Re: [Ifeffit] about wolframite crystallographic file
Yordy, I'll look into this when I get a chance, but that might not be until later in the week (I am on travel at the moment). B -- Bruce Ravel --- [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ -Original Message- From: [EMAIL PROTECTED] on behalf of Yordy Licea Fonseca Sent: Sat 11/15/2008 6:36 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] about wolframite crystallographic file Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: Artemis trapped one or more errors! Error message dumped to screen. I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: [EMAIL PROTECTED] winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] about wolframite crystallographic file
Dear Yordy, this error message actually occured because the crystallographic data in the .cif file is somewhat ambigous. The space group is P 2/c (number 13), which is a monoclinic cell (with two different settings, as additional complication: unique axis b or c). Now, if you look in the .cif file, the unit cell parameters are given as follows: -- snip _cell_length_a 4.6698(9) _cell_length_b 5.6873(23) _cell_length_c 4.9515(17) _cell_angle_alpha 90. _cell_angle_beta 90.(0) _cell_angle_gamma 90. -- snip You can see, that in the cif file, all angles are 90. degrees. This however would be an orthorhombic cell, not a monoclinic. That's exactly the contents of the Artemis/Atoms error message: Monoclinic cells have all unequal axes and one non-right angle. Unknown setting for a monoclinic cell. Fatal error(s) in cell parameters. The atoms code in this case is not able to determine the setting of the monoclinic cell, because it cannot find the unique axis. For humans, the unique axis is denoted by the standard deviation (0) behind beta, making it unique axis b. This however is not interpreted by Artemis. This means, that you have to tell Artemis in some way, which angle deviates from 90°. For this, I usually change the beta angle in the cif file by some tiny amount, to -say- 90.0001 degrees. This is far below the standard deviation, so it's crystallographically still valid. -- snip _cell_angle_alpha 90. _cell_angle_beta 90.0001(0) _cell_angle_gamma 90. -- snip Cheers, dominik Yordy Licea Fonseca wrote: Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: Artemis trapped one or more errors! Error message dumped to screen. I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Dominik Samuelis [EMAIL PROTECTED] Max-Planck-Institut für Festkörperforschung Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] about wolframite crystallographic file
Yordy, Bruce Apparently Atoms doesn't like it that the beta angle in a monoclinic cell is 90 degrees. When I change the beta angle to 91 degrees or even 90.0001 (and change nothing else), Atoms runs normally. It's interesting that although Artemis says it has written a message nothing shows up in the messages palette but the echo palette does show that an error was caught. Carl From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yordy Licea Fonseca Sent: Saturday, November 15, 2008 6:36 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] about wolframite crystallographic file Hi all, As soon as I load this attached CIF crystallographic file from ISCD in Artemis0.8.012 the software says: Artemis trapped one or more errors! Error message dumped to screen. I can`t go on runnig Atoms as it seems to be a problem with the file. I have read the suggestion made in FAQ, but I can not manage to find the error. Could you help me, please? It would be nice once the problem been fixed to add this structure to Matt's atoms.inp database. Thanks you very much, Yordy -- Yordy E. Licea Fonseca Departamento de Físico-Química Instituto de Química-IQ/UFRJ Laboratório de Catálise Heterogênea Rio de Janeiro, RJ, CEP 21.949-909 Brasil Email: [EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
Hi, This is my fault... and I apologize for the sloppiness and for being late in fixing this. I've been mixing 'development/testing' and 'production' versions, and haven't been very good at keeping them cleanly separated. I think I have this mostly under control now, but I will have to work on a decent test suite. I think I found another reason to make a 1.2.11c version too, that the mixing of devel and production caused an experiment in how fitting was done to be the default, so that the reported chi-square doesn't actually match the documentation (instead of summing real and imaginary parts, it sums real and magnitude components of the misfit, which is part of an experiment to see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for another way to report chi-square and misfits is potentially a useful approach, but it's not what is documented. Anyway, mixing devel and production versions like this (for the past couple years, really) is very sloppy on my part, and I apologize again. I actually have an ubuntu box now, though I built pgplot from source, and have never made a .deb file. There is a new source kit at http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll post this to sourceforge this afternoon, and I'll also make a new DLL for Windows and post all of these on the download page. I'll also make a new updater for Windows. --Matt On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi [EMAIL PROTECTED] wrote: Carlo Segre wrote: Hi Mauro: I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository deb http://debian-xray.iit.edu intrepid main contrib non-free Carlo, Thank you very much for the package. Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no HoraeFriends from Bruce SVN. Well, now I have pgplot5, ifeffit, perl-ifeffit and python-ifeffit from binaries and libperlxray horae and demeter built from source (Bruce SVN). Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these IFF str = * output as stated also by Gareth in his Ifeffit 1.2.11b terminal output post. Is it normal? Cheers, Mauro ___ 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] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls compiled in. Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville [EMAIL PROTECTED] wrote: Hi, This is my fault... and I apologize for the sloppiness and for being late in fixing this. I've been mixing 'development/testing' and 'production' versions, and haven't been very good at keeping them cleanly separated. I think I have this mostly under control now, but I will have to work on a decent test suite. I think I found another reason to make a 1.2.11c version too, that the mixing of devel and production caused an experiment in how fitting was done to be the default, so that the reported chi-square doesn't actually match the documentation (instead of summing real and imaginary parts, it sums real and magnitude components of the misfit, which is part of an experiment to see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for another way to report chi-square and misfits is potentially a useful approach, but it's not what is documented. Anyway, mixing devel and production versions like this (for the past couple years, really) is very sloppy on my part, and I apologize again. I actually have an ubuntu box now, though I built pgplot from source, and have never made a .deb file. There is a new source kit at http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll post this to sourceforge this afternoon, and I'll also make a new DLL for Windows and post all of these on the download page. I'll also make a new updater for Windows. --Matt On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi [EMAIL PROTECTED] wrote: Carlo Segre wrote: Hi Mauro: I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository deb http://debian-xray.iit.edu intrepid main contrib non-free Carlo, Thank you very much for the package. Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no HoraeFriends from Bruce SVN. Well, now I have pgplot5, ifeffit, perl-ifeffit and python-ifeffit from binaries and libperlxray horae and demeter built from source (Bruce SVN). Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these IFF str = * output as stated also by Gareth in his Ifeffit 1.2.11b terminal output post. Is it normal? Cheers, Mauro ___ 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 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
Debian packages have been uploaded to unstable and I am in the process of building Ubuntu packages for my repository. i expect that they will be up tonight. carlo On Mon, 17 Nov 2008, Matt Newville wrote: Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls compiled in. Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville [EMAIL PROTECTED] wrote: Hi, This is my fault... and I apologize for the sloppiness and for being late in fixing this. I've been mixing 'development/testing' and 'production' versions, and haven't been very good at keeping them cleanly separated. I think I have this mostly under control now, but I will have to work on a decent test suite. I think I found another reason to make a 1.2.11c version too, that the mixing of devel and production caused an experiment in how fitting was done to be the default, so that the reported chi-square doesn't actually match the documentation (instead of summing real and imaginary parts, it sums real and magnitude components of the misfit, which is part of an experiment to see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for another way to report chi-square and misfits is potentially a useful approach, but it's not what is documented. Anyway, mixing devel and production versions like this (for the past couple years, really) is very sloppy on my part, and I apologize again. I actually have an ubuntu box now, though I built pgplot from source, and have never made a .deb file. There is a new source kit at http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll post this to sourceforge this afternoon, and I'll also make a new DLL for Windows and post all of these on the download page. I'll also make a new updater for Windows. --Matt On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi [EMAIL PROTECTED] wrote: Carlo Segre wrote: Hi Mauro: I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository deb http://debian-xray.iit.edu intrepid main contrib non-free Carlo, Thank you very much for the package. Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no HoraeFriends from Bruce SVN. Well, now I have pgplot5, ifeffit, perl-ifeffit and python-ifeffit from binaries and libperlxray horae and demeter built from source (Bruce SVN). Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these IFF str = * output as stated also by Gareth in his Ifeffit 1.2.11b terminal output post. Is it normal? Cheers, Mauro ___ 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 -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498Fax: 312.567.3494 [EMAIL PROTECTED] http://www.iit.edu/~segre [EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit 1.2.11c (was Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source)
Thanks, Carlo! --Matt On Mon, Nov 17, 2008 at 8:03 PM, Carlo Segre [EMAIL PROTECTED] wrote: Debian packages have been uploaded to unstable and I am in the process of building Ubuntu packages for my repository. i expect that they will be up tonight. carlo On Mon, 17 Nov 2008, Matt Newville wrote: Hi Folks, I've uploaded source kits for Ifeffit 1.2.11c to the cars.uchicago.edu and sourceforge.net download sites. I have a Windows dll made for this bug fix version. If anyone is interested, this is currently at http://cars.uchicago.edu/~ifeffit/updates/011/bin/ifeffit_12.dll This should be a drop-in replacement for the IFEFFIT_DIR\bin\ifeffit_12.dll on your system. Artemis.exe will not be updated from this dll, as it has this dlls compiled in. Bruce will have to make a new Artemis.exe, and then we'll make a automatic update. Sorry for all the trouble, --Matt On Mon, Nov 17, 2008 at 12:30 PM, Matt Newville [EMAIL PROTECTED] wrote: Hi, This is my fault... and I apologize for the sloppiness and for being late in fixing this. I've been mixing 'development/testing' and 'production' versions, and haven't been very good at keeping them cleanly separated. I think I have this mostly under control now, but I will have to work on a decent test suite. I think I found another reason to make a 1.2.11c version too, that the mixing of devel and production caused an experiment in how fitting was done to be the default, so that the reported chi-square doesn't actually match the documentation (instead of summing real and imaginary parts, it sums real and magnitude components of the misfit, which is part of an experiment to see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for another way to report chi-square and misfits is potentially a useful approach, but it's not what is documented. Anyway, mixing devel and production versions like this (for the past couple years, really) is very sloppy on my part, and I apologize again. I actually have an ubuntu box now, though I built pgplot from source, and have never made a .deb file. There is a new source kit at http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll post this to sourceforge this afternoon, and I'll also make a new DLL for Windows and post all of these on the download page. I'll also make a new updater for Windows. --Matt On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi [EMAIL PROTECTED] wrote: Carlo Segre wrote: Hi Mauro: I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository deb http://debian-xray.iit.edu intrepid main contrib non-free Carlo, Thank you very much for the package. Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no HoraeFriends from Bruce SVN. Well, now I have pgplot5, ifeffit, perl-ifeffit and python-ifeffit from binaries and libperlxray horae and demeter built from source (Bruce SVN). Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these IFF str = * output as stated also by Gareth in his Ifeffit 1.2.11b terminal output post. Is it normal? Cheers, Mauro ___ 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 -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498Fax: 312.567.3494 [EMAIL PROTECTED] http://www.iit.edu/~segre [EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
