[Octopus-users] XCrysden output format

[David Strubbe]

Bob,

Actually, that file out.oct only tells you what Octopus thinks was in your
input file. What is definitive is the block in standard output like this:

******************************** Grid ********************************
Simulation Box:
  Type = sphere
  Radius  [b] =  22.000
  Octopus will run in 3 dimension(s).
  Octopus will treat the system as periodic in 0 dimension(s).
Main mesh:
  Spacing [b] = ( 0.250, 0.250, 0.250)    volume/point [b^3] =  0.01562
  # inner mesh =    2854025
  # total mesh =    3203265
  Grid Cutoff [H] =    78.957
**********************************************************************

Check that this is really 0.2.

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
> >
>
>
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