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LAMMPS (15 Feb 2016)
# 2d indenter simulation with minimization instead of dynamics
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)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 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
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
#dump 1 all atom 10 dump.indent
#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 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 = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558
20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033
30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033
35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082
Loop time of 0.00924516 on 1 procs for 35 steps with 420 atoms
97.3% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19093697812 -3.19093855395
Force two-norm initial, final = 6.74302 0.230475
Force max component initial, final = 1.46877 0.0236603
Final line search alpha, max atom move = 1 0.0236603
Iterations, force evaluations = 35 70
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0078757 | 0.0078757 | 0.0078757 | 0.0 | 85.19
Neigh | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 4.89
Comm | 8.0109e-05 | 8.0109e-05 | 8.0109e-05 | 0.0 | 0.87
Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.28
Modify | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 1.16
Other | | 0.0007045 | | | 7.62
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3580 ave 3580 max 3580 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574
40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534
50 0 -3.174757 0 -3.173603 -0.34916248 436.00326
60 0 -3.1789904 0 -3.1780198 -0.31146423 436.06053
70 0 -3.1800572 0 -3.1792392 -0.27664904 436.09293
80 0 -3.1808315 0 -3.1799813 -0.24091474 435.00572
90 0 -3.1810856 0 -3.1803991 -0.1771392 433.03804
100 0 -3.1812307 0 -3.1805381 -0.15305004 434.96379
110 0 -3.1812588 0 -3.1805938 -0.12504604 432.50683
111 0 -3.1812728 0 -3.1805961 -0.12407116 432.50683
Loop time of 0.0215449 on 1 procs for 76 steps with 420 atoms
102.1% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.17436899358 -3.18059381924 -3.18059607055
Force two-norm initial, final = 1618.56 0.444006
Force max component initial, final = 1191.42 0.168708
Final line search alpha, max atom move = 0.428869 0.0723538
Iterations, force evaluations = 76 147
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016444 | 0.016444 | 0.016444 | 0.0 | 76.33
Neigh | 0.0022733 | 0.0022733 | 0.0022733 | 0.0 | 10.55
Comm | 0.0001955 | 0.0001955 | 0.0001955 | 0.0 | 0.91
Output | 5.7459e-05 | 5.7459e-05 | 5.7459e-05 | 0.0 | 0.27
Modify | 0.00096774 | 0.00096774 | 0.00096774 | 0.0 | 4.49
Other | | 0.001607 | | | 7.46
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3596 ave 3596 max 3596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3596
Ave neighs/atom = 8.5619
Neighbor list builds = 19
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
111 0 -3.1812728 0 -0.21796953 -0.12362158 434.07977
120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832
130 0 -3.0632093 0 -3.0453082 1.4275815 434.09622
140 0 -3.0947739 0 -3.0852867 1.2276154 434.51983
150 0 -3.1008901 0 -3.0931811 1.1938163 434.52998
160 0 -3.1026159 0 -3.0950306 1.2229151 434.35672
170 0 -3.1032959 0 -3.0962512 1.3134391 432.20445
180 0 -3.1041304 0 -3.0969544 1.3751461 430.37017
190 0 -3.1043441 0 -3.0970791 1.392095 430.37017
193 0 -3.1043345 0 -3.0970891 1.3934777 430.37017
Loop time of 0.022316 on 1 procs for 82 steps with 420 atoms
103.1% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.217969533586 -3.09708660422 -3.09708908043
Force two-norm initial, final = 1754.38 0.648372
Force max component initial, final = 924.68 0.156564
Final line search alpha, max atom move = 0.961384 0.150518
Iterations, force evaluations = 82 156
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017607 | 0.017607 | 0.017607 | 0.0 | 78.90
Neigh | 0.0018115 | 0.0018115 | 0.0018115 | 0.0 | 8.12
Comm | 0.00016046 | 0.00016046 | 0.00016046 | 0.0 | 0.72
Output | 5.8413e-05 | 5.8413e-05 | 5.8413e-05 | 0.0 | 0.26
Modify | 0.0010521 | 0.0010521 | 0.0010521 | 0.0 | 4.71
Other | | 0.001626 | | | 7.29
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3666 ave 3666 max 3666 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3666
Ave neighs/atom = 8.72857
Neighbor list builds = 14
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
193 0 -3.1043345 0 2.0111862 1.3910056 431.13503
200 0 -2.5918177 0 -1.931934 5.51119 430.91952
210 0 -2.8122285 0 -2.7440908 4.2686845 440.18379
220 0 -2.9102892 0 -2.8879734 3.5957736 444.98944
230 0 -2.9492295 0 -2.9335905 3.2079493 451.92209
240 0 -2.9611099 0 -2.9486963 3.1240398 452.59159
250 0 -2.9644912 0 -2.9549723 3.0493724 455.54273
260 0 -2.9716881 0 -2.9621479 2.8585653 458.29826
270 0 -3.0142839 0 -3.0048107 2.1183076 462.48471
280 0 -3.0666108 0 -3.0590819 1.4342986 470.61174
290 0 -3.1004306 0 -3.0944504 1.1550298 472.70399
300 0 -3.1107855 0 -3.1043751 1.0663324 470.76888
310 0 -3.1124671 0 -3.1059633 1.0375877 473.02275
316 0 -3.1126981 0 -3.1061297 1.0266662 473.02275
Loop time of 0.0393021 on 1 procs for 123 steps with 420 atoms
99.2% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
2.01118618013 -3.10612971775 -3.10612971775
Force two-norm initial, final = 2329.79 2.56384
Force max component initial, final = 1038.4 0.558457
Final line search alpha, max atom move = 6.21371e-07 3.47009e-07
Iterations, force evaluations = 123 270
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030668 | 0.030668 | 0.030668 | 0.0 | 78.03
Neigh | 0.0037498 | 0.0037498 | 0.0037498 | 0.0 | 9.54
Comm | 0.00033641 | 0.00033641 | 0.00033641 | 0.0 | 0.86
Output | 8.6069e-05 | 8.6069e-05 | 8.6069e-05 | 0.0 | 0.22
Modify | 0.0017693 | 0.0017693 | 0.0017693 | 0.0 | 4.50
Other | | 0.002692 | | | 6.85
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3583 ave 3583 max 3583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3583
Ave neighs/atom = 8.53095
Neighbor list builds = 29
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
316 0 -3.1126981 0 5.3552772 1.0307152 471.16452
320 0 -2.7131804 0 0.70918694 3.910187 471.16482
330 0 -2.5180572 0 -2.2327154 5.9511047 472.82589
340 0 -2.8183947 0 -2.790733 4.18655 477.34785
350 0 -2.9132456 0 -2.8943586 3.4322048 481.94491
360 0 -2.9337359 0 -2.9225123 3.2341233 484.63169
370 0 -2.9463892 0 -2.9382426 3.0071366 485.20235
380 0 -2.9682176 0 -2.9597318 2.6056737 490.5653
390 0 -2.9878255 0 -2.974755 2.3632883 491.02616
400 0 -3.0033473 0 -2.9915257 2.205124 490.20353
410 0 -3.0130231 0 -3.001125 2.0531631 492.78365
420 0 -3.0146089 0 -3.0030496 1.9865701 492.35543
430 0 -3.0344603 0 -3.0225619 1.6795534 494.30371
440 0 -3.03943 0 -3.0271752 1.64578 494.30371
450 0 -3.0420658 0 -3.0294992 1.6461313 493.96169
460 0 -3.0443144 0 -3.0312966 1.6701433 493.56812
465 0 -3.0444584 0 -3.0313908 1.6713796 493.56812
Loop time of 0.0470922 on 1 procs for 149 steps with 420 atoms
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
5.35527716926 -3.03139082546 -3.03139082546
Force two-norm initial, final = 3151.59 4.64631
Force max component initial, final = 1384.28 2.19626
Final line search alpha, max atom move = 1.88135e-07 4.13193e-07
Iterations, force evaluations = 149 323
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036967 | 0.036967 | 0.036967 | 0.0 | 78.50
Neigh | 0.004194 | 0.004194 | 0.004194 | 0.0 | 8.91
Comm | 0.00037503 | 0.00037503 | 0.00037503 | 0.0 | 0.80
Output | 0.00010633 | 0.00010633 | 0.00010633 | 0.0 | 0.23
Modify | 0.002212 | 0.002212 | 0.002212 | 0.0 | 4.70
Other | | 0.003238 | | | 6.88
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 113 ave 113 max 113 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3693 ave 3693 max 3693 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3693
Ave neighs/atom = 8.79286
Neighbor list builds = 33
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Memory usage per processor = 3.59478 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
465 0 -3.0444584 0 -2.5580192 1.6715946 493.50462
470 0 -2.9426683 0 -2.8814986 2.6421083 493.54443
480 0 -2.9569251 0 -2.9256743 2.6206554 493.55709
490 0 -2.961805 0 -2.9376884 2.6095523 493.40001
500 0 -2.9651536 0 -2.9450214 2.6314399 493.06356
510 0 -2.9667772 0 -2.9489178 2.6710408 492.70775
520 0 -2.9728188 0 -2.9566496 2.7182742 492.38186
530 0 -2.9791224 0 -2.9651707 2.7038256 493.19977
540 0 -2.9968316 0 -2.984276 2.5920672 495.29778
550 0 -3.0029515 0 -2.9915532 2.4491025 500.52622
560 0 -3.0160794 0 -3.0057787 2.0399831 513.34527
570 0 -3.0363001 0 -3.0306173 1.6834763 520.40445
580 0 -3.0548101 0 -3.0490935 1.501103 521.5353
590 0 -3.0640876 0 -3.0585539 1.3888581 520.17883
600 0 -3.0713144 0 -3.0649318 1.3341898 518.99349
610 0 -3.0727361 0 -3.0662278 1.2983097 519.87058
620 0 -3.0732598 0 -3.0671664 1.2611866 520.9829
630 0 -3.076528 0 -3.069576 1.1930176 520.18857
640 0 -3.0778611 0 -3.0710808 1.1946248 520.31492
650 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
651 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
Loop time of 0.057997 on 1 procs for 186 steps with 420 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.55801918976 -3.07153633363 -3.07153633363
Force two-norm initial, final = 440.856 1.45625
Force max component initial, final = 245.987 0.411517
Final line search alpha, max atom move = 1.25651e-06 5.17073e-07
Iterations, force evaluations = 186 403
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.045592 | 0.045592 | 0.045592 | 0.0 | 78.61
Neigh | 0.0050173 | 0.0050173 | 0.0050173 | 0.0 | 8.65
Comm | 0.00052071 | 0.00052071 | 0.00052071 | 0.0 | 0.90
Output | 0.00014472 | 0.00014472 | 0.00014472 | 0.0 | 0.25
Modify | 0.0027096 | 0.0027096 | 0.0027096 | 0.0 | 4.67
Other | | 0.004013 | | | 6.92
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 116 ave 116 max 116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3622 ave 3622 max 3622 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3622
Ave neighs/atom = 8.62381
Neighbor list builds = 39
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Memory usage per processor = 3.59487 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
651 0 -3.0781525 0 -2.6488207 1.2032064 520.29591
660 0 -3.0085949 0 -2.9796645 1.9715308 520.26872
670 0 -3.014536 0 -2.9989599 2.0077209 520.35057
680 0 -3.0193861 0 -3.0073499 2.0050119 520.52555
690 0 -3.0214256 0 -3.0087927 2.0056587 520.37174
700 0 -3.0218644 0 -3.0095894 2.0386389 520.05804
710 0 -3.0262571 0 -3.0142277 2.1356802 520.14691
720 0 -3.0325017 0 -3.0216037 2.1065924 521.43634
730 0 -3.0400735 0 -3.0302631 2.0146233 523.09133
740 0 -3.048476 0 -3.0386288 1.9305047 523.14231
750 0 -3.0523937 0 -3.042131 1.9025403 522.0453
760 0 -3.0544932 0 -3.044222 1.9106706 521.73287
770 0 -3.0587698 0 -3.048907 1.9552463 521.6899
780 0 -3.065994 0 -3.0566273 1.931796 521.52157
790 0 -3.0675084 0 -3.0577936 1.9283059 520.99202
799 0 -3.0677005 0 -3.057959 1.9288603 520.99202
Loop time of 0.046221 on 1 procs for 148 steps with 420 atoms
99.5% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.64882068661 -3.05795898949 -3.05795898949
Force two-norm initial, final = 420.333 1.17649
Force max component initial, final = 194.656 0.28552
Final line search alpha, max atom move = 1.95857e-06 5.5921e-07
Iterations, force evaluations = 148 327
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036542 | 0.036542 | 0.036542 | 0.0 | 79.06
Neigh | 0.0038009 | 0.0038009 | 0.0038009 | 0.0 | 8.22
Comm | 0.00038958 | 0.00038958 | 0.00038958 | 0.0 | 0.84
Output | 9.8705e-05 | 9.8705e-05 | 9.8705e-05 | 0.0 | 0.21
Modify | 0.0021958 | 0.0021958 | 0.0021958 | 0.0 | 4.75
Other | | 0.003194 | | | 6.91
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 122 ave 122 max 122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3612 ave 3612 max 3612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3612
Ave neighs/atom = 8.6
Neighbor list builds = 30
Dangerous builds = 0
Total wall time: 0:00:00
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