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Topics - 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 / 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?

4
General Questions and Answers / Band structure (route) setup
« on: November 14, 2014, 12:48 »
Dear, all

I try to calculate the band structure from the optimized structures. (orthorhombic structure). However, there is no guide line to setup the k-path (e.g., G, X, Z, ...). From the wikipedia, the high symmetry points for simple orthorhombic system is represented by (G -> X -> U -> Z ->G ) http://en.wikipedia.org/wiki/Brillouin_zone#mediaviewer/File:Simple_Orthorhombic_Lattice_(Brillouin_zone).png
Is it right? How can I check the path is right?


Actually, I wanted to calculate the band along the k-path [0,0,0] -> [0,0.5,0] -> [0,0,0.5] -> [0,0,0].
However, I got the error message using below input file.

The error is about the using of "points_per_segment=20,"

Why it cannot use "points_per_segment=20," with kpoints option?


configuration = nlread('../analysis.nc', object_id='gID001')[0]

# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=configuration,
    kpoints=[[0.0,0.0,0.0],[0.0,0.5,0.0],[0.0,0.5,0.5],[0.0,0.0,0.5],[0.0,0.0,0.0]],
    points_per_segment=20,
    bands_above_fermi_level=All,
    projection_list=ProjectionList(elements=[Lanthanum,Manganese,Strontium,Oxygen]),
    )
nlsave('0Vo_Band_LSMO_part.nc', bandstructure)


5
General Questions and Answers / Export CIF files using the linux command
« on: October 18, 2014, 10:15 »
Dear all,

Is it possible to export CIF files for both initial and optimized geometries after geometry optimization in the linux command line?
(I'm using ver. ATK 13.8.1)


6
General Questions and Answers / Required memory check
« on: June 9, 2014, 07:23 »
Dear, all

Is it possible to check the required memory in the linux command lines or python scripts?


7
General Questions and Answers / Energy calculation under the gate bias
« on: May 16, 2014, 03:00 »
Dear all,

Is it possible to calculate the energy of the system (not device model) under the bias?
I means just add the metallic region above the model system (like gate) which has the large vacuum slab.
 


# Add metallic region
metallic_region_0 = BoxRegion(
    -2.0*Volt,
    xmin = 0.0*Angstrom, xmax = 2.464*Angstrom,
    ymin = 22.275134*Angstrom, ymax = 25.0*Angstrom,
    zmin = 6.38542*Angstrom, zmax = 19.641547*Angstrom,
)

metallic_regions = [metallic_region_0]
bulk_configuration.setMetallicRegions(metallic_regions)

8
General Questions and Answers / Density of States (with Gaussian Smearing)
« on: March 25, 2014, 15:29 »
Dear QuantumWise staff members,

I can get the density of states following input options. However, the DOS is smeared with tetrahedron method with so many energy points. Actually, I wanted to analysis the partial density of states with gaussian smearing in the VNL. It's very quick and easy to analyze which atoms or orbitals are affected to the specific peaks in the DOS.

The problems are ...
1. I can't see the DOS with gaussian broadening in VNL.
2. The energy points are so big... -> very slow to analyze the partial density of states in VNL because so many data.

How can I ...
1. Calculate the DOS with gaussian smearing (default)
2. set the energy range and the number of points.

in following input options.

Code
density_of_states = DensityOfStates(
    configuration=bulk_configuration,
    kpoints=MonkhorstPackGrid(40,4,1),
    energy_zero_parameter=FermiLevel,
    bands_above_fermi_level=None,
    )
nlsave('analysis.nc', density_of_states)
nlprint(density_of_states)

9
General Questions and Answers / I-V reverse bias
« on: March 24, 2014, 13:33 »
I have a question for reverse bias calculation.

When I perform the forward bias from 0 to 0.15 V, it starts from 0 V.
    biases=numpy.linspace(0,0.15,7)*Volt,

| Left electrode chemical potential  =   -3.927765 eV                          |
| Right electrode chemical potential =   -3.927765 eV                          |
| Left electrode chemical potential  =   -3.940265 eV                          |
| Right electrode chemical potential =   -3.915265 eV                          |
| Left electrode chemical potential  =   -3.952765 eV                          |
| Right electrode chemical potential =   -3.902765 eV                          |
| Left electrode chemical potential  =   -3.965265 eV                          |
| Right electrode chemical potential =   -3.890265 eV                          |
| Left electrode chemical potential  =   -3.977765 eV                          |
| Right electrode chemical potential =   -3.877765 eV                          |
| Left electrode chemical potential  =   -3.990265 eV                          |
| Right electrode chemical potential =   -3.865265 eV                          |
| Left electrode chemical potential  =   -4.002765 eV                          |
| Right electrode chemical potential =   -3.852765 eV                          |


However, when I calculate the reverse bias, it start from -0.15 V. Is that right? I think the reverse bias also start from 0 bias ....

    biases=numpy.linspace(0,-0.15,7)*Volt,

| Left electrode chemical potential  =   -3.852765 eV                          |
| Right electrode chemical potential =   -4.002765 eV                          |
| Left electrode chemical potential  =   -3.865265 eV                          |
| Right electrode chemical potential =   -3.990265 eV                          |
| Left electrode chemical potential  =   -3.877765 eV                          |
| Right electrode chemical potential =   -3.977765 eV                          |
| Left electrode chemical potential  =   -3.890265 eV                          |
| Right electrode chemical potential =   -3.965265 eV                          |
| Left electrode chemical potential  =   -3.902765 eV                          |
| Right electrode chemical potential =   -3.952765 eV                          |
| Left electrode chemical potential  =   -3.915265 eV                          |
| Right electrode chemical potential =   -3.940265 eV                          |
| Left electrode chemical potential  =   -3.927765 eV                          |
| Right electrode chemical potential =   -3.927765 eV                          |


10
General Questions and Answers / Extract analysis data from .nc file
« on: March 15, 2014, 16:58 »
Dear all,

I'm running ATK on Linux environment.
VNL is very convenient tool for visualize the structure and analysis data such as I-V, Transmission, and Density of States.
However, it is sometimes very time consuming to compare several analysis data.

I want to extract directly specific data such as I-V, Transmission, and Density of States data from .nc file on the linux without VNL.
Is it possible to directly extract each data from the analysis by using python scripts?

If it is possible, could you let me know how to build the script and running?


Thank you very much.


11
General Questions and Answers / Electrode validator in ATK 13.8.1
« on: March 5, 2014, 03:01 »
There is a new function (Electrode validator)  in the new version of ATK 13.8.1.

What's the Electrode validator? How could I use this function?

Is there any manual for study this function? ???

12
General Questions and Answers / absolute value of I-V
« on: March 3, 2014, 13:42 »
Dear all,

I'm testing the I-V calculations for Al(100) / Al(100) / Al(100) very simple structure.
If I consider the supercell of 2x2 along the x and y direction, the current values are increased.
The current values are depends on the size of the model structures? That means the absolute current values are meaningless?

How can I define the absolute current values?

Also,

The direct comparison of I-V data with different stoichiometric system in central (scattering) region (Al2O3, AlO etc.; total number of atoms are different) is possible?



13
General Questions and Answers / Geometry Optimization
« on: February 27, 2014, 13:16 »
Dear all,

I am try to calculate the Al unit cell with OptimizeGeometry.
However, the geometry is not changed... (Lattice parameters)
I did not consider Constrain cell and Optimizer Method is QuasiNewton, PBE functional, and DZP basis sets.

I don't know what's the problem. Could you help me?

 

14
General Questions and Answers / I-V Calculation Density Matrix
« on: February 19, 2014, 05:16 »
Dear all,

I try to calculate I-V characteristics of two terminal devices. I set the voltage range from 0 to 1 V (11 points).
The calculation results shows 0, 0.1, 0.2, 0.3, ... 1.0 V. The log represent the calculation performed step by step from 0 V to 1V.

I have a question about I-V calculation procedure.
After calculation of specific voltage point (0 V or something), the next step voltage (0.1V or something) continuously calculate by considering the density matrix of previous step voltage (0V)?  ???

or

Each voltage steps are independently calculated? ???

15
General Questions and Answers / Error message (Transmission Analyzer)
« on: February 17, 2014, 07:41 »
Dear all,

After calculation of I-V and Transmission Spectrum, there was always an error message running Transmission Analyzer...

The following error message was generated when attempting to run the Transmission Analyzer...


Error on AnalysisBar Add-on

  An error occurred while performing an operation with AnalysisBar Add-on TransmissionAnalyzerPlugin. total size of new array must be unchanged

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