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lammps/examples/meam/log.19May17.meam.shear.g++.4
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LAMMPS (19 May 2017)
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)
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 meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam 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 (../thermo.cpp:489)
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 = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 27 17 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
Loop time of 0.482293 on 4 procs for 100 steps with 1912 atoms
Performance: 17.914 ns/day, 1.340 hours/ns, 207.343 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.44374 | 0.45604 | 0.46922 | 1.4 | 94.56
Neigh | 0.0047338 | 0.0049097 | 0.0051899 | 0.2 | 1.02
Comm | 0.0054841 | 0.019044 | 0.031472 | 6.9 | 3.95
Output | 0.00012755 | 0.00013644 | 0.00015831 | 0.0 | 0.03
Modify | 0.0011139 | 0.0011852 | 0.0012643 | 0.2 | 0.25
Other | | 0.0009753 | | | 0.20
Nlocal: 478 ave 492 max 465 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 809 ave 822 max 795 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 5916 ave 6133 max 5658 min
Histogram: 1 0 0 1 0 0 0 0 1 1
FullNghs: 11832 ave 12277 max 11299 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 47328
Ave neighs/atom = 24.7531
Neighbor list builds = 5
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 500 dump.meam.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 (../thermo.cpp:489)
reset_timestep 0
run 3000
Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93
100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765
200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877
300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714
400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012
500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256
600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848
700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046
800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183
900 304.61422 -8126.9246 0 -8090.6214 6654.0963 20640.213
1000 300 -8113.8464 0 -8078.0931 7760.1239 20768.465
1100 300.17873 -8097.7469 0 -8061.9722 8438.126 20874.731
1200 306.01441 -8083.3367 0 -8046.8665 10835.586 20994.432
1300 300 -8067.022 0 -8031.2686 11216.067 21126.348
1400 300 -8053.223 0 -8017.4697 10570.206 21253.378
1500 300 -8043.4849 0 -8007.7315 11360.766 21375.523
1600 300 -8034.621 0 -7998.8676 11371.584 21498.889
1700 300 -8028.6783 0 -7992.925 9596.524 21613.705
1800 300 -8033.0818 0 -7997.3285 8767.2651 21743.178
1900 303.18912 -8035.194 0 -7999.0606 8059.9558 21859.215
2000 300 -8025.0327 0 -7989.2794 9305.7521 21980.138
2100 300 -8041.4626 0 -8005.7092 6623.8789 22108.39
2200 300 -8040.3133 0 -8004.5599 7512.9368 22225.648
2300 300 -8055.6567 0 -8019.9033 8281.354 22344.128
2400 304.05922 -8050.289 0 -8014.0518 11964.826 22476.044
2500 305.75646 -8037.0481 0 -8000.6087 16594.032 22595.746
2600 307.71105 -8031.2253 0 -7994.5529 18381.745 22708.119
2700 307.397 -8026.5338 0 -7989.8988 13944.653 22829.042
2800 309.3455 -8020.2305 0 -7983.3634 7037.4046 22954.851
2900 301.2859 -8010.4731 0 -7974.5665 3843.8972 23072.109
3000 303.29908 -8000.0395 0 -7963.8929 364.90172 23207.69
Loop time of 14.5278 on 4 procs for 3000 steps with 1912 atoms
Performance: 17.842 ns/day, 1.345 hours/ns, 206.500 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.872 | 13.929 | 13.998 | 1.4 | 95.88
Neigh | 0.20891 | 0.21114 | 0.21272 | 0.3 | 1.45
Comm | 0.25364 | 0.32377 | 0.37706 | 8.9 | 2.23
Output | 0.0011427 | 0.0012097 | 0.0013931 | 0.3 | 0.01
Modify | 0.033687 | 0.033991 | 0.034694 | 0.2 | 0.23
Other | | 0.02871 | | | 0.20
Nlocal: 478 ave 509 max 445 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 804 ave 845 max 759 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 5827 ave 6177 max 5496 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 11654 ave 12330 max 11039 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 46616
Ave neighs/atom = 24.3808
Neighbor list builds = 223
Dangerous builds = 0
Total wall time: 0:00:15
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