Error regarding the self energies when calculating transmission pathways

[Mohammed]

I am trying to run a script calculating the transmission pathways at 3 different energies. I am using a Recursion self energy calculator. At first I didnt specify any arguments and it gave me the error "save_self_energies is deprecated, use storage_strategy". I returned and added this argument to the calculator and still getting this error. Generally the simualation ran when I was using the Direct self energy but I understand that Recursion is a more accurate approach, hence I want to keep with it.

The scrpit is shown below / attached.

# -------------------------------------------------------------
# Analysis from File
# -------------------------------------------------------------
path = u'/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc'
configuration = nlread(path, object_id='gID000')[0]

# -------------------------------------------------------------
# Transmission Pathways
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_pathways = TransmissionPathways(
    configuration=configuration,
    energy=-0.36*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    contributions=Left,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=SaveInMemory()),
    )
nlsave('/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc', transmission_pathways)
nlprint(transmission_pathways)

# -------------------------------------------------------------
# Transmission Pathways
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_pathways = TransmissionPathways(
    configuration=configuration,
    energy=-1.48*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    contributions=Left,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=SaveInMemory()),
    )
nlsave('/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc', transmission_pathways)
nlprint(transmission_pathways)

# -------------------------------------------------------------
# Transmission Pathways
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_pathways = TransmissionPathways(
    configuration=configuration,
    energy=-2.46*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    contributions=Left,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=SaveInMemory()),
    )
nlsave('/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc', transmission_pathways)
nlprint(transmission_pathways)

[Mohammed]

Any help ??

[Petr Khomyakov]

Which version of the ATK are you using? Did you set up your calculation through the VNL (GUI)?  Please provide all the scripts and corresponding log files related to this calculation.

[Mohammed]

I am using ATK 2017.12, and I ran the calculation through the GUI.

The script is attached (same as in my first message) and the log file with the error message as well

[Petr Khomyakov]

I would also like to see the py and log files related to the original SCF calculation that produced the nc file. 

[Mohammed]

They are attached.  I zipped the log file because its size was too large

[Petr Khomyakov]

The issue is due to the fact that the nc file has been obtained with a much older version of ATK (2015.1), and you are trying to compute the transmission paths with the latest 2017.12 version. In principle, it should have worked, but there seems to exist a compatibility bug.

Could you send all the py and log files together with your nc file to quantumatk-support@synopsys.com? If your files are too bulky, then you may post a zip file with all the information, e.g., in Dropbox or any other server, sent us a link, so that we will be able to download the files.

[Mohammed]

The email has been sent.

Thank you Petr for your assistance 

[Petr Khomyakov]

Did you sent it to quantumatk-support@synopsys.com? I cannot see your message.

[Mohammed]

Yes I did

[Jess Wellendorff]

We received your email now.