LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified) # 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) 1 by 1 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 = 0.005 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) = 4.148 | 4.148 | 4.148 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 0.0365221 on 1 procs for 500 steps with 1200 atoms Performance: 5914221.123 tau/day, 13690.327 timesteps/s, 16.428 Matom-step/s 89.2% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022939 | 0.022939 | 0.022939 | 0.0 | 62.81 Bond | 0.00073851 | 0.00073851 | 0.00073851 | 0.0 | 2.02 Neigh | 0.0078339 | 0.0078339 | 0.0078339 | 0.0 | 21.45 Comm | 0.00072134 | 0.00072134 | 0.00072134 | 0.0 | 1.98 Output | 7.1419e-05 | 7.1419e-05 | 7.1419e-05 | 0.0 | 0.20 Modify | 0.0034868 | 0.0034868 | 0.0034868 | 0.0 | 9.55 Other | | 0.0007314 | | | 2.00 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 = 2.5783333 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) = 5.391 | 5.391 | 5.391 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 0.0650638 on 1 procs for 500 steps with 1200 atoms Performance: 3319817.322 tau/day, 7684.762 timesteps/s, 9.222 Matom-step/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.027565 | 0.027565 | 0.027565 | 0.0 | 42.37 Bond | 0.0007043 | 0.0007043 | 0.0007043 | 0.0 | 1.08 Neigh | 0.012724 | 0.012724 | 0.012724 | 0.0 | 19.56 Comm | 0.00091442 | 0.00091442 | 0.00091442 | 0.0 | 1.41 Output | 6.004e-05 | 6.004e-05 | 6.004e-05 | 0.0 | 0.09 Modify | 0.022329 | 0.022329 | 0.022329 | 0.0 | 34.32 Other | | 0.0007666 | | | 1.18 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 411 ave 411 max 411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8759 ave 8759 max 8759 min Histogram: 1 0 0 0 0 0 0 0 0 0 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) = 9.306 | 9.306 | 9.306 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 2.1630988 Loop time of 0.0592806 on 1 procs for 500 steps with 1200 atoms Performance: 3643690.276 tau/day, 8434.468 timesteps/s, 10.121 Matom-step/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026866 | 0.026866 | 0.026866 | 0.0 | 45.32 Bond | 0.00071863 | 0.00071863 | 0.00071863 | 0.0 | 1.21 Neigh | 0.010927 | 0.010927 | 0.010927 | 0.0 | 18.43 Comm | 0.00084187 | 0.00084187 | 0.00084187 | 0.0 | 1.42 Output | 6.8106e-05 | 6.8106e-05 | 6.8106e-05 | 0.0 | 0.11 Modify | 0.019075 | 0.019075 | 0.019075 | 0.0 | 32.18 Other | | 0.000783 | | | 1.32 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 417 ave 417 max 417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8654 ave 8654 max 8654 min Histogram: 1 0 0 0 0 0 0 0 0 0 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