forked from lijiext/lammps
224 lines
9.5 KiB
Plaintext
224 lines
9.5 KiB
Plaintext
LAMMPS (12 Feb 2014)
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# sample LAMMPS input script for diffusion of 2d LJ liquid
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# mean-squared displacement via compute msd
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# settings
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variable x equal 40
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variable y equal 40
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variable rho equal 0.6
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variable t equal 1.0
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variable rc equal 2.5
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# problem setup
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units lj
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dimension 2
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atom_style atomic
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neigh_modify delay 0 every 1
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lattice sq2 ${rho}
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lattice sq2 0.6
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region simbox block 0 $x 0 $y -0.1 0.1
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region simbox block 0 40 0 $y -0.1 0.1
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region simbox block 0 40 0 40 -0.1 0.1
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create_box 1 simbox
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Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
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4 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 3200 atoms
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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mass * 1.0
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velocity all create $t 97287
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velocity all create 1 97287
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fix 1 all nve
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fix 2 all langevin $t $t 0.1 498094
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fix 2 all langevin 1 $t 0.1 498094
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fix 2 all langevin 1 1 0.1 498094
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fix 3 all enforce2d
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# equilibration run
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thermo 1000
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run 5000
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Memory usage per processor = 2.06238 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -1.56492 0 -0.5652325 -1.5346995
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1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
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2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
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3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
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4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
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5000 0.97069909 -1.5851114 0 -0.61471562 0.90108296
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Loop time of 0.548328 on 8 procs for 5000 steps with 3200 atoms
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Pair time (%) = 0.242437 (44.2139)
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Neigh time (%) = 0.0589295 (10.7471)
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Comm time (%) = 0.0797399 (14.5424)
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Outpt time (%) = 0.00014773 (0.0269419)
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Other time (%) = 0.167074 (30.4697)
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Nlocal: 400 ave 406 max 394 min
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Histogram: 1 1 0 1 0 2 1 0 1 1
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Nghost: 202.5 ave 212 max 191 min
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Histogram: 1 0 0 0 3 1 0 2 0 1
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Neighs: 2800.88 ave 2903 max 2690 min
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Histogram: 1 1 0 0 1 2 1 0 1 1
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Total # of neighbors = 22407
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Ave neighs/atom = 7.00219
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Neighbor list builds = 599
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Dangerous builds = 0
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unfix 2
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# data gathering run
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reset_timestep 0
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# factor of 4 in 2 variables is for 2d
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compute msd all msd com yes
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variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
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fix 9 all vector 10 c_msd[4]
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variable fitslope equal slope(f_9)/4/(10*dt)
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thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
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# only need to run for 10K steps to make a good 100-frame movie
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#dump 1 all custom 1 tmp.dump id type vx vy vz
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#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
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thermo 1000
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run 100000
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Memory usage per processor = 2.29126 Mbytes
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Step Temp msd[4] twopoint fitslope
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0 0.97069909 5.6797985e-31 1.4199496e-25 5e+20
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1000 0.98259938 4.018182 0.20090906 0.18018405
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2000 0.98866167 9.1771673 0.22942916 0.20819132
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3000 0.98066292 14.377973 0.23963287 0.2226381
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4000 0.97384109 19.666022 0.24582526 0.23154108
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5000 0.97843004 25.570023 0.25570022 0.23873417
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6000 0.98703537 31.182236 0.25985196 0.2446473
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7000 0.97169186 36.915546 0.26368246 0.24892937
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8000 0.9823893 42.723242 0.26702026 0.25284158
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9000 0.9998457 49.159596 0.27310886 0.25648405
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10000 0.98782869 55.95808 0.27979039 0.26026001
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11000 0.99481941 63.387246 0.28812384 0.26436008
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12000 0.9760981 70.325901 0.29302458 0.26836823
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13000 0.97774297 77.590396 0.2984246 0.2723266
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14000 0.96752038 85.055703 0.30377036 0.27627449
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15000 0.98697717 92.723433 0.3090781 0.28007928
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16000 0.98385955 100.89787 0.31530583 0.28396785
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17000 0.9839555 108.44716 0.31896223 0.28772551
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18000 0.98000182 115.932 0.32203333 0.29120847
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19000 0.96633821 123.99378 0.32629942 0.2945701
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20000 0.98641362 131.63233 0.32908082 0.29781576
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21000 0.9763779 140.20546 0.33382253 0.30091009
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22000 0.97984221 149.3632 0.33946182 0.30410181
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23000 0.98384014 157.80278 0.34304952 0.30727461
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24000 0.97601102 165.78405 0.34538343 0.31026343
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25000 0.99623187 173.8015 0.347603 0.31311142
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26000 0.98943691 182.06075 0.35011683 0.31582297
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27000 0.98992058 188.30114 0.34870582 0.31827868
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28000 0.97957751 196.93202 0.35166432 0.32053702
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29000 0.99513582 206.48445 0.35600767 0.32277974
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30000 0.99754125 213.2124 0.355354 0.32491307
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31000 0.98894929 221.74208 0.35764851 0.32691848
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32000 0.973493 229.28872 0.35826363 0.3288054
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33000 0.99989261 236.7565 0.35872197 0.33061911
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34000 0.97192218 243.57374 0.35819667 0.33225106
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35000 0.99711642 250.65118 0.35807311 0.33369124
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36000 0.97718259 258.94971 0.35965237 0.33507325
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37000 0.98194807 265.83921 0.35924218 0.33634589
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38000 0.97195138 272.94984 0.35914453 0.33755459
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39000 0.98219017 280.07692 0.35907297 0.33864166
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40000 0.98039694 288.4453 0.36055663 0.33967254
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41000 0.97621359 295.85108 0.360794 0.3406849
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42000 0.97460413 303.13769 0.3608782 0.34161073
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43000 0.9799912 312.06356 0.3628646 0.34254857
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44000 0.96313376 320.55123 0.36426276 0.34347747
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45000 0.97643796 329.68761 0.36631956 0.34443057
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46000 0.98641729 338.40463 0.36783111 0.34540729
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47000 0.97811939 345.46683 0.3675179 0.34634877
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48000 0.99744864 352.87823 0.36758148 0.34720815
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49000 0.97480356 362.60002 0.37000002 0.34807624
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50000 0.97841509 368.44194 0.36844193 0.34892214
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51000 0.97865859 375.44238 0.36808076 0.34966222
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52000 0.97415415 382.95453 0.36822551 0.35036495
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53000 0.97984491 390.33776 0.36824317 0.35103186
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54000 0.99289379 396.4986 0.36712833 0.35162842
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55000 0.98606668 403.49336 0.36681214 0.35217399
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56000 0.98585489 411.98283 0.36784182 0.35270646
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57000 0.98507959 418.14272 0.36679186 0.35321673
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58000 0.98030805 423.23791 0.36486026 0.353654
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59000 0.98315137 429.40554 0.36390299 0.35400654
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60000 0.98762585 437.17376 0.36431146 0.35433653
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61000 0.96937507 442.38698 0.36261228 0.3546452
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62000 0.97194792 450.91689 0.36364265 0.3549106
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63000 0.99877655 460.61733 0.36556931 0.3552122
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64000 0.98525211 469.26926 0.36661661 0.35554833
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65000 0.9833149 477.52571 0.36732747 0.35589823
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66000 0.97191797 485.72618 0.36797438 0.35624251
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67000 0.98479592 492.83716 0.36778892 0.35657544
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68000 0.98418943 498.90452 0.36684156 0.35688872
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69000 0.96953928 507.57013 0.36780444 0.35718476
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70000 0.98373337 515.05745 0.36789818 0.35749562
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71000 0.98260952 522.33093 0.36783868 0.35778626
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72000 0.98906053 527.99215 0.36666121 0.35804724
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73000 0.99569597 534.99359 0.36643396 0.35827372
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74000 0.97627362 540.94769 0.3655052 0.35847643
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75000 0.97276792 546.45533 0.36430355 0.35864641
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76000 0.97659072 554.59353 0.36486417 0.35879714
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77000 0.9807196 562.96571 0.36556215 0.35896542
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78000 0.97398601 571.22804 0.36617182 0.35914269
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79000 0.98124212 577.92968 0.36577828 0.35930881
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80000 0.98506783 586.73568 0.3667098 0.35948276
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81000 0.97926561 596.68206 0.36832226 0.35968089
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82000 0.97906184 604.24971 0.36844495 0.35988893
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83000 0.96540502 610.7078 0.36789626 0.3600856
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84000 0.98726761 619.32703 0.36864704 0.36027536
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85000 0.98133061 627.20955 0.36894679 0.3604747
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86000 0.99142106 634.68836 0.36900486 0.36067069
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87000 0.97917566 641.73186 0.36881141 0.36086497
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88000 0.99391197 649.76607 0.36918527 0.36105571
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89000 0.98521911 655.50224 0.36825969 0.36123298
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90000 0.97419059 664.0397 0.36891095 0.36139717
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91000 0.98687774 671.19045 0.36878596 0.36156016
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92000 0.97816545 677.37724 0.36813981 0.36171235
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93000 0.98734859 684.56734 0.36804696 0.3618463
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94000 0.99116168 691.47221 0.36780437 0.36197063
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95000 0.99982024 698.01624 0.36737697 0.36208597
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96000 0.99232404 703.53179 0.3664228 0.36218818
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97000 0.97829693 707.91832 0.36490635 0.36225634
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98000 0.99878715 713.77777 0.36417233 0.36230715
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99000 0.97026354 717.24468 0.36224478 0.3623226
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100000 0.98911409 722.1539 0.36107695 0.36230617
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Loop time of 9.28795 on 8 procs for 100000 steps with 3200 atoms
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Pair time (%) = 4.87621 (52.5003)
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Neigh time (%) = 1.26444 (13.6138)
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Comm time (%) = 1.60752 (17.3076)
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Outpt time (%) = 0.00843725 (0.0908408)
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Other time (%) = 1.53135 (16.4875)
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Nlocal: 400 ave 410 max 389 min
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Histogram: 1 1 1 0 1 1 0 0 1 2
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Nghost: 205.375 ave 216 max 194 min
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Histogram: 1 0 0 2 2 0 1 0 0 2
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Neighs: 2818 ave 3010 max 2683 min
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Histogram: 2 0 2 0 1 1 0 1 0 1
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Total # of neighbors = 22544
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Ave neighs/atom = 7.045
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Neighbor list builds = 12748
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Dangerous builds = 0
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