forked from lijiext/lammps
223 lines
10 KiB
Groff
223 lines
10 KiB
Groff
LAMMPS (27 Nov 2018)
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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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orthogonal box = (0 0 -0.5) to (12 12 0.5)
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1 by 1 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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replicate $r $r 1
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replicate 4 $r 1
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replicate 4 4 1
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orthogonal box = (0 0 -0.5) to (48 48 0.5)
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1 by 1 by 1 MPI processor grid
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32 atoms
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Time spent = 0.000279665 secs
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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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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 1
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variable c_t equal 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 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
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pair_style body/rounded/polygon 1 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 y 0.001 $P 1.0 couple xy 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 y 0.001 $P 1.0 couple xy 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 y 0.001 $P 1.0 couple xy 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 y 0.001 $P 1.0 couple xy 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 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
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fix 2 all enforce2d
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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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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 = 6.15685
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ghost atom cutoff = 6.15685
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binsize = 3.07843, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 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 0.38428256 0.0014168922 0.38569945 0.0020468171
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2000 0.41372193 0.015263236 0.42898517 0.0029343462
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3000 0.54844547 0.014870378 0.56331585 0.001978353
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4000 0.73816048 0.031668204 0.76982869 0.0025939718
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5000 0.84536165 0.011504649 0.8568663 0.0037990517
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6000 0.73776478 0.14445932 0.8822241 0.0086538113
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7000 0.52022565 0.069507637 0.58973329 0.0072098694
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8000 0.72653213 0.12783368 0.85436581 0.023907183
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9000 0.87685727 0.1239819 1.0008392 0.0064590959
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10000 0.7250918 0.097243508 0.82233531 0.0012448267
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11000 0.62302234 0.05597557 0.67899791 0.00080239872
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12000 0.57159363 0.18199602 0.75358965 0.01033626
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13000 0.7505295 0.071545266 0.82207477 0.011480236
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14000 0.84703598 0.15914379 1.0061798 0.032814039
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15000 0.41905013 0.090552572 0.5096027 0.015717153
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16000 0.41805189 0.042916881 0.46096877 0.020702707
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17000 0.59966233 0.05285043 0.65251275 0.016526024
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18000 0.54282285 0.20835047 0.75117332 0.036414059
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19000 0.777922 0.034754101 0.8126761 0.036467537
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20000 0.54703924 0.14633506 0.6933743 0.012917248
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21000 0.49337931 0.1858754 0.67925471 0.037890735
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22000 0.64916623 0.19281344 0.84197967 0.011996773
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23000 0.66958738 0.20459682 0.8741842 0.023639466
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24000 0.63729755 0.1111959 0.74849345 0.025049919
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25000 0.60094316 0.13375799 0.73470115 0.035286376
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26000 0.35419589 0.22049451 0.5746904 0.0024215291
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27000 0.33789786 0.18494942 0.52284728 0.0066457643
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28000 0.32376056 0.13151726 0.45527782 0.010773856
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29000 0.36198203 0.11044834 0.47243037 0.063012638
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30000 0.22624436 0.19690087 0.42314523 0.037422734
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31000 0.32284312 0.059623656 0.38246677 0.0287682
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32000 0.4457193 0.042396136 0.48811544 0.022025252
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33000 0.61078662 0.059447221 0.67023384 0.030335089
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34000 0.63157762 0.062056279 0.6936339 0.044624352
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35000 0.69577644 0.086216204 0.78199264 0.0319995
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36000 0.76814336 0.062105963 0.83024933 0.044316891
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37000 0.58641664 0.095034548 0.68145119 0.03234133
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38000 0.48772813 0.12911854 0.61684667 0.038732146
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39000 0.74957742 0.09823432 0.84781174 0.053181162
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40000 0.57881374 0.2932491 0.87206284 0.065740126
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41000 0.4415176 0.22899179 0.67050939 0.026159841
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42000 0.5260339 0.2048105 0.7308444 0.046294432
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43000 0.33493572 0.32500572 0.65994144 -0.01250241
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44000 0.46467243 0.07907132 0.54374375 0.13386238
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45000 0.48135518 0.2618908 0.74324598 -0.016767159
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46000 0.27223209 0.24562643 0.51785852 0.052118439
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47000 0.26402739 0.1838767 0.44790409 -0.0015878764
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48000 0.10229166 0.25519169 0.35748335 -0.033927088
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49000 0.24313495 0.16578185 0.40891679 0.12414926
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50000 0.27400066 0.27688032 0.55088098 0.10421157
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51000 0.43081855 0.18111733 0.61193587 0.16373371
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52000 0.81969298 0.060995894 0.88068887 0.057285357
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53000 0.99936159 0.029137886 1.0284995 0.19425015
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54000 0.69750047 0.038079774 0.73558024 -0.089236384
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55000 0.54823746 0.056369886 0.60460734 -0.021320579
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56000 0.6752322 0.050322917 0.72555512 0.25303548
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57000 0.90328009 0.061107142 0.96438723 -0.1962713
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58000 0.81463148 0.050387847 0.86501933 0.35952157
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59000 0.61636455 0.064910223 0.68127478 -0.27208497
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60000 0.62573918 0.052264617 0.67800379 0.4493407
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61000 0.81065726 0.071269668 0.88192693 -0.34643283
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62000 0.86420318 0.052799365 0.91700254 0.48308047
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63000 0.67848508 0.069087342 0.74757242 -0.31814526
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64000 0.61430417 0.052109373 0.66641354 0.38336646
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65000 0.75782937 0.063488206 0.82131757 -0.19113322
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66000 0.88735857 0.051779306 0.93913787 0.29410996
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67000 0.70684373 0.061786313 0.76863005 -0.16503578
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68000 0.58571951 0.052402151 0.63812166 0.30173228
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69000 0.64997491 0.064435462 0.71441037 -0.1920633
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70000 0.75071821 0.053416991 0.8041352 0.3846747
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71000 0.8124718 0.06877986 0.88125166 -0.26852566
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72000 0.71352066 0.05358784 0.7671085 0.41321806
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73000 0.55151827 0.066470642 0.61798891 -0.2211738
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74000 0.65473635 0.061946814 0.71668316 0.29536873
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75000 0.88704613 0.059476353 0.94652248 -0.0312656
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76000 0.76899803 0.057351665 0.8263497 0.017885214
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77000 0.65149455 0.05407174 0.70556629 0.25192449
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78000 0.68614394 0.074251169 0.76039511 -0.19369404
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79000 0.97451567 0.06262739 1.0371431 0.4217182
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80000 0.88207775 0.070157004 0.95223476 -0.27318477
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81000 0.69294455 0.062623957 0.75556851 0.40150141
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82000 0.70748016 0.073924331 0.78140449 -0.17128794
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83000 0.78180774 0.063513978 0.84532172 0.22033652
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84000 0.80170993 0.065812223 0.86752216 0.083202913
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85000 0.64788122 0.070348079 0.7182293 -0.066913668
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86000 0.56575431 0.064865112 0.63061942 0.33905786
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87000 0.78205358 0.07983702 0.8618906 -0.22844912
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88000 0.87426443 0.065703482 0.93996791 0.448573
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89000 0.73269893 0.079827385 0.81252632 -0.24183162
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90000 0.66703106 0.065630146 0.73266121 0.35410109
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91000 0.73107154 0.07402702 0.80509856 -0.085492997
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92000 1.043635 0.067156523 1.1107915 0.14311135
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93000 0.86063344 0.065607238 0.92624068 0.20750649
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94000 0.68304235 0.075962239 0.75900459 -0.14594625
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95000 0.7069191 0.067125732 0.77404483 0.39459759
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96000 0.79860046 0.090957588 0.88955805 -0.24202125
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97000 0.81366777 0.071387081 0.88505485 0.32217266
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98000 0.61885746 0.041524228 0.66038169 0.31635364
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99000 0.57007759 0.055438456 0.62551604 -0.21172902
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100000 0.80462394 0.045542313 0.85016626 0.099207503
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Loop time of 6.34495 on 1 procs for 100000 steps with 32 atoms
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Performance: 1361713.788 tau/day, 15760.576 timesteps/s
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99.7% 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 | 5.0158 | 5.0158 | 5.0158 | 0.0 | 79.05
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Neigh | 0.0072868 | 0.0072868 | 0.0072868 | 0.0 | 0.11
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Comm | 0.18669 | 0.18669 | 0.18669 | 0.0 | 2.94
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Output | 0.00098681 | 0.00098681 | 0.00098681 | 0.0 | 0.02
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Modify | 1.0417 | 1.0417 | 1.0417 | 0.0 | 16.42
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Other | | 0.09245 | | | 1.46
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Nlocal: 32 ave 32 max 32 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 35 ave 35 max 35 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 61 ave 61 max 61 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 61
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Ave neighs/atom = 1.90625
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Neighbor list builds = 1545
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Dangerous builds = 0
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Total wall time: 0:00:06
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