[Ifeffit] JFEFF/FEFF9 SaveRun no longer works after Java Update -- FEFFgroup announcement
Dear iFEFFIT community, a short update from the FEFF developers team: A recent Java update (Java 7 Update 21) broke some functionality of the JFEFF interface for the FEFF program. Users who update to J7U21 have noticed that when they click SaveRun nothing happens: the FEFF programs do not run and there is no output. We think this issue will affect people on all Operating Systems. To fix this issue there are two possibilities: * Roll back Java to a previous version. For security reasons please have at least Java 7 Update 11, which was an important security update, or newer. Instructions for rolling back Java can be found online. * We have updated JFEFF to work with the latest Java. This latest (J)FEFF version is not yet available on the official download website, but FEFF users with a valid license can contact us and we will provide them with a download link for the latest (J)FEFF. Please contact us directly. Users who currently have FEFF8 can upgrade to FEFF9 at any time at a discounted rate. Thank you to Linda Lim for her earlier post on the iFEFFIT ML. Cheers, Kevin Jorissen FEFFgroup - University of Washington ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] FEFF report: Hard tests failed in fovrg.
Dear Ifeffit community, a short reaction from the FEFFgroup. 1/ It's true that we don't follow up on the ifeffit ML 100%. Important issues usually do get through to us. We highly value the ifeffit community. We can also be contacted directly for problems that are FEFF related rather than iFEFFit related ( contacthttp://www.feffproject.org/feffproject-contact.html ). We'll likely ask you for the feff.inp file that generates the problem. 2/ We're glad that FEFF6 is so successful. Meanwhile FEFF6 is about as old as Windows95, and development is now focused on FEFF9http://www.feffproject.org/feffproject-feff.html, which has 15-20 years of improvements over FEFF6. It's a big improvement for anyone running FEFF calculations. It costs $500, or $250 upgrade from any paid version of FEFF. 3/ The OP posted 5 input files. 4 of these run without problems in FEFF9. The last has I atoms (Z=53) at a spacing of 0.8A, and doesn't run out of the box. I expect the same result from FEFF8. 4/ There has been some effort to bring a FEFF9lite to the analysis codes, analogous to the FEFF6lite discussed here. We would be very happy to see that effort succeed. 5/ FWIW the fovrg routine was retired in 1996 and replaced by a relativistic version called dfovrg. The hard error does not exist anymore. 6/ We're a small team; we apologize for all the 'bothering' we don't get around to. We do care about supporting our users and put a lot of energy into support. Please reach out ot us when you need us. Cheers from Seattle, Kevin Jorissen PS I posted a while back about a problem with JFEFF and Java updates but I'm not sure the message made it through: I asked the mod, but no reply. I hope this msg makes it :). On Wed, Aug 7, 2013 at 8:24 AM, Bruce Ravel bra...@bnl.gov wrote: On 08/06/2013 11:55 AM, Naumova, Maria wrote: May I use this FEFF calculation as a valid base for future fit? Or this error means that FEFF doesn't work correct and I can't rely on its output? If the phase-shift program failed to converge does it mean that it could stop in some completely unrealistic result? Maria, You are correct that the version of Feff6 that we are allowed to give away for free reliably complains about failing something called a hard test. This is some kind of convergence test on the computation of the muffin tin potential. The test is made in the lines just prior to this: https://github.com/newville/**ifeffit/blob/master/src/feff6/**fovrg.f#L158https://github.com/newville/ifeffit/blob/master/src/feff6/fovrg.f#L158 The error is reported here: https://github.com/newville/**ifeffit/blob/master/src/feff6/**phase.f#L127https://github.com/newville/ifeffit/blob/master/src/feff6/phase.f#L127 If you can make heads to tails out of the calculation in fovrg.f, you are vastly smarter than me, vastly more patient than me, or both! I have 2 comments on the main point of your post: 1. As you noted, this question has been asked many times before. Not once has anyone from the Feff project (i.e. anyone who might actually have a working knowledge of that bit of code) bothered to comment. It would be lovely to hear from one of them. 2. This very version of Feff has been included with Ifeffit and with the packages I build for my software for years. Over a decade, in fact. In that time, Feff, Ifeffit, and my software have been used for defensible data analysis thousands of times and by hundreds of practitioners. That does not mean that any part of the software stack is actually correct. But it does mean that lots of article writers and lots of article reviewers have accepted the results coming from this stack of software. That does not mean that you should accept it. Quite the contrary -- you would be wise to question every part of the software stack. You may even find that you will need to discard any or all parts of that software stack and replace them with something you trust more -- perhaps even with something that you, yourself have written. To summarize, I am saying the same thing I have said in the past. I don't understand the code that generates that message. No one from the Feff project has ever bothered weighing in on what it means. No one has demonstrated that it represents an actionable problem. The codes which use Feff have been in use for years to produce defensible science. So, in conclusion, what should you do? I have no idea. My advice is to continue using the software, but my advice may not be any more reliable than the software itself. I hope that helps. Probably doesn't, but it's the best I can do. 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
Re: [Ifeffit] FEFF report: Hard tests failed in fovrg.
Hi Bruce, thanks for your answer. I'm glad that we seem to be in agreement about the main point, which is that a FEFF9L is the best way forward (integrates with analysis tools; has all improvements and bugfixes; free). I'll fire up developer communication about this (including you). Thank you for bringing the $$ problem to my attention; I did not know that it was a problem for a large number of users. As for the original question, the algorithm fovrg had some problems (meaning that it would fail; not that it would produce bad results), as explained by John Rehr in the 2005 message cited by the OP. The needed improvements are exactly those changes made in later versions. That is why I am more drawn to a FEFF9L than to fitting some of the improvements into the old FEFF6L, but I will discuss it with the other developers. I have not tried to make the OP's files work in FEFF6L. I would look at the RGRID/AFOLP/FOLP/POTENTIALS cards first. I'll give this a try later myself, but it's possible that there is no solution within FEFF6L. Let me finish by reiterating that people are welcome to contact us directly with FEFF questions, as we may not see all messages reported here. Cheers, Kevin On Wed, Aug 7, 2013 at 11:58 AM, Bruce Ravel bra...@bnl.gov wrote: Kevin, Thank you for your email. I apologize if I expressed myself in a way that was too mean-spirited in my earlier email, but the basic point was true. The hard test in fovrg question has been asked repeatedly. Your response today is, by my memory, the first we've seen on this topic, from your group, and on this mailing list. I have a few comments. 1. The original question remains unanswered. 2. A lot of people use the software stack at the top of which Artemis sits. For many of those people a $250 or $500 expense is completely out of reach. Not a few. Lots. We have users who are impoverished grad students. We have users who are researchers in developing countries. To be so blithe about a $500 expense is unfair to those people. 3. Feff6 is unambiguously not dead. Feff6L is the only version (the *ONLY* version) I am allowed to package with my software. That not only makes it alive -- it makes it the de-facto version for many people. 4. Is Feff9L a thing? I would be thrilled to put Feff6L out of our misery and replace it with something that post-dates Windows 95. I agree that it has been discussed, but no one has ever asked me to take a look at such a thing. Perhaps I flatter myself, but I would think that I would be involved somehow, given that one of the main reasons to make Feff9L is to see it included in a package with Artemis. So, let me end this on a positive note by reaching out to you with some actionable questions: 1. What should I tell my users who ask about the hard test failure in fovrg that is not a solicitation to spend money on Feff9? 2. Can I take a look at Feff9L? Cheers, B On 08/07/2013 02:29 PM, Kevin Jorissen wrote: Dear Ifeffit community, a short reaction from the FEFFgroup. 1/ It's true that we don't follow up on the ifeffit ML 100%. Important issues usually do get through to us. We highly value the ifeffit community. We can also be contacted directly for problems that are FEFF related rather than iFEFFit related ( contact http://www.feffproject.org/**feffproject-contact.htmlhttp://www.feffproject.org/feffproject-contact.html ). We'll likely ask you for the feff.inp file that generates the problem. 2/ We're glad that FEFF6 is so successful. Meanwhile FEFF6 is about as old as Windows95, and development is now focused on FEFF9 http://www.feffproject.org/**feffproject-feff.htmlhttp://www.feffproject.org/feffproject-feff.html, which has 15-20 years of improvements over FEFF6. It's a big improvement for anyone running FEFF calculations. It costs $500, or $250 upgrade from any paid version of FEFF. 3/ The OP posted 5 input files. 4 of these run without problems in FEFF9. The last has I atoms (Z=53) at a spacing of 0.8A, and doesn't run out of the box. I expect the same result from FEFF8. 4/ There has been some effort to bring a FEFF9lite to the analysis codes, analogous to the FEFF6lite discussed here. We would be very happy to see that effort succeed. 5/ FWIW the fovrg routine was retired in 1996 and replaced by a relativistic version called dfovrg. The hard error does not exist anymore. 6/ We're a small team; we apologize for all the 'bothering' we don't get around to. We do care about supporting our users and put a lot of energy into support. Please reach out ot us when you need us. -- 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
Re: [Ifeffit] FEFF report: Hard tests failed in fovrg.
Hi all, I think that several of the points raised in the last few replies will be better addressed off-ML. (See above) As for the benefits of FEFF9: * calculation of potentials is more stable and more accurate * improved self-energy (- better peak positions and widths) * ability to use high-quality ab initio Debye-Waller factors (this will currently be beyond the skill of many users, but will be semi-automated in an upcoming release of FEFF9) * alternative RPA core hole * ... and don't forget: * 15 years of ironing out problems Cheers, Kevin Jorissen On Wed, Aug 7, 2013 at 12:47 PM, Bruce Ravel bra...@bnl.gov wrote: Hi Matthew, On 08/07/2013 03:35 PM, Matthew Marcus wrote: 2.The later FEFFs use a different structure, in which the modules are separate programs. Can this be integrated into Artemis? I don't see that as a problem. Demeter already does a lot of crazy things, including playing around with the CONTROL values and replacing Feff's pathfinder with one that I wrote. Going back to point 1, any FEFF9L would need to be a wrapper which executes the modules in correct sequence. I doubt that Feff9L would be a drop-in replacement in Artemis, but if Feff9L were a defined thing, then I (and other software authors -- yourself, for example) would have a defined target to work against. 5.Is there some documentation showimg how FEFF(6) is better than FEFF6L for EXAFS alone? Under what conditions should we be dissatisfied with FEFF6L? Umm ... well ... perhaps when fovrg fails its hard test? :) I know that FEFF9 has all kinds of nice things that it does, but many of these are irrelevant for Artemis use. This is a recurring topic on this list and a most excellent question. As I have written before, there is some anecdotal evidence that self consistent muffin tins are an improvement in terms of the values of E0 needed for a good fit. But I am not aware of a rigorous investigation that has been published in any form (journal article on down to wiki page). I think that simply having a version of FeffN (with N6) in a form that I can properly target in Demeter would be a real boon in that it would be a lot easier to automate such tests. 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 ifef...@millenia.cars.aps.anl.**gov Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.**gov/mailman/listinfo/ifeffithttp://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] Lecture/tutorials required on FeFF 9.x
Hi Sanjeev, Depending on what you're doing exactly we may be able to contribute something. We have taught several workshops, although I'm not 100% sure what we have in terms of lecture materials as our workshops tend to be very hands-on. In any case we'd be happy to host contributed tutorials on our website for the whole community to enjoy. Thanks very much for your interest in using and sharing the FEFF code, Kevin Jorissen On Wed, Aug 21, 2013 at 8:40 PM, S. Gautam sgauta...@gmail.com wrote: Dear All, I have been trying to find out some lectures/tutorials on FeFF 9.x (J.J. Rehr) to deliver my XAFS users, other than it's UserGuide as available on the website. If someone has made for their users, it would help me to deliver with acknowledging you. thanks in advance sincerely Sanjeev - Dr. Sanjeev Gautam KIST -PAL , South Korea -- http://orcid.org/-0003-3123-9906 - ___ 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] Demeter 0.9.19
I can concur with others here that making something work on Mac can be a miserable experience. Sometimes you have to admit defeat and change the approach. Anyway, I tried sudo port install p5.16-ifeffit and failed: ~/Downloads% sudo port install p5.16-ifeffit --- Computing dependencies for p5.16-ifeffit --- Dependencies to be installed: ifeffit pgplot perl5.16 gdbm --- Extracting pgplot Error: org.macports.extract for port pgplot returned: command execution failed Error: Failed to install pgplot Please see the log file for port pgplot for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_pgplot/pgplot/main.log Error: The following dependencies were not installed: ifeffit pgplot perl5.16 gdbm To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port p5.16-ifeffit failed ~/Downloads% (This is upon rerunning the command - the first time, it installed many more dependencies -- does anyone else suspect port of being designed to fill hard disks as fast as possible?) System is 10.9 generally up-to-date with most things. pgplot seems to fail during extraction. I doubt that I'd be able to contribute a lot to this project, but I can test things. Also I'm surprised to read so much about gfortran about this thread, but maybe I'm missing some common knowledge on the project ... I am generally much happier with Ifort. Cheers, Kevin On Thu, Jan 9, 2014 at 8:47 AM, Schima, Frank frank.sch...@nist.gov wrote: Hi all, On Jan 9, 2014, at 8:26 AM, Matt Newville newvi...@cars.uchicago.edu wrote: On Thu, Jan 9, 2014 at 8:04 AM, Bruce Ravel bra...@bnl.gov wrote: On 01/09/2014 08:24 AM, Stefano Luciano Ciurli wrote: Hello Bruce and thank you for your hard work! instructions to install on OS X 10.6.8? There is not a Mac package. I do not own a Mac and and so do not have the ability to develop a Mac package on my own. Over the years, no one has ever stepped up to help me develop a Mac package for Demeter. (Or Debian packages, or RedHat packages, for that matter.) Well, I have *tried* many times, and put a fair amount of time in getting Demeter to work on a Mac. What I have not done is *succeed*. I can tell you that getting wxPerl to work on Mac OSX is far from simple. Though Demeter is many years old now, and I've tried many times over the years (and I using wxPython on Mac all the time), it is only within the past few months that I have ever gotten wxPerl to actually build on any Mac, and this was a 10.8 machine. Currently (though I haven't looked at it in more than a month), getting the Ifeffit-Perl interface to build properly with Mac OS 10.8 has me stumped, as Apple is now using llvm/clang, making it challenging to work well with gfortran. Migrating Demeter to use Larch should simplify the situation, as it would remove the need for the Ifeffit-Perl interface. Frankly, the work I do on the Windows package takes a lot of time. The only way I can claim that time fits in my job description is because my group uses Windows machines at our beamlines. Help would be welcome to develop packages for Mac and other platforms, but despite repeated requests over many years, no one has ever volunteered and actually seen it through to completion. Yes, help building Demeter for Mac OSX would be great. I too have put a lot of work into making Demeter run on OS X. I have been attempting to make a port of it in Macports [1] so it is easy to install and/or have a package installer created. The good news is that along the way I have successfully created a port of ifeffit [2] that builds fine for me on 10.9 and should work all the way down to 10.6. I utilize gcc for gfortran. I believe the ifeffit-perl bindings [3] work too. After you install Macports [4], you can simply type: sudo port install p5.16-ifeffit The bad news is that my in progress Demeter port does not work yet. The problem I’m stuck on is getting the perl-wx port [5] built. I have not been able to get it built with the new wx-widgets version 3.0.0 that is in Macports. The perl-wx people apparently don’t have support for that version of wx yet and they never respond to my queries about it on the mailing list. I encourage people to test out ifeffit on OS X through Macports and give me feedback - positive or negative. Thanks to Bruce for his support during this endeavor. Cheers! Frank [1] http://www.macports.org [2] https://trac.macports.org/browser/trunk/dports/science/ifeffit/Portfile [3] https://trac.macports.org/browser/trunk/dports/perl/p5-ifeffit/Portfile [4] http://www.macports.org/install.php [5] https://trac.macports.org/browser/trunk/dports/perl/p5-wx/Portfile ___ Ifeffit mailing list
Re: [Ifeffit] Demeter 0.9.19
Hi Matt, I agree with everything you say. Thanks for taking the time to explain. As someone who uses fortran all the time, it makes sense for me to own Ifort, but since it's only free for academics on Linux, that's not true for most people. Actually, for FEFF our philosophy is also that it should compile with any compiler on any platform. We respond to EVERY compilation issue and never tell people to use another compiler. However -- most of our users don't want to compile code at all: they like a nice binary that I've compiled for them. (I doubt that the ifeffit/demeter users would object to this option ;).) For that, I like to use Ifort - for my purpose it's the better compiler. But we make sure that FEFF compiles well using gfortran etc. also. If I were to successfully built the codes on this mailing list, I'll definitely share the recipe, as well as any kind of binary other people can use without having to build/compile/... . It won't be for today, unfortunately :). Cheers, Kevin On Fri, Jan 10, 2014 at 7:28 AM, Matt Newville newvi...@cars.uchicago.eduwrote: Hi Kevin, On Thu, Jan 9, 2014 at 11:37 PM, Kevin Jorissen kevinjorissen...@gmail.com wrote: I can concur with others here that making something work on Mac can be a miserable experience. Sometimes you have to admit defeat and change the approach. Anyway, I tried sudo port install p5.16-ifeffit and failed: ~/Downloads% sudo port install p5.16-ifeffit --- Computing dependencies for p5.16-ifeffit --- Dependencies to be installed: ifeffit pgplot perl5.16 gdbm --- Extracting pgplot Error: org.macports.extract for port pgplot returned: command execution failed Error: Failed to install pgplot Please see the log file for port pgplot for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_pgplot/pgplot/main.log Error: The following dependencies were not installed: ifeffit pgplot perl5.16 gdbm To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port p5.16-ifeffit failed ~/Downloads% (This is upon rerunning the command - the first time, it installed many more dependencies -- does anyone else suspect port of being designed to fill hard disks as fast as possible?) System is 10.9 generally up-to-date with most things. pgplot seems to fail during extraction. I doubt that I'd be able to contribute a lot to this project, but I can test things. Also I'm surprised to read so much about gfortran about this thread, but maybe I'm missing some common knowledge on the project ... I am generally much happier with Ifort. If you or anyone else wants to use ifort or any other compiler, that would be fine. For many years, I did keep a license for Digital/Compaq/Intel Fortran on Windows in order to make the Windows dlls for distribution of the Ifeffit package. Even on Windows, this stopped being necessary, as the MinGW suite began including gfortran. Unlike Feff, these are open source projects, and we absolutely insist that anyone interested can use, (try to) build, and distribute these programs -- both Bruce and I are begging for such help, actually. Requiring non-free tools simply to build these programs would definitely put a burden on potential developers. I don't see any reason for why that would be necessary, especially on Linux and Mac, for which the system compilers are gcc (or gcc/llvm) which includes a working fortran compiler. Many free software projects (notably for me, scipy, but also the macports that Frank mentioned) use gfortran on Macs. And gfortran works fine for me for many things on 10.6 and 10.8. I can compile the basic ifeffit library and other fortran libraries used in Larch (though I did recently notice some dependency issues between 10.6 and 10.8, as the compiler version changed, and haven't tried 10.9 yet). I have not been able to build PGPLOT (perhaps not crucial for Demeter) or the Ifeffit-Perl bridge successfully on 10.8. I believe this is probably a matter of getting the compiler / linker arguments correct If you or anyone else can get these codes to build using ifort, more power to you. If so, can you post your solution? --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] Demeter 0.9.19
Hi Frank, thanks for responding ... I merely wanted to do you the favor of giving feedback on an experimental solution you solicited feedback for. After wiping and reinstalling macports, your port also installs. I probably don't want to know why. Cheers, Kevin On Fri, Jan 10, 2014 at 10:43 AM, Schima, Frank frank.sch...@nist.govwrote: On Jan 9, 2014, at 10:37 PM, Kevin Jorissen kevinjorissen...@gmail.com wrote: I can concur with others here that making something work on Mac can be a miserable experience. That’s the opposite of my experience. Anyway, I tried sudo port install p5.16-ifeffit and failed: ~/Downloads% sudo port install p5.16-ifeffit --- Computing dependencies for p5.16-ifeffit --- Dependencies to be installed: ifeffit pgplot perl5.16 gdbm --- Extracting pgplot Error: org.macports.extract for port pgplot returned: command execution failed Error: Failed to install pgplot Please see the log file for port pgplot for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_pgplot/pgplot/main.log Error: The following dependencies were not installed: ifeffit pgplot perl5.16 gdbm To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port p5.16-ifeffit failed ~/Downloads% (This is upon rerunning the command - the first time, it installed many more dependencies -- does anyone else suspect port of being designed to fill hard disks as fast as possible?) System is 10.9 generally up-to-date with most things. pgplot seems to fail during extraction. The pgplot port extracts and installs fine for me on OS X (10.6 through 10.9). But this is completely off-topic for this list. Please go to the Macports users mailing list [1] for support about this issue. I doubt that I'd be able to contribute a lot to this project, but I can test things. That is helpful. Also I'm surprised to read so much about gfortran about this thread, but maybe I'm missing some common knowledge on the project ... I am generally much happier with Ifort. gfortran is the only fortran compiler that will work with Macports since it is open source. Cheers! Frank [1] https://lists.macosforge.org/mailman/listinfo/macports-users ___ 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] Connecting Artemis to FEFF9.6.4
Hi Bao and Bruce, There has indeed been progress since FEFF6 -- the newer versions of the program have new input options that the old program will not recognize. E.g., as described in the post Bruce linked to, we now generally use the EDGE card rather than the HOLE card to specify the absorption edge. However the HOLE card is still recognized by the current FEFF9. Someone mentioned FEFF breaking support for older input files. To the contrary I expect FEFF6 input files to work smoothly with the FEFF9 code. E.g. the Cu example in the FEFF6 distribution works with today's FEFF9. FEFF6 and FEFF9 may produce somewhat different output for the same input file because some internal defaults and algorithms have changed. FEFF9 is not meant to be run through the GUI exclusively. Many users (myself included) love working from the command line, and that will always be 100% supported. The GUI is just another way to control the input file and run the same compiled fortran executables. Occasional users and users unfamiliar with the command-line terminal (the majority of our users work in a Windows environment) seem fairly happy with it. But you can always do the same thing by typing feff on the command line. Our interface still consists of a single text file with 10-20 lines of keywords with options; and then a list of x,y,z coordinates. It's kind of old-fashioned; if something fancier is needed, I'm willing to help or translate it or show interested parties the code. On to the physics: I indeed expect that the improved self-energy (we call it MPSE, for Many-Pole Self-Energy) would improve EXAFS for many (not all) materials by shifting peak positions and correcting broadening. Other improvements might come from new options for Debye-Waller factors, TDLDA, or self-consistent SCF potentials (I think some on this mailing may have questioned the value of SCF potentials). The thread referenced by Bruce asks how well one would have to know the dielectric function of a material (that in itself may not be known very precisely) in order to get an advantage from the MPSE. In my own calculations a primitive built-in model requiring no knowledge from the user already seems to provide some of the improvement. It's not a conclusive answer, but it's encouraging. My personal opinion is that the dielectric function does not need to be provided with high accuracy. Josh Kas may be able to make a more qualified statement. Like Bruce, I would be delighted to see a comprehensive study done. It's certainly on our minds and if anyone else has plans in this direction, I'm sure we would be glad to support the effort. Finally ... Reading the referenced thread, I feel the need to clarify a few things about the FEFF group... We care a lot about our users and in particular about this community. It's a priority to make our codes useful to this community as well as the wider FEFF community. Personally I spend loads of time responding to questions, testing other people's input files, implementing requests, teaching, ... and wishing I had more time to implement all the remaining things I would like to provide! -- just like Matt or Bruce. I invite everyone to contact me with any FEFF requests that would benefit users, or to include me in ongoing developments. And to end on a cheerful note, I can happily report that FEFF8 for ifeffit EXAFS analysis is ready to be given out! Cheers and a late happy new year to everyone, Kevin Jorissen On Fri, Jan 10, 2014 at 8:13 AM, Bruce Ravel bra...@bnl.gov wrote: Hi Bao, This posting and its conversation thread is relevant to your question: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl. gov/msg03810.html The one thing that has changed since then is that progress has been made on making a version of feff8 with its XANES functionality stripped out and which can be redistributed. One thing that has not changed is that its integration into Artemis is very incomplete. Following the instructions in my first response to that post may work for you with feff9.6.4. Or maybe not. I have no idea. Another thing that has not changed is my skepticism that feffN (where N6) offers a substantial improvement for EXAFS data analysis. As I said in that conversation, it may, but no one has demonstrated it tomy satistfaction. Multi-pole self-energies are likely to represent a significant improvement in the EXAFS, but again, that systematic study has not been done. B PS: FWIW, getting feff8-for-EXAFS ready for use is something that neither Matt nor I have found much time for. A volunteer would be very welcome. On 01/10/2014 11:00 AM, Bao Nguyen wrote: Dear all, I’m new and have a daff question which must have been asked before: Can I refer Artemis to FEFF9.6.4, which I have, rather than the standard-issued FEFF6 for more streamlined structural refinement? Many thanks! Bao Nguyen Tenure-track Research Fellow School of Chemistry
Re: [Ifeffit] Demeter not working on Windows 8.1 64bit
Out of curiosity, I installed 09.19 on a fresh Win8.1 64bit under VMWare.
No problems during installation. I opened the cyanobacteria.prj data from
Bruce's sample data repo in Athena. After clicking around a few times
(specifically, clicking the green arrow and the magnifying glass+red curve
next to it in the toolbar of the plot window), I caused a gnu plot.exe has
stopped working error. Going into the monitor for the plotting log, I see
a similar x-range problem as discovered by Robert Gordon:
## energy quadrant
set title {/*1.6 Energy}
set xlabel {/*1.4 Energy{aa}(eV)}
set ylabel {/*1.4 x{/Symbol m}(E)}
#set xrange [ 11918.952 : 11918.952 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_lydqknai' using
1:2 with lines ls 2,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_kpklgmnh' using
1:2 with lines ls 1,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_djrhchms' using
1:2 with lines ls 3,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_geakjukk' using
1:2 with lines ls 4
## k quadrant
set title {/*1.5 k-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 k^{2} {\267} {/Symbol c}(k){aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_vyutwjzc' using
1:2 with lines ls 1
## R quadrant
set title {/*1.5 R-space}
set xlabel {/*1.2 Radial distance{aa}({\305})}
set ylabel {/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}{aa}({\305}^{-3})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_qeqqfnof' using
1:2 with lines ls 1,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_njjlolaa' using
1:2 with lines ls 2
## q quadrant
set title {/*1.5 q-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25 ]}{aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_ydrraees' using
1:2 with lines ls 1
So, I'm not offering anything new in this message, but perhaps confirming
someone else's experience can help. To be clear, this VM has never seen
any kind of Demeter, perl, gnu plot, ... before this experiment. It's a
clean Windows (I only added java and feff9 on it at an earlier time) and
current with all windows updates.
Cheers,
Kevin
On Tue, Jan 14, 2014 at 2:17 PM, Robert Gordon ragor...@alumni.sfu.cawrote:
Installing 0.9.19 overtop of 0.9.18.2 and Athena works fine.
Installing 0.9.19 clean (deleting demeter directory under appdata/roaming)
2nd attempt to open file in DAthena results in only 1 mini-graph.
Ranges are 0 for Emin/max, kmin/max, Rmin/max - putting a valid range
restores
full graph e.g. Rmin = 0 , Rmax = 6 gives full-size R-space graph...ditto
for fixing other
ranges. Fixed 3 out of 4 and read in a new file...obtained 3
mini-graphs...reset q range
as well and that one appears too.
Exited. Restarted. Read in file -
Show Command Buffer/Plot Buffer
## energy quadrant
set title {/*1.6 Energy}
set xlabel {/*1.4 Energy{aa}(eV)}
set ylabel {/*1.4 x{/Symbol m}(E)}
#set xrange [ 11870.11617648 : 11870.11617648 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vlxtfjcm' using
1:2 with lines ls 2,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_tfoziltm' using
1:2 with lines ls 1,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_fthredqy' using
1:2 with lines ls 3,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_iebbuian' using
1:2 with lines ls 4
## k quadrant
set title {/*1.5 k-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 k^{2} {\267} {/Symbol c}(k){aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_xizghpwm' using
1:2 with lines ls 1
## R quadrant
set title {/*1.5 R-space}
set xlabel {/*1.2 Radial distance{aa}({\305})}
set ylabel {/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}{aa}({\305}^{-3})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_nwtxpqxm' using
1:2 with lines ls 1,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vysurgrh' using
1:2 with lines ls 2
## q quadrant
set title {/*1.5 q-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25 ]}{aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_hxroumyr' using
1:2 with lines ls 1
unset multiplot
So, seems to be setting the xranges to zero for a clean install these
plots, and gnuplot
doesn't plot if no xrange. If I reset, then I can move around and use
DAthena 9.19
without issue...DArtemis is still an unhappy DHuntress with fpj files...
On 1/14/2014 3:28 PM, Bruce Ravel wrote:
On 01/14/2014 04:11 PM, Robert Gordon wrote:
Hi Matt, Shoaib (and Bruce lurking in the luminiferous ether),
I have 8.1 x64 on my laptop and just upgraded to 0.9.19 - clean install.
I can offer some additional
Re: [Ifeffit] Demeter not working on Windows 8.1 64bit
-- just to be clear, the pasted section of the log is not the bottom part.
It is followed by many more lines containing gnu plot settings (but no
plot commands).
Cheers,
Kevin
On Tue, Jan 14, 2014 at 5:38 PM, Kevin Jorissen
kevinjorissen...@gmail.comwrote:
Out of curiosity, I installed 09.19 on a fresh Win8.1 64bit under VMWare.
No problems during installation. I opened the cyanobacteria.prj data from
Bruce's sample data repo in Athena. After clicking around a few times
(specifically, clicking the green arrow and the magnifying glass+red curve
next to it in the toolbar of the plot window), I caused a gnu plot.exe has
stopped working error. Going into the monitor for the plotting log, I see
a similar x-range problem as discovered by Robert Gordon:
## energy quadrant
set title {/*1.6 Energy}
set xlabel {/*1.4 Energy{aa}(eV)}
set ylabel {/*1.4 x{/Symbol m}(E)}
#set xrange [ 11918.952 : 11918.952 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_lydqknai' using
1:2 with lines ls 2,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_kpklgmnh' using
1:2 with lines ls 1,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_djrhchms' using
1:2 with lines ls 3,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_geakjukk' using
1:2 with lines ls 4
## k quadrant
set title {/*1.5 k-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 k^{2} {\267} {/Symbol c}(k){aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_vyutwjzc' using
1:2 with lines ls 1
## R quadrant
set title {/*1.5 R-space}
set xlabel {/*1.2 Radial distance{aa}({\305})}
set ylabel {/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}{aa}({\305}^{-3})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_qeqqfnof' using
1:2 with lines ls 1,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_njjlolaa' using
1:2 with lines ls 2
## q quadrant
set title {/*1.5 q-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25 ]}{aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_ydrraees' using
1:2 with lines ls 1
So, I'm not offering anything new in this message, but perhaps confirming
someone else's experience can help. To be clear, this VM has never seen
any kind of Demeter, perl, gnu plot, ... before this experiment. It's a
clean Windows (I only added java and feff9 on it at an earlier time) and
current with all windows updates.
Cheers,
Kevin
On Tue, Jan 14, 2014 at 2:17 PM, Robert Gordon ragor...@alumni.sfu.cawrote:
Installing 0.9.19 overtop of 0.9.18.2 and Athena works fine.
Installing 0.9.19 clean (deleting demeter directory under appdata/roaming)
2nd attempt to open file in DAthena results in only 1 mini-graph.
Ranges are 0 for Emin/max, kmin/max, Rmin/max - putting a valid range
restores
full graph e.g. Rmin = 0 , Rmax = 6 gives full-size R-space graph...ditto
for fixing other
ranges. Fixed 3 out of 4 and read in a new file...obtained 3
mini-graphs...reset q range
as well and that one appears too.
Exited. Restarted. Read in file -
Show Command Buffer/Plot Buffer
## energy quadrant
set title {/*1.6 Energy}
set xlabel {/*1.4 Energy{aa}(eV)}
set ylabel {/*1.4 x{/Symbol m}(E)}
#set xrange [ 11870.11617648 : 11870.11617648 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vlxtfjcm' using
1:2 with lines ls 2,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_tfoziltm' using
1:2 with lines ls 1,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_fthredqy' using
1:2 with lines ls 3,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_iebbuian' using
1:2 with lines ls 4
## k quadrant
set title {/*1.5 k-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 k^{2} {\267} {/Symbol c}(k){aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_xizghpwm' using
1:2 with lines ls 1
## R quadrant
set title {/*1.5 R-space}
set xlabel {/*1.2 Radial distance{aa}({\305})}
set ylabel {/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}{aa}({\305}^{-3})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_nwtxpqxm' using
1:2 with lines ls 1,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vysurgrh' using
1:2 with lines ls 2
## q quadrant
set title {/*1.5 q-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25
]}{aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_hxroumyr' using
1:2 with lines ls 1
unset multiplot
So, seems to be setting the xranges to zero for a clean install these
plots, and gnuplot
doesn't plot if no xrange. If I reset, then I can move around and use
DAthena 9.19
without issue...DArtemis
Re: [Ifeffit] Demeter not working on Windows 8.1 64bit
1:2 with lines ls 1
unset multiplot
On Tue, Jan 14, 2014 at 5:47 PM, Kevin Jorissen
kevinjorissen...@gmail.comwrote:
-- just to be clear, the pasted section of the log is not the bottom part.
It is followed by many more lines containing gnu plot settings (but no
plot commands).
Cheers,
Kevin
On Tue, Jan 14, 2014 at 5:38 PM, Kevin Jorissen
kevinjorissen...@gmail.com wrote:
Out of curiosity, I installed 09.19 on a fresh Win8.1 64bit under VMWare.
No problems during installation. I opened the cyanobacteria.prj data from
Bruce's sample data repo in Athena. After clicking around a few times
(specifically, clicking the green arrow and the magnifying glass+red curve
next to it in the toolbar of the plot window), I caused a gnu plot.exe has
stopped working error. Going into the monitor for the plotting log, I see
a similar x-range problem as discovered by Robert Gordon:
## energy quadrant
set title {/*1.6 Energy}
set xlabel {/*1.4 Energy{aa}(eV)}
set ylabel {/*1.4 x{/Symbol m}(E)}
#set xrange [ 11918.952 : 11918.952 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_lydqknai' using
1:2 with lines ls 2,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_kpklgmnh' using
1:2 with lines ls 1,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_djrhchms' using
1:2 with lines ls 3,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_geakjukk' using
1:2 with lines ls 4
## k quadrant
set title {/*1.5 k-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 k^{2} {\267} {/Symbol c}(k){aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_vyutwjzc' using
1:2 with lines ls 1
## R quadrant
set title {/*1.5 R-space}
set xlabel {/*1.2 Radial distance{aa}({\305})}
set ylabel {/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}{aa}({\305}^{-3})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_qeqqfnof' using
1:2 with lines ls 1,\
'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_njjlolaa' using
1:2 with lines ls 2
## q quadrant
set title {/*1.5 q-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25
]}{aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\jorissen\AppData\Roaming\demeter\stash\gp_ydrraees' using
1:2 with lines ls 1
So, I'm not offering anything new in this message, but perhaps confirming
someone else's experience can help. To be clear, this VM has never seen
any kind of Demeter, perl, gnu plot, ... before this experiment. It's a
clean Windows (I only added java and feff9 on it at an earlier time) and
current with all windows updates.
Cheers,
Kevin
On Tue, Jan 14, 2014 at 2:17 PM, Robert Gordon ragor...@alumni.sfu.cawrote:
Installing 0.9.19 overtop of 0.9.18.2 and Athena works fine.
Installing 0.9.19 clean (deleting demeter directory under
appdata/roaming)
2nd attempt to open file in DAthena results in only 1 mini-graph.
Ranges are 0 for Emin/max, kmin/max, Rmin/max - putting a valid range
restores
full graph e.g. Rmin = 0 , Rmax = 6 gives full-size R-space
graph...ditto for fixing other
ranges. Fixed 3 out of 4 and read in a new file...obtained 3
mini-graphs...reset q range
as well and that one appears too.
Exited. Restarted. Read in file -
Show Command Buffer/Plot Buffer
## energy quadrant
set title {/*1.6 Energy}
set xlabel {/*1.4 Energy{aa}(eV)}
set ylabel {/*1.4 x{/Symbol m}(E)}
#set xrange [ 11870.11617648 : 11870.11617648 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vlxtfjcm'
using 1:2 with lines ls 2,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_tfoziltm'
using 1:2 with lines ls 1,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_fthredqy'
using 1:2 with lines ls 3,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_iebbuian'
using 1:2 with lines ls 4
## k quadrant
set title {/*1.5 k-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 k^{2} {\267} {/Symbol c}(k){aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_xizghpwm'
using 1:2 with lines ls 1
## R quadrant
set title {/*1.5 R-space}
set xlabel {/*1.2 Radial distance{aa}({\305})}
set ylabel {/*1.2 {/*1.25 |}{/Symbol c}(R){/*1.25 |}{aa}({\305}^{-3})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_nwtxpqxm'
using 1:2 with lines ls 1,\
'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_vysurgrh'
using 1:2 with lines ls 2
## q quadrant
set title {/*1.5 q-space}
set xlabel {/*1.2 Wavenumber{aa}({\305}^{-1})}
set ylabel {/*1.2 {/*1.25 Re[}{/Symbol c}(q){/*1.25
]}{aa}({\305}^{-2})}
set xrange [ 0 : 0 ]
plot 'C:\Users\ragordon\AppData\Roaming\demeter\stash\gp_hxroumyr'
using 1:2 with lines ls 1
unset multiplot
So, seems to be setting the xranges to zero for a clean install
Re: [Ifeffit] EXAFS with multiple absorbers
Hi Francisco No. If you e.g. want to sum contributions from several scatterers with different environment/fine structure, the right procedure is to do a separate feff calculation for each of these scatterers. Cheers Kevin Jorissen On Feb 21, 2014, at 4:38 PM, Francisco Garcia garcia.ff@gmail.com wrote: Dear users, I would like to know if FEFF8 or FEFF9 can compute the EXAFS when multiple absorbers are present in the sample. Thank you. ___ 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] Demeter on Mac OS X
There was a recent update of XCode (5.1.1), which could be a suspect (depending on when you installed it) and might have broken some dependency? (I don't know what the Demeter port depends on.) E.g. it might update some of the libraries/compilers used in demeter (I'm not sure), and sometimes the command line tools need to be reinstalled to restore softlinks etc. The error message you see might be related to a changed c runtime library or something (just guessing). I tried a clean install of demeter today and I can open Athena properly. Have you tried reinstalling demeter? This is always a good thing to try. - Use port to remove demeter and dependencies. - Reinstall XCode command line tools (xcode-select --install) if you haven't already. - sudo port install demeter Cheers, Kevin PS It's clearly harmless but I get a couple of these warnings: ~% /opt/local/bin/athena 2014-06-06 11:50:01.909 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:01.909 perl5.16[31186:303] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug. 2014-06-06 11:50:01.989 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.040 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.085 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.091 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.096 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.404 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name .Lucida Grande UI and got font with PostScript name .LucidaGrandeUI. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.407 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name .Lucida Grande UI and got font with PostScript name .LucidaGrandeUI. For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:03.202 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name Lucida Grande and got font with PostScript name LucidaGrande. For best performance, only use PostScript names when calling this API. ~% ~% On Fri, Jun 6, 2014 at 10:16 AM, Schima, Frank frank.sch...@nist.gov wrote: On Jun 6, 2014, at 7:11 AM, Bruce Ravel bra...@bnl.gov wrote: On 06/05/2014 06:09 AM, Juliana Fonseca de Lima wrote: Hi all, I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that? perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! PS: I have 8 GB of physical memory. Juliana, I suspect the reason no one has answered your post is that you have not provided much information to work with. /Something/ must have happened to your computer in the last week. Did you do a system update? Did you install new software? Perhaps a block of RAM went bad -- you could run a hardware test to find out. (That happened recently on one of my laptops.) The bottom line is that I cannot see any way to diagnose the problem simply on the basis of the information provided. That Athena worked one day and not the next suggests something changed on your computer. Agreed. I can tell you that all of the programs launch fine for me on OS X 10.9.3 and 10.8.5 using the latest Demeter port in Macports. I would suggest making sure you are up to date in Macports: sudo port selfupdate sudo port upgrade outdated Cheers! Frank ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Demeter-devel MacPorts Athena issues work-around
It's kinda what I do on this mailing list.
And I think I'm unsubscribing for that reason (although, like many others
undoubtedly, I am probably professionally condemned to return eventually).
In ten years of helping countless users as an expert on WIEN2k resp. FEFF,
and encountering all the frustrations that come with mailing lists and
novice users, I have not seen people treated the way they sometimes are on
this mailing list. It goes against my values around helping users; it
makes me uncomfortable; and I don't want to see it anymore.
Much to your credit, you proceeded to type also several long and detailed
paragraphs addressing the issue, which were helpful to the user.
I would be delighted if you were willing to protect your time and energy (a
valid need) in a friendlier way.
Best regards,
Kevin Jorissen
PS still reachable through www.feffproject.org or at by e-mail for
FEFF-related questions.
On Sat, Jul 5, 2014 at 9:06 PM, Bruce Ravel bra...@bnl.gov wrote:
On 07/04/2014 12:11 PM, Margaret Hinkle wrote:
Thanks for your help your quick reply. I did not expect my altering
one character in the code to fix the problem -- I had just hoped it
would tell me if the Tip of the Day was indeed the culprit. I did as you
suggested, and the problem is completely fixed. Thanks!
Per your comment regarding Issue 2 -- I have attached two files, one
with the header removed (filename: '...NoHeader_exafsscan.dat'), and the
other with the header left in with #s commenting it out (filename:
'...Header_exafsscan.dat'). Note that these are transmission samples,
with I0 in column 56, and I1 in column 57.
Margaret Anne,
By the end of this email, I am going to thoroughly solve your problem.
But, first, I am going to step up on my soapbox and pontificate. It's
kinda what I do on this mailing list
You started this by writing I can only load data files into Athena if
there are no headers of any sort. That is a demonstrably untrue
statement, and easily so. Were it true, this mailing list would be either
(a) filled with nothing but posts about people complaining that they cannot
import their data, or (b) silent because no one would use software so
completely fucked up and useless.
A true statement might have been that you had examples of data files that
could not be imported into Athena. But you did not include an example of
the troublesome data file -- I had to ask for it.
When you ask a question, you should try to put yourself in the shoes of
the person answering. I am not in the same room as you, I am not looking
at your computer, and I do not have the example that triggers the problem
here in front of me. And I do not possess telepathy. When you ask a
question, you have to give the person who wants to help a fighting chance
of being able to help.
All right. Enough of that. Let's solve your problem.
Find the installation location of Demeter on your computer. If you do not
know where that is, then open a command terminal and enter the following
command:
perl -e 'use Demeter; print $INC{Demeter.pm}, $/'
The thing that gets printed is the folder containing the main Demeter
module file. Everything else is beneath that folder.
Download this file:
https://s3.amazonaws.com/demeter4xas/SpecFileLongLine.pm
and save it as
Demeter/Plugins/SpecFileLongLine.pm
where Demeter/ is a folder inside the folder we identified above.
Make sure that the file is called SpecFileLongLines.pm -- exactly as
written there -- and that your web browser does not help you out by
changing the extension of the file to .txt or any other such shenanigans.
Now fire up Athena and select Plugin Registry from the main menu. This
will display the view shown here:
http://bruceravel.github.io/demeter/aug/other/plugin.html#
athena%27spluginregistry
There should be an row that says SpecFileLongLine. Click it on.
You should now be able to import your files without needing to edit the
header.
Note that if you attempt to import one of your data files *without*
enabling the SpecFileLongLine plugin, Athena will continue to crash. The
mere presence of the SpecFileLongLine.pm file is not enough -- you *must*
enable in the plugin registry.
So, what was the problem?
Well, Ifeffit -- which is the math and XAS engine underneath the hood of
Athena -- is written in Fortran. Fortran does not have dynamic memory
allocation. Thus there are some hardwired limits to things in Ifeffit, not
all of which get handled gracefully when exceeded.
The line in your data file causing the problem is the one that starts with
#L. It contains the column labels and is about 330 characters long. As
one point, Ifeffit attempts to stuff those 330 characters in a variable
configured to be 256 characters long. That is the cause and location of
the error message you cited.
The plugin does the simplest possible thing. It makes a copy of the data
file, copying every
