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[lammps-users] Voronoi/atom issue
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[lammps-users] Voronoi/atom issue


From: Rajdeep Behera <rajdeepbehera87@...24...>
Date: Wed, 8 Nov 2017 13:01:51 -0500

Hi all,
I want to calculate the volume of a spherical nano-particle resides inside of a cubical simulation box (see the attached figure) utilizing Voronoi tessellation. My input commands are given below,

_________________________________________________________
units      metal
dimension  3
boundary   p p p
atom_style  atomic

lattice      fcc 4.247
region       whole  block 0 50 0 50 0 50 units box
create_box   2 whole
region       Domain sphere 25 25 25 10 units box 
lattice      fcc 4.247
create_atoms 2 region Domain

region         Core sphere 25 25 25 6 units box 
group          Core region Core 

pair_style       eam/alloy
pair_coeff      * * AlGa.eam Al Ga
neighbor        2.0 bin
neigh_modify    delay 10 check yes

minimize        1e-15 1e-15 1000 100000

compute         v Core voronoi/atom only_group
compute         tv Core  reduce sum c_v[1]

dump            1 all custom 100 dat.test.*.cfg id type xs ys zs vx vy vz

thermo_style    custom step time temp vol c_tv

thermo          10
timestep        0.001

fix             relax all nvt temp 2.5 2.5 0.001

run 1000
write_data      Eql-NVT-1 
______________________________________________________________

But, interestingly the volume of the nanoparticle is computed almost double of the simulation box. Here is my output,

Step Time Temp Volume c_tv 
      64            0            0                       125000    265676.44 
      70        0.006    50.253752             125000    265675.37 
      80        0.016 1.4260517e-010       125000    265682.03 
      90        0.026 3.2938985e-006       125000    265682.01 
     100        0.036  0.040481345          125000    265679.68 
........

Am I missing anything? 

Please make your comment/suggestion in this regard.

Thanks,
R

  

Attachment: nano-particle.png
Description: PNG image