LAMMPS (29 Sep 2021) # test script for fix mol/swap # initial system is 50/50 chains of type 1 and type 2 # b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the # system will stay in equilibrium as a mix of both chain types # fix mol/swap helps this happen quickly # see the last 2 columns of thermo output for counts of 2 chain types units lj atom_style angle neighbor 0.36 bin neigh_modify delay 0 pair_style lj/cut 1.1224620483 bond_style fene angle_style cosine special_bonds lj 0.0 1.0 1.0 read_data data.bead Reading data file ... orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700) 1 by 2 by 2 MPI processor grid reading atoms ... 4000 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 3900 bonds reading angles ... 3800 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.028 seconds pair_coeff * * 1.0 1.0 1.1224620483 pair_coeff 1 2 1.02 1.0 1.1224620483 bond_coeff 1 30.0 1.5 1.0 1.0 angle_coeff 1 1.500 pair_modify shift yes variable vt1 atom type==1 variable vt2 atom type==2 group g1 dynamic all var vt1 every 100 dynamic group g1 defined group g2 dynamic all var vt2 every 100 dynamic group g2 defined variable count1 equal count(g1) variable count2 equal count(g2) timestep 0.010 fix 1 all langevin 1.0 1.0 100.0 702547 fix 2 all nve fix 3 all mol/swap 100 1 1 2 482794 1.0 compute p all pressure thermo_temp thermo 1000 thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2 run 50000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.482462 ghost atom cutoff = 1.482462 binsize = 0.74123102, bins = 23 23 23 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/3d bin: standard WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728) Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2 0 0 21.451627 5.079399 0 0 2000 2000 1000 0.49011138 21.59359 4.2337989 10 10 2000 2000 2000 0.55288866 21.724374 4.4596786 20 20 2080 1920 3000 0.59299724 21.844178 4.6112243 30 29 2280 1720 4000 0.64746348 21.964318 4.9463669 40 39 2280 1720 5000 0.67853936 22.053147 5.1950218 50 48 2320 1680 6000 0.70751144 22.147453 5.0636869 60 58 2240 1760 7000 0.73570064 22.233705 5.4872622 70 68 2160 1840 8000 0.7677554 22.312938 5.4283736 80 77 2360 1640 9000 0.78493237 22.383155 5.8547233 90 87 2440 1560 10000 0.80634514 22.449402 5.8785731 100 96 2400 1600 11000 0.82563194 22.475286 5.8193738 110 104 2400 1600 12000 0.81684024 22.527492 6.0323967 120 114 2320 1680 13000 0.84497155 22.567888 6.0488755 130 122 2240 1760 14000 0.85452242 22.606908 6.1983634 140 132 2080 1920 15000 0.88109242 22.654336 6.1408279 150 141 1960 2040 16000 0.88925915 22.707597 6.1560975 160 150 2000 2000 17000 0.91598439 22.762791 6.1071728 170 160 2000 2000 18000 0.92453211 22.778304 6.3330693 180 170 2240 1760 19000 0.92839551 22.797316 6.2917909 190 180 2000 2000 20000 0.93054033 22.819289 6.091701 200 189 2200 1800 21000 0.93955351 22.844135 6.5833013 210 198 2000 2000 22000 0.94454858 22.856272 6.5661753 220 207 2200 1800 23000 0.95446407 22.878735 6.5957294 230 216 2160 1840 24000 0.94748257 22.894539 6.6187447 240 226 1920 2080 25000 0.95732202 22.912292 6.4795471 250 236 1680 2320 26000 0.96970172 22.908988 6.537366 260 245 1720 2280 27000 0.96032166 22.924899 6.6238248 270 255 1960 2040 28000 0.96197769 22.9358 6.8926097 280 264 1920 2080 29000 0.98745595 22.964694 6.5839025 290 271 2040 1960 30000 0.99264869 22.947884 6.3893499 300 280 1920 2080 31000 0.96953069 22.957927 6.6616047 310 289 1800 2200 32000 0.99955117 22.963979 6.5958456 320 298 1680 2320 33000 0.97090103 22.969029 6.9087296 330 307 1800 2200 34000 0.99818457 22.988477 6.6471994 340 316 1920 2080 35000 0.9965288 22.992883 6.9691785 350 325 2040 1960 36000 0.99533174 22.983774 6.6585089 360 334 2000 2000 37000 0.98819278 22.995387 6.618802 370 344 2080 1920 38000 0.99598576 22.991892 6.7536669 380 354 2080 1920 39000 0.99312702 22.989239 6.4028165 390 364 2080 1920 40000 1.0035821 23.001944 6.9307671 400 374 1920 2080 41000 0.99914733 23.00134 6.6251677 410 383 1880 2120 42000 0.98054536 22.981781 6.5918554 420 393 1880 2120 43000 0.99413829 23.008 6.7390795 430 403 1720 2280 44000 0.98867961 23.00521 6.8505543 440 412 1600 2400 45000 0.99626811 23.019995 6.827741 450 421 1640 2360 46000 1.0186043 23.020759 6.6195562 460 430 1680 2320 47000 1.0121335 23.019271 6.6022102 470 439 1800 2200 48000 0.99883756 23.013973 6.5255522 480 448 1920 2080 49000 0.99425223 23.022708 6.609746 490 458 2240 1760 50000 0.99505489 23.012641 6.4592863 500 468 2240 1760 Loop time of 19.4175 on 4 procs for 50000 steps with 4000 atoms Performance: 2224796.830 tau/day, 2574.996 timesteps/s 95.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5467 | 2.6684 | 2.7896 | 6.3 | 13.74 Bond | 2.3037 | 2.4117 | 2.5085 | 5.3 | 12.42 Neigh | 7.3597 | 7.3633 | 7.3673 | 0.1 | 37.92 Comm | 3.0482 | 3.2694 | 3.4997 | 10.2 | 16.84 Output | 0.0014609 | 0.0017069 | 0.0021793 | 0.7 | 0.01 Modify | 2.9624 | 3.0581 | 3.1424 | 4.7 | 15.75 Other | | 0.6447 | | | 3.32 Nlocal: 1000.00 ave 1013 max 986 min Histogram: 1 0 0 1 0 0 0 1 0 1 Nghost: 1186.25 ave 1198 max 1178 min Histogram: 2 0 0 0 0 0 1 0 0 1 Neighs: 4927.00 ave 5028 max 4790 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 19708 Ave neighs/atom = 4.9270000 Ave special neighs/atom = 5.7000000 Neighbor list builds = 10721 Dangerous builds = 0 Total wall time: 0:00:19