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lammps/examples/shear/log.15Feb16.shear.void.g++.4
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LAMMPS (15 Feb 2016)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
timestep 0.001
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.1
ghost atom cutoff = 5.1
binsize = 2.55 -> bins = 23 14 4
Memory usage per processor = 2.7752 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02
25 220.57465 -7320.4003 0 -7286.7852 832.69858 19547.02
50 300 -7292.1121 0 -7246.3928 7101.9213 19686.075
75 295.2793 -7286.9013 0 -7241.9014 5282.1114 19746.39
100 300 -7301.0026 0 -7255.2833 -1939.7714 19790.975
Loop time of 0.0633137 on 4 procs for 100 steps with 1708 atoms
Performance: 136.463 ns/day, 0.176 hours/ns, 1579.436 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.056509 | 0.057388 | 0.058275 | 0.3 | 90.64
Neigh | 0.001965 | 0.0020149 | 0.0020759 | 0.1 | 3.18
Comm | 0.0013819 | 0.0022985 | 0.003196 | 1.6 | 3.63
Output | 9.8705e-05 | 0.0001052 | 0.00012016 | 0.1 | 0.17
Modify | 0.00085497 | 0.00087214 | 0.00089121 | 0.1 | 1.38
Other | | 0.0006346 | | | 1.00
Nlocal: 427 ave 437 max 419 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 780 ave 788 max 774 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 9859.75 ave 10248 max 9544 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 39439
Ave neighs/atom = 23.0907
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
#dump 1 all atom 100 dump.shear.void
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
reset_timestep 0
run 3000
Memory usage per processor = 2.7752 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 299.05825 -7301.0026 0 -7270.6316 -2766.8643 19799.958
100 301.19116 -7308.1272 0 -7277.5397 -8905.8025 19851.046
200 296.34396 -7306.2167 0 -7276.1214 -9976.4707 19977.676
300 301.10727 -7303.6912 0 -7273.1122 -9863.5572 20024.08
400 303.06413 -7299.743 0 -7268.9652 -7947.839 20095.051
500 298.67442 -7297.287 0 -7266.955 -5764.8779 20168.374
600 296.13094 -7292.6877 0 -7262.614 -1786.0615 20265.23
700 305.86337 -7287.378 0 -7256.3159 -1049.7285 20413.77
800 297.25967 -7280.2104 0 -7250.0221 -1484.4549 20516.847
900 305.16151 -7272.5608 0 -7241.57 -808.36942 20629.22
1000 303.28807 -7264.3771 0 -7233.5765 -2139.5907 20763.579
1100 297.67659 -7258.2851 0 -7228.0544 -770.05741 20890.609
1200 309.60751 -7254.7626 0 -7223.3203 819.60099 20995.654
1300 300 -7251.8704 0 -7221.4038 -1919.6357 21121.462
1400 300 -7258.7732 0 -7228.3066 -5164.6854 21253.378
1500 304.51839 -7269.5164 0 -7238.5909 -8462.6306 21376.744
1600 302.30135 -7270.4656 0 -7239.7653 -10283.715 21489.117
1700 300 -7273.6082 0 -7243.1416 -11338.311 21616.147
1800 306.59272 -7269.4364 0 -7238.3003 -14218.514 21740.735
1900 306.24897 -7271.6064 0 -7240.5052 -19238.112 21854.329
2000 302.17783 -7267.1183 0 -7236.4305 -20204.467 21975.252
2100 308.30693 -7268.4528 0 -7237.1425 -25338.75 22097.397
2200 306.39487 -7266.6795 0 -7235.5635 -27066.965 22230.534
2300 300 -7262.1576 0 -7231.691 -24009.895 22351.457
2400 300 -7261.5352 0 -7231.0686 -20454.104 22478.487
2500 300.08812 -7260.6902 0 -7230.2146 -15315.132 22587.196
2600 296.32147 -7257.4049 0 -7227.3118 -13410.947 22722.776
2700 300 -7256.5862 0 -7226.1196 -15961.676 22830.263
2800 298.83111 -7256.171 0 -7225.8231 -20667.094 22960.958
2900 291.53879 -7248.9903 0 -7219.3829 -23968.563 23081.881
3000 293.96302 -7243.6435 0 -7213.79 -25021.209 23200.361
Loop time of 1.9353 on 4 procs for 3000 steps with 1708 atoms
Performance: 133.933 ns/day, 0.179 hours/ns, 1550.145 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6683 | 1.6925 | 1.736 | 2.0 | 87.46
Neigh | 0.10491 | 0.10797 | 0.11187 | 0.8 | 5.58
Comm | 0.041337 | 0.089808 | 0.11691 | 9.6 | 4.64
Output | 0.00081921 | 0.00085014 | 0.00093603 | 0.2 | 0.04
Modify | 0.025656 | 0.026361 | 0.027086 | 0.3 | 1.36
Other | | 0.01777 | | | 0.92
Nlocal: 427 ave 450 max 403 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 785 ave 843 max 722 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 9576.75 ave 10183 max 9094 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 38307
Ave neighs/atom = 22.428
Neighbor list builds = 215
Dangerous builds = 0
Total wall time: 0:00:02
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