Messages

256

General Questions and Answers / Re: gate voltage sweep

« on: May 18, 2016, 09:13 »

Dear Dipankar,
there must be some error in your script. Using the script:

for i in numpy.arange(-1.0,1.0,0.2):
    print i

I get as expected:

stradi@stradi:Desktop$ atkpython test.py
# ---------------------------------------------------------------- #
# This time-limited pre-release version will expire on 2016-08-10. #
# ---------------------------------------------------------------- #
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 2016.dev [Build 5a2e684]                                   |
|                                                                              |
+------------------------------------------------------------------------------+
-1.0
-0.8
-0.6
-0.4
-0.2
-2.22044604925e-16
0.2
0.4
0.6
0.8

Timing:                          Total     Per Step        %

--------------------------------------------------------------------------------

Loading Modules + MPI   :       1.24 s       1.24 s      99.95% |=============|
--------------------------------------------------------------------------------
Total                   :       1.24 s

I also suggest to use numpy.linspace instead of numpy.arange, since the former also includes the endpoints.

257

General Questions and Answers / Re: Spin-orbit Coupling in MoS2 Monolayer Structure

« on: April 29, 2016, 09:17 »

Hello,

you should use a basis set and functional which supports spin-orbit coupling Please refer to this tutorial:
http://docs.quantumwise.com/tutorials/spin_orbit_bandstructures.html

258

General Questions and Answers / Re: Qestion about the two probe system optimization

« on: April 21, 2016, 09:11 »

Dear Zhuangping,

- Is my understanding right, please correct it if there is any misundertanding?
You are right about the differences between the BRR and 1DMIN methods.  Regarding the BRR method, notice that in ATK you can treat those region that you don't need to optimize as rigid bodies. When you set a part of the system as rigid body, you constrain only its interatomic angles and distances, but not its center of mass, which is still free to move.

- Yet, I have qestions about the 1DMIN method. What is the total energy for?
It is the energy of the central systems. Please read section: http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/chap.negf.html#sect1.negf.totalEnergy

- In ATK, if one use a vacum large enough, then the dipole correction can be ignored?
In principle you are correct, but consider that a better choice is to use the multigrid solver implemented in ATK, with which you can use different boundary conditions. Therefore you don't have to care about the dipole.
See for example: http://docs.quantumwise.com/tutorials/geometry_optimization.html

- If we use ghost atoms at the metal surface, do the ghost atoms be chosen to move or fix during the geometry optimization?
No the ghost atoms are fixed.

- In addition, I find one can not use ATK-Classical method to do a geometric relaxation for two probe systems if there are molecules and metal electrodes. How to solve this problem? Can we define the potentials for different kinds of atoms, respectively? If not, we can only use ATK-SE to speed up the geometry optimization?

This is probably because there is no set of potentials available for the atoms in your system. However, you can use ATK-SE for the geometry optmization. See for example:
http://docs.quantumwise.com/tutorials/neb_dftb.html?highlight=neb

- Also, I find the ATK-Classical gives a wrong geometry results. For a molecule that is optimzed by ATK-DFT, the ATK-Classical gives a dissociation molecule structure. So, use the ATK-Classical with care.

I think a more general statement would be: "use classical potentials with care!"

Let me know if I left something out or unclear

Regards,
Daniele.

259

General Questions and Answers / Re: The problem of calculated curent

« on: April 19, 2016, 09:27 »

Dear fan0221,

The current in both system is essentially zero, (~10-4 nA), because your bias window (-0.25 V to +0.25 V) lies within the semiconductor band gap. It is difficult to say more without having a look at how the actual device configuration looks like. However, by looking at the transmission curves, it looks like to have an appreciable current, you should increase the bias voltage quite a lot, so that some of the peaks in the transmission spectrum lies within the bias window (this might be difficult, depending on the system).

best regards,
Daniele.
 

260

General Questions and Answers / Re: Use of a user specified norm conserving pseudopotentials in the calculations

« on: April 15, 2016, 16:23 »

Dear Guangping,

I have investigated the issue. It looks like the projectors automatically generated by APE are too long ranged for the default ATK basis set. Unfortunately, we cannot support all the pseudopotential generators. There are 2 solutions to this problem:

1) Increase the "radial_cutoff_radius" in your script, until the error disappear. Notice the the required cutoff radius could be much larger (approx. 1.5x-2x) than the default one.
2) Generate the *.psf pseudopotentials with the SIESTA pseudopotential generator. In this case, the generated projectors are much more compatible with our basis set, and ATK should run without problems. I have tested this for Ag, with a *.psf pseudopotential generated using the same configuration of your *.upf pseudopotential.

Regards,
Daniele.

261

General Questions and Answers / Re: How can we define a nonorthogonal BoxRegion ?

« on: April 15, 2016, 10:42 »

Dear Guangping,

in principle the fact that the a rectangle box usually does not match the unit cell in the xy plane is not a problem. You just have to ensure that the rectangle box is larger than the unit cell in the xy plane itself. See for example the tutorial:

http://quantumwise.com/publications/tutorials/item/512-opening-a-band-gap-in-silicene-and-bilayer-graphene-with-an-electric-field

The Poisson equation will be calculated taking into account only the part of the rectangle box within the unit cell.

Regards,
Daniele.

262

General Questions and Answers / Re: Use of a user specified norm conserving pseudopotentials in the calculations

« on: April 14, 2016, 09:15 »

Dear zhangguangping,

I have tested *.psf pseudos with ATK and never had this kind of problems. Could you please attach your pseudo so that we can test it?

Thanks,
Daniele.

263

General Questions and Answers / Re: Potential profile in tunnel junction?

« on: April 4, 2016, 10:22 »

Dear Chust,

please look at the section "Voltage Drop" (an alternative name for the electrostatic potential drop) in this tutorial:
http://docs.quantumwise.com/tutorials/atk_transport_calculations.html?highlight=potential%20drop

264

General Questions and Answers / Re: How to create a TiO2 nanotube

« on: April 2, 2016, 10:03 »

You can use the Bulk -> Surface (cleave) tool to create a periodic cell with the (110) direction oriented along the C axis - select "Periodic and normal" in the options for the out-of-plane cell vector. Starting from this configuration, you can build the nanotube following the same steps as before. 

265

General Questions and Answers / Re: Transmission eigenvalue and eigenstates

« on: April 1, 2016, 13:51 »

Dear iconxicon,

please find attached a script that reads a DeviceConfiguration, calculate the k-resolved transmission for a specified number of k-points, and save the results to a file that can be analyzed using VNL.

266

General Questions and Answers / Re: Transmission eigenvalue and eigenstates

« on: April 1, 2016, 10:41 »

Another small comment, I think that the increase in the current with bias is due to the fact that at a bias of 0.4 V the tail of the resonance at -0.45 eV starts to enter the bias window.

267

General Questions and Answers / Re: Transmission eigenvalue and eigenstates

« on: April 1, 2016, 10:38 »

Dear iconxicon,

The number of transmission modes is zero because you are probably evaluating the transmission at the Gamma point. Instead, the peak at E-Ef = -0.45 eV is associated with transmitting states away from the Gamma point. Try with the Trasmission Analyzer to evaluate the eigenvalues at k_A = 0.0, k_B = 0.5, and you should get some eigenvalue. To do this you can set the values of k_A and k_B directly in the Bottom-Right panel of the Transmission Analyzer.

I am preparing a script to plot the k-resolved transmission, to make it easier to analyze.

Regarding the relation between transmission and current: I don't this the correlation is that straightforward, because in the Landauer formalism the current is calculated from the convolution between the Transmission and the Fermi functions of the electrodes. Therefore, also the electronic structure of the electrodes play a role.

268

General Questions and Answers / Re: How to create a TiO2 nanotube

« on: March 31, 2016, 11:09 »

Dear raissamartins,

The wrapper should work, please see the structure TiO2 nanotube structure attached.

In order to build the tube correctly, make sure of two things:
1) Use a bulk TiO2 orthogonal cell: starting from the database structure, go to Bulk Tools -> Supercell and press (i) Conventional and (ii) Transform;
2) Before using the Tube Wrapper, make sure that the repeated TiO2 supercell is aligned along the B cell vector, and that the B vector is aligned along the Y cartesian axis. To do this, use Bulk Tools -> Swap Axes

269

General Questions and Answers / Re: How to create a TiO2 nanotube

« on: March 30, 2016, 08:43 »

Dear raissamartins,

did you try to follow the steps in this tutorial?
http://docs.quantumwise.com/tutorials/mos2_cnt.html?highlight=wrapper

Otherwise, we would be happy to help, it would be great if you could provide some more explanation of what went wrong.

Daniele

270

General Questions and Answers / Re: Transmission eigenvalue and eigenstates

« on: March 29, 2016, 10:25 »

Dear Iconxicon,
Could you please attach a script of your calculation and your reference data? It is difficult to figure out what it is actually wrong with the information you provided.
Thanks