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Date: 2023/02/13 18:19
Name: Nima

I am new in OPENMX,and I started calculation of PDOS. I  calculate PDOS for perovskite structure such az (C4H12N)2 (CH3NH3)PbBr3,i want to plot PDOS of C4H12N, but at the result there is PDOS for each atoms separately. How can I plot total PDOS for C4H12N?
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Re: PDOS ( No.1 )
Date: 2023/02/15 15:11
Name: Vipin Kumar

Dear Nima,
Could you please tell me your definition of PDOS? I think you are talking about the total DOS of a whole system where all the constituent atoms contribute to the total DOS. Then you need to calculate the total DOS instead PDOS using the tetrahedron or Gaussian method.
Re: PDOS ( No.2 )
Date: 2023/02/15 17:08
Name: Nima

Thank you for your answer

I want plot PDOS of just organic compound, not C ,H, N atoms. Whole system is incloud (CH3NH3) organic cation, Pb and Br are other compound, that I want plot only CH3NH3 compound PODS.
Re: PDOS ( No.3 )
Date: 2023/02/16 14:52
Name: Vipin Kumar

Then you need to calculate the total DOS. see the following

% ./DosMain cdia.Dos.val cdia.Dos.vec
    Max of Spe_Total_CNO = 8
    1 1 101 102 103 101 102 103
    Which method do you use?, Tetrahedron(1), Gaussian Broadeninig(2)
    Do you want Dos(1) or PDos(2)?
    1 (you need to choose 1 here, then it will give you your desired result)

Re: PDOS ( No.4 )
Date: 2023/02/18 21:42
Name: Yung-Ting Lee

The way of plotting partial density of states (PDOS) for specific atoms in the system by gnuplot is listed as below.

Step (a): Type in the command "./DosMain *.Dos.val *.Dos.vec"

For example:
% ./DosMain *.Dos.val *.Dos.vec
Which method do you use?, Tetrahedron(1), Gaussian Broadening(2)
2      (I usually use the Gaussian broadening method for broadening.)
Please input a value of gaussian (double) (eV)
0.02  (for example)
Do you want Dos(1) or PDos(2)?

Number of atoms=6    (if the total number of atoms is 6 in the system)
Which atoms for PDOS : (1,...,6), ex 1 2
2 3 4      (selecting the specific atom' index that you want to project)

Step (b): Type in the command, e.g. " paste *.PDOS.Gaussian.atom2 *.PDOS.Gaussian.atom3 *.PDOS.Gaussian.atom4 > *.PDOS.Gaussian.atom2-4 "

The three input files are *.PDOS.Gaussian.atom2 , *.PDOS.Gaussian.atom3 , and *.PDOS.Gaussian.atom4 .
The output file is *.PDOS.Gaussian.atom2-4 .
The function of the "paste" command is used to join files horizontally (parallel merging) by outputting lines consisting of lines from each file to the standard output. (  Reference:  )

Step (c):
The 3-column format in a PDOS file is "Energy  PDOS  accumulated-PDOS ".
Therefore, in this example, the output format will be "Energy  PDOS  accumulated-PDOS    Energy  PDOS  accumulated-PDOS    Energy  PDOS  accumulated-PDOS".

Step (d): The command line by Gnuplot is listed below.

plot "*.PDOS.Gaussian.atom2-4" 1:($2+$5+$8) lc rgb "#ff0000"
pause -1

1 = data from column index 1 in the output file, i.e. Energy
$2 = data from column index 2 in the output file, i.e. PDOS from atom2
$5 = data from column index 5 in the output file, i.e. PDOS from atom3
$8 = data from column index 8 in the output file, i.e. PDOS from atom4
lc rgb "#ff0000"=> "lc" = line color, "rgb" stands for Red-Green-Blue, "#ff0000" = RGB red color.

Then, a combined PDOS contribution from atom2, atom3, and atom4 will be shown by Gnuplot. (The x-axis is energy and the y-axis is PDOS.)

Best regards,
Yung-Ting Lee
Re: PDOS ( No.5 )
Date: 2023/02/21 18:51
Name: Nima

Thank you so much

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