Author Topic: Questions about the functions of Molecular Dynamics  (Read 341 times)

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Offline shyoun

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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?
« Last Edit: March 8, 2021, 02:54 by shyoun »

Offline mlee

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Re: Questions about the functions of Molecular Dynamics
« Reply #1 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. 
« Last Edit: March 9, 2021, 16:30 by mlee »

Offline shyoun

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Re: Questions about the functions of Molecular Dynamics
« Reply #2 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?

Offline shyoun

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Re: Questions about the functions of Molecular Dynamics
« Reply #3 on: March 10, 2021, 03:56 »
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?

Offline mlee

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Re: Questions about the functions of Molecular Dynamics
« Reply #4 on: March 10, 2021, 15:47 »
You need to define the force field parameter with bonded and non-bonded terms.

Offline shyoun

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Re: Questions about the functions of Molecular Dynamics
« Reply #5 on: March 11, 2021, 05:10 »
Thank you!
I'll try it!

Offline shyoun

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Re: Questions about the functions of Molecular Dynamics
« Reply #6 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.

Offline mlee

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Re: Questions about the functions of Molecular Dynamics
« Reply #7 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.

Offline mlee

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Re: Questions about the functions of Molecular Dynamics
« Reply #8 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. 

Offline shyoun

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Re: Questions about the functions of Molecular Dynamics
« Reply #9 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.