LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 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) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms Time spent = 0.000351191 secs 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 (src/thermo.cpp:488) #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 ... 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 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333 1000 0.11974254 -3.0876892 0 -2.9853378 -0.037059247 440.78771 2000 0.12086797 -3.0886512 0 -2.9853378 -0.39883289 444.3556 3000 0.11671309 -3.0840074 0 -2.9842455 -0.34859991 442.95428 4000 0.12339115 -3.1000529 0 -2.9945828 -0.049696765 438.99297 5000 0.10860594 -3.0866045 0 -2.9937722 -0.47973882 443.99855 6000 0.11839788 -3.0929689 0 -2.9917669 -0.033454196 442.70339 7000 0.12194527 -3.0835584 0 -2.9793242 -0.13981611 443.36261 8000 0.11671309 -3.0862884 0 -2.9865265 0.073952568 441.71327 9000 0.12449823 -3.0880806 0 -2.9816643 0.28647997 439.28167 10000 0.12475263 -3.0830722 0 -2.9764384 0.38101457 440.50309 11000 0.11198118 -3.0743549 0 -2.9786377 0.67583952 438.50252 12000 0.10823034 -3.0621355 0 -2.9696244 0.66485023 441.13781 13000 0.1194298 -3.0579575 0 -2.9558734 1.0884087 437.72805 14000 0.12310404 -3.051382 0 -2.9461573 0.87077685 445.54012 15000 0.11148458 -3.0402208 0 -2.944928 1.0040641 451.9079 16000 0.12322323 -3.041552 0 -2.9362254 0.7581871 456.90367 17000 0.12311085 -3.0300334 0 -2.9248029 1.0483261 452.91646 18000 0.12062509 -3.0261636 0 -2.9230579 1.3983564 451.71896 19000 0.11957854 -3.0142948 0 -2.9120836 1.3961883 457.92501 20000 0.12230825 -3.0015681 0 -2.8970237 1.1238267 470.13177 21000 0.1206722 -3.0280371 0 -2.9248911 0.77173089 472.88673 22000 0.11522969 -3.0159631 0 -2.9174691 0.58945089 474.56136 23000 0.1169292 -3.0257398 0 -2.9257932 0.90016236 473.58055 24000 0.11814748 -3.0288882 0 -2.9279002 0.85469502 469.82134 25000 0.11141357 -3.0218783 0 -2.9266463 1.0469177 471.01085 26000 0.11159246 -3.0122701 0 -2.9168851 1.1216321 471.99194 27000 0.10918089 -3.0045635 0 -2.9112398 1.2920286 474.41152 28000 0.1183178 -3.0017823 0 -2.9006488 1.3477212 474.08453 29000 0.118332 -2.9855957 0 -2.88445 1.4002777 478.49231 30000 0.11691453 -2.9721091 0 -2.872175 1.6266108 479.0394 Loop time of 2.58797 on 1 procs for 30000 steps with 420 atoms Performance: 3004676.853 tau/day, 11592.117 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 | 1.7803 | 1.7803 | 1.7803 | 0.0 | 68.79 Neigh | 0.074505 | 0.074505 | 0.074505 | 0.0 | 2.88 Comm | 0.038266 | 0.038266 | 0.038266 | 0.0 | 1.48 Output | 0.00033927 | 0.00033927 | 0.00033927 | 0.0 | 0.01 Modify | 0.61562 | 0.61562 | 0.61562 | 0.0 | 23.79 Other | | 0.07897 | | | 3.05 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 111 ave 111 max 111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3711 ave 3711 max 3711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3711 Ave neighs/atom = 8.83571 Neighbor list builds = 614 Dangerous builds = 0 # run without indenter unfix 4 run 30000 Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30000 0.11691453 -2.9721091 0 -2.872175 1.6267079 479.0108 31000 0.10925212 -3.0270482 0 -2.9336637 -0.33277278 488.93429 32000 0.11439597 -2.9975157 0 -2.8997344 -0.41937391 489.30458 33000 0.1202415 -3.0272086 0 -2.9244307 0.45435486 481.29876 34000 0.12236916 -3.0291826 0 -2.9245861 0.060773047 480.57112 35000 0.10701052 -3.0155083 0 -2.9240398 -0.32828426 491.34913 36000 0.11671309 -3.0501978 0 -2.9504359 0.17774604 480.03548 37000 0.11311041 -3.0472325 0 -2.9505501 -0.096250401 480.52043 38000 0.11671309 -3.0386964 0 -2.9389345 -0.26914235 481.1656 39000 0.127378 -3.0478959 0 -2.9390181 -0.11503417 478.38488 40000 0.11422635 -3.0479185 0 -2.9502821 -0.11840551 479.29223 41000 0.11339443 -3.0470107 0 -2.9500855 -0.36658233 484.33262 42000 0.11750945 -3.0506884 0 -2.9502458 -0.18687218 482.18706 43000 0.10968886 -3.0433967 0 -2.9496388 -0.23827778 483.87888 44000 0.11163929 -3.0449886 0 -2.9495636 -0.2241347 482.09898 45000 0.11726053 -3.0498339 0 -2.9496041 -0.03707734 480.27988 46000 0.10971187 -3.0434544 0 -2.9496769 -0.311219 482.26813 47000 0.11448154 -3.0476146 0 -2.9497602 -0.10374643 480.75372 48000 0.11796515 -3.0503583 0 -2.9495262 -0.18534074 479.03433 49000 0.11331324 -3.0464609 0 -2.9496051 -0.38382421 483.23363 50000 0.1102072 -3.043921 0 -2.94972 -0.11678189 481.28121 51000 0.11169997 -3.0449271 0 -2.9494503 -0.22869529 483.39421 52000 0.1052379 -3.0396306 0 -2.9496773 -0.264831 479.77275 53000 0.12170796 -3.0536766 0 -2.9496453 -0.14056206 482.58519 54000 0.11347849 -3.0465613 0 -2.9495642 -0.23137478 481.27 55000 0.115223 -3.0480538 0 -2.9495655 -0.32336031 485.15401 56000 0.11115417 -3.044689 0 -2.9496787 -0.066353134 481.37281 57000 0.10783414 -3.0418895 0 -2.949717 -0.20380917 482.14483 58000 0.10703451 -3.04105 0 -2.949561 -0.2673909 482.03847 59000 0.11041464 -3.0439806 0 -2.9496023 -0.17616699 481.33957 60000 0.12014097 -3.05226 0 -2.949568 -0.21176633 481.15213 Loop time of 2.20628 on 1 procs for 30000 steps with 420 atoms Performance: 3524485.426 tau/day, 13597.552 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7599 | 1.7599 | 1.7599 | 0.0 | 79.77 Neigh | 0.074152 | 0.074152 | 0.074152 | 0.0 | 3.36 Comm | 0.037216 | 0.037216 | 0.037216 | 0.0 | 1.69 Output | 0.00033259 | 0.00033259 | 0.00033259 | 0.0 | 0.02 Modify | 0.25688 | 0.25688 | 0.25688 | 0.0 | 11.64 Other | | 0.07779 | | | 3.53 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 106 ave 106 max 106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3578 ave 3578 max 3578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3578 Ave neighs/atom = 8.51905 Neighbor list builds = 617 Dangerous builds = 0 Total wall time: 0:00:04