[Octopus-users] XCrysden output format

[David Strubbe]

Bob,

Ok, so what version of Octopus are you using? And was it the same for both
runs? The number of elements in XCrySDen output was off by one from the
correct value earlier but was fixed, and you could be dealing with
inconsistent versions.

David

On Mon, May 10, 2010 at 7:47 PM, Robertson Burgess <
Robertson.Burgess at newcastle.edu.au> wrote:

> Hi David,
>
> Thanks for the reply. I checked the out.oct file in my exec folder, and the
> Spacing is 0.2 as it is in my input. Also I'm not using a periodic system,
> as I'm simulating an isolated cluster.
>
> Bob
>
> >>> David Strubbe <dstrubbe at berkeley.edu> 11/05/2010 12:10 pm >>>
> Hi Bob,
>
> Check the spacing listed in your output file and see how that compares to
> what you requested in the inp file. If you are using a periodic system,
> only
> certain spacings are possible, and Octopus will pick the one that is
> closest
> to what you asked, but smaller.
>
> David
>
> On Mon, May 10, 2010 at 6:00 PM, Robertson Burgess <
> Robertson.Burgess at newcastle.edu.au> wrote:
>
> > Dear Octopus Users,
> >
> > I've been outputting the electron density data in the XCrysden format.
> For
> > the first structure it tried it on it worked fine, and the last part of
> the
> > file before all the data was as follows;
> >
> > BEGIN_BLOCK_DATAGRID3D
> > units: coords = A, function = A^-3
> > DATAGRID_3D_function
> >     87     87     87
> > 0.0 0.0 0.0
> >   17.200000    0.000000    0.000000
> >    0.000000   17.200000    0.000000
> >    0.000000    0.000000   17.200000
> >
> > This was exactly as expected, giving my a data grid spacing of
> > 17.2/(87-1)=0.2 exactly. This is exactly the value of my Spacing input,
> so
> > this is what I expected.
> > When I ran the same thing for a larger system, however, I got the
> following
> > block:
> >
> > BEGIN_BLOCK_DATAGRID3D
> > units: coords = A, function = A^-3
> > DATAGRID_3D_function
> >    117    117    117
> > 0.0 0.0 0.0
> >   23.457460    0.000000    0.000000
> >    0.000000   23.457460    0.000000
> >    0.000000    0.000000   23.457460
> >
> > which gives me a grid spacing of ~0.202219. However my Spacing value in
> my
> > inp file is the same as before, exactly 0.2, but that would mean that the
> > size of my grid should instead be 23.2. Why is it for this larger system
> > that the grid spacing has changed? I would have thought the grid spacing
> > should follow exactly from the input in Octopus? The reason that this is
> > important to me is because my smaller system above is actually a
> sub-section
> > of my larger system, and if the grid spacings are the same then it would
> be
> > very straight forward to subtract the electron density of my top system
> from
> > that of my bottom system. If the densities are not the same, that
> obviously
> > makes things substantially more problematic.
> >
> > Thanks,
> > Bob Burgess
> > University of Newcastle, Australia
> >
> > _______________________________________________
> > Octopus-users mailing list
> > Octopus-users at tddft.org
> > http://www.tddft.org/mailman/listinfo/octopus-users
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.tddft.org/pipermail/octopus-users/attachments/20100510/2db11e46/attachment.html