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lammps/examples/voronoi/log.5Oct16.voronoi.data.g++.4
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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)
2 by 2 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 = 9.29039 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 3.4106051e-13 0 186 12 36 0
Loop time of 5.00679e-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 | | 5.007e-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: 81.25 ave 84 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
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 = 8.03996 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 1.90735e-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: 81.25 ave 84 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
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