error in extraction of vnl file

[quantum2009]

i am trying to extract the data from vnl file with a scirpt from your forum. when i run through Job manager i got this error

Running: C:\Program Files\QuantumWise\Virtual NanoLab 2008.10.0\atk\bin\atk.exe c:/docume~1/admini~1/locals~1/temp/tmpibuyq5.nl
Please enter VNL file name:
Traceback (most recent call last):
  File "c:/docume~1/admini~1/locals~1/temp/tmpibuyq5.nl", line 3, in ?
    filename = raw_input('Please enter VNL file name: ')
EOFError: EOF when reading a line
Terminated Abnormally

help me to solve this issue

[serhan]

Welcome to the forum!

When I looked at the py file, it seems that it will get input from the console, that means you have to use ATK in command window. The job manager also starts ATK, however I think it is not possible to input a filename on job manager window. So, in Windows terminal,  try please giving the command 'atk extract_transmission_from_VNL_file.py' command. Then it will run as expected.

Cheers,
Serhan

[Anders Blom]

Alternatively, you can modify the script to not ask for the file name interactively, but just enter the VNL file name manually into the script before you run it. In this case you also need to hardcode the sample name into the script. See http://quantumwise.com/forum/index.php?topic=300.0 for a discussion on precisely this.

[quantum2009]

yes i got the data from vnl file. Now i need to do the same for a vnl file which contains density of states Vs energy. i modified that script. but got some error.

Running: C:\Program Files\QuantumWise\Virtual NanoLab 2008.10.0\atk\bin\atk.exe c:/docume~1/admini~1/locals~1/temp/tmp6u9xny.nl
The following samples are present in this VNL file:
['twoprobe_configuration']
['Local Density Of States Local Density Of States', 'Density Of States Density of states']
Traceback (most recent call last):
  File "c:/docume~1/admini~1/locals~1/temp/tmp6u9xny.nl", line 69, in ?
    trans = data['Desnsity Of States Desnity of states']
KeyError: 'Desnsity Of States Desnity of states'
Terminated Abnormally

what is the problem with the script?

[Anders Blom]

Just a typo

The key should be 'Density Of States Density of states', but you put 'Desnsity Of States Desnity of states' in your script.

[quantum2009]

now i got this follwoing error

Running: C:\Program Files\QuantumWise\Virtual NanoLab 2008.10.0\atk\bin\atk.exe c:/docume~1/admini~1/locals~1/temp/tmpdx271j.nl
The following samples are present in this VNL file:
['twoprobe_configuration']
['Local Density Of States Local Density Of States', 'Density Of States Density of states']
Energy (eV)    Desnity of states
----------------------------------
Traceback (most recent call last):
  File "c:/docume~1/admini~1/locals~1/temp/tmpdx271j.nl", line 81, in ?
    T = trans.density_of_states()
AttributeError: TransmissionSpectrumTimeReversalSymmetryReduced instance has no attribute 'density_of_states'
Terminated Abnormally

[Anders Blom]

It should be

Code

T = trans.average_density_of_states()

The reason is that the DOS, like the transmission, is an average over the k-points in the Brillouin zone sampling. Are you familiar with the very useful command "dir"? It can really help in situations like this. You can insert "print dir(trans)" and then you will see all properties of the object "trans"