Artem,
On Thu, Oct 14, 2010 at 6:06 PM, Artem Baskin <[email protected]> wrote:
> Dear Siesta 3.0 beta users! Thank you for you time.
> I have three simple (hope that) questions about processing SIESTA.
>
> 1) how to fix the coordinates of atoms that I choose relaxing the rest
> part of my system?
>
> I used
> %block GeometryConstraints
> position # of atom which position I want to be fixed
> %endblock GeometryConstraints
> to control coordinates of atoms to be fixed. BUT AT THE END OF RELAXATION
> PROCEDURE final coordinates ARE CHANGED. Why? How to overcome this
>
> problem?
In principle it should work well. However, try
%block GeometryConstraints
position 10 11 12 1.0 0.0 0.0
position 10 11 12 0.0 1.0 0.0
position 10 11 12 0.0 0.0 1.0
%endblock GeometryConstraints
as a radical measure. Check the manual for the meaning.
>
> 2)I run SIESTA jobs at remote cluster with limited time of each job. If
> the granted time elapsed before the calculations are finished how can I
> restart the same job (using something like check file in Gaussian) without
>
> running it from the very begging? Is there any specific file containing
> that information, and how to restart it (I mean, the particular command
> etc.)?
>
http://www.icmab.es/siesta/manuales/manual-3.0-b/node119.html and
check the entry "reading saved data"
> 3)I want to study interaction between neutral lattice and ions. Is there
>
> any way (besides that mentioned in manual) to do that associating the
> charge with ions (but not with the whole system)? If not, how to interpret
> the results? If I have, for example, Na(+) should I look for a specific
>
> pseudopotential for that particle or pseudopotential for neutral Na is
> enough?
Sorry I can't help you with that.
Cheers,
Marcos
>
> Any help will be appreciated,
> Thank you in advance
>
> Artem Baskin,
> PhD student,
> University of Illinois at Chicago
>
