Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?
Hi Bruce I have spent 1 month to learn the Athena by using your ATHENA User's Guide updated at Aug. 31,2007. I am very satisfied with it and thank you very much. Now I am learning the ARTEMIS. However, till now I can not find a suitable guide for a beginner. The PPT wrote by Shelly is not suitable for me. And the artemisdoc.pod is also puzzled me. Is there a Artemis User's Guide like the Athena? Thanks Kefan -- Kefan Wang School of Physics and Electronics Henan University, 475004 E-mail: [EMAIL PROTECTED]; [EMAIL PROTECTED] Hi Kefan, I suspect that my answer to this question will be of broad interest, so I am taking the liberty of CCing the Ifeffit mailing list. Thank you for the very kind words regaridng Athena. I am pleased that you found the Athena User's Guide so helpful. Sadly, I have not yet written a document of comparable extent for Artemis. I certainly understand that there is a need for comparable user guide, but finding the time and energy to write one has not yet happened. Writing the Athena User's Guide was fairly exhausting and I need to take a break before embarking on a similarly large document for Artemis. I have to defend Shelly's various presentations. I think they have a lot of good information in them. I think that using them along with other resources can give you enough of an overview of Artemis to get started. I strongly recommend that you work through Scott Calvin's ZnO example, which can be foun at http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib ZnO is somewhat of an idealized example -- many of us work on problems that are pretty far removed from a simple crystal like ZnO. However, Scott's example is quite thorough. Working through it while carefully following his comments in the project journals will introduce many of Artemis' features. As for the pod file -- those are the files that get displayed when you click on one of the documentation buttons from within Artemis. I acknowledge that they are thin on details and somewhat out of date. The last bit of advice I can give you is to read the papers written by the names you see on the Ifeffit mailing list. The folks who offer answers to question on the list are also some of the best practitioners of EXAFS analysis using Feff. Although it might seem funny to read papers by Anatoly Frenkel or Paul Fons if you are studying environmental science (or Shelly Kelly's if you are a materials scientist), I strongly recommend doing so anyway. Their science might be pretty far away from what you do, but the EXAFS analysis strategies are quite instructive and are certainly transferable. I know that is not the answer you were hoping for, but it may be helpful nonetheless. Regards, B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?
What would be really useful is to make a searchable database with links to original publications (many of them are more than 20 years old but are still the best resources on many issues) on many subjects discussed in this list. For example: Number of independent data points: see Stern and Heald arcticle in Handbook on Synchrotron Radiation, Ed Stern PRB article, etc. Thickness effects: Kim and Stern PRB Cumulants: G. Bunker, Nucl. Instrum. Methods in 1980s Background removal: Newville, Livins, PRB etc. Multiple scattering collinear paths and angular dependence of f(k): Lee and Pendry PRB (1975?) Transferability of photoelectron phase: Citrin, Kincaid, et al, Phys Rev B, 1970s (I may be wrong in the years and order of authors, but this this the idea). It would be so useful if someone (I cannot do it but will be happy to help) took care of putting together a backbone version of it and set it up as, say, wiki (which is Bruce's idea as I once brought it up to him). I am sure most of us will be happy to contribute references that we know. Thus, such database may become an exhaustive resource of information that should be a primer for every XAFS user. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Richard Mayes Sent: Friday, December 14, 2007 11:02 AM To: XAFS Analysis using Ifeffit Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [Ifeffit] Is there a Artemis User's Guide like the Athena? Kefan, As someone who was in your place 2 years ago, one thing Bruce mentioned was reading the papers of people you find on the mail list, however he didn't specifically mention searching the mail list. When I had questions, the answers were often already discussed on the mail-list. If you're not a member of the mail-list, I highly recommend you join. As I currently struggle writing a how-to manual that's supposed to shorten the XAFS learning curve for our group, I find myself searching the mail-list archives often to see how different people approach different issues. Good luck on your quest! -Richard Hi Bruce I have spent 1 month to learn the Athena by using your ATHENA User's Guide updated at Aug. 31,2007. I am very satisfied with it and thank you very much. Now I am learning the ARTEMIS. However, till now I can not find a suitable guide for a beginner. The PPT wrote by Shelly is not suitable for me. And the artemisdoc.pod is also puzzled me. Is there a Artemis User's Guide like the Athena? Thanks Kefan -- Kefan Wang School of Physics and Electronics Henan University, 475004 E-mail: [EMAIL PROTECTED]; [EMAIL PROTECTED] Hi Kefan, I suspect that my answer to this question will be of broad interest, so I am taking the liberty of CCing the Ifeffit mailing list. Thank you for the very kind words regaridng Athena. I am pleased that you found the Athena User's Guide so helpful. Sadly, I have not yet written a document of comparable extent for Artemis. I certainly understand that there is a need for comparable user guide, but finding the time and energy to write one has not yet happened. Writing the Athena User's Guide was fairly exhausting and I need to take a break before embarking on a similarly large document for Artemis. I have to defend Shelly's various presentations. I think they have a lot of good information in them. I think that using them along with other resources can give you enough of an overview of Artemis to get started. I strongly recommend that you work through Scott Calvin's ZnO example, which can be foun at http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib ZnO is somewhat of an idealized example -- many of us work on problems that are pretty far removed from a simple crystal like ZnO. However, Scott's example is quite thorough. Working through it while carefully following his comments in the project journals will introduce many of Artemis' features. As for the pod file -- those are the files that get displayed when you click on one of the documentation buttons from within Artemis. I acknowledge that they are thin on details and somewhat out of date. The last bit of advice I can give you is to read the papers written by the names you see on the Ifeffit mailing list. The folks who offer answers to question on the list are also some of the best practitioners of EXAFS analysis using Feff. Although it might seem funny to read papers by Anatoly Frenkel or Paul Fons if you are studying environmental science (or Shelly Kelly's if you are a materials scientist), I strongly recommend doing so anyway. Their science might be pretty far away from what you do, but the EXAFS analysis strategies are quite instructive and are certainly transferable. I know that is not the answer you were hoping for, but it may be helpful nonetheless. Regards, B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of
Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?
What would be really useful is to make a searchable database with links to original publications (many of them are more than 20 years old but are still the best resources on many issues) on many subjects discussed in this list. Anatoly, This seems like an awfully good start: http://scon155.phys.msu.su/~papers/ In fact, you seem to be the first hit for a search of cumulants! Alexander seems to have done a very nice job. Some more web-fu would be nice -- for instance, actual links to the articles or to their DOI numbers would be very helpful for those of us lucky enough tobe at institutions with extensive subscription collections. Mirrors of the database and web page on other continents might also be helpful. B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] two issues with Athena on Windows and one with Artemis
Hi, For the last few weeks, I have been doing experiments at beamlines with Windows machines. This has afforded me more time than normal using my programs under Windows. I am appreciating my linux machines more than normal, but that is not the point of this email ;-) I have found a few issues that I wanted to address even though no one has yet mentioned them on this list. 1. Combo-box menus: In Athena, combo boxes are used for a variety of purposes. For instance, in the alignment dialog, a combo box is used to select the data group for use as the alignment standard. It seems that selecting items from the drop-down list does not work as expected. Clicking to post the drop down menu then clicking on your choice does not cause your choice to be inserted into the combo-box text area. The work-around that I have found is to first *right* click on your selection, then *left* click on it. I cannot explain why this works and I wish the whole thing just worked correctly. At least there is a work-around! (Another work-around is to move the appropriate group to the top of the list, but I dislike the right-click/left-click solution less ;-/ .) 2. Several people have mentioned privately that the most recent version of Athena seems very sluggish on Windows. I agree and so, I think, does Matt. We changed how the compiled parts get compiled for the most recent release and perhaps some bed seeting were used. We'll look into for the next release. While doing some profiling on my new coding project, Demeter, I figured out a reasonably simple and very fruitful optimization for the interaction between my perl code and the Ifeffit library. I will implement that for the next release of Athena. Hopefully the next version will be snappier. For now, I apologize that the performance of Athena is less than it should be. 3. In Artemis, there are two or three menu items which involve importing something from a file. One example is Import variables from text file under the GDS menu. On Windows, this fails to post the file selection dialog and spews error messages to the console. This bug will be fixed in the next release. Sadly, there is no work-around that I know of. Regards, B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?
Kefan, I suggest starting with Bruce's lecture and example of fitting methyl tin: http://xafs.org/Workshops/APS2007?action=AttachFiledo=gettarget=Ravel_artemis.pdf http://xafs.org/Workshops/APS2007?action=AttachFiledo=gettarget=Ravel.zip as it really gives a nice approach to building up from the beginning and shows not only the concepts but enough of which buttons to push to actually get a real fit yourself. Fitting with Artemis/Ifeffit definitely takes some study. That's why there are training courses and online notes and mailing lists. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
