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glotzerlab / hoomd-blue

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
http://glotzerlab.engin.umich.edu/hoomd-blue
BSD 3-Clause "New" or "Revised" License
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Simulation of Physical Vapor Deposition #251

Closed joaander closed 7 years ago

joaander commented 7 years ago

Original report by Yuan-Chao (Bitbucket: Yuan-Chao, GitHub: Yuan-Chao).

Dear Sir/Madam,

There is a growing interest in modelling physical vapor deposition of different materials recently in various disciplines, including material sciences, condensed matter physics and engineering. If you could develop a reliable feature to simulate physical vapor deposition, it would be great for many people. I hope you could consider it as soon as you can. Thank you very much

Best Wishes,

Yuan-Chao

joaander commented 7 years ago

What specific functionality is lacking from HOOMD that is preventing you from running the simulation you want to? The topic of "physical vapor deposition" is broad and it is not clear what you are asking for.

joaander commented 7 years ago

Reporter did not provide a clear description of what functionality is needed. Feel free to re-open with such a description.

joaander commented 7 years ago

Original comment by Yuan-Chao (Bitbucket: Yuan-Chao, GitHub: Yuan-Chao).

Dear Mr. Anderson,

Thank you for the reminder. We want to deposit some amorphous & metallic films using the EAM potential in simulations to mimic the experimental physical vapor deposition. However, such functionality seems to be not reliable in LAMMPS. I am wondering whether HOOMD could realize this function. Please also refer to the references: DOI: 10.1038/NMAT3521; DOI: 10.1038/ncomms13062. Please contact me if you need any further information. Thank you very much

Best Regards,

Yuan-Chao

joaander commented 7 years ago

Original comment by Yuan-Chao (Bitbucket: Yuan-Chao, GitHub: Yuan-Chao).

Dear Mr. Anderson,

Thank you for the reminder. We want to deposit some amorphous & metallic films using the EAM potential in simulations to mimic the experimental physical vapor deposition. However, such functionality seems to be not reliable in LAMMPS. I am wondering whether HOOMD could realize this function. Please also refer to the references: DOI: 10.1038/NMAT3521; DOI: 10.1038/ncomms13062. Please contact me if you need any further information. Thank you very much

Best Regards,

Yuan-Chao

joaander commented 7 years ago

I have reviewed the methods sections of the two papers you reference. HOOMD-blue is already capable of 1) Lennard-Jones simulations 2) Harmonic bonds 3) Adding particles as the simulation progresses 4) Adjusting the box size as the simulation progresses and 5) FIRE energy minimization. This is sufficient to execute these simulations.

If you have questions about how to use these existing functionalities in HOOMD, please refer to the documentation: http://hoomd-blue.readthedocs.io/en/stable/ . The hoomd-users mailing list (https://groups.google.com/forum/#!forum/hoomd-users) is the best resource to ask for help.

joaander commented 7 years ago

Original comment by Yuan-Chao (Bitbucket: Yuan-Chao, GitHub: Yuan-Chao).

Dear Joshua,

Thank you very much for your nice reply. Since I am new to HOOMD and I heard it is multi-functional, I want yo try it for future studies. Could you please give some examples on how to add particles in the simulation processes and integrate them in HOOMD?

Thank you.

Best Regards,

Yuan-Chao

joaander commented 7 years ago

Original comment by Michael Howard (Bitbucket: mphoward, GitHub: mphoward).

As Josh said, these questions will be best answered on the mailing list:

https://groups.google.com/forum/#!forum/hoomd-users