Hong"
To: siesta-l@uam.es
Sent: Friday, January 15, 2010 2:17:07 AM GMT -05:00 US/Canada Eastern
Subject: Re: [SIESTA-L] the surface was totally changed after calculation
Heiko-san,
thank you very much.
I cannot understand that " choose some larger value for the axis perpendicula
Heiko-san,
thank you very much.
I cannot understand that " choose some larger value for the axis
perpendicular to the surface to simulate a surface layer" so I have to add
vacuum layer to this system? Thank you very much
Fen Hong
Hi Fen Hong,
the unit cell results from your parameters:
LatticeConstant 4.0782 Ang
%block Latticeparameters
4.0782 4.0782 4.0782 90. 90. 90.
%endblock
The lattice constant is multiplied by the Latticeparameters block
values: 4.0782*4.0782=16.631715 and you choose 90° at all angles
The output file shows that:
"outcell: Unit cell vectors (Ang):
16.6317150.000.00
0.00 16.6317150.00
0.000.00 16.631715"
It seems wrong again , I think.
FenHong
Dear all,
Thank you for your replay. Actually, I want to calculate absorption energy
for only one cubic, only one gold layer. My purpose is to compare the
viboration frequency difference between Siesta and another software. By the
way, The gold layer was constructed by VESTA, it is different from t
Hi Marcos
Yes sure ... its clear that the system is creating a cell, what is weird is:
the manual states ( pg 30 item 6.4.1):
" Firstly, the size of the cell itself should be speci ed, using some
combination of the options
LatticeConstant, LatticeParameters, and LatticeVectors, and SuperCell. I
Ney,
I agree with you on much of what you say. However, the fact that
siesta automatically specifies a cell is not weird. In tha manual it
says that, if no cell is specified (or LatticeConstant, now I don't
remember it by heart and feel too lazy to check it out), siesta will
assume the system is a
Dear Min Gao
Excuse me if I miss the aim of your calculation, but It seems that there are
some problems with the definition of your syste:
Your geometry just contain 6 Au atoms, which in my opinion is not enough to
isolate two consecutive surfaces in slab calculations (this is how surfaces
are u
Dear Fen Hong,
I think you should fix only one axis of the gold atoms, as it is
expected that the molecule has at least some influence on the surface
spot where it connects. So it might be better for the in-plane movement
to be not totally fixed. But you have to decide whether you want to
inc
Dear Heiko Dumlich:
Thank you for your suggestions. I have checked the input file, it seems ok,
no spelling mistake and wrong structure. So what I should do is add *"%block
GeometryConstraints
position from 1 to 6 (This is the gold
number )
Dear Fen Hong,
you should freeze the gold atoms axis perpendicular to the plane. The
problem is that you just put one layer of gold atoms. This means there
are no more layers to counteract the force of the adsorbed molecule. If
there were more layers in your simulation then you would see a dif
In fact,I did not freeze it. You mean it is necessary to freeze it when do
the calculation? But finally we should unfreeze it,right?
On Thu, Jan 14, 2010 at 12:25 PM, Christopher Rowan
wrote:
> Maybe you want to freeze the gold surface atoms?
>
> Chris Rowan
>
> 2010/1/13 Min Gao
>
> Dear all,
Maybe you want to freeze the gold surface atoms?
Chris Rowan
2010/1/13 Min Gao
> Dear all,
> I was going to calculated the absorption energy. while during the
> calculation the surface was totally changed,Au-Au bond distance, the
> angle,even the shape of the surface. I attacted the inputfile a
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