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)
1 by 1 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 = 2.37519 Mbytes
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 5.6843419e-14
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: 2415 ave 2415 max 2415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8256 ave 8256 max 8256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
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 = 7.05652 Mbytes
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 3.4106051e-13
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: 496 ave 496 max 496 min
Histogram: 1 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