Messages

46

General Questions and Answers / Re: KeyError

« on: February 11, 2010, 09:17 »

Dr. Blom,

Thanks for your reply, however when I use:
...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
twoprobe_config=configs[configs.keys()[0]]

I get:

Traceback (most recent call last):
  File "Li_SW15_2-Trans.Spec.py", line 9, in ?
    twoprobe_config=configs[configs.keys()[0]]
IndexError: list index out of range

And, when I try to get the configuration name using
...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
print configs.keys()

I get only []

Besides that I have also used the configuration name in the Result Browser in VNL and again it gives KeyError.

Is there any other reason?

Thanks,

47

General Questions and Answers / KeyError

« on: February 10, 2010, 21:56 »

Hi,

I have an input:

....
system = "system_name"
vnlfile=VNLFile(system + ".vnl")
twoprobe_config=vnlfile.readAtomicConfigurations()[system]
....

Upon running I get the following error:

Traceback (most recent call last):
  File "system_name_file.py", line 7, in ?
    twoprobe_config=vnlfile.readAtomicConfigurations()[system]
KeyError: 'system_name'

What can be the reason?
Thanks

48

General Questions and Answers / Re: Decision of Iteration control parameters

« on: October 21, 2009, 09:30 »

Many thanks for your quick reply,

49

General Questions and Answers / Re: Decision of Iteration control parameters

« on: October 21, 2009, 09:03 »

Thanks for your reply A.Blom, then how can I insert the increasing step number in this script?

50

General Questions and Answers / Decision of Iteration control parameters

« on: October 20, 2009, 14:11 »

Hi,

I am running the VNL to calculate the transmission coefficients for some systems including around 500 atoms. For some systems we need to increase the max. step the under  "Iteration control parameters " otherwise we get:

"ATKError: Exceeded maximum number of self-consistent iterations.
Terminated Abnormally"

and of course it takes time!

1) Is there anyway to decide  the max. steps roughly before starting the calculation, so that we are able to save time?

2) Is there any other reason(s) of that error?

3) If we get this error and program terminates abnormally, using the produced nc file, is it possible to start the calculation at this point by increasing the step number?

Many Thanks,

51

General Questions and Answers / Hopping energy(nearest-neighbour) and on-site energy

« on: October 7, 2009, 09:16 »

Hi,

I wonder how I can define or introduce nearest-neighbour hopping energy and on-site energies (defined in tight-binding Hamiltonian) for one dimensional chains.

Thanks for your answer(s)

52

General Questions and Answers / Re: Python Files in VNL

« on: July 29, 2009, 14:48 »

Dr. Blom,

Thanks for your reply. I will check the system in Nanoscope as well.

53

General Questions and Answers / Re: Python Files in VNL

« on: July 29, 2009, 12:54 »

Thanks for your replies. In this way I can make some calculations. Actually the main reason that I have asked this question is that, when I drop the python file, without producing .vnl file,  to atomic manipulator there are some changes in the geometry(expecially in coordinates) of the system. For example there can be shift in the sample placed in the central region of the two probe system. In addtion to that even if I introduced surface layers in the python file, in the left panel of the atomic manipulator surface layers get zero value. Is this because of completed two-probe system in the python file as ZH indicated?

Thanks

54

General Questions and Answers / Python Files in VNL

« on: July 28, 2009, 23:05 »

Hi,

I am using VNL. I have edited python files and added some lines into them to get some specific two probe systems. However when I drag and drop this python file directly to atomic manipulator, somehow the system configured in the python file has some modifications, it is deteriorating. Also in the atomic manipulator on the left panel repetition tab comes out instead of surface tab. Is this because of not exporting the python file to vnl file? If it is so, how can I export the python file to vnl file in VNL?

Many Thanks for your help,

55

Installation and License Questions / License feature checkout failed:License server machine is down or not responding

« on: July 22, 2009, 11:25 »

Hi,

I am trying to configuring the client in Windows to load the floating license server installed in Linux server. However Filexible License Manager gives the following error:

ERROR: License feature checkout failed:License server machine is down or not responding. See the system administrator about starting the license server system, or make sure you're referring to the right host (see LM_LICENSE_FILE).
Feature: VNL
Hostname:      license_server
License path:  27001@license_server
FLEXnet Licensing error:-96,491.  For further information, refer to the FLEXnet Licensing End User Guide,
available at "www.macrovision.com".

I know that License server machine is running. How can I resolve this problem?

Thanks,

56

Installation and License Questions / No Display found. Running in console mode not supported.

« on: June 17, 2009, 07:47 »

Hi,

I have installed the VNL into the server, through the license server and it was working! Upon logging out and logging in I was not able to run VNL, giving the error " No Display found. Running in console mode not supported.". Could you please elucidate the problem?

Thanks!

Sergio!