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/old/newton
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stencil: half/multi/old/2d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 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 -0.090814168 1.8042332 0.075557943 77825.289
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4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521
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5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581
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6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994
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7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068
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8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899
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9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69
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10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271
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11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223
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12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869
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13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441
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14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432
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15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491
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16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633
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17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582
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18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933
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19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945
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20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271
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21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934
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22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03
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23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999
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24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323
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25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848
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26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597
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27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24
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28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441
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29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266
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30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051
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31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903
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32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077
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33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987
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34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964
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35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433
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36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246
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37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664
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38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421
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39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293
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40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176
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41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599
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42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922
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43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928
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44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954
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45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662
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46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162
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47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453
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48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543
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49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823
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50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277
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Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms
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Performance: 1921872.705 tau/day, 4448.779 timesteps/s
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98.0% 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 | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39
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Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81
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Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48
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Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37
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Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92
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Other | | 0.5666 | | | 5.04
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Nlocal: 756.500 ave 838 max 693 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Nghost: 1282.50 ave 1333 max 1216 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 6426.25 ave 7350 max 5786 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Total # of neighbors = 25705
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Ave neighs/atom = 8.4947125
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Neighbor list builds = 4326
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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: 0:00:11
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