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.


Messages - shyoun

Pages: [1] 2
1
Hello,

I want to compare the tunneling barrier of Metal/2D semiconductor contact.
So I want to add a fermi energy at the effective voltage like 2nd image (https://doi.org/10.1038/s41699-021-00251-y). But I can't find a tutorial about it.
How can I add it?


2
Questions and Answers / Re: MD error
« on: July 1, 2021, 06:15 »
Thank you! I will take it, too :)

3
Questions and Answers / Re: MD error
« on: June 29, 2021, 04:17 »
Thank you for your answer.

I made potential by referring to the parameters of several papers.
And the 'webinar' means the webinar held on 2021/6/22?
I haven't heard it yet, but I'm glad it's related to my problem.

Thank you so much. I'll listen to the webinar and try it.

4
Questions and Answers / Re: MD error
« on: June 29, 2021, 03:52 »
Thank you for your advice.

I tested it in low temperature. Unfortunately, I found that simulation with 10K(and also 1K) results in the same error.
The speed of atoms does not exceed 0.01 Angstrom/fs just before an error occurs.
Is this just a matter of potential parameter?
There are several combinations that is not among torsion term in the potential parameter. Is this the cause?

5
Questions and Answers / MD error
« on: June 23, 2021, 04:29 »
Hello,

I calculated a simulation of deposition of GeH4 on MoS2 with a ReaxFF potential parameter that I made.
And as soon as GeH4 got closer to MoS2, all of atom's information was deleted.

This is part of the structure information.
# Define elements
elements = [Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, .... Hydrogen, Hydrogen]

# Define coordinates
fractional_coordinates = [[ nan,  nan,  nan],
                          [ nan,  nan,  nan],
                          [ nan,  nan,  nan],
                          [ nan,  nan,  nan], ....  [ nan,  nan,  nan]]

# Define velocities
velocities = [[ nan,  nan,  nan],
              [ nan,  nan,  nan],
              [ nan,  nan,  nan], .... [ nan,  nan,  nan]]*Angstrom/fs

Is there any known cause of this kind of error? I wonder why this error is happening.
I'll put up the code and potential information together, just in case it helps.

6
Thank you for your answer
That was a great help!

7
Thank you for the details.

I have a question about the code,
What's the meaning of the [-1] in 'ldos_bulk = nlread("LDOS_Heterostructure_Au&BI2O2Se_Bilayer.hdf5", LocalDensityOfStates)[-1]' at the first paragraph

Regards

8
Thank you for your kind reply!

9
Dear ATK staff,

I want to identify the bands of specific parts in bandstructure of Metal/Semiconductor Heterostructure
And I found the post of forum
https://forum.quantumatk.com/index.php?topic=4161.msg18983#msg18983

But the link of this forum is dead. So, can you give me a new tutorial or link?

Thank you.

10
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?

11
Thank you for your advice.
Let me check it!

12
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.

13
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.

14
Thank you!
I'll try it!

15
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?

Pages: [1] 2