LAMMPS (29 Mar 2019) 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 = 0.000422001 secs read_data CPU = 0.00473404 secs special_bonds fene 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 0.000183344 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 500 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 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 200 0.45 1.01454 0.10663502 1.5708 4.7598476 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms Performance: 5066547.720 tau/day, 11728.120 timesteps/s 98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 Other | | 0.002669 | | | 6.26 Nlocal: 300 ave 304 max 292 min Histogram: 1 0 0 0 0 0 0 0 2 1 Nghost: 103.5 ave 108 max 98 min Histogram: 1 0 0 1 0 0 0 0 0 2 Neighs: 773.5 ave 792 max 735 min Histogram: 1 0 0 0 0 0 0 0 2 1 Total # of neighbors = 3094 Ave neighs/atom = 2.57833 Ave special neighs/atom = 0.5 Neighbor list builds = 52 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 50 #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 500 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 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms Performance: 2434100.210 tau/day, 5634.491 timesteps/s 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 Other | | 0.002938 | | | 3.31 Nlocal: 300 ave 309 max 291 min Histogram: 1 0 0 1 0 0 1 0 0 1 Nghost: 218.75 ave 223 max 216 min Histogram: 1 0 2 0 0 0 0 0 0 1 Neighs: 2192.25 ave 2251 max 2113 min Histogram: 1 0 0 1 0 0 0 0 0 2 Total # of neighbors = 8769 Ave neighs/atom = 7.3075 Ave special neighs/atom = 0.5 Neighbor list builds = 47 Dangerous builds = 2 unfix 2 unfix 4 unfix 5 fix 5 solute rigid/small molecule create bodies CPU = 7.70092e-05 secs 150 rigid bodies with 450 atoms 1.30435 = max distance from body owner to body atom fix 4 all enforce2d run 500 Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes Step Temp E_pair E_mol TotEng Press 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms Performance: 3671840.233 tau/day, 8499.630 timesteps/s 98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 Other | | 0.00224 | | | 3.81 Nlocal: 300 ave 303 max 295 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 219 ave 224 max 215 min Histogram: 1 0 0 1 1 0 0 0 0 1 Neighs: 2185.75 ave 2244 max 2143 min Histogram: 1 1 0 0 0 1 0 0 0 1 Total # of neighbors = 8743 Ave neighs/atom = 7.28583 Ave special neighs/atom = 0.5 Neighbor list builds = 40 Dangerous builds = 0 Total wall time: 0:00:00