forked from lijiext/lammps
253 lines
9.6 KiB
Groff
253 lines
9.6 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 = 0.000712872 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 0.648098 on 8 procs for 5000 steps with 3200 atoms
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Performance: 3332829.949 tau/day, 7714.884 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 | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96
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Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01
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Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66
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Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02
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Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02
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Other | | 0.05398 | | | 8.33
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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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Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
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Step Temp c_vacf[4] v_vacf
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0 0.97069905 1.9407914 0
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1000 0.98138076 0.029239763 0.22157396
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2000 0.97606079 -0.0015179052 0.23974121
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3000 0.97924866 -0.013873067 0.21877575
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4000 0.98568451 0.026969065 0.24052934
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5000 0.97551815 0.050232557 0.24508207
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6000 0.98482252 -0.0018424259 0.25686293
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7000 0.9672559 0.018499957 0.27279836
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8000 0.9836541 -0.022683127 0.27022734
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9000 0.99087147 0.0071767632 0.25267902
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10000 0.99663166 -0.011971734 0.2645822
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11000 0.97776688 0.01601675 0.27801788
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12000 0.98246011 0.0085456779 0.29207728
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13000 0.98788732 0.0054252587 0.29148533
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14000 0.96872483 0.0087976064 0.29645689
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15000 0.98955796 -0.060068996 0.28904116
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16000 0.99855196 -0.0066979853 0.24964957
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17000 0.98600861 0.021334454 0.23410452
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18000 0.98696963 -0.01971883 0.23190572
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19000 0.9881192 -0.022828159 0.20882183
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20000 0.98527319 -0.0085783561 0.20610922
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21000 0.99015191 -0.0061019744 0.20199693
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22000 0.97972418 -0.04380952 0.22099864
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23000 0.98911012 -0.0031381071 0.19304223
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24000 0.98810498 0.023131507 0.18483784
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25000 0.96961962 -0.020892151 0.17128259
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26000 0.99118408 0.02918818 0.15353531
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27000 0.98515159 -0.026417648 0.1457756
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28000 0.98951677 0.010372147 0.13321212
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29000 0.9832026 0.00058150905 0.13262151
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30000 0.98449493 0.0012256712 0.13576655
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31000 0.96585993 0.0053021384 0.10734708
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32000 0.98758117 -0.011513109 0.11473375
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33000 0.98875584 -0.0089140499 0.13003947
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34000 0.98007229 0.023423116 0.145185
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35000 0.98415295 -0.0078343607 0.16513809
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36000 0.98101154 0.025471963 0.1296799
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37000 0.97606878 -0.016931612 0.11515595
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38000 0.97220293 -0.015288346 0.12046935
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39000 0.979783 0.039556949 0.10596988
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40000 0.98375673 0.0098704124 0.15651085
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41000 0.97506523 -0.029457701 0.14822207
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42000 0.97106749 -0.024867475 0.12266294
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43000 0.97717259 0.010866403 0.14228602
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44000 0.98541435 -0.031545234 0.13017093
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45000 0.97678287 -0.011024372 0.11824999
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46000 0.98169719 0.011925437 0.1390346
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47000 0.99471466 0.0048178625 0.13076123
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48000 0.98332437 0.045576305 0.12667585
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49000 0.98126947 -0.044123768 0.13582991
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50000 0.98809751 0.014296599 0.12323107
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51000 0.95919516 -0.0091171161 0.1494511
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52000 0.98097913 0.010081012 0.12805794
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53000 0.97774072 0.043349117 0.14524942
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54000 0.99096915 0.021179196 0.1355801
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55000 0.97652739 -0.015118967 0.14955035
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56000 0.99185306 0.0018045061 0.16706629
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57000 0.96289342 0.0095090659 0.19215008
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58000 0.97871716 -0.028989119 0.20370326
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59000 0.98637393 0.0067841088 0.21820001
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60000 0.98009845 0.011559251 0.24504916
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61000 0.99416712 0.0099372548 0.24882366
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62000 0.97612483 0.014677063 0.25146482
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63000 0.97786531 -0.0047938112 0.26052305
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64000 0.99080668 -0.01632121 0.24744267
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65000 0.97952497 0.0070583633 0.22323997
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66000 0.98095955 0.036296232 0.2151706
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67000 0.98370788 -0.0040313363 0.22236193
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68000 0.96931818 0.0231486 0.20397659
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69000 0.98512552 -0.017450997 0.21854935
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70000 0.98065743 0.046916694 0.2080453
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71000 0.98971283 0.010974871 0.21628306
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72000 0.99890324 -0.023780184 0.23385876
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73000 0.98649924 0.012862733 0.23458964
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74000 0.98723422 -0.0096252165 0.23873216
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75000 1.0025633 -0.070387674 0.2275029
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76000 0.97859959 0.0058897922 0.22954358
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77000 0.97973006 -0.0082868083 0.25189797
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78000 0.9903944 -0.042368536 0.26564349
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79000 0.96847518 -0.050630573 0.25344248
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80000 0.99171112 0.012126001 0.23257751
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81000 0.97202573 -0.029816198 0.27354387
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82000 0.99368438 0.030082951 0.27859495
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83000 0.97932483 -0.0081664387 0.27409123
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84000 0.99078651 0.056610231 0.27593659
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85000 0.98973457 0.020424285 0.31002605
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86000 0.9835873 -0.0016980943 0.30158255
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87000 0.97180564 -0.0051924508 0.27401969
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88000 0.99743353 -0.030700753 0.24105471
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89000 0.98993437 0.0087866525 0.23913724
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90000 0.9926071 -0.014023378 0.24202489
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91000 0.98800458 0.033613695 0.2238248
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92000 0.98501879 -0.0406599 0.21809043
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93000 0.98810082 0.027637634 0.21550897
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94000 0.97563748 0.0014112208 0.18954766
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95000 0.97283448 0.0093796591 0.17838358
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96000 0.9883071 0.033049994 0.18594703
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97000 0.97717678 0.01070451 0.19203994
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98000 0.97190208 0.015065013 0.20906937
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99000 0.98687379 -0.036869401 0.22993959
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100000 0.97559757 0.045464091 0.23369283
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Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms
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Performance: 5289636.190 tau/day, 12244.528 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 | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83
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Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15
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Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95
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Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21
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Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42
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Other | | 0.363 | | | 4.45
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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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