#159 Wien2k + vibrations

[Laurence Marks]

Can you please provide a reader for Wien2k DFT files www.wien2k.at (I can provide format info etc). Also, can you provide information on how to input vibrational modes; I am writing an interface for these so can produce a file in the "appropriate" format, if someone tells me what!

[Bob Hanson]

Glad to hear hydroxy.struct has the gap. That was what I was worried about. There are still a few general issues I know we need to consider, but yes, I think we can say we have a Wien2k reader. Happy day! I hope you enjoy it. I'd like to close this feature request.

Vibrations -- I'd be very interested in discussing this. Right now you can read vibrations independently from a file. Vibrations are a "settable" quantity, meaning that you can create them on the fly using a script:

{atomno=3}.vxyz = {1/2 0 0}

note the factional coordinates here. So really the "file" that would be read would simply be a Jmol script file. Since you apparently have no specific file format for these vibrations, why not simply put them out in this format? You have to be a little careful, because "atomno=3" might mean more than one atom when more than one model is loaded.

Or you could create a "data" file, read it using the file() function:

mydata = file("datafile.txt")

and have it be a list of the three vector quantities for all atoms loaded.
and then manipulate that file as desired to create the vibrations.

I would say the thing to do would be to try that and see how it goes, then consider working with an official specification. One thing I am loath to do is to create readers for ad hoc data types that really aren't anybody's standard.

Symmetry and vibrations. Now there's an interesting thought. I wonder how that works. A single point can be generated by several different operations, but these in general would transform a vector (a pair of points) differently. So while the same point can come from two different symmetry operations, transformation of a vector by the same two operations might produce different results.

Bob

[Bob Hanson]

by the way, the latest version allows

load andalusite.struct {1 1 1} spacegroup "none"

meaning "load the "MULT" atoms and disregard the symmetry matrices.

This might be handy for testing.

[Laurence Marks]

I was buried in some other things. I tried reading in the vibrations as you mentioned, but it does not look like they are implemented in anything except the xyz mode although I may be wrong. Are they available in other modes?

Symmetry and vibrations get complicated. In general one needs to reduce down to P1 symmetry or produce structures without the symmetry elements broken by the vibration; I think this would get too complicated to do within Jmol in the general case and should be left to the code which produces the input.

[Bob Hanson]

One of the interesting things you can do in Jmol is refer to coordinates (and vectors) in terms of fractional coordinates. For example:

x = {1/2 1/2 1/2}

is interpreted correctly based on the current file loaded. It's the "/" sign there that flags this. The latest incarnation of Jmol, 11.7.37 also allows for coordinates to be expressed in decimal, followed by ".xyz"

x = {0.5 0.5 0.5}.xyz

but really that could just be:

x = {0.5 0.5 0.5/1}

because just one "/" in a coordinate does it.

In addition, if you want to select all atoms of a given position in the unit cell (in a P1 sense, but across multiple unit cells), you can use:

select within(-0.1, {1/2 1/2 1/2})

where that negative distance means "normalized to the unit cell". That now means that you can assign vibrational vectors from a file just to the P1 atoms, and Jmol will at least take care of all translations that are needed to apply those vibrations to all similar atoms.

If you start working on vibrations and need some help, please contact Jmol-users.

Closing this request now.

Bob Hanson