Topics

1

General Questions and Answers / About the unit of external potential

« on: December 24, 2012, 08:57 »

Dear Quantumwise Staff:
    Recently I calculate the external potential and get confused by its unit. Why is it in the unit of eV? Shouldn't it be V?
   
    PS: The manual says "ExternalPotential, returns the electrostatic potential due to the electrodes and gates in the system". How to tell the external potential from the internal one? Is the screening effect included in the external potential calculation?

    Thank you!

2

General Questions and Answers / Question about annealing and current calculation

« on: November 14, 2012, 06:31 »

Dear Quantumwise Staff:

I have two questions and they may be related or not.

First, when I find it hard to converge for a certain device, I raise the temperature in both electrode and central region to a higher one, say 1000 K. Then the obtained .nc file is used as the initial state for the room temperature calculation by manually reading and adjusting the former "electron_temperature" in electrodes' and central region's calculators. Is such annealing procedure correct?

Second, when I calculate the current of room temperature .nc file obtained by annealing, a great discrepancy occurs between the current of "transmission_spectrum.current()" (I added it to the script) and the one shown by the analyzer. Such mismatch can be up to 2 orders of magnitude. Which current is reliable? Or neither?

Thank you!

3

General Questions and Answers / Question about hydrogenation in builder 12.2.1

« on: June 29, 2012, 17:31 »

Dear Quantumwise staff:

    Recently I'm trying to learn the new builder, it looks cool but does have some defect. I have scanned the tutorials with no answers, or maybe I just missed them...
    First, where can I choose the form of hydrogenation? I'm curious about silicene, in which the hydrogenation is probably sp2 like and only edge atoms get hydrogenated, but the hydrogenate button always gives an sp3 form and make every Si atom connected with at least an H.
    Second, edge Boron in h-BN can't be hydrogenated, but Nitride is no problem.
    Finally, how can I add a single atom in the builder without directly modifying the python script? I hope there is some way to add atoms and make their distance to edge reasonable. Imagine the edge of GNR is functionalized by atoms with a variety of bond lengths. Such system is hard to build using current builder.
    Last but not least, is there anyway to reset camera to xy, yz and xz plane? And may I save current work place as a whole project and reload all needed parts in the stash at a time?

    The new builder is really cool in the selection function and many other things. Tags are convenient. I have used Materials Studio and it has a really strong builder system, you can learn something from it. I think everything will be better in ATK:)

4

General Questions and Answers / Convergence Problem

« on: April 17, 2012, 17:26 »

Dear Quantum Staff:

Recently I've tested some silicene FET structures. The first structure was hard to converge but I managed to make it. However, when I come to the second one (attached, very similar to the first one), it doesn't converge at the equivalent bulk calculation. The dH is 1E+9! I've no idea about the reason. Could you please test my script? Any advise will be appreciated.

By the way, is it necessary to set the kpoint number in the z direction of central region? In this case (2D silicene FET in yz plain), may I use (1,50,1) instead of (1,50,50) as the central region kpoints? Thank you for your answer!

5

General Questions and Answers / Question about initial state

« on: April 3, 2012, 14:09 »

Recently I noticed that if I use previously converged structures stored in .nc file as the initial state to start a new SCF cycle (with probably some changes, say, in the voltages of metallic regions), the electrodes' calculation will be skipped. Is it reasonable?

Particularly, if the bias voltages (and some parameters such as gate voltages) are changed while the structure is unchanged, is it still a good way to converge with previous converged states as initials?

6

General Questions and Answers / Convergence problem in 11.8b1

« on: November 3, 2011, 09:02 »

Recently I tried mGGA in bulk calculation. It converges well and yields a good bandgap result, so I think mGGA should give better results in device calculation. However, when I tried 11.8b1 with my old device structures (which means they converge well in 11.2.3 using PBE), severe convergence problem occured in all part of Two Probe calculation using mGGA. Every part of Two Probe calculation is not able to converge, from the electrode to central region SCF. I've tried methods like anneling, pre-conditioner, tuning the iteration parameters and using the previous PBE .nc file as the initial state, but all didn't work. Even the electrode calculation is not able to converge.

Is there anyone else having such convergence problem?

My system is all made up of Si atoms, having 8 atoms in electrode and 50-100 atoms in central region (I've changed it from 144 to 72 and still got such problem) and two metallic regions.

PS: Have 11.8.b1 expired now?

7

General Questions and Answers / Trouble with Segmentation fault

« on: June 18, 2011, 16:14 »

Recently I calculated a system with ATK DFT pack. I wrote a script for the system with a controllable channel length to learn the dependence of transmission spectrum on it. It works well with any length <= 19 cells, whereas systems with lengths above 19 cells encounter the segmentation fault just after equivalent bulk calculation and before device SCF.

Code

+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 11.2.0 [Build 3044]                                        |
|                                                                              |
+------------------------------------------------------------------------------+

.....omitted for the maximum allowed length of this message^_^

Calculating Eigenvalues    : ==================================================
Calculating Density Matrix : ==================================================

+------------------------------------------------------------------------------+
| Density Matrix Report                             DM        DD               |
+------------------------------------------------------------------------------+
|   0  Si   [   15.666 ,   15.465 ,    0.000 ]    4.00008   0.00008            |
|   1  Si   [   16.119 ,   17.398 ,    1.116 ]    3.99996  -0.00004            |
|   2  Si   [   15.666 ,   17.398 ,    3.348 ]    4.00000   0.00000            |
|   3  Si   [   16.119 ,   15.465 ,    4.464 ]    4.00001   0.00001            |
|   4  Si   [   15.666 ,   15.465 ,    6.696 ]    4.00003   0.00003            |
|   5  Si   [   16.119 ,   17.398 ,    7.812 ]    3.99992  -0.00008            |
|   6  Si   [   15.666 ,   17.398 ,   10.044 ]    4.00006   0.00006            |
|   7  Si   [   16.119 ,   15.465 ,   11.160 ]    3.99997  -0.00003            |
|   8  Si   [   15.666 ,   15.465 ,   13.392 ]    4.00003   0.00003            |
|   9  Si   [   16.119 ,   17.398 ,   14.508 ]    3.99999  -0.00001            |
|  10  Si   [   15.666 ,   17.398 ,   16.740 ]    3.99999  -0.00001            |
|  11  Si   [   16.119 ,   15.465 ,   17.856 ]    3.99996  -0.00004            |
|  12  Si   [   15.666 ,   15.465 ,   20.088 ]    4.00008   0.00008            |
|  13  Si   [   16.119 ,   17.398 ,   21.204 ]    3.99994  -0.00006            |
|  14  Si   [   15.666 ,   17.398 ,   23.436 ]    4.00002   0.00002            |
|  15  Si   [   16.119 ,   15.465 ,   24.552 ]    4.00002   0.00002            |
|  16  Si   [   15.666 ,   15.465 ,   26.784 ]    4.00002   0.00002            |
|  17  Si   [   16.119 ,   17.398 ,   27.900 ]    3.99994  -0.00006            |
|  18  Si   [   15.666 ,   17.398 ,   30.132 ]    4.00005   0.00005            |
|  19  Si   [   16.119 ,   15.465 ,   31.249 ]    3.99996  -0.00004            |
|  20  Si   [   15.666 ,   15.465 ,   33.481 ]    4.00005   0.00005            |
|  21  Si   [   16.119 ,   17.398 ,   34.597 ]    3.99999  -0.00001            |
|  22  Si   [   15.666 ,   17.398 ,   36.829 ]    3.99998  -0.00002            |
|  23  Si   [   16.119 ,   15.465 ,   37.945 ]    3.99997  -0.00003            |
|  24  Si   [   15.666 ,   15.465 ,   40.177 ]    4.00007   0.00007            |
|  25  Si   [   16.119 ,   17.398 ,   41.293 ]    3.99993  -0.00007            |
|  26  Si   [   15.666 ,   17.398 ,   43.525 ]    4.00003   0.00003            |
|  27  Si   [   16.119 ,   15.465 ,   44.641 ]    4.00001   0.00001            |
|  28  Si   [   15.666 ,   15.465 ,   46.873 ]    4.00001   0.00001            |
|  29  Si   [   16.119 ,   17.398 ,   47.989 ]    3.99995  -0.00005            |
|  30  Si   [   15.666 ,   17.398 ,   50.221 ]    4.00004   0.00004            |
|  31  Si   [   16.119 ,   15.465 ,   51.337 ]    3.99995  -0.00005            |
|  32  Si   [   15.666 ,   15.465 ,   53.569 ]    4.00007   0.00007            |
|  33  Si   [   16.119 ,   17.398 ,   54.685 ]    3.99998  -0.00002            |
|  34  Si   [   15.666 ,   17.398 ,   56.917 ]    3.99998  -0.00002            |
|  35  Si   [   16.119 ,   15.465 ,   58.033 ]    3.99999  -0.00001            |
|  36  Si   [   15.666 ,   15.465 ,   60.265 ]    4.00006   0.00006            |
|  37  Si   [   16.119 ,   17.398 ,   61.381 ]    3.99992  -0.00008            |
|  38  Si   [   15.666 ,   17.398 ,   63.613 ]    4.00005   0.00005            |
|  39  Si   [   16.119 ,   15.465 ,   64.729 ]    4.00000   0.00000            |
|  40  Si   [   15.666 ,   15.465 ,   66.961 ]    4.00001   0.00001            |
|  41  Si   [   16.119 ,   17.398 ,   68.077 ]    3.99997  -0.00003            |
|  42  Si   [   15.666 ,   17.398 ,   70.309 ]    4.00002   0.00002            |
|  43  Si   [   16.119 ,   15.465 ,   71.425 ]    3.99994  -0.00006            |
|  44  Si   [   15.666 ,   15.465 ,   73.657 ]    4.00008   0.00008            |
|  45  Si   [   16.119 ,   17.398 ,   74.773 ]    3.99997  -0.00003            |
|  46  Si   [   15.666 ,   17.398 ,   77.005 ]    3.99999  -0.00001            |
|  47  Si   [   16.119 ,   15.465 ,   78.121 ]    4.00000   0.00000            |
|  48  Si   [   15.666 ,   15.465 ,   80.353 ]    4.00004   0.00004            |
|  49  Si   [   16.119 ,   17.398 ,   81.469 ]    3.99992  -0.00008            |
|  50  Si   [   15.666 ,   17.398 ,   83.701 ]    4.00006   0.00006            |
|  51  Si   [   16.119 ,   15.465 ,   84.817 ]    3.99999  -0.00001            |
|  52  Si   [   15.666 ,   15.465 ,   87.049 ]    4.00002   0.00002            |
|  53  Si   [   16.119 ,   17.398 ,   88.165 ]    3.99998  -0.00002            |
|  54  Si   [   15.666 ,   17.398 ,   90.397 ]    4.00001   0.00001            |
|  55  Si   [   16.119 ,   15.465 ,   91.514 ]    3.99995  -0.00005            |
|  56  Si   [   15.666 ,   15.465 ,   93.746 ]    4.00008   0.00008            |
|  57  Si   [   16.119 ,   17.398 ,   94.862 ]    3.99996  -0.00004            |
|  58  Si   [   15.666 ,   17.398 ,   97.094 ]    4.00000   0.00000            |
|  59  Si   [   16.119 ,   15.465 ,   98.210 ]    4.00001   0.00001            |
|  60  Si   [   15.666 ,   15.465 ,  100.442 ]    4.00003   0.00003            |
|  61  Si   [   16.119 ,   17.398 ,  101.558 ]    3.99992  -0.00008            |
|  62  Si   [   15.666 ,   17.398 ,  103.790 ]    4.00006   0.00006            |
|  63  Si   [   16.119 ,   15.465 ,  104.906 ]    3.99997  -0.00003            |
|  64  Si   [   15.666 ,   15.465 ,  107.138 ]    4.00003   0.00003            |
|  65  Si   [   16.119 ,   17.398 ,  108.254 ]    3.99999  -0.00001            |
|  66  Si   [   15.666 ,   17.398 ,  110.486 ]    3.99999  -0.00001            |
|  67  Si   [   16.119 ,   15.465 ,  111.602 ]    3.99996  -0.00004            |
|  68  Si   [   15.666 ,   15.465 ,  113.834 ]    4.00008   0.00008            |
|  69  Si   [   16.119 ,   17.398 ,  114.950 ]    3.99994  -0.00006            |
|  70  Si   [   15.666 ,   17.398 ,  117.182 ]    4.00002   0.00002            |
|  71  Si   [   16.119 ,   15.465 ,  118.298 ]    4.00002   0.00002            |
|  72  Si   [   15.666 ,   15.465 ,  120.530 ]    4.00002   0.00002            |
|  73  Si   [   16.119 ,   17.398 ,  121.646 ]    3.99994  -0.00006            |
|  74  Si   [   15.666 ,   17.398 ,  123.878 ]    4.00005   0.00005            |
|  75  Si   [   16.119 ,   15.465 ,  124.994 ]    3.99996  -0.00004            |
|  76  Si   [   15.666 ,   15.465 ,  127.226 ]    4.00005   0.00005            |
|  77  Si   [   16.119 ,   17.398 ,  128.342 ]    3.99999  -0.00001            |
|  78  Si   [   15.666 ,   17.398 ,  130.574 ]    3.99998  -0.00002            |
|  79  Si   [   16.119 ,   15.465 ,  131.690 ]    3.99997  -0.00003            |
|  80  Si   [   15.666 ,   15.465 ,  133.922 ]    4.00007   0.00007            |
|  81  Si   [   16.119 ,   17.398 ,  135.038 ]    3.99993  -0.00007            |
|  82  Si   [   15.666 ,   17.398 ,  137.270 ]    4.00003   0.00003            |
|  83  Si   [   16.119 ,   15.465 ,  138.386 ]    4.00001   0.00001            |
|  84  Si   [   15.666 ,   15.465 ,  140.618 ]    4.00001   0.00001            |
|  85  Si   [   16.119 ,   17.398 ,  141.734 ]    3.99995  -0.00005            |
|  86  Si   [   15.666 ,   17.398 ,  143.966 ]    4.00004   0.00004            |
|  87  Si   [   16.119 ,   15.465 ,  145.082 ]    3.99995  -0.00005            |
|  88  Si   [   15.666 ,   15.465 ,  147.314 ]    4.00007   0.00007            |
|  89  Si   [   16.119 ,   17.398 ,  148.430 ]    3.99998  -0.00002            |
|  90  Si   [   15.666 ,   17.398 ,  150.662 ]    3.99998  -0.00002            |
|  91  Si   [   16.119 ,   15.465 ,  151.779 ]    3.99999  -0.00001            |
|  92  Si   [   15.666 ,   15.465 ,  154.011 ]    4.00006   0.00006            |
|  93  Si   [   16.119 ,   17.398 ,  155.127 ]    3.99992  -0.00008            |
|  94  Si   [   15.666 ,   17.398 ,  157.359 ]    4.00005   0.00005            |
|  95  Si   [   16.119 ,   15.465 ,  158.475 ]    4.00000   0.00000            |
|  96  Si   [   15.666 ,   15.465 ,  160.707 ]    4.00001   0.00001            |
|  97  Si   [   16.119 ,   17.398 ,  161.823 ]    3.99997  -0.00003            |
|  98  Si   [   15.666 ,   17.398 ,  164.055 ]    4.00002   0.00002            |
|  99  Si   [   16.119 ,   15.465 ,  165.171 ]    3.99994  -0.00006            |
|  100  Si   [   15.666 ,   15.465 ,  167.403 ]    4.00008   0.00008           |
|  101  Si   [   16.119 ,   17.398 ,  168.519 ]    3.99997  -0.00003           |
|  102  Si   [   15.666 ,   17.398 ,  170.751 ]    3.99999  -0.00001           |
|  103  Si   [   16.119 ,   15.465 ,  171.867 ]    4.00000   0.00000           |
|  104  Si   [   15.666 ,   15.465 ,  174.099 ]    4.00004   0.00004           |
|  105  Si   [   16.119 ,   17.398 ,  175.215 ]    3.99992  -0.00008           |
|  106  Si   [   15.666 ,   17.398 ,  177.447 ]    4.00006   0.00006           |
|  107  Si   [   16.119 ,   15.465 ,  178.563 ]    3.99999  -0.00001           |
|  108  Si   [   15.666 ,   15.465 ,  180.795 ]    4.00002   0.00002           |
|  109  Si   [   16.119 ,   17.398 ,  181.911 ]    3.99998  -0.00002           |
|  110  Si   [   15.666 ,   17.398 ,  184.143 ]    4.00001   0.00001           |
|  111  Si   [   16.119 ,   15.465 ,  185.259 ]    3.99995  -0.00005           |
+------------------------------------------------------------------------------+
|   2 E = -144.593 dE =  3.562179e-03 dH =  1.152072e-03                       |
+------------------------------------------------------------------------------+
| Calculation Converged in 2 steps                                             |
|                                                                              |
| Fermi Level  = -3.679114 eV                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Equivalent Bulk  [Finished Mon Apr 11 23:23:39 2011]                         |
|                                                                              |
+------------------------------------------------------------------------------+
/home/zxgao/QuantumWise/atk-11.2.0/atkpython/bin/atkpython: line 3: 18596 Segmentation fault      PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../share/pseudopotentials GPAW_SETUP_PATH=$EXEC_DIR/../share/gpaw-setups/ PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atkpython_exec $*

Is it a problem of lacking memory? My machine has 24G mems and my structure has 92 atoms in 19-cell system and 96 atoms in 20-cell one, buffer layers and electrodes included. SZ basis is chosen. I have examined the calculation of 19-cell system and found the maximum mem no more than 60%. So I think it is probably not a problem of mem, nor is a problem of my script since it works well with shorter channels. I'm really confused with such problem. Is there any other possible cause？My atk ver is 11.2.0. Do I have to update it?

Thank you for your answer!