I have two questions:
Q1, how to import the structure file "Au-DTB-Au.VNL" from the example folder of VNL2008.10 to VNL10.8.0, since the VNL format file is invalid in 10.8.0?
(I try to open the Au-DTB-Au.VNL file in 2008.10 and save as to Au-DTB-Au.py file, and then import it into 10.8. However, an error shows "An error occurred
The following error message was generated when running the script:
The last 27 atoms of the central region must match the last 27 atoms of the right electrode region. Atom 75 of the central region was Au at (4.32537207 Ang, 2.497254786 Ang, 23.85660639 Ang), it should have been Au at (0.0 Ang, 0.0 Ang, 23.85660639 Ang).
Typically this is caused by a syntax error or a spelling mistake; the message above should be helpful in correcting the issue in such cases.
If you believe the error is caused by VNL itself, please report the issue to QuantumWise, and make sure to include the traceback (click "Show Details...") and the script")
Q2, I want to optimize the above structure under a bias (4 V) in the VNL10.8.0, since it argues that the new version (10.
can do the real optimizaion under bias. The optimization calculaion is fine (
| Optimization Information Fx Fy Fz |
+------------------------------------------------------------------------------+
| 0 Au [ 7.930 , 0.416 , 1.177 ] 0.00000 0.00000 0.00000 |
...
| 26 Au [ 2.163 , 7.076 , 5.886 ] 0.00000 0.00000 0.00000 |
| 27 C [ 2.163 , 3.746 , 9.340 ] 0.00002 -0.37070 -0.47289 |
| 28 C [ 2.163 , 2.537 , 10.038 ] 0.00012 0.15417 1.02052 |
| 29 C [ 2.163 , 2.537 , 11.434 ] -0.00002 0.58899 -2.46883 |
| 30 C [ 2.163 , 3.746 , 12.132 ] -0.00014 0.45219 0.79718 |
| 31 C [ 2.163 , 4.955 , 11.434 ] -0.00001 -1.06966 -2.09744 |
| 32 C [ 2.163 , 4.955 , 10.038 ] 0.00019 0.22143 0.79862 |
| 33 S [ 2.163 , 3.746 , 7.586 ] 0.00144 -0.06909 0.41823 |
| 34 H [ 2.163 , 1.599 , 9.496 ] -0.00001 -3.08222 -1.47391 |
| 35 H [ 2.163 , 1.599 , 11.976 ] 0.00003 -3.46500 2.21446 |
| 36 S [ 2.163 , 3.746 , 13.886 ] -0.00004 0.09841 -3.48203 |
| 37 H [ 2.163 , 5.893 , 11.976 ] -0.00008 3.48056 2.25191 |
| 38 H [ 2.163 , 5.893 , 9.496 ] -0.00010 3.06288 -1.45637 |
| 39 Au [ 7.930 , 0.416 , 15.586 ] 0.00000 0.00000 0.00000 |
...
| 65 Au [ 2.163 , 7.076 , 20.296 ] 0.00000 0.00000 0.00000 |
+------------------------------------------------------------------------------+
| Optimization step = 0 E = -7.1426e+04 eV Maximum force = 3.4806e+00 eV/Ang |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Device Calculation [Started Tue Aug 17 15:50:42 2010])
My question is why there is only one step of optimization before the device property calculation? What is the meaning of values of Forcexyz? The force difference before and after optimization? How to view the optimized structure? Why the structure of analysis.nc file is the same as the initial structure?
Sorry for too many questions. Many thanks.
BTW: I have 3 year experience in using ATK, but I still cannot manipulate the new version. Therefore, a detail manual/tutorial of the new version is necessory and important!