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lammps/examples/meam/log.19May17.meam.shear.g++.1
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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)
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 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) = 9.788 | 9.788 | 9.788 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
Loop time of 1.58103 on 1 procs for 100 steps with 1912 atoms
Performance: 5.465 ns/day, 4.392 hours/ns, 63.250 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5561 | 1.5561 | 1.5561 | 0.0 | 98.42
Neigh | 0.018544 | 0.018544 | 0.018544 | 0.0 | 1.17
Comm | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 0.09
Output | 0.00011396 | 0.00011396 | 0.00011396 | 0.0 | 0.01
Modify | 0.0038245 | 0.0038245 | 0.0038245 | 0.0 | 0.24
Other | | 0.001096 | | | 0.07
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1672 ave 1672 max 1672 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23806 ave 23806 max 23806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47612 ave 47612 max 47612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47612
Ave neighs/atom = 24.9017
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) = 9.964 | 9.964 | 9.964 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297
100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53
200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24
300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759
400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698
500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813
600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887
700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302
800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519
900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992
1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243
1100 304.14047 -8096.5041 0 -8060.2573 9646.6976 20888.167
1200 302.78457 -8080.5931 0 -8044.5079 11516.209 20995.917
1300 308.67054 -8061.6724 0 -8024.8857 11496.479 21130.013
1400 309.8301 -8046.27 0 -8009.3452 12926.835 21247.271
1500 300 -8035.0321 0 -7999.2788 15346.455 21370.637
1600 300 -8030.6657 0 -7994.9123 14802.869 21496.446
1700 300 -8024.5251 0 -7988.7718 13176.923 21611.262
1800 300 -8022.9963 0 -7987.243 10260.665 21741.956
1900 300 -8028.0522 0 -7992.2988 6955.1367 21867.765
2000 300 -8037.2708 0 -8001.5175 3520.3749 21987.467
2100 300 -8035.9945 0 -8000.2412 3237.6121 22109.611
2200 300 -8036.1882 0 -8000.4348 4295.1386 22223.205
2300 300 -8032.7689 0 -7997.0155 6231.2346 22355.121
2400 300 -8034.6621 0 -7998.9088 8585.3799 22468.716
2500 300 -8031.7774 0 -7996.0241 11627.871 22587.196
2600 300 -8024.032 0 -7988.2786 16254.69 22716.669
2700 308.64215 -8017.407 0 -7980.6237 18440.226 22835.149
2800 300 -8015.7348 0 -7979.9814 17601.716 22957.293
2900 305.82558 -8013.7448 0 -7977.2972 14123.494 23089.209
3000 300 -8011.0289 0 -7975.2755 9957.2884 23205.247
Loop time of 51.9315 on 1 procs for 3000 steps with 1912 atoms
Performance: 4.991 ns/day, 4.808 hours/ns, 57.768 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 50.918 | 50.918 | 50.918 | 0.0 | 98.05
Neigh | 0.81033 | 0.81033 | 0.81033 | 0.0 | 1.56
Comm | 0.047331 | 0.047331 | 0.047331 | 0.0 | 0.09
Output | 0.0011976 | 0.0011976 | 0.0011976 | 0.0 | 0.00
Modify | 0.11889 | 0.11889 | 0.11889 | 0.0 | 0.23
Other | | 0.03606 | | | 0.07
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1672 ave 1672 max 1672 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23557 ave 23557 max 23557 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47114 ave 47114 max 47114 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47114
Ave neighs/atom = 24.6412
Neighbor list builds = 221
Dangerous builds = 0
Total wall time: 0:00:53
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