LAMMPS (5 Oct 2016)
# Test volume definitions for 2d and finite systems

variable        rcut equal 10.0
variable        rskin equal 2.0
variable        rcomm equal 20.0
variable        len equal 4.0
variable        lenz equal 10.0

dimension       2
units		metal
boundary	p p p

#lattice         sq 1.0 origin 0.5 0.5 0.0
lattice         hex 1.0 origin 0.5 0.5 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)
  2 by 2 by 1 MPI processor grid
create_atoms    1 region atoms
Created 32 atoms

mass 		1 1.0

pair_style      lj/cut ${rcut}
pair_style      lj/cut 10
pair_coeff      1 1 0.0 1.0

neighbor	${rskin} nsq
neighbor	2 nsq

# set the minimum communication cut-off
comm_modify     cutoff ${rcomm}
comm_modify     cutoff 20

compute 	v1 all voronoi/atom neighbors yes
compute 	volvor all reduce sum c_v1[1]
variable 	volsys equal lz*lx*ly
variable 	err equal c_volvor-v_volsys
thermo_style 	custom c_volvor v_volsys vol v_err
thermo 		1

#
# TEST 1: Volume check for 2d bulk system
#

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 = 12
  ghost atom cutoff = 20
Memory usage per processor = 2.41069 Mbytes
c_volvor v_volsys Volume v_err 
   277.12813    277.12813    27.712813 5.1159077e-13 
Loop time of 4.05312e-06 on 4 procs for 0 steps with 32 atoms

0.0% CPU use with 4 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   |            | 4.053e-06  |            |       |100.00

Nlocal:    8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    2159 ave 2159 max 2159 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    2064 ave 2077 max 2051 min
Histogram: 1 0 0 1 0 0 1 0 0 1

Total # of neighbors = 8256
Ave neighs/atom = 258
Neighbor list builds = 0
Dangerous builds = 0

#
# TEST 2: Volume check for 2d finite system
#         add margins in x and y directions
#

change_box 	all boundary f f p
run  		0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 7.04625 Mbytes
c_volvor v_volsys Volume v_err 
   277.12813    277.12813    27.712813 3.4106051e-13 
Loop time of 1.90735e-06 on 4 procs for 0 steps with 32 atoms

0.0% CPU use with 4 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   |            | 1.907e-06  |            |       |100.00

Nlocal:    8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    24 ave 24 max 24 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    124 ave 124 max 124 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 496
Ave neighs/atom = 15.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00