Re: [Ifeffit] Fitting EXAFS simulation to experimental
Hi Carl, I'm not sure what level you were asking your question from. Bruce provided an answer to one interpretation of the question. If the question is, however, has anyone written an automated script that allows the user to choose parameters given to ATOMS as fitting parameters for all space groups, then my answer is that I'm not aware of that having been done. For example, it is very easy to make the lattice parameter for a cubic space group be a fitting parameter, as changes to it will result in a uniform fractional change to the length of all paths, and the reff keyword makes it easy to implement a uniform fractional change. Plenty of people have computed the relationship between ATOMS parameters and path parameters for specific geometries (including more complicated ones), and used that for fitting. But in each case that requires some effort to think about the geometry involved. That's different from having a script that allows you to designate a shift in, say, the x-coordinate in fractional coordinates of one kind of atom in the input file and automatically have that result in the generation of the correct function of that fitting parameter in each of the paths used in FEFF, including multiple-scattering paths. And that's the thing that I don't think currently exists. --Scott Calvin Sarah Lawrence College On May 29, 2014, at 9:04 AM, Bruce Ravel bra...@bnl.gov wrote: On 05/28/2014 06:58 PM, Carl Brozek wrote: Dear listhost, I'm using Artemis as a front end for ATOMS and FEFF and I would like to build a simulated EXAFS spectrum based on experimental data I have. I know how to generate a simulation based on a .cif or .xyz file, but is it possible to vary parameters in these input geometries to best match the experimental? Has someone implemented this in artemis or matlab? thanks, Carl, In Artemis, this is called a VPath. http://bruceravel.github.io/demeter/artug/plot/vpaths.html You will need to import data of some sort because a VPath is created from paths that have been associated with a data set. Run Feff. Drag and drop any number of paths from the Path tab in the Feff window onto your data Window. Mark the paths paths you want to include in your VPath by clicking their little check buttons. From the Actions menu, select Make VPath from marked. This will prompt you for a name for the VPath and insert the VPath into the plotting list, as described in the page whose URL is given above. As for varying structural parameters, that is what we call a fit. You can parameterize the various Delta R parameters to represent changes in lattice positions. There are plenty of examples of this using Ifeffit -- Daniel Haskel's papers on cuprate superconductors, my own papers on titanate perovskites, lots of work buy Anatoly Frenkel on various catalyst materials, Sam Webb's work on manganites, just to name a few. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://xafs.org/BruceRavel Software:https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting EXAFS simulation to experimental
Yes, it is possible to vary atomic positions in the fitting process and evaluate their effect on the fit, or just use them as adjustable parameters in the fit as any other fitting variables. This process was historically started by Yizhak Yacoby (see papers from his group in the 1990s), who introduced structural distortions into the fit. We had a somewhat similar approach in this work: https://pubweb.bnl.gov/~frenkel/KNbO3/kno.pdf where we have parameterized the fractional coordinates of oxygen atoms in the perovskite structure and traced their effect on EXAFS equation (most non-trivially, on the scattering amplitude of multiple scattering (Equations 6,7) paths, the rest was pretty trivial: Equations 4,5). I think Bruce also had done such parameterization in some of his papers and in his Thesis. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Scott Calvin [scal...@sarahlawrence.edu] Sent: Thursday, May 29, 2014 10:40 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting EXAFS simulation to experimental Hi Carl, I'm not sure what level you were asking your question from. Bruce provided an answer to one interpretation of the question. If the question is, however, has anyone written an automated script that allows the user to choose parameters given to ATOMS as fitting parameters for all space groups, then my answer is that I'm not aware of that having been done. For example, it is very easy to make the lattice parameter for a cubic space group be a fitting parameter, as changes to it will result in a uniform fractional change to the length of all paths, and the reff keyword makes it easy to implement a uniform fractional change. Plenty of people have computed the relationship between ATOMS parameters and path parameters for specific geometries (including more complicated ones), and used that for fitting. But in each case that requires some effort to think about the geometry involved. That's different from having a script that allows you to designate a shift in, say, the x-coordinate in fractional coordinates of one kind of atom in the input file and automatically have that result in the generation of the correct function of that fitting parameter in each of the paths used in FEFF, including multiple-scattering paths. And that's the thing that I don't think currently exists. --Scott Calvin Sarah Lawrence College On May 29, 2014, at 9:04 AM, Bruce Ravel bra...@bnl.gov wrote: On 05/28/2014 06:58 PM, Carl Brozek wrote: Dear listhost, I'm using Artemis as a front end for ATOMS and FEFF and I would like to build a simulated EXAFS spectrum based on experimental data I have. I know how to generate a simulation based on a .cif or .xyz file, but is it possible to vary parameters in these input geometries to best match the experimental? Has someone implemented this in artemis or matlab? thanks, Carl, In Artemis, this is called a VPath. http://bruceravel.github.io/demeter/artug/plot/vpaths.html You will need to import data of some sort because a VPath is created from paths that have been associated with a data set. Run Feff. Drag and drop any number of paths from the Path tab in the Feff window onto your data Window. Mark the paths paths you want to include in your VPath by clicking their little check buttons. From the Actions menu, select Make VPath from marked. This will prompt you for a name for the VPath and insert the VPath into the plotting list, as described in the page whose URL is given above. As for varying structural parameters, that is what we call a fit. You can parameterize the various Delta R parameters to represent changes in lattice positions. There are plenty of examples of this using Ifeffit -- Daniel Haskel's papers on cuprate superconductors, my own papers on titanate perovskites, lots of work buy Anatoly Frenkel on various catalyst materials, Sam Webb's work on manganites, just to name a few. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://xafs.org/BruceRavel Software:https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting EXAFS simulation to experimental
Hi All, As Scott, Bruce, Anatoly have said, it is certainly possible to map certain crystallographic distortions to local structure, and so predict the effect on EXAFS, and model EXAFS in terms of those distortions. But to be clear for the original question, EXAFS is inherently a local structure probe and is not actually sensitive to crystallographic parameters. That is, one *must* make the mapping from crystlalographic parameters to local structure, often making important assumptions (such as there is a crystal structure and I know what the space group is) that EXAFS is not actually able to deny or confirm. Anyway, yes it is certainly possible to do things like model the extent of a tetragonal distortion. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting EXAFS simulation to experimental
I wonder if what he was asking about is an automated way of mapping the position parameters for a given space group, that is, fractional atomic coordinates as listed in a .cif, onto the various path distances. As it is now, it's impractically hard to do it except for very simple cases. Maybe what is needed is a language for specifying local structures in which atom positions and occupancies can be given by variables, and the program would automatically parameterize the paths. As a hypothetical toy example, consider a simple model of a substitutional model of Fe in bcc W (atoms chosen more or less at random). Here, we suspect that since Fe is a smaller atom than W, the first neighbors would be displaced inward. Thus, we might have a specification something like SET a0 = 3.165 /* lattice parameter of pure W */ CENTRAL Fe 0 0 0 ATOM W /* 1st NN */ POS a0*(1-dist1)*(sqrt(3),sqrt(3),sqrt(3))/2 OCC 1 SS SS1 ATOM W POS a0*(1-dist1)*(-sqrt(3),sqrt(3),sqrt(3))/2 OCC 1 SS SS1 ... add the other 6 ATOM W /* 2nd NN */ POS a0*(1-dist2)*(1,0,0) OCC 1 SS SS2 ... add the other 5 The program would then automatically compute not only the distances for the SS paths, but those for the MS paths as well, and perhaps even estimate the ss values based on the ss's for the shells. This is a relatively trivial example in which the scripting isn't needed. However, it gets bigger. For instance, suppose that some of the 1NN atoms might have Fe on them. Then, the W sites would have OCC 1-xFe and there would be ATOM Fe sites specifications like: ATOM Fe POS a0*(1-dist1Fe)*(sqrt(3),sqrt(3),sqrt(3))/2 OCC xFe SS SS1Fe and the program would automatically work up MS paths with the proper weighting for the number of W and Fe atoms involved. Now, consider an octahedral cage in which the central atom may be off-center: SET a0 = appropriate value CENTRAL Ti a0*(d_off,d_off,d_off)/sqrt(3) ATOM O POS (a0/2)*(1+d1,d2,d2) OCC 1 SS SS1 ATOM O POS (a0/2)*(d2,1+d1,d2) OCC 1 SS SS1 ATOM O POS (a0/2)*(d2,d2,1+d1) OCC 1 SS SS1 ATOM O POS (a0/2)*(-1+d1,d2,d2) OCC 1 SS SS1 ... The distortions shown are intended to keep the 3-fold symmetry about 111. Now, when you consider the higher shells, you can see that it could get pretty messy to work out what the distances would be as a function of d_off, even if you don't allow displacements of higher neighbors. This sort of specification only becomes sort of practical because computers can now handle the multitudes of paths which will appear. Funny that the Vpath thing should have just got discussed; that tool would be extra-important for distorted structures. For the POS parameters, the above are given in Cartesian coords, but it would be good to have the option to do it in crystal coords, invoking the crystal symmetry. I'm not sure how to do that for impurities. I realize that this would be a HUGE job, but whoever does it would win the hearts of EXAFS people everywhere :-) mam On 5/29/2014 8:14 AM, Matt Newville wrote: Hi All, As Scott, Bruce, Anatoly have said, it is certainly possible to map certain crystallographic distortions to local structure, and so predict the effect on EXAFS, and model EXAFS in terms of those distortions. But to be clear for the original question, EXAFS is inherently a local structure probe and is not actually sensitive to crystallographic parameters. That is, one *must* make the mapping from crystlalographic parameters to local structure, often making important assumptions (such as there is a crystal structure and I know what the space group is) that EXAFS is not actually able to deny or confirm. Anyway, yes it is certainly possible to do things like model the extent of a tetragonal distortion. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting EXAFS simulation to experimental
Dear Carl, The short answer is yes, but it takes a little bit of effort. One method is to actually figure out how stretching the c-axis impacts the lengths of each path geometrically, and then use the functions determine to express the delr's of each path in terms of the change in c. This method is rigorously correct, but requires digging in to the geometry, and entering somewhat lengthy expressions for many of the scattering paths. A related method is to in effect use a first-order approximation of those changes. To do that, create two atoms files with slightly different values of c. Generate the corresponding paths, and see how the reff of those paths changes. For example, changing c by 0.01 might result in a certain path having a reff change by 0.014. Use the ratio of the change in reff to the change in c to scale the delr of those paths with respect to a guessed parameter delc. In the example I just provided the delr of the path in question would be chosen to be 1.4*delc. The second method is, of course, approximate, but for small changes in a parameter such as c can work pretty well, and can be easier to implement than the first. --Scott Calvin Sarah Lawrence College On May 29, 2014, at 12:33 PM, Carl Brozek bro...@mit.edu wrote: Dear All, Thank you for your responses so far and I apologize for not being clearer. Here is the problem at hand: I have a material that is best thought of as organic, graphene-like 2-D sheets connected by infinite chains of Fe-S. Based on PXRD and other techniques, we know the structure of the AB plane (the 2-D organic part), but we aren't able to make sense of what is going on with the Fe-S chain. We can simulate the PXRD based on proposed .cif files, but it's off most likely because of the c direction (Fe-S chain). We collected Fe K edge XAS to tease out Fe-S bond angles and distances, hoping we could feed this into our simulation for the PXRD to improve the fit. Modifying the ATOMS input by hand, by constructing different reasonable geometries, was improving the simulation, but using a error minimization fitting program would be best. So, is it possible to vary specific angles and distances between atoms along the c-direction only in an error minimization program based on our experimental data? I apologize if you have already responded to this reformulated question. best, Carl ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting EXAFS simulation to experimental
Hi Matthew, On Thu, May 29, 2014 at 11:18 AM, Matthew Marcus mamar...@lbl.gov wrote: I wonder if what he was asking about is an automated way of mapping the position parameters for a given space group, that is, fractional atomic coordinates as listed in a .cif, onto the various path distances. As it is now, it's impractically hard to do it except for very simple cases. I completely agree. Maybe what is needed is a language for specifying local structures in which atom positions and occupancies can be given by variables, and the program would automatically parameterize the paths. As a hypothetical toy example, consider a simple model of a substitutional model of Fe in bcc W (atoms chosen more or less at random). Here, we suspect that since Fe is a smaller atom than W, the first neighbors would be displaced inward. This is an excellent suggestion... Thus, we might have a specification something like SET a0 = 3.165 /* lattice parameter of pure W */ CENTRAL Fe 0 0 0 ATOM W /* 1st NN */ POS a0*(1-dist1)*(sqrt(3),sqrt(3),sqrt(3))/2 OCC 1 SS SS1 ATOM W POS a0*(1-dist1)*(-sqrt(3),sqrt(3),sqrt(3))/2 OCC 1 SS SS1 ... add the other 6 ATOM W /* 2nd NN */ POS a0*(1-dist2)*(1,0,0) OCC 1 SS SS2 ... add the other 5 The program would then automatically compute not only the distances for the SS paths, but those for the MS paths as well, and perhaps even estimate the ss values based on the ss's for the shells. This is a relatively trivial example in which the scripting isn't needed. However, it gets bigger. For instance, suppose that some of the 1NN atoms might have Fe on them. Then, the W sites would have OCC 1-xFe and there would be ATOM Fe sites specifications like: ATOM Fe POS a0*(1-dist1Fe)*(sqrt(3),sqrt(3),sqrt(3))/2 OCC xFe SS SS1Fe and the program would automatically work up MS paths with the proper weighting for the number of W and Fe atoms involved. Now, consider an octahedral cage in which the central atom may be off-center: SET a0 = appropriate value CENTRAL Ti a0*(d_off,d_off,d_off)/sqrt(3) ATOM O POS (a0/2)*(1+d1,d2,d2) OCC 1 SS SS1 ATOM O POS (a0/2)*(d2,1+d1,d2) OCC 1 SS SS1 ATOM O POS (a0/2)*(d2,d2,1+d1) OCC 1 SS SS1 ATOM O POS (a0/2)*(-1+d1,d2,d2) OCC 1 SS SS1 ... The distortions shown are intended to keep the 3-fold symmetry about 111. Now, when you consider the higher shells, you can see that it could get pretty messy to work out what the distances would be as a function of d_off, even if you don't allow displacements of higher neighbors. This sort of specification only becomes sort of practical because computers can now handle the multitudes of paths which will appear. Funny that the Vpath thing should have just got discussed; that tool would be extra-important for distorted structures. For the POS parameters, the above are given in Cartesian coords, but it would be good to have the option to do it in crystal coords, invoking the crystal symmetry. I'm not sure how to do that for impurities. I realize that this would be a HUGE job, but whoever does it would win the hearts of EXAFS people everywhere :-) mam Yes, that's a very nice way to do it, and I think such a distortion language would be a great way to map the problem to EXAFS. I think such ideas have been kicked around for a long time, and I'm pretty sure something like this was part of Bruce's motivation for Virtual Paths. A confounding, persistent issue for many years was that Feff's pathfinder (purposely?) loses all information about the atomic positions for a path. Basically, the pathfinder needs to be able to retain the full path in order to model distortions in the way you're talking about. I believe Bruce's pathfinder in Artemis does this. I agree it's real work, but would be highly useful. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fitting EXAFS simulation to experimental
Hi Scott, Thanks a lot for the insight. It seems like it'll take a bit of work, but I'm happy to hear it's doable. best, Carl On Thu, May 29, 2014 at 12:54 PM, Scott Calvin scal...@sarahlawrence.eduwrote: Dear Carl, The short answer is yes, but it takes a little bit of effort. One method is to actually figure out how stretching the c-axis impacts the lengths of each path geometrically, and then use the functions determine to express the delr's of each path in terms of the change in c. This method is rigorously correct, but requires digging in to the geometry, and entering somewhat lengthy expressions for many of the scattering paths. A related method is to in effect use a first-order approximation of those changes. To do that, create two atoms files with slightly different values of c. Generate the corresponding paths, and see how the reff of those paths changes. For example, changing c by 0.01 might result in a certain path having a reff change by 0.014. Use the ratio of the change in reff to the change in c to scale the delr of those paths with respect to a guessed parameter delc. In the example I just provided the delr of the path in question would be chosen to be 1.4*delc. The second method is, of course, approximate, but for small changes in a parameter such as c can work pretty well, and can be easier to implement than the first. --Scott Calvin Sarah Lawrence College On May 29, 2014, at 12:33 PM, Carl Brozek bro...@mit.edu wrote: Dear All, Thank you for your responses so far and I apologize for not being clearer. Here is the problem at hand: I have a material that is best thought of as organic, graphene-like 2-D sheets connected by infinite chains of Fe-S. Based on PXRD and other techniques, we know the structure of the AB plane (the 2-D organic part), but we aren't able to make sense of what is going on with the Fe-S chain. We can simulate the PXRD based on proposed .cif files, but it's off most likely because of the c direction (Fe-S chain). We collected Fe K edge XAS to tease out Fe-S bond angles and distances, hoping we could feed this into our simulation for the PXRD to improve the fit. Modifying the ATOMS input by hand, by constructing different reasonable geometries, was improving the simulation, but using a error minimization fitting program would be best. So, is it possible to vary specific angles and distances between atoms along the c-direction only in an error minimization program based on our experimental data? I apologize if you have already responded to this reformulated question. best, Carl ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Fitting EXAFS simulation to experimental
Dear listhost, I'm using Artemis as a front end for ATOMS and FEFF and I would like to build a simulated EXAFS spectrum based on experimental data I have. I know how to generate a simulation based on a .cif or .xyz file, but is it possible to vary parameters in these input geometries to best match the experimental? Has someone implemented this in artemis or matlab? thanks, Carl -- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
