QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: shyoun on March 7, 2021, 13:34

Title: Questions about the functions of Molecular Dynamics
Post by: shyoun on March 7, 2021, 13:34

I want to try the simulation in this paper through the QuantumATK Nanolab.
https://pubs.acs.org/doi/abs/10.1021/acs.nanolett.7b01727
It is a simulation in which predeposited MoO3 adds S2 gas to create MoS2.

I wonder if the following functions are possible in QuantumATK.
1. Can I graph the energy of the structure that changes through the NEB like Fig2?   I saw that there was the NEB tab in the Builder, but I couldn't find a way to see the change of energy.
2. I want to use ForceFieldCalculater, but there is no information about Mo. Is there no problem to proceed with Molecular Dynamics even if it's not ForceFiledCalculater?

Title: Re: Questions about the functions of Molecular Dynamics
Post by: mlee on March 9, 2021, 16:19

You can use the NEB calculation. After finishing the NEB calculation, you can see it in the movie tool.
Available force fields in QuantumATK are shown in the ForceFieldCalculator. If you cannot find the force field of Mo in the ForceFieldCalculator, QuantumATK doesn't include it. You need to add the Mo force field parameter using the Potential Editor. Otherwise you need to use DFT code instead of force field parameter. 

Title: Re: Questions about the functions of Molecular Dynamics
Post by: shyoun on March 10, 2021, 03:54

Thank you for your answer!

And.. I have another question. When I press the Particle Type part of the edit tab of ReaxFF in ForceFieldCalculator, the epsilon and sigma of all atoms are zero. Is there no problem with this? Is it automatically calculated and entered by a parameter? If so, is it okay to add Molybdenum as an Add tab without any additional information?

Title: Re: Questions about the functions of Molecular Dynamics
Post by: shyoun on March 10, 2021, 03:56

Quote from: shyoun on March 10, 2021, 03:54

Thank you for your answer!

And.. I have another question. When I press the Particle Type part of the edit tab of ReaxFF in ForceFieldCalculator, the Lennard-Jones parameter: epsilon and sigma of all atoms are zero. Is there no problem with this? Is it automatically calculated and entered by a parameter? If so, is it okay to add Molybdenum as an Add tab without any additional information?

Title: Re: Questions about the functions of Molecular Dynamics
Post by: mlee on March 10, 2021, 15:47

You need to define the force field parameter with bonded and non-bonded terms.

Title: Re: Questions about the functions of Molecular Dynamics
Post by: shyoun on March 11, 2021, 05:10

Thank you!
I'll try it!

Title: Re: Questions about the functions of Molecular Dynamics
Post by: shyoun on April 2, 2021, 08:04

I found the potential parameter of Molybdenum and Oxygen.
Supporting information of
https://doi.org/10.1002/anie.200902574

And I made a new potential like the other potentials that were previously installed. But some errors occur.

Error is :
Traceback (most recent call last):
  File "MoO3.py", line 1442, in <module>
    bulk_configuration.update()
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 2393, in update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 432, in _update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 417, in _update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 1405, in _configure_tremolo_model
tremolox.RuntimeError: Error in /slowfs/qatkdev2/bamboo/de02vlbamboo09/bamboo-agent-home/xml-data/build-dir/QL-Q2009-BLD/external-libs/src/tremolox/src/reaxff.c line 5575: ReaxFF data file /home/shyoun/Downloads/QuantumATK-Q-2019.12/lib/python3.6/site-packages/tremolox/potentials/ReaxFF/ysh_Mo&O_2 not valid: could not read number of bonds
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8

How can I make the program read the number of bonds without any problems?
I upload the potential set I made.

Title: Re: Questions about the functions of Molecular Dynamics
Post by: mlee on April 6, 2021, 15:17

You would like to count the number of bonds after the MD simulation using the ReaxFF. Right? Unfortunately the current version doesn't include the feature. Upcoming release will be included.

Title: Re: Questions about the functions of Molecular Dynamics
Post by: mlee on April 6, 2021, 15:21

When I add the new reaxFF in your attachment, it works well. I think you also succeeded to create the new ReaxFF such as the attached image. 

Title: Re: Questions about the functions of Molecular Dynamics
Post by: shyoun on April 19, 2021, 09:04

Thank you for your answer

And I also create the potential set in the script generator without any problems. However, there is an error like the reply above when executing it on Python.

Title: Re: Questions about the functions of Molecular Dynamics
Post by: mlee on April 23, 2021, 12:26

Sorry to reply lately.
I encountered the same problem with the attached ReaxFF.
Probably it seems not to fit in QuantumATK or your model may not suit on the attached ReaxFF.
Can you double check the all parameters including the space and empty lines? Sometimes typo makes this issues. 

Title: Re: Questions about the functions of Molecular Dynamics
Post by: shyoun on April 26, 2021, 05:45

Thank you for your advice.
Let me check it!