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lammps/examples/indent/log.5Oct16.indent.g++.4
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LAMMPS (5 Oct 2016)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
#dump 1 all atom 250 dump.indent
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 30000
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 = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 17 15 1
Memory usage per processor = 2.47636 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
1000 0.11573595 -3.0964873 0 -2.9975606 -0.20448672 441.83732
2000 0.11519605 -3.0960246 0 -2.9975594 -0.38133491 442.33058
3000 0.11367906 -3.0839597 0 -2.9867912 -0.42579765 444.59119
4000 0.11618844 -3.0860897 0 -2.9867762 -0.041580916 439.84614
5000 0.11327789 -3.0848614 0 -2.9880358 -0.48898867 446.19202
6000 0.12058424 -3.0869438 0 -2.983873 0.011477134 440.56887
7000 0.11772522 -3.0833477 0 -2.9827207 -0.090378245 442.56787
8000 0.12533514 -3.0970033 0 -2.9898715 0.13263189 441.23478
9000 0.1198683 -3.0867062 0 -2.9842473 0.34046664 439.4706
10000 0.12234014 -3.0835007 0 -2.9789291 0.28399731 441.94307
11000 0.11082436 -3.0754796 0 -2.9807511 0.62194284 441.32012
12000 0.1084272 -3.0646379 0 -2.9719584 0.65383569 442.64668
13000 0.11686417 -3.0600388 0 -2.9601477 1.0041123 438.50135
14000 0.12557378 -3.0570017 0 -2.949666 0.85709169 442.10189
15000 0.11934084 -3.0498848 0 -2.9478768 1.0392201 451.74396
16000 0.12576913 -3.045218 0 -2.9377154 1.3479479 441.2702
17000 0.11546579 -3.0348367 0 -2.9361409 1.631821 439.48441
18000 0.12148869 -3.0221152 0 -2.9182713 1.6088855 449.25443
19000 0.11883863 -3.0036777 0 -2.902099 1.5201108 447.12736
20000 0.11163567 -3.0038144 0 -2.9083924 1.4078554 461.76339
21000 0.11361999 -2.9900869 0 -2.8929688 1.1334192 473.91362
22000 0.12696379 -3.0207381 0 -2.9122143 0.83288039 473.02925
23000 0.1188706 -3.01731 0 -2.915704 1.1482286 468.57874
24000 0.11820885 -3.0098527 0 -2.9088123 0.98884958 472.75675
25000 0.11671309 -3.0101308 0 -2.9103689 1.2402973 469.77097
26000 0.11965934 -3.0091118 0 -2.9068315 0.94844832 469.04458
27000 0.12147721 -3.0085715 0 -2.9047374 1.2363584 474.98572
28000 0.11718062 -2.993818 0 -2.8936565 1.143781 478.94786
29000 0.10922042 -2.9873887 0 -2.8940313 1.6184815 473.13968
30000 0.11475456 -2.9749758 0 -2.876888 1.8682946 472.49357
Loop time of 1.05783 on 4 procs for 30000 steps with 420 atoms
Performance: 7350928.409 tau/day, 28360.063 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40826 | 0.46628 | 0.5198 | 6.6 | 44.08
Neigh | 0.017807 | 0.019817 | 0.021682 | 1.1 | 1.87
Comm | 0.22255 | 0.26884 | 0.31893 | 8.2 | 25.41
Output | 0.0005722 | 0.00060749 | 0.00070214 | 0.2 | 0.06
Modify | 0.18744 | 0.19364 | 0.20341 | 1.5 | 18.31
Other | | 0.1086 | | | 10.27
Nlocal: 105 ave 115 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 96.25 ave 104 max 87 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 931.25 ave 1078 max 743 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3725
Ave neighs/atom = 8.86905
Neighbor list builds = 608
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.47641 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11475456 -2.9749758 0 -2.876888 1.8675667 472.67773
31000 0.11574891 -3.0442299 0 -2.9452921 -0.72600606 489.16618
32000 0.11316772 -3.0299575 0 -2.933226 -0.74912451 483.50803
33000 0.12321675 -3.052617 0 -2.947296 0.29368262 473.07336
34000 0.11671309 -3.0470741 0 -2.9473122 -0.46988097 480.59621
35000 0.11671309 -3.0456501 0 -2.9458882 -0.74504498 475.07349
36000 0.11980973 -3.0797043 0 -2.9772955 0.083053833 461.14624
37000 0.10992033 -3.0712499 0 -2.9772942 -0.6447083 468.1598
38000 0.11831288 -3.0676136 0 -2.9664842 -0.59676518 469.61724
39000 0.11663782 -3.0775961 0 -2.9778985 0.21776888 460.87504
40000 0.10805913 -3.0688733 0 -2.9765084 -0.59632811 469.15555
41000 0.12118734 -3.0800988 0 -2.9765125 -0.32401944 466.81124
42000 0.12373313 -3.0822746 0 -2.9765123 -0.0033603954 462.85792
43000 0.1078275 -3.0686759 0 -2.976509 -0.71758451 469.60392
44000 0.12315017 -3.0787716 0 -2.9735076 -0.05619902 463.06786
45000 0.11564078 -3.0833684 0 -2.9845231 -0.36953273 465.92986
46000 0.10640706 -3.0654913 0 -2.9745386 -0.53685976 469.3539
47000 0.11810977 -3.0754985 0 -2.9745428 0.088083121 463.20699
48000 0.11241387 -3.0828874 0 -2.9868003 -0.54828531 466.25548
49000 0.11679121 -3.0748686 0 -2.9750399 -0.33781022 465.50451
50000 0.11656344 -3.07471 0 -2.9750761 -0.054088803 461.22814
51000 0.12060058 -3.0781622 0 -2.9750774 -0.55815121 468.81379
52000 0.11936306 -3.0876851 0 -2.9856581 -0.34773758 464.10154
53000 0.11032135 -3.0799138 0 -2.9856153 -0.1735616 465.533
54000 0.12365261 -3.0737021 0 -2.9680086 -0.52954909 468.29003
55000 0.12763641 -3.0771061 0 -2.9680074 -0.17884875 464.79749
56000 0.12638245 -3.0879132 0 -2.9798863 -0.2754242 464.35767
57000 0.11481136 -3.0780176 0 -2.9798812 -0.45547532 468.09393
58000 0.11858604 -3.0812503 0 -2.9798874 -0.17502776 463.2168
59000 0.11344551 -3.0768536 0 -2.9798847 -0.32382437 465.29204
60000 0.11637998 -3.0793607 0 -2.9798836 -0.45942931 466.04868
Loop time of 0.87344 on 4 procs for 30000 steps with 420 atoms
Performance: 8902734.020 tau/day, 34346.968 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38824 | 0.45201 | 0.49914 | 6.9 | 51.75
Neigh | 0.0175 | 0.020234 | 0.022472 | 1.5 | 2.32
Comm | 0.21322 | 0.26426 | 0.33067 | 10.0 | 30.25
Output | 0.00049305 | 0.00051773 | 0.00058699 | 0.2 | 0.06
Modify | 0.04793 | 0.053404 | 0.05745 | 1.8 | 6.11
Other | | 0.08302 | | | 9.50
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 92.5 ave 96 max 89 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 892.25 ave 1003 max 788 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 634
Dangerous builds = 0
Total wall time: 0:00:01
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