QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: amitwsu on February 10, 2017, 21:49

Title: Error in emulating wrap and hook function
Post by: amitwsu on February 10, 2017, 21:49

Hi,
I am emulating the Thin film growth example with hook function - and in doing that I am getting the following error. The original example works fine. I am not sure what the error is telling me. Attached is the python script.

Thanks
Amit

Traceback (most recent call last):
  File "He_deposit_Tungsten (100).py", line 719, in <module>
    method=method
  File "./zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 262, in MolecularDynamics
  File "./zipdir/NL/Dynamics/MolecularDynamics/NVTNoseHoover.py", line 102, in _initialize
  File "./zipdir/NL/Dynamics/MolecularDynamics/NVTNoseHoover.py", line 248, in _initializeThermostats
NL.ComputerScienceUtilities.Exceptions.NLValueError: Nose-Hoover requires at least one unconstrained degree of freedomwithin each temperature group.

Title: Re: Error in emulating wrap and hook function
Post by: Julian Schneider on February 13, 2017, 14:59

The script looks ok at first glance, we'll need to look into this a bit more. We'll let you know as soon as we have found the problem.

Title: Re: Error in emulating wrap and hook function
Post by: Julian Schneider on February 14, 2017, 12:08

The script is correct, it is a small bug in the MD-functionality. We'll try and fix it as soon as possible.

For now, the workaround is to include all atoms the W-surface (i.e. also the constrained bottom atoms) into the group "substrate", as shown  in the attached script.

Title: Re: Error in emulating wrap and hook function
Post by: amitwsu on February 14, 2017, 18:41

Julian,
Thank you for your reply and looking into the script. I tried your suggestion and I still got an error when running the complete simulation   (multiple MD)

In trying to resolve the issue I noticed that it was not the Tags that was generating the error but infact it is the reservoir_temperature that is generating the error. For example the line

reservoir_temperature = [('substrate',300*Kelvin)]  gives and error whereas if I replace the line with
reservoir_temperature = 300*Kelvin then the code runs fine with the same Atom tags, as was in my original file.

Also, what I dont understand is why does it work for the  Script_Sic  example and does not work for my script.

Any suggestion on how to set reservoir_temperature for a selected atoms?

Thanks
Amit

Title: Re: Error in emulating wrap and hook function
Post by: amitwsu on February 14, 2017, 20:09

I misread your response. You solution works.

Thanks
Amit