LAMMPS (5 Oct 2016)
# Exercise different output data options

variable        len equal 4.0
variable        lenz equal 10.0

dimension       2
units		metal
boundary	f f p

lattice         hex 1.0 origin 0.25 0.25 0.0
Lattice spacing in x,y,z = 1 1.73205 1

atom_style	atomic

region          box block 0 ${len}  0 ${len} 0.0 ${lenz}
region          box block 0 4  0 ${len} 0.0 ${lenz}
region          box block 0 4  0 4 0.0 ${lenz}
region          box block 0 4  0 4 0.0 10
region          atoms block 0 ${len}  0 ${len} 0.0 0.0
region          atoms block 0 4  0 ${len} 0.0 0.0
region          atoms block 0 4  0 4 0.0 0.0
create_box      1 box
Created orthogonal box = (0 0 0) to (4 6.9282 10)
  1 by 1 by 1 MPI processor grid
create_atoms    1 region atoms
Created 32 atoms

mass 		1 1.0

pair_style      lj/cut 2.5
pair_coeff      1 1 0.0 1.0

neighbor	1.0 nsq

#
# TEST 1:
#

# This compute voronoi generates all three
# types of quantity: per-atom, local, and global

compute 	v1 all voronoi/atom neighbors yes edge_histo 6

# write voronoi per-atom quantities to a file

dump    	dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]

# writing voronoi local quantities to a file

dump            dlocal all local  1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]

# sum up a voronoi per-atom quantity

compute 	volvor all reduce sum c_v1[1]

variable 	volsys equal lz*lx*ly
variable 	err equal c_volvor-v_volsys

# output voronoi global quantities

thermo_style 	custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
thermo 		1

run  		0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.5
  ghost atom cutoff = 3.5
Memory usage per processor = 9.40674 Mbytes
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 
   277.12813    277.12813    27.712813 3.9790393e-13            0          186           12           36            0 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms

0.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 9.537e-07  |            |       |100.00

Nlocal:    32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    325 ave 325 max 325 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0

uncompute       v1
uncompute       volvor
undump          dperatom
undump          dlocal

#
# TEST 2:
#

# This compute voronoi generates
# local and global quantities, but
# not per-atom quantities

compute 	v2 all voronoi/atom neighbors yes edge_histo 6 peratom no

# write voronoi local quantities to a file

dump            d2 all local  1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]

# sum up a voronoi local quantity

compute 	sumarea all reduce sum c_v2[3]

# output voronoi global quantities

thermo_style 	custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
thermo 		1

run  		0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 8.15503 Mbytes
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] 
   1215.0706            0          186           12           36            0 
Loop time of 1.19209e-06 on 1 procs for 0 steps with 32 atoms

0.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 1.192e-06  |            |       |100.00

Nlocal:    32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    325 ave 325 max 325 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0



Total wall time: 0:00:00
