Messages

16

General Questions and Answers / Re: Basis set superposition error correction

« on: September 9, 2020, 09:57 »

Hi,

It is difficult to answer this question very generally. But sometimes basis set superposition errors (BSSE) can be significant leading to an overbinding, i.e. too large binding energy. If you get very different binding energies with and without the Counterpoise correction, it is probably important. In order to address the problem for a particular case, I would suggest that you try to compare your results with plane-wave calculations, using the PlaneWaveCalculator, since this does not suffer from BSSE.

Regards,
Troels

17

General Questions and Answers / Re: Query Regarding high symmetry points in band structure calculation

« on: September 9, 2020, 09:50 »

Why not just leave out one of the points which have the same energy as another high-symmetry point. Did you know, that you can get a visual representation of the high-symmetry points using the Builder->Bulk Tools->Brillouin Zone Viewer.

18

General Questions and Answers / Re: ampacity / current carrying capacity

« on: September 9, 2020, 09:45 »

Hi,

In my understanding, a detailed calculation of the current carrying capacity is an extremely complicated task involving (i) electron-phonon coupling giving rise to current induced heating (i.e. energy transfer from the electrons to the phonon bath and vice versa); (ii) current-induced forces; (iii) this should be coupled with some kind of molecular dynamics simulation to actually model the break-down of the conductor.
Such a full calculation cannot be done with QuantumATK (or with any other tool as far as I am aware).

You can address parts of the problem individually such as electron-phonon coupling or to some extend current-induced forces (calculate the force at finite bias).

Regards,
Troels

19

General Questions and Answers / Re: Geometry Optimization in Germanene Zigzag nanoribbon incorrect results

« on: August 31, 2020, 14:16 »

Hi,

It seems that your unit cell in the C-direction for the ZZNR is too long, since there are no bonds in the C-direction crossing the unit cell edge. I would guess your structure should look more like the attached figure.

Regards,
Troels

20

General Questions and Answers / Re: Query Regarding high symmetry points in band structure calculation

« on: August 31, 2020, 14:08 »

Hi,

You will never create problems in the bandstructure calculation by removing some high-symmetry points. The reason that (Gamma, Z)  and (X, R) have the same energy in your case is probably that you have a vacuum region in the z-direction. In this case, there is no interactions in the z-direction whereby the bands become flat. If this is not the case, then please share your script.

Regards,
Troels

21

General Questions and Answers / Re: 3D band structure plot

« on: August 28, 2020, 14:28 »

Hi,

1) We currently don't have a built-in analysis tool for visualizing 3D bandstructures. However, it is possibly to make your own plot using e.g. the Eigenvalues analysis object, which calculates the energy eigenvalues of a given configuration for a list of k-points. I have attached a script that calculates and plots the valence- and conduction band structure of graphene in a similar way as your attached plot. I hope you can use this as a starting point and modify it for your own applications.

2) We currently don't have an analysis object for calculating projected phonon density of states. However, I have previously shared a script that you can hopefully use. See the attachment here:
https://forum.quantumatk.com/index.php?topic=6427.msg27005#new

Regards,
Troels

22

General Questions and Answers / Re: Phonon DOS

« on: August 27, 2020, 10:42 »

Hi,
We currently don't have an analysis object for calculating projected phonon density of states. However, I have previously shared a script that you can hopefully use. See the attachment here:
https://forum.quantumatk.com/index.php?topic=6427.msg27005#new

Regards,
Troels

23

General Questions and Answers / Re: Query regarding thermoelectric calculation

« on: August 5, 2020, 12:53 »

Hi,
Concerning 1):It sounds like you are doing the right  things. However, it is hard to judge if your results are correct. Can you please share some pictures of the phonon transmissions or hdf5-file with the results. It would also be helpful to compare DFT and FF phonon bandstructures for the electrodes.
Concerning 2): You can add doping to your structure in the Builder ->  Miscellaneous -> Doping.

24

General Questions and Answers / Re: Rashba effect

« on: August 4, 2020, 11:55 »

Hi,

I'm nut sure if I compkletely understand your question, but I would say that the interaction included in QuantumATK will always be between the electron spins and the screened electric field. In addition to this, as you probably know, you can also have Rashba effects from surfaces and interface, i.e. without an external field.

Regards,
Troels

25

General Questions and Answers / Re: projection of phonon band

« on: August 4, 2020, 11:46 »

Hi,

Sure you can project on each atom. I have attached a slightly modified script, which projects on each atom (and plots the contribution from atom 0 and 1 - in this case they are all the same).

Regards,
Troels

26

General Questions and Answers / Re: Query regarding thermoelectric calculation

« on: August 4, 2020, 11:25 »

Hi,

1) In general you need to do a very careful optimization (relaxation) of the atomic structure when calculating phonons. In your case, the device seems to be a simple continuation of the electrodes, so it should be enough to do a fine relaxation of the electrode structure using OptimizeGeometry with a Force tolerance of 0.01 eV/Ang. At this point I would suggest to calculate the PhononBandstructure for the electrode to check that it looks reasonable. There shouldn't be phonon modes with negative energy.
From the relaxed electrode structure you make the device and calculate the DynamicalMatrix for the device.

You should only expect integer phonon transmissions for each individual transverse k-point. In your case the structure is periodic in the B-direction and if you calculate the phonon transmission for multiple k-points in the B-direction, you should not expect to get integer values. This is only true for a single k-point - or for a one-dimensional structure (where you only have the Gamma-point).

2) The thermoelectric properties are changing with doping concentration. So you should either plot the properties vs. doping (or vs. Fermi level) or pick a relevant one.

3) That depends on your doping level (position of Fermi level) - see answer to 2). The peaks closes to the valence/conduction band edges gives you the maximal ZT for p/n doped structures.

Regards,
Troels

27

General Questions and Answers / Re: Regarding phonon transmission calculation using quantumATK

« on: August 3, 2020, 13:41 »

Hi,
Sorry for the late reply, but this is vacation times...

I didn't see any obvious errors in your script. Also did you see any error messages - there are none in the Phonon_Trans.log file.

You can maybe try with this slightly modified script:

Code

path = '/home/utpal/Utpal/Jyoti/ATK/Thermoelectric_BeX2/BeX/device_pentag/DFT/Device_Pentag_DM.hdf5'
dynamical_matrix = nlread(path, object_id='dynamical_matrix')[0]
dynamical_matrix.update()

configuration = nlread(path, object_id='DeviceConfiguration_0')[0]

qpoint_grid = MonkhorstPackGrid()

phonon_transmission_spectrum = PhononTransmissionSpectrum(
    configuration=configuration,
    dynamical_matrix=dynamical_matrix,
    energies=numpy.linspace(0,0.5,101)*eV,
    qpoints=qpoint_grid,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(),
    )
nlsave('Phonon_Trans.hdf5', phonon_transmission_spectrum)
nlprint(phonon_transmission_spectrum)

28

General Questions and Answers / Re: mobility_error

« on: July 9, 2020, 14:14 »

Hi,

This looks strange and should not happen. How many processes did you run with?  I was unable to reproduce the error, with a slightly modified script. Perhaps try to run with fewer processes. Also, I noticed that your k-point sampling for the ElectronPhononCoupling is around the Gamma-point (ka_range=[-0.1, 0.1], kb_range=[-0.1, 0.1]), while I guess you would rather have it around the K-point, i.e.

Code

kpoints = RegularKpointGrid(
    ka_range=[0.23, 0.43],
    kb_range=[0.23, 0.43],
    kc_range=[0.0, 0.0],
    na=20,
    nb=20,
    nc=1,
    )

Regards,
Troels

29

General Questions and Answers / Re: Query Regarding thermoelectric coefficient calculation

« on: July 7, 2020, 12:19 »

Hi,

Currently the ZT is only shown in the table if both the phonon transmission and electron transmission spectra are available. However, the ZT which is shown in the plot is calculated from the usual formula ZT=G*S^2*T/k_tot,
where k_tot = k_el + k_ph. In the case where the phonon transmission spectrum is not calculated, the phonon thermal conductance, k_ph, is just set to zero.

Notice that often k_ph > k_el, which means that the ZT calculated without the phonon contribution is way too large. However, the values in the plot of ZT are fine, given that you are aware of the overestimation of ZT. In scientific papers, this quantity if sometimes denoted ZT_el, highlighting that it is calculated only from the electronic transmission. The "real" ZT is the ZT  = ZT_el * k_el / (k_el + k_ph).

Regards,
Troels

30

General Questions and Answers / Re: Regarding phonon transmission calculation using quantumATK

« on: July 7, 2020, 09:46 »

You can (and should) run the calculation of the DynamicalMatrix in parallel. This is the most expensive part of the calculation. When the DynamicalMatrix is calculated, you run a different script in serial to do the phonon transmission. The phonon transmission calculation can easily be done in serial for 144 atoms.

Regarding device optimization: If you simply repeat the unit cell and don't introduce defects, if should not be necessary to relax the device configuration.

Concerning the K-point sampling, this will depend on the system and in general convergence  with respect to number of K-points should be checked. But usually the default values in QuantumATK are good.