The ABINIT Users Mailing List ( CLOSED )

[Xavier Gonze <gonze@pcpm.ucl.ac.be>]

Dear Y. Okuno,

There are several experts in the interaction of grphite (or graphitic
structure) with molecules, that you might contact. I will give you their
address. As a first reaction, I think that you might try (OH)- instead
of just OH ... but this might not be relevant ...

X. Gonze

-------------------------------------------------------------------------

okuno@osa.sci.jri.co.jp wrote:
> Dear Abinit Users.
>
> I use Abinit for estimation of  the bond length of the HO-C length of the Graphite surface 
> with its C atom is terminated by OH group, the distance between O atom of OH group and  
> C atom of the graphite,  because Graghite in the solvant is always 
> terminated by some functional group like OH.
>
> We assume OH group density on the Graphite surface is very tiny, 
> (we do not know this assumption is right), and set one sheet of Graphite 
> in the unit  cell with 24 atoms and set OH group on the top of one Carbon atom. 
>
> We calculate surface energy by E(Graphite + OH) -E(OH) -E(Graphite) 
> (where E(x) is x's total energy) with changing the distance between  the Oxygen 
>  and Carbon.
>
> But the results shows the energy minimum of the surface energy is located the 
> distance 6.5Bohr, and when the case of the distance 2.5Bohr (the distance of 
> CH3-OH) the results show positive surface energy and indicate the OH group 
> are not absorbed by Graphite. 
>
> Are there some need for attention to treat the functional group like OH?
>
>
> Our input file for the Graphite(one sheet with 24 atoms and one OH group)
> is like below.
>
>
>
> nsppol 2
>
> #Definition of the unit cell
> acell      13.9235010838      16.0774741976      25.3072104390
> rprim     1.000000000000     0.000000000000     0.000000000000
>           0.000000000000     1.000000000000     0.000000000000
>           0.000000000000     0.000000000000     1.000000000000
> ntypat    3 
> znucl 1 6 8 
> natom   26 
> typat 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 1 
> xcart 
>     0.000000000000     0.000000000000     0.000000000000 
>     2.320583513975     1.339789516470     0.000000000000 
>     2.320583513975     4.019368549411     0.000000000000 
>     0.000000000000     5.359158065882     0.000000000000 
>     0.000000000000     8.038737098823     0.000000000000 
>     2.320583513975     9.378526615293     0.000000000000 
>     2.320583513975    12.058105648234     0.000000000000 
>     0.000000000000    13.397895164704     0.000000000000 
>     4.641167027950     0.000000000000     0.000000000000 
>     6.961750541925     1.339789516470     0.000000000000 
>     6.961750541925     4.019368549411     0.000000000000 
>     4.641167027950     5.359158065882     0.000000000000 
>     4.641167027950     8.038737098823     0.000000000000 
>     6.961750541925     9.378526615293     0.000000000000 
>     6.961750541925    12.058105648234     0.000000000000 
>     4.641167027950    13.397895164704     0.000000000000 
>     9.282334055900     0.000000000000     0.000000000000 
>    11.602917569875     1.339789516470     0.000000000000 
>    11.602917569875     4.019368549411     0.000000000000 
>     9.282334055900     5.359158065882     0.000000000000 
>     9.282334055900     8.038737098823     0.000000000000 
>    11.602917569875     9.378526615293     0.000000000000 
>    11.602917569875    12.058105648234     0.000000000000 
>     9.282334055900    13.397895164704     0.000000000000 
>     4.641167027950     5.359158065882     2.500000000000 
>     4.641167027950     5.359158065882     4.500000000000 
>
> tsmear 0.04 
> kptopt 1
> ngkpt 1 1 1 
> ecut 60 
> nstep 50 
> toldfe 1.0d-6 
>
>
>
> Y. OKuno 
> Japan Research Institute.