[gpaw-users] Probing the character of molecular orbitals

[Miguel Caro]

Hi again,

Thanks Thomas for your email. I've kept working on this problem and I
think I came up with a much better solution, but I'm having trouble with
the implementation.

Now, I focus on bonds between C atoms, rather than atoms themselves. I
pick any two C atoms in my network and calculate the Wannier functions
corresponding to those two atoms when they form an ethane molecule:
basically I put three hydrogens at the right positions from each carbon
so that they form a modified ethane molecule where the carbons occupy
the same positions as in my amorphous carbon network. One of the Wannier
functions is localized in between the carbons, and corresponds to a
sigma orbital.

The approach can be better pictured here for the ethane
(mcaroba.dyndns.org/misc/ethane.png) and for the same Wannier function
overlayed on the amorphous carbon cell (mcaroba.dyndns.org/misc/a-C.png)
[sorry about the crappy rendering - VMD somehow managed to mess it up].
I had to write an interpolation routine for the Wannier function because
my carbon network lives in a hexagonal cell, and the Wannier calculator
cannot handle that - that explains why the orbitals don't look exactly
the same.

Now I use the LDOS calculator passing my Wannier function (wf_new)
instead of the KS orbitals:

    e, dos = calc_aC.get_all_electron_ldos(mol=atoms, spin=0, npts=501,
                                           width=0.2, wf_k=wf_new,
    P_aui=P_aui)

My problem at the moment is that I do not have the correct projectors.
To get a first result (quick and dirty) I simply set the projectors to
zero. This is a very bad solution and the summed overlaps between the
amorphous carbon orbitals and my Wannier function are far from 1.
However, qualitatively my DOS looks "promising"
(mcaroba.dyndns.org/misc/wannier_dos.png - note that the Wannier DOS had
to be scaled up by a lot). The pi orbitals that live in the mobility gap
of amorphous carbon (10 - 15 eV in the graph) do not show in the
projection onto my Wannier function, which should have no pi character -
exactly what I expected.

Now my question is about how to obtain/construct the required
projectors. Are they readily available from the Wannier calculator?

Many thanks,
Miguel


On 2016-04-21 22:03, Thomas Olsen wrote:
>
> Hi Miguel
>
>  
>
> It sounds like a tricky problem and I think that the characterization
> of your system in terms of pi/sigma bonds is not a completely
> well-defined problem - at least not quantitatively. It seems that the
> approach you are pursuing might give you a qualitative idea about the
> nature of the bonds though.
>
>  
>
> You want some measure of sigma orbitals that you can project onto
> everywhere and I guess the methane molecule can be used for that
> purpose. As you suggest, you could obtain a measure of the
> total "sigma" PDOS by calculating the PDOS on individual methane
> molecules centered on  all C atoms in your system and then add all the
> individual PDOS. But bear in mind that all the states you project onto
> does not form an orthonormal set so you will never obtain something
> that sums up to the total DOS in your system. Also, the result will be
> specific to "Methane sigma orbitals" and you would get something else
> if using another molecule having sigma bonds. Nevertheless, comparing
> the summed PDOS of sigma orbitals and pi orbitals (for some
> molcule) might give you a good idea of the bonding in your system
>
>  
>
> /Thomas
>
>  
>
>  
>
> ------------------------------------------------------------------------
> *Fra:* gpaw-users-bounces at listserv.fysik.dtu.dk
> [gpaw-users-bounces at listserv.fysik.dtu.dk] på vegne af Miguel Caro via
> gpaw-users [gpaw-users at listserv.fysik.dtu.dk]
> *Sendt:* 21. april 2016 15:11
> *Til:* gpaw-users at listserv.fysik.dtu.dk
> *Emne:* [gpaw-users] Probing the character of molecular orbitals
>
> Hi all,
>
> I am trying to use the scheme to project DOS onto molecular orbitals
> in order to probe the sigma/pi character of an amorphous carbon
> network. I have gone through the tutorial at
>
> https://wiki.fysik.dtu.dk/gpaw/documentation/pdos/pdos.html#molecular-orbital-pdos
>
> but still can't figure out how to do this properly.
>
> At the moment I'm calculating the Kohn-Sham orbitals for an isolated
> methane molecule whose C atom is centered at the same position as some
> C atom in my amorphous network, and in a supercell of the same size.
> In this way I make sure that the wave functions are commensurate (i.e.
> they are given on the same grid). Methane has 4 sigma bonds, so I'm
> seeking to probe the sigma character of my amorphous carbon KS states.
> To achieve that, I calculate the PDOS from the overlap of the
> amorphous carbon KS states and the methane KS states using the method
> outlined in the online tutorial. The overlaps are nicely close to 1 in
> every case. But obviously, the methane KS orbitals are nowhere near a
> complete basis for my amorphous network, where I have of the order of
> 100s of atoms. So basically I get a very poor description of the
> original DOS with this approach.
>
> I was thinking about constructing the KS basis set for the projection
> from an array consisting of several copies of my methane orbitals
> shifted in space so that they are centered at each and all of the C
> atoms in the amorphous carbon network. But I'm not sure if this makes
> much sense or if it's going to work at all.
>
> I was wondering if someone has already tried to do something like this
> before and how they went about it.
>
> Many thanks,
> Miguel
> -- 
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcaroba at gmail.com*
> Work: *miguel.caro at aalto.fi*
> Website: http://mcaroba.dyndns.org

-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcaroba at gmail.com*
Work: *miguel.caro at aalto.fi*
Website: http://mcaroba.dyndns.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20160425/55d8213b/attachment.html>