Examples and documentation
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Joel Clemmer
175
examples/multi/log.30Nov20.granular.old.intel.4
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examples/multi/log.30Nov20.granular.old.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/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/old/newton/tri
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stencil: half/multi/old/2d/tri
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 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 0.063669588 3607.6622
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20000 0.0091390255 0 0.0091362477 0.088165402 3408.567
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21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936
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22000 0.00601731 0 0.0060154811 0.15261994 3064.3873
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23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782
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24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897
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25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164
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26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312
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27000 0.001700508 0 0.0016999912 0.37665013 2487.1626
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28000 0.0014434246 0 0.0014429859 0.41572163 2409.327
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29000 0.00089885063 0 0.00089857742 0.453431 2340.2313
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30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155
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31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349
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32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738
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33000 0.00044719326 0 0.00044705733 0.59696179 2142.571
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34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282
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35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008
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36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242
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37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235
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38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706
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39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838
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40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034
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41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108
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42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649
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43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672
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44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284
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45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755
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46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989
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47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606
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48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258
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49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032
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50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534
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Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms
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Performance: 698235.574 tau/day, 1616.286 timesteps/s
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89.8% 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 | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36
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Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78
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Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56
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Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29
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Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28
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Other | | 0.8418 | | | 2.72
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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: 3049.75 ave 3089 max 2999 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Neighs: 13440.5 ave 14459 max 11964 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Total # of neighbors = 53762
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Ave neighs/atom = 16.341033
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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: 0:00:30
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