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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)
2 by 2 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 = 3.60136 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 0.00339699 on 4 procs for 35 steps with 420 atoms
95.7% CPU use with 4 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 | 0.0019855 | 0.002022 | 0.0020628 | 0.1 | 59.52
Neigh | 0.00012016 | 0.00012463 | 0.00012922 | 0.0 | 3.67
Comm | 0.00034857 | 0.00041682 | 0.00048089 | 0.3 | 12.27
Output | 3.7909e-05 | 4.0412e-05 | 4.6968e-05 | 0.1 | 1.19
Modify | 3.2663e-05 | 3.8743e-05 | 4.4823e-05 | 0.1 | 1.14
Other | | 0.0007544 | | | 22.21
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 84 ave 90 max 78 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 895 ave 999 max 798 min
Histogram: 2 0 0 0 0 0 0 0 0 2
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 = 3.60136 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 -0.17713919 433.03804
100 0 -3.1812307 0 -3.1805381 -0.15305002 434.96379
110 0 -3.1812588 0 -3.1805938 -0.12504601 432.50683
111 0 -3.1812728 0 -3.1805961 -0.12407115 432.50683
Loop time of 0.00934356 on 4 procs for 76 steps with 420 atoms
91.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.17436899358 -3.18059381928 -3.18059607058
Force two-norm initial, final = 1618.56 0.444005
Force max component initial, final = 1191.42 0.168709
Final line search alpha, max atom move = 0.428871 0.0723543
Iterations, force evaluations = 76 147
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0039222 | 0.0042289 | 0.0045605 | 0.5 | 45.26
Neigh | 0.00056624 | 0.00060999 | 0.00065136 | 0.2 | 6.53
Comm | 0.0011964 | 0.0017179 | 0.0022454 | 1.1 | 18.39
Output | 0.00011611 | 0.0001232 | 0.000139 | 0.1 | 1.32
Modify | 0.00025821 | 0.00028563 | 0.0003078 | 0.1 | 3.06
Other | | 0.002378 | | | 25.45
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 87 ave 90 max 84 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 899 ave 1001 max 797 min
Histogram: 1 1 0 0 0 0 0 0 1 1
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 = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
111 0 -3.1812728 0 -0.21796955 -0.12362156 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 1.3134388 432.20444
180 0 -3.1041304 0 -3.0969544 1.3751455 430.37021
190 0 -3.1043441 0 -3.0970791 1.3920926 430.37021
193 0 -3.1043346 0 -3.0970891 1.3934753 430.37021
Loop time of 0.0095458 on 4 procs for 82 steps with 420 atoms
94.3% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.217969552445 -3.09708660005 -3.09708907864
Force two-norm initial, final = 1754.38 0.649535
Force max component initial, final = 924.68 0.156756
Final line search alpha, max atom move = 0.962047 0.150807
Iterations, force evaluations = 82 156
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0040784 | 0.0045295 | 0.00495 | 0.6 | 47.45
Neigh | 0.00041556 | 0.00045681 | 0.0004952 | 0.2 | 4.79
Comm | 0.0011504 | 0.0016876 | 0.0022304 | 1.2 | 17.68
Output | 0.00012088 | 0.00012857 | 0.000144 | 0.1 | 1.35
Modify | 0.00027156 | 0.00029528 | 0.00032377 | 0.1 | 3.09
Other | | 0.002448 | | | 25.65
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 94 ave 97 max 91 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 916.5 ave 1013 max 831 min
Histogram: 1 1 0 0 0 0 0 1 0 1
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 = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
193 0 -3.1043346 0 2.0111873 1.3910032 431.13505
200 0 -2.5918062 0 -1.93191 5.511262 430.91953
210 0 -2.8122299 0 -2.7440894 4.2686747 440.18337
220 0 -2.910295 0 -2.8879715 3.5956981 444.98997
230 0 -2.949231 0 -2.9335905 3.2079519 451.9225
240 0 -2.9611012 0 -2.9486911 3.1241334 452.5907
250 0 -2.9644798 0 -2.9549529 3.0499305 455.51712
260 0 -2.9716705 0 -2.9621358 2.8593553 458.27346
270 0 -3.0143454 0 -3.0048234 2.1158458 462.52748
280 0 -3.0656896 0 -3.0590412 1.4428324 470.69566
290 0 -3.1008608 0 -3.0951203 1.1487473 472.80734
300 0 -3.1109522 0 -3.1046995 1.064904 470.50807
310 0 -3.1123989 0 -3.105985 1.0430839 470.40952
313 0 -3.1125022 0 -3.1060453 1.0390872 470.40952
Loop time of 0.0165539 on 4 procs for 120 steps with 420 atoms
92.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
2.01118731028 -3.10604533837 -3.10604533837
Force two-norm initial, final = 2329.79 2.39232
Force max component initial, final = 1038.4 0.571422
Final line search alpha, max atom move = 7.76258e-07 4.43571e-07
Iterations, force evaluations = 120 264
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0066144 | 0.0077118 | 0.0089424 | 1.2 | 46.59
Neigh | 0.0008266 | 0.00094324 | 0.0010567 | 0.3 | 5.70
Comm | 0.0018625 | 0.0032995 | 0.0045738 | 2.2 | 19.93
Output | 0.00018287 | 0.00019288 | 0.00021982 | 0.1 | 1.17
Modify | 0.00045705 | 0.00051093 | 0.00056267 | 0.2 | 3.09
Other | | 0.003896 | | | 23.53
Nlocal: 105 ave 123 max 90 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 91 ave 100 max 85 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 892.25 ave 1107 max 699 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 28
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 = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
313 0 -3.1125022 0 5.3341053 1.0377311 471.02427
320 0 -2.402824 0 -0.86170235 6.1550233 471.02943
330 0 -2.5964265 0 -2.4563494 5.5893601 473.87197
340 0 -2.857458 0 -2.8325789 3.9156904 478.37268
350 0 -2.923244 0 -2.9056267 3.3461026 481.81668
360 0 -2.9355414 0 -2.924236 3.2437289 484.05209
370 0 -2.9486011 0 -2.9405396 2.9295065 487.64545
380 0 -2.9695687 0 -2.9616077 2.5116249 491.53648
390 0 -2.991356 0 -2.9786736 2.2788393 491.056
400 0 -3.0098108 0 -2.9963408 2.0798685 490.87751
410 0 -3.0142937 0 -3.0017605 2.0015139 491.52711
417 0 -3.0148998 0 -3.0024932 1.9909706 492.48053
Loop time of 0.0134063 on 4 procs for 104 steps with 420 atoms
95.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
5.33410533222 -3.00249023582 -3.00249317367
Force two-norm initial, final = 3147.64 2.97401
Force max component initial, final = 1384.36 0.679769
Final line search alpha, max atom move = 0.14124 0.0960107
Iterations, force evaluations = 104 200
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0046661 | 0.0059155 | 0.0071743 | 1.5 | 44.13
Neigh | 0.00073218 | 0.00090402 | 0.0010717 | 0.5 | 6.74
Comm | 0.001442 | 0.0029395 | 0.0044417 | 2.5 | 21.93
Output | 0.00014901 | 0.00015819 | 0.00018287 | 0.1 | 1.18
Modify | 0.0003469 | 0.00039375 | 0.0004406 | 0.2 | 2.94
Other | | 0.003095 | | | 23.09
Nlocal: 105 ave 121 max 89 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 93.5 ave 101 max 86 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 936 ave 1121 max 741 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3744
Ave neighs/atom = 8.91429
Neighbor list builds = 27
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 = 3.60141 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
417 0 -3.0148998 0 -2.4816986 1.9918498 492.26314
420 0 -2.9209943 0 -2.7871779 2.8201475 492.26417
430 0 -2.9210322 0 -2.8866221 3.0115293 492.22119
440 0 -2.930174 0 -2.9072946 3.0289241 491.74253
450 0 -2.9423694 0 -2.9251127 3.0269322 491.55578
460 0 -2.9595882 0 -2.9424058 2.8769376 491.29122
470 0 -2.9716874 0 -2.9531385 2.7820875 491.71167
480 0 -2.9967793 0 -2.9798492 2.5135722 493.20335
490 0 -3.0077594 0 -2.9927399 2.3652753 495.90598
500 0 -3.0156527 0 -3.0064227 2.2002124 502.94121
510 0 -3.0389075 0 -3.0316863 1.8518803 512.1298
520 0 -3.0533374 0 -3.0444153 1.6968184 511.35747
530 0 -3.0643133 0 -3.0573978 1.5165159 516.34223
540 0 -3.0958216 0 -3.0905446 1.0627598 519.02979
550 0 -3.1051578 0 -3.1009512 1.0050567 517.17039
560 0 -3.1119271 0 -3.1069923 0.92711525 515.78315
570 0 -3.114104 0 -3.1090684 0.9237051 515.34157
580 0 -3.114576 0 -3.1094219 0.9181339 515.34157
590 0 -3.114722 0 -3.1095528 0.90665975 515.99746
600 0 -3.1149189 0 -3.1096744 0.88783587 515.99746
605 0 -3.1149612 0 -3.1097106 0.88187936 515.99746
Loop time of 0.0259686 on 4 procs for 188 steps with 420 atoms
100.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.48169863396 -3.10971061979 -3.10971061979
Force two-norm initial, final = 470.636 1.194
Force max component initial, final = 222.162 0.376608
Final line search alpha, max atom move = 2.92234e-06 1.10058e-06
Iterations, force evaluations = 188 401
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0087585 | 0.011606 | 0.014545 | 2.6 | 44.69
Neigh | 0.00098324 | 0.0012714 | 0.0015543 | 0.8 | 4.90
Comm | 0.0028691 | 0.006242 | 0.0094991 | 4.1 | 24.04
Output | 0.00028014 | 0.00029546 | 0.00033355 | 0.1 | 1.14
Modify | 0.00066638 | 0.00077331 | 0.00089598 | 0.4 | 2.98
Other | | 0.005781 | | | 22.26
Nlocal: 105 ave 125 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 94.25 ave 104 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 895.75 ave 1159 max 648 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3583
Ave neighs/atom = 8.53095
Neighbor list builds = 38
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 = 3.60141 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
605 0 -3.1149612 0 -2.7562264 0.88153856 516.19694
610 0 -3.0480145 0 -3.0046036 1.5377628 516.18952
620 0 -3.0581364 0 -3.0393996 1.5790644 516.23694
630 0 -3.058957 0 -3.0461523 1.6279637 515.82575
640 0 -3.0608654 0 -3.0476936 1.631809 515.82575
650 0 -3.059954 0 -3.0488507 1.7016953 514.58992
660 0 -3.0601043 0 -3.0495387 1.7749452 513.2301
670 0 -3.0600329 0 -3.0503272 1.8525614 512.87295
680 0 -3.0618342 0 -3.0532875 1.9461671 512.7735
690 0 -3.0681709 0 -3.0588644 1.8339583 513.83989
700 0 -3.0723671 0 -3.0624663 1.7080165 515.99424
710 0 -3.0738836 0 -3.0635305 1.6674853 516.40455
720 0 -3.0744809 0 -3.0640016 1.6430059 516.40455
729 0 -3.074692 0 -3.0641622 1.6351234 517.12194
Loop time of 0.0175288 on 4 procs for 124 steps with 420 atoms
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.75622643697 -3.06416218566 -3.06416218566
Force two-norm initial, final = 387.971 1.75423
Force max component initial, final = 226.888 0.425447
Final line search alpha, max atom move = 9.47831e-07 4.03252e-07
Iterations, force evaluations = 124 275
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0053589 | 0.0078858 | 0.010479 | 2.7 | 44.99
Neigh | 0.00037146 | 0.00052333 | 0.00067759 | 0.6 | 2.99
Comm | 0.0017581 | 0.0046017 | 0.0073204 | 3.9 | 26.25
Output | 0.00017619 | 0.00018531 | 0.00021076 | 0.1 | 1.06
Modify | 0.00044012 | 0.00054049 | 0.00064754 | 0.4 | 3.08
Other | | 0.003792 | | | 21.63
Nlocal: 105 ave 131 max 78 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 97.25 ave 110 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 900.25 ave 1197 max 607 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3601
Ave neighs/atom = 8.57381
Neighbor list builds = 16
Dangerous builds = 0
Total wall time: 0:00:00
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