[Wien] Determine primitive cell and positions, CXZ LATTICE 15_B2/b

[Laurence Marks]

A slightly tangential comment: unless your CIF came from a neutron
diffraction analysis the H positions can be very wrong. Many refinement
codes such as Shelx are very good, but just put H into "reasonable"
positions as they are unstable in the refinements with XRD data.

In principle the CIF file should have information about how the H positions
were determined.

___________________________
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
On Mar 20, 2015 6:56 AM, "Peter Blaha" <pblaha at theochem.tuwien.ac.at> wrote:
>
> Of course, for "better" positions it will be easier, but you would still
> run into the same problems with the default inputs.
>
> The problem with ghostbands is either connected with
> i) a WRONG case.struct file (not in your case)  or
> ii) ALWAYS connected with the VERY SMALL spheres (for atoms like C,N,O
> or in your case P and O)  AND the s- (l=0) states of these atoms.
>
> Typically the 3s (2s) state of P or O (or C,N) is lower in energy than
> the actual valence states and for a BIG sphere it is therefore necessary
> (more accurate) to describe these states with an additional LO and 2
> lines in case.in1 like:
>
>   0   -1.55      0.002 CONT 1
>   0    0.30      0.000 CONT 1
>
> For SMALL spheres, however, this leads to ghostbands and the case.scf2
> file indicates for you for which atom and l it happens (atom 3 for l=0).
>
> Thus you have to edit case.in1 and either set the "second" energy very
> high (O):
>
>   0   -1.55      0.002 CONT 1
>   0    5.30      0.000 CONT 1
>
> or even remove the second line (and change the number of "exceptions" in
> the line above from 3 to 2 (P-atom):
>
>    0.30    2  0      (GLOBAL E-PARAMETER WITH n OTHER CHOICES,
>   0   -1.79      0.002 CONT 1
>   1    0.30      0.000 CONT 1
>
> Then do a "crude":
>
> run (-p) -fc 10
>
> and you see enormous forces on many atoms (in particular H, because
> their distance is VERY wrong, leading to these extremely small H and O
> radii).
>
> run -p -min -fc 1
>
> optimizes the positions seamlessly. I've stopped this at a very early
> stage, but the struct file is attached.
>
> With this struct file I would rerun setrmt again, because the much more
> realistic O-H distances allow now for larger H and O spheres making the
> calculations MUCH faster. Then continue with the position optimization.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20150320/2821184e/attachment.html>