176 lines
7.8 KiB
Groff
176 lines
7.8 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 0.5
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Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
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region box block 0 60 0 60 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
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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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change_box all triclinic
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Changing box ...
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triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
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# remove two spheres of small particles and add large particles in the voids
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region sphere1 sphere 20.0 20.0 0.0 10.0 units box
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region sphere2 sphere 60.0 60.0 0.0 10.0 units box
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delete_atoms region sphere1
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Deleted 154 atoms, new total = 3446
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delete_atoms region sphere2
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Deleted 158 atoms, new total = 3288
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create_atoms 2 single 20.0 20.0 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 2 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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set type 2 mass 400
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Setting atom values ...
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2 settings made for mass
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set type 1 mass 1
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Setting atom values ...
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3288 settings made for mass
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set type 2 diameter 20
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Setting atom values ...
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2 settings made for diameter
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set type 1 diameter 1
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Setting atom values ...
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3288 settings made for diameter
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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/interval 2 1 20
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comm_modify mode multi vel yes reduce/multi #multi/old
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# colloid potential
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pair_style granular
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pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
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fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
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fix 2 all enforce2d
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fix 3 all deform 1 xy erate 1e-3
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#dump 1 all custom 1000 dump.granular id x y z radius
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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 = 21
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ghost atom cutoff = 21
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binsize = 1, bins = 85 85 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair granular, perpetual
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attributes: half, newton on, size, history
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pair build: half/size/multi/newton/tri
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stencil: half/multi/2d/tri
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bin: multi
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Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes
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Step Temp E_pair TotEng Press Volume
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0 1.44 0 1.4395623 0.66837658 7200
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1000 0.32605303 0 0.32595393 0.17341558 7862.5037
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2000 0.12631567 0 0.12627728 0.069188881 8216.7174
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3000 0.069373812 0 0.069352726 0.040740832 8344.2982
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4000 0.045084633 0 0.045070929 0.029328609 8239.3656
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5000 0.032681746 0 0.032671813 0.025416741 7943.7831
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6000 0.026301239 0 0.026293245 0.021418793 7617.8426
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7000 0.021666723 0 0.021660138 0.018961011 7255.9338
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8000 0.018141337 0 0.018135823 0.019306113 6887.4963
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9000 0.015922309 0 0.015917469 0.020033398 6524.016
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10000 0.014744547 0 0.014740066 0.020959503 6168.1945
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11000 0.013872852 0 0.013868636 0.021708943 5823.3153
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12000 0.013321594 0 0.013317545 0.02332141 5491.4979
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13000 0.01269964 0 0.012695779 0.024796428 5174.6263
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14000 0.01227055 0 0.012266821 0.027785072 4873.4516
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15000 0.012120508 0 0.012116824 0.029656636 4588.8603
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16000 0.011612027 0 0.011608498 0.034695109 4320.4674
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17000 0.011216697 0 0.011213288 0.042746966 4069.4275
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18000 0.010950166 0 0.010946838 0.053528994 3835.5439
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19000 0.010887635 0 0.010884325 0.069684492 3619.562
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20000 0.010563449 0 0.010560238 0.08654561 3420.2636
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21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408
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22000 0.006929086 0 0.0069269799 0.15018917 3072.0438
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23000 0.0052239156 0 0.0052223277 0.19067193 2924.441
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24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426
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25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912
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26000 0.002549072 0 0.0025482972 0.33567824 2579.3738
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27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502
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28000 0.001772982 0 0.0017724431 0.41079958 2411.9111
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29000 0.001127719 0 0.0011273762 0.44752241 2341.1888
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30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611
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31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328
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32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674
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33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696
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34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504
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35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077
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36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251
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37000 0.0003540723 0 0.00035396468 0.68803919 2005.497
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38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345
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39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979
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40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695
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41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326
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42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474
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43000 0.00021545017 0 0.00021538468 0.82803644 1872.073
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44000 0.00017293257 0 0.00017288 0.85436769 1852.6548
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45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087
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46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977
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47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913
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48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082
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49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875
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50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247
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Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms
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Performance: 1217551.996 tau/day, 2818.407 timesteps/s
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100.0% 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 | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21
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Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31
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Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10
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Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01
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Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32
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Other | | 0.5419 | | | 3.05
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Nlocal: 822.500 ave 897 max 779 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 190.500 ave 211 max 179 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 6665.75 ave 7329 max 6104 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Total # of neighbors = 26663
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Ave neighs/atom = 8.1042553
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Neighbor list builds = 342
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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: 0:00:17
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