LAMMPS (12 Feb 2014) # 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 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 Memory usage per processor = 2.06238 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 0.97069909 -1.5851114 0 -0.61471562 0.90108296 Loop time of 0.548328 on 8 procs for 5000 steps with 3200 atoms Pair time (%) = 0.242437 (44.2139) Neigh time (%) = 0.0589295 (10.7471) Comm time (%) = 0.0797399 (14.5424) Outpt time (%) = 0.00014773 (0.0269419) Other time (%) = 0.167074 (30.4697) 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 # factor of 4 in 2 variables is for 2d compute msd all msd com yes variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6) fix 9 all vector 10 c_msd[4] variable fitslope equal slope(f_9)/4/(10*dt) thermo_style custom step temp c_msd[4] v_twopoint v_fitslope # 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 Memory usage per processor = 2.29126 Mbytes Step Temp msd[4] twopoint fitslope 0 0.97069909 5.6797985e-31 1.4199496e-25 5e+20 1000 0.98259938 4.018182 0.20090906 0.18018405 2000 0.98866167 9.1771673 0.22942916 0.20819132 3000 0.98066292 14.377973 0.23963287 0.2226381 4000 0.97384109 19.666022 0.24582526 0.23154108 5000 0.97843004 25.570023 0.25570022 0.23873417 6000 0.98703537 31.182236 0.25985196 0.2446473 7000 0.97169186 36.915546 0.26368246 0.24892937 8000 0.9823893 42.723242 0.26702026 0.25284158 9000 0.9998457 49.159596 0.27310886 0.25648405 10000 0.98782869 55.95808 0.27979039 0.26026001 11000 0.99481941 63.387246 0.28812384 0.26436008 12000 0.9760981 70.325901 0.29302458 0.26836823 13000 0.97774297 77.590396 0.2984246 0.2723266 14000 0.96752038 85.055703 0.30377036 0.27627449 15000 0.98697717 92.723433 0.3090781 0.28007928 16000 0.98385955 100.89787 0.31530583 0.28396785 17000 0.9839555 108.44716 0.31896223 0.28772551 18000 0.98000182 115.932 0.32203333 0.29120847 19000 0.96633821 123.99378 0.32629942 0.2945701 20000 0.98641362 131.63233 0.32908082 0.29781576 21000 0.9763779 140.20546 0.33382253 0.30091009 22000 0.97984221 149.3632 0.33946182 0.30410181 23000 0.98384014 157.80278 0.34304952 0.30727461 24000 0.97601102 165.78405 0.34538343 0.31026343 25000 0.99623187 173.8015 0.347603 0.31311142 26000 0.98943691 182.06075 0.35011683 0.31582297 27000 0.98992058 188.30114 0.34870582 0.31827868 28000 0.97957751 196.93202 0.35166432 0.32053702 29000 0.99513582 206.48445 0.35600767 0.32277974 30000 0.99754125 213.2124 0.355354 0.32491307 31000 0.98894929 221.74208 0.35764851 0.32691848 32000 0.973493 229.28872 0.35826363 0.3288054 33000 0.99989261 236.7565 0.35872197 0.33061911 34000 0.97192218 243.57374 0.35819667 0.33225106 35000 0.99711642 250.65118 0.35807311 0.33369124 36000 0.97718259 258.94971 0.35965237 0.33507325 37000 0.98194807 265.83921 0.35924218 0.33634589 38000 0.97195138 272.94984 0.35914453 0.33755459 39000 0.98219017 280.07692 0.35907297 0.33864166 40000 0.98039694 288.4453 0.36055663 0.33967254 41000 0.97621359 295.85108 0.360794 0.3406849 42000 0.97460413 303.13769 0.3608782 0.34161073 43000 0.9799912 312.06356 0.3628646 0.34254857 44000 0.96313376 320.55123 0.36426276 0.34347747 45000 0.97643796 329.68761 0.36631956 0.34443057 46000 0.98641729 338.40463 0.36783111 0.34540729 47000 0.97811939 345.46683 0.3675179 0.34634877 48000 0.99744864 352.87823 0.36758148 0.34720815 49000 0.97480356 362.60002 0.37000002 0.34807624 50000 0.97841509 368.44194 0.36844193 0.34892214 51000 0.97865859 375.44238 0.36808076 0.34966222 52000 0.97415415 382.95453 0.36822551 0.35036495 53000 0.97984491 390.33776 0.36824317 0.35103186 54000 0.99289379 396.4986 0.36712833 0.35162842 55000 0.98606668 403.49336 0.36681214 0.35217399 56000 0.98585489 411.98283 0.36784182 0.35270646 57000 0.98507959 418.14272 0.36679186 0.35321673 58000 0.98030805 423.23791 0.36486026 0.353654 59000 0.98315137 429.40554 0.36390299 0.35400654 60000 0.98762585 437.17376 0.36431146 0.35433653 61000 0.96937507 442.38698 0.36261228 0.3546452 62000 0.97194792 450.91689 0.36364265 0.3549106 63000 0.99877655 460.61733 0.36556931 0.3552122 64000 0.98525211 469.26926 0.36661661 0.35554833 65000 0.9833149 477.52571 0.36732747 0.35589823 66000 0.97191797 485.72618 0.36797438 0.35624251 67000 0.98479592 492.83716 0.36778892 0.35657544 68000 0.98418943 498.90452 0.36684156 0.35688872 69000 0.96953928 507.57013 0.36780444 0.35718476 70000 0.98373337 515.05745 0.36789818 0.35749562 71000 0.98260952 522.33093 0.36783868 0.35778626 72000 0.98906053 527.99215 0.36666121 0.35804724 73000 0.99569597 534.99359 0.36643396 0.35827372 74000 0.97627362 540.94769 0.3655052 0.35847643 75000 0.97276792 546.45533 0.36430355 0.35864641 76000 0.97659072 554.59353 0.36486417 0.35879714 77000 0.9807196 562.96571 0.36556215 0.35896542 78000 0.97398601 571.22804 0.36617182 0.35914269 79000 0.98124212 577.92968 0.36577828 0.35930881 80000 0.98506783 586.73568 0.3667098 0.35948276 81000 0.97926561 596.68206 0.36832226 0.35968089 82000 0.97906184 604.24971 0.36844495 0.35988893 83000 0.96540502 610.7078 0.36789626 0.3600856 84000 0.98726761 619.32703 0.36864704 0.36027536 85000 0.98133061 627.20955 0.36894679 0.3604747 86000 0.99142106 634.68836 0.36900486 0.36067069 87000 0.97917566 641.73186 0.36881141 0.36086497 88000 0.99391197 649.76607 0.36918527 0.36105571 89000 0.98521911 655.50224 0.36825969 0.36123298 90000 0.97419059 664.0397 0.36891095 0.36139717 91000 0.98687774 671.19045 0.36878596 0.36156016 92000 0.97816545 677.37724 0.36813981 0.36171235 93000 0.98734859 684.56734 0.36804696 0.3618463 94000 0.99116168 691.47221 0.36780437 0.36197063 95000 0.99982024 698.01624 0.36737697 0.36208597 96000 0.99232404 703.53179 0.3664228 0.36218818 97000 0.97829693 707.91832 0.36490635 0.36225634 98000 0.99878715 713.77777 0.36417233 0.36230715 99000 0.97026354 717.24468 0.36224478 0.3623226 100000 0.98911409 722.1539 0.36107695 0.36230617 Loop time of 9.28795 on 8 procs for 100000 steps with 3200 atoms Pair time (%) = 4.87621 (52.5003) Neigh time (%) = 1.26444 (13.6138) Comm time (%) = 1.60752 (17.3076) Outpt time (%) = 0.00843725 (0.0908408) Other time (%) = 1.53135 (16.4875) Nlocal: 400 ave 410 max 389 min Histogram: 1 1 1 0 1 1 0 0 1 2 Nghost: 205.375 ave 216 max 194 min Histogram: 1 0 0 2 2 0 1 0 0 2 Neighs: 2818 ave 3010 max 2683 min Histogram: 2 0 2 0 1 1 0 1 0 1 Total # of neighbors = 22544 Ave neighs/atom = 7.045 Neighbor list builds = 12748 Dangerous builds = 0