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 = 0.000706911 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 0.667446 on 8 procs for 5000 steps with 3200 atoms Performance: 3236214.756 tau/day, 7491.238 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 | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27 Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68 Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06 Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02 Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43 Other | | 0.05701 | | | 8.54 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 Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes Step Temp c_msd[4] v_twopoint v_fitslope 0 0.97069905 0 0 5e+20 1000 0.98138076 4.0484996 0.20242494 0.20685564 2000 0.97606079 9.2121392 0.23030346 0.23687918 3000 0.97924866 14.815034 0.24691721 0.25405247 4000 0.98568451 20.516817 0.25646019 0.26353644 5000 0.97551815 27.33922 0.27339219 0.27544492 6000 0.98482252 34.37734 0.28647782 0.28966619 7000 0.9672559 41.696689 0.29783348 0.30165524 8000 0.9836541 48.340277 0.30212673 0.31085371 9000 0.99087147 56.042692 0.31134828 0.31811489 10000 0.99663166 63.69663 0.31848314 0.32589374 11000 0.97776688 71.144109 0.32338231 0.33219745 12000 0.98246011 78.301774 0.32625739 0.33723 13000 0.98788732 85.061923 0.32716124 0.34053027 14000 0.96872483 91.1658 0.32559214 0.34231162 15000 0.98955796 97.278388 0.32426129 0.34229511 16000 0.99855196 104.23997 0.3257499 0.34217252 17000 0.98600861 110.66055 0.3254722 0.34172446 18000 0.98696963 116.90111 0.32472531 0.3408227 19000 0.9881192 124.21305 0.32687644 0.34036538 20000 0.98527319 131.09874 0.32774685 0.34003478 21000 0.99015191 137.89263 0.32831579 0.33987868 22000 0.97972418 146.68982 0.33338595 0.34060035 23000 0.98911012 155.1264 0.33723129 0.34201036 24000 0.98810498 162.88634 0.33934653 0.34371488 25000 0.96961962 170.37907 0.34075814 0.34531409 26000 0.99118408 179.26511 0.34474059 0.34717195 27000 0.98515159 185.90764 0.3442734 0.34898035 28000 0.98951677 192.12183 0.34307469 0.35021808 29000 0.9832026 196.99457 0.33964581 0.35075459 30000 0.98449493 203.48475 0.33914124 0.35066186 31000 0.96585993 210.06193 0.33880956 0.35046715 32000 0.98758117 218.94174 0.34209646 0.35046623 33000 0.98875584 225.96489 0.34237104 0.35073944 34000 0.98007229 233.5792 0.34349882 0.35109188 35000 0.98415295 241.98148 0.34568783 0.35157879 36000 0.98101154 250.30876 0.34765106 0.3523013 37000 0.97606878 258.2127 0.34893608 0.35318097 38000 0.97220293 266.40464 0.35053242 0.3540743 39000 0.979783 272.8578 0.34981769 0.35496561 40000 0.98375673 279.87598 0.34984497 0.35558182 41000 0.97506523 288.07676 0.35131312 0.35618259 42000 0.97106749 296.11647 0.3525196 0.35698571 43000 0.97717259 304.46747 0.35403194 0.3577736 44000 0.98541435 312.57228 0.35519578 0.35865003 45000 0.97678287 321.82674 0.35758527 0.35958623 46000 0.98169719 329.78197 0.35845866 0.36062236 47000 0.99471466 337.11283 0.35863066 0.36158322 48000 0.98332437 346.0754 0.3604952 0.36255042 49000 0.98126947 356.11859 0.36338631 0.3636628 50000 0.98809751 365.65248 0.36565248 0.36496809 51000 0.95919516 373.91833 0.36658659 0.36628073 52000 0.98097913 381.26492 0.36660089 0.36752237 53000 0.97774072 388.81031 0.36680218 0.36863962 54000 0.99096915 395.56767 0.36626636 0.36961521 55000 0.97652739 401.72735 0.36520668 0.37038579 56000 0.99185306 407.28834 0.3636503 0.37094092 57000 0.96289342 414.75298 0.3638184 0.37130039 58000 0.97871716 424.69443 0.36611588 0.37180428 59000 0.98637393 433.14205 0.36706953 0.37239862 60000 0.98009845 438.14533 0.36512111 0.37288487 61000 0.99416712 446.08007 0.3656394 0.37321496 62000 0.97612483 450.90846 0.36363585 0.37345792 63000 0.97786531 455.36749 0.36140277 0.37344803 64000 0.99080668 458.04873 0.35785057 0.37313914 65000 0.97952497 461.31241 0.3548557 0.3725875 66000 0.98095955 463.91727 0.35145248 0.37174735 67000 0.98370788 468.93 0.34994776 0.37076942 68000 0.96931818 471.07765 0.34638063 0.36961868 69000 0.98512552 474.59146 0.34390685 0.36830908 70000 0.98065743 478.66071 0.3419005 0.36686789 71000 0.98971283 482.57357 0.33984054 0.36535224 72000 0.99890324 485.32018 0.3370279 0.36373174 73000 0.98649924 490.19497 0.33574998 0.36200692 74000 0.98723422 496.04991 0.33516886 0.36034919 75000 1.0025633 501.6313 0.33442087 0.35872052 76000 0.97859959 505.97813 0.33288035 0.35714939 77000 0.97973006 510.55334 0.33152814 0.35553808 78000 0.9903944 515.06966 0.33017286 0.35391584 79000 0.96847518 518.76483 0.32833217 0.35226287 80000 0.99171112 524.18127 0.32761329 0.35065267 81000 0.97202573 529.09959 0.32660468 0.34904364 82000 0.99368438 535.80271 0.32670897 0.34747913 83000 0.97932483 543.08233 0.32715803 0.34605097 84000 0.99078651 547.57861 0.32593965 0.34469765 85000 0.98973457 552.24581 0.32485048 0.34332115 86000 0.9835873 557.3493 0.32404029 0.34197018 87000 0.97180564 564.93434 0.32467491 0.34069702 88000 0.99743353 571.39837 0.32465817 0.33951258 89000 0.98993437 577.81703 0.32461631 0.33838511 90000 0.9926071 583.39378 0.32410765 0.33730429 91000 0.98800458 591.08741 0.3247733 0.33630505 92000 0.98501879 596.10133 0.32396811 0.33534725 93000 0.98810082 604.02652 0.32474544 0.33445545 94000 0.97563748 609.43676 0.32416849 0.33361404 95000 0.97283448 615.15754 0.32376713 0.33278044 96000 0.9883071 622.30912 0.32411933 0.33199212 97000 0.97717678 628.84457 0.32414669 0.33125729 98000 0.97190208 634.37377 0.32366009 0.33054877 99000 0.98687379 640.66666 0.32356902 0.32986014 100000 0.97559757 646.96406 0.32348203 0.32920186 Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms Performance: 5670494.518 tau/day, 13126.145 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 | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19 Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11 Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34 Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06 Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60 Other | | 0.4348 | | | 5.71 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