On 04/26/2011 08:36 AM, Laurence Marks wrote:
> This is the exception, but then this is not "saturating" this is
> calculating the thermodynamics of wet/hydrogenated graphene.
> Saturating is, for instance, calculating a silicon surface and
> terminating with hydrogen to model the bulk rather than
On 04/26/2011 02:49 AM, Lorenzo Paulatto wrote:
> Dear Hongsheng Zhao,
> there are many ways to saturate the bonds, and not all of them actually
> make sense in experimental conditions. The matter is discussed quite in
> depth in Phys. Rev. Lett. 101, 096402 (2008).
Thanks a lot for all the helps f
Well, you literally add the coordinates of H atoms, and the definition
of H atom itself...
If you are asking how I do it, depending on the system, I either write
a simple script, or, if it is small enough, I extract the coordinates
to a standart from, and then use a freely available "geometry edit
On Tue, 26 Apr 2011 14:29:23 +0200, Laurence Marks
wrote:
> A personal opinion: saturating "bonds" with hydrogen is bad science,
> just as "fixing atoms" is also bad science. These are relics of the
> days when it was hard to calculate a big system, but 100's (1000's) of
> atoms are no longer pa
In data 26 aprile 2011 alle ore 14:15:36, Hongsheng Zhao
ha scritto:
> -
> The carbon atoms at the edges are saturated with H atoms.
> --
>
> So, according to the above description, what should I revise the input
> file in order to saturating the edges with H atoms?
Dear Hongshe
On 04/25/2011 07:04 AM, O. Baris Malcioglu wrote:
> Dear Hongsheng Zhao,
>
> Unless you are asking if someone ever tried forcing a particular
> "bond" or aromaticity in PW explicitly (one can try to constrain some
> number of KS states trying to estimate a particular bond, but I don't
> think this
This is the exception, but then this is not "saturating" this is
calculating the thermodynamics of wet/hydrogenated graphene.
Saturating is, for instance, calculating a silicon surface and
terminating with hydrogen to model the bulk rather than using a big,
centro-symmetric slab.
On Tue, Apr 26, 2
A personal opinion: saturating "bonds" with hydrogen is bad science,
just as "fixing atoms" is also bad science. These are relics of the
days when it was hard to calculate a big system, but 100's (1000's) of
atoms are no longer particularly difficult. Do it right.
On Tue, Apr 26, 2011 at 7:07 PM,
Dear All,
This issues is somehow not so pertained to the PWSCF, but a gerneral DFT
modelling problem, sorry for this request on this list.
We all know that the H atoms is often used to saturate the dangling bonds in
the system's edge, say, for graphene nanoribbon. My issue is: as far as the
Dear Hongsheng Zhao,
Unless you are asking if someone ever tried forcing a particular
"bond" or aromaticity in PW explicitly (one can try to constrain some
number of KS states trying to estimate a particular bond, but I don't
think this is a good idea to do in a pw DFT code), I think you might
be
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