Morning all, I finally decided to try using Demeter and this morning went to use Athena. Opening my data was all fine but importing the cif file into atoms got me in trouble. Upon selecting the file I got a pop-up saying "Choose a record from this CIF file" however there is nothing listed. If I click OK, the program crashes. This is also reproducible if I run stand-alone ATOMS. I have generated the CIF files from VESTA where I modify the crystal structure manually. This hasn't caused an issue in the past but with Demeter, perhaps there is a header I need to add? Attached is the CIF file I'm trying to use along with the error logs. Also I am using Windows 7 and the previous IFEFFIT is still installed. Thanks for the help and continued development, Andy Korinda Notestein Lab Chemical & Biological Engineering Northwestern University
On Monday, February 20, 2012 09:16:59 AM Andrew Korinda wrote:
Morning all,
I finally decided to try using Demeter and this morning went to use Athena. Opening my data was all fine but importing the cif file into atoms got me in trouble. Upon selecting the file I got a pop-up saying "Choose a record from this CIF file" however there is nothing listed. If I click OK, the program crashes. This is also reproducible if I run stand-alone ATOMS. I have generated the CIF files from VESTA where I modify the crystal structure manually. This hasn't caused an issue in the past but with Demeter, perhaps there is a header I need to add? Attached is the CIF file I'm trying to use along with the error logs. Also I am using Windows 7 and the previous IFEFFIT is still installed.
Hi Andy, I haven't been wanting to ignore your question -- it's just been a particularly busy week so far. I should have a moment to look into your CIF file tomorrow, so hopefully I'll be responding substantively soon. B -- Bruce Ravel ------------------------------------ bravel at bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
On Monday, February 20, 2012 10:16:59 am Andrew Korinda wrote:
I finally decided to try using Demeter and this morning went to use Athena. Opening my data was all fine but importing the cif file into atoms got me in trouble. Upon selecting the file I got a pop-up saying "Choose a record from this CIF file" however there is nothing listed. If I click OK, the program crashes. This is also reproducible if I run stand-alone ATOMS. I have generated the CIF files from VESTA where I modify the crystal structure manually. This hasn't caused an issue in the past but with Demeter, perhaps there is a header I need to add? Attached is the CIF file I'm trying to use along with the error logs. Also I am using Windows 7 and the previous IFEFFIT is still installed.
Hi Andrew, I know that I am grossly overdue in responding to this email. I found the bug that resulted in the record selection dialog being posted with no content. Thanks for that. As far as I can tell, VESTA -- if I got the correct VESTA off of Google -- is a biomolecule visualization program. You edit a moelcule and have it write out coordinates. It seems a little convoluted to write out a large volume unit cell in the P1 space group. To my mind, it would be more straightforward to have VESTA write out cartesian coordinates and drop them in some feff.inp boilerplate. On one hand that is a bit more fussy work. On the other hand, it avoids having to rely upon Demeter's CIF implementation, which relies upon a fairly crappy CIF parser (which was not written by me, I hasten to add!). But anything that works is worth doing, I suppose. Your bug will be fixed in the next release. Sorry again for the long wait -- I really do take all bug reports very seriously. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
Thanks Bruce.
My route certainly hasn't been the most direct but more of a temporary
bridge between two collaborators. I'll look into implementing your
suggestions the next go-round.
Andy K.
On Thu, Mar 22, 2012 at 2:55 PM, Bruce Ravel
On Monday, February 20, 2012 10:16:59 am Andrew Korinda wrote:
I finally decided to try using Demeter and this morning went to use Athena. Opening my data was all fine but importing the cif file into atoms got me in trouble. Upon selecting the file I got a pop-up saying "Choose a record from this CIF file" however there is nothing listed. If I click OK, the program crashes. This is also reproducible if I run stand-alone ATOMS. I have generated the CIF files from VESTA where I modify the crystal structure manually. This hasn't caused an issue in the past but with Demeter, perhaps there is a header I need to add? Attached is the CIF file I'm trying to use along with the error logs. Also I am using Windows 7 and the previous IFEFFIT is still installed.
Hi Andrew,
I know that I am grossly overdue in responding to this email.
I found the bug that resulted in the record selection dialog being posted with no content. Thanks for that.
As far as I can tell, VESTA -- if I got the correct VESTA off of Google -- is a biomolecule visualization program. You edit a moelcule and have it write out coordinates. It seems a little convoluted to write out a large volume unit cell in the P1 space group. To my mind, it would be more straightforward to have VESTA write out cartesian coordinates and drop them in some feff.inp boilerplate.
On one hand that is a bit more fussy work. On the other hand, it avoids having to rely upon Demeter's CIF implementation, which relies upon a fairly crappy CIF parser (which was not written by me, I hasten to add!).
But anything that works is worth doing, I suppose.
Your bug will be fixed in the next release. Sorry again for the long wait -- I really do take all bug reports very seriously.
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (2)
-
Andrew Korinda -
Bruce Ravel