Re: [SIESTA-L] doping

[I. Camps]

Dear Masoudeh,

Be aware that doping is not the same of make atom substitution. We talk in
doping when the doping concentration is << that the system atom
concentrations. Using a 2x2x2 supercell will not give the decided
proportions in concentrations, so, you are simulating a ternary alloy
system TiOX.

Also, in working with alloys or doping, a big issue is to decide where to
"put/add" the third atom (in this case). There are techniques like
quase-random structure theory that can help with this.

Regarding your questions:

> 1. After doping should I find optimized lattice constant or optimized
> lattice constant of pure structure is acceptable?
>
If you know how your system behave (aka: is there experimental evidence of
crystal lattice parameter modifications) based on that, you select whether
or not make the lattice optimization. Normally, in doping, as the dopant
concentrations is low, there is no lattice modification. On the other hand,
working with alloys may not only change the lattice parameters but the
crystal symmetry as well.


> 2. after doping how can I measure the increasment or decreasment of the
> structure volume?
>
The structure volume can directly calculated from the crystal lattice
parameters. If you decided to not optimize the lattice then the volume will
not change. If you optimize the lattice, take the lattice parameters from
the output file (be sure the optimizations is completed) and calculate
manually the volume (I think that in the output, SIESTA write the crystal
volume).


> 2. I plot diagram of Pdos of pure tinoxide with 48 atoms, and I want to
> shift top of the valance band to zero. But the quantity of energy read from
> the filename.eig file (5.0578) is different from the value in the diagram
> of pdos( about 0.6). Why?
>
With the data you gave, I can not answer this question. What I do is take
the value of the Fermi level and then, using a graphical software
(OriginLab, Excel, Scigrapgh, GnuPlot, etc.) or a spreadsheet soft, shift
the data manually (maybe there is a tool or script in the SIESTA package).


> 2. For shifting the diagram of doped tinoxide, howmuch Should I shift it?
> As much as pure tinoxide read from the filename.eig or from the
> filename.eig of doped tinoxide?
>
It is your decision. It have to do with what you want to
show/study/discuss. Normally, I let the data as it, without making any
shift in the energy, but choose an energy scale of +/- 4eV around the Fermi
energy.

[]'s,

Camps

Re: [SIESTA-L] Help regarding pdosxml and Eig2dos utility

[Mostafa Shabani]

Dear siesta user
Inside the pdosxml folder, there is a file "m_orbital_chooser.f90" and you
should edit it based on your interest atoms and orbitals. The line you
should edit it is
wantit = (( orbid%species == "Fe" ) .and. ( orbid%n == 3 ) .and. (orbid%l
== 2 ))this line extract  (n=3, l=2 , Fe)   3d orbital for Fe
atoms datas from pdos output file.
after you edit this file type make in terminal . and by this command
pdosxml > filename.txt you can obtain the results you want and you can plot
it easily by xmgrace.

On Tue, Nov 21, 2017 at 6:35 AM, BISWAJIT BALL 
wrote:

> Dear Siesta Users,
>
>
>   I am trying to plot pdos using pdosxml and Eig2dos utility. While
> using pdosxml I have systemlabel.pdos file and after running job by using
> command ./pdosxml systemlabel.pdos>x.dat I am getting a x.dat file.
> But the plotting gives only a straight line i.e in the x.dat file out
> of three columns two columns are zero although my system is not spin
> polarised. I want to calculate the individual atoms pdos and understand the
> meaning of each line in m_orbitalchooser.f90 file.
>
>  I have the systemlabel.EIG file and after running job by using
> command Eig2dos -s 0.2 -n 400 -m -15 -M 15 system label, i am getting an
> outputfile but the plotting gives only total pdos.
>   I want to plot individual atoms pdos by using Eig2dos and pdosxml
> utility. So, kindly help me in this regard.
>
>  With best regards
>