How are you calculating neighbours in matlab ?. What algorithm are you using ?. The best way to check this is to download voro ++ source code compile and get the executable. The command line option is pretty easy to use.
voro++ [opts] <x_min> <x_max> <y_min> <y_max> <z_min> <z_max>
use this option -o -c %n
Arun
Thank you Arun. I tried with voro++. It came out that for 2D when it calculates neighbouring lists of a particle it considers same particles up and down.
For example, in the output file
9939 5479 6085 5781 6085 5481 9585 10034
…
….
…
In the first line the Id of the particles is 6085 and in the neighbor list it appears twice where it should not be in the neighbour list at all. Consequently, it shows that it has 8 neighbours. I need the voronoi area. I am suspicious whether it will give the perfect area.
In matlab there is one function called voronoi which calculates number of neighbours.
With best regards,
Pritam
On the compute voronoi/atom doc page, there is a note
about using it for 2d systems. You might have to
play with the z-size of your 2d box to get Voro++ to
avoid counting images of the atom itself in the z dimension.
Are you actually using “dimension 2” in LAMMPS?
Or are you using dimension 3, with a small box in z?
Steve
Yes, I am using dimension 2 in LAMMPS. But when the simulation is run it ask for length of the box along z. So, I put a box length. But During run of the simulation there is no change of the z coordinates.
units lj
atom_style atomic
dimension 2
boundary p p p
read_data system1.data
and the starting of the system1.data file is
LAMMPS data file via write_data, version 15 May 2015, timestep = 10
22525 atoms
2 atom types
0.000000 158.113876 xlo xhi
0.000000 158.113876 ylo yhi
-0.105409 0.105409 zlo zhi
0.000000 0.000000 0.000000 xy xz yz
with best regards,
Pritam
More precisely,
region box prism 0 90.0 0 90.0 -0.1 0.1 0 0 0
if I do not mention box length in z direction, it shows error with illegal region command. Though dimension 2 is used.
With best regards,
Pritam
This is just a feature of the tessellation method. Whenever a Voronoi cell extends to a boundary, a cell face is created at the boundary and this is treated as another neighbor. Hence in your 2d example, the upper and lower free surfaces are treated as two neighbors. I will update the documentation to make this clearer.
Dear Aidan,
Thank you very much. In addition to that I need voronoi cell area. According to the calculation, Voronoi cell area (in 2D) is changed with the length of the box along the z dimension which is not expected in case 2D. Is it like the value which is obtained as voronoi cell area, it is basically volume and we need to divide it by the box height to get the cell area?
With best regards,
Pritam
yes, the Voro++ lib is always computing 3d volumes. Divide
by the z-box length (even for a 2d simulation) and you
will have voronoi “area”. The tesselation is the same,
i.e. it is always 2d, provided your atoms all have the same
z coord, which they should for a 2d model.
Steve
Ok, Thank you very much.
With best
Pritam