Examples and documentation
This commit is contained in:
Joel Clemmer
175
examples/multi/log.30Nov20.granular.intel.4
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175
examples/multi/log.30Nov20.granular.intel.4
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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 0.5
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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
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comm_modify mode multi vel yes multi/reduce
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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) = 11.33 | 11.33 | 11.33 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 0.32273428 0 0.32263619 0.17174972 7859.8897
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2000 0.12441598 0 0.12437817 0.067078155 8212.9946
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3000 0.067389284 0 0.067368801 0.040425551 8336.7112
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4000 0.044312733 0 0.044299264 0.028220228 8229.0658
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5000 0.032702163 0 0.032692223 0.024302012 7931.1298
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6000 0.025856 0 0.025848141 0.021241317 7603.5534
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7000 0.021437473 0 0.021430957 0.019285494 7243.5757
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8000 0.018129567 0 0.018124057 0.020738727 6877.4816
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9000 0.01637016 0 0.016365184 0.020261904 6515.3445
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10000 0.01500918 0 0.015004618 0.020551803 6160.4475
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11000 0.014156553 0 0.01415225 0.021324818 5815.4665
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12000 0.013725412 0 0.01372124 0.021159958 5483.6304
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13000 0.013215733 0 0.013211716 0.021685624 5165.4758
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14000 0.012398179 0 0.012394411 0.024155572 4862.8657
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15000 0.01184269 0 0.01183909 0.028504106 4577.901
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16000 0.01143291 0 0.011429435 0.033564204 4309.88
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17000 0.011166204 0 0.01116281 0.040588854 4058.9972
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18000 0.011000875 0 0.010997532 0.048998904 3825.1569
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19000 0.010225905 0 0.010222797 0.063669586 3607.6622
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20000 0.0091390249 0 0.0091362471 0.088165396 3408.567
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21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936
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22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873
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23000 0.0046667554 0 0.004665337 0.19453813 2917.9782
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24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897
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25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164
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26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313
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27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628
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28000 0.001443434 0 0.0014429952 0.41572112 2409.3271
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29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314
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30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156
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31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347
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32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736
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33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709
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34000 0.00060927898 0 0.00060909379 0.61734988 2107.128
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35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004
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36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237
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37000 0.0003140158 0 0.00031392035 0.69018918 2007.323
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38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702
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39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837
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40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032
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41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103
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42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646
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43000 0.00020544063 0 0.00020537818 0.82714181 1872.768
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44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303
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45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779
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46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004
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47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601
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48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244
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49000 0.00018647711 0 0.00018642043 0.95733125 1779.401
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50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506
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Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms
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Performance: 964340.770 tau/day, 2232.270 timesteps/s
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99.9% 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 | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99
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Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51
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Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83
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Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39
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Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59
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Other | | 0.6017 | | | 2.69
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Nlocal: 822.500 ave 859 max 785 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 395.750 ave 424 max 368 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 13439.5 ave 14346 max 12017 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Total # of neighbors = 53758
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Ave neighs/atom = 16.339818
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Neighbor list builds = 348
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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: 0:00:22
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