Messages

16

General Questions and Answers / How to initial decide the molecule position in a two probe device

« on: March 11, 2014, 03:46 »

    The left and right electrode had been completed and the distance between the two electrode was set. Then the molecule was put in the center of the device by using "center" option in the "Coordinate Tools".
    But I was not sure whether the center was the perfect position for the molecule. And It would cost much time by using the "Optimize Geometry" in "Script Generator" to optimize the position of the molecule.
   Another problem was the it would change the molecule structure during optimization.
   I didn`t know how to deal with that.

17

General Questions and Answers / DOS difference

« on: February 21, 2014, 13:23 »

     I have used VNL 13.8.0 to calculate electrode-molecule-electrode Device Density of State and the result is shown in figure1. So I used VNL2008.10 calculate this device`s DOS again and the result is shown in figure2. Both the result shows that they have the similar trend, but their value are very different, about one order of magnitude difference. I`m not sure which one is right?
     The primary parameters in VNL2008.10 are set as attachment3.
      
  

18

General Questions and Answers / Re: "internal error"

« on: February 21, 2014, 08:21 »

Yes! It works now! Thank you!

19

General Questions and Answers / "internal error"

« on: February 21, 2014, 03:05 »

  There is always an error happens when I try to use the VNL 2008.10 to open a "py" file. Restarting or reinstallation still cannot solve this problem. Is it because the incomplete software i got or it is incompatible with my computer?

20

General Questions and Answers / Re: "PeriodicAtomConfiguration" error

« on: February 20, 2014, 08:24 »

In the VNL 13.8, Is it still necessary to set these following parameters when I use a "New Calculator"?
    type = DoubleZetaPolarized,
    radial_sampling_dr = 0.001*Bohr,
    energy_shift = 0.01*Rydberg,
    delta_rinn = 0.8,
    v0 = 40.0*Rydberg,
    charge = 0.0,
    split_norm = 0.15
They are the "basis set" parameters in VNL2008. I am not sure whether they are still the same default value in VNL13.8.

21

General Questions and Answers / Re: "PeriodicAtomConfiguration" error

« on: February 20, 2014, 03:07 »

Thank you, Mr. Martinez. That really helps a lot! But there is still some questions including sensitive aspects. Can I send my message to you by email,  Mr. Martinez?

22

General Questions and Answers / "PeriodicAtomConfiguration" error

« on: February 19, 2014, 08:09 »

Dear all,
I had constructed a two probe configuration-[Au electrode-Molecule-Au electrode] by using VNL 2008.10. Now I want to use VNL 13.8.0 to run the script. But there`re always error existing. I don`t know how to adjust my code to VNL13.8.0. The attachment is the code.

23

General Questions and Answers / Re: error message

« on: January 23, 2014, 11:53 »

They were created by other person at least one year ago and the both software and licence were lost. So just the files were left. Now I want to use the files for some data. Can I email these files to your company to use the old verson software opening these files or translating them to the new verson files?

24

General Questions and Answers / Re: error message

« on: January 22, 2014, 12:30 »

But I really need to open these files edited by the old version software. They are very important. Is there any other methods any more?

25

General Questions and Answers / Re: error message

« on: January 19, 2014, 05:00 »

Where can I get the old VNL software! Is there any website link?

26

General Questions and Answers / Re: error message

« on: January 18, 2014, 09:28 »

I now know the file may be  created by using Virtual NanoLab 2008.2. But i didn

27

General Questions and Answers / error message

« on: January 18, 2014, 04:10 »

Dear all,
   When I run a complete .VNL file using Virtual nanoLab 13.8.0, there was always an error message:

   The following error message was generated when attempting to read a file:
The format of the file C:/Users/think/Desktop/1.vnl cannot be determined
If the message does reveal the cause of the error, please report the issue to QuantumWise, and make sure to include the traceback (click "Show Details...").
  Traceback (most recent call last):
  File ".\zipdir\NL\GUI\DnD\MimeData.py", line 253, in _urlTypes
  File ".\zipdir\NL\IO\ConfigurationsImporter.py", line 151, in __init__
  File ".\zipdir\NL\IO\ConfigurationsImporter.py", line 254, in inspect
NLIOError: The format of the file C:/Users/think/Desktop/1.vnl cannot be determined

   The file cannot be open. Is this the reason of different computer system or anything else. How to deal with it.
   Thanks in advance!

28

General Questions and Answers / How to optimize the molecule in device.

« on: January 16, 2014, 13:54 »

Dear friends,
  I have made a two probe configuration:[Au electrode]-[molecule]-[Au electrode]. The structure of molecule(a cubic) had been optimised individually before used to construct the two probe device.
The distance between two electrode was based on experience parameter.

  The initial structure of the device is shown in figure1.
  The electrode is two layers, and the Unit Vector is:
           vector_a = [5.89465425896, 0.0, 0.0]*Angstrom
           vector_b = [0.0, 5.89465425896, 0.0]*Angstrom
           vector_c = [0.0, 0.0, 4.16814999926]*Angstrom
  Five layers of Au slab were chosen in z direction as left electrode and electrode extension just for a fast computational speed.  
  The perpendicular distance between the left electrode and the leftmost atom of the molecule as well as counterpart in the right is 2.0 Å as experience.
  More detail parameters are in the attached script.
  
  So I decided to optimized structure of the molecule in this device. We kept all gold atoms fixed and relax the molecule in the center until the forces on each atom are smaller than 0.05 eV/ Å in the
optimization.

  But the result I got was unstatisfied, because the change of molecule`s shape is too big, not cubic any more, as in figure2. So I think there must be someting wrong.
  1.The perpendicular distance between the left electrode and the leftmost atom of the molecule is 2.0 Å according to experience. But I am not sure whether it is the cause of the mistake.
  2. In this work, only five layers of Au slab are used because they are enough for such small molecule. Also I am not sure it is reasonable.
  
  The two above is just the reasons I speculated. And this problem is still making me confused.
  
 Thanks in advance!

29

General Questions and Answers / Re: construct Au electrode with 2 × 2 layers in x and y directions

« on: January 15, 2014, 13:15 »

     Thank you, Mr Martinez. I think I now know how to deal with it and I will check again with the two links above. Thanks a lot.
     

30

General Questions and Answers / Re: construct Au electrode with 2 × 2 layers in x and y directions

« on: January 14, 2014, 08:25 »

Thank you, Mr Martinez. You`ve maken a very clear guidance. thank you, again!
I think I have made some improvements by follwing your guide and the figure1 shows the structure I got.

Then I made some trials to construct a whole two probe model including both left and right parts. But I am not sure whether the processes are reasonable.
After getting the figure1, the structure was repeated in C direaction 2 times, using the "repeat" plugin in Bulk Tools. So there are 4 layers in C direction.
Then I "drag" repeated structure itself into the builder. After that,  Z`=Z+10 was inputted into Transform by Expression plugin in the Coordinate Tools to seperated them.
Then using Device Tools->Device From Bulk, so there is a two probe with right and left electrodes, as figure3.

But the  "Screening Region" is 4 layers which may be slightly more. And I am not sure whether the whole processes are reasonable.