[CP2K-user] [CP2K:15480] Reg pdos
Gayathri Vijayakumar
gayathr... at gmail.com
Sat May 29 19:02:21 UTC 2021
Thank you so much lucas. as suggested i will try using coop tool.
Cu is of a single element type.
i am also attaching the geometry file. the yellow highlighted atoms are
hydrogen getting adsorbed on Cu.
The red and blue atoms are O and Si of zeolites. Though pdos files were
generated for them as well, zeolite is a periodic lattice and hence the
interaction between the hydrogen molecule and Cu atom is localized indeed.
that is the reason i plotted the pdos file of h and pdos file of Cu alone
in the same plot. pl find the plot attached.
Thanking you
On Saturday, 29 May 2021 at 23:03:10 UTC+5:30 Lucas Lodeiro wrote:
> 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 (<
> gay... 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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>
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