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m3g / packmol

Packmol - Initial configurations for molecular dynamics simulations
http://m3g.github.io/packmol
MIT License
214 stars 48 forks source link

packing molecules in a hexagonal unit cell #24

Closed goodwilling closed 3 years ago

goodwilling commented 3 years ago

Hi. Packmol is a great tool in creating initial configurations. I am wondering if it can now be used for packing molecules into a hexagonal unit cell. Thank you very much.

lmiq commented 3 years ago

No, no directly. We are hoping to release a new improved version of Packmol until the end of the year with that and other improvements. Currently one would have to build a cubic box and cut it with an external tool to make it hexagonal.

pfebrer commented 2 years ago

Hi, I discovered your code today and it was a very nice surprise!

However I also need to constrain the coordinates to a non-orthogonal cell. I haven't found anything in the documentation, is the implementation you mentioned here already in the code? Thanks!

lmiq commented 2 years ago

No, it is not. It will actually be a complete rewrite of the code, with new features. The most important core part is written already and supports general PBCs, but I still need to write the actual interface. Maybe for the end of the year, but I cannot guarantee that.

pfebrer commented 2 years ago

Ok, thanks for the info! I've been reading your papers and if it's urgent I'll probably give it a shot at implementing it in our python package (sisl), since we already have the efficient neighbour search with optional PBC and some generic optimization methods. For a simple implementation (all that I need since my systems are "DFT-sized") the only missing part would be to compute the gradients I think.

The papers were an interesting read!