Dear,
I don't get a couple of things you question?
A) What exactly have you done in your calculations is unclear to me
B) What does "weird" mean? You haven't shown a plot.
C) What is "job method"?
For graphene you typically need a decent number of k-points to capture the
Dirac cone. See e.g. https://doi.org/10.1088/1361-648X/aac4dd which details
out some PDOS calculations with graphene.
%block ProjectedDensityOfStates
-20.00 6.00 0.1 5000 eV
%endblock ProjectedDensityOfStates
%block PDOS.kgrid_Monkhorst_Pack
96 0 0 0.0
0 96 0 0.0
0 0 1 0.0
%endblock PDOS.kgrid_Monkhorst_Pack
Then you subsequently need to post-process the PDOS.xml files using the
pdosxml utility.
Alternatively you may use https://github.com/zerothi/sisl to extract PDOS
information, see
http://zerothi.github.io/sisl/docs/latest/api-generated/sisl.io.siesta.pdosSileSiesta.html#sisl.io.siesta.pdosSileSiesta
which
enables such interaction with siesta (you do need to use the development
version of sisl for this to work).
For instance this small Python snippet will assume all atoms are equal and
take out the first pz-orbital contribution
from all atoms in the unit-cell, you can easily adapt it to take out other
orbitals as well.
# code-snippet
import sisl as s
g, E, PDOS = s.get_sile('siesta.PDOS.xml').read_data()
# Find pz orbital on first atom
idx_pz = -1
for i, orb in enumerate(g.atoms[0]):
if orb.l == 1 and orb.m == 0:
idx_pz = i
break
# Clever function to get all orbital indices in the geometry (and hence the
orbital indices in the XML output)
all_pz = g.a2o(range(len(g))) + idx_pz
# Now extract PDOS (this is for an unpolarized calculation)
DOS = PDOS.sum(0)
pz = PDOS[all_pz, :].sum(0)
###
Hope this helped.
Den ons. 20. jun. 2018 kl. 22.01 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:
> Good afternoon,
>
> I am emailing you all to ask for assistance concerning finding the right
> pdos for graphene.
>
> So far i have successfully done it in VASP similar to the paper result
> shown in dosgraphene.png.
>
> However it did not work for me in SIESTA and getting weird dos plots.
>
> I followed How to DOS properly was shown on slide 34 (also shown in
> DOS.png) from the following link:
>
>
> http://personales.unican.es/junqueraj/JavierJunquera_files/Talks/Visualization.pdf
>
>
> Despite that and following very carefully by deleting all files and
> keeping the original fdf and psf files, I still i did not get the results I
> am hoping for.
>
> I am using job method since I am using high energy cut off and thus not
> losing the calculation.
>
> I am not sure what to do next. I tried playing around with the numbers one
> factor at a time.
>
> Any suggestions I am more than happy to listen to.
>
> Thank you and looking forward to your reply.
>
> EL-abed
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
> Condensed Matter Theory (CMT) Group
> | School of Physics
> THE UNIVERSITY OF SYDNEY | NSW | 2006
>
>
>
>
>
--
Kind regards Nick
