forked from lijiext/lammps
225 lines
8.2 KiB
Plaintext
225 lines
8.2 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 0.556362 on 8 procs for 5000 steps with 3200 atoms
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Pair time (%) = 0.242478 (43.5828)
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Neigh time (%) = 0.0590148 (10.6073)
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Comm time (%) = 0.0862918 (15.51)
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Outpt time (%) = 0.000148952 (0.0267725)
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Other time (%) = 0.168428 (30.2731)
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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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compute vacf all vacf
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fix 4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
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# factor of 0.5 is for 2d
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fix 5 all vector 1 c_vacf[4]
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variable vacf equal 0.5*dt*trap(f_5)
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thermo_style custom step temp c_vacf[4] v_vacf
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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 vacf[4] vacf
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0 0.97069909 1.9407915 0
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1000 0.98259938 0.068345562 0.21424576
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2000 0.98866167 0.028205164 0.24370013
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3000 0.98066292 0.008852823 0.27439588
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4000 0.97384109 0.011903564 0.3159275
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5000 0.97843004 0.019295534 0.33596598
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6000 0.98703537 0.01070801 0.34517088
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7000 0.97169186 -0.0082938435 0.33784119
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8000 0.9823893 0.038402174 0.32756669
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9000 0.9998457 0.045317593 0.33379383
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10000 0.98782869 0.027148675 0.34751149
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11000 0.99481941 0.035783937 0.36009047
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12000 0.9760981 -0.0010825507 0.36059769
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13000 0.97774297 0.048323885 0.36103752
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14000 0.96752038 0.0008189784 0.34988029
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15000 0.98697717 -0.0339338 0.35841003
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16000 0.98385955 0.03729417 0.36378228
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17000 0.9839555 -0.0063931744 0.37486488
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18000 0.98000182 0.065439765 0.39975619
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19000 0.96633821 0.0034363237 0.39585239
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20000 0.98641362 -0.020284 0.39696422
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21000 0.9763779 0.013683539 0.36183593
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22000 0.97984221 -0.0077108606 0.32642476
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23000 0.98384014 -0.030550764 0.32775468
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24000 0.97601102 -0.0047287909 0.3294707
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25000 0.99623187 0.00653461 0.34586445
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26000 0.98943691 -0.05047279 0.3283058
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27000 0.98992058 -0.01720223 0.30840611
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28000 0.97957751 0.020915942 0.3149002
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29000 0.99513582 0.03712206 0.30525251
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30000 0.99754125 -0.022509889 0.29511243
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31000 0.98894929 0.015289267 0.25586423
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32000 0.973493 0.015971435 0.25226411
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33000 0.99989261 0.026989142 0.29050941
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34000 0.97192218 0.043710515 0.29067058
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35000 0.99711642 0.047231436 0.27989734
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36000 0.97718259 0.0059969847 0.28843181
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37000 0.98194807 0.017440303 0.30325718
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38000 0.97195138 -0.040449666 0.29696592
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39000 0.98219017 0.0063692991 0.28915832
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40000 0.98039694 -0.0038122219 0.24799014
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41000 0.97621359 0.012624961 0.2374766
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42000 0.97460413 -0.0024187 0.24693474
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43000 0.9799912 0.015928618 0.26238505
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44000 0.96313376 -0.067284605 0.24397772
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45000 0.97643796 -0.0039001998 0.22733962
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46000 0.98641729 -0.026949085 0.24167989
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47000 0.97811939 -0.050859011 0.2335985
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48000 0.99744864 -0.008154229 0.2417371
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49000 0.97480356 -0.011051498 0.25474033
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50000 0.97841509 -0.00531423 0.25357072
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51000 0.97865859 0.067722096 0.25086864
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52000 0.97415415 0.015863025 0.2516842
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53000 0.97984491 0.021332829 0.28226376
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54000 0.99289379 -0.0192578 0.28300764
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55000 0.98606668 0.029307891 0.27592186
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56000 0.98585489 0.0062922121 0.2687204
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57000 0.98507959 -0.0068688582 0.27868708
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58000 0.98030805 0.013766115 0.31008116
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59000 0.98315137 0.033068034 0.32211415
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60000 0.98762585 0.050662295 0.30109082
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61000 0.96937507 -0.02797113 0.29968066
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62000 0.97194792 -0.0032022157 0.2866526
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63000 0.99877655 -0.010154313 0.31701083
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64000 0.98525211 -0.020415497 0.31774092
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65000 0.9833149 0.0087192442 0.31256891
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66000 0.97191797 0.0047184494 0.29880531
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67000 0.98479592 -0.010779275 0.294197
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68000 0.98418943 -0.035264623 0.29993828
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69000 0.96953928 -0.028114432 0.27403611
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70000 0.98373337 -0.057363336 0.25554163
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71000 0.98260952 0.048742037 0.27102884
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72000 0.98906053 0.010799224 0.26908376
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73000 0.99569597 -0.0092675754 0.26927752
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74000 0.97627362 0.013945821 0.2730712
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75000 0.97276792 0.015036012 0.25847255
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76000 0.97659072 -0.027078556 0.26783118
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77000 0.9807196 -0.044553679 0.25993053
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78000 0.97398601 -0.00027444729 0.26127735
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79000 0.98124212 -0.012488833 0.27454966
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80000 0.98506783 -0.015190822 0.2676633
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81000 0.97926561 -0.012755191 0.27046398
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82000 0.97906184 0.012564185 0.2835038
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83000 0.96540502 -0.007372877 0.29622738
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84000 0.98726761 0.021015365 0.32432233
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85000 0.98133061 0.020043402 0.3540913
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86000 0.99142106 0.025350024 0.36697674
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87000 0.97917566 0.0061562414 0.37456288
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88000 0.99391197 0.0068565008 0.39150922
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89000 0.98521911 0.015500816 0.38121119
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90000 0.97419059 0.00037609894 0.34181128
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91000 0.98687774 -0.0073221495 0.35316892
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92000 0.97816545 0.014057005 0.33181146
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93000 0.98734859 0.016570523 0.34546487
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94000 0.99116168 -0.0068196043 0.36316635
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95000 0.99982024 0.076723346 0.38376316
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96000 0.99232404 -0.048534983 0.38369657
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97000 0.97829693 0.0041180664 0.38022523
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98000 0.99878715 -0.00089133295 0.40289006
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99000 0.97026354 -0.0039532716 0.43650647
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100000 0.98911409 0.028647976 0.4499919
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Loop time of 10.5771 on 8 procs for 100000 steps with 3200 atoms
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Pair time (%) = 4.88134 (46.1499)
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Neigh time (%) = 1.2657 (11.9664)
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Comm time (%) = 1.78371 (16.8638)
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Outpt time (%) = 0.0207323 (0.196011)
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Other time (%) = 2.62565 (24.8239)
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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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