RE: on high pressure data indexing and unit cell reduction
?hello everyone - thank you so much to those who have helped me thus far. I'm replying just to say that I sorted through the results from GSAS II this morning and I don't believe it was able to index this cell! since I failed to do so the first time, I am including the unit cell parameters I was working with from topas for those curious (p2 space group): a, b, c = 21.95 x 8.49 x 14.45, alpha, beta, gamma = 90, 142.1, 90 volume = 1655 a, b, c = 13.78 x 8.49 x 14.47, alpha, beta, gamma = 90, 78.0, 90 volume = 1657? I will be looking into all suggestions and seeing what I can do. Thank you again to everyone! From: rietveld_l-requ...@ill.fr rietveld_l-requ...@ill.fr on behalf of Leonid Solovyov l_solov...@yahoo.com Sent: Tuesday, March 04, 2014 1:49 AM To: rietveld_l@ill.fr Subject: Re: on high pressure data indexing and unit cell reduction Unit cell standardization may be done in VESTA http://jp-minerals.org/vesta Load a CIF to VESTA and go to Utilities-Standardization of Crystal Data then File-Export Data *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660036, Akademgorodok 50/24, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** On Tuesday, March 4, 2014 3:56 AM, Young, Lindsay lindsay.yo...@rockets.utoledo.edu wrote: Hello all - I've gotten stuck at a point in my data refinement, I'd appreciate it if someone has any suggestions for me. I have been trying to index high pressure data. It was collected using a diamond anvil cell with a 2d detector. I integrated the data on GSAS II, using the penetration correction. I opened this data on Jade to do peak fitting, and indexed the resulting peak list in Topas. I managed to get a reasonable monoclinic cell - but it is not in standard cell notation - the angle for beta is 142 degrees, and I would like see this cell represented such that is between 90 and 130 degrees. I tried indexing this peak list in Treor and Dicvol, with no results. I then tried putting the unit cell from Topas into hklgen, taking the peaks it generated (which do match those in the pattern), and indexing them with Treor and Dicvol, but neither program turns out any results. I did tweak the standard settings of both programs to try to get results, but this was not successful. The idea is, if we can get the same result in another program as we did in Topas, it could further show that the result is correct. Does anyone know how I can convert this cell? Is there a unit cell reduction program I could use? If you need any additional information please let me know! ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.commailto:alan.he...@neutronoptics.com Send commands to lists...@ill.frmailto:lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++ ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: on high pressure data indexing and unit cell reduction
In some regards I believe a true check of a cell form indexing is a pawley or lebail fit. If such a fit is good enough (i.e. fits all the peaks of interest and does not have too many extra unobserved peaks and yes I know this is kind of a subjective criterion), I would call the indexing a preliminary success (hopefully later confirmed by a structure solution and refinement, or some other sanity check). Goodness of fit measures from an indexing program can only tell one so much. Saul Lapidus On Mon, Mar 3, 2014 at 2:55 PM, Young, Lindsay lindsay.yo...@rockets.utoledo.edu wrote: Hello all - I've gotten stuck at a point in my data refinement, I'd appreciate it if someone has any suggestions for me. I have been trying to index high pressure data. It was collected using a diamond anvil cell with a 2d detector. I integrated the data on GSAS II, using the penetration correction. I opened this data on Jade to do peak fitting, and indexed the resulting peak list in Topas. I managed to get a reasonable monoclinic cell - but it is not in standard cell notation - the angle for beta is 142 degrees, and I would like see this cell represented such that is between 90 and 130 degrees. I tried indexing this peak list in Treor and Dicvol, with no results. I then tried putting the unit cell from Topas into hklgen, taking the peaks it generated (which do match those in the pattern), and indexing them with Treor and Dicvol, but neither program turns out any results. I did tweak the standard settings of both programs to try to get results, but this was not successful. The idea is, if we can get the same result in another program as we did in Topas, it could further show that the result is correct. Does anyone know how I can convert this cell? Is there a unit cell reduction program I could use? If you need any additional information please let me know! ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++ ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
on high pressure data indexing and unit cell reduction
Hello all - I've gotten stuck at a point in my data refinement, I'd appreciate it if someone has any suggestions for me. I have been trying to index high pressure data. It was collected using a diamond anvil cell with a 2d detector. I integrated the data on GSAS II, using the penetration correction. I opened this data on Jade to do peak fitting, and indexed the resulting peak list in Topas. I managed to get a reasonable monoclinic cell - but it is not in standard cell notation - the angle for beta is 142 degrees, and I would like see this cell represented such that is between 90 and 130 degrees. I tried indexing this peak list in Treor and Dicvol, with no results. I then tried putting the unit cell from Topas into hklgen, taking the peaks it generated (which do match those in the pattern), and indexing them with Treor and Dicvol, but neither program turns out any results. I did tweak the standard settings of both programs to try to get results, but this was not successful. The idea is, if we can get the same result in another program as we did in Topas, it could further show that the result is correct. Does anyone know how I can convert this cell? Is there a unit cell reduction program I could use? If you need any additional information please let me know! ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: on high pressure data indexing and unit cell reduction
Hi, I really enjoy your arguing ... The cell got by Topas is correct and the other programs fail to support this idea. Try ITO ... if you have at least 20 peaks. Back to real life where gems do not rule. To check a cell I can only recommend a standalone program nicknamed LePage, which is really good. A good trick I frequently use is to take any working input to Platon in any format, edit the cell and run it with Calc all. Of course, you will get a lot of rubbish, but at the very beginning there's also a good cell analysis. A hint : if you have troubles with a cell, why not to post it :-) ? Happy indexing, lubo On Mon, 3 Mar 2014, Young, Lindsay wrote: Hello all - I've gotten stuck at a point in my data refinement, I'd appreciate it if someone has any suggestions for me. I have been trying to index high pressure data. It was collected using a diamond anvil cell with a 2d detector. I integrated the data on GSAS II, using the penetration correction. I opened this data on Jade to do peak fitting, and indexed the resulting peak list in Topas. I managed to get a reasonable monoclinic cell - but it is not in standard cell notation - the angle for beta is 142 degrees, and I would like see this cell represented such that is between 90 and 130 degrees. I tried indexing this peak list in Treor and Dicvol, with no results. I then tried putting the unit cell from Topas into hklgen, taking the peaks it generated (which do match those in the pattern), and indexing them with Treor and Dicvol, but neither program turns out any results. I did tweak the standard settings of both programs to try to get results, but this was not successful. The idea is, if we can get the same result in another program as we did in Topas, it could further show that the result is correct. Does anyone know how I can convert this cell? Is there a unit cell reduction program I could use? If you need any additional information please let me know! ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: on high pressure data indexing and unit cell reduction
Cell conversion may be done with the programs provided by Bilbao Crystallography Server (http://www.cryst.ehu.es/). Consider using the programs: GENPOS and CELLTRAN. On 03/03/2014 05:55 PM, Young, Lindsay wrote: Hello all - I've gotten stuck at a point in my data refinement, I'd appreciate it if someone has any suggestions for me. I have been trying to index high pressure data. It was collected using a diamond anvil cell with a 2d detector. I integrated the data on GSAS II, using the penetration correction. I opened this data on Jade to do peak fitting, and indexed the resulting peak list in Topas. I managed to get a reasonable monoclinic cell - but it is not in standard cell notation - the angle for beta is 142 degrees, and I would like see this cell represented such that is between 90 and 130 degrees. I tried indexing this peak list in Treor and Dicvol, with no results. I then tried putting the unit cell from Topas into hklgen, taking the peaks it generated (which do match those in the pattern), and indexing them with Treor and Dicvol, but neither program turns out any results. I did tweak the standard settings of both programs to try to get results, but this was not successful. The idea is, if we can get the same result in another program as we did in Topas, it could further show that the result is correct. Does anyone know how I can convert this cell? Is there a unit cell reduction program I could use? If you need any additional information please let me know! ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: on high pressure data indexing and unit cell reduction
Unit cell standardization may be done in VESTA http://jp-minerals.org/vesta Load a CIF to VESTA and go to Utilities-Standardization of Crystal Data then File-Export Data *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660036, Akademgorodok 50/24, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** On Tuesday, March 4, 2014 3:56 AM, Young, Lindsay lindsay.yo...@rockets.utoledo.edu wrote: Hello all - I've gotten stuck at a point in my data refinement, I'd appreciate it if someone has any suggestions for me. I have been trying to index high pressure data. It was collected using a diamond anvil cell with a 2d detector. I integrated the data on GSAS II, using the penetration correction. I opened this data on Jade to do peak fitting, and indexed the resulting peak list in Topas. I managed to get a reasonable monoclinic cell - but it is not in standard cell notation - the angle for beta is 142 degrees, and I would like see this cell represented such that is between 90 and 130 degrees. I tried indexing this peak list in Treor and Dicvol, with no results. I then tried putting the unit cell from Topas into hklgen, taking the peaks it generated (which do match those in the pattern), and indexing them with Treor and Dicvol, but neither program turns out any results. I did tweak the standard settings of both programs to try to get results, but this was not successful. The idea is, if we can get the same result in another program as we did in Topas, it could further show that the result is correct. Does anyone know how I can convert this cell? Is there a unit cell reduction program I could use? If you need any additional information please let me know! ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
