LAMMPS (28 Feb 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # 2d micelle simulation dimension 2 neighbor 0.3 bin neigh_modify delay 5 atom_style bond # Soft potential push-off read_data data.micelle orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) 2 by 2 by 1 MPI processor grid reading atoms ... 1200 atoms scanning bonds ... 1 = max bonds/atom reading bonds ... 300 bonds 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.000175714 secs read_data CPU = 0.00145626 secs special_bonds fene 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 7.22408e-05 secs pair_style soft 1.12246 pair_coeff * * 0.0 1.12246 bond_style harmonic bond_coeff 1 50.0 0.75 velocity all create 0.45 2349852 variable prefactor equal ramp(1.0,20.0) fix 1 all nve fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 fix 3 all adapt 1 pair soft a * * v_prefactor fix 4 all enforce2d thermo 50 run 1000 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 binsize = 0.71123, bins = 51 51 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair soft, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 600 0.45 0.58193041 0.088386617 1.119942 5.131481 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 Loop time of 0.0389124 on 4 procs for 1000 steps with 1200 atoms Performance: 11101855.138 tau/day, 25698.739 timesteps/s 95.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73 Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08 Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59 Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12 Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71 Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34 Other | | 0.002501 | | | 6.43 Nlocal: 300 ave 305 max 292 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 100.25 ave 108 max 93 min Histogram: 1 0 1 0 0 0 1 0 0 1 Neighs: 784 ave 815 max 739 min Histogram: 1 0 0 0 0 0 1 1 0 1 Total # of neighbors = 3136 Ave neighs/atom = 2.61333 Ave special neighs/atom = 0.5 Neighbor list builds = 92 Dangerous builds = 0 unfix 3 # Main run pair_style lj/cut 2.5 # solvent/head - full-size and long-range pair_coeff 1 1 1.0 1.0 2.5 pair_coeff 2 2 1.0 1.0 2.5 pair_coeff 1 2 1.0 1.0 2.5 # tail/tail - size-averaged and long-range pair_coeff 3 3 1.0 0.75 2.5 pair_coeff 4 4 1.0 0.50 2.5 pair_coeff 3 4 1.0 0.67 2.5 # solvent/tail - full-size and repulsive pair_coeff 1 3 1.0 1.0 1.12246 pair_coeff 1 4 1.0 1.0 1.12246 # head/tail - size-averaged and repulsive pair_coeff 2 3 1.0 0.88 1.12246 pair_coeff 2 4 1.0 0.75 1.12246 thermo 1000 #dump 1 all atom 2000 dump.micelle #dump 2 all image 2000 image.*.jpg type type zoom 1.6 #dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 #dump 3 all movie 2000 movie.mpg type type zoom 1.6 #dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 reset_timestep 0 group solvent molecule 0 750 atoms in group solvent group solute subtract all solvent 450 atoms in group solute unfix 1 unfix 2 unfix 4 fix 1 solvent nve fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 150 rigid bodies with 450 atoms fix 4 all enforce2d run 20000 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 = 26 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736 1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869 2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671 3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553 4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215 5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897 6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512 7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309 8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852 9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071 10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464 11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699 12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823 13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171 14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645 15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206 16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281 17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975 18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943 19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952 Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms Performance: 5025468.853 tau/day, 11633.030 timesteps/s 98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77 Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27 Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16 Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92 Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03 Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76 Other | | 0.05327 | | | 3.10 Nlocal: 300 ave 303 max 298 min Histogram: 1 0 1 0 1 0 0 0 0 1 Nghost: 218.5 ave 226 max 215 min Histogram: 2 1 0 0 0 0 0 0 0 1 Neighs: 2258.75 ave 2283 max 2216 min Histogram: 1 0 0 0 0 0 1 0 1 1 Total # of neighbors = 9035 Ave neighs/atom = 7.52917 Ave special neighs/atom = 0.5 Neighbor list builds = 1580 Dangerous builds = 0 unfix 5 unfix 4 fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 create bodies CPU = 5.43594e-05 secs 150 rigid bodies with 450 atoms 0.916597 = max distance from body owner to body atom fix 4 all enforce2d run 20000 Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes Step Temp E_pair E_mol TotEng Press 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643 21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285 22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965 23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871 24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675 25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122 26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501 27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661 28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448 29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989 30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951 31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891 32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966 33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641 34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091 35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508 36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696 37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854 38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763 39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345 40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727 Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms Performance: 6885775.862 tau/day, 15939.296 timesteps/s 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30 Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72 Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51 Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27 Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04 Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52 Other | | 0.03321 | | | 2.65 Nlocal: 300 ave 304 max 293 min Histogram: 1 0 0 0 0 1 0 0 0 2 Nghost: 215.25 ave 217 max 213 min Histogram: 1 0 0 0 0 1 0 1 0 1 Neighs: 2340 ave 2378 max 2290 min Histogram: 1 0 0 1 0 0 0 0 0 2 Total # of neighbors = 9360 Ave neighs/atom = 7.8 Ave special neighs/atom = 0.5 Neighbor list builds = 1579 Dangerous builds = 0 Total wall time: 0:00:03