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) 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 = 0.000473022 secs read_data CPU = 0.0024147 secs special_bonds fene 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 0.00022316 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) = 3.799 | 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 0.54981866 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 0.103162 on 1 procs for 500 steps with 1200 atoms Performance: 2093802.885 tau/day, 4846.766 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 Other | | 0.002726 | | | 2.64 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 197 ave 197 max 197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3094 ave 3094 max 3094 min Histogram: 1 0 0 0 0 0 0 0 0 0 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) = 5.274 | 5.274 | 5.274 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 0.178806 on 1 procs for 500 steps with 1200 atoms Performance: 1208012.705 tau/day, 2796.326 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 Other | | 0.00293 | | | 1.64 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 416 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8769 ave 8769 max 8769 min Histogram: 1 0 0 0 0 0 0 0 0 0 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 = 0.00015378 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) = 8.64 | 8.64 | 8.64 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 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms Performance: 1297278.008 tau/day, 3002.958 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 Other | | 0.003141 | | | 1.89 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 415 ave 415 max 415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8743 ave 8743 max 8743 min Histogram: 1 0 0 0 0 0 0 0 0 0 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