1LAMMPS (29 Mar 2019) 2 using 1 OpenMP thread(s) per MPI task 3# 2d micelle simulation 4 5dimension 2 6 7neighbor 0.3 bin 8neigh_modify delay 5 9 10atom_style bond 11 12# Soft potential push-off 13 14read_data data.micelle 15 orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) 16 2 by 2 by 1 MPI processor grid 17 reading atoms ... 18 1200 atoms 19 scanning bonds ... 20 1 = max bonds/atom 21 reading bonds ... 22 300 bonds 23 2 = max # of 1-2 neighbors 24 1 = max # of 1-3 neighbors 25 1 = max # of 1-4 neighbors 26 2 = max # of special neighbors 27 special bonds CPU = 0.000422001 secs 28 read_data CPU = 0.00473404 secs 29special_bonds fene 30 2 = max # of 1-2 neighbors 31 2 = max # of special neighbors 32 special bonds CPU = 0.000183344 secs 33 34pair_style soft 1.12246 35pair_coeff * * 0.0 1.12246 36 37bond_style harmonic 38bond_coeff 1 50.0 0.75 39 40velocity all create 0.45 2349852 41 42variable prefactor equal ramp(1.0,20.0) 43 44fix 1 all nve 45fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 46fix 3 all adapt 1 pair soft a * * v_prefactor 47fix 4 all enforce2d 48 49thermo 50 50run 500 51Neighbor list info ... 52 update every 1 steps, delay 5 steps, check yes 53 max neighbors/atom: 2000, page size: 100000 54 master list distance cutoff = 1.42246 55 ghost atom cutoff = 1.42246 56 binsize = 0.71123, bins = 51 51 1 57 1 neighbor lists, perpetual/occasional/extra = 1 0 0 58 (1) pair soft, perpetual 59 attributes: half, newton on 60 pair build: half/bin/newton 61 stencil: half/bin/2d/newton 62 bin: standard 63Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes 64Step Temp E_pair E_mol TotEng Press 65 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 66 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 67 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 68 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 69 200 0.45 1.01454 0.10663502 1.5708 4.7598476 70 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 71 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 72 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 73 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 74 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 75 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 76Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms 77 78Performance: 5066547.720 tau/day, 11728.120 timesteps/s 7998.7% CPU use with 4 MPI tasks x 1 OpenMP threads 80 81MPI task timing breakdown: 82Section | min time | avg time | max time |%varavg| %total 83--------------------------------------------------------------- 84Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 85Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 86Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 87Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 88Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 89Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 90Other | | 0.002669 | | | 6.26 91 92Nlocal: 300 ave 304 max 292 min 93Histogram: 1 0 0 0 0 0 0 0 2 1 94Nghost: 103.5 ave 108 max 98 min 95Histogram: 1 0 0 1 0 0 0 0 0 2 96Neighs: 773.5 ave 792 max 735 min 97Histogram: 1 0 0 0 0 0 0 0 2 1 98 99Total # of neighbors = 3094 100Ave neighs/atom = 2.57833 101Ave special neighs/atom = 0.5 102Neighbor list builds = 52 103Dangerous builds = 0 104 105unfix 3 106 107# Main run 108 109pair_style lj/cut 2.5 110 111# solvent/head - full-size and long-range 112 113pair_coeff 1 1 1.0 1.0 2.5 114pair_coeff 2 2 1.0 1.0 2.5 115pair_coeff 1 2 1.0 1.0 2.5 116 117# tail/tail - size-averaged and long-range 118 119pair_coeff 3 3 1.0 0.75 2.5 120pair_coeff 4 4 1.0 0.50 2.5 121pair_coeff 3 4 1.0 0.67 2.5 122 123# solvent/tail - full-size and repulsive 124 125pair_coeff 1 3 1.0 1.0 1.12246 126pair_coeff 1 4 1.0 1.0 1.12246 127 128# head/tail - size-averaged and repulsive 129 130pair_coeff 2 3 1.0 0.88 1.12246 131pair_coeff 2 4 1.0 0.75 1.12246 132 133thermo 50 134 135#dump 1 all atom 2000 dump.micelle 136 137#dump 2 all image 2000 image.*.jpg type type zoom 1.6 138#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 139 140#dump 3 all movie 2000 movie.mpg type type zoom 1.6 141#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 142 143reset_timestep 0 144group solvent molecule 0 145750 atoms in group solvent 146group solute subtract all solvent 147450 atoms in group solute 148unfix 1 149unfix 2 150unfix 4 151fix 1 solvent nve 152fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 153fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 154150 rigid bodies with 450 atoms 155fix 4 all enforce2d 156run 500 157Neighbor list info ... 158 update every 1 steps, delay 5 steps, check yes 159 max neighbors/atom: 2000, page size: 100000 160 master list distance cutoff = 2.8 161 ghost atom cutoff = 2.8 162 binsize = 1.4, bins = 26 26 1 163 1 neighbor lists, perpetual/occasional/extra = 1 0 0 164 (1) pair lj/cut, perpetual 165 attributes: half, newton on 166 pair build: half/bin/newton 167 stencil: half/bin/2d/newton 168 bin: standard 169Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes 170Step Temp E_pair E_mol TotEng Press 171 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 172 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 173 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 174 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 175 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 176 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 177 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 178 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 179 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 180 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 181 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 182Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms 183 184Performance: 2434100.210 tau/day, 5634.491 timesteps/s 18598.9% CPU use with 4 MPI tasks x 1 OpenMP threads 186 187MPI task timing breakdown: 188Section | min time | avg time | max time |%varavg| %total 189--------------------------------------------------------------- 190Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 191Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 192Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 193Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 194Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 195Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 196Other | | 0.002938 | | | 3.31 197 198Nlocal: 300 ave 309 max 291 min 199Histogram: 1 0 0 1 0 0 1 0 0 1 200Nghost: 218.75 ave 223 max 216 min 201Histogram: 1 0 2 0 0 0 0 0 0 1 202Neighs: 2192.25 ave 2251 max 2113 min 203Histogram: 1 0 0 1 0 0 0 0 0 2 204 205Total # of neighbors = 8769 206Ave neighs/atom = 7.3075 207Ave special neighs/atom = 0.5 208Neighbor list builds = 47 209Dangerous builds = 2 210unfix 2 211unfix 4 212unfix 5 213fix 5 solute rigid/small molecule 214 create bodies CPU = 7.70092e-05 secs 215150 rigid bodies with 450 atoms 216 1.30435 = max distance from body owner to body atom 217fix 4 all enforce2d 218run 500 219Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes 220Step Temp E_pair E_mol TotEng Press 221 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 222 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 223 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 224 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 225 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 226 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 227 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 228 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 229 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 230 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 231 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 232Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms 233 234Performance: 3671840.233 tau/day, 8499.630 timesteps/s 23598.3% CPU use with 4 MPI tasks x 1 OpenMP threads 236 237MPI task timing breakdown: 238Section | min time | avg time | max time |%varavg| %total 239--------------------------------------------------------------- 240Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 241Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 242Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 243Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 244Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 245Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 246Other | | 0.00224 | | | 3.81 247 248Nlocal: 300 ave 303 max 295 min 249Histogram: 1 0 0 0 0 0 1 0 1 1 250Nghost: 219 ave 224 max 215 min 251Histogram: 1 0 0 1 1 0 0 0 0 1 252Neighs: 2185.75 ave 2244 max 2143 min 253Histogram: 1 1 0 0 0 1 0 0 0 1 254 255Total # of neighbors = 8743 256Ave neighs/atom = 7.28583 257Ave special neighs/atom = 0.5 258Neighbor list builds = 40 259Dangerous builds = 0 260Total wall time: 0:00:00 261