LAMMPS (2 Aug 2018) # sample LAMMPS input script for diffusion of 2d LJ liquid # mean-squared displacement via compute msd # settings variable x equal 40 variable y equal 40 variable rho equal 0.6 variable t equal 1.0 variable rc equal 2.5 # problem setup units lj dimension 2 atom_style atomic neigh_modify delay 0 every 1 lattice sq2 ${rho} lattice sq2 0.6 Lattice spacing in x,y,z = 1.82574 1.82574 1.82574 region simbox block 0 $x 0 $y -0.1 0.1 region simbox block 0 40 0 $y -0.1 0.1 region simbox block 0 40 0 40 -0.1 0.1 create_box 1 simbox Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) 4 by 2 by 1 MPI processor grid create_atoms 1 box Created 3200 atoms Time spent = 0.000712872 secs pair_style lj/cut ${rc} pair_style lj/cut 2.5 pair_coeff * * 1 1 mass * 1.0 velocity all create $t 97287 velocity all create 1 97287 fix 1 all nve fix 2 all langevin $t $t 0.1 498094 fix 2 all langevin 1 $t 0.1 498094 fix 2 all langevin 1 1 0.1 498094 fix 3 all enforce2d # equilibration run thermo 1000 run 5000 Neighbor list info ... update every 1 steps, delay 0 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 = 53 53 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 -1.56492 0 -0.5652325 -1.5346995 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms Performance: 3332829.949 tau/day, 7714.884 timesteps/s 99.9% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96 Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01 Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66 Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02 Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02 Other | | 0.05398 | | | 8.33 Nlocal: 400 ave 406 max 394 min Histogram: 1 1 0 1 0 2 1 0 1 1 Nghost: 202.5 ave 212 max 191 min Histogram: 1 0 0 0 3 1 0 2 0 1 Neighs: 2800.88 ave 2903 max 2690 min Histogram: 1 1 0 0 1 2 1 0 1 1 Total # of neighbors = 22407 Ave neighs/atom = 7.00219 Neighbor list builds = 599 Dangerous builds = 0 unfix 2 # data gathering run reset_timestep 0 compute vacf all vacf fix 4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf # factor of 0.5 is for 2d fix 5 all vector 1 c_vacf[4] variable vacf equal 0.5*dt*trap(f_5) thermo_style custom step temp c_vacf[4] v_vacf # only need to run for 10K steps to make a good 100-frame movie #dump 1 all custom 1 tmp.dump id type vx vy vz #dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2 thermo 1000 run 100000 Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes Step Temp c_vacf[4] v_vacf 0 0.97069905 1.9407914 0 1000 0.98138076 0.029239763 0.22157396 2000 0.97606079 -0.0015179052 0.23974121 3000 0.97924866 -0.013873067 0.21877575 4000 0.98568451 0.026969065 0.24052934 5000 0.97551815 0.050232557 0.24508207 6000 0.98482252 -0.0018424259 0.25686293 7000 0.9672559 0.018499957 0.27279836 8000 0.9836541 -0.022683127 0.27022734 9000 0.99087147 0.0071767632 0.25267902 10000 0.99663166 -0.011971734 0.2645822 11000 0.97776688 0.01601675 0.27801788 12000 0.98246011 0.0085456779 0.29207728 13000 0.98788732 0.0054252587 0.29148533 14000 0.96872483 0.0087976064 0.29645689 15000 0.98955796 -0.060068996 0.28904116 16000 0.99855196 -0.0066979853 0.24964957 17000 0.98600861 0.021334454 0.23410452 18000 0.98696963 -0.01971883 0.23190572 19000 0.9881192 -0.022828159 0.20882183 20000 0.98527319 -0.0085783561 0.20610922 21000 0.99015191 -0.0061019744 0.20199693 22000 0.97972418 -0.04380952 0.22099864 23000 0.98911012 -0.0031381071 0.19304223 24000 0.98810498 0.023131507 0.18483784 25000 0.96961962 -0.020892151 0.17128259 26000 0.99118408 0.02918818 0.15353531 27000 0.98515159 -0.026417648 0.1457756 28000 0.98951677 0.010372147 0.13321212 29000 0.9832026 0.00058150905 0.13262151 30000 0.98449493 0.0012256712 0.13576655 31000 0.96585993 0.0053021384 0.10734708 32000 0.98758117 -0.011513109 0.11473375 33000 0.98875584 -0.0089140499 0.13003947 34000 0.98007229 0.023423116 0.145185 35000 0.98415295 -0.0078343607 0.16513809 36000 0.98101154 0.025471963 0.1296799 37000 0.97606878 -0.016931612 0.11515595 38000 0.97220293 -0.015288346 0.12046935 39000 0.979783 0.039556949 0.10596988 40000 0.98375673 0.0098704124 0.15651085 41000 0.97506523 -0.029457701 0.14822207 42000 0.97106749 -0.024867475 0.12266294 43000 0.97717259 0.010866403 0.14228602 44000 0.98541435 -0.031545234 0.13017093 45000 0.97678287 -0.011024372 0.11824999 46000 0.98169719 0.011925437 0.1390346 47000 0.99471466 0.0048178625 0.13076123 48000 0.98332437 0.045576305 0.12667585 49000 0.98126947 -0.044123768 0.13582991 50000 0.98809751 0.014296599 0.12323107 51000 0.95919516 -0.0091171161 0.1494511 52000 0.98097913 0.010081012 0.12805794 53000 0.97774072 0.043349117 0.14524942 54000 0.99096915 0.021179196 0.1355801 55000 0.97652739 -0.015118967 0.14955035 56000 0.99185306 0.0018045061 0.16706629 57000 0.96289342 0.0095090659 0.19215008 58000 0.97871716 -0.028989119 0.20370326 59000 0.98637393 0.0067841088 0.21820001 60000 0.98009845 0.011559251 0.24504916 61000 0.99416712 0.0099372548 0.24882366 62000 0.97612483 0.014677063 0.25146482 63000 0.97786531 -0.0047938112 0.26052305 64000 0.99080668 -0.01632121 0.24744267 65000 0.97952497 0.0070583633 0.22323997 66000 0.98095955 0.036296232 0.2151706 67000 0.98370788 -0.0040313363 0.22236193 68000 0.96931818 0.0231486 0.20397659 69000 0.98512552 -0.017450997 0.21854935 70000 0.98065743 0.046916694 0.2080453 71000 0.98971283 0.010974871 0.21628306 72000 0.99890324 -0.023780184 0.23385876 73000 0.98649924 0.012862733 0.23458964 74000 0.98723422 -0.0096252165 0.23873216 75000 1.0025633 -0.070387674 0.2275029 76000 0.97859959 0.0058897922 0.22954358 77000 0.97973006 -0.0082868083 0.25189797 78000 0.9903944 -0.042368536 0.26564349 79000 0.96847518 -0.050630573 0.25344248 80000 0.99171112 0.012126001 0.23257751 81000 0.97202573 -0.029816198 0.27354387 82000 0.99368438 0.030082951 0.27859495 83000 0.97932483 -0.0081664387 0.27409123 84000 0.99078651 0.056610231 0.27593659 85000 0.98973457 0.020424285 0.31002605 86000 0.9835873 -0.0016980943 0.30158255 87000 0.97180564 -0.0051924508 0.27401969 88000 0.99743353 -0.030700753 0.24105471 89000 0.98993437 0.0087866525 0.23913724 90000 0.9926071 -0.014023378 0.24202489 91000 0.98800458 0.033613695 0.2238248 92000 0.98501879 -0.0406599 0.21809043 93000 0.98810082 0.027637634 0.21550897 94000 0.97563748 0.0014112208 0.18954766 95000 0.97283448 0.0093796591 0.17838358 96000 0.9883071 0.033049994 0.18594703 97000 0.97717678 0.01070451 0.19203994 98000 0.97190208 0.015065013 0.20906937 99000 0.98687379 -0.036869401 0.22993959 100000 0.97559757 0.045464091 0.23369283 Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms Performance: 5289636.190 tau/day, 12244.528 timesteps/s 100.0% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83 Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15 Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95 Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21 Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42 Other | | 0.363 | | | 4.45 Nlocal: 400 ave 413 max 391 min Histogram: 2 1 0 2 0 0 1 1 0 1 Nghost: 204.75 ave 213 max 197 min Histogram: 1 1 0 1 0 3 0 1 0 1 Neighs: 2800.62 ave 2959 max 2661 min Histogram: 1 1 1 2 0 0 0 1 1 1 Total # of neighbors = 22405 Ave neighs/atom = 7.00156 Neighbor list builds = 12728 Dangerous builds = 0 Total wall time: 0:00:08