[Octopus-users] XCrysden output format

[Robertson Burgess]

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
>
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