KeyError

[sergio]

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

[Anders Blom]

For this code to work, you would have had to save the configuration to the VNL with the name "system_name". If you know that the VNL file only contains a single configuration, you can always use the construction

Code

...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
twoprobe_config=configs[configs.keys()[0]]

where "file.vnl" should be the proper name of the VNL file. Otherwise, if you forgot the name used to store the configuration, use this code:

Code

...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
print configs.keys()

This will print the configuration name; let's say it is "my_system". Then use that in

Code

twoprobe_config=vnlfile.readAtomicConfigurations()["my_system"]

You can also open the VNL file in the Result Browser in VNL, then you will see the configuration name.

[sergio]

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,

[Anders Blom]

Most likely only the results are stored in the VNL file, not the geometry. This typically happens for PeriodicAtomConfigurations, like nanotubes, if you are unlucky...

Is the VNL file large? You can email it to me and I can check.

Did you lose the script used to run the calculation? Is there any other way to restore the geometry?

[sergio]

Dr. Blom,

Sorry for late reply, I was dealing with some reports....Actually I have just realized that upon defining the exact path of the vnl file, the code that you have written works!

Thanks,

[hellboy]

Dear Sir, I was trying to obtain the atoms in the central region for nanotube using the below mentioned code:

Code

from ATK.TwoProbe import *
from displayCentralRegion import displayCentralRegionAtoms

vnl_file=VNLFile("CNT.vnl")
atomic_configuration_dict = vnl_file.readAtomicConfigurations()
atomic_configuration = atomic_configuration_dict["twoprobe_configuration"]
displayCentralRegionAtoms(atomic_configuration)
      

then i tried using code mentioned below, but got errors:

Code

...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
twoprobe_config=configs[configs.keys()[0]]

I get:

Code

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

And, when I try to get the configuration name using

Code

...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
print configs.keys()

I get only [] How do i obtain the central region atoms with periodic_atom_configuration such as in nanotubes?

[Anders Blom]

And, when I try to get the configuration name using

Code

...
vnlfile=VNLFile("file.vnl")
configs=vnlfile.readAtomicConfigurations()
print configs.keys()

I get only []

Then the VNL file does not contain any configurations. To extract a configuration from a VNL file, the easiest way is to use the Result Browser in VNL, and not use these complex scripts. Just open the file in the Result Browser, select the configuration and you will see the Python code that defines it.