Strange relation between simulation box size and computed data

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1

​please always reply to the mailing list and not only individual people.​

Thanks a lot for your response Aidan and Axel!!

Maybe it could be a way to modify the Voronoi method for approximate
calculation of the cluster volume, or at least of it's change.

i don't see how. ​voronoi tessellation is a method for *dividing* a given
volume, not for determining a volume.​

​axel.​

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Thanks a lot for your response Aidan and Axel!!

Maybe it could be a way to modify the Voronoi method for approximate calculation of the cluster volume, or at least of it’s change.

With all respect,
Ruslan

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The voronoi package in lammps is built over the voro++ library. That library has features to deal with a case like the one you are describing: http://math.lbl.gov/voro++/examples/irregular/
Note however that the solution described there is purely geomettrical and other techniques such a probe particle approaches as Axel mentioned may be more suitable to construct volume descriptors that suit better your needs.
Carlos

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Thanks a lot for your suggestions Carlos!

It may be a good solution, however I first time hear about probe particle
approach technique and have no idea what it stands for. Could you, or
someone else, give me a link?

With all respect,
Ruslan

5

Thanks a lot for your suggestions Carlos!

It may be a good solution, however I first time hear about probe particle
approach technique and have no idea what it stands for. Could you, or
someone else, give me a link?

​this method is widely used in biomolecular simulations to assess the
solvent accessible surface are, for example. of course, that surface - by
definition - also defines an effective volume of the biomolecule.

https://en.wikipedia.org/wiki/Accessible_surface_area

please note that the dependency of the resulting surface (or volume) on the
size of the probe particle highlights the inherent arbitrariness of such
definitions.

axel.​

6

The particle probe approach results may end up being very similar to the one I linked because “I believe” in the Voro++ you can initialize the WZ cell of each particle to be a sphere. Take my words with a grain of salt as I have never done it but just repeated for you what the docs state.
Carlos