Thank you Chris for the suggestion. The occupancies are 1 for each given atom. I tried to read the .cif file with ‘from pymatgen.io.cif import CifParser’ module and it works without any issues. ‘ parser = CifParser(cif_file) structure = parser.get_structures()[0] ‘ Thanks, Anis From: Christopher Patridge via Ifeffit Sent: November 14, 2024 10:54 AM To: XAFS Analysis using Ifeffit Cc: Christopher Patridge Subject: [Ifeffit] Re: Generating feff.inp from .cif file issues I think full occupancies might be the problem. Chris ********************************************* Dr. Chris Patridge Associate Professor of Chemistry Faculty Senate President SASE 314 D’Youville University 320 Porter Ave Buffalo, NY 14201 716-829-8124 ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd I think full occupancies might be the problem. Chris ********************************************* Dr. Chris Patridge Associate Professor of Chemistry Faculty Senate President SASE 314 D’Youville University 320 Porter Ave Buffalo, NY 14201 716-829-8124 patridgc@dyc.edumailto:patridgc@dyc.edu On Nov 14, 2024, at 1:32 PM, Anis Attiaoui via Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov> wrote:  Dear Ifeffit Community, I am struggling to generate the feff. inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch. xrd. cif2feff import cif2feffinp and from larch. xrd. structure2feff ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Dear Ifeffit Community, I am struggling to generate the feff.inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch.xrd.cif2feff import cif2feffinp and from larch.xrd.structure2feff import structure2feffinp. For some reason both of them, they cannot seem to read the cif cluster file (attached). The snippet of the code I am using is : inp_file = cif2feffinp(cif_file, 'Sn', edge='K', absorber_site=1, version8=False) I am trying to generating inp_file using feff6. I keep getting the error output of inp_file: “# could not read CIF file”. I am wondering if this is because the .cif file is bad or there is sthg else going on. Any suggestions will be tremendously helpful. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!fs... https://urldefense.us/v3/__https:/mcintyre.stanford.edu/__;!!G_uCfscf7eWS!ak... ifeffit mailing list: https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists/... https://urldefense.us/v3/__https:/millenia.cars.aps.anl.gov/mailman3/lists/i... to unsubscribe, send mail to ifeffit-leave@millenia.cars.aps.anl.govmailto:ifeffit-leave@millenia.cars.aps.anl.gov

Thank you, Matt. I did try to pip install larixite but it doesn’t seem to work for some reason. So I tried to directly build it after downloading the app. Still It seems not to be working. Below is the output. Sorry for this inconvenience. A. With pip install larixite [cid:image001.png@01DB3696.C979D240] [cid:image002.png@01DB3696.B495C4B0] From: Matt Newville Sent: November 14, 2024 12:50 PM To: XAFS Analysis using Ifeffit Cc: Anis Attiaoui Subject: Re: [Ifeffit] Generating feff.inp from .cif file issues Hi Anis, I think we fixed a few problems that might apply here for larixite. This CIF file should work if you upload it to https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite/__;!!G... When I do this, it seems like it works fine. See: https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite/cifs/G... We intend that xraylarch will use this newer code soon. On Thu, Nov 14, 2024 at 12:32 PM Anis Attiaoui via Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov> wrote: Dear Ifeffit Community, I am struggling to generate the feff. inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch. xrd. cif2feff import cif2feffinp and from larch. xrd. structure2feff ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Dear Ifeffit Community, I am struggling to generate the feff.inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch.xrd.cif2feff import cif2feffinp and from larch.xrd.structure2feff import structure2feffinp. For some reason both of them, they cannot seem to read the cif cluster file (attached). The snippet of the code I am using is : inp_file = cif2feffinp(cif_file, 'Sn', edge='K', absorber_site=1, version8=False) I am trying to generating inp_file using feff6. I keep getting the error output of inp_file: “# could not read CIF file”. I am wondering if this is because the .cif file is bad or there is sthg else going on. Any suggestions will be tremendously helpful. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!dO... https://urldefense.us/v3/__https:/mcintyre.stanford.edu/__;!!G_uCfscf7eWS!ak... ifeffit mailing list: https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists/... to unsubscribe, send mail to ifeffit-leave@millenia.cars.aps.anl.govmailto:ifeffit-leave@millenia.cars.aps.anl.gov -- --Matt Newville https://urldefense.us/v3/__http://cars.uchicago.edu__;!!G_uCfscf7eWS!dOIUJ_g... >> 630-327-7411

No I do not. But I circumvented the python compatibility of Larixite, and now it works fine. I am using python 3.8 and Larixite is compatible with >3.9. That was the issue. Now I can generate the .inp file from .cif using Larixite. Thank you all for your help. A. Get Outlook for Android<https://urldefense.us/v3/__https://aka.ms/AAb9ysg__;!!G_uCfscf7eWS!ZKbPjZJDx... > ________________________________ From: Robert Gordon via Ifeffit Sent: Thursday, November 14, 2024 3:22:58 PM To: ifeffit@millenia.cars.aps.anl.gov Cc: Robert Gordon Subject: [Ifeffit] Re: Generating feff.inp from .cif file issues Hi Anis, Do you have the Demeter package (predecessor to Larch) installed? The stand-alone atoms version there can read your cif file and outputs the attached feff. inp. -R. On 2024-11-14 1: 12 p. m. , Anis Attiaoui via Ifeffit wrote: Thank you, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hi Anis, Do you have the Demeter package (predecessor to Larch) installed? The stand-alone atoms version there can read your cif file and outputs the attached feff.inp. -R. On 2024-11-14 1:12 p.m., Anis Attiaoui via Ifeffit wrote: Thank you, Matt. I did try to pip install larixite but it doesn’t seem to work for some reason. So I tried to directly build it after downloading the app. Still It seems not to be working. Below is the output. Sorry for this inconvenience. A.  ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Thank you, Matt. I did try to pip install larixite but it doesn’t seem to work for some reason. So I tried to directly build it after downloading the app. Still It seems not to be working. Below is the output. Sorry for this inconvenience. A. With pip install larixite [cid:part1.VYsquTLg.1OaytLFM@gmail.com] [cid:part2.BuWrhhjX.RNDoV9tc@gmail.com] From: Matt Newville mailto:newville@cars.uchicago.edu Sent: November 14, 2024 12:50 PM To: XAFS Analysis using Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov Cc: Anis Attiaoui mailto:anatt@stanford.edu Subject: Re: [Ifeffit] Generating feff.inp from .cif file issues Hi Anis, I think we fixed a few problems that might apply here for larixite. This CIF file should work if you upload it to https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite/__;!!G... https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite/__;!!G... When I do this, it seems like it works fine. See: https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite/cifs/G... https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite/cifs/G... We intend that xraylarch will use this newer code soon. On Thu, Nov 14, 2024 at 12:32 PM Anis Attiaoui via Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov> wrote: Dear Ifeffit Community, I am struggling to generate the feff. inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch. xrd. cif2feff import cif2feffinp and from larch. xrd. structure2feff ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Dear Ifeffit Community, I am struggling to generate the feff.inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch.xrd.cif2feff import cif2feffinp and from larch.xrd.structure2feff import structure2feffinp. For some reason both of them, they cannot seem to read the cif cluster file (attached). The snippet of the code I am using is : inp_file = cif2feffinp(cif_file, 'Sn', edge='K', absorber_site=1, version8=False) I am trying to generating inp_file using feff6. I keep getting the error output of inp_file: “# could not read CIF file”. I am wondering if this is because the .cif file is bad or there is sthg else going on. Any suggestions will be tremendously helpful. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!ZK... https://urldefense.us/v3/__https:/mcintyre.stanford.edu/__;!!G_uCfscf7eWS!ak... ifeffit mailing list: https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists/... https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists/... to unsubscribe, send mail to ifeffit-leave@millenia.cars.aps.anl.govmailto:ifeffit-leave@millenia.cars.aps.anl.gov -- --Matt Newville https://urldefense.us/v3/__http://cars.uchicago.edu__;!!G_uCfscf7eWS!dOIUJ_g...> 630-327-7411 ifeffit mailing list: https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists/... https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists/... to unsubscribe, send mail to ifeffit-leave@millenia.cars.aps.anl.govmailto:ifeffit-leave@millenia.cars.aps.anl.gov