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Messages - Pieter Vancraeyveld

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1
You have discovered a bug in the Q-2019.12 version of QuantumATK that has been fixed for the upcoming R-2020.09 release.

As a workaround, you can select the option 'Set up electrode cross-section as a supercell' in the 'Device from Bulk' widget as indicated in the attached screenshot.

2
Can you share your script? Perhaps we can give you some suggestions based on what you have written already.

4
Based on your input, it appears that one of your bash startup scripts (.profile, .bashrc, .bash_profile) contains an error. After you have fixed it, you should be able to execute

ssh liuxiaolin@10.10.114.204 'echo $0; echo $SHELL; env'

as a single command without getting error messages.

5
Please ssh to your login node and execute the following command:

bash -c 'echo $0; echo $-; env'

What output do you get?

6
Your output contains a lot of "command not found" errors. This indicates errors in the scripts being sourced at login. Can you check or share ~/.bashrc on your login node? It is likely that PATH is set incorrectly.

7
I can see that my instructions were not 100% clear. Can you also execute

ssh liuxiaolin@10.10.114.204 'echo $0; echo $SHELL; env'

as a single command and provide the output?

8
Can you execute the following commands one by one and share the output?

ssh liuxiaolin@10.10.114.204 'echo $0; echo $SHELL; env'
ssh liuxiaolin@10.10.114.204
echo $0
echo $SHELL
env
exit

Thanks, Pieter

9
It is not clear why the diagnostic check fails if you can manually execute 'which bash'.

Can you empty the 'Scripts to source' field in the 'Environment' tab of the machine settings and submit a new script using the job manager?

10
Hi Aanand,

The reason that you can run some, but not all of the configurations, is related to the electrodes. Some of your devices have transverse electrode repetitions, while others don't. DeviceDensityOfStates does not support all definitions in Q-2019.12 and we will address this for the R-2020.09 release.

For now, you can pass method=LocalDeviceDensityOfStates to the ProjectedLocalDensityOfStates definition in your scripts. You might considering lowering the density_mesh_cutoff passed to ProjectedLocalDensityOfStates to improve performance.

Regards,
Pieter

11
It appears that 'bash' is not available on the server. Can you manually login and execute the command 'which bash'?

12
Hi Nayab,

Where are you running Nanolab? On Linux or Windows, inside a virtual machine or not? Please share the script of a structure that cannot be dropped and a screenshot of the About box under Help > About.

Thanks,
Pieter

13
Hi Aanand,

You have run into the issue that DDOS currently does not support devices with transverse electrode repetitions. We will make sure to address this in the next release.

In the meantime, you can run PLDOS using the LDOS method as follows:
Code: [Select]
projected_local_density_of_states = ProjectedLocalDensityOfStates(
    configuration=configuration,
    method=LocalDeviceDensityOfStates,
    energies=numpy.linspace(-4, 3, 351)*eV,
    kpoints=kpoint_grid,
    contributions=All,
    self_energy_calculator=RecursionSelfEnergy(),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    density_mesh_cutoff=75.0*Hartree,
    processes_per_energy=All,
    )

Does this solution work for you?

Sorry for the inconvenience,
Pieter


14
Can you share the input scripts and log output of the device and PLDOS calculations?

15
Questions and Answers / Re: Error during runing
« on: June 10, 2020, 08:47 »
The file containing your job manager settings has been corrupted. Please remove $HOME/.vnl/Jobs_2019.12.hdf5 and restart QuantumATK Nanolab.


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