forked from lijiext/lammps
184 lines
7.9 KiB
Groff
184 lines
7.9 KiB
Groff
LAMMPS (24 Dec 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
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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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1 by 1 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 #multi/old
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neigh_modify delay 0 collection/type 2 1*4 5
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comm_modify mode multi reduce/multi #multi/old
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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) = 4.385 | 4.385 | 4.385 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 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
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3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
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4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
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5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
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6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702
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7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386
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8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372
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9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764
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10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941
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11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993
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12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363
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13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226
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14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372
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15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715
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16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607
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17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6
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18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856
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19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867
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20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666
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21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277
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22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593
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23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968
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24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941
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25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154
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26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774
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27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521
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28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093
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29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945
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30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305
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31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392
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32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609
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33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572
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34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49
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35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819
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36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608
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37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772
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38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511
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39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647
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40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198
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41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649
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42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804
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43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893
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44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262
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45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842
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46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151
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47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334
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48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246
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49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093
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50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715
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Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms
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Performance: 1093493.133 tau/day, 2531.234 timesteps/s
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100.0% CPU use with 1 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 | 10.789 | 10.789 | 10.789 | 0.0 | 54.62
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Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59
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Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70
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Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01
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Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11
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Other | | 0.7856 | | | 3.98
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Nlocal: 3026.00 ave 3026 max 3026 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 584.000 ave 584 max 584 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 25892.0 ave 25892 max 25892 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 25892
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Ave neighs/atom = 8.5565102
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Neighbor list builds = 4330
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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: 0:00:19
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