[Ifeffit] Correct Crystallographic parameters for Todorokite EXAFS fitting in Artemis

Robert Gordon ragordon at alumni.sfu.ca
Thu Feb 6 16:05:30 CST 2014

Hi Satty,

The crystal data in your inp file came from the paper. I checked the 
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 

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:


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 at millenia.cars.aps.anl.gov
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Dr. Robert Gordon
Staff Scientist, PNCSRF
APS Sector 20 (PNC/XSD)
9700 S Cass Ave. 435E
Argonne, IL, USA  60439

630-252-0580 fax

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