Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit
Dear Dr. Robert Thanks a lot for your information that's very helpful. I checked the ICSD, but unfortunately we don't have access to the crystal data. It would be great, if you or someone has the access to the crystal data to provide me the coordinates, the *collection code: 202727, Author: Post, Year: 1988. * *Please let me know, if someone has the access to the data.* Regards Sathish On Thu, Feb 6, 2014 at 11:05 PM, ifeffit-requ...@millenia.cars.aps.anl.govwrote: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. Re: Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis (Robert Gordon) -- Message: 1 Date: Thu, 06 Feb 2014 16:05:30 -0600 From: Robert Gordon ragor...@alumni.sfu.ca To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis Message-ID: 52f4072a.1070...@alumni.sfu.ca Content-Type: text/plain; charset=iso-8859-1; Format=flowed Hi Satty, The crystal data in your inp file came from the paper. I checked the International Crystal Structure Database (ICSD) - printout attached. The structure data in the paper are not in standard form - atoms might not give the correct results if the input is bad- and there are typos for two of the O5 coordinates according to the ICSD warning. Does your institution have access to the ICSD - Online or on disc? If you are not familiar with it, try talking to one of your institution's reference librarians. I'm not certain what you mean by the corner-corner Mn. You were choosing Mn1 as the core in your inp. When I look at the structure, Mn1 sits in the middle of the set of 3 octahedra that make up a side of the tunnel. Where would the corner-corner distance be relative to the middle of the chain? You have 4 different Mn sites. Fitting in R-space is common. As for learning about crystal structures, try sitting in on a coordination chemistry or solid state chemistry course. For a basic learning book, I like West's Basic Solid State Chemistry or Muller's Inorganic Structural Chemistry (again, try the library if you don't want to buy a copy). More recent books may be available. A bit of googling may reveal some online lessons, like: http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html regards, Robert On 2/6/2014 3:16 AM, Sathish Mayanna wrote: Hi I am having some problem to get the real crystallographic parameters for Todorokite (I know there are many literature available) I used the parameters from Post et al 1988 (/Rietveld refinement of the Todorokite structure/) and others as well (*attached Todorokite.inp file*). I except the corner corner Mn in Todorokite, since its a tunnel structure, but the Feff calculations do not provide any corner corner Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn. But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is also a tunnel structure, I could get the Corner-Corner Mn and can fit perfectly the Mn-O, Mn-Mn, but cannot fit in K space. It would be really great, if anyone could provide me the model Tunnel type-Mn oxide crystallographic parameters to fit the data *(attached Mn Spectra.prj)* p.s: I tried my best to learn and understand the crystallographic parameters and miller indices, but still I feel that I am very poor, it would be nice, if someone suggest some good and basic source to learn more about pure mineralogy (which is crucial to know the basic parameters for fitting in Artemis). -- Satty ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140206/b269b2f3/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: todorokite.pdf Type: application/pdf Size: 30762 bytes Desc: not available URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140206/b269b2f3/attachment.pdf
Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fit
Was there no attachment to my earlier response? I printed out the ICSD page with the correct parameters and attached it as a pdf. My outgoing message indicates the attachment is there. -R. On 2/9/2014 7:40 AM, Sathish Mayanna wrote: Dear Dr. Robert Thanks a lot for your information that's very helpful. I checked the ICSD, but unfortunately we don't have access to the crystal data. It would be great, if you or someone has the access to the crystal data to provide me the coordinates, the *collection code: 202727, Author: Post, Year: 1988. * * * *Please let me know, if someone has the access to the data.* * * Regards Sathish * * ** On Thu, Feb 6, 2014 at 11:05 PM, ifeffit-requ...@millenia.cars.aps.anl.gov mailto:ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov mailto:ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov mailto:ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov mailto:ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. Re: Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis (Robert Gordon) -- Message: 1 Date: Thu, 06 Feb 2014 16:05:30 -0600 From: Robert Gordon ragor...@alumni.sfu.ca mailto:ragor...@alumni.sfu.ca To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov mailto:ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis Message-ID: 52f4072a.1070...@alumni.sfu.ca mailto:52f4072a.1070...@alumni.sfu.ca Content-Type: text/plain; charset=iso-8859-1; Format=flowed Hi Satty, The crystal data in your inp file came from the paper. I checked the International Crystal Structure Database (ICSD) - printout attached. The structure data in the paper are not in standard form - atoms might not give the correct results if the input is bad- and there are typos for two of the O5 coordinates according to the ICSD warning. Does your institution have access to the ICSD - Online or on disc? If you are not familiar with it, try talking to one of your institution's reference librarians. I'm not certain what you mean by the corner-corner Mn. You were choosing Mn1 as the core in your inp. When I look at the structure, Mn1 sits in the middle of the set of 3 octahedra that make up a side of the tunnel. Where would the corner-corner distance be relative to the middle of the chain? You have 4 different Mn sites. Fitting in R-space is common. As for learning about crystal structures, try sitting in on a coordination chemistry or solid state chemistry course. For a basic learning book, I like West's Basic Solid State Chemistry or Muller's Inorganic Structural Chemistry (again, try the library if you don't want to buy a copy). More recent books may be available. A bit of googling may reveal some online lessons, like: http://www.seas.upenn.edu/~chem101/sschem/solidstatechem.html http://www.seas.upenn.edu/%7Echem101/sschem/solidstatechem.html regards, Robert On 2/6/2014 3:16 AM, Sathish Mayanna wrote: Hi I am having some problem to get the real crystallographic parameters for Todorokite (I know there are many literature available) I used the parameters from Post et al 1988 (/Rietveld refinement of the Todorokite structure/) and others as well (*attached Todorokite.inp file*). I except the corner corner Mn in Todorokite, since its a tunnel structure, but the Feff calculations do not provide any corner corner Mn, in addition I cannot fit exactly even Mn-O or Mn-Mn. But If I use Ramsdellite (*attached Ramsdellite.inp file*), which is also a tunnel structure, I could get the Corner-Corner Mn and can fit perfectly the Mn-O, Mn-Mn, but cannot fit in K space. It would be really great, if anyone could provide me the model Tunnel type-Mn oxide crystallographic parameters to fit the data *(attached Mn Spectra.prj)* p.s: I tried my best to learn and understand the crystallographic parameters and miller indices, but still I feel that I am very poor, it would be nice, if someone suggest some good and basic source to learn more about pure mineralogy (which is
