > > Software: https://github.com/bruceravel > > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Thu, 30 Jul 2015 10:51:30 -0400 > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > > based cluster > > > Message-ID: <55BA39F2.4090609(a)bnl.gov> > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > > > >> 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > > >> extending upto 18 A in radial distance from the central cobalt atom. > > But > > > >> there are quite a few instances of Hydrogen atoms that are too > close. > > I > > > >> tried the FOLP with the recommendation for Hydrogen of 0.8, I seem > to > > > >> get a syntax type error, that i cant figure out. I checked the > crystal > > > >> structure and the smallest hydrogen bond distance is 0.89 A. (I have > > > >> attached the corresponding input and log file with suffix 'full > > > cluster') > > > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at > you > > > > when you have atoms that are separated by 1.75 Angstroms or less. > That > > > > message has nothing to do with the FOLP setting. > > > > > > Oops! That message is triggered for atoms separated by 1.75 bohr, > which > > > is about 0.92 Angstrom. > > > > > > B > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 535A > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ > > > Software: https://github.com/bruceravel > > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Thu, 30 Jul 2015 15:58:12 +0000 > > > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > > <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > > > Content-Type: text/plain; charset="windows-1252" > > > > > > Dear Ie-Rang, > > > > > > I?m the demeter maintainer on MacPorts, but I admit I am anything but a > > > MacPorts guru. > > > > > > I notice that the error you showed is a failure to install gcc49. I > don?t > > > know if that new GCC is compatible with your old version of OS X, but > > > that?s an issue that?s beyond my expertise. You might edit your > variants > > > file (it?s /opt/local/etc/macports/variants.conf on my installation) to > > > insist on an earlier version by adding a line containing, e.g., > ?+gcc47? > > or > > > whatever is your installed and preferred version of GCC. > > > > > > In fact, the port demeter does not depend (directly) on gcc, which you > > can > > > see by issuing the command > > > > > > > port echo depof:demeter > > > > port echo depof:demeter-devel > > > > > > So it looks to me like you have several steps to get ready for > installing > > > demeter. > > > > > > I admit that I recently discovered?but have not fixed?a flaw in the > > > demeter port description file. The code depends on ports > p5.16-file-which > > > and p5.16-math-round, but these are not made explicit. I need to figure > > out > > > how to add these to the explicit dependency list. I?m just back from > > > vacation and a conference, so I have no excuses now. If you get far > > enough > > > that you can install *but not run* demeter?s executables, then a > > workaround > > > for this is > > > > > > > sudo port install p5.16-file-which p5.16-math-round > > > > > > And for MacPorts users in general: I understand that the project as a > > > whole is in the process of trying to move to Perl 5.22 instead of 5.16. > > > I?ll be updating the port file to reflect that change, too. > > > > > > Joe Fowler > > > NIST Boulder Laboratories > > > > > > > > > On Jul 29, 2015, at 4:01 PM, ifeffit-request(a)millenia.cars.aps.anl.gov > > > <mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: > > > > > > Send Ifeffit mailing list submissions to > > > ifeffit(a)millenia.cars.aps.anl.gov<mailto: > > 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. HELP: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) > > > 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) > > > 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster > > > (Ganesh Subramanian) > > > > > > From: Ie-Rang Jeon <jeon(a)northwestern.edu> > > > Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Date: July 29, 2015 at 1:11:08 PM MDT > > > To: "ifeffit(a)millenia.cars.aps.anl.gov" < > > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > Reply-To: XAFS Analysis using Ifeffit < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > > > > > Hello, > > > > > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I > can't > > > do this. Below are error messages that I got. > > > Could you please help me to figure out what the problem is? > > > > > > Thank you. > > > Ie-Rang > > > > > > > > > ----------------------------------- > > > > > > ---> Building gcc49 > > > Error: org.macports.build for port gcc49 returned: command execution > > failed > > > Error: Failed to install gcc49 > > > Please see the log file for port gcc49 for details: > > > > > > > > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > > > Error: The following dependencies were not installed: > > > . > > > . > > > . > > > Error: Processing of port demeter-devel failed > > > > > > > > > > > > > > > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Date: July 29, 2015 at 1:21:06 PM MDT > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Reply-To: XAFS Analysis using Ifeffit < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > > > > > On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: > > > Hello, > > > > > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I > can't > > > do this. Below are error messages that I got. > > > Could you please help me to figure out what the problem is? > > > > > > Thank you. > > > Ie-Rang > > > > > > Perhaps there's anything useful in that log file? > > > B > > > > > > > > > > > > > > > ----------------------------------- > > > > > > ---> Building gcc49 > > > Error: org.macports.build for port gcc49 returned: command execution > > failed > > > Error: Failed to install gcc49 > > > Please see the log file for port gcc49 for details: > > > > > > > > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > > > Error: The following dependencies were not installed: > > > . > > > . > > > . > > > Error: Processing of port demeter-devel failed > > > > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 535A > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ > > > Software: https://github.com/bruceravel > > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > > > > > >

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