Hi,
I’d like to divide my simulation box into smaller boxes (regions).
Specifically, I want to have 24 smaller boxes on each axis (24x24x24).
In the region command, apart from defining the boundaries of each region separately, is there any faster way to divide the cell into 24 regions on each direction, because I didn’t manage to find sth.
Thanks,
Nikos.
What do you want to do with those regions?
I have a solution of particles and I want to measure the volumes of the voids between them.
After creating these small pieces, I’ll see which of those pieces contain no particles (which means that they are in the void regions) and then, calculate the distances from the center of each piece to the closest particle. The void volume will be the volume of a sphere with radius equal to this distance.
I’m aware of the Voronoi tessellation method for the calculation of the voids, but it does not give me the results that I want.
You could do binning with compute chunk/atom and then counting of atoms per bin with compute property/chunk. The void volume would be approximated by the number of cells without any atoms.
If you want a more accurate approximation of the void you probably need to write a custom compute. That compute would have to set up a rather fine grid and then also have an effective atom radius. Then you loop over all atoms and determine which voxels they overlap with and flag those as occupied. The sum of the volume of the unoccupied voxels is the void volume.
If you are familiar with VMD, you can also have a look at its volmap command (or the Volmap Tool dialog) and then post-process the resulting grid after writing it to a .dx file.
ok understood.
Thank you so much Axel.