Re: [Ifeffit] S02 selection from reviewer
Peng, I think what everyone has said is quite useful, but there is likely another aspect to consider as you make revisions. Based on the reviewer comments, it sounds like you are trying to interpret your fitted N values as being statistically distinct. My guess is that is not correct, as Matt suggested, and the fact that the N is lower in fluorescence suggests that overabsorption is attenuating the EXAFS amplitude, as Matthew suggested. If you really want to make the claim of differences in coordination environment then you should also look at R. A lower coordination number should be accompanied by a decrease in R. How R shifts will be impacted by the resolution of the data, determined by your k-range, but I think if fitting a single Sb-O path then in most cases you should see R change if N is truly going down. It can get more complicated, clearly, and the S02 you are using may not be a perfect value, as Shelly's paper indicates, but if N is truly going down in one sample then R definitely should be changing. I do not think about Sb very often, so if the only way for coordination to change is from a change in redox state then you should see a shift in the XANES spectrum. However, be cautious here because overabsorption will increase the intensity of a XANES spectrum for normalized absorbances below 1 and decrease the intensity above 1. If the XANES fine structure features of all samples are the same (in position) but you see what I describe in the overall absorbance, then your fluorescence samples is likely just suffering from overabsorption effects and your N will appear smaller. This gives a lower apparent S02, which is likely what the reviewer is getting at. My sense is that what the reviewer is really criticizing is your interpretations based on differences in fitted N values, which may not be valid. Jeff On 10/2/2021 9:48 AM, Kelly, Shelly D. wrote: Hi Peng: It might be helpful to understanding some of Matt's points regarding S02 transferability, Ei and energy resolution by looking at this paper. Comparison of EXAFS foil spectra from around the world DOI: 10.1088/1742-6596/190/1/012032 Kind regards, Shelly -Original Message- From: Ifeffit On Behalf Of Matthew Marcus Sent: Saturday, October 2, 2021 9:04 AM To:ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] S02 selection from reviewer Since S02 is a parameter in the description of EXAFS and not of the experiment, it's independent of technique. Overabsorption (misnamed 'self-absorption') can reduce the *measured* amplitude, an effect which can be fudged in analysis by reducing S02. If the sample is truly homogeneous (on the scale of the absorption length), then you can calculate the amount of overabsorption to see if it's significant. However, many kinds of samples, such as concentrated powders mixed with a diluent such as BN, this condition is not met. If the particles are large enough for each to have significant absorption edge jumps, then diluting them in BN doesn't fix the problem. mam On 10/2/2021 12:49 AM, Peng Liu wrote: Dear IFEFFIT members, I am sorry to bother you again. I asked about S02 selection for the first major revision. I just received the second revision. The reviewer is not satisfied with one S02 value for all our samples. " 1. I am still not satisfied with selected SO2 value (it is set to 0.85). SO2 is not transferable between different samples and detection methods. It is not possible to use a value obtained from different compound using transmission measurement mode to completely different other compound measured using fluorescence mode. One method to fix SO2 value is to measure diluted solution (to avoid self-absorption) of reference material in fluorescence mode. Other is to use multiple spectra fitting for all samples of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 parameter is the same for all samples. At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in fluorescence mode. " We do get the S02 from a similar reference material measured in transmission mode, and our samples were all measured in fluorescence mode. It is not possible to measure the diluted reference material in fluorescence mode in one or two months. If you could give me some suggestions, that would be great. -- Best Regards, Peng Liu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe:http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe:http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing
[Ifeffit] Substantial problems running ATOMS in Demeter 0.9.24
The message sequence from this morning prompted me to inquire if anyone can provide help with ATOMS crashing on my own computer. I am running Demeter 0.9.24 on Windows 10 Pro 64. I did a fresh install of Demeter after having removed all older versions of Demeter 0.9, including the Demeter folders in C:\Users\\AppData\Roaming\. My problem is unfortunately simple and something I do not know how to fix: Whenever I hit the "Run Atoms" button, stand-alone atoms crashes. The program simply dies, and no files are written. I am able to enter text, save an atoms.inp file, and reload an atoms.inp file, but "Run Atoms" crashes the program. I have tested this with a simple compound, NaCl, using the attached atoms.inp file. Note that I don't want to work on NaCl, I just used this to test a simple structure. The log file associated with the crash is attached. The log file says Windows 8, but I think this is just hows Windows 10 shows up as that is what I am running, from a clean Windows 10 install. Anyway, when I load this atoms.inp file or enter the same information by hand the program crashes. I was able to load and run this atoms.inp file in the old version of atoms (3.0.1) and produced the attached feff_oldATOMS.inp file. I thus don't think it is a data entry problem. I hope that I have provided enough information. I have no problems running ATHENA, ARTEMIS, or HEPHAESTUS. Given the log file I suspect this is something unique to my computer, but I am stumped as to what it could be as I am running a standard OS with a standard install on Demeter. Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/ ## This Atoms file was generated by Demeter 0.9.24 ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015 title = Halite space = Fm3m a = 5.64010b= 5.64010c = 5.64010 alpha = 90.0beta = 90.0gamma = 90.0 rmax = 8.0core = Cl # polarization = 0.0 0.0 0.0 shift = 0.00.00.0 atoms # el. x y ztag Na 0.0 0.0 0.0 Na Cl 0.5 0.5 0.5 Cl Started at 2016-06-03T12:54:07 Win8Professional (64-bit) 6292002002561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\catal\AppData\Roaming\DemeterPerl\c\bin;C:\Users\catal\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\catal\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\catal\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin perl version: v5.18.2 @INC: C:/Users/catal/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/catal/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/catal/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/catal/AppData/Roaming/DemeterPerl/perl/lib . Demeter version 0.9.24 Can't call method "workspace" on an undefined value at C:/Users/catal/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Atoms/Xtal.pm line 1004. * This feff6 input file was generated by Atoms 3.0.1 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 3.89 microns, unit edge step:21.71 microns * specific gravity = 2.164 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction:0.00105 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * - * The following crystallographic data were used: * * titleHalite * space = F m -3 m * a =5.64010 b = 5.64010 c = 5.64010 * alpha = 90.0 beta = 90.0 gamma = 90.0 * core = Cl edge = K * atoms * ! elem x y z tagocc * Na0.00.00.0 Na1.0 * Cl0.50.50.5 Cl1.0 * - TITLE Halite HOLE 1 1.0 * Cl K edge (2822.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX8.0 *CRITERIA curved plane *DEBYEtemp debye-temp NLEG 4 POTENTIALS *ipot Z element 0 17 Cl 1 11 Na 2 17 Cl ATOMS * this list contains 93 atoms * x y z ipot tag distance 0.00.00.0 0 Cl 0.0 2.820050.00.0 1 Na_12.82005 -2.820050.00.0 1 Na_12.82005 0.02.82005
Re: [Ifeffit] Unable to export flattened normalized XANES spectra from Athena 0.9.24
Hi Bruce, I appreciate the reply. It looks like what I want is the flattend column of data, which is not column 2 in the version 0.9.24 norm(E) files, it is column 3. I was unaware both flattened and unflatten normalized data were exported in the file. In Athena 0.8 if "Flatten normalized data" was selected then column 2 was this flattened data in a norm(E) file. I had no idea that the export format for norm(E) files changed in version 0.9. To make sure I have this correct, below are the column labels from norm(E) files exported from Athena 0.8.061 and Athena 0.9.24: 0.8.061: # energy norm bkg_norm der_norm 0.9.24: # e normflatfbkg ndernsec I have plotting code that expects columns 1 and 2 and I was unaware that flattened data is now output separately (in column 3). In version 0.8 a flattened normalized spectra was outputted if the box was checked, and if it was unchecked then column 2 was the unflattened data, from what I can tell. Can you please confirm that I understand this correctly? I admit that I had not looked at the documentation before writing since I understood the Athena 0.8 file format and had not anticipated a format change in the new version. It clearly would have been informative to look at the current documentation! Of course, as you note that the columns listed in the documentation for norm(E) files are wrong, with the current output format being columns 1 4 2 3 6 7 from what is listed in the documentation (column 5 does not appear in my file). Should this be looked at? I actually would prefer the column order that is listed in the documentation. The file format is clearly not what you intended. Thank you, Jeff On 12/8/2015 9:15 PM, Bruce Ravel wrote: Here's what the manual has to say http://bruceravel.github.io/demeter/aug/output/column.html Looking at the code, however, it seems the document has swapped columns 2/3 and columns 4/5. I think what you are looking for is in column 4, not column 2. If that's right, I'll treat this as a documentation bug. If that is not the case, then I'll prod you for more information so I can understand the software bug. In either case, thanks for the report. Cheers, B On 12/08/2015 06:09 PM, Jeff Catalano wrote: I am looking for some help with a possible error on my part or bug associated with exporting normalized mu(E) spectra from Athena 0.9.24 64-bit on Windows 10 Pro 64-bit. I have some Si XANES data with a challenging background shape that is well removed through careful normalization in Athena, as long as the "Flatten normalized data" option is checked. When I save the current group as norm(E), what is saved is the non-flattened normalized data. The checkbox for flattening the data has no effect on what is exported despite changing what is plotted. I have verified this by comparing the files exported the the flatten box checked or unchecked. I have tried this with multiple data files loaded in multiple formats (raw beamline data, simple two-column E and mu data, PRJ files) and the effect is always the same. It is also unaffected by the normalization ranges I select. No matter what options I select Athena 0.9.24 will only save non-flattened norm(E) data. This behavior is different from what I remember, and I have verified that in version 0.8 of Athena the exported norm(E) was the flattened data, provided that the flatten box was checked (of course). I have been unable to determine if I have any errors in the settings in version 0.9.24 but all parameters that I can find are identical in both 0.9.24 and 0.8. I have also uninstalled and reinstalled Athena 0.9.24 and the effect is still the same. Has anyone else noticed this problem? Is this a bug? Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Unable to export flattened normalized XANES spectra from Athena 0.9.24
I am looking for some help with a possible error on my part or bug associated with exporting normalized mu(E) spectra from Athena 0.9.24 64-bit on Windows 10 Pro 64-bit. I have some Si XANES data with a challenging background shape that is well removed through careful normalization in Athena, as long as the "Flatten normalized data" option is checked. When I save the current group as norm(E), what is saved is the non-flattened normalized data. The checkbox for flattening the data has no effect on what is exported despite changing what is plotted. I have verified this by comparing the files exported the the flatten box checked or unchecked. I have tried this with multiple data files loaded in multiple formats (raw beamline data, simple two-column E and mu data, PRJ files) and the effect is always the same. It is also unaffected by the normalization ranges I select. No matter what options I select Athena 0.9.24 will only save non-flattened norm(E) data. This behavior is different from what I remember, and I have verified that in version 0.8 of Athena the exported norm(E) was the flattened data, provided that the flatten box was checked (of course). I have been unable to determine if I have any errors in the settings in version 0.9.24 but all parameters that I can find are identical in both 0.9.24 and 0.8. I have also uninstalled and reinstalled Athena 0.9.24 and the effect is still the same. Has anyone else noticed this problem? Is this a bug? Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
