[CP2K-user] [CP2K:17190] Reg pdos

[Anjali ganai]

Hello,

I have just started using cp2k. Can you please say which tool to use to 
plot the PDOS after running the python script on .pdos file?

Regards
Anjali

On Sunday, May 30, 2021 at 12:32:21 AM UTC+5:30 gayathr... at gmail.com wrote:

> 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 (<
>> 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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>>>
>>

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