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Axel Kohlmeyer authoredAxel Kohlmeyer authored
log.27Nov18.shear.void.g++.4 7.97 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)
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
Time spent = 0.000400543 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 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 (src/thermo.cpp:488)
timestep 0.001
run 100Neighbor 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) = 3.356 | 3.356 | 3.356 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 0.0688287 on 4 procs for 100 steps with 1708 atoms
Performance: 125.529 ns/day, 0.191 hours/ns, 1452.882 timesteps/s
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.059247 | 0.060771 | 0.062449 | 0.5 | 88.29
Neigh | 0.0022693 | 0.0023552 | 0.0024772 | 0.2 | 3.42
Comm | 0.0018966 | 0.0037905 | 0.005276 | 2.1 | 5.51
Output | 8.297e-05 | 0.00011259 | 0.00019741 | 0.0 | 0.16
Modify | 0.00082994 | 0.00084907 | 0.00086927 | 0.0 | 1.23
Other | | 0.0009506 | | | 1.38
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 (src/thermo.cpp:488)
reset_timestep 0
run 3000
Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 MbytesStep Temp E_pair E_mol TotEng Press Volume
0 298.93143 -7301.0026 0 -7270.6316 -2766.8643 19799.958
100 301.13545 -7308.1131 0 -7277.5182 -8902.3332 19851.054
200 296.29577 -7306.2042 0 -7276.101 -9974.9354 19977.713
300 301.05914 -7303.6788 0 -7273.0916 -9862.4944 20024.1
400 303.0153 -7299.731 0 -7268.9451 -7947.0168 20095.075
500 298.65447 -7297.2717 0 -7266.9288 -5763.5283 20168.398
600 296.11526 -7292.6719 0 -7262.5871 -1784.5157 20265.23
700 305.84406 -7287.3611 0 -7256.2878 -1047.7333 20413.775
800 297.24737 -7280.1938 0 -7249.9939 -1482.5729 20516.847
900 305.15166 -7272.5442 0 -7241.5412 -806.41836 20629.22
1000 303.27519 -7264.3603 0 -7233.548 -2138.7382 20763.579
1100 297.64923 -7258.2644 0 -7228.0237 -768.39318 20890.609
1200 309.57038 -7254.7251 0 -7223.2732 826.2357 20995.654
1300 300 -7251.8391 0 -7221.3595 -1913.381 21121.462
1400 300 -7258.6892 0 -7228.2096 -5149.1767 21253.378
1500 304.55119 -7269.4714 0 -7238.5294 -8459.0382 21376.744
1600 302.21492 -7270.4103 0 -7239.7057 -10281.182 21489.117
1700 300 -7273.5589 0 -7243.0794 -11327.559 21616.147
1800 306.43021 -7269.3385 0 -7238.2057 -14197.412 21741.956
1900 306.23041 -7271.5332 0 -7240.4207 -19223.302 21854.329
2000 302.23263 -7267.091 0 -7236.3847 -20191.798 21975.252
2100 308.71627 -7268.4269 0 -7237.0618 -25282.39 22097.397
2200 306.77342 -7266.6664 0 -7235.4987 -27060.48 22230.534
2300 300 -7262.0978 0 -7231.6182 -24060.909 22351.457
2400 300 -7261.4125 0 -7230.9329 -20517.199 22462.608
2500 300.21813 -7260.6381 0 -7230.1364 -15407.463 22589.639
2600 296.24006 -7257.2142 0 -7227.1167 -13436.36 22711.783
2700 300 -7256.4647 0 -7225.9852 -15922.92 22830.263
2800 298.94765 -7255.6331 0 -7225.2605 -20555.015 22959.736
2900 294.98551 -7249.0201 0 -7219.05 -23986.374 23079.438
3000 291.21483 -7244.1837 0 -7214.5967 -25356.925 23197.918
Loop time of 2.21357 on 4 procs for 3000 steps with 1708 atoms
Performance: 117.096 ns/day, 0.205 hours/ns, 1355.278 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8072 | 1.86 | 1.9192 | 3.7 | 84.03
Neigh | 0.11667 | 0.12264 | 0.13213 | 1.7 | 5.54
Comm | 0.10804 | 0.17878 | 0.23557 | 13.3 | 8.08
Output | 0.00073075 | 0.0012527 | 0.002811 | 2.5 | 0.06
Modify | 0.024781 | 0.025831 | 0.02754 | 0.7 | 1.17
Other | | 0.02508 | | | 1.13
Nlocal: 427 ave 450 max 403 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 785.25 ave 844 max 723 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 9581.25 ave 10185 max 9102 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 38325
Ave neighs/atom = 22.4385
Neighbor list builds = 215
Dangerous builds = 0
Total wall time: 0:00:02