Messages

16

General Questions and Answers / Re: Is it a bug?

« on: October 26, 2017, 17:13 »

What about operating system? I have noticed that you are using the 2016.3 version. It is always a good idea of using an updated version, in your case this would be 2016.4.

It seems that at that time, Mar, 2017, we don't update ATK to 2016.4(or this version is still not available at that time?). But now I have decided to update it to 2017version

17

General Questions and Answers / Re: Is it a bug?

« on: October 26, 2017, 16:56 »

It's a 1D system, Petr, not 2D.
The eigenvalues should add up to the transmission, at any given k-point, so there is definitely something odd going on.

Thank you for your reply, Blom.
Now I think I can confirm that the issue is a bug, please see the figures in the doc file in the attachment.

18

General Questions and Answers / Re: Is it a bug?

« on: October 26, 2017, 16:42 »

@bubble Please post the actual script and log file related to this calculation. What version of ATK and operating system are you using?

For the py file, please see the attachment. The log file is too large to upload, thus I only paste some useful information (see below)
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 2016.3 [Build 7eb51b6]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Device DFT Calculation  [Started Mon Mar 06 18:39:30 2017]                   |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| CPU Information                                                              |
|                                                                              |
+------------------------------------------------------------------------------+
|  Process ID 0 at Caculation                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Size of dense matrices =   342 x   342 [2 MB per matrix]                     |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================

                            |--------------------------------------------------|
Calculating Nonlocal Part  : ==================================================
+------------------------------------------------------------------------------+






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

Density Matrix          :  316916.52 s     309.49 s      52.07% |=============|
Exchange-Correlation    :  237723.35 s     215.92 s      39.06% |==========|
Real Space Integral     :   22425.83 s      20.37 s       3.68% ||
Parallel Mixing         :   10362.81 s       9.57 s       1.70% |
Transmission Spectrum   :    7524.17 s     684.02 s       1.24% |
Valence Density         :    4493.48 s       4.08 s       0.74% |
Hartree Potential       :    3758.31 s       3.41 s       0.62% |
Diagonalization         :    2131.62 s      36.13 s       0.35% |
Setting Density Matrix  :    2028.00 s     507.00 s       0.33% |
Real Space Basis        :      59.85 s       3.33 s       0.01% |
Constant Terms          :      50.46 s       4.21 s       0.01% |
Difference Density      :      20.52 s       0.31 s       0.00% |
Core Density            :       6.88 s       0.10 s       0.00% |
Neutral Atom Potential  :       3.93 s       0.56 s       0.00% |
Loading Modules + MPI   :       2.42 s       2.42 s       0.00% |
Basis Set Generation    :       2.40 s       0.13 s       0.00% |
File IO, nlsave         :       1.94 s       0.08 s       0.00% |
Hubbard Term            :       0.02 s       0.00 s       0.00% |
Fixed Spins Term        :       0.00 s       0.00 s       0.00% |
--------------------------------------------------------------------------------
Total                   :  608594.55 s (7d01h03m14.55s)

19

General Questions and Answers / Is it a bug?

« on: October 24, 2017, 16:58 »

Hi,
   recently, I investigated a 1D nanodevice with spin-polarized calcualation. The attachment is three files. You can see that for the down spin, the average T(E) and the k-resovled transmision coiffiences is of 10^(-6) order of magnitude (the first figure). Therefore, the IV show that Idown is nearly zero (the third figure). However, the calculated the eigenvalue of the spin-down channel is about 0.38 (see the left-down cornor of the first figure) and the corresponding states (the second figure) are delocalized.

I want to know whether it is a bug? OR, how to explain this strange phenominon?
THANK YOU

20

General Questions and Answers / Re: What dose DD mean in the log file

« on: October 18, 2017, 12:59 »

Thank you for your reply.

However, what is the relationship betwenn, DM(U), DM(D) and DD? is there any more related   information?

21

General Questions and Answers / What dose DD mean in the log file

« on: October 18, 2017, 10:30 »

Hi, I have three questions
1. In the log file, what dose DD mean?
2. Do the DM(U) and DM (D) represent the spin-up and -down components of density matrix?
3. For a given calculation, we use PBE-SGGA and SZP basis set, even though the basis set is relatively small, for my system the SZP contains, for example, 2s, 2p,3d orbitals. I wonder why in the loge file for a given atom,the  DM(U) and DM (D) are only two numbers rather than matrix?   

Thank you!

22

General Questions and Answers / Re: Why Ne=48?

« on: September 22, 2017, 10:42 »

Thank you for your reply!

23

General Questions and Answers / Why Ne=48?

« on: September 22, 2017, 10:24 »

Hi,

https://docs.quantumwise.com/tutorials/parallelization/parallelization.html

Recently, I found in the above tutorial, in the 'unit-of-work' section, the tutorial indicates that the 'contour energy point' Ne is usually 48, and this confused me.

To my knowledge, the  contour intergral is divided into equilibrim and non-equilibrim parts. For the former the default value is 30, as indicated in the 'New calculator' panel. However, for the latter, only the default 'Real axis point density', 0.001Ha (about 0.0272eV), is given in the 'New calculator' . What I want to know is:

1. Is the energy point in the  non-equilibrim part equal to (about) 18 (i.e. 48-30=18)?
2. How to fix the number 18 or 48? To my knowledge, in the real axis the integral length should be dependent on the chemmical potential difference (i.e. uL-uR)? If so,  whether the energy point used in the real axis should be equal to (uL-uR)/0.001Ha, rather than 18?

Thank you!

24

General Questions and Answers / Spectra current

« on: September 19, 2017, 14:14 »

Hi,
In the IV-analyzer,  what is the expression for the 'spectral current' ?  is it equal to T(E)(fL-fR)? (Here, T(E) transmission spetrum of the given bias, f the fermi function of the L, R electrode), i.e. the integral of the spectra current is the corresponding current?

Thank you!

25

General Questions and Answers / Re: How to understand this point in the tutorial?

« on: September 19, 2017, 04:21 »

Thank you for your reply.

Another question is, what is the expression for the 'spectral current' in the IVcurve section of the tutorial? is it equal to T(E)(fL-fR)? (Here, T(E) transmission spetrum of the given bias, f the fermi function of the L, R electrode)

26

General Questions and Answers / How to understand this point in the tutorial?

« on: September 18, 2017, 11:37 »

Hi
In the tutorial
http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html
For the "Check the electrode geometry and size" section, the "Note" indicates that 'The reason for this is that only the nearest-neighbor interactions of the electrode along C are kept in the device calculation (this is necessary in order to describe the electrodes as semi-infinite rather than fully periodic along C).'

Is this point only suitable for the SE method considered here ? Is is suitable for the DFT method? and how to understand it?

It means that the NN interaction along, for example, A or B direction is discarded? I think this will cause incorrect results for the actural devices.

 Thank you!

27

General Questions and Answers / The phonon spectrum

« on: September 13, 2017, 15:39 »

Hi,
   Recently, I want to calculate the phonon sprectrum of 2D boron sheet. The experiment has shown that this system is stable. But I found negative frequencies at PBE/DZP level. I wonder whether the theoretical level that I considered is too low? Any suggestion?

Thank you!

28

General Questions and Answers / the degeneracy of CH4 molecular orbital

« on: September 6, 2017, 16:24 »

Hi,
I have a question. Now I want to get the degeneracy of a molecule. Using CH4 as an example (ATK 2017 version), I calculated its molecular energy spectrum. The input py file is in the attachment. But after calculation in the log file there exits a mistake, i.e., '  'float' object has no attribute '__getitem__'.

According to the manual, the return type of degeneracy() in keyword MolecularEnergySpectrum is list of float. Whether the notation degen[0]【i】 that I used in the script is wrong? If so, however, I found the notation of 'occupation()' (the return type of which is also list of float) can give correct results in the log file. In addition, if I change the notation degen[0]【i】 to degen, the result is also correct.

Thank you for your reply.

29

General Questions and Answers / How to obtain the different components of DOS

« on: September 4, 2017, 10:33 »

Hi
   Does the ATK2017 version provide different components of DOS? To my knowledage, the old version could only provide s p d...for DOS. In the new version, are the px, py, pz, dxy, dyz.... components avaible?

Thank you!

30

General Questions and Answers / transmission eigenstate

« on: July 28, 2017, 02:50 »

Hi,
   What is the difference between the left and right contributions for the transmission eigenstate (TE) calculation? 
   For example, If the bias voltage is finite, I think that, for a given energy, the electron can be viewed as incident from the left and right electrodes at the same time, and the final current is the result of, e.g.  'right contribution minus left contribution'. And based on this consideration,  we can obtain the left and right contributions for the TE?
  Am I right?
Thank you !