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
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
-- Bruce Ravel ------------------------------------ bravel@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/