document (using ACE in Molly) update

[YangshuaiWang]

I have identified an opportunity for enhancement in the document. In this particular instance, no output was generated. Consequently, I initiated the simulation, conducted a simple temperature analysis, and subsequently exported the trajectory to both a .xyz file and a .gif format. Should time permit and a consensus be reached, I intend to incorporate additional examples and analysis functions (static, thermodynamics, ...) to further augment the document's content.

[tjjarvinen]

Thanks for the initiative.

I would like to have few changes to be made.

1. The main point with ACEmd is to replace JuLIP with a newer AtomsBase compatible framework. So, I would like for you to replace JuLIP with AtomsIO in examples.
2. Also you could add that Ovito is one example program, VMD and PyMol few others.
3. Molly also has functionality to generate visualizations when GlMakie has been loaded that could be very useful to add too (look for Molly docs and example use in Molly basics).

I have not yet added Molly v0.18 to the support list. But will do it soon, that should fix some issues with AtomsBase compatibility...

[YangshuaiWang]

Thanks for the comments, I will change the first one and add the second one accordingly, as for the third one, I think the visualization in Molly is a bit ugly (just my personal preference), but yes, maybe you're right, just adding it is not bad at all.

[tjjarvinen]

Yep we can mention that the Molly visualization is there. And I do agree that it is not up to what Ovito, MD, etc. are.

[YangshuaiWang]

Hi,

According to your suggestion, I am trying to replace JuLIP with AtomsIO, but I get stuck, I try to run:
fname_xyz = joinpath(pkgdir(ACEmd), "data", "TiAl-big.xyz")
data = ExtXYZ.Atoms(read_frame(fname_xyz))
sys = Molly.System(data, pot)
save_system("test.xyz", sys)
but I got this:

julia> ERROR: MethodError: no method matching element(::Missing)

Any comment for this? I try to read the document of AtomsIO, but unfortunately it is not friendly enough to be read.

My package status is:

[69e0c927] ACEmd v0.1.5
[3b96b61c] ACEpotentials v0.6.3
[1692102d] AtomsIO v0.2.2
[352459e4] ExtXYZ v0.1.12
[945c410c] JuLIP v0.14.3
⌃ [aa0f7f06] Molly v0.17.0
[91a5bcdd] Plots v1.39.0
[1986cc42] Unitful v1.17.0

[tjjarvinen]

This seems to be a bug in Molly (or several of them) related to AtomsBase support.

Probably the best way forward is for me to make a PR(s) for Molly to fix these issues.

I hopefully have time for that later this week...

[YangshuaiWang]

Thank you!

…

2023年9月14日 11:03，Teemu Järvinen ***@***.***> 写道： This seems to be a bug in Molly (or several of them) related to AtomsBase support. Probably the best way forward is for me to make a PR(s) for Molly to fix these issues. I hopefully have time for that later this week... — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFQACPRVOTX26IUTNXNSZ4TX2JXY3ANCNFSM6AAAAAA4VMSKNQ>. You are receiving this because you authored the thread.