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Messages - atk_user

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1
General Questions and Answers / LDOS energy range
« on: November 28, 2014, 13:01 »
Dear all,

I'm trying to calculate the real-space projected local density of states (LDOS) for the device configurations.
I want to get the LDOS for the energy range i.e., -0.5 eV to Fermi level or Fermi level to 0.5 eV. Is it possible?



# -------------------------------------------------------------
# Local device density of states
# -------------------------------------------------------------
local_device_density_of_states = LocalDeviceDensityOfStates(
    configuration=configuration,
    energy=0*eV,
    kpoints=MonkhorstPackGrid(24,24),
    contributions=All,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(),
    )
nlsave('analysis.nc', local_device_density_of_states)

2
General Questions and Answers / Extract optimized structures
« on: November 28, 2014, 12:46 »
Dear, all

Is it possible to extract the optimized geometry file (.py) in the linux command line using Python script after complete the geometry optimization?
I know it is possible to extract the geometry in the VNL but this process is not handy in the linux.


3
General Questions and Answers / Re: vacancy formation energy
« on: November 19, 2014, 15:42 »
I think the energy is correspond to the LaMnO3 !!

How about calculate the energy for the LaMnO3-x ??

After that could I using this formula?


E (LaMnO3-x) + 1/2 E (O2) - E (LaMnO3)

4
General Questions and Answers / Re: vacancy formation energy
« on: November 19, 2014, 13:30 »
then,

<  the LaMnO3-x part of the system would then correspond to "layer1" in the tutorial, and the oxygen atom would correspond to "layer2".  >   <--  the energy from this calculation is correspond to the energy for LaMnO3-x ??

5
General Questions and Answers / Re: vacancy formation energy
« on: November 19, 2014, 10:10 »
How can I setup to consider BSSE for the vacancy formation energy. I found only an example of interlayer distance of graphite. Could you explain more details? I trying to calculate the BSSE correction but in manual there is an comment using GHOST atom instead of actually removing them from the configuration. (in the page 2)

http://quantumwise.com/documents/tutorials/latest/Grimme/Grimme.pdf


6
General Questions and Answers / vacancy formation energy
« on: November 19, 2014, 06:35 »
Dear, all

I'm trying to calculate the oxygen vacancy formation in LaMnO3 bulk crystal by using above formula.

E (LaMnO3-x) + 1/2 E (O2) - E (LaMnO3)

E (LaMnO3-x) : total energy of crystal with single oxygen vacancy (with fully relaxation; cell and atom positions)
E (O2) : total energy of O2 molecule in 30 A cubic box
E (LaMnO3) : total energy of LaMnO3 perfect crystal (with fully relaxation; cell and atom positions)

However, the calculated formation energy is quite high compare to the result from VASP (plane-wave calculation) (same PBE functional). What's the problem? BSSE correction is needed due to basis sets?

How can I solve this problem? I need a detailed calculation procedure. Could you help me?

7
General Questions and Answers / Re: Band structure (route) setup
« on: November 14, 2014, 16:04 »
Actually, my system is slightly distorted,

alpha, beta, gamma is 89.95, 90.05, 89.92 and a, b, and c are 8.04, 8.04, and 23.29 ..

The route G Z T, Y G is calculated.

8
General Questions and Answers / Re: band structure decomposition
« on: November 14, 2014, 14:49 »
Thank you very much. I'll try it.  :D

9
General Questions and Answers / Re: Band structure (route) setup
« on: November 14, 2014, 14:49 »
I got the error messages for the route setup.

bandstructure = Bandstructure(
    configuration=configuration,
    route=['G', 'X', 'S', 'Y', 'G'],
    points_per_segment=20,
    bands_above_fermi_level=4,
    )
nlsave('Band_GXSYG.nc', bandstructure)



Traceback (most recent call last):
  File "input.py", line 12, in <module>
    projection_list=ProjectionList(elements=[Lanthanum,Manganese,Strontium,Oxygen]),
  File "./zipdir/NL/Analysis/Bandstructure.py", line 67, in __init__
  File "./zipdir/NL/Analysis/BaseBandstructure.py", line 71, in __init__
  File "./zipdir/NL/Analysis/BaseBandstructure.py", line 495, in setupPathMethod
  File "./zipdir/NL/Analysis/BaseBandstructure.py", line 429, in determinePath
KeyError: 'S'


10
General Questions and Answers / Re: Band structure (route) setup
« on: November 14, 2014, 14:38 »
I see  :) how can I assign the name of points.

Thank you very much for your time.

11
General Questions and Answers / Re: Band structure (route) setup
« on: November 14, 2014, 14:37 »
That's the T and L point I think.

12
General Questions and Answers / Re: Band structure (route) setup
« on: November 14, 2014, 14:28 »
I missing a point (0, 0.5, 0.5)

How can I call that point in orthorhombic and hexagonal symmetry.

Is there any guide line or manual to assign that points?

13
General Questions and Answers / Re: band structure decomposition
« on: November 14, 2014, 14:06 »
I'm little confusing... ???

If I first projection on elements or angular momenta from reading the analysis.nc (optimized file) using below input file. Is that the same or different with the band from the script?

# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=configuration,
    route=['G', 'X', 'U', 'Z', 'G'],
    points_per_segment=20,
    bands_above_fermi_level=4,
    projection_list=ProjectionList(elements=[Silicon, Oxygen]),
    )
nlsave('Band1.nc', bandstructure)

# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=configuration,
    route=['G', 'X', 'U', 'Z', 'G'],
    points_per_segment=20,
    bands_above_fermi_level=4,
    projection_list=ProjectionList(elements=[Silicone]),
    )
nlsave('Band2.nc', bandstructure)

14
General Questions and Answers / Re: Band structure (route) setup
« on: November 14, 2014, 14:01 »
Then.....

How can I call the same points in hexagonal symmetry?


[0,0,0] -> [0,0.5,0] -> [0,0,0.5] -> [0,0,0]. in hexagonal?

15
General Questions and Answers / Re: band structure decomposition
« on: November 14, 2014, 13:47 »
Thank you very much. It looks little complicate. I'll try.

In VNL, I found the "band structure Analyzer..." In the Bandstructure Analyzer, I found the drop down menu for "sum", "up", and "down". It looks spin sum, up, and down component of band structure.

Is it different from the band extracted by using the script you gave above?

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