Messages

166

General Questions and Answers / Re: Fermi surface

« on: January 12, 2017, 10:56 »

I guess that what you mean is to have the weights of the individual k-points, as by definition the DOS is a weighed integral over the Brillouin zone.

For a given Monkhorst-Pack grid, you can retrieve (i) all the k-points before symmetry reduction and (ii) all the corresponding weights by querying the  MonkhorstPackGrid class with (i) allKpoints and (ii) allKpointsWeights:

http://docs.quantumwise.com/manuals/Types/MonkhorstPackGrid/MonkhorstPackGrid.html

167

General Questions and Answers / Re: Device supercell heterojunction

« on: January 6, 2017, 09:01 »

Yes, you are correct.

Just make sure of one thing: a dipole will form at the interface between A and B because of the chemical/physical interaction between the two materials. You have to make sure that this dipole is well screened at the boundary with the electrodes. To do this, just unsure that the A and B parts in the central region are long enough. You can check that the potential is well screened by looking at the Hartree difference potential of the device, which has to be flat close to the electrodes. There is a more technical explanation of this in the tutorial I posted above.

Regards,
Daniele.

168

General Questions and Answers / Re: problem displaying Bandstructure of Graphene: VNL as QE GUI

« on: January 5, 2017, 14:34 »

Try these input files and make sure to update to the last version of the QE plugin (v2.3). Then you should be able to visualize the bands of graphene correctly.

Notice that we have found out a small numerical issue with the way k-points labeling is handled for the K point, so the "K" label will now show up in your band structure plot.

Also, make sure to run the calculations in a clean folder, I manage to reproduce your problem only when I re-run the calculation in a folder that already had some QE output in it.

Regards,
Daniele.

169

General Questions and Answers / Re: problem displaying Bandstructure of Graphene: VNL as QE GUI

« on: January 5, 2017, 09:05 »

That is weird. In the VNL figure the band structure from Gamma to Gamma, that is, no k-points path is selected in the Brillouin zone.

Did you also set up the system using VNL? Which version of QE are you using?

Regards,
Daniele.

170

General Questions and Answers / Re: Device supercell heterojunction

« on: January 5, 2017, 09:00 »

The electrodes are constructed by internal routines that find periodic patterns starting from the left/right hand side of the central region. A structure like the one you mentioned A-B-A-B-A-B will be transformed in a device (A)-A-B-A-B-A-B-(B), where the letters in parenthesis indicate semi-infinite electrodes, if a periodic pattern can be recognized in A and B.

However, please let me notice that the device configuration is best suited for geometries like L-C-R, where L and R are left and right semi-infinite electrodes and C is a central region where scattering occurs. Check:
http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html

In order to simulate transport in a fully periodic A-B system, I would rather calculate the transmission of the A-B BulkConfiguration.

Regards,
Daniele.

171

General Questions and Answers / Re: Fermi surface

« on: January 4, 2017, 09:50 »

Fermi surface plotting will be available starting from ATK 2017.

172

General Questions and Answers / Re: how to transform the picture of k-depended transmission

« on: January 4, 2017, 09:41 »

KA and KB indicate the same coordinate system in both plots. 

The data you show contain the first Brillouin zone, but unfortunately at the moment the transmission analyzer does not support plotting of hexagonal Brillouin zones.

If you right-click on the image you can export the data as a standard ASCII file, and then plot these data using an hexagonal structure. Notice that KA and KB are expressed as reciprocal coordinates, so in order to plot the hexagonal Brillouin zone, you should express them in Cartesian coordiantes. you can do the following:

(i) retrieve the Bravais lattice from the device configuration:
http://docs.quantumwise.com/manuals/Types/DeviceConfiguration/DeviceConfiguration.html

(ii) get the reciprocal vectors of this Bravais lattice:
http://docs.quantumwise.com/manuals/includes/BravaisLattices.html#NL.CommonConcepts.Configurations.BravaisLattice.BravaisLattice

173

General Questions and Answers / Re: band structure of bulk Black phosphorus

« on: December 30, 2016, 11:02 »

Dear Victor,

the calculations in the paper you mention have been performed using the HSE06 hybrid functional. GGA functionals such as PBE (the one you used in your calculations if you followed the tutorial) give too small band gap and in your particular case predict BP to be metallic.
Hybrid functionals will be available in ATK starting from ATK2017. In the meanwhile you can try the MGGA functional and the PseudoPotentialProjectorShift method, which also can be used to get a better gap compared to PBE:

http://docs.quantumwise.com/manuals/Types/ExchangeCorrelation/ExchangeCorrelation.html
http://docs.quantumwise.com/manuals/Types/PseudoPotentialProjectorShift/PseudoPotentialProjectorShift.html

Regards,
Daniele.

174

General Questions and Answers / Re: is there any way to calculate the transmission spectrum gap ?

« on: December 30, 2016, 09:45 »

To evaluate the gap you can easily use the TransmissionSpectrum analyzer in VNL.

Unfortunately, there is no script available at the moment, but it should not be too difficult to write a script that:

1. nlreads the TransmissionSpectrum object from the transmissionspectrum.nc file. See: http://docs.quantumwise.com/manuals/Types/nlread/nlread.html

2. extracts from the TransmissionSpectrum object (i) the energy using the query function .energy(), and (ii) the k-point averaged transmission using the query function .evaluate(). See: http://docs.quantumwise.com/manuals/Types/TransmissionSpectrum/TransmissionSpectrum.html

3. scans over all energies and prints out the energies where the corresponding transmission goes below/above a certain threshold (e.g. 0.01).

You can follow the instruction on atkpython in the manual:
http://docs.quantumwise.com/manuals/Python.html

175

General Questions and Answers / Re: band structure of bulk Black phosphorus

« on: December 30, 2016, 09:27 »

If you want to calculate the band structure of BP and compare it that of phosporene, once you have built the BP conventional cell as described in the tutorial (http://docs.quantumwise.com/tutorials/crystal_builder/crystal_builder.html) do the following operations:

1. Open the Bulk Tools ‣ Swap Axes tool and click B-C and Y-Z in order to align the phosphorene plane perpendicular to the C axis.
2. The lattice type has now been reset. You therefore need to open Bulk Tools ‣ Lattice Parameters and select Simple Orthorhombic as the lattice type.

Then you can calculate the band structure of BP in the same way as explained in the tutorial for phosphorene (same k-point sampling, same basis set, same exchange-correlation functional).

176

General Questions and Answers / Re: band structure of bulk Black phosphorus

« on: December 29, 2016, 08:54 »

As far as I can see the cell vectors in the bulk BP are not aligned in the same way as in Phosphorene. In the former, the C axis lies parallel to the staking plane, whereas in the latter is lies perpendicular to this plane. This second orientation of the cell vectors is the correct one.

I would try to repeat the calculation for BP by swapping the axes so that the C axis lies perpendicular to the stacking plane.

177

General Questions and Answers / Re: TMR Negative percentage

« on: December 28, 2016, 15:32 »

Did you read the TMR tutorial for Fe-MgO-Fe?

http://docs.quantumwise.com/tutorials/fe_mgo_fe/fe_mgo_fe.html

Do you manage to get the correct TMR for Fe-MgO-Fe as described in the tutorial?

What makes you think that you should get the same for Fe-MgO-Ni?

178

General Questions and Answers / Re: TMR Negative percentage

« on: December 28, 2016, 08:45 »

Difficult to say without even seeing the system structure    It would be great if you can attach it.

179

General Questions and Answers / Re: band structure of bulk Black phosphorus

« on: December 28, 2016, 08:42 »

It is difficult to say what's wrong without seeing your atkpython input and log files. If you can attach them here, we could have a look...

180

General Questions and Answers / Re: Generation of es states and MPSH states during IETS run

« on: December 27, 2016, 08:48 »

Hello,

the calculation of MPSH states considers only elastic scattering. In principle, if you want to use it to analyse a IETS signal, you should extract the normal modes of the vibrating system, and calculate the MPSH when the geometry is displaced along a particular normal mode.

We could have a closer look at the reason why your calculation fails if you attach your atkpython script.

Regards,
Daniele.