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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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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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) = 10.29 | 10.29 | 10.29 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 0.32604952 0 0.32595042 0.17341597 7862.5013
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2000 0.12631038 0 0.12627198 0.069126477 8216.6956
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3000 0.069351715 0 0.069330635 0.040799593 8344.1931
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4000 0.045023755 0 0.04501007 0.029184795 8239.1832
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5000 0.032735149 0 0.0327252 0.025640841 7943.5691
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6000 0.026205227 0 0.026197262 0.021206924 7617.6672
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7000 0.02165475 0 0.021648168 0.018789365 7255.2897
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8000 0.018299317 0 0.018293755 0.019272158 6887.3386
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9000 0.016283763 0 0.016278813 0.020434892 6524.0274
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10000 0.015148918 0 0.015144313 0.021650465 6168.4941
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11000 0.014180465 0 0.014176155 0.022320009 5823.98
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12000 0.013505744 0 0.013501639 0.023978674 5492.4853
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13000 0.013009585 0 0.01300563 0.024391329 5175.7455
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14000 0.012494373 0 0.012490576 0.027331543 4874.3212
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15000 0.012057669 0 0.012054004 0.030561239 4589.518
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16000 0.011510988 0 0.01150749 0.034613772 4321.1694
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17000 0.011198594 0 0.01119519 0.042263536 4070.0115
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18000 0.010978603 0 0.010975266 0.053637275 3836.0304
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19000 0.010768789 0 0.010765516 0.069472547 3619.75
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20000 0.0102256 0 0.010222492 0.085332898 3420.2738
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21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821
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22000 0.006565581 0 0.0065635854 0.14807426 3071.3012
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23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162
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24000 0.0040345997 0 0.0040333734 0.237983 2792.2658
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25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475
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26000 0.0024157863 0 0.002415052 0.33851944 2578.4972
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27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264
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28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871
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29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208
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30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452
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31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456
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32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224
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33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345
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34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045
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35000 0.00075804791 0 0.0007578175 0.6359631 2072.525
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36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907
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37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831
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38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441
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39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127
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40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006
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41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939
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42000 0.00025394755 0 0.00025387036 0.80529272 1893.064
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43000 0.00021067821 0 0.00021061418 0.82962095 1872.365
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44000 0.00017927684 0 0.00017922235 0.85522899 1853.531
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45000 0.0001464225 0 0.000146378 0.87925998 1837.2423
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46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227
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47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605
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48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227
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49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811
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50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507
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Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms
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Performance: 393345.914 tau/day, 910.523 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 | 44.691 | 44.691 | 44.691 | 0.0 | 81.38
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Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39
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Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37
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Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00
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Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43
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Other | | 0.7794 | | | 1.42
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Nlocal: 3290.00 ave 3290 max 3290 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 525.000 ave 525 max 525 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 26732.0 ave 26732 max 26732 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 26732
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Ave neighs/atom = 8.1252280
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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: 0:00:54
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