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) 1 by 1 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 = 0.000271559 secs read_data CPU = 0.00115585 secs special_bonds fene 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 8.39233e-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) = 3.799 | 3.799 | 3.799 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 0.107201 on 1 procs for 1000 steps with 1200 atoms Performance: 4029800.456 tau/day, 9328.242 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20 Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72 Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00 Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71 Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15 Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95 Other | | 0.002429 | | | 2.27 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 195 ave 195 max 195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3136 ave 3136 max 3136 min Histogram: 1 0 0 0 0 0 0 0 0 0 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) = 5.274 | 5.274 | 5.274 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736 1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457 2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896 3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634 4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178 5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284 6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653 7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099 8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769 9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447 10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582 11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418 12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497 13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173 14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767 15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999 16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066 17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295 18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102 19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746 Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms Performance: 2347175.802 tau/day, 5433.277 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13 Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16 Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33 Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33 Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01 Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58 Other | | 0.05369 | | | 1.46 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 395 ave 395 max 395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8915 ave 8915 max 8915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8915 Ave neighs/atom = 7.42917 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 = 0.00012517 secs 150 rigid bodies with 450 atoms 1.04536 = max distance from body owner to body atom fix 4 all enforce2d run 20000 Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes Step Temp E_pair E_mol TotEng Press 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893 21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317 22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077 23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349 24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923 25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811 26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018 27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673 28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888 29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141 30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915 31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009 32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148 33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113 34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843 35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697 36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963 37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678 38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487 39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123 40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536 Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms Performance: 2341388.948 tau/day, 5419.882 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.756 | 1.756 | 1.756 | 0.0 | 47.59 Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15 Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30 Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31 Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01 Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19 Other | | 0.05386 | | | 1.46 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 393 ave 393 max 393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9091 ave 9091 max 9091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9091 Ave neighs/atom = 7.57583 Ave special neighs/atom = 0.5 Neighbor list builds = 1582 Dangerous builds = 0 Total wall time: 0:00:07