184 lines
7.9 KiB
Groff
184 lines
7.9 KiB
Groff
LAMMPS (30 Nov 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
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using 1 OpenMP thread(s) per MPI task
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# Big colloid particles and small LJ particles
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units lj
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atom_style sphere
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dimension 2
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lattice sq 0.1
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Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
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region box block 0 60 0 60 -0.5 0.5
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create_box 5 box
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Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 3600 atoms
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create_atoms CPU = 0.001 seconds
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#Roughly equally partition atoms between types 1-4
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set group all type/fraction 2 0.500 23984
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Setting atom values ...
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1768 settings made for type/fraction
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set group all type/fraction 3 0.333 43684
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Setting atom values ...
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1255 settings made for type/fraction
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set group all type/fraction 4 0.250 87811
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Setting atom values ...
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927 settings made for type/fraction
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# remove two spheres of small particles and add large particles in the voids
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region sphere1 sphere 60.0 60.0 0.0 30.0 units box
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region sphere2 sphere 130.0 130.0 0.0 30.0 units box
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delete_atoms region sphere1
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Deleted 289 atoms, new total = 3311
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delete_atoms region sphere2
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Deleted 287 atoms, new total = 3024
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create_atoms 5 single 60.0 60.0 0.0 units box
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Created 1 atoms
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create_atoms CPU = 0.000 seconds
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create_atoms 5 single 130.0 130.0 0.0 units box
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Created 1 atoms
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create_atoms CPU = 0.000 seconds
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set type 1 mass 400
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Setting atom values ...
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753 settings made for mass
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set type 2 mass 1
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Setting atom values ...
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722 settings made for mass
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velocity all create 1.44 87287 loop geom
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# multi neighbor and comm for efficiency
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neighbor 1 multi #/old
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neigh_modify delay 0 multi/custom 2 1*4 5
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comm_modify mode multi multi/reduce
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# colloid potential
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pair_style colloid 20.0
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pair_coeff * * 144.0 1.0 0.0 0.0 3.0
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pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
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fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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dump 1 all atom 1000 dump.colloid
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#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
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#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
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thermo_style custom step temp epair etotal press vol
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thermo 1000
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timestep 0.005
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run 50000
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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 = 31
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ghost atom cutoff = 31
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binsize = 2, bins = 95 95 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair colloid, perpetual
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attributes: half, newton on
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pair build: half/multi/newton
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stencil: half/multi/2d
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bin: multi
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Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes
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Step Temp E_pair TotEng Press Volume
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0 1.44 0 1.4395241 0.121 36000
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1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
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2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
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3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289
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4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708
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5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295
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6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648
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7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448
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8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484
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9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609
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10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542
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11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927
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12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009
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13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654
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14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89
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15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786
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16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792
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17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809
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18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172
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19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244
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20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884
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21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487
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22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812
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23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427
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24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79
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25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756
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26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645
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27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657
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28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079
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29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99
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30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355
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31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196
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32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934
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33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442
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34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628
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35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725
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36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049
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37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825
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38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497
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39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469
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40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846
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41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515
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42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657
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43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024
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44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224
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45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959
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46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822
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47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892
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48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453
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49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918
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50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268
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Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms
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Performance: 2966022.789 tau/day, 6865.793 timesteps/s
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99.8% CPU use with 4 MPI tasks x 1 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 | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59
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Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21
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Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96
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Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69
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Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04
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Other | | 0.4737 | | | 6.50
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Nlocal: 756.500 ave 839 max 673 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Nghost: 292.500 ave 307 max 282 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Neighs: 6435.25 ave 7367 max 5493 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 25741
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Ave neighs/atom = 8.5066094
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Neighbor list builds = 4335
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:07
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