Dear Andrei,
thank you very much for the reply. Below I commented the points you arised.
In data 22/10/10 13:44:04, apost...@uni-osnabrueck.de ha scritto:
> Dear Roberto,
> it seems (please correct if I am wrong) that the cube format
> is intended to describe finite system a priori, so there is
> no periodicity in it taken into account. Moreover I think that
> for any practical reason you'd like to have a FINITE figure anyway...
> So whatever you'd like to use of periodicity, you take it into account
> WHILE, or PRIOR TO, cutting your visualisation box - how many
> periodic cells / parts of cells you want to include into it.
That's not what I meant. Obviously you plot only a finite region of space, but
such region is consistent with periodic boundaries only if it's boundered by
your lattice vectors. That's evident for example in a Si3N4 sample with cell
defined by:
%block LatticeVectors
15.204 7.602 0.0000
0.0000 13.16705 0.0000
0.0000 0.0000 11.624
%endblock LatticeVectors
Clearly, it would be inappropriate to use a cubic region for plotting a
wavefunction of this system. Especially for publication purposes.
> A limitation - indeed - of cube format (and of Denchar) is that this
> visualisation box must be orthogonal.
didn't know that
> Probably, for big majority of applications this is good enough.
> If you insist on non-orthogonality,
> then for instance XCrySDen allows to define non-orthogonal boxes,
> and my Sies2xsf suite of tools
> http://www.home.uni-osnabrueck.de/apostnik/Software/Sies2xsf.tar.gz
> allows to generate corresponding inputs to XCrySDen -
> for grid properties, e.g., RHO et al. (but not for wave functions).
Great, I will try that. But why not for wavefunctions? isn't the format of
prefix.RHO.cube identical to that of a prefix.K1.WF1.MOD.cube?
> In your case, the deviation from orthogonality seems to be
> purely numerical and negligible for any purpose of visualisation.
Indeed. But I have other cases like the one above that are more difficult to
adapt.
> Another question is, whether you absolutely need to cut your
> visualisation box identical (or almost) with your unit cell,
> or are there other reasonable choices, smaller or bigger cuts,
> which may better emphasize what you want to emphasize in your figure...
Well, I have to think about that, but I don't think so.
Best,
RG
> Best regards
>
> Andrei Postnikov
>
> > Hi,
> >
> > I couldn't figure out how to generate the cube files within the
> > boundaries defined by my lattice vectors:
> >
> > %block LatticeVectors
> >
> > 20.804198 -0.109425 -0.024170
> > -0.109478 20.785394 -0.082819
> > -0.024133 -0.083005 20.788121
> >
> > %endblock LatticeVectors
> >
> > The system is a bulk, and therefore I have to take into account the
> > periodic
> > boundary conditions; using Denchar.MniX,Y,Z and Denchar.MaxX,Y,Z I can
> > only
> > define cubic boundaries. Is there a way to do that? Is this planned for a
> > future feature?
> >
> > RG
