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Axel Kohlmeyer authoredAxel Kohlmeyer authored
log.27Nov18.shear.g++.1 7.92 KiB
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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
Time spent = 0.001899 secs
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 5 2.5 INF INF
#delete_atoms region void
# 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 (src/thermo.cpp:488)
timestep 0.001
run 100
Neighbor list info ... 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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam, 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) = 3.49 | 3.49 | 3.49 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02
25 220.34459 -8272.5701 0 -8233.1798 5168.6655 19547.02
50 300 -8237.7876 0 -8184.1576 13741.264 19686.493
75 292.67269 -8229.8093 0 -8177.4891 14319.387 19744.946
100 300 -8245.8191 0 -8192.189 9034.8776 19778.592
Loop time of 0.284035 on 1 procs for 100 steps with 1912 atoms
Performance: 30.419 ns/day, 0.789 hours/ns, 352.069 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26775 | 0.26775 | 0.26775 | 0.0 | 94.27
Neigh | 0.0096006 | 0.0096006 | 0.0096006 | 0.0 | 3.38
Comm | 0.0018885 | 0.0018885 | 0.0018885 | 0.0 | 0.66
Output | 9.8228e-05 | 9.8228e-05 | 9.8228e-05 | 0.0 | 0.03
Modify | 0.0035083 | 0.0035083 | 0.0035083 | 0.0 | 1.24
Other | | 0.001191 | | | 0.42
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2122 ave 2122 max 2122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45975 ave 45975 max 45975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45975
Ave neighs/atom = 24.0455
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
#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 (src/thermo.cpp:488)
reset_timestep 0
run 3000
Per MPI rank memory allocation (min/avg/max) = 3.492 | 3.492 | 3.492 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 0 298.42546 -8245.8191 0 -8210.2533 8056.2702 19786.12
100 300 -8260.779 0 -8225.0257 3180.8817 19817.51
200 298.49477 -8257.8274 0 -8222.2534 1700.0333 19934.216
300 296.80877 -8250.217 0 -8214.8439 -335.0728 20058.906
400 306.4648 -8245.2088 0 -8208.6849 12.980341 20142.437
500 298.68513 -8240.2265 0 -8204.6298 724.74628 20168.921
600 302.36747 -8230.4475 0 -8194.412 4008.1803 20287.313
700 300 -8222.0049 0 -8186.2515 6769.0085 20413.548
800 303.21455 -8210.9809 0 -8174.8444 8151.2853 20518.069
900 297.73976 -8197.2227 0 -8161.7387 10762.493 20642.656
1000 300 -8180.7322 0 -8144.9788 14223.501 20768.465
1100 305.90212 -8166.6385 0 -8130.1817 18071.031 20883.281
1200 295.28708 -8152.0566 0 -8116.865 21319.983 21009.09
1300 300 -8141.735 0 -8105.9817 22789.953 21123.905
1400 300 -8130.0945 0 -8094.3412 23506.161 21254.6
1500 300 -8125.491 0 -8089.7376 21984.112 21364.53
1600 300 -8129.0114 0 -8093.2581 18298.088 21494.003
1700 300 -8151.5114 0 -8115.758 11476.041 21608.819
1800 300 -8160.1734 0 -8124.42 7531.8995 21732.185
1900 309.49207 -8153.8281 0 -8116.9435 8365.4734 21865.322
2000 300 -8160.422 0 -8124.6687 5899.5578 21983.802
2100 308.20427 -8156.5089 0 -8119.7778 4890.4919 22102.282
2200 300 -8157.3295 0 -8121.5761 2430.2444 22223.205
2300 300 -8162.8531 0 -8127.0998 -196.01631 22340.464
2400 309.85806 -8165.8024 0 -8128.8741 -1402.5251 22463.83
2500 300 -8168.8805 0 -8133.1271 -60.525408 22599.41
2600 300 -8161.8771 0 -8126.1237 2356.1773 22720.333
2700 300 -8165.9618 0 -8130.2084 239.23169 22841.256
2800 306.61457 -8165.9986 0 -8129.457 -2360.5296 22954.851
2900 305.42952 -8161.9351 0 -8125.5347 -6928.3135 23081.881
3000 292.3109 -8156.8668 0 -8122.0298 -9481.3532 23197.918
Loop time of 8.5487 on 1 procs for 3000 steps with 1912 atoms
Performance: 30.320 ns/day, 0.792 hours/ns, 350.931 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7964 | 7.7964 | 7.7964 | 0.0 | 91.20
Neigh | 0.54999 | 0.54999 | 0.54999 | 0.0 | 6.43
Comm | 0.061907 | 0.061907 | 0.061907 | 0.0 | 0.72
Output | 0.00085449 | 0.00085449 | 0.00085449 | 0.0 | 0.01
Modify | 0.10321 | 0.10321 | 0.10321 | 0.0 | 1.21
Other | | 0.03637 | | | 0.43
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2095 ave 2095 max 2095 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45027 ave 45027 max 45027 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45027
Ave neighs/atom = 23.5497
Neighbor list builds = 222
Dangerous builds = 0
Total wall time: 0:00:08