forked from lijiext/lammps
104 lines
3.4 KiB
Groff
104 lines
3.4 KiB
Groff
LAMMPS (16 Mar 2018)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Gay-Berne benchmark
|
|
# biaxial ellipsoid mesogens in isotropic phase
|
|
# shape: 2 1.5 1
|
|
# cutoff 4.0 with skin 0.8
|
|
# NPT, T=2.4, P=8.0
|
|
|
|
units lj
|
|
atom_style ellipsoid
|
|
|
|
# creation
|
|
#lattice sc 0.22
|
|
#region box block 0 32 0 32 0 32
|
|
#create_box 1 box
|
|
#create_atoms 1 box
|
|
#set group all quat/random 982381
|
|
|
|
read_data data.gb
|
|
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
32768 atoms
|
|
reading velocities ...
|
|
32768 velocities
|
|
32768 ellipsoids
|
|
|
|
compute rot all temp/asphere
|
|
group spheroid type 1
|
|
32768 atoms in group spheroid
|
|
variable dof equal count(spheroid)+3
|
|
compute_modify rot extra ${dof}
|
|
compute_modify rot extra 32771
|
|
|
|
velocity all create 2.4 41787 loop geom
|
|
|
|
pair_style gayberne 1.0 3.0 1.0 4.0
|
|
pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
|
|
|
|
neighbor 0.8 bin
|
|
|
|
timestep 0.002
|
|
thermo 20
|
|
|
|
# equilibration
|
|
#fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
|
|
#compute_modify 1_temp extra ${dof}
|
|
#run 100
|
|
#write_restart tmp.restart
|
|
|
|
fix 1 all npt/asphere temp 2.4 2.4 0.2 iso 8.0 8.0 0.2
|
|
run 100
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 4.8
|
|
ghost atom cutoff = 4.8
|
|
binsize = 2.4, bins = 21 21 21
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair gayberne, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
|
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
|
|
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
|
|
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
|
|
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
|
|
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
|
|
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
|
|
Loop time of 11.3124 on 4 procs for 100 steps with 32768 atoms
|
|
|
|
Performance: 1527.522 tau/day, 8.840 timesteps/s
|
|
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 10.778 | 10.849 | 10.934 | 2.0 | 95.90
|
|
Neigh | 0.088265 | 0.08871 | 0.089238 | 0.1 | 0.78
|
|
Comm | 0.1384 | 0.22518 | 0.29662 | 14.1 | 1.99
|
|
Output | 0.00020599 | 0.00024837 | 0.00036836 | 0.0 | 0.00
|
|
Modify | 0.13828 | 0.13899 | 0.13984 | 0.2 | 1.23
|
|
Other | | 0.01053 | | | 0.09
|
|
|
|
Nlocal: 8192 ave 8215 max 8166 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
Nghost: 11972.5 ave 11984 max 11959 min
|
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
|
Neighs: 576083 ave 579616 max 572161 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 2304332
|
|
Ave neighs/atom = 70.3226
|
|
Neighbor list builds = 6
|
|
Dangerous builds = 3
|
|
|
|
Please see the log.cite file for references relevant to this simulation
|
|
|
|
Total wall time: 0:00:11
|