[CP2K-user] [CP2K:15480] Reg pdos

[Lucas Lodeiro]

Hi,

When you do the pdos, if all Cu atoms are the same atom kind, you will get
the pdos for all of them in only one file. But if you change the name of Cu
adsorption site from Cu to Cu1 for example, the Cu adsorption site will be
a different kind from other Cu atoms, and you will get it in a different
pdos file. With it, you could plot only the H_2 and Cu1, and analize with
detail. I do not know if this is sufficient... maybe the acceptor orbitals
are not only localized on Cu, maybe the neighbor atoms apport. Usually, a
pdos analisis is partner with HOMO-LUMO analysis, and specific interaction
orbital analisis...
Also, if you want to analyze the bonding antibonding nature of interaction
and pdos, the COOP is a good tool.

Regards

El sáb, 29 may 2021 a las 5:44, Gayathri Vijayakumar (<
gayathr... at gmail.com>) escribió:

> Dear cp2k users,
>
> I am currently studying the binding energy of a hydrogen molecule on a
> active site in zeolite. Zeolites is modelled as a periodic system. The
> active site is a metal (Cu).  So I have used diagonalization scheme and
> fermi dirac smearing.  There are total of 5 element kinds (Si, O, Al, Cu,H)
> and i got pdos file specifically for each of them. The fermi energy was
> also printed in the pdos file.  I got something like this for each element.
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> # Projected DOS for atomic kind Cu at iteration step i = 238, E(Fermi) =
>    0.134594 a.u.
> #     MO Eigenvalue [a.u.]      Occupation                 s
>    p                 d                 f
>        1         -0.766875        1.000000        0.00040816
> 0.00019927        0.00040976        0.00005599
>        2         -0.763958        1.000000        0.00001065
> 0.00106732        0.00035579        0.00024586
>        3         -0.763400        1.000000        0.00039341
> 0.00081615        0.00058844        0.00014208
>        4         -0.761087        1.000000        0.00051101
> 0.00026805        0.00069802        0.00005593
>        5         -0.760405        1.000000        0.00000217
> 0.00067203        0.00037474        0.00014099
>        6         -0.760013        1.000000        0.00020776
> 0.00043195        0.00020688        0.00008696
>        7         -0.757958        1.000000        0.00015781
> 0.00109346        0.00043777        0.00053473
>        8         -0.757330        1.000000        0.00002862
> 0.00006718        0.00012050        0.00002821
>        9         -0.756220        1.000000        0.00018373
> 0.00016449        0.00013811        0.00005944
>       10         -0.754529        1.000000        0.00075570
> 0.00054211        0.00150433        0.00010640
>       11         -0.754317        1.000000        0.00026342
> 0.00027469        0.00036698        0.00004827
>       12         -0.753713        1.000000        0.00046664
> 0.00102621        0.00045793        0.00035679
>       13         -0.752123        1.000000        0.00062391
> 0.00049449        0.00075069        0.00023401
>       14         -0.751470        1.000000        0.00000664
> 0.00025988        0.00018482        0.00020862
>       15         -0.751237        1.000000        0.00000305
> 0.00025721        0.00032981        0.00009450
>       16         -0.750955        1.000000        0.00008902
> 0.00172526        0.00128286        0.00043091
>       17         -0.750701        1.000000        0.00006711
> 0.00017480
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Then i smeared it and plotted Cu and H data in the same plot to understand
> the orbital contribution to adsorption in terms of bonding and anti bonding
> states position with respect to fermi level.
>
> But now i am confused because  there is only 1 active Cu site and 1 gas
> molecule in the entire periodic lattice of zeolites with 287 atoms and
> adsorption is happening on the active site.  does plotting pdos make any
> sense in this case?
>
> or simply plotting HUMO and LUMO makes more sense?
>
> I will be very thankful to your suggestions and help.
>
> Thanking you.
>
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