forked from lijiext/lammps
252 lines
11 KiB
Groff
252 lines
11 KiB
Groff
LAMMPS (2 Aug 2018)
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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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Time spent = 0.000706911 secs
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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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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 53 53 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 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 0.97069905 -1.5851114 0 -0.61471567 0.90108287
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Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms
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Performance: 3236214.756 tau/day, 7491.238 timesteps/s
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99.9% CPU use with 8 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27
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Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68
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Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06
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Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02
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Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43
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Other | | 0.05701 | | | 8.54
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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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Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
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Step Temp c_msd[4] v_twopoint v_fitslope
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0 0.97069905 0 0 5e+20
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1000 0.98138076 4.0484996 0.20242494 0.20685564
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2000 0.97606079 9.2121392 0.23030346 0.23687918
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3000 0.97924866 14.815034 0.24691721 0.25405247
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4000 0.98568451 20.516817 0.25646019 0.26353644
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5000 0.97551815 27.33922 0.27339219 0.27544492
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6000 0.98482252 34.37734 0.28647782 0.28966619
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7000 0.9672559 41.696689 0.29783348 0.30165524
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8000 0.9836541 48.340277 0.30212673 0.31085371
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9000 0.99087147 56.042692 0.31134828 0.31811489
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10000 0.99663166 63.69663 0.31848314 0.32589374
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11000 0.97776688 71.144109 0.32338231 0.33219745
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12000 0.98246011 78.301774 0.32625739 0.33723
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13000 0.98788732 85.061923 0.32716124 0.34053027
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14000 0.96872483 91.1658 0.32559214 0.34231162
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15000 0.98955796 97.278388 0.32426129 0.34229511
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16000 0.99855196 104.23997 0.3257499 0.34217252
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17000 0.98600861 110.66055 0.3254722 0.34172446
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18000 0.98696963 116.90111 0.32472531 0.3408227
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19000 0.9881192 124.21305 0.32687644 0.34036538
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20000 0.98527319 131.09874 0.32774685 0.34003478
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21000 0.99015191 137.89263 0.32831579 0.33987868
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22000 0.97972418 146.68982 0.33338595 0.34060035
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23000 0.98911012 155.1264 0.33723129 0.34201036
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24000 0.98810498 162.88634 0.33934653 0.34371488
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25000 0.96961962 170.37907 0.34075814 0.34531409
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26000 0.99118408 179.26511 0.34474059 0.34717195
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27000 0.98515159 185.90764 0.3442734 0.34898035
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28000 0.98951677 192.12183 0.34307469 0.35021808
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29000 0.9832026 196.99457 0.33964581 0.35075459
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30000 0.98449493 203.48475 0.33914124 0.35066186
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31000 0.96585993 210.06193 0.33880956 0.35046715
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32000 0.98758117 218.94174 0.34209646 0.35046623
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33000 0.98875584 225.96489 0.34237104 0.35073944
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34000 0.98007229 233.5792 0.34349882 0.35109188
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35000 0.98415295 241.98148 0.34568783 0.35157879
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36000 0.98101154 250.30876 0.34765106 0.3523013
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37000 0.97606878 258.2127 0.34893608 0.35318097
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38000 0.97220293 266.40464 0.35053242 0.3540743
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39000 0.979783 272.8578 0.34981769 0.35496561
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40000 0.98375673 279.87598 0.34984497 0.35558182
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41000 0.97506523 288.07676 0.35131312 0.35618259
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42000 0.97106749 296.11647 0.3525196 0.35698571
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43000 0.97717259 304.46747 0.35403194 0.3577736
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44000 0.98541435 312.57228 0.35519578 0.35865003
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45000 0.97678287 321.82674 0.35758527 0.35958623
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46000 0.98169719 329.78197 0.35845866 0.36062236
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47000 0.99471466 337.11283 0.35863066 0.36158322
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48000 0.98332437 346.0754 0.3604952 0.36255042
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49000 0.98126947 356.11859 0.36338631 0.3636628
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50000 0.98809751 365.65248 0.36565248 0.36496809
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51000 0.95919516 373.91833 0.36658659 0.36628073
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52000 0.98097913 381.26492 0.36660089 0.36752237
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53000 0.97774072 388.81031 0.36680218 0.36863962
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54000 0.99096915 395.56767 0.36626636 0.36961521
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55000 0.97652739 401.72735 0.36520668 0.37038579
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56000 0.99185306 407.28834 0.3636503 0.37094092
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57000 0.96289342 414.75298 0.3638184 0.37130039
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58000 0.97871716 424.69443 0.36611588 0.37180428
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59000 0.98637393 433.14205 0.36706953 0.37239862
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60000 0.98009845 438.14533 0.36512111 0.37288487
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61000 0.99416712 446.08007 0.3656394 0.37321496
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62000 0.97612483 450.90846 0.36363585 0.37345792
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63000 0.97786531 455.36749 0.36140277 0.37344803
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64000 0.99080668 458.04873 0.35785057 0.37313914
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65000 0.97952497 461.31241 0.3548557 0.3725875
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66000 0.98095955 463.91727 0.35145248 0.37174735
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67000 0.98370788 468.93 0.34994776 0.37076942
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68000 0.96931818 471.07765 0.34638063 0.36961868
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69000 0.98512552 474.59146 0.34390685 0.36830908
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70000 0.98065743 478.66071 0.3419005 0.36686789
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71000 0.98971283 482.57357 0.33984054 0.36535224
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72000 0.99890324 485.32018 0.3370279 0.36373174
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73000 0.98649924 490.19497 0.33574998 0.36200692
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74000 0.98723422 496.04991 0.33516886 0.36034919
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75000 1.0025633 501.6313 0.33442087 0.35872052
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76000 0.97859959 505.97813 0.33288035 0.35714939
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77000 0.97973006 510.55334 0.33152814 0.35553808
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78000 0.9903944 515.06966 0.33017286 0.35391584
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79000 0.96847518 518.76483 0.32833217 0.35226287
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80000 0.99171112 524.18127 0.32761329 0.35065267
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81000 0.97202573 529.09959 0.32660468 0.34904364
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82000 0.99368438 535.80271 0.32670897 0.34747913
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83000 0.97932483 543.08233 0.32715803 0.34605097
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84000 0.99078651 547.57861 0.32593965 0.34469765
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85000 0.98973457 552.24581 0.32485048 0.34332115
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86000 0.9835873 557.3493 0.32404029 0.34197018
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87000 0.97180564 564.93434 0.32467491 0.34069702
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88000 0.99743353 571.39837 0.32465817 0.33951258
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89000 0.98993437 577.81703 0.32461631 0.33838511
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90000 0.9926071 583.39378 0.32410765 0.33730429
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91000 0.98800458 591.08741 0.3247733 0.33630505
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92000 0.98501879 596.10133 0.32396811 0.33534725
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93000 0.98810082 604.02652 0.32474544 0.33445545
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94000 0.97563748 609.43676 0.32416849 0.33361404
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95000 0.97283448 615.15754 0.32376713 0.33278044
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96000 0.9883071 622.30912 0.32411933 0.33199212
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97000 0.97717678 628.84457 0.32414669 0.33125729
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98000 0.97190208 634.37377 0.32366009 0.33054877
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99000 0.98687379 640.66666 0.32356902 0.32986014
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100000 0.97559757 646.96406 0.32348203 0.32920186
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Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms
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Performance: 5670494.518 tau/day, 13126.145 timesteps/s
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100.0% CPU use with 8 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19
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Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11
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Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34
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Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06
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Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60
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Other | | 0.4348 | | | 5.71
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Nlocal: 400 ave 413 max 391 min
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Histogram: 2 1 0 2 0 0 1 1 0 1
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Nghost: 204.75 ave 213 max 197 min
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Histogram: 1 1 0 1 0 3 0 1 0 1
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Neighs: 2800.62 ave 2959 max 2661 min
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Histogram: 1 1 1 2 0 0 0 1 1 1
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Total # of neighbors = 22405
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Ave neighs/atom = 7.00156
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Neighbor list builds = 12728
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Dangerous builds = 0
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Total wall time: 0:00:08
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