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 1.1 (stronger than 1/1 or 2/2) the # system will go to equilibrium as mostly one type or the other # 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 = 0.034 seconds pair_coeff * * 1.0 1.0 1.1224620483 pair_coeff 1 2 1.1 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 21.4699 5.230121 0 0 2000 2000 1000 0.50228459 21.61044 4.3659303 10 9 1960 2040 2000 0.55721903 21.75955 4.5695439 20 17 1960 2040 3000 0.61139287 21.892943 4.6514755 30 26 2240 1760 4000 0.65767189 22.002303 5.1854503 40 33 2280 1720 5000 0.69383416 22.110271 5.3803498 50 41 2280 1720 6000 0.72692038 22.205887 5.1756569 60 49 2280 1720 7000 0.77151336 22.306777 5.5743555 70 56 2240 1760 8000 0.78606858 22.37036 5.7745208 80 64 2560 1440 9000 0.79363653 22.420931 5.7369418 90 71 2680 1320 10000 0.82352629 22.488759 6.0238896 100 76 2720 1280 11000 0.83867685 22.534887 6.1263771 110 82 2800 1200 12000 0.85335127 22.590281 6.1499954 120 86 2800 1200 13000 0.86430985 22.632068 6.1654016 130 89 2760 1240 14000 0.88057592 22.680253 6.2162735 140 94 2800 1200 15000 0.89326694 22.719731 6.4789839 150 97 2760 1240 16000 0.90667644 22.737367 6.214481 160 101 2760 1240 17000 0.91190336 22.758572 6.2293336 170 105 2600 1400 18000 0.93182455 22.782019 6.2865382 180 111 2680 1320 19000 0.93002139 22.797048 6.5579988 190 117 2600 1400 20000 0.92396243 22.796108 6.6207461 200 122 2800 1200 21000 0.92949808 22.802813 6.3753268 210 125 2920 1080 22000 0.93415719 22.807112 6.4696121 220 130 3040 960 23000 0.9214833 22.82116 6.4146288 230 131 3080 920 24000 0.95693685 22.839738 6.4035728 240 135 2920 1080 25000 0.95421851 22.865199 6.4510751 250 138 2880 1120 26000 0.95476555 22.878082 6.4652888 260 145 3000 1000 27000 0.95773535 22.880671 6.757952 270 149 3000 1000 28000 0.95405332 22.896053 6.7425175 280 155 3080 920 29000 0.95955713 22.904144 6.6672832 290 161 3240 760 30000 0.95521498 22.886699 6.6197941 300 164 3360 640 31000 0.96431176 22.91094 6.6373887 310 168 3440 560 32000 0.96592495 22.903679 6.4245884 320 172 3520 480 33000 0.96457971 22.922681 6.6987987 330 175 3480 520 34000 0.96541889 22.92116 6.5992755 340 178 3600 400 35000 0.96892691 22.923361 6.7973298 350 178 3600 400 36000 0.97267726 22.923431 6.6577403 360 179 3640 360 37000 0.97514714 22.939979 6.4028068 370 183 3640 360 38000 0.98638599 22.952022 6.6518868 380 183 3640 360 39000 0.97864891 22.962534 6.3906837 390 184 3680 320 40000 0.9933016 22.975785 6.6819613 400 185 3720 280 41000 0.9861477 22.977271 6.6747347 410 187 3800 200 42000 0.98157369 22.963129 6.830028 420 187 3800 200 43000 0.98202452 22.966947 6.5257905 430 187 3800 200 44000 0.99540503 22.971262 6.5546513 440 187 3800 200 45000 0.98433653 22.978028 6.4316725 450 189 3800 200 46000 0.97912775 22.981328 6.9139851 460 189 3800 200 47000 0.9791927 22.981131 6.6417971 470 190 3840 160 48000 0.99601024 22.998536 6.6756953 480 191 3880 120 49000 0.99589958 22.998489 6.9262843 490 191 3880 120 50000 0.99294715 23.00399 6.6976013 500 192 3920 80 Loop time of 19.5161 on 4 procs for 50000 steps with 4000 atoms Performance: 2213556.537 tau/day, 2561.987 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 | 2.6256 | 2.7183 | 2.8265 | 5.2 | 13.93 Bond | 2.3363 | 2.4406 | 2.5197 | 4.8 | 12.51 Neigh | 7.382 | 7.3884 | 7.3936 | 0.2 | 37.86 Comm | 3.014 | 3.2136 | 3.3994 | 9.4 | 16.47 Output | 0.0014574 | 0.0017086 | 0.0020613 | 0.5 | 0.01 Modify | 3.0282 | 3.1295 | 3.2034 | 4.1 | 16.04 Other | | 0.624 | | | 3.20 Nlocal: 1000.00 ave 1011 max 993 min Histogram: 2 0 0 0 0 1 0 0 0 1 Nghost: 1187.25 ave 1202 max 1179 min Histogram: 2 0 0 1 0 0 0 0 0 1 Neighs: 4939.25 ave 5067 max 4850 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 19757 Ave neighs/atom = 4.9392500 Ave special neighs/atom = 5.7000000 Neighbor list builds = 10714 Dangerous builds = 0 Total wall time: 0:00:19