hi all,
when I am calculating voronoi volume for a square lattice in 50x50x1 box and lattice spacing of 1. Total voronoi volume is not summing up with the box volume.
Does it calculate any normalized value or it gives the exact value?
Help is highly appreciated
Are you using periodic boundaries? Note that it
is a “volume” not an area. And see this note
on the compute voronoi/atom doc page:
IMPORTANT NOTE: The Voro++ package performs its calculation in 3d. This should still work for a 2d LAMMPS simulation, to effectively compute Voronoi “areas”, so long as the z-dimension of the box is roughly the same (or smaller) compared to the separation of the atoms. Typical values for the z box dimensions in a 2d LAMMPS model are -0.5 to 0.5, which satisfies the criterion for most units systems. Note that you define the z extent of the simulation box for 2d simulations when using the create_box or read_data commands.
Steve
Input file please!
Daniel
Input file please!
Daniel
units lj
atom_style sphere
dimension 2
boundary p p p
neighbor 0.55 bin
neigh_modify every 1 delay 0
lattice sq 1 origin 0.5 0.5 0
region simbox block 0 50 0 50 -0.5 0.5
create_box 1 simbox
create_atoms 1 region simbox units lattice
set type 1 diameter 1
pair_style soft 0.5
pair_coeff 1 1 1000.0 0.5
fix 1 all enforce2d
compute 1 all voronoi/atom
compute 2 all contact/atom
dump 1 all custom 1 dump.colloid id c_1[1] c_2 x y z
dump 2 all image 1 image.*.jpg type type &
zoom 1.6 adiam 1
dump_modify 2 pad 4
min_style sd
minimize 1.0e-4 1.0e-6 10000 100000
write_data data2.min
Hmmm. If I set the system up as 3d (with a corresponding sc lattice,
same box size, same atomic positions) the per-atom volumes come out
correctly as 1.0 each.
I don't quite see what breaks the 2d case. I'll have to investigate.
yes
hi,
did you find anything…reducing the thickness of the z dimension is reducing the volume…now i am getting 2.13
although this is the same thing…ignore the last email…problem still remains the same… whenever you find anything please let me know…your help is highly appreciated
Hi Daniel
Voro ++ is giving the perfect result for the same thing…I think there is a problem how this package has been linked with the LAMMPS