[Ifeffit] fitting of S XANES with arctans and gaussians
I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica Acta 99 (2012) 206–223. In this paper, they fit spectra to two arctangents and 6 gaussians, with widths of the arctans slaved together and widths of gaussians 1-3 and 4-6 slaved (or all 6 to one value). I'm looking for recommendations as to how to do the fit. They give prescriptions for how to set the initial estimates to give robust values. Manceau has told me that 'Athena works quite well', but I don't see any obvious way there to do the parameter constraints called for, or to keep peak heights from going negative. Athena also has a habit of assuming you want it to do the normalization for you; I've already done that and need no further 'help'. Any ideas? I've tried using Genplot, but that offers no way to restrain parametsrs to ranges to keep them from going nuts. PCA seems to want 6-8 components, so it's not all that helpful. These spectra were taken at various spots on a biological structure (abalone radula) so there's no sense of sequence which would enable the use of evolving factor analysis or something like that. LCF doesn't give satisfying fits with the references I have. I've attached a couple of the files, truncated to the range Manceau&Nagy fit to. The originas were taken over the range 2460-2550eV. mam 2459.8733 0.016383041 2460.1233 0.016094189 2460.3735 0.022025956 2460.6238 0.016678091 2460.8738 0.01631 2461.1240.019483142 2461.3743 0.01770903 2461.6245 0.022848981 2461.8745 0.018562062 2462.1248 0.020740321 2462.3748 0.020652939 2462.6250.017123673 2462.8752 0.025094582 2463.1252 0.019867383 2463.3755 0.022139577 2463.6257 0.023213524 2463.8757 0.020676881 2464.1260.025052877 2464.3762 0.029113997 2464.6262 0.026324339 2464.8765 0.023671083 2465.1267 0.028306101 2465.3767 0.026002042 2465.6270.030652333 2465.8772 0.028775895 2466.1272 0.032816786 2466.3774 0.033937715 2466.6277 0.032948535 2466.8777 0.034721162 2467.1279 0.035310403 2467.3782 0.044202648 2467.6282 0.038343795 2467.8784 0.044291645 2468.1287 0.045460965 2468.3787 0.051915355 2468.6289 0.064561076 2468.8789 0.064293481 2469.1292 0.06745372 2469.3794 0.076904655 2469.6294 0.078936517 2469.8794 0.083785988 2470.1292 0.09224768 2470.3789 0.10311307 2470.6287 0.12705681 2470.8784 0.15507881 2471.1279 0.19775756 2471.3777 0.24674262 2471.6274 0.38095856 2471.8772 0.61600226 2472.1270.95312738 2472.3767 1.3190417 2472.6262 1.579319 2472.8761.6359525 2473.1257 1.5544981 2473.3755 1.4989064 2473.6252 1.5021619 2473.8751.5229028 2474.1245 1.4984316 2474.3743 1.3305453 2474.6241.0569189 2474.8738 0.83871508 2475.1235 0.74043173 2475.3733 0.70619929 2475.6228 0.73935717 2475.8726 0.8194145 2476.1223 0.87513489 2476.3721 0.88144314 2476.6218 0.90261424 2476.8716 0.89132398 2477.1211 0.89018643 2477.3708 0.8967182 2477.6206 0.90281725 2477.8704 0.94701087 2478.1201 0.94702822 2478.3699 0.97867304 2478.6194 1.0008969 2478.8691 1.0092386 2479.1189 1.0287796 2479.3687 1.08442 2479.6184 1.1615053 2479.8679 1.3039225 2480.1179 1.5145243 2480.3674 1.797269 2480.6172 2.0798359 2480.8669 2.2775149 2481.1167 2.3608608 2481.3662 2.3488405 2481.6162.2907579 2481.8657 2.2880797 2482.1155 2.3719938 2482.3652 2.5308979 2482.6152.589304 2482.8645 2.5814075 2483.1143 2.3856504 2483.3642.1799946 2483.6138 1.9504212 2483.8635 1.7527013 2484.1133 1.5563732 2484.3628 1.4446132 2484.6125 1.3397398 2484.8623 1.2488514 2485.1121 1.2062074 2485.3618 1.141425 2485.6116 1.1280848 2485.8611 1.0882412 2486.1108 1.0844127 2486.3606 1.0722013 2486.6104 1.0759245 2486.8601 1.050091 2487.1099 1.0626349 2487.3596 1.0662534 2487.6091 1.0521868 2487.8589 1.0660895 2459.8232 0.0086620357 2460.0735 0.0090417974 2460.3235 0.033545561 2460.5737 0.0085842237 2460.8240.0051017846 2461.0740.011186908 2461.3242 0.017373042 2461.5742 0.015282798 2461.8245 0.020608777 2462.0747 0.030159647 2462.3247 0.037008617 2462.5750.019812036 2462.8250.017694598 2463.0752 0.021219229 2463.3252 0.025639383 2463.5754 0.
[Ifeffit] Artemis - Atom/Feff issues
Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent model3_occ.cif Description: model3_occ.cif structure_xyzformat.xyz Description: structure_xyzformat.xyz ___ 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
Re: [Ifeffit] Artemis - Atom/Feff issues
Hi Marcus, Your cif file is confusing to me in several ways. It will also be confusing to the tool in Demeter that interprets crystal data. Firstly, your space group is tetragonal (P -4 21 m), but you have a=b=c and alpha=beta=gamma. That's not exactly wrong, per se, but it is an unusual way of expressing the dimensions of your unit cell. You lattice constants are surprising and problematic. You have a=b=c=1. 1 Angstrom is a highly unusual lattice constant and almost certainly not what you want. At least, not what you want when interacting with Demeter. Most problematically, your positions in the unit cell are expressed in numbers that suggest Angstrom units rather than fractional position in the unit cell. Perhaps this point is not made clearly enough in the document, but Demeter expects that atom positions are in fractional units. For example, germanium is diamond structure, space group Fd3m, a=5.658. The position of the Ge atom is (0.125,0.125,0.125). The position is !NOT! (0.70725,0.70725,0.70725). When Demeter finds a position less than 0 or greater than 1, it moves that position back into the first unit cell in the upper, right quadrant. So, when it sees a position like (2.69220, 1.31120, 2.64190), which is your La position, it moves that to (0.69220, 0.31120, 0.64190). That behavior makes a lot of sense when working with fractional coordinates, but is clearly problematic given that your cif file has weird lattice constants and (I think) Cartesian coordinates for the atoms positions. It's very hard for me to know how best to advise you because I don't really know what what you are trying to do. Perhaps you are using Mercury or some other tool to generate a cluster of Cartesian coordinates. That's fine. In that case, you want to convert that cluster to a feff.inp file and skip the Atoms page entirely. See, for instance: https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples?slide=9 Executive summary: you seem to be trying to do something differently from how Demeter actually works. Think about fitting your work flow to what Demeter does rather than the other way around. B On 07/18/2016 12:59 PM, M.F.Bertuzzo wrote: Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Artemis - Atoms/Feff issues
Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent structure_xyzformat.xyz Description: structure_xyzformat.xyz model3_occ.cif Description: model3_occ.cif ___ 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
