Re: [Ifeffit] correlating number of nearest neighborst to the particle
Dear Scott and Anatoly, Thanks a lot for your valuable suggestions. I may get back to you for any questions, once I go through both the approaches in literature and implement them in the form of a fit. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 09 January, 2014 19:18 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 10 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. Re: correlating number of nearest neighborst to the particle size (Scott Calvin) 2. Re: correlating number of nearest neighborst to the particle size (Anatoly I Frenkel) -- Message: 1 Date: Thu, 9 Jan 2014 13:11:41 -0500 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] correlating number of nearest neighborst to the particlesize Message-ID: e6fe5676-5821-46a2-abad-b383ae402...@slc.edu Content-Type: text/plain; charset=utf-8 Hi Jatin, There are two strategies that have been used to do this that you can find in the literature, both of which are by members who frequent this list (myself and Anatoly Frenkel). I have published articles outlining a strategy where you assume the shape of the particles. Most often in my case that has been spheres, but it could be plates or hemispheres or whatever. Then you derive how the coordination number depends on dimensions for that shape (as I said, I an others have done that for spheres), and make those dimensions free parameters in an Ifeffit (e.g. Artemis) fit. Anatoly has published articles outlining a strategy where you treat the coordination numbers themselves as free parameters, and then check for consistency with various shapes. I think Anatoly's method is better when the nanoparticles are very consistent; i.e. they have a narrow size distribution and consistent shapes, and when data quality is good. I think my method may work better when the nanoparticles are messier or when the data is more limited, if only because it requires fewer free parameters. A typical reference for Anatoly's method is A View from the Inside:? Complexity in the Atomic Scale Ordering of Supported Metal Nanoparticles Anatoly I. Frenkel,*,?,?, Charles W. Hills,? and, and Ralph G. Nuzzo*,?,? The Journal of Physical Chemistry B 2001 105 (51), 12689-12703 A typical reference for my method is ?Estimating crystallite size in polydispersed samples using EXAFS,? S. Calvin, C. J. Riedel,* E. E. Carpenter, S. A. Morrison, R. M. Stroud, and V. G. Harris, Physica Scripta T115, 744 (2005). although that can be a little hard to find. Another reference which is more widely available is ?Comparison of extended X-ray absorption fine structure and Scherrer analysis of x-ray diffraction as methods for determining mean sizes of polydisperse nanoparticles,? S. Calvin, S. X. Luo, C. C. Broadbridge, J. K. McGuinness, E. Anderson, A. Lehman, K. H. Wee, S. A. Morrison, and L. K. Kurihara, Appl. Phys. Lett. 87, 233102 (2005). --Scott Calvin Sarah Lawrence College On Jan 9, 2014, at 12:55 PM, Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de wrote: Hi All, I would like to estimate the size of Cu nanoparticles grown in my sample by EXAFS fitting. I can refine the number of nearest neighbors in these Cu nanoparticles up to 4 shells (say NN1, NN2, NN3 and NN4), by constraining S02 to the value obtained by fitting the data of Cu reference foil. But, how do I correlate the refined values of nearest neighbors to the actual size of Cu nanoparticles ? Any help in this regard would be much appreciated. Regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You
Re: [Ifeffit] Demeter 0.9.19
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] cannot run demeter 0.9.19
Hi, I'd like to report a bug in which I can't run any of the demeter programs (athena, artemis, hephaestus) after updating to 0.9.19. My computer is running windows 7 - I either install Demeter 0.9.19 without removing 0.9.18 (the installer automatically uninstalls it anyways), or after removing 0.9.18 in add/remove programs - In either case I get an error message from perl.exe saying This program can't start because libgcc_s_dw2-1.dll is missing from your computer. Try reinstalling the program to fix this problem - i click ok and program closes I can re-install 0.9.18 and it works fine, but no matter what i've tried 0.9.19 wont run for me. I attached the logfile for artemis (identical to log file for athena) thanks for your help, georges dartemis.log Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] cannot run demeter 0.9.19
George, I think this may be a problem with the splashscreen. (One that, frustratingly, I don't see on any of my Windows computers. Grrr) Could you try an experiment for me? Open the file C:\strawberry\perl\site\bin\dathena.bat and comment out line 23, the one that says use Wx::Perl::SplashFast Demeter::Here-here.'UI/Athena/share/logo.jpg', 4000; Comment it out with a # mark, like so: # use Wx::Perl::SplashFast Demeter::Here-here.'UI/Athena/share/logo.jpg', 4000; Save it and try launching Athena again. Let me know what happens. Thanks, B On 01/10/2014 10:39 AM, Georges Siddiqi wrote: Hi, I'd like to report a bug in which I can't run any of the demeter programs (athena, artemis, hephaestus) after updating to 0.9.19. My computer is running windows 7 - I either install Demeter 0.9.19 without removing 0.9.18 (the installer automatically uninstalls it anyways), or after removing 0.9.18 in add/remove programs - In either case I get an error message from perl.exe saying This program can't start because libgcc_s_dw2-1.dll is missing from your computer. Try reinstalling the program to fix this problem - i click ok and program closes I can re-install 0.9.18 and it works fine, but no matter what i've tried 0.9.19 wont run for me. I attached the logfile for artemis (identical to log file for athena) thanks for your help, georges ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- 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
Re: [Ifeffit] Connecting Artemis to FEFF9.6.4
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 University of Leeds Woodhouse Lane Leeds, UK Tel: +44 (0)1133430109 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- 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
Re: [Ifeffit] cannot run demeter 0.9.19
Hi Bruce, Interestingly, when I reinstall demeter 0.9.19, I get a different error (but the same effect, cannot open athena/artemis). this time it reads The procedure entry point _gxx_personality_v0 could not be located in the dynamic link library libstdc++-6.dll but either way, commenting out line 23 makes no apparent difference. sorry! georges On Fri, Jan 10, 2014 at 4:45 PM, Bruce Ravel bra...@bnl.gov wrote: George, I think this may be a problem with the splashscreen. (One that, frustratingly, I don't see on any of my Windows computers. Grrr) Could you try an experiment for me? Open the file C:\strawberry\perl\site\bin\dathena.bat and comment out line 23, the one that says use Wx::Perl::SplashFast Demeter::Here-here.'UI/Athena/share/logo.jpg', 4000; Comment it out with a # mark, like so: # use Wx::Perl::SplashFast Demeter::Here-here.'UI/Athena/share/logo.jpg', 4000; Save it and try launching Athena again. Let me know what happens. Thanks, B On 01/10/2014 10:39 AM, Georges Siddiqi wrote: Hi, I'd like to report a bug in which I can't run any of the demeter programs (athena, artemis, hephaestus) after updating to 0.9.19. My computer is running windows 7 - I either install Demeter 0.9.19 without removing 0.9.18 (the installer automatically uninstalls it anyways), or after removing 0.9.18 in add/remove programs - In either case I get an error message from perl.exe saying This program can't start because libgcc_s_dw2-1.dll is missing from your computer. Try reinstalling the program to fix this problem - i click ok and program closes I can re-install 0.9.18 and it works fine, but no matter what i've tried 0.9.19 wont run for me. I attached the logfile for artemis (identical to log file for athena) thanks for your help, georges ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- 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] cannot run demeter 0.9.19
On 01/10/2014 11:30 AM, Georges Siddiqi wrote: Interestingly, when I reinstall demeter 0.9.19, I get a different error (but the same effect, cannot open athena/artemis). this time it reads The procedure entry point _gxx_personality_v0 could not be located in the dynamic link library libstdc++-6.dll but either way, commenting out line 23 makes no apparent difference. That's troubling. I had another person here at BNL who say that same error message. Commenting out the line with SplashFast in it worked for him. If that doesn't do the trick, then I am genuinely puzzled. Let me think about it during lunch and get back to you. 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
Re: [Ifeffit] Demeter 0.9.19
On Jan 9, 2014, at 8:33 PM, Matt Newville newvi...@cars.uchicago.edu wrote: Hi Frank, On Thu, Jan 9, 2014 at 10:47 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 Thanks! I'm very glad you're working on this too. I wasn't able to build wxPerl with macports either, but it did work with citrusperl. I don't have a strong preference, but citrusperl does seem reasonable as a standalone perl install. I don't know how likely it wold be to package this up into an App, but I suspect it would be possible. I don’t know anything about citrusperl - besides the 1 minute of looking at the site since you mentioned it - but I’m working on a Macports based solution to install Demeter and so I will be using perl from Macports only. I feel that is the best way forward and where my knowledge lies. FWIW, I think that Demeter does not need wxWidgets verision 3, and that 2.8 or 2.9 would be fine From recent experience with wxPython and wxWidgets 3, I'd take the conservative approach and see if Demeter can work with a not-too-old version like 2.9. Does that help you build with macports? It used to build for me, I think with wxWidgets 2.9. But for reasons that I’ve now forgotten, Demeter did not completely run correctly when I built it. I believe one of the sub programs did work for me however. But now that wxWidgets has been updated in Macports to version 3, the perl-wx project has apparently not been updated to accommodate this new version yet. wxWidgets has been a major problem in Macports because it was 32-bit code and not 64-bit ready. My understanding is that version 3.0 is 64-bit finally. This is the desired state that will allow it to work better with OS X and Macports in
Re: [Ifeffit] Demeter 0.9.19
On Jan 9, 2014, at 10:37 PM, Kevin Jorissen kevinjorissen...@gmail.commailto: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
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, On Fri, Jan 10, 2014 at 12:33 PM, Schima, Frank frank.sch...@nist.gov wrote: On Jan 9, 2014, at 8:33 PM, Matt Newville newvi...@cars.uchicago.edu wrote: Hi Frank, On Thu, Jan 9, 2014 at 10:47 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 Thanks! I'm very glad you're working on this too. I wasn't able to build wxPerl with macports either, but it did work with citrusperl. I don't have a strong preference, but citrusperl does seem reasonable as a standalone perl install. I don't know how likely it wold be to package this up into an App, but I suspect it would be possible. I don’t know anything about citrusperl - besides the 1 minute of looking at the site since you mentioned it - but I’m working on a Macports based solution to install Demeter and so I will be using perl from Macports only. I feel that is the best way forward and where my knowledge lies. FWIW, I think that Demeter does not need wxWidgets verision 3, and that 2.8 or 2.9 would be fine From recent experience with wxPython and wxWidgets 3, I'd take the conservative approach and see if Demeter can work with a not-too-old version like 2.9. Does that help you build with macports? It used to build for me, I think with wxWidgets 2.9. But for reasons that I’ve now forgotten, Demeter did not completely run correctly when I built it. I believe one of the sub programs did work for me however. But now that wxWidgets has been updated in Macports to version 3, the perl-wx project has apparently not been updated to accommodate this new version yet. wxWidgets has been a major problem in Macports because it was 32-bit code and not 64-bit ready. My understanding is that version 3.0 is 64-bit finally. This is the
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
