Re: [Ifeffit] Artemis error message
The program icon for artemis and athena is a short applescript application (that in turn calls a unix script). The source code is in the Ifeffit/applescript folder (the top level artemis is a compiled applescript applescript). It goes like this:display dialog "Please pick an output device" buttons {"X11 graphics", "Aquaterm"} default button "X11 graphics"set mydevice to the button returned of the resultif mydevice contains "Aquaterm" then do shell script "/Applications/Ifeffit/bin/runprog -q -m -x -a artemis"else do shell script "/Applications/Ifeffit/bin/runprog -q -x -a artemis"end ifAs you can see depending on the answer received the script /Applications/Ifeffit/bin/runprog is invoked (with different options). The shell script runprog is a bourne shell script (written by Matt and hacked by me). The -m option just sets the environment variable PGPLOT_DEV to the value /AQT before ifeffit is invoked. The option list is: -a) app=$2 ; shift ;; -x) $open_x ;; -q) show_out=0 ;; -d) show_dir=1 ;; -m) device='/AQT' ;; *) files="$files $1" ;;It should be possible to invoke artemis with an aquaterm graphics output by using the line "/Applications/Ifeffit/bin/runprog -q -m -x -a artemis" (without the quotes) in an X11 window. Does this command work? I should add that some of the linking is dynamic (at runtime) and by installing other dynamic libraries, it is conceivable that aquaterm could get confused (but of course, I should say that I have never seen this on my machines and I install a lot of stuff). Hope this helps, PaulOn Sep 14, 2006, at 9:34 PM, Stefano Ciurli wrote:Hello Matt, Did you try using /Applications/Ifeffit/bin/feff6 as the preferredfeff executable in Artemis? That's what the error message wassuggesting you try. I did try, no success Can you verify that you have /Applications/Ifeffit/bin/feff6? verified, I do have it.In the meantime I made an interesting discovery that some of you will certainly be able to explain:If I launch Artemis using the double click on the application icon I DO get the error message and feff does not run, regardless of which application I choose for the graphicsHowever:If I launch the program from the terminal window, I do not get the question on whether to choose Xwindow or Aquaterm, the default being apparently Xwindow PGPLOT, and everything runs smoothly.So, what is the origin of the error message that I get when I launch the program from the icon?Stefano-- Stefano CiurliProfessor of ChemistryLaboratory of Bioinorganic ChemistryDepartment of Agro-Environmental Science and TechnologyUniversity of BolognaViale Giuseppe Fanin, 40I-40127 BolognaItalyPhone: +39-051-209-6204Fax: +39-051-209-6203"Fatti non foste a viver come bruti,ma per seguir virtute e canoscenza"Dante Alighieri - Inferno - Canto XXVI"Ihr seid bestimmt, nicht Tieren gleich zu leben,Nein, Tugend zu erringen und Erkenntnis""Ye were not form'd to live the life of brutes,But virtue to pursue and knowledge high"___Ifeffit mailing listIfeffit@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___
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[Ifeffit] Artemis error message and paths
Hi Stefano (Bruce/Matt), Looking over your comments, I must admit I am a little confused as to what could be causing the problem. If you can invoke aquaterm complete with functioning graphics, the only difference that I can guess could exist is a difference in shell paths. The runprog program with its attendant shell variable changes seems to work fine. The AppleScript program is pretty minimalist, so the only viable explanation I can think of is somehow the shell environment getting corrupted. As the AppleScript that invokes artemis works fine here (and apparently elsewhere as well), a possible cause is the difference in startup initialization at the shell script level. Bruce, Matt, what do you think about this? If a shell is started by AppleScript, it would be a non-interactive shell, whereas if it is started manually via X11 and the default shell is bash, the startup initialization file ~/.bashrc would be read in. If it were invoked via the AppleScript program, it would not. Sounds like something is screwy with the PATH environment variable. Of course, this implies that it is something unique to Stefano's system and not general (never mind the fact that the user can switch shells -- I am using bash on one system and tcsh on another!). If a path was set incorrectly (e.g. affecting a perl library or otherwise), could this cause the symptoms that Stefano is seeing? I might add that I notice the default path for feff6 is feff6 so this would seem to implicitly assume that feff6 is on the users path (and it obviously isn't in this case, although it is for me). One fix would be to hardwire all of the paths needed into the runprog shells script by appending to the PATH variable (e.g. the location of artemis is wired). Any suggestions? p.s. I noticed there is a dump paths option in the help menu (which is broken in that at least on my system apparently tries to dump to root and fails). I hacked the artemis.dump path to dump to /tmp/ artemis.dump and it worked, however, there is no information on the feff executable variable. smime.p7s Description: S/MIME cryptographic signature ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Artemis error message and paths
Hi Stephano, I don't see the directory /Applications/Ifeffit/bin on your search path. It should be there. It is usually automatically included via a script installed by the Ifeffit installer, but it seems to be missing here (perhaps another installer deleted it by mistake). Add the following line to your .cshrc file in your home directory and see if it fixes things. Be careful to use a text editor that understands unix line endings (like the free editor smultron from http://smultron.sourceforge.net). source /Applications/Ifeffit/bin/iff_init.csh PaulOn Sep 19, 2006, at 6:00 PM, Stefano Ciurli wrote: Hi Paul, Looking over your comments, I must admit I am a little confused as to what could be causing the problem. If you can invoke aquaterm complete with functioning graphics, the only difference that I can guess could exist is a difference in shell paths. The runprog program with its attendant shell variable changes seems to work fine. The AppleScript program is pretty minimalist, so the only viable explanation I can think of is somehow the shell environment getting corrupted. As the AppleScript that invokes artemis works fine here (and apparently elsewhere as well), a possible cause is the difference in startup initialization at the shell script level. if you need my .cshrc file, here it is below, maybe you can guess if something is wrong: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source ~/Library/Scripts/iterminal_custom.tcsh source /Applications/XtalView/XtalView.env source /sw/bin/init.csh setenv PATH `echo $PATH`:/Applications/Sparky.app/Contents/Resources/bin:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Applications/XtalView/bin/powermacDarwin:/Applications/vnmrj1.1d/bin:/Applications/cyana-2.1:/Applications/cara_1.2_osx:/Users/stefano/AutoAssign2.3.0:/Users/stefano/bin defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv MARSHOME /Applications/mars-1.1.3_OSX setenv CCPNMR_TOP_DIR /usr/local/ccpnmr setenv PYTHONPATH .:$CCPNMR_TOP_DIR/ccpnmr1.0/python setenv LD_LIBRARY_PATH /sw/lib:/sw/lib:/usr/X11R6/lib setenv LD_LIBRARY_PATH ${CCPNMR_TOP_DIR}/tcl8.3/lib:${CCPNMR_TOP_DIR}/tk8.3/lib setenv TCL_LIBRARY /sw/lib/tcl8.4 setenv TK_LIBRARY /sw/lib/tk8.4 alias runmars $MARSHOME/bin/runmars alias ono osx_ono alias cara /Applications/cara_1.5.2_osx if (-e /Applications/NMRPipe/com/nmrInit.mac.com) then source /Applications/NMRPipe/com/nmrInit.mac.com endif if (-e /Applications/NMRPipe/dynamo/com/dynInit.com) then source /Applications/NMRPipe/dynamo/com/dynInit.com endif # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~ Bruce, Matt, what do you think about this? If a shell is started by AppleScript, it would be a non-interactive shell, whereas if it is started manually via X11 and the default shell is bash, the startup initialization file ~/.bashrc would be read in. my default shell is tcsh If it were invoked via the AppleScript program, it would not. Sounds like something is screwy with the PATH environment variable. Of course, this implies that it is something unique to Stefano's system and not general (never mind the fact that the user can switch shells -- I am using bash on one system and tcsh on another!). let me know which configuration file I should look at If a path was set incorrectly (e.g. affecting a perl library or otherwise), could this cause the symptoms that Stefano is seeing? I might add that I notice the default path for feff6 is "feff6" so this would seem to implicitly assume that feff6 is on the users path (and it obviously isn't in this case, although it is for me). One fix would be to hardwire all of the paths needed into the runprog shells script by appending to the PATH variable (e.g. the location of artemis is wired). Any suggestions? will see what Matt and Bruce have to say Stefano --
Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"___Ifeffit mailing listIfeffit@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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[Ifeffit] Hack and slash
I hacked and slashed and have succeeded in building the wrapper and making a new version of horae. It is getting rather late here so I will have to turn in, but I think the idea of making a different Makefile for the wrapper is a good one. As it didn't seem to be particularly difficult, I assume that I will have no trouble putting one together. I will post a new tarball later tommorrow on sourceforge with a new Mac installer (power pc). This problem with the tarball was new -- there was no conflict before (or was there). The error associated warning message occurred when tar attempted to write the file atoms on top of the directory Atoms. I wonder if the archive order was different before hiding the conflict? Paul On Dec 6, 2006, at 11:59 PM, Bruce Ravel wrote: On Wednesday 06 December 2006 08:30, Paul Fons wrote: Alas Bruce, not everyone has a unix without training wheels. The darwin OS is case insensitive. Sort of a good thing in many ways. For instance take the example of atoms and Atoms in the horae-063 directory. This frozzed tar in the unpacking stage and I didn't realize the conflict until today (I was in Italy until last Friday so didn't get a chance to compile horae until today). Hmmm... not so trivial. But I'll try to have a trial tarball for you later today. Can you remove the conflict with uppercase and lowercase atoms/ Atoms in the horae directory so this doesn' happen every time. It would also be sort of neat if there were a some sort of honest way to compile the ifeffit_wrapper.c source without having to hack the ucky MakeMaker output (a switch perhaps). All this is of course, when you have time. Thanks for the new release. If I knew how to honestly compile the wrapper, I'd be happy to do so. Are you able to compile other C code from perl packages out of the box? For example, if you downloaded (to suggest an example that horae uses) Compress::Zlib and did the typical perl-y build incantation, does it run to completion without further input? If so, then I can simply remove all darwin-specific code from my makefile.PL. If not, then you need to tell me what to do. One option is for you to provide me with a makefile that builds ifeffit_wrapper. I'll add that to the tarball and simply have Makefile.PL skip the compilation of ifeffit_wrapper. Then your external makefile can be used to build ifeffit_wrapper. That adds a step to the build incantation, but that's not so bad. Perhaps better, I can simply skip the build of ifeffit_wrapper for darwin on the assuption that it is already installed or has been installed some other way. That way, the wrapper can be part of the installer package, not part of the tarball update for darwin. That is, in fact, what my Makefile.PL does for debian. B -- Bruce Ravel -- [EMAIL PROTECTED] Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USAfax: (1) 630 252 9793 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] statistical vicissitudes and dead links
Hi Shelly, I noticed that the link you posted either is dead or doesn't work from outside anl (the message from the server is ambiguous). Paul ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] ERROR in getting feff8 input file for YBCO from Webatoms
Just to follow on this -- I can access the YBCO atoms entry (via a search). The atoms.inp pops up correctly, but when I attempted to run atoms, I got the same error message. The error doesn't come from my end (as far as I can tell). The problem seems to be with the execution of atoms (e.g. hitting the button Run atoms.). The cgi is probably broken. Paul ERROR Access Denied Access Denied by security policy The security policy for your network prevents your request from being allowed at this time. Please contact your administrator if you feel this is incorrect. On Feb 3, 2007, at 2:42 AM, Matt Newville wrote: Hi Feng, Sorry for the trouble. I'm not sure where the problem is. I can get files from the Atoms archive from home (ie, outside the Argonne network), and I don't see any recent errors in the logs, suggesting that both the server connections and the access through the Argonne and APS firewalls are working.Could it be that the trouble is at your end? Perhaps we can troubleshoot this a little better. Does the 'search for Atoms.inp' page http://cars9.uchicago.edu/~newville/adb/search.html appear for you? Is it responsive? Can you select a central atoms, a structure, and then hit 'Run Webatoms'? Can you browse to http://cars9.uchicago.edu/atomsdb/ and see a large number of atoms.inp files? Can you select and download some of these files? Hope that helps, --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] ERROR in getting feff8 input file for YBCO from Web atoms
I must admit that at least inside of the ANL lan, I was very (un) impressed with the firewall and the questionable judgments it made based upon content for access of material from outside ANL. I never suspected that it would try a filter scheme for things inside ANL. Bizarre. On Feb 8, 2007, at 4:14 AM, Matt Newville wrote: Feng, Paul, Dave,Bruce, Thanks for the reports. I can reproduce this problem, and I'm pretty sure it's not exactly a problem with the cgi script, but more of an APS/ANL firewall issue.That is, inside the APS firewall, I can run webatoms on this file (unmodified) and get the correct result. It's not simply an issue with 'refer2', because even outside the firewall, I can get other files with a 'refer2' tag in them (try ZnOH2.inp, for example). In addition, leaving the 'refer2' in, and taking the 'refer1' line out also generates a correct output. Also: even outside the firewall, I can get http://cars9.uchicago.edu/atomsdb/YBa2Cu3O7.inp In addition, generating the feff.inp file, and copying this file to http://cars9.uchicago.edu/atomsdb/ybco_feff1.inp I can access that file as well (which might help Feng) So, it appears that the firewall is not simply blocking files that contain the string: refer2: Cava, et al, Physica C 165, p.419, (1990) but does appear to be blocking URLs that contain certain strings (or perhaps strings of a certain length??). I would guess that changing the cgi script to use POST instead of GET would be the simplest way to solve this problem. --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] Hephaestus
I should have mentioned as well that there is a link on the ifeffit wiki page (under Macintosh) to the Jeff's intel version as well as the powerpc version (http://cars9.uchicago.edu/iffwiki/Downloads). There is an also an explanation there stating X11 is necessary under platform notes. I did find something that might be improved. On the ifeffit page, there is a link on the first page (http:// cars9.uchicago.edu/ifeffit/) to Get the latest version and if you follow that link (http://cars9.uchicago.edu/ifeffit/download.html), you are lead to believe that the power pc version is the only version for the Mac (there is no explanation otherwise) and the only link leads to the powerpc version. We could probably solve some of the confusion by adding an Intel Mac to the list. Ultimately, the best solution would be to make a universal installer. First fixing the link on the Get the latest version would seem to be an easy fix (note this isn't a wiki page or I would have fixed it already). Paul On Feb 23, 2007, at 12:57 AM, Jeff Terry wrote: Hi all, I believe that there is a link to a Mac Intel version of these at the MRCAT home page: http://mrcat.iit.edu/ There should be an installer for the Intel Macs there. It does require X11 to be installed already. Jeff On Feb 22, 2007, at 8:51 AM, Paul Fons wrote: Yes, This is the case -- as I made the mac installer. The x86 mac cpu version was made by Jeff Terry. I am getting a new macpro notebook this week so I will start working on the installer sometime soon hopefully. I am still a little scared by Jeff's saying it wasn't trivial. Were there a lot of changes necessary? Jeff, could some of these be fed back upstream to Matt? Paul On Feb 22, 2007, at 12:27 PM, Matt Newville wrote: Hi Carloine, On 2/21/07, Caroline Peacock [EMAIL PROTECTED] wrote: Have just installed the Ifeffit package (feffit-1.2.9-Mac10.4_horae64pre_pkg.dmg) on my Intel Mac (OS X 10.4.8)... Upon double clicking Hephaestus (as instructed in the readme) i am prompted to choose either X11 graphics or Aquaterm - either way X11 opens and then nothing...Is this a UNIX based program - from the screenshots i guessed it wasn't? Any ideas why it isn't working? I'm copying this to the Ifeffit mailing list, as I think someone else may have a better answer than I can give. Hephaestus does require X11, but I think the problem is that the Ifeffit-1.2.9 disk installers are all PPC only. That is, I think no one has made an installer for Intel Mac. --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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Line endings
On the Mac a command line way to remove line endings would be something like tr '\r' '\n' this command translates all carriage returns into new lines. You can then use it in a shell loop e.g. #!/bin/bash for file in *dat; do cat $file | tr '\r' '\n' $file.out end On May 25, 2007, at 3:35 AM, Scott Calvin wrote: Hi Bruce, Thnks--your response helped me track down the nature of the problem. It turns out that if I wash the files.dat and paths.dat files by opening them on a pc and then saving them again, Artemis then does a little better, allowing me to read in path files that have themselves been washed. I suspect if I washed every text file in the directory, it might work smoothly (maybe I'll try running a calculation with only a handful of paths and doing that). The interesting thing to me is that the behavior is indeed platform-independent...Artemis on the Mac apparently needs the Feff files to have the pc end-of-line termination. :) Does anyone out there have a simple way to btach convert a whole bunch of files from Mac CR line breaks to pc CR/LF line breaks? I'm not part of the linux or unix worlds, but can use either Windows XP or OS X methods. --Scott Calvin Sarah Lawrence College At 02:11 PM 5/24/2007, Bruce Ravel wrote: I see the same problem using the two files you sent. My best guess for the source of the problem is that Artemis is not finding the files.dat and paths.data (or possibly path00.dat) files in the same place as the feff.inp and feff.dat files. Artemis needs those files to build the interpretation page and does not handle their absence gracefully. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Paul Fons Team Leader Nano-Optics Research Team [EMAIL PROTECTED] Center for Applied Near-Field Optics National Institute of Advanced Industrial Technology Tsukuba Central 4, Higashi 1-1-1 Tsukuba, Ibaraki Japan 305-8562 tel. +81-298-61-5635 fax. +81-298-61-2939 The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 近接場光応用工学研究センター 近接場光基礎研究チーム チーム長 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Debye Waller factors for Water Molecules
Hi Matt, I took a look at the paper you mentioned and as in my case, the water is appears to be pretty much only bonded to the Zn at 1.96 Angstroms for the isolated enzyme. I guess this implies that Anatoly's idea of using a Zn+2 solution as a starting point might make sense. I have no idea how much the DW varies for water in these types of systems. Is the usual idea to just set it at some reasonable value (e.g. from the idea of Anatoly) and then keep it fixed? Paul On Jul 30, 2007, at 3:51 PM, Paul Fons wrote: Thanks everyone (Shelly, Matt, and Anatoly) for the info. I thought it would be fun to learn while trying to work out a (relatively) simple system. I have EXAFS data about a Zn site. The Zn is bonded to three cystedines so I have the DW pretty much under control, but for the water molecules. I will investigate the approaches mentioned here and see which one the data is most consistent with (I did have the foresight to choose a system for which I have high resolution x-ray crystallography data). Thanks Paul On Jul 29, 2007, at 12:57 AM, Matt Newville wrote: Hi Paul, A. Vogel et al (Biochemistry 43, p10379, 2004) report a Zn water (or OH) at 2.0Ang with sigma2=0.007Ang^2 for data collected at 30K. This is for a binuclear Zn compound, and the OH is a bridging ligand (with the other ligands being dominated by histidine-like rings), so I don't know how close it is to your structure. But it might be a good place to start. Also, the results came from EXCURVE. That's not to suggest that the results are not reliable, but you might want to check carefully the meaning of sigma2. I'm not 100% sure of this (or what the Vogel et al paper is reporting), but I think the EXCURVE sigma2 might be a factor of 2 bigger than the Ifeffit sigma2. I'd be a little wary of using an Einstein model for water ligands down to 30K. It would be interesting to hear how well an Einstein model compares to the DFT modeling for any ligands in a bio-molecule. --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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on BlueWhite64)
Hi Matt, Sitting here at Elettra during a run, I downloaded the rc1 of ifeffit10 on my MacBook Pro (intel cpu) and found that the gfortran compiler had trouble with one of the sources: rand.f and attempted a build using gfortran 4.2.1 and found that the make crashed due to an overflow in a constant in rand.f. The same makefile worked fine with the intel compiler. If I get time later this week, I will try and build the latest version of ifeffit and horae using the intel compiler on the MacBook Pro I have here. gfortran -g -O2 -fPIC -c misc_rand.f misc_rand.f:111.36: parameter(umask = -2147483648) ! most significant w-r bits 1 Error: Integer too big for its kind at (1) make[3]: *** [misc_rand.o] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive-am] Error 2 Ciao, Paul On Aug 22, 2007, at 10:56 PM, Matt Newville wrote: Hi Chachi, all I believe I have a source kit that will build correctly for you using gfortran. I've tested on three different generations of Fedora/Redhat linux systems, one with only g77, one with only gfortran, and one with both, and the installation now works on all of them. Please try http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz With this tar ball, you will need to install pgplot: tar xvzf ifeffit-1.2.10_rc1.tar.gz cd ifeffit-1.2.10 sh PGPLOT_install ./configure make make install (doing the two 'install steps' with sufficient privilege). Again, you need to install PGPLOT with the provided script. Both the PGPLOT and Ifeffit installations will use gfortran if available, and g77 if gfortran is not available. I think it would not be too difficult to attempt to use Intel's ifort compiler or g95, though I do not know that it's needed-- all linux distribution come with gcc so have easy-to-use packages for gfortran (and, for legacy, g77). I did get horae-065 and the python wrappers to build with no trouble (once the Tk modules were installed) on all systems, though I haven't done much more than trivial testing. Since I tested only on a few linux boxes, I'd be interested in hearing reports for other systems. I'll wait a few days (or more) to hear reports before uploading this as ifeffit-1.2.10. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Paul Fons Team Leader Nano-Optics Research Team [EMAIL PROTECTED] Center for Applied Near-Field Optics National Institute of Advanced Industrial Technology Tsukuba Central 4, Higashi 1-1-1 Tsukuba, Ibaraki Japan 305-8562 tel. +81-298-61-5635 fax. +81-298-61-2939 The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 近接場光応用工学研究センター 近接場光基礎研究チーム チーム長 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on BlueWhite64)
Buona Mattina Matt, I tried moving the def of umask to the main body of misc_rand as an executable statement and the same problem with overflow occurred (at least the compiler is consistent) gfortran -g -O2 -fPIC -c misc_rand.f misc_rand.f:130.26: umask = -2147483648 ! most significant w-r bits 1 Error: Integer too big for its kind at (1) make[3]: *** [misc_rand.o] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive-am] Error 2 Paul On Aug 23, 2007, at 6:40 PM, Matt Newville wrote: Hi Paul, On 8/23/07, paul fons [EMAIL PROTECTED] wrote: gfortran -g -O2 -fPIC -c misc_rand.f misc_rand.f:111.36: parameter(umask = -2147483648) ! most significant w-r bits 1 Error: Integer too big for its kind at (1) Thanks for the report. This compiled for me on linux, using gfortran 4.1.1 and 4.1.2, and obviously works in g77. I do see a reference that -2**31 is no longer a valid integer _constant_ in gfortran, but that it can be (oddly enough), a valid integer _value_. Weird. I don't have an installation of gfortran 4.2 easily available. Would you be willing to try this change? Comment out the parameter(umask ...) line, and simply set umask at the beginning of the executable statements ** misc_rand.f lines 110,111,112 should read: parameter(mata = -1727483681) ! constant vector a c parameter(umask = -2147483648) ! most significant w-r bits parameter(lmask = 2147483647) ! least significant r bits misc_rand.f lines 129,130,131,132 should read: cmag01(x) = x * mata for x=0,1 c umask = -2147483648 ! most significant w-r bits if(mti.ge.n) then ** That seems like it would be the easiest fix to me. Thanks, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Paul Fons Team Leader Nano-Optics Research Team [EMAIL PROTECTED] Center for Applied Near-Field Optics National Institute of Advanced Industrial Technology Tsukuba Central 4, Higashi 1-1-1 Tsukuba, Ibaraki Japan 305-8562 tel. +81-298-61-5635 fax. +81-298-61-2939 The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 近接場光応用工学研究センター 近接場光基礎研究チーム チーム長 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit 1.2.10
Hi Matt. I downloaded (on the Intel Mac) the latest Ifeffit and both g95 and gfortran have the same problem with the umask variable (I did try an assignment and had the same error -- at least it is consistent!). Intel fortran has trouble with linking (at least in the current ./ configure setup), but I assume Jeff has found a way around this. I should be able to build the powerpc version with no problem (g77 is available) gfortran 4.2.1 g95 4.0.3 gfortran -g -O2 -fPIC -c get_inpfile.f gfortran -g -O2 -fPIC -c misc_rand.f misc_rand.f:131.15: umask = lmask + 1 1 Error: Arithmetic overflow at (1) make[3]: *** [misc_rand.o] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 Paul On Sep 20, 2007, at 7:35 AM, Matt Newville wrote: Hi Folks, I've just uploaded Ifeffit 1.2.10 to the cars.uchicago.edu and sourceforge.net sites. I'm posting both source code (ifeffit-1.2.10.tar.gz) and a Windows installer (ifeffit-1.2.10.exe) which includes the latest versions of Hephaestus, Athena, and Artemis. Installers for Mac users shouldn't be too far behind. For now, the downloads page at http://cars9.uchicago.edu/ifeffit/ Downloads links to both 1.2.10 and 1.2.9 versions. It may take a day or so for the files to show up on all the sourceforge.net mirrors. The new Windows Installer reflects a new build process for the underlying library. This took some time to work out (you may recall some emails about this over the summer) , but we think it is working as well as any previous version. There are quite a few changes to Bruce's codes, all for the better. And this version does install and work on Windows Vista. For the source code kit, this now uses a new install location for PGPLOT, so if you're installing you must run PGPLOT_Install before installing ifeffit. Also in this version is support for (and default use of) gfortran instead of g77. If you need to use a different fortran compiler from the one found by default, you can use ./PGPLOT_Install --with-fortran=g77 ./configure --with-fortran=g77 make install As always, let us know if there are any problems. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Paul Fons Team Leader Nano-Optics Research Team [EMAIL PROTECTED] Center for Applied Near-Field Optics National Institute of Advanced Industrial Technology Tsukuba Central 4, Higashi 1-1-1 Tsukuba, Ibaraki Japan 305-8562 tel. +81-298-61-5635 fax. +81-298-61-2939 The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 近接場光応用工学研究センター 近接場光基礎研究チーム チーム長 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Ifeffit 1.2.10 + Athena 0.8.54, Artemis 0.8.011, Hephaestus 0.17 Mac PPC installer
I have made a Mac installer for Ifeffit 1.2.10 and have uploaded it to sourceforge.net. The link should be http:// downloads.sourceforge.net/ifeffit/Ifeffit-1.2.10- Mac10.4_PPC_horae066_pkg.dmg. I have updated the wiki as well to mention the new version. Let me know of any problems. It seems to work fine here. Paul On Sep 21, 2007, at 4:25 AM, Bruce Ravel wrote: Hi all, I just uploaded the new tarball for my codes to SourceForge and to my web site. The versions in this source tarball are the versions in the Windows installer Matt announced yesterday. There are a number of changes for the Windows users. This version uses more up-to-date versions of Perl amd of perl/Tk. Also, ini files and other files written by the programs are now written to personal space rather than system space. This means that in the future you will be able to upgrade without blowing away any customizations you may have made. == We STRONGLY encourage all Windows users to download the latest installer and upgrade their computers. == There are no major changes in any of the programs, however a large number of bugs and problems discovered since the APS XAFS summer school have been fixed. Details at http://cars9.uchicago.edu/iffwiki/HoraeVersion066 B On Wednesday 19 September 2007, Matt Newville wrote: Hi Folks, I've just uploaded Ifeffit 1.2.10 to the cars.uchicago.edu and sourceforge.net sites. I'm posting both source code (ifeffit-1.2.10.tar.gz) and a Windows installer (ifeffit-1.2.10.exe) which includes the latest versions of Hephaestus, Athena, and Artemis. Installers for Mac users shouldn't be too far behind. For now, the downloads page at http://cars9.uchicago.edu/ifeffit/ Downloads links to both 1.2.10 and 1.2.9 versions. It may take a day or so for the files to show up on all the sourceforge.net mirrors. The new Windows Installer reflects a new build process for the underlying library. This took some time to work out (you may recall some emails about this over the summer) , but we think it is working as well as any previous version. There are quite a few changes to Bruce's codes, all for the better. And this version does install and work on Windows Vista. For the source code kit, this now uses a new install location for PGPLOT, so if you're installing you must run PGPLOT_Install before installing ifeffit. Also in this version is support for (and default use of) gfortran instead of g77. If you need to use a different fortran compiler from the one found by default, you can use ./PGPLOT_Install --with-fortran=g77 ./configure --with-fortran=g77 make install As always, let us know if there are any problems. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel -- [EMAIL PROTECTED] Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USAfax: (1) 630 252 9793 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Intel Mac release of latest horae package 066
I know Jeff Terry is busy and I wanted the latest release for the Intel Mac my own purposes so I built a release using the traditional (/Applications/Ifeffit) file structure (I said I needed quickly, right?) using gfortran. The new installer is on the sourceforge site under the ifeffit project (http://downloads.sourceforge.net/ifeffit/ Ifeffit-1.2.10-Mac10.4_Intel_horae66.dmg?use_mirror=osdn). I will update the Wiki as well to the new release. As I said, I made the release for myself and am sharing it -- meaning I have only tested it on the system I built it on (Mac Pro) and my Mac Book Pro laptop (for which I used the installer). It works on both of these systems just fine, but they are of course setup in a similar way. If anyone has any problems let me know (although I have an extended series of synchrotron runs coming up and my focus will be on my (day and night) job. Note that you *must* have installed the X11 environment (an optional install located on the restore disks that come with new Macs) for this to work (it runs under X11). Paul Dr. Paul Fons Nano-Optics Reseach Team Team Leader National Institute for Advanced Industrial Science Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: [EMAIL PROTECTED] The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 近接場光応用工学研究センター 近接場光基礎研究チーム チーム長 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Intel Mac release of latest horae package 066
I figured this out actually when I tried using the same software on my notebook. The cause was a shared library not being found due to dynamic linking. I have since done a static link for the binary and reposted it (it works fine on my laptop now). I also noticed, but still haven't fixed that the aquaterm I included was a powerpc version (it runs fine under emulation, but is a little bit of a waste of cpu). I already fixed it here on the laptop, but I am in the middle of an experiment here at SPring-8 and haven't had time to upload that version. I would be curious to know if the new version on sourceforge has fixed the graphics problem for others as well. I will upload the intel version of aquaterm later as it doesn't really have any visible effect. Paul On Oct 12, 2007, at 1:02 PM, Xue Rui wrote: Hi, all. I come with some software problems. I am using a Mac with System Version: Mac OS X 10.4.10 (8R4031) Kernel Version: Darwin 8.10.3 I just installed the new version of horae package 066 released by Dr Paul Fons. Everything works ok except for the plot window: it just shows the lines, but not any words, numbers, not the scale of the coordinate, not the name of the file. Another problem is I can not print the plot. I tried the previous version written by Jeff, these problems went away but the feff6 did not work then. Anything I need to figure out for the system? Best wishes. Snow On Oct 4, 2007, at 1:00 PM, ifeffit- [EMAIL PROTECTED] wrote: [Ifeffit] Intel Mac release of latest horae package 066 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Paul Fons Team Leader Nano-Optics Research Team [EMAIL PROTECTED] Center for Applied Near-Field Optics National Institute of Advanced Industrial Technology Tsukuba Central 4, Higashi 1-1-1 Tsukuba, Ibaraki Japan 305-8562 tel. +81-298-61-5635 fax. +81-298-61-2939 The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 近接場光応用工学研究センター 近接場光基礎研究チーム チーム長 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Debye-Waller factors from first principles
Hi John, Hello from Japan! The cherry blossoms have just finished falling off the trees here and we are enjoying a beautiful spring. Speaking of spring ... we have been doing a lot of DFT calculations in my group recently for phase change materials and I was very curious about the possibility of calculating Debye-Waller factors within abinit using some of the same DFT structural models we have been optimizing. If it is possible to do so as a joint research project or if it is possible to just use the code. Either is fine. We have temperature dependence data for all edges of the materials in question so checking the DW factors might give us some insight into the correct structural models. Thanks in any case! Cheers, Paul ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit/iXAFS won't launch in OS 10.6 (Snow Leopard)
The problem with iXAFS is that it is attempting to run a 32 bit version of perl contained within the application in a 64 bit process. The new version of perl that ships with Snow Leopard is 5.10.0. I pasted the error message from the ixafs shell below. The solution would seem to be to repackage the perl libraries in 5.10.0 and use 64 bit binaries for the Intel compiler. I have the Intel compiler as well so if you need help, please drop me a line. Note Perl 5.8 is included with Snow Leopard as well and can be invoked by changing the defaults of the system, but this is probably a bad thing to do as it will change the perl application for all programs and will undoubtably cause more problems in the long run than it will solve. Cheers, Paul p.s. lines below are from perl and iXAFS under Snow Leopard (10.6.1) $perl --version This is perl, v5.10.0 built for darwin-thread-multi-2level (with 2 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall athena Can't load '/Applications/iXAFS.app/Contents/Resources/Horae/lib/perl5/ site_perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle' for module Tk::Event: /Applications/iXAFS.app/Contents/Resources/Horae/ lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Event/ Event.bundle: no appropriate 64-bit architecture (see man perl for running in 32-bit mode) at /System/Library/Perl/5.10.0/darwin-thread- multi-2level/XSLoader.pm line 67. at /Applications/iXAFS.app/Contents/Resources/Horae/lib/perl5/ site_perl/5.8.6/darwin-thread-multi-2level/Tk/Event.pm line 10 Compilation failed in require at /Applications/iXAFS.app/Contents/ Resources/Horae/lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/ Tk.pm line 13. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/ Tk.pm line 13. Compilation failed in require at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. Undefined subroutine Tk::Event::CleanupGlue called at /Applications/ iXAFS.app/Contents/Resources/Horae/lib/perl5/site_perl/5.8.6/darwin- thread-multi-2level/Tk/Event.pm line 3. END failed--call queue aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Installation ifeffit-1.2.4.dmg OS X 10.2.8
Have you tried some of the older releases in the ifeffit project on SourceForge (http://sf.net). Iffefit relies on Perl as well as PerlTK for the X11 based interface. I helped make some of the earlier versions of the installer (the newest version iXAFS has a launcher included in it -- although it is still being updated for Snow Leopard) so I remember some of the details. PerlTK needs to be compiled for a particular version of perl (which is different on each MacOS release). There were also some binary compatibilities introduced in the perl environment at some point I recall (older binaries were not usable). It is thus important to build ifeffit for each release. You can download the sourcecode for ifeffit on sf.net as well and build it yourself if you can't find an appropriate binary installer there (the appropriate PerlTK would have to be downloaded from perl.org). The build is fairly straightforward (you need f77 which is still out there on the net). The older OS appropriate binary installer would be the easiest solution. I would offer to help more, but I don't have a machine that can run the older OS. Paul On Oct 15, 2009, at 11:46 PM, Juergen Roehler wrote: Hi, I am trying to run Ifeffit on MacOSX 10.2.8 from ifeffit-1.2.4.dmg on a Wallstreet Powerbook (a good old companion ) Ifeffit successfully installed in Applications folder [noname:/Applications/Ifeffit] jroehler% ls artemis icons lib perl5 tkatoms athena include man pgplot XDarwin started (XFree86 4.2 installed from Fink, runs fine for other X applications) Click the perl scripts athena or friends, or run them explicitly with perl 5.6 - athena friends won´t start. Asked to choose a program. Which one? Try to start from terminal: [noname:/Applications/Ifeffit] jroehler % ./athena Can't locate Tk.pm in @INC (@INC contains: /sw/lib/perl5/5.6.0/ darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin /sw/lib/perl5 /sw/ lib/perl5/darwin /System/Library/Perl/darwin /System/Library/Perl / Library/Perl/darwin /Library/Perl /Library/Perl /Network/Library/ Perl/darwin /Network/Library/Perl /Network/Library/Perl .) at ./ athena line 53. BEGIN failed--compilation aborted at ./athena line 53. Well, the *.pm´s and everything else is in /Applications/Ifeffit/lib/ perl5 or /Applications/Ifeffit/, being not in the search tree. Don´t want to modify the system architecture copying /lib/perl5 and the other stuff to somewhere else. How to modify the scripts athena friends. Other solutions? Would like to start jsut from the icons. Thanks in advance. Juergen *** Juergen Roehler Universitaet zu Koeln Fachgruppe Physik Zuelpicher Str. 77 50937 Koeln mailto:juergen.roeh...@uni-koeln.de http://www.uni-koeln.de/~abb12 *** ___ 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] iXAFS for OS X 10.6
Hi Jeff, Hello from a sunny and warm Japan. I would love to upgrade to snow leopard... but ixafs is a must have for me hence I am still at 10.5. Would it be possible to test whatever version you have ready on my mac? So long as I can select a file from X11 and fit stuff, any functional problems with the pretty front end are something I can live with. Please let me know if I can help. Cheers, Paul On Jan 14, 2010, at 1:26 PM, Jeff Terry wrote: Hi All, We have a beta version of iXAFS for Snow Leopard (OS X 10.6). Please email me if you would like to test this version. We hope to have a full release shortly, but would like to have a small group look for major issues for a short time. Thanks, Jeff ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Manual update to iXAFS
Hi Bruce, Regards from a far too hot Japan, Thanks for the update suggestions for iXAFS Bruce. I managed to get it to work, but I found a couple of problems. 1. There is another intermediate directory in your steps (3,4,5), e.g. /Applications/iXAFS/Contents/Resources/bin should read /Applications/iXAFS/Contents/Resources/Horae/bin The intermediate directory Horae is missing in each case. 2. SVN is installed by default on the Mac. When I tried to run the mkartemis.pl and friends after downloading the latest svn release, however, I found that the rc.pl files were missing. How does one generate these from the svn files? I used a rc.pl from a horae-70 release I had around and it apparently worked. 3. The version numbers in the SVN release conflict within the files from the SVN (at least when following the procedure you mentioned above). Some of the files from the SVN release have (ArtemisLog) $VERSION set to 0.8.014 while others (e.g. Group.pm had $VERSION = 0.0.8.061). This triggers an error in the athena and artemis of a version mismatch. I fixed this by disabling the check, as the logic of the versioning is not very clear from a simple examination of the files. What should the $VERSION string (and any other version related strings) be set to in each of the files? In any case it work, but it sure would be nice to have a nice new official release! paul ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Mac OS X Mountain Lion iXAFS
The problem I suspect stems from the internal script of iXAFS calling the package X11 instead of the new name XQuartz. The fix would be either to modify the source code to use either or you may be able to make an Mac OS X alias to the X11 application (either this or a Unix alias should work). I have yet to install mountain lion myself yet, so I cannot verify this. It would be arguably best to change the source code to use either X11 or XQuartz if present I think. Is this something you can do Matt? Cheers, Paul On Aug 13, 2012, at 5:18 AM, George Sterbinsky wrote: Hi Kyler, It may be possible to install ifeffit and Demeter from source code. Instructions of a sort can be found here http://cars9.uchicago.edu/ifeffit/Downloads#MACOSX and here http://bruceravel.github.com/demeter/pods/installation.pod.html#Installing_source_code I'm not sure how the installation from source code would be affected by the lack of X11, but perhaps someone else could chime in if they have more insight into that. Best, George On Thu, Aug 9, 2012 at 2:19 PM, Kyler Carroll kyler.carr...@gmail.com wrote: Hello, I havent seen a post yet pertaining to this issue so I thought I would share and perhaps see if there are solutions to my problem. I have recently upgraded my mac to run the new OS X Mountain Lion and in the process noticed that apple no longer supports or includes X11. They instead have moved to XQuartz http://xquartz.macosforge.org. I downloaded the new XQuartz to my computer and obviously still cannot access iXAFS. I was wondering if someone could offer some advice for me so that I can still run iXAFS on my macbook (Macbook pro OS X version 10.8, 2.3 GHz intel core i5). Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego ___ 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 Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-f...@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 主任研究員 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Recommendations for DFT/computational chemistry software?
Hi Scott, I have been dabbling in DFT for a while. There are many free packages around, but if you would like to model XAFS as well, I would suggest an all electron code for accuracy (such as Wien2K). For general purposes, I am also using VASP and CASTEP. The former uses projector augmented waves and the other ultrasoft pseudopotentials. VASP is fast and scalable to the largest machines and is designed from the ground up for quantum molecular dynamics. Both VASP and CASTEP use pseudopotentials whereas Wien2K uses a linearized augmented plane wave basis (read as radial wavefunctions and Ylms in a sphere about each atom and plane waves between spheres with boundary condition matching at the surface of the spheres. This way it is possible to model even the 1s electrons for heavier atoms and yes it does affect valence electron wavefunctions via orthogonality. All of these approaches are single particle DFT approaches, but it should be good enough for a start, if you want to go beyond these, with solutions of the Bethe-Saltpeter equation (electron and a hole) things get complicated and expensive (in terms of computer time) very quickly. If you are interested in free software I would suggest gpaw, quantum espresso, and abinit. I would also suggest learning the atomic simulation environment in which you can program multiple codes in python (and even solve for maximally localized Wannier functions in a few lines of code!) (Atomic Simulation Environment — ASE 3.8.0.3329 documentation). What exactly are you trying to do? If you are looking for a non-spherical approximation for EXAFS beyond feff8's spheres, you might try FNDMES by Joly as well. Cheers, Paul On Aug 12, 2013, at 10:30 PM, Scott Calvin scal...@sarahlawrence.edu wrote: Hi all, I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose? --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Dr. Paul Fons Chief Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-f...@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 上級主究員 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Recommendations for DFT/computational chemistry software?
Hi Matthew, You are absolutely correct in that the old adage still applies, garbage in equals garbage out. There is no substitute for knowing what you are doing. On the other hand, the great increases in computer power have made what was a nearly intractable problem much more manageable and it is a distinct advantage to be able to use ab-initio software to get insight into the chemistry. Of course, the scaling problem with plane-wave DFT is still there (memory = cube of the number of atoms), but even on a Mac Pro with 32 GB of memory you can simulate the ground state of hundreds of atoms in reasonable times whereas ten years ago, you would have had to use a supercomputer for the same problem. The codes themselves are much easier to use and their associated mailing lists make it a great way to learn the details of a given calculation. It certainly beats writing your own code from scratch (which I did back in 1990 when I was at the Univ. of Illinois on the NCSA machines)! On the other hand, I realize that I should have recommended a couple of books for background reading. A relatively easy read on solid state physics including some details of DFT Efthimios Kaxiras: Atomic and Electronic Structure of Solids My favourite book is a more comprehensive work. Richard M. Martin: Electronic Structure: Basic Theory and Practical Methods I should also add that abinit (http://www.abinit.org) is a free (as in gnu copyleft) code that has a set of very nice tutorials online starting with bonding two hydrogen atoms with references to appropriate papers to read for deeper information. To summarize, my point is that the hardware/software barriers to using DFT codes have gotten much smaller over the years and then investing the time in learning them can potentially offer greater insight into hard to understand problems. It is certainly useful for EXAFS in that one can obtain the relaxed structures in a 0 K calculation to compare for instance different possible XANES structures while at the same time potentially offering calculated material properties (optical reflectivity, Raman, etc.) that can offer additional results that can be compared to experiment. Certainly the ASE environment allows one to program a series of calculations using python and helps shorten the time necessary for writing input files and keeping track of the voluminous output. I give all of my postdocs extensive training in using DFT to get insight into material science problems. While it is not always useful, it can provide useful information in many cases. Paul On Aug 17, 2013, at 1:45 AM, Matthew Marcus mamar...@lbl.gov wrote: Please correct me if I'm wrong, but I get the impression that if you don't know exactly what you're doing, these programs will cheerfully return wrong answers. There seem to be many parameters and choices to be made. I once looked at Quantum Espresso but gave up when I saw that the script for doing MD on a single water molecule ran for over a page of incomprehensible code. I didn't see anything that looked like a step-by-step tutorial or manual. Gaussian with the Gaussview UI is simple enough for an experimentalist like me to use; are there better packages out there which are as well? I also get the impression that you need some pretty hefty compute power. A Linux system is probably to be preferred over Windows. One of these days I should learn Python, not just for this stuff. mam On 8/16/2013 7:27 AM, Paul Fons wrote: Hi Scott, I have been dabbling in DFT for a while. There are many free packages around, but if you would like to model XAFS as well, I would suggest an all electron code for accuracy (such as Wien2K). For general purposes, I am also using VASP and CASTEP. The former uses projector augmented waves and the other ultrasoft pseudopotentials. VASP is fast and scalable to the largest machines and is designed from the ground up for quantum molecular dynamics. Both VASP and CASTEP use pseudopotentials whereas Wien2K uses a linearized augmented plane wave basis (read as radial wavefunctions and Ylms in a sphere about each atom and plane waves between spheres with boundary condition matching at the surface of the spheres. This way it is possible to model even the 1s electrons for heavier atoms and yes it does affect valence electron wavefunctions via orthogonality. All of these approaches are single particle DFT approaches, but it should be good enough for a start, if you want to go beyond these, with solutions of the Bethe-Saltpeter equation (electron and a hole) things get complicated and expensive (in terms of computer time) very quickly. If you are interested in free software I would suggest gpaw, quantum espresso, and abinit. I would also suggest learning the atomic simulation environment in which you can program multiple codes in python (and even solve for maximally
[Ifeffit] Demeter OS X macports build failure
Hi Frank, Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command port upgrade outdated. Here is the content of the log file. Do you have any advise as to how to proceed? Best wishes, Paul FOns ~ $cat /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/main.log version:1 :msg:clean --- Computing dependencies for p5.16-ifeffit:info:clean .:debug:clean p5.16-ifeffit has no conflicts :debug:clean Searching for dependency: perl5.16 :debug:clean Found Dependency: receipt exists for perl5.16 :debug:clean Searching for dependency: ifeffit :debug:clean Found Dependency: receipt exists for ifeffit :msg:clean :debug:main Executing org.macports.main (p5.16-ifeffit) :debug:main changing euid/egid - current euid: 0 - current egid: 0 :debug:main egid changed to: 502 :debug:main euid changed to: 503 :debug:main Skipping completed org.macports.archivefetch (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.fetch (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.checksum (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.extract (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.patch (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.configure (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:build build phase started at Mon Aug 25 11:25:07 JST 2014 :notice:build --- Building p5.16-ifeffit :debug:build Executing org.macports.build (p5.16-ifeffit) :debug:build Environment: CC_PRINT_OPTIONS='YES' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/.CC_PRINT_OPTIONS' CPATH='/opt/local/include' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' :debug:build Assembled command: 'cd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl /usr/bin/make -j8 -w all' :debug:build Executing command line: cd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl /usr/bin/make -j8 -w all :info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build rm -f blib/arch/auto/Ifeffit/Ifeffit.bundle :info:build LD_RUN_PATH=/usr/lib /usr/bin/clang -shared ifeffit_wrap.o -arch x86_64 -o blib/arch/auto/Ifeffit/Ifeffit.bundle \ :info:build /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -lifeffit -lnopgplot -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build __gfortran_compare_string, referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build _setsca_ in libifeffit.a(misc_vars.o) :info:build ... :info:build __gfortran_concat_string, referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build __gfortran_getenv, referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build __gfortran_st_close, referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build
Re: [Ifeffit] Demeter OS X macports build failure
Hi Frank, The suggestion you made allowed me to successfully get artemis, athena, and hephestus running with one problem. The windows are black for artemis (although the other two are fine). Any suggestions as to how to fix this problem? Cheers, Paul On Aug 26, 2014, at 0:50, Schima, Frank frank.sch...@nist.gov wrote: On Aug 25, 2014, at 6:17 AM, Bruce Ravel bra...@bnl.gov wrote: On 08/24/2014 10:33 PM, Paul Fons wrote: Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command port upgrade outdated. Here is the content of the log file. Do you have any advise as to how to proceed? Paul, Errors like this: :info:build Undefined symbols for architecture x86_64: :info:build __gfortran_compare_string, referenced from: suggest a missing library that is being referenced but which cannot be linked to. Perhaps you are missing some package associated with gfortran...? I'd likely know how to solve this problem on Ubuntu, but on macports….. Thanks for responding Bruce. You are correct and this is a new bug I have seen recently. While I don’t know why this is happening exactly, fortunately the workaround is easy. sudo port install ifeffit +gcc49 sudo port clean p5.16-ifeffit sudo port upgrade outdated Cheers! Frank ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-f...@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 上級主究員 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Demeter OS X macports build failure
Hi (again) Frank, The problem with the black windows in artemis was solved last time by installing the demeter-devel package, however, you suggested installing the ifeffit package. I had assumed that this version would have solved the black window problem. I then tried installing demeter-devel and all programs ran without error. I am a little confused as to what is the most recent version -- am I now running an older version of demeter than before? Is this black window problem something wrong on my end (with the version installed by port install ifeffit +gcc49)? In any case, thank you very much for your efforts. Best wishes, Paul On Aug 26, 2014, at 0:50, Schima, Frank frank.sch...@nist.gov wrote: On Aug 25, 2014, at 6:17 AM, Bruce Ravel bra...@bnl.gov wrote: On 08/24/2014 10:33 PM, Paul Fons wrote: Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command port upgrade outdated. Here is the content of the log file. Do you have any advise as to how to proceed? Paul, Errors like this: :info:build Undefined symbols for architecture x86_64: :info:build __gfortran_compare_string, referenced from: suggest a missing library that is being referenced but which cannot be linked to. Perhaps you are missing some package associated with gfortran...? I'd likely know how to solve this problem on Ubuntu, but on macports….. Thanks for responding Bruce. You are correct and this is a new bug I have seen recently. While I don’t know why this is happening exactly, fortunately the workaround is easy. sudo port install ifeffit +gcc49 sudo port clean p5.16-ifeffit sudo port upgrade outdated Cheers! Frank ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-f...@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 上級主究員 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Demeter OS X macports build failure
Hi Bruce, Thank you for the suggestion. I would have tried addressing this directly, but the macports is supposed to handle dependencies automatically (like yum or yast in linux). The suggestion by Frank apparently solved the installation problem, but there is a potential black window problem in artemis. I can avoid this by using the package demeter-devel, but it was my impression that the package ifeffit was the most recent version. Hope I figure this out soon. Cheers, Paul On Aug 25, 2014, at 21:17, Bruce Ravel bra...@bnl.gov wrote: On 08/24/2014 10:33 PM, Paul Fons wrote: Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command port upgrade outdated. Here is the content of the log file. Do you have any advise as to how to proceed? Paul, Errors like this: :info:build Undefined symbols for architecture x86_64: :info:build __gfortran_compare_string, referenced from: suggest a missing library that is being referenced but which cannot be linked to. Perhaps you are missing some package associated with gfortran...? I'd likely know how to solve this problem on Ubuntu, but on macports. 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://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-f...@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 上級主究員 ポール・フォンス ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Update on importing Hephaestus Fe standard
Hi All, I wanted to add a quick update in that the Fe standard from Hephaestus can be imported as a mu(E) file in athena. Perhaps the file type assigned by Hephaestus is the only problem here. Cheers, Paul ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] PCA not enabled on Mac version of Demeter: Athena
I just wanted to add the comment works here for @0.9.20pre10. This is probably more helpful to Frank than Ellen, but it would seem that it something unique to Ellen's configuration. I am running Mavericks 10.9.5 by the way. Cheers, Paul On Oct 4, 2014, at 3:50, Ellen Daugherty ellen.daughe...@colostate.edu wrote: Hello XAFS community, I recently upgraded to the new version of Demeter (0.9.20) for Mac and am trying to run principal components analysis on my spectra. When I click on Principle components analysis from the main menu, the window shows the following message: PCA is not enabled on this computer. The most likely reason is that the perl modules PDL and/or PDL::Stats are not available. Perhaps the solution here is simple, but I am not familiar with perl modules and do not understand the source of the issue. I could not find information about this problem in the Mail Archive, though I may have missed something. Do I need to download the PDL perl modules separately from the Demeter installation? Could there be files that are not located in the proper directory? Or perhaps PCA is simply not available for Macs? Please let me know if further information would help in solving this problem. Thank you! Ellen -- Graduate Student Research Assistant Department of Chemistry Colorado State University ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Problems with gnuplot graphics on Mac OS 10.12.1
Hi All,
I have installed demeter using Macports on 10.12.1 and while hephaestus seems
to run normally, athena has some trouble with graphics. The usual athena perl
based panel shows up just fine, but upon loading some data, there is always an
error when gnuplot is invoked to plot graphics (as reproduced below). It would
seem that the command “set” is missing the first letter. Does anyone have a
suggestion as to what to check to fix this?
Axion:perl5.24 $ use_macports.sh athena
gnuplot> et label '{/Symbol \305}' at 400.7,853.0387 center front textcolor
ls 12
^
line 0: invalid command___
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[Ifeffit] Problems with gnuplot graphics on Mac OS 10.12.1
Hi All, I just wanted to give an update to my earlier problems with the mysterious gnuplot errors. After editing the file Matt mentioned earlier, I decided to uninstall and install demeter to no avail. I then realized that I had been relying on the latest version of xquartz (the x11 system) and installed x11 using macports. After a bit of trouble with installation (I had to break the installation into pieces — but this is a typical macports problem), the x11 installation completed and athena worked fine. Thus my conclusion is that there was some sort of weird interference between x11 subsystems. In any case, all is well now. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] xraylarch
Hi. Due to the difficulties of getting demeter to work on the Apple M1 machines, I have started to use xraylarch and so far I like the interface as well as the possibility of scripting later on. I had a couple of observations and a question regarding xraylarch usage that I hope could be addressed here. First, one can load multiple spectra into the (feff) fitting window. It seems, however, that which paths are selected are universal (the selected paths are used for all exafs spectra). Does this mean that multiple edge fitting is not possible. If multiple edge fitting is possible, how is it done? In the fitting window, one can have several spectra loaded and one can select all or some of the spectra to be fit. The interface seems like it was designed for multiple edge fitting, but is it? Second, it is strange that whenever a parameter is changed that the fitting variable settings (fixed, vary, constrain) are reset. For complex fits, this generates a lot of unnecessary clicking (and the corresponding mistake possibilities) Third, when one reads in several different feff calculations, one would, in principle, like to have a different value of e0 (the origin of energy offset) for each feff calculation. By default when a feff calculation is read in the variable e0 is defined. When one defines alternative energy offset variables for the different feff calculations and deletes the original e0 value, something strange happens. Accessing the “Edit Parameters” window results in e0 reappearing (even though it has been manually deleted previously). Is this a feature? The same thing may happen for other “automatic” variables as well. Four. This is really a feature request. When a variable is unused (lets say some additional paths are introduced in the fitting process and a new fit without them is attempted), the choices in the parameter list are (fix, vary, and constrain). There is no option to “skip” like in Artemis. Obviously, one can choose fix, but in doing so the unused variable shows up in the fit result summary and is somewhat confusing. It would be subjectively better to have the option to “skip” a variable and not have it show up in the fit summary. Just some initial thoughts... ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
