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Topics - lknife

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16
General Questions and Answers / Why I cannot find the pathway in the right part of the device?
« on: July 27, 2017, 17:34 »
Dear expert,

After the IV curve calculation of a in-plane interface based device, I wanted to have a look at the pathway under a specific bias. However, although it showed the pathway in the left part of the device, there is no pathway in the right part. I cannot understand it since in my view, the two-probe device is just like a “Serial circuit“, the current flow along the route should be equal. The current in this case is 3.64 nA (0.15V), not very low.

Why I cannot find the pathway in the right part of the device? Can anyone here help me with this problem?

Attached are three files related to this problem:
1. the transmission spectrum under bias 0.15V;
2. the .py file for the post-calculation  from the transmission spectrum;
3. the result of the second step: the pathway

17
General Questions and Answers / What's the difference among the three concepts about DensityofStates?
« on: July 25, 2017, 20:19 »
Dear experts,

I have been using ATK for nearly a year but I am still confused about these three concepts: DeviceDensityofStates, LocalDeviceDensityofStates and ProjectedLocalDensityofStates. Can anyone give me a simplified explanation about the difference among them?

Thank you very much for your kind help!

18
General Questions and Answers / cannot use "device from bulk"
« on: July 25, 2017, 17:14 »
Dear all,

I finished the optimization of the central region of a device as described in tutorial "Advanced device relaxation" http://docs.quantumwise.com/tutorials/device_relaxation/device_relaxation.html

In consideration of the time consuming, I used a relatively shorter central region for the optimization process. The original length of the central region is 20.0871 angstom which can be converted to device configuration using "device from bulk" plugin. However, after the optimization, the length of the central region reduced a little to 19.9862 angstrom and the "device from bulk" plugin cannot work on this optimized central region. I wonder if the minimum length for "Device from bulk" plugin is 20 angstrom so that it doesn't work on the optimized (shorter than 20) one.

Please see the attached files: before_opt.py and after_opt.py are the two configurations before and after the optimization. the file 1HB-TdB*.py is the .py file for the optimization calculation.

Can anyone here help me with this problem?
Thank you very much for your time and kind help!

19
General Questions and Answers / how to improve the convergence of the calculation?
« on: July 20, 2017, 15:32 »
Dear experts,

I encountered a convergence problem when I wanted to calculate the bandstructure of a configuration using SOGGA method. The calculation did not converge even though the iteration step had been set up to 500. I am afraid that even I set the iteration step to 1000, it cannot converge, either. Please see the attached .py file for this calculation. The .log file is too large to be posted here.

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

+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0   W   [   2.961 ,   5.159 ,  29.857 ]    7.33600   7.19113   0.52713     |
|   1  Te   [   0.988 ,   0.578 ,  31.435 ]    8.71712   7.13326  -0.14962     |
|   2  Te   [   2.961 ,   3.572 ,  32.096 ]    7.82671   7.79577  -0.37752     |
|   3   W   [   0.987 ,   3.136 ,  30.152 ]    7.33618   7.19098   0.52716     |
|   4  Te   [   2.962 ,   1.701 ,  28.576 ]    8.71509   7.13522  -0.14969     |
|   5  Te   [   0.987 ,   4.724 ,  27.914 ]    7.82768   7.79486  -0.37746     |
+------------------------------------------------------------------------------+
| 496 E =  -114.21 dE =  7.083951e-05 dH =  7.248292e-04                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0   W   [   2.961 ,   5.159 ,  29.857 ]    7.33598   7.19116   0.52713     |
|   1  Te   [   0.988 ,   0.578 ,  31.435 ]    8.71710   7.13328  -0.14962     |
|   2  Te   [   2.961 ,   3.572 ,  32.096 ]    7.82688   7.79559  -0.37753     |
|   3   W   [   0.987 ,   3.136 ,  30.152 ]    7.33621   7.19094   0.52715     |
|   4  Te   [   2.962 ,   1.701 ,  28.576 ]    8.71502   7.13529  -0.14968     |
|   5  Te   [   0.987 ,   4.724 ,  27.914 ]    7.82764   7.79491  -0.37745     |
+------------------------------------------------------------------------------+
| 497 E =  -114.21 dE =  1.379775e-05 dH =  1.007962e-03                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0   W   [   2.961 ,   5.159 ,  29.857 ]    7.33595   7.19118   0.52713     |
|   1  Te   [   0.988 ,   0.578 ,  31.435 ]    8.71709   7.13329  -0.14962     |
|   2  Te   [   2.961 ,   3.572 ,  32.096 ]    7.82666   7.79581  -0.37753     |
|   3   W   [   0.987 ,   3.136 ,  30.152 ]    7.33616   7.19100   0.52716     |
|   4  Te   [   2.962 ,   1.701 ,  28.576 ]    8.71503   7.13528  -0.14969     |
|   5  Te   [   0.987 ,   4.724 ,  27.914 ]    7.82758   7.79498  -0.37744     |
+------------------------------------------------------------------------------+
| 498 E = -114.209 dE =  1.085760e-04 dH =  8.330157e-04                       |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0   W   [   2.961 ,   5.159 ,  29.857 ]    7.33575   7.19138   0.52713     |
|   1  Te   [   0.988 ,   0.578 ,  31.435 ]    8.71713   7.13325  -0.14961     |
|   2  Te   [   2.961 ,   3.572 ,  32.096 ]    7.82588   7.79662  -0.37750     |
|   3   W   [   0.987 ,   3.136 ,  30.152 ]    7.33604   7.19112   0.52716     |
|   4  Te   [   2.962 ,   1.701 ,  28.576 ]    8.71514   7.13516  -0.14969     |
|   5  Te   [   0.987 ,   4.724 ,  27.914 ]    7.82658   7.79594  -0.37748     |
+------------------------------------------------------------------------------+
| 499 E = -114.209 dE =  1.434497e-05 dH =  8.131609e-04                       |
+------------------------------------------------------------------------------+
|                                                                              |
| Fermi Level  = -5.478226 eV                                                  |
+------------------------------------------------------------------------------+
################################################################################
#                                                                              #
# Warning: The calculation did not converge to the requested tolerance!        #
#                                                                              #
################################################################################
+------------------------------------------------------------------------------+
|                                                                              |
| DFT Calculation  [Finished Wed Jul 19 14:56:15 2017]                         |
|                                                                              |
+------------------------------------------------------------------------------+
------------------------------------------------------------------------------------------------------


I want to know, if there is something I can do to improve the convergence of the calculation?

Thank you very much for your time and kind help!

20
General Questions and Answers / why the hdp.py did not show full length of the device?
« on: July 17, 2017, 19:51 »
Dear experts,

I used the hdp.py file from tutorial "Modeling metal–semiconductor contacts: The Ag–Si interface" to make average of my EDP result. http://docs.quantumwise.com/casestudies/ag_si_interface/ag_si_interface.html

Please see the attached figure of the device: the total length of the device is about 90nm. However, the result from hdp.py just showed me a region from 10nm-80nm.  Since I am not very familiar with python script, can anyone here help me to explain why it cannot display the full length of the device in the hdp.py?

BTW, I am using ATK2015.1, together with ATK2016.4.

Thank you very much for your time and kind help!

21
General Questions and Answers / How to get the transmission pathway
« on: July 13, 2017, 02:58 »
Dear ATK experts,

I calculated the I-V curve of a device using ATK SE: Huckel method. The ATK version for calculating the IV curve is 2015.1. All the self-consistent-configuration were saved in one .nc file with different ID. After the IV calculation, I wanted to have a look at the transmission pathway under a certain bias. So I used "analysis from file" block and calculated the transmission pathway for each of the self-consistent-configuration. However, the transmission pathway obtained were not correct, I think. Please see the attached IV curve and one of the transmission pathways (all the others are similar).  I don't know what's wrong with the transmission pathway calculation, since the IV curve is a normal one and there must be something transported through the device. Why I cannot get the correct transmission pathway result?

I am looking forward to your kind help! Thank you very much for your time!

22
General Questions and Answers / Is the IV curve correct?
« on: July 8, 2017, 16:48 »
Dear experts,

I got my IV curve using ATKSE:Extended Huckel method, seen in the attached figure. I have a question on the spectral current. Since the energy did not cover the current region (the blue area), I am not sure if the IV curve is correct. Can anybody here help me with this problem?

Thank you very much for your help!

23
General Questions and Answers / why are the band structures calculated by GGA and SOGGA totally different?
« on: June 18, 2017, 05:17 »
I can understand some minors difference between the results calculated by GGA and SOGGA.

However, seen attached pictures, for calculations with the same bulk configuration and all other identical parameters, the band structures calculated by GGA and SOGGA are totally different. I don't know which one should be more reasonable, since there is no reference for this new bulk configuration. Can anyone here help me with this problem?

Thank you very much for you time and kind help!

24
General Questions and Answers / what's wrong with the website of the Forum?
« on: June 18, 2017, 04:50 »
During the past several days, when I tried to connect to the Forum, a warning message always appeared saying that this website is not safe. Thus I failed to get access to the Forum. Today is the first time to be here again and I want to know what's wrong with this website. Can anybody help me with this problem, since  there is no problem for me to get to the Forum before and the problem is still there even though I have successfully got to the Forum.

25
General Questions and Answers / Can I run this command using VNL?
« on: June 14, 2017, 16:48 »
Dear experts,

I am studying the tutorial "Modeling metal–semiconductor contacts: The Ag–Si interface". There is a script named "hdp.py" and need to be run by "atkpython hdp.py device.nc". Since I am using the windows system, I don't know how to run it through VNL.

Can anybody here help me with this problem?

Thank you very much for your kind help!

26
General Questions and Answers / something wrong with the "viewer" plug-in？
« on: June 13, 2017, 22:48 »
After I changed the fuzz factor in order to have a better view of the bond, the color and font size of the label, as well as the border line of the lattice cannot be changed any more. I am not sure if it is a bug of the "viewer" plug-in.

27
General Questions and Answers / How to restart a geometry optimization calculation with previous trajectory file
« on: June 12, 2017, 15:49 »
Dear all,

I want to restart the geometry optimization calculation which was stopped without finishing. I saved the trajectory file as doing the optimization. Then, how to use the trajectory file to restart the calculation? I have read the tutorial "Restarting a stopped calculation". However, in that tutorial, it was just said "you can take out some of the later images and set up a new optimization using this geometry as a starting point".

The question is: how can I do it? how to use the trajectory file as a starting point?

Thanks very much for your time and kind help!
 

28
General Questions and Answers / What's wrong with my ElectrostaticDifferencePotential result?
« on: June 12, 2017, 00:42 »
Dear experts,

I tried to calculated the ElectrostaticDifferencePotential of a device using the attached .py file. And the attached .png file shows the 1D plot of the potential along c direction. It seems that the length of the screening region is not long enough. My questions are, what's the y coordinate of this plot? why the value of y coordinate is so large?

Thanks a lot for anyone willing to help me!

29
General Questions and Answers / What is the "device relaxation" for?
« on: June 8, 2017, 05:22 »
Dear experts,

I am now studying the geometry optimization of an interface based device. From the tutorial "Advanced device relaxation", we can see that the geometry optimization of such a device includes these steps:

(1) constructing the interface using the "Interface" plug-in;
(2) using the "device from bulk" plug-in to build the two-probe device;
(3) splitting the device into three parts: the left electrode, the right electrode and the central region;
(4) geometry optimizing the two electrodes (sometimes only one electrode needs to be optimized);
(5) applying the effect of the geometry optimization of the electrode onto the corresponding atoms in the central region by stretching the atoms;
(6) geometry optimizing the central region using Bulk Rigid Relaxation (BRR) method as described in the tutorial. Sometimes a 1DMIN method will also be used to improve the accuracy;
(7) the final device configuration can be obtained by applying "device from bulk" again onto the relaxed central region;

However, in tutorial "Modeling metal–semiconductor contacts: The Ag–Si interface", after relaxing the central region of the Ag-Si interface device, an additional "Device relaxation" was carried out. I don't know what's this step for. Is it necessary to do so?

And, it was said in this tutorial that the time consuming for the relaxation of the central region needs about 20 hours on a 16-core node, while the time consuming for the relaxation of the whole device only takes about 2 hours on 16 cores. Since the whole device is larger than the central region, why is the time consuming for the relaxation of the whole device far less than that needed for the relaxation of the central?

Thank you very much for you time and kind help!



30
General Questions and Answers / How to get the electron affinity from the band structure?
« on: June 4, 2017, 05:48 »
Dear experts,

I want to extract the electron affinity from the band structure where the electron affinity is defined as the difference between the minimum energy of the conduction band (CBM) and free electron level in vacuum. Can anybody here tell me how to do it?

Thank a lot for your time and kind help!

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