[Ifeffit] Artemis - Atom/Feff issues

[Bruce Ravel]

Hi Marcus,

Your cif file is confusing to me in several ways.  It will also be 
confusing to the tool in Demeter that interprets crystal data.

Firstly, your space group is tetragonal (P -4 21 m), but you have a=b=c 
and alpha=beta=gamma.  That's not exactly wrong, per se, but it is an 
unusual way of expressing the dimensions of your unit cell.

You lattice constants are surprising and problematic.  You have a=b=c=1. 
  1 Angstrom is a highly unusual lattice constant and almost certainly 
not what you want.  At least, not what you want when interacting with 
Demeter.

Most problematically, your positions in the unit cell are expressed in 
numbers that suggest Angstrom units rather than fractional position in 
the unit cell.  Perhaps this point is not made clearly enough in the 
document, but Demeter expects that atom positions are in fractional units.

For example, germanium is diamond structure, space group Fd3m, a=5.658. 
The position of the Ge atom is (0.125,0.125,0.125).  The position is 
!NOT! (0.70725,0.70725,0.70725).

When Demeter finds a position less than 0 or greater than 1, it moves 
that position back into the first unit cell in the upper, right 
quadrant.  So, when it sees a position like (2.69220, 1.31120, 2.64190), 
which is your La position, it moves that to (0.69220, 0.31120, 0.64190). 
  That behavior makes a lot of sense when working with fractional 
coordinates, but is clearly problematic given that your cif file has 
weird lattice constants and (I think) Cartesian coordinates for the 
atoms positions.

It's very hard for me to know how best to advise you because I don't 
really know what what you are trying to do.  Perhaps you are using 
Mercury or some other tool to generate a cluster of Cartesian 
coordinates.  That's fine.  In that case, you want to convert that 
cluster to a feff.inp file and skip the Atoms page entirely.  See, for 
instance:

https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples?slide=9



Executive summary: you seem to be trying to do something differently 
from how Demeter actually works.  Think about fitting your work flow to 
what Demeter does rather than the other way around.


B



On 07/18/2016 12:59 PM, M.F.Bertuzzo wrote:
> Dear all,
>
>
> Having a spot of trouble with Feff calculations at the moment, any help
> would be much appreciated.
>
>
> A little info before I describe the problem:
>
>
> I have performed Crystal14 calculations on a system to optimise its
> geometry. After completing this, I opened the output file in J-Ice so
> that I could then save the file in .pdb format, so I could then open it
> inside of Mercury (v3.8) which would then allow me to save the file as a
> .CIF, to be used for Feff a calculation in Artemis. All okay so far.
>
>
> But, when I open the CIF file inside of Artemis it thinks that some of
> the atoms sit only 0.02Angstroms apart from one another - obviously
> wrong. Yet when the file is viewed in Mercury (or whatever graphical
> interface you wish to use) it correctly displays the atoms, as opposed
> to Artemis which is somehow populating 500+ atoms within a small
> distance of just 5 Angstroms.
>
> Is this something to do with the Cluster size? I have tried to
> arbitrarily increase it to a higher number to prevent it from finding
> atoms just 0.02Angstroms apart, but even then it locates atoms
> 0.14Angstroms apart which is still wrong.
>
>
> I have attached the structure (in .XYZ format) I am trying to work on so
> you can view it as well as its CIF format that I have been trying to
> open up inside of Artemis to run Feff.
>
>
>
> Thanks for any assistance!
>
>
> Marcus
>
> Postgraduate Researcher in Chemistry
> University of Kent
>
>
>
>
>
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-- 
  Bruce Ravel  ------------------------------------ bravel at 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/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/