LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified) WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) # 2d micelle simulation dimension 2 neighbor 0.3 bin neigh_modify delay 5 atom_style bond # Soft potential push-off read_data data.micelle Reading data file ... orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) 2 by 2 by 1 MPI processor grid reading atoms ... 1200 atoms scanning bonds ... 1 = max bonds/atom reading bonds ... 300 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 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 = 0.000 seconds read_data CPU = 0.004 seconds special_bonds fene Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 1 1 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds 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 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) 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 bin: standard WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 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 0.0138659 on 4 procs for 500 steps with 1200 atoms Performance: 15577811.312 tau/day, 36059.748 timesteps/s, 43.272 Matom-step/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0053896 | 0.0057144 | 0.0060899 | 0.4 | 41.21 Bond | 0.00020074 | 0.00021422 | 0.00022291 | 0.0 | 1.54 Neigh | 0.0025301 | 0.0025401 | 0.0025501 | 0.0 | 18.32 Comm | 0.0031194 | 0.0035074 | 0.0038196 | 0.4 | 25.30 Output | 6.4137e-05 | 6.7743e-05 | 7.7909e-05 | 0.0 | 0.49 Modify | 0.0013391 | 0.0013582 | 0.0013972 | 0.1 | 9.80 Other | | 0.0004638 | | | 3.34 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 = 2.5783333 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 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 Loop time of 0.0381773 on 4 procs for 500 steps with 1200 atoms Performance: 5657810.772 tau/day, 13096.784 timesteps/s, 15.716 Matom-step/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0059651 | 0.0062314 | 0.0066404 | 0.3 | 16.32 Bond | 0.00021057 | 0.00022477 | 0.0002333 | 0.0 | 0.59 Neigh | 0.0041424 | 0.0041487 | 0.0041512 | 0.0 | 10.87 Comm | 0.004264 | 0.0047244 | 0.0050297 | 0.4 | 12.37 Output | 8.2396e-05 | 8.6559e-05 | 9.6749e-05 | 0.0 | 0.23 Modify | 0.021833 | 0.021946 | 0.022094 | 0.1 | 57.48 Other | | 0.0008157 | | | 2.14 Nlocal: 300 ave 303 max 296 min Histogram: 1 0 0 0 1 0 0 0 1 1 Nghost: 216.25 ave 219 max 214 min Histogram: 1 0 1 0 0 0 1 0 0 1 Neighs: 2189.75 ave 2205 max 2173 min Histogram: 1 0 0 0 1 0 1 0 0 1 Total # of neighbors = 8759 Ave neighs/atom = 7.2991667 Ave special neighs/atom = 0.5 Neighbor list builds = 46 Dangerous builds = 2 unfix 2 unfix 4 unfix 5 fix 5 solute rigid/small molecule create bodies CPU = 0.000 seconds 150 rigid bodies with 450 atoms 1.3043524 = max distance from body owner to body atom fix 4 all enforce2d run 500 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes Step Temp E_pair E_mol TotEng Press 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 Loop time of 0.0236819 on 4 procs for 500 steps with 1200 atoms Performance: 9120883.727 tau/day, 21113.157 timesteps/s, 25.336 Matom-step/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0058656 | 0.0059718 | 0.0061355 | 0.1 | 25.22 Bond | 0.0002083 | 0.00022447 | 0.00023485 | 0.0 | 0.95 Neigh | 0.0035477 | 0.0035644 | 0.0035824 | 0.0 | 15.05 Comm | 0.0041037 | 0.0042227 | 0.0043024 | 0.1 | 17.83 Output | 7.4355e-05 | 7.8273e-05 | 8.7777e-05 | 0.0 | 0.33 Modify | 0.008976 | 0.0090549 | 0.0091663 | 0.1 | 38.24 Other | | 0.0005654 | | | 2.39 Nlocal: 300 ave 306 max 295 min Histogram: 1 0 1 0 0 1 0 0 0 1 Nghost: 221 ave 226 max 217 min Histogram: 1 0 0 1 1 0 0 0 0 1 Neighs: 2163.5 ave 2271 max 2100 min Histogram: 1 1 0 1 0 0 0 0 0 1 Total # of neighbors = 8654 Ave neighs/atom = 7.2116667 Ave special neighs/atom = 0.5 Neighbor list builds = 39 Dangerous builds = 0 Total wall time: 0:00:00