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lammps/examples/shear/log.15Feb16.shear.void.g++.1
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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)
1 by 1 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 = 2.86988 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02
25 222.66197 -7321.4403 0 -7287.5071 562.28854 19547.02
50 300 -7292.2273 0 -7246.508 7555.5059 19688.542
75 292.67603 -7286.2016 0 -7241.5984 6825.409 19746.217
100 300 -7297.4174 0 -7251.698 1627.2455 19775.648
Loop time of 0.228758 on 1 procs for 100 steps with 1708 atoms
Performance: 37.769 ns/day, 0.635 hours/ns, 437.143 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21504 | 0.21504 | 0.21504 | 0.0 | 94.00
Neigh | 0.0082476 | 0.0082476 | 0.0082476 | 0.0 | 3.61
Comm | 0.0012808 | 0.0012808 | 0.0012808 | 0.0 | 0.56
Output | 8.2016e-05 | 8.2016e-05 | 8.2016e-05 | 0.0 | 0.04
Modify | 0.0031452 | 0.0031452 | 0.0031452 | 0.0 | 1.37
Other | | 0.0009589 | | | 0.42
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39444 ave 39444 max 39444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39444
Ave neighs/atom = 23.0937
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 = 2.86988 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 296.81549 -7297.4174 0 -7267.2741 785.80272 19779.424
100 290.32156 -7309.73 0 -7280.2463 -5960.68 19838.822
200 290.76236 -7306.4805 0 -7276.952 -7418.7514 19927.076
300 293.25821 -7304.1086 0 -7274.3267 -11009.15 20043.748
400 293.84766 -7299.0985 0 -7269.2567 -7883.11 20105.777
500 291.74499 -7299.9751 0 -7270.3468 -5633.9534 20145.528
600 303.46664 -7291.5162 0 -7260.6975 -1009.8362 20277.444
700 300 -7287.9569 0 -7257.4903 -2204.427 20399.405
800 300 -7280.4222 0 -7249.9555 -2875.1442 20520.781
900 292.92463 -7272.7361 0 -7242.9881 -1776.2948 20641.435
1000 307.93499 -7265.1866 0 -7233.9141 -1238.1504 20758.693
1100 300.17079 -7260.1229 0 -7229.6389 -1842.3017 20889.388
1200 302.06128 -7255.9277 0 -7225.2517 -1888.5899 21012.754
1300 300 -7259.2664 0 -7228.7998 -3184.8863 21119.02
1400 300 -7265.444 0 -7234.9774 -6107.2621 21252.157
1500 308.79162 -7271.0073 0 -7239.6478 -6104.8023 21369.416
1600 300 -7275.2324 0 -7244.7658 -8516.6115 21500.11
1700 309.22602 -7278.5756 0 -7247.172 -13747.711 21618.59
1800 300 -7284.3068 0 -7253.8402 -14332.302 21728.52
1900 299.75827 -7283.413 0 -7252.9709 -14457.778 21854.329
2000 297.70312 -7274.9007 0 -7244.6674 -20473.262 21986.245
2100 304.09482 -7269.8328 0 -7238.9503 -19783.936 22101.061
2200 299.66443 -7269.2566 0 -7238.8241 -16596.846 22224.427
2300 299.27231 -7268.2781 0 -7237.8853 -15841.479 22345.35
2400 300.69324 -7259.5316 0 -7228.9946 -14593.472 22471.159
2500 297.44581 -7258.0006 0 -7227.7934 -17840.459 22589.639
2600 300 -7253.3731 0 -7222.9065 -18551.141 22719.112
2700 305.12651 -7253.1648 0 -7222.1775 -20324.426 22832.706
2800 294.14063 -7249.1464 0 -7219.2748 -17535.191 22960.958
2900 307.30441 -7249.4895 0 -7218.281 -17444.188 23079.438
3000 304.44871 -7244.9559 0 -7214.0374 -15836.731 23207.69
Loop time of 6.93892 on 1 procs for 3000 steps with 1708 atoms
Performance: 37.355 ns/day, 0.642 hours/ns, 432.344 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3414 | 6.3414 | 6.3414 | 0.0 | 91.39
Neigh | 0.43388 | 0.43388 | 0.43388 | 0.0 | 6.25
Comm | 0.041184 | 0.041184 | 0.041184 | 0.0 | 0.59
Output | 0.00080252 | 0.00080252 | 0.00080252 | 0.0 | 0.01
Modify | 0.093581 | 0.093581 | 0.093581 | 0.0 | 1.35
Other | | 0.02807 | | | 0.40
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1879 ave 1879 max 1879 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38632 ave 38632 max 38632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38632
Ave neighs/atom = 22.6183
Neighbor list builds = 209
Dangerous builds = 0
Total wall time: 0:00:07
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