ATOMS for XANES simulation by FEFF8.4
Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/
Dear all, After reading again the FEFF8.4 Manual, I decided that using WebATOMS is a good option. If you have another suggestion, please let me know. Best regards María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/ 2015-09-12 17:52 GMT-06:00 María Elena Montero Cabrera < elena.montero@cimav.edu.mx>:
Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance
María Elena
Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/
Hello Maria, You can use the stand-alone Atoms application included in demeter to prepare feff8 input files from crystallographic data, in the application under the "atoms" tab there is a button called "export" and then you can select feff8 as an output format. You should be able to do the same thing with webatoms in your browser and get a similar result. In either case for a XANES calculation you will probably edit the input file manually afterwards to set the desired input parameters for the calculation. I believe that EXAFS fitting in Artemis can only be done with feff6 which is included in demeter so you probably need to prepare a separate input file for that without any input cards specific to later versions of feff. Best wishes, Johan ________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of María Elena Montero Cabrera [elena.montero@cimav.edu.mx] Sent: 13 September 2015 01:52 To: XAFS Analysis using Ifeffit Subject: [Ifeffit] ATOMS for XANES simulation by FEFF8.4 Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/
Thank you very much, Johan.
I have another question, probably for Bruce:
In the latest version of Artemis (before the release of Demeter) it was
possible to edit preferences for running FEFF. I mean, when I acquired the
FEFF version 8.4, I could tell Artemis to run this FEFF, instead of FEFF6.
In the current version of Artemis may be it is, but I didn't find this
possibility. Would somebody advice me in this task?
Thanking in advance
Maria Elena
María Elena
Dra. María Elena Montero Cabrera
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua
Chihuahua CP 31136, Chih. México
Tel (614) 4391123
http://redtuls.org/
2015-09-15 10:26 GMT-06:00 Johan Nilsson
Hello Maria,
You can use the stand-alone Atoms application included in demeter to prepare feff8 input files from crystallographic data, in the application under the "atoms" tab there is a button called "export" and then you can select feff8 as an output format. You should be able to do the same thing with webatoms in your browser and get a similar result. In either case for a XANES calculation you will probably edit the input file manually afterwards to set the desired input parameters for the calculation.
I believe that EXAFS fitting in Artemis can only be done with feff6 which is included in demeter so you probably need to prepare a separate input file for that without any input cards specific to later versions of feff.
Best wishes, Johan
------------------------------ *From:* ifeffit-bounces@millenia.cars.aps.anl.gov [ ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of María Elena Montero Cabrera [elena.montero@cimav.edu.mx] *Sent:* 13 September 2015 01:52 *To:* XAFS Analysis using Ifeffit *Subject:* [Ifeffit] ATOMS for XANES simulation by FEFF8.4
Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance
María Elena
Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/
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On 09/16/2015 11:20 AM, María Elena Montero Cabrera wrote:
In the latest version of Artemis (before the release of Demeter) it was possible to edit preferences for running FEFF. I mean, when I acquired the FEFF version 8.4, I could tell Artemis to run this FEFF, instead of FEFF6. In the current version of Artemis may be it is, but I didn't find this possibility. Would somebody advice me in this task?
Feff8 is poorly supported in the current version of Artemis. That said, this has been discussed many times on the mailing list and can be found in the archives. I am working towards transitioning Artemis to use feff85exafs (https://github.com/xraypy/feff85exafs), but that will take a few months. This is relevant to the feff6/feff8 discussion: http://bruceravel.github.io/SCFtests/scf.html B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Thank you, Bruce. No problems, I can wait.
Regards
Maria Elena
María Elena
Dra. María Elena Montero Cabrera
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua
Chihuahua CP 31136, Chih. México
Tel (614) 4391123
http://redtuls.org/
2015-09-16 9:33 GMT-06:00 Bruce Ravel
On 09/16/2015 11:20 AM, María Elena Montero Cabrera wrote:
In the latest version of Artemis (before the release of Demeter) it was possible to edit preferences for running FEFF. I mean, when I acquired the FEFF version 8.4, I could tell Artemis to run this FEFF, instead of FEFF6. In the current version of Artemis may be it is, but I didn't find this possibility. Would somebody advice me in this task?
Feff8 is poorly supported in the current version of Artemis. That said, this has been discussed many times on the mailing list and can be found in the archives.
I am working towards transitioning Artemis to use feff85exafs ( https://github.com/xraypy/feff85exafs), but that will take a few months.
This is relevant to the feff6/feff8 discussion: http://bruceravel.github.io/SCFtests/scf.html
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
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participants (3)
-
Bruce Ravel -
Johan Nilsson -
María Elena Montero Cabrera