MoS2 and Au

[dwh]

Hello everyone ,how can I plot the Gaussian and tetrahedron spectrum within pylab for specific atoms of the periodic bulk systems？ For example, I want to get the PDOS or 3sp orbit of S atom of  MoS2 and Au contact system, but I want to use the Gaussian and tetrahedron spectrum ways ,rather than using more k-points. could you give me a specific way? thanks

[zh]

In  principles, on has to use a sufficiently dense k-mesh in the DOS calculations in order to get smooth curves of DOS plot.

[dwh]

Thanks, I know that we usually use a sufficiently dense k-mesh in the DOS calculations, but I want to use the Gaussian and tetrahedron spectrum ways for specific atoms of the periodic bulk systems. I just want to know how can I do? please give me a way,thank you very much, I am looking forward to your reply

[zh]

The following webpage shows an example for the calculations of DOS using the Gaussian smearing method and the tetrahedron technique:
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.densityofstates.html

[dwh]

Thanks, I know the links you give me,but I want to get the PDOS of S atom of  MoS2 and Au contact system by using the Gaussian and tetrahedron spectrum ways. Could you have a specific way?

[Anders Blom]

Once you have DensityOfStates object you can just ask it for the two types of spectra, with the relevant projection:

Code: python

dos = DensityOfStates(configuration, ...)
projection_list = ProjectionList(elements=Sulphur)
ts = dos.tetrahedronSpectrum(projection_list)
gs = dos.gaussianSpectrum(projection_list)

You may be interested in the projection on individual atoms, then use ProjectionList(atoms=[12]) etc where 12 is the atom index (starting at 0) of the atom to project on; you can project on more than one at the time. Tips on plotting are in the reference manual under the link above.

[dwh]

Thanks, could you give me a complete py file?

[Anders Blom]

I'm a bit hesitant to do that, because the details matter, and I don't want you to get the wrong results because of any assumption I'm forced to make. For instance, you need to consider the proper k-point sampling for your system. Also, I don't know precisely what you want in terms of projection. The above is almost a complete script, you just need the DOS part, which you can copy from a script made with the Script Generator, or if you already computed the DOS you can just nlread it from the NC file.

[dwh]

Thank you very much. my input and output files : g-oh.py, g-oh.log, g-oh.nc .  how can I add your code that you give me in the follow code:

# read DOS object from file
dos = nlread('g-oh.nc', DensityOfStates)[0]

# make list of energies
energies = numpy.arange(-14,5,0.01)*eV

# calculate the DOS spectrum with two different methods
dos_t = dos.tetrahedronSpectrum(energies)
dos_g = dos.gaussianSpectrum(energies, broadening = 0.2*eV)

#plot the spectra using pylab
import pylab
pylab.figure()
pylab.plot(energies.inUnitsOf(eV), dos_t.inUnitsOf(eV**-1))
pylab.plot(energies.inUnitsOf(eV), dos_g.inUnitsOf(eV**-1))
pylab.xlabel("Energy (eV)")
pylab.ylabel("DOS (1/eV)")
pylab.show()


In the script file, the Hydrogen and Oxygen atoms number: 33 and 32. I just want to get the PDOS of Hydrogen and Oxygen atoms by using  the Gaussian and tetrahedron spectrum ways.  I am very looking forward to your reply,Thanks .

[kstokbro]

try something like this:

projection_list = ProjectionList([32])
dos_t = dos.tetrahedronSpectrum(energies, projection_list = projection_list)

[dwh]

Thank you very very much, it was successful.And now, I want to calculate the S or P orbits PDOS of Hydrogen and Oxygen atoms by using  the Gaussian and tetrahedron spectrum ways.  , Could you give me the code?  I am very very looking forward to your reply,Thanks .

[kstokbro]

please check the manual:
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.projectionlist.html
s- hydrogen is:
projection_list=ProjectionList(elements=[Hydrogen], angular_momenta = [ 0 ])