Hi I have a really strange problem with the new version of athena. After updating to iffefit 1.2.7 I lose the possibility to use athena, but the rest of the package works well. I already try do deinstall everything and install ifeffit again but nothing changed. This problem is present only on my computer while in the computer of my colleagues athena works well. The file 1.txt is the answer of calling from the shell "athena.exe" the file 2.txt is the answer of calling from the shell "athena.bat" I'm using a windows 2000 sistem Any idea? Bye Carmelo -- ************************************************************************ Carmelo Prestipino(*) Department of Inorganic, Physical and Material Chemistry Via P. Giuria 7 I-10125 Torino Italy Tel +39011-6707841> Fax +39011-6707855 E-mail carmelo.prestipino@unito.it (*) also with INFM UdR di Torino Universita' ************************************************************************* C:\Programmi\Ifeffit>athena.bat Ifeffit checked for updates recently. Untagged opnames: recv i_predec localtime sassign rewinddir untie sockpair scope seekdir ucfirst fteowned i_negate rv2cv leave accept ge redo stringify substcont index right_shift aelem hex sservent send gt multiply bit_or unlink gv wantarray i_ne exi t lcfirst semctl open rv2sv gprotoent backtick syswrite getlogin grepstart subtract ftsize eof warn ehostent nextstate dofile aassign ftatime gvsv null gmtime shift stat flip substr postinc open_dir cond_expr atan2 left_shift time hslice leaveeval ret urn grepwhile socket preinc telldir seq link ftfile setstate sysread chdir each av2arylen ioctl reset ftewrite refgen gpwuid ord join modulo chown pop padav shmread ftsvtx pos and pow sgrent oct rindex chr sge aelemfast regcomp andassign fteexec rv2gv ftpipe ftsuid sort i_divide sprotoent fork entersub sgt ftbinary chmod unpack fteread bind tell eservent entertry semop push getpriority flock rv2hv lc ftrowned gpwnam system le gsbyport dump concat pushmark ftctime lt mapstart i_postdec repeat pack leaveloop stub exists sin threadsv syscall utime quotemeta ftchr padsv bit_xor log mapwhile rcatline sysopen readdir alarm truncate seek const padany sselect entereval abs ftzero ne helem close ftblk i_eq gpwent gpbynumber values pushre leavesub proto type die dbmclose aslice binmode wait complement list reverse flop snetent gsbyname fttty ftrexec leavetry match unstack eprotoent i_preinc gpbyname shutdown ftrwrite crypt postdec iter listen anoncode trans lineseq ftrread length ftsgid sprintf print chomp or add enter predec lock epwent tie fttext chop i_ge sle schop umask closedir gnetent subst tied i_add setpgrp i_modulo defined scmp negate getpeername undef rmdir ftlink slt regcreset i_gt rename ghostent msgsnd method_named kill orassign requ ire sqrt method ftis lstat splice mkdir leavesublv gsockopt ftdir i_ncmp scalar getpgrp chroot padhv ncmp vec exp unshift caller qr dbstate ggrnam cos sne ftmtime symlink srefgen ftsock enterloop schomp keys msgrcv msgget shmget anonhash exec waitpid xor sleep read range goto getppid delete prtf shostent int next fcntl getsockname shmwrite i_multiply setpriority gelem sysseek regcmaybe getc enterwrite semget not gservent ggrent anonlist formline glob fileno ssockopt rv2av spwent i_subtract ggrgid tms gnbyname rand divide srand enteriter bit_and study eq dbmopen gnbyaddr leavewrite i_le pipe_op ghbyname connect ref lslice bless uc readline enetent select readlink msgctl i_lt i_postinc split last egrent ghbyaddr shmctl Can't locate Tk/Popup.pm in @INC (@INC contains: C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc/lib C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc CODE(0x12d32 6c) .) at Tk/Widget.pm line 259. BEGIN failed--compilation aborted at -e line 835. C:\Programmi\Ifeffit> C:\Programmi\Ifeffit>athena.exe can't open \perl\Xray\space_groups.db: No such file or directory at Xray/Xtal.pm line 115 Compilation failed in require at Ifeffit/Files.pm line 50. BEGIN failed--compilation aborted at Ifeffit/Files.pm line 50. Compilation failed in require at script/athena line 86. BEGIN failed--compilation aborted at script/athena line 86. BEGIN failed--compilation aborted at -e line 835. C:\Programmi\Ifeffit>
Hi Carmelo, You probably need to clear out any stale "PAR" directories, which probably live in a temporary folder, such as C:\Documents and Settings\USER\Local Settings\Temp\par-USER\ where USER is your Windows login name. Note that some of these folders may be hidden by default. You'll need to find the par-USER folder and delete the old 'cach-******' folders there. You might need to search for folders named 'par-USER'. This seems to be a common issue with recent versions of athena, artemis, and hepheastus on Windows. We're working on a better solution, and hope to have it ready soon. --Matt On Tue, 2 Aug 2005, Carmelo Prestipino wrote:
Hi I have a really strange problem with the new version of athena. After updating to iffefit 1.2.7 I lose the possibility to use athena, but the rest of the package works well. I already try do deinstall everything and install ifeffit again but nothing changed. This problem is present only on my computer while in the computer of my colleagues athena works well. The file 1.txt is the answer of calling from the shell "athena.exe" the file 2.txt is the answer of calling from the shell "athena.bat" I'm using a windows 2000 sistem Any idea? Bye Carmelo
Hi
I am also experiencing the similar problem. But
instead of Athena, Hephaestus doesn't run at all
after I updated my IFEFFIT 1.2.6 to 1.2.7. I
reinstalled the program several times but still
experienced the same problem. Anyone has similar
problems?
Li Yang
--- Carmelo Prestipino
Hi I have a really strange problem with the new version of athena. After updating to iffefit 1.2.7 I lose the possibility to use athena, but the rest of the package works well. I already try do deinstall everything and install ifeffit again but nothing changed. This problem is present only on my computer while in the computer of my colleagues athena works well. The file 1.txt is the answer of calling from the shell "athena.exe" the file 2.txt is the answer of calling from the shell "athena.bat" I'm using a windows 2000 sistem Any idea? Bye Carmelo
--
************************************************************************
Carmelo Prestipino(*) Department of Inorganic, Physical and Material Chemistry Via P. Giuria 7 I-10125 Torino Italy Tel +39011-6707841> Fax +39011-6707855 E-mail carmelo.prestipino@unito.it (*) also with INFM UdR di Torino Universita'
*************************************************************************
C:\Programmi\Ifeffit>athena.bat
Ifeffit checked for updates recently. Untagged opnames: recv i_predec localtime sassign rewinddir untie sockpair scope seekdir ucfirst fteowned i_negate rv2cv leave accept ge redo stringify substcont index right_shift aelem hex sservent send gt multiply bit_or unlink gv wantarray i_ne exi t lcfirst semctl open rv2sv gprotoent backtick syswrite getlogin grepstart subtract ftsize eof warn ehostent nextstate dofile aassign ftatime gvsv null gmtime shift stat flip substr postinc open_dir cond_expr atan2 left_shift time hslice leaveeval ret urn grepwhile socket preinc telldir seq link ftfile setstate sysread chdir each av2arylen ioctl reset ftewrite refgen gpwuid ord join modulo chown pop padav shmread ftsvtx pos and pow sgrent oct rindex chr sge aelemfast regcomp andassign fteexec rv2gv ftpipe ftsuid sort i_divide sprotoent fork entersub sgt ftbinary chmod unpack fteread bind tell eservent entertry semop push getpriority flock rv2hv lc ftrowned gpwnam system le gsbyport dump concat pushmark ftctime lt mapstart i_postdec repeat pack leaveloop stub exists sin threadsv syscall utime quotemeta ftchr padsv bit_xor log mapwhile rcatline sysopen readdir alarm truncate seek const padany sselect entereval abs ftzero ne helem close ftblk i_eq gpwent gpbynumber values pushre leavesub proto type die dbmclose aslice binmode wait complement list reverse flop snetent gsbyname fttty ftrexec leavetry match unstack eprotoent i_preinc gpbyname shutdown ftrwrite crypt postdec iter listen anoncode trans lineseq ftrread length ftsgid sprintf print chomp or add enter predec lock epwent tie fttext chop i_ge sle schop umask closedir gnetent subst tied i_add setpgrp i_modulo defined scmp negate getpeername undef rmdir ftlink slt regcreset i_gt rename ghostent msgsnd method_named kill orassign requ ire sqrt method ftis lstat splice mkdir leavesublv gsockopt ftdir i_ncmp scalar getpgrp chroot padhv ncmp vec exp unshift caller qr dbstate ggrnam cos sne ftmtime symlink srefgen ftsock enterloop schomp keys msgrcv msgget shmget anonhash exec waitpid xor sleep read range goto getppid delete prtf shostent int next fcntl getsockname shmwrite i_multiply setpriority gelem sysseek regcmaybe getc enterwrite semget not gservent ggrent anonlist formline glob fileno ssockopt rv2av spwent i_subtract ggrgid tms gnbyname rand divide srand enteriter bit_and study eq dbmopen gnbyaddr leavewrite i_le pipe_op ghbyname connect ref lslice bless uc readline enetent select readlink msgctl i_lt i_postinc split last egrent ghbyaddr shmctl
Can't locate Tk/Popup.pm in @INC (@INC contains:
C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc/lib
C:\DOCUME~1\lello\IMPOST~1\Temp\par-lello\cache-5d90d4330465c124b0c34b24a7275a8a36486b2a/inc
CODE(0x12d32 6c) .) at Tk/Widget.pm line 259.
BEGIN failed--compilation aborted at -e line 835.
C:\Programmi\Ifeffit>
> C:\Programmi\Ifeffit>athena.exe can't open \perl\Xray\space_groups.db: No such file or directory at Xray/Xtal.pm line 115 Compilation failed in require at Ifeffit/Files.pm line 50. BEGIN failed--compilation aborted at Ifeffit/Files.pm line 50. Compilation failed in require at script/athena line 86. BEGIN failed--compilation aborted at script/athena line 86. BEGIN failed--compilation aborted at -e line 835.
C:\Programmi\Ifeffit>>
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Hi Li, Yes, other people have had similar problems.... As you noticed, re-installing is probably not the issue. Did you try looking for and deleting PAR-* directories under your Document and Settings folder? --Matt On Wed, 3 Aug 2005, li yang wrote:
Hi
I am also experiencing the similar problem. But instead of Athena, Hephaestus doesn't run at all after I updated my IFEFFIT 1.2.6 to 1.2.7. I reinstalled the program several times but still experienced the same problem. Anyone has similar problems?
Li Yang
On Thursday 04 August 2005 10:06, Matt Newville wrote:
Hi Li,
Yes, other people have had similar problems....
As you noticed, re-installing is probably not the issue. Did you try looking for and deleting PAR-* directories under your Document and Settings folder?
--Matt
On Wed, 3 Aug 2005, li yang wrote:
Hi
I am also experiencing the similar problem. But instead of Athena, Hephaestus doesn't run at all after I updated my IFEFFIT 1.2.6 to 1.2.7. I reinstalled the program several times but still experienced the same problem. Anyone has similar problems?
This post from about 6 weeks ago is relevant to the current thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-June/001815.html Given how many people are having trouble with the new way of building windows executables (using PAR), I am considering going back to using PerlApp. Any substantive suggestions or offers of help from the Windows-using portion of the Ifeffit community would be welcome. B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi all, First of all, kudos to Bruce and Matt on the new versions. One of my summer students more than once uttered the phrase "This is <italic>awesome</italic>" as she tried out yet another new feature. I concur. :) * * * I thought I'd share some non-transparent behavior on the part of feff6L as embedded in Artemis. It happens in a <italic>very</italic> common situation; I suspect many of you have been aware of this for years; for some reason I didn't really notice it enough to investigate until today: Use Artemis to put in an atoms file for Cu (fcc; a=3.61; one copper at 0,0,0). Choose a cluster size of 6. Run atoms, then feff. I get 22 paths ranging up to 6 angstroms. No problem. Repeat with cluster size 7. 41 paths now, up to 7 ansgstroms. Again, no problem. Now try cluster size 8. Now there are only 30 paths, with a maximum r of 6.35 angstroms! It turns out that what is happening is that feff is giving the error "internal path finder limit exceeded -- path list may be incomplete." And indeed it is. It just surprises me a little the manner in which it is incomplete...it's considerably worse off than the 7 angstrom cluster. There's an easy fix: feff defaults to evaluating paths with up to 8 (!) legs. If I override that to max out at 4 legs, then the cluster size can be pushed up as large as 9 without exceeding the path finder limit. In my opinion, the path finder limit in feff is high enough for most applications. I frequently fit up to 5 angstroms, which, considering the difference between reff and r and the width of EXAFS peaks, means I feel I have to include paths up to about 6 angstroms. But that means I need to have feff compute a cluster bigger than that (as has been discussed on this list a few times)...which makes a 7 angstrom cluster seem reasonable; maybe 8 for safety. I have never encountered a path with more than 4 legs that I found to be significant. So for me this is not a problem. But with novices in mind, I see two improvements that could be made: 1) Artemis now does a decent job of flagging users when iffeffit encounters a problem. Perhaps it should do the same for feff. (I know the feff error messages are often somewhat obscure. But if Artemis simply stated that "FEFF has encountered a possible problem" and advised users to check the messages screen, the behavior might seem a tad less baffling.) 2) Does anyone out there run into cases where paths with more than 4 legs are significant? If not, Artemis should just stick the card NLEG 4 into the feff.inp file automatically...that's probably a better default value. Of course, a knowledgeable user could still override that to include more legs if they wished. --Scott Calvin Sarah Lawrence College
First of all, kudos to Bruce and Matt on the new versions. One of my summer students more than once uttered the phrase "This is <italic>awesome</italic>" as she tried out yet another new feature. I concur. :)
Awwwww..... now I'm blushing.....
In my opinion, the path finder limit in feff is high enough for most applications. I frequently fit up to 5 angstroms, which, considering the difference between reff and r and the width of EXAFS peaks, means I feel I have to include paths up to about 6 angstroms. But that means I need to have feff compute a cluster bigger than that (as has been discussed on this list a few times)...which makes a 7 angstrom cluster seem reasonable; maybe 8 for safety. I have never encountered a path with more than 4 legs that I found to be significant.
2) Does anyone out there run into cases where paths with more than 4 legs are significant? If not, Artemis should just stick the card NLEG 4 into the feff.inp file automatically...that's probably a better default value. Of course, a knowledgeable user could still override that to include more legs if they wished.
The NLEGS suggestion is a good one. I'll probably take you up on it. The fix is very simple and is one that anyone can implement immediately without modification to the artemis source code. Search among the files installed as part of my software for a file called "feff.atp". This is template that Artemis uses to write input data for feff. In short, it provides a sort of outline for what the feff.inp file should look like. Simply add a line that says NLEG 4 somewhere in that file. On a unix machine, you will probably need to copy the feff.atp file to ~/.horae/atp/ before editing it.
1) Artemis now does a decent job of flagging users when iffeffit encounters a problem. Perhaps it should do the same for feff. (I know the feff error messages are often somewhat obscure. But if Artemis simply stated that "FEFF has encountered a possible problem" and advised users to check the messages screen, the behavior might seem a tad less baffling.)
Actually, I have been building a database of feff6 error messages. When Feff is finished, artemis parses the text in the window where the feff output is displayed. If it recognizes the error message, it displays an explanation in gaudy red-on-white text at the end of feff's run time messages. If you find a feff error for which Artemis does not provide an explanation, send me a project file that triggers the error so I can add it to the database for the next release. I am only making responses to the error messages from feff6L, the version that comes with Ifeffit, at this time. If you use another version of feff, you are on your own for now as far as recognizing what feff's error means. I have also been auditing the code this week to make sure that the messages window rises to the top of the screen when an informational message of this sort gets displayed. B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Bruce: I have implemented your proposed change in the Debian packages. There should be a new revision on my server soon. Carlo On Thu, 4 Aug 2005, Bruce Ravel wrote:
The fix is very simple and is one that anyone can implement immediately without modification to the artemis source code. Search among the files installed as part of my software for a file called "feff.atp". This is template that Artemis uses to write input data for feff. In short, it provides a sort of outline for what the feff.inp file should look like. Simply add a line that says
NLEG 4
somewhere in that file. On a unix machine, you will probably need to copy the feff.atp file to ~/.horae/atp/ before editing it.
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
Hi all, the recent messages on error messages written by the feff6L module of artemis prompted me to pose the following question here. Since the very first trials with the program, last year, every time I run feff using a feff.inp file derived from a structural model that includes the metal ion and the few amino acids that would act as ligands to it, I get error messages of the type I am including here. Is there something wrong or is everything Ok and I should disregard the messages? Regards Stefano phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 4 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 5 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 6 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 7 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... WARNING in PATHS Module: rmax > distance to most distant atom. Some paths may be missing. rmax, ratx 6.00000 5.87504 Rmax 6.0000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table nfound nheap nheapx nsc r Paths found 701 (nheapx, nbx 180 8) Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% Unique paths 153, total paths 264 -- ____________________________________________ 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"
Bruce,
my feff.atp file now is the following. Is it OK??? I am puzzled by
the stars in front of NLEG 8 and then the line I have added stating
NLEG 4 without a star, but I simply followed instruction,
monkey-wise, so I am not sure.
Stefano
Hi Stefano, The stars are "commented out" lines to make it easy for the user to change options without remembering the exact code word. Since we are specifying a value for NLEG other than the default, there is no need to have the starred line with NLEG 8 on it. It won't actually hurt since it's treated as a comment, but could confuse users. I recommend removing it. --Scott Calvin Sarah Lawrence College At 10:47 PM 8/10/2005 +0200, you wrote:
Bruce,
my feff.atp file now is the following. Is it OK??? I am puzzled by the stars in front of NLEG 8 and then the line I have added stating NLEG 4 without a star, but I simply followed instruction, monkey-wise, so I am not sure. Stefano
Hi Scott,
The stars are "commented out" lines to make it easy for the user to change options without remembering the exact code word.
that's what I though, but did not dare to change :-)
Since we are specifying a value for NLEG other than the default, there is no need to have the starred line with NLEG 8 on it. It won't actually hurt since it's treated as a comment, but could confuse users. I recommend removing it.
OK Thanks, now reading your comment of the other day I better understand the issue. 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"
participants (7)
-
Bruce Ravel -
Carlo Segre -
Carmelo Prestipino -
li yang -
Matt Newville -
Scott Calvin -
Stefano Ciurli