Ah, ok. I see. Right, Jmol can read the input files. Since we are reading
frequency data from CRYSTAL, it would be nice to expand that capability to
CASTEP. There is a new SUPERCELL option for LOAD that allows reading
supercells, and of course one can in any event read any number of unit
cells. (Not sure how that relates to frequency modes or if that would be
equivalent to what you describe.) Jmol does a nice job with trajectory files
and can read all sorts of electron density file formats. If CUBE is working
for you, that's fine. Otherwise we could talk about that, too. Doesn't
CASTEP output electron density in one of the standard formats?
Let me write a reader for that phonon file as a starting point. Looks simple
enough.
On Thu, Sep 8, 2011 at 12:55 PM, Keith Refson <[email protected]> wrote:
> Dear Robert,
>
>
> Robert Hanson wrote:
>
>> I guess we are reading the .cell file. Is this a different file?
>>
>
> The .cell file is an input file. As far as I know Jmol can not read any
> CASTEP output files (unless you care to contradict me!).
>
> The main output file - the .castep file - does not include any eigenvector
> information from a phonon calculation, so while you could read the
> frequencies, that would not help with animation. The full phonon data file
> has suffix ".phonon" and is designed to be more easily machine readable. A
> small example is attached, along with my conversion to xyz.
> However my scripts does more - including generating a supercell to display
> phonons at commensurate q/=0 wavevectors. It would be rather neat if JMol
> could do all of that directly.
>
> There are also trajectory files for MD and geometry optimtimisation,
> again which we currently convert to xyz, and electron density files,
> which we convert to Gaussian CUBE.
>
> I'm very happy to discuss and help with extensions to read these formats.
>
> Keith
>
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