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QuantumATK => General Questions and Answers => Topic started by: J.g_johnson on February 19, 2014, 08:09

Title: "PeriodicAtomConfiguration" error
Post by: J.g_johnson 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.

Title: Re: "PeriodicAtomConfiguration" error
Post by: Umberto Martinez on February 19, 2014, 09:36

You can import old scripts form VNL 2008 if you include these two lines at the beginning of your script (the new version will check for these two lines and recognize the file format):

Code

from ATK.KohnSham import *
from ATK.TwoProbe import *

Drag and Drop your file directly from the Project Files list to the Builder or Viewer.
You will see that it still not properly imported due to some particular keywords that are present in your script.

Still, you are able extract the three regions (device+electrodes) from the builder using the Split device tool (http://www.quantumwise.com/documents/tutorials/latest/BuilderManual/index.html/chap.plugins.html#sect1.plugins.toolbar), play around a bit and reconstruct your device. :)
Please, check the attachment.

Another solution is to simply open you old script and adapt your old TwoProbeConfiguration to the new DeviceConfiguration class following the Manual
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.deviceconfiguration.html
 (http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.deviceconfiguration.html)

Title: Re: "PeriodicAtomConfiguration" error
Post by: J.g_johnson 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?

Title: Re: "PeriodicAtomConfiguration" error
Post by: J.g_johnson 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.

Title: Re: "PeriodicAtomConfiguration" error
Post by: Umberto Martinez on February 20, 2014, 09:05

Quote from: J.g_johnson 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.

You can see all the available parameters and the default values used in the new version in the new Manual.
In particular, check:
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.lcaocalculator.html (http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.lcaocalculator.html)
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.basisset.html (http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.basisset.html)
and the specific links therein.