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Messages - shyoun

Pages: 1 [2]
16
Hello,

I want to print the DOS graph like Fig 15. in   https://doi.org/10.1103/PhysRevX.4.031005
So I calculated LDOS with the attached code

And calculating was over well, and I can see the result. But I cannot export the data from the result.
How can I get the raw data from the calculation result?

17
Thank you for your advice.
Let me check it!

18
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.

19
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.

20
Thank you!
I'll try it!

21
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?

22
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?

23
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?

25
In tutorial https://docs.quantumatk.com/tutorials/deposition/deposition.html

Deposition can be simulated in the following ways:
1. Run a new simulation for each newly introduced atom or molecule. The entire deposition simulation can then be performed in an outer loop over the deposited atoms/molecules.
2. Keep all atoms or molecules that should be deposited in a reservoir in the simulation cell. For each new deposition event, take one of these atoms out of the reservoir and place it above the substrate.

And tutorial said 'However, in QuantumATK it is not possible to save the entire simulation into a single MDTrajectory object for later visualization and analysis, due to the varying number of atoms'. I wonder if the latest version is still impossible too. If not, I wonder if there is a tutorial on it.

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