1
General Questions and Answers / Re: Problem regarding job submission in 2019.12
« on: August 7, 2020, 14:23 »
The workaround posted in https://forum.quantumatk.com/index.php?topic=6437.msg27030#msg27030 will solve your issue.
Show Posts
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Pages: [1] 2
2
General Questions and Answers / Re: Job Manager won't work
« on: August 7, 2020, 14:22 »
The procedure on Windows is the same.
3
General Questions and Answers / Re: Getting error message while converting from bulk to device
« on: August 7, 2020, 14:21 »
You can create your device configuration by pasting the following code snippet at the bottom of the script that defines your bulk configuration:
The issue in Nanolab will be resolved in the R-2020.09 release scheduled for September 8.
Code
from NL.CommonConcepts.Configurations.DeviceFromBulk import deviceFromBulk, findBothElectrodeLengths
device_configuration = deviceFromBulk(
electrode_lengths=findBothElectrodeLengths(bulk_configuration) * Angstrom,
bulk_configuration=bulk_configuration,
enable_minimal_electrodes=True,
enable_transverse_electrode_repetitions=False,
)The issue in Nanolab will be resolved in the R-2020.09 release scheduled for September 8.
4
General Questions and Answers / Re: Getting error message while converting from bulk to device
« on: July 31, 2020, 09:13 »
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.
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.
5
Scripts, Tutorials and Applications / Re: script for transmission spectrum various bias
« on: July 21, 2020, 15:30 »
Can you share your script? Perhaps we can give you some suggestions based on what you have written already.
6
General Questions and Answers / Re: DOS vs PDOS
« on: July 16, 2020, 11:16 »
You can read how PDOS relates to DOS at https://docs.quantumatk.com/manual/Types/ProjectedDensityOfStates/ProjectedDensityOfStates.html#notes.
7
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: July 8, 2020, 17:43 »
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.
ssh liuxiaolin@10.10.114.204 'echo $0; echo $SHELL; env'
as a single command without getting error messages.
8
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: July 8, 2020, 11:31 »
Please ssh to your login node and execute the following command:
bash -c 'echo $0; echo $-; env'
What output do you get?
bash -c 'echo $0; echo $-; env'
What output do you get?
9
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: July 8, 2020, 10:54 »
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.
10
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: July 8, 2020, 08:32 »
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?
ssh liuxiaolin@10.10.114.204 'echo $0; echo $SHELL; env'
as a single command and provide the output?
11
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: July 7, 2020, 11:53 »
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
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
12
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: July 6, 2020, 10:59 »
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?
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?
13
General Questions and Answers / Re: Error running DDOS/PLDOS analysis on QuantumATK 2019.12
« on: June 30, 2020, 12:01 »
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
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
14
General Questions and Answers / Re: Job Manager for remote SLURM execution of QuantumATK scripts
« on: June 30, 2020, 10:05 »
It appears that 'bash' is not available on the server. Can you manually login and execute the command 'which bash'?
15
General Questions and Answers / Re: moving geometry from labfloor to builder
« on: June 12, 2020, 09:36 »
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
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
Pages: [1] 2