230 lines
11 KiB
Groff
230 lines
11 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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# 2d rounded polygon bodies
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variable r index 4
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variable steps index 100000
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variable T index 0.5
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variable P index 0.1
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variable seed index 980411
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units lj
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dimension 2
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atom_style body rounded/polygon 1 6
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atom_modify map array
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read_data data.squares
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Reading data file ...
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orthogonal box = (0 0 -0.5) to (12 12 0.5)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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2 atoms
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2 bodies
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read_data CPU = 0.001 seconds
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replicate $r $r 1
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replicate 4 $r 1
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replicate 4 4 1
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Replication is creating a 4x4x1 = 16 times larger system...
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orthogonal box = (0 0 -0.5) to (48 48 0.5)
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2 by 2 by 1 MPI processor grid
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32 atoms
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replicate CPU = 0.001 seconds
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velocity all create $T ${seed} dist gaussian mom yes rot yes
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velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
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velocity all create 0.5 980411 dist gaussian mom yes rot yes
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change_box all boundary p f p
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Changing box ...
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variable cut_inner equal 0.5
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variable k_n equal 100
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variable k_na equal 2
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variable c_n equal 0.1
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variable c_t equal 0.1
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variable mu equal 0.1
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variable delta_ua equal 0.5
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pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
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pair_coeff * * ${k_n} ${k_na}
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pair_coeff * * 100 ${k_na}
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pair_coeff * * 100 2
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comm_modify vel yes
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neighbor 0.5 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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#fix 1 all nve/body
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#fix 1 all nvt/body temp $T $T 1.0
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fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
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fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
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fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
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fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
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fix 2 all enforce2d
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fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
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#compute 1 all body/local id 1 2 3
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#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
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thermo_style custom step ke pe etotal press
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thermo 1000
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#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
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#dump_modify 2 pad 6
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run ${steps}
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run 100000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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 = 6.1568542
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ghost atom cutoff = 6.1568542
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binsize = 3.0784271, bins = 16 16 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair body/rounded/polygon, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.378 | 5.378 | 5.379 Mbytes
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Step KinEng PotEng TotEng Press
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0 0.484375 0.25 0.734375 0.0067274306
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1000 0.51464289 0.00099012638 0.51563301 0.013444625
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2000 0.55653313 0.0040982283 0.56063136 0.0034505512
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3000 0.75323998 0.023578898 0.77681887 0.0036652891
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4000 0.70044978 0.092406287 0.79285607 0.0089262842
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5000 0.54548803 0.096501313 0.64198934 0.0051379522
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6000 0.48208828 0.097798868 0.57988715 0.01529805
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7000 0.68219182 0.038843949 0.72103577 0.016842202
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8000 0.53792445 0.01298383 0.55090828 0.0066797984
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9000 0.49980358 0.029397965 0.52920155 0.0046731992
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10000 0.48705755 0.10138831 0.58844586 -1.9690665e-05
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11000 0.52151879 0.065897951 0.58741674 0.0049324908
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12000 0.59065198 0.03929683 0.62994881 0.0014198454
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13000 0.46076897 0.073363984 0.53413295 0.0057849056
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14000 0.38058168 0.16336914 0.54395082 0.0099910111
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15000 0.58924494 0.13219579 0.72144074 0.012781632
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16000 0.65163924 0.10979538 0.76143462 0.015088945
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17000 0.51431594 0.036344433 0.55066037 0.001446035
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18000 0.42677394 0.093297234 0.52007117 0.00093775852
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19000 0.62399853 0.13309136 0.75708989 0.0095351169
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20000 0.52835966 0.085936455 0.61429611 0.013158115
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21000 0.42999051 0.12857394 0.55856445 0.024369485
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22000 0.56770038 0.19738636 0.76508675 0.024211788
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23000 0.55137392 0.18212359 0.7334975 0.024095463
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24000 0.6225794 0.13091248 0.75349189 0.032707954
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25000 0.47106345 0.10241626 0.57347971 0.0059731265
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26000 0.60567231 0.055894222 0.66156653 0.010614697
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27000 0.49075416 0.13914345 0.62989761 0.00048442735
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28000 0.48902573 0.21423204 0.70325777 0.021295043
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29000 0.42728391 0.24136135 0.66864527 0.031633766
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30000 0.64658635 0.15368867 0.80027502 0.0084616839
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31000 0.71370199 0.18014549 0.89384748 0.02367184
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32000 0.40141173 0.1833294 0.58474113 0.034918949
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33000 0.55780706 0.14130843 0.69911549 0.012266172
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34000 0.36544303 0.15788143 0.52332446 0.0084938225
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35000 0.56844142 0.17507842 0.74351984 0.061506713
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36000 0.5048707 0.15834563 0.66321633 0.0286909
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37000 0.4371274 0.087735559 0.52486296 -0.0016289252
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38000 0.49941117 0.22576207 0.72517324 0.059233327
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39000 0.69480051 0.15465372 0.84945423 0.039061293
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40000 0.52881719 0.29110071 0.8199179 0.032439208
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41000 0.56931201 0.38596881 0.95528082 0.045284803
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42000 0.46759969 0.21337568 0.68097537 0.086759715
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43000 0.63416318 0.44687151 1.0810347 0.072272415
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44000 0.43914666 0.20832735 0.64747401 0.026280272
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45000 0.38329718 0.25407815 0.63737533 0.017356403
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46000 0.59511045 0.32148788 0.91659833 -0.0076184601
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47000 0.50635988 0.37243112 0.878791 0.025435347
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48000 0.42316224 0.29368731 0.71684954 0.00067040329
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49000 0.40194259 0.26659105 0.66853364 0.069225504
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50000 0.4740342 0.305674 0.77970819 0.014813566
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51000 0.57279011 0.32080139 0.8935915 0.0091332017
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52000 0.54543481 0.34482955 0.89026435 -0.021131696
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53000 0.39241519 0.36432403 0.75673922 0.0077163816
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54000 0.62021406 0.32010094 0.940315 0.044477965
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55000 0.45160485 0.29442122 0.74602607 0.02563201
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56000 0.41737028 0.31207675 0.72944704 0.050342936
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57000 0.53454189 0.29192181 0.8264637 0.068452573
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58000 0.65449932 0.33567481 0.99017413 0.055352019
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59000 0.58742699 0.37317432 0.96060131 0.012805462
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60000 0.42430458 0.33744246 0.76174704 0.018744436
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61000 0.65433333 0.40723506 1.0615684 0.019757611
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62000 0.64472397 0.34658649 0.99131047 0.090688735
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63000 0.65381774 0.47452792 1.1283457 0.2090513
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64000 0.44107995 0.60507044 1.0461504 0.03144844
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65000 0.38159186 0.45527276 0.83686462 0.090856608
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66000 0.48842595 0.49445721 0.98288316 0.08753844
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67000 0.65088575 0.4611542 1.11204 0.066602605
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68000 0.5155131 0.38693864 0.90245174 0.0062596909
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69000 0.41477899 0.45120406 0.86598306 0.037396561
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70000 0.60305022 0.47624271 1.0792929 0.040607751
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71000 0.67077877 0.51044906 1.1812278 0.029084971
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72000 0.50912034 0.34340114 0.85252148 0.055767674
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73000 0.55167778 0.43795801 0.98963579 0.083371911
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74000 0.53603549 0.37357862 0.90961411 0.058762722
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75000 0.47521522 0.529749 1.0049642 0.12419171
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76000 0.48952134 0.63953611 1.1290574 0.09709472
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77000 0.63445283 0.57542295 1.2098758 0.11868116
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78000 0.62184463 0.60025138 1.222096 0.079417229
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79000 0.52715665 0.54847579 1.0756324 0.033981154
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80000 0.6264593 0.39323366 1.019693 0.05627332
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81000 0.78582235 0.47541992 1.2612423 0.031287815
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82000 0.69665491 0.58355423 1.2802091 -0.04433392
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83000 0.4994351 0.40089694 0.90033204 -0.0019687817
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84000 0.50932093 0.62716285 1.1364838 0.095177695
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85000 0.56251638 0.56010929 1.1226257 0.013989132
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86000 0.67155822 0.51326814 1.1848264 0.10616402
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87000 0.61317511 0.52704394 1.140219 0.076578899
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88000 0.57436568 0.60641096 1.1807766 0.042050421
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89000 0.62350614 0.65896923 1.2824754 0.15949038
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90000 0.57445242 0.65085438 1.2253068 0.034123951
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91000 0.50043488 0.69213026 1.1925651 -0.076403957
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92000 0.57345231 0.74801993 1.3214722 0.033715387
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93000 0.63056204 0.64474627 1.2753083 0.051205732
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94000 0.70948937 0.61081243 1.3203018 -0.0069457836
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95000 0.66048722 0.61001641 1.2705036 0.16072266
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96000 0.48720026 0.64888522 1.1360855 0.12573765
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97000 0.41570988 0.68810987 1.1038198 -0.033070846
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98000 0.53689925 0.83787736 1.3747766 0.098173219
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99000 0.5147061 0.92360546 1.4383116 0.12155736
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100000 0.5793939 0.63393822 1.2133321 0.090967465
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Loop time of 2.08698 on 4 procs for 100000 steps with 32 atoms
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Performance: 4139957.491 tau/day, 47916.175 timesteps/s, 1.533 Matom-step/s
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92.1% 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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Pair | 0.31 | 0.33594 | 0.35254 | 2.8 | 16.10
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Neigh | 0.001991 | 0.0021241 | 0.0022581 | 0.2 | 0.10
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Comm | 0.40717 | 0.43106 | 0.46731 | 3.4 | 20.65
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Output | 0.00076842 | 0.002908 | 0.0092082 | 6.7 | 0.14
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Modify | 1.1389 | 1.1624 | 1.1753 | 1.3 | 55.70
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Other | | 0.1525 | | | 7.31
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Nlocal: 8 ave 9 max 7 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 14 ave 16 max 12 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 13.25 ave 17 max 11 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 53
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Ave neighs/atom = 1.65625
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Neighbor list builds = 3000
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Dangerous builds = 0
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Total wall time: 0:00:02
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