184 lines
7.9 KiB
Groff
184 lines
7.9 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 0.1
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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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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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#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 #multi
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neigh_modify delay 0 #multi/custom 2 1*4 5
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comm_modify mode multi/old #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) = 4.496 | 4.496 | 4.496 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 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
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3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
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4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
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5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
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6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702
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7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387
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8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802
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9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722
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10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135
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11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116
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12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208
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13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901
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14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344
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15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963
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16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043
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17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977
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18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99
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19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325
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20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745
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21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298
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22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199
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23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71
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24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334
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25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577
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26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041
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27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392
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28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419
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29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642
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30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15
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31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091
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32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726
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33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866
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34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869
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35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285
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36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264
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37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274
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38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252
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39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857
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40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905
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41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981
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42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931
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43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82
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44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18
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45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013
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46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611
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47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083
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48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933
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49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165
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50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069
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Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms
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Performance: 756994.490 tau/day, 1752.302 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 | 10.918 | 10.918 | 10.918 | 0.0 | 38.26
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Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36
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Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51
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Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00
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Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57
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Other | | 0.9412 | | | 3.30
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Nlocal: 3026.00 ave 3026 max 3026 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2292.00 ave 2292 max 2292 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 25767.0 ave 25767 max 25767 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 25767
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Ave neighs/atom = 8.5152016
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Neighbor list builds = 4332
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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: 0:00:28
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