Re: [Ifeffit] Error in Atoms output
Hi Bruce/All, I've recently (before this bug was reported) done some monoclinic analyses; consequently, I'm wondering if this bug impacts all monoclinic CIFs, or only certain cases (and if so, is there any easy way to confirm whether it had an impact?)? I think my data was fine - the path list matched what I was expecting and what has been reported previously - but I'd like to be certain before publishing etc.. Thanks, Ian From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of Bruce Ravel <bra...@bnl.gov> Sent: 27 February 2018 17:07:59 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Error in Atoms output On 02/19/2018 06:23 AM, Kaustubh Priolkar wrote: > We are trying to fit low temperature V K edge EXAFS data in V2O3. As per > the cif files available (attached herewith – V2O3_10K data.cif) the > structure is described by I2/a space group. When this file is read by > ATOMS it gives an erroneous output ( attached herewith - feff.inp). In > particular the values of V-O and V-V bond distances are not correct and > do not match with bond distances reported in literature (Phys. Rev. B 2 > (1970) 3771). > > Could anyone tell me where am I making a mistake. I am aware that I2/a > is a non standard space group but I am not sure if I need to take any > precaution while reading the cif file in ATOMS. > > Thanks and regards, Hi Kaustubh, Thanks for this bug report. This uncovered not one but two bugs in how Atoms handles monoclinic space groups. How economical! I will be pushing a fix to github soon and I will try to find some time to make a new windows installer. I should point out that, even with the bug fix, the distances using the CIF file you attached will not match Phys. Rev. B 2 (1970) 3771. The CIF file that you supplied is from doi:10.1016/S0022-4596(03)00295-0, which reports slightly different numbers for the undoped V2O3 compared to the 1970 paper. I have attached a feff.inp file that I think is correct. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM 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 Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Error in Atoms output
Thanks Bruce. I agree that the paper and the cif file had no relation. I merely wanted to emphasize the point that ATOMS was giving an erroneous output. Cheers, Kaustubh Sent from Mail for Windows 10 From: Bruce Ravel Sent: Tuesday, February 27, 2018 10:54 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Error in Atoms output On 02/19/2018 06:23 AM, Kaustubh Priolkar wrote: > We are trying to fit low temperature V K edge EXAFS data in V2O3. As per > the cif files available (attached herewith – V2O3_10K data.cif) the > structure is described by I2/a space group. When this file is read by > ATOMS it gives an erroneous output ( attached herewith - feff.inp). In > particular the values of V-O and V-V bond distances are not correct and > do not match with bond distances reported in literature (Phys. Rev. B 2 > (1970) 3771). > > Could anyone tell me where am I making a mistake. I am aware that I2/a > is a non standard space group but I am not sure if I need to take any > precaution while reading the cif file in ATOMS. > > Thanks and regards, Hi Kaustubh, Thanks for this bug report. This uncovered not one but two bugs in how Atoms handles monoclinic space groups. How economical! I will be pushing a fix to github soon and I will try to find some time to make a new windows installer. I should point out that, even with the bug fix, the distances using the CIF file you attached will not match Phys. Rev. B 2 (1970) 3771. The CIF file that you supplied is from doi:10.1016/S0022-4596(03)00295-0, which reports slightly different numbers for the undoped V2O3 compared to the 1970 paper. I have attached a feff.inp file that I think is correct. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM 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 Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Error in Atoms output
On 02/19/2018 06:23 AM, Kaustubh Priolkar wrote: We are trying to fit low temperature V K edge EXAFS data in V2O3. As per the cif files available (attached herewith – V2O3_10K data.cif) the structure is described by I2/a space group. When this file is read by ATOMS it gives an erroneous output ( attached herewith - feff.inp). In particular the values of V-O and V-V bond distances are not correct and do not match with bond distances reported in literature (Phys. Rev. B 2 (1970) 3771). Could anyone tell me where am I making a mistake. I am aware that I2/a is a non standard space group but I am not sure if I need to take any precaution while reading the cif file in ATOMS. Thanks and regards, Hi Kaustubh, Thanks for this bug report. This uncovered not one but two bugs in how Atoms handles monoclinic space groups. How economical! I will be pushing a fix to github soon and I will try to find some time to make a new windows installer. I should point out that, even with the bug fix, the distances using the CIF file you attached will not match Phys. Rev. B 2 (1970) 3771. The CIF file that you supplied is from doi:10.1016/S0022-4596(03)00295-0, which reports slightly different numbers for the undoped V2O3 compared to the 1970 paper. I have attached a feff.inp file that I think is correct. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ V2O3_feff.inp Description: chemical/gamess-input ___ 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
