forked from lijiext/lammps
387 lines
19 KiB
Plaintext
387 lines
19 KiB
Plaintext
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LAMMPS (1 Feb 2014)
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# sample LAMMPS input script for viscosity of 2d LJ liquid
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# Green-Kubo method via fix ave/correlate
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# settings
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variable x equal 20
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variable y equal 20
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variable rho equal 0.6
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variable t equal 1.0
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variable rc equal 2.5
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variable p equal 400 # correlation length
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variable s equal 5 # sample interval
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variable d equal $p*$s # dump interval
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variable d equal 400*$s
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variable d equal 400*5
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# problem setup
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units lj
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dimension 2
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atom_style atomic
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neigh_modify delay 0 every 1
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lattice sq2 ${rho}
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lattice sq2 0.6
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region simbox block 0 $x 0 $y -0.1 0.1
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region simbox block 0 20 0 $y -0.1 0.1
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region simbox block 0 20 0 20 -0.1 0.1
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create_box 1 simbox
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Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
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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 800 atoms
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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mass * 1.0
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velocity all create $t 97287
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velocity all create 1 97287
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# equilibration run
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fix 1 all nve
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fix 2 all langevin $t $t 0.1 498094
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fix 2 all langevin 1 $t 0.1 498094
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fix 2 all langevin 1 1 0.1 498094
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fix 3 all enforce2d
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thermo $d
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thermo 2000
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run 10000
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Memory usage per processor = 2.06394 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -1.56492 0 -0.56617 -1.535262
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2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
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4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
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6000 1.0384043 -1.6029205 0 -0.5658142 0.82862869
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8000 1.0288194 -1.5760462 0 -0.54851284 1.1299693
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10000 0.97521893 -1.5752855 0 -0.60128557 1.0982639
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Loop time of 1.72441 on 1 procs for 10000 steps with 800 atoms
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Pair time (%) = 0.929897 (53.9255)
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Neigh time (%) = 0.203868 (11.8225)
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Comm time (%) = 0.0357857 (2.07524)
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Outpt time (%) = 5.60284e-05 (0.00324913)
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Other time (%) = 0.554805 (32.1736)
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Nlocal: 800 ave 800 max 800 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 261 ave 261 max 261 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5617 ave 5617 max 5617 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5617
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Ave neighs/atom = 7.02125
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Neighbor list builds = 1101
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Dangerous builds = 0
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velocity all scale $t
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velocity all scale 1
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unfix 2
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# Green-Kubo viscosity calculation
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reset_timestep 0
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variable pxy equal pxy
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fix SS all ave/correlate $s $p $d v_pxy type auto file profile.gk.2d ave running
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fix SS all ave/correlate 5 $p $d v_pxy type auto file profile.gk.2d ave running
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fix SS all ave/correlate 5 400 $d v_pxy type auto file profile.gk.2d ave running
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fix SS all ave/correlate 5 400 2000 v_pxy type auto file profile.gk.2d ave running
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variable scale equal 1.0/$t*vol*$s*dt
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variable scale equal 1.0/1*vol*$s*dt
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variable scale equal 1.0/1*vol*5*dt
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variable v11 equal trap(f_SS[3])*${scale}
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variable v11 equal trap(f_SS[3])*33.3333333333333
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thermo_style custom step temp press pxy v_v11
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run 500000
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Memory usage per processor = 2.06394 Mbytes
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Step Temp Press Pxy v11
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0 1 1.1131139 -0.062970733 0.066088554
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2000 1.0080895 1.0200888 -0.11243616 -1.2606591
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4000 0.99653513 1.0745982 -0.0075361431 -1.2260153
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6000 1.015614 1.0288859 -0.045052789 2.2423387
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8000 1.0480587 1.0090528 -0.16941968 1.4483022
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10000 1.0340413 0.8935734 -0.016265599 1.367264
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12000 1.0208142 0.98827028 -0.098494798 0.96391762
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14000 1.0063108 1.1900869 0.041555635 0.71920668
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16000 1.0104133 1.0341648 -0.08539107 0.87216885
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18000 1.0324239 0.78956816 -0.022393354 0.99812938
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20000 0.98065939 1.1290253 0.088823616 0.86856675
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22000 1.0456522 0.79585972 -0.10649734 1.3811196
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24000 1.0120651 1.0552123 0.21725489 1.648588
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26000 1.0441983 0.959829 0.0053239549 1.6192642
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28000 0.9936521 1.1033308 -0.0013213764 1.4830182
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30000 1.0106141 1.0845812 0.048019524 1.3015283
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32000 1.0138237 0.96535384 -0.18328359 1.1659494
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34000 0.99897229 1.2265577 -0.057168503 1.3064819
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36000 0.98508691 1.1289173 -0.18839382 1.5336228
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38000 1.0419001 0.79249301 -0.20846158 1.4200528
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40000 1.0152017 0.98214979 -0.0067504119 1.3792256
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42000 1.0113905 1.0421477 -0.047659129 1.3414456
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44000 1.0201365 1.112008 0.01373301 1.3159903
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46000 1.018482 0.93142144 -0.10476936 1.3358778
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48000 1.0362661 0.77862744 -0.073200405 1.2925615
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50000 1.0200063 0.96817572 -0.082635361 1.2477558
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52000 1.018602 1.0281262 0.059387055 1.253828
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54000 1.0465938 0.78372671 -0.04203004 1.2411918
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56000 1.0376258 1.031501 -0.043675881 1.3662686
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58000 0.97830162 1.239229 0.033252127 1.2677821
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60000 0.99938589 1.2023844 0.05306354 1.191899
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62000 1.010291 0.93962979 0.047429505 1.0726624
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64000 1.0233048 0.93855809 0.17161686 1.0641676
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66000 1.0124208 1.0309115 -0.0040419968 1.0550472
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68000 0.98507874 1.0281731 -0.090367158 1.070317
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70000 1.0012103 1.0065752 0.11646809 1.2306811
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72000 1.0257593 0.94487824 0.047164906 1.2402116
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74000 0.99773444 1.0006634 -0.16947105 1.3458531
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76000 0.99053502 1.1802621 -0.011315672 1.4050256
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78000 1.0266873 0.92896952 0.053862201 1.4183056
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80000 1.0181396 1.0028774 -0.1669873 1.3918642
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82000 1.0183891 1.0045513 0.12750581 1.3598925
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84000 1.0054008 1.1361355 0.11127961 1.3235664
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86000 1.0153982 1.0270658 0.032996007 1.244148
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88000 1.0089441 0.94065248 -0.14958385 1.2504534
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90000 1.0090826 0.96386446 0.04002849 1.19906
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92000 0.98701529 1.0170739 0.048669738 1.230085
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94000 1.0271895 0.90965645 0.16524668 1.2111807
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96000 1.0588564 0.64666046 -0.012052311 1.1865422
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98000 1.01362 1.02233 0.015426298 1.198456
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100000 0.99253832 1.1498855 -0.11430916 1.1821222
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102000 1.0260594 0.8604477 -0.038050842 1.1482599
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104000 1.0248424 1.0639555 -0.08295859 1.1390154
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106000 1.0069076 1.2491555 0.010334731 1.1352025
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108000 1.0350323 0.9938777 0.028015622 1.1395354
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110000 1.0090965 1.0811591 -0.069761835 1.1641264
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112000 0.98126774 1.2677506 0.03105149 1.1417489
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114000 1.0053548 1.05943 -0.053492802 1.1435347
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116000 1.0116531 1.1377687 0.08984011 1.1290702
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118000 1.0441155 0.94024004 0.069880409 1.1352496
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120000 0.99682009 1.1603848 -0.09404725 1.2100588
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122000 1.0155742 1.0078645 -0.027651839 1.173532
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124000 0.99222072 1.1821546 -0.0308041 1.2037919
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126000 1.0405098 1.155637 0.030664374 1.1715576
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128000 1.0187941 0.98070733 0.0059064696 1.2064639
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130000 1.0399447 0.99686501 0.14875158 1.26474
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132000 1.0409005 1.0086593 0.021338889 1.2817848
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134000 1.0476219 0.8026445 0.036028195 1.269031
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136000 1.0361278 0.82017002 0.12410098 1.2516208
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138000 1.0118377 1.017853 -0.051473869 1.2497683
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140000 1.0150827 1.0187598 -0.021626098 1.2422255
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142000 1.0299632 0.85581133 0.0020789713 1.3028929
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144000 1.0299864 0.75409682 0.067708051 1.2807235
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146000 1.0300343 0.95486967 -0.12805174 1.2639701
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148000 0.99833371 1.0636801 -0.012957113 1.2450247
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150000 1.0218031 1.0345594 -0.0076210772 1.238176
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152000 1.0166582 1.000406 0.048913573 1.2350809
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154000 1.0200436 0.9620376 0.016990704 1.2277908
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156000 1.0174714 0.97523697 -0.089095058 1.2333756
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158000 1.0057212 0.98373273 0.10571489 1.2207665
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160000 1.0116139 1.0531268 0.040970831 1.1908489
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162000 1.0141586 0.97503702 -0.12255418 1.1835675
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164000 0.96779259 1.1194358 0.17756759 1.1540165
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166000 1.0009628 1.1253418 0.050763812 1.141318
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168000 0.99014049 1.1155831 -0.14569673 1.1317473
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170000 1.0298577 0.98702864 -0.00084160851 1.1904372
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172000 1.0202995 0.96163813 0.0045819305 1.1873872
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174000 1.0359389 0.89018321 0.011677378 1.1807412
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176000 1.0256185 1.0300041 0.02536302 1.1857003
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178000 1.0271101 1.0152692 -0.13910986 1.2068771
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180000 1.0194759 0.87873048 -0.12169124 1.1850476
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182000 1.0319658 1.0033092 -0.095869229 1.1660609
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184000 1.0078723 1.2412606 -0.049703306 1.1654829
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186000 1.0442603 0.79824994 -0.093218879 1.1463494
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188000 1.0004515 0.90810497 -0.048680818 1.1105332
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190000 1.000942 0.94373473 0.10613178 1.1009497
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192000 1.048449 0.97658358 -0.17712897 1.1263395
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194000 1.0290391 0.98531851 -0.012106089 1.0921536
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196000 1.0315571 1.1564407 0.057141413 1.0858253
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198000 1.0142691 1.0606813 0.029671093 1.0716634
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200000 1.0456713 0.84981128 0.11494717 1.0676611
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202000 1.0260155 1.0217822 -0.040530429 1.0674862
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204000 0.99472169 1.1602851 0.0051321303 1.0579412
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206000 1.0014916 1.0461488 0.0060656173 1.0549157
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208000 1.0022353 1.0846052 -0.11185825 1.0596996
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210000 1.015275 1.0276323 -0.030737448 1.0550317
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212000 1.0039546 1.1104646 0.10845813 1.0540841
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214000 1.007432 1.024032 -0.11046904 1.0455342
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216000 0.99740694 1.140278 -0.065900867 1.048484
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218000 1.0237293 0.94527063 -0.20653618 1.0406664
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220000 1.0069562 1.1273839 -0.0067054642 1.0387632
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222000 1.0342064 1.0131146 0.035157231 1.0296557
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224000 1.003096 1.0550729 0.03305911 1.0335
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226000 1.0144191 1.0049718 0.042900611 1.0650019
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228000 1.0268793 0.90872396 -0.17661877 1.0602896
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230000 1.0237908 0.98063448 -0.029475684 1.0685714
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232000 1.0069934 1.1044794 0.13426396 1.0662281
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234000 0.98863378 0.95248555 -0.024211245 1.0765215
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236000 1.0134171 1.0478432 -0.17292923 1.0525098
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238000 1.0120921 0.99042234 0.025333354 1.0420108
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240000 1.0042316 1.1071855 -0.02061948 1.0468243
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242000 1.0086548 1.0773029 -0.10892118 1.0462304
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244000 1.0016487 1.0120587 -0.11220572 1.0530018
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246000 1.0206702 0.96270397 0.076386758 1.0399964
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248000 1.0106322 0.97979007 -0.056885564 1.0285937
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250000 1.0521704 0.90240063 -0.098004463 1.0680676
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252000 1.0031792 1.1298376 -0.12700293 1.0572962
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254000 1.0023361 1.0397687 -0.042138767 1.055246
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256000 1.0207399 0.99843942 -0.067694614 1.0678481
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258000 0.98874431 1.228494 0.040793426 1.0558317
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260000 1.0183455 1.0188006 -0.17725132 1.0629806
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262000 1.0018425 0.94317435 0.10076842 1.0548939
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264000 1.0166318 0.8436724 -0.056681878 1.0488651
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266000 1.0091103 1.0775158 0.028771667 1.0371622
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268000 1.0013292 0.95251758 -0.050343862 1.0496861
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270000 0.99674492 1.1472622 -0.11346408 1.1092918
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272000 1.0049198 1.0673533 -0.064343803 1.0881727
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274000 1.0303169 0.97093144 -0.010278759 1.0846913
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276000 1.0273615 0.84473644 -0.017151036 1.0688783
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278000 1.0127363 1.2089228 -0.039397817 1.0875618
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280000 0.98505511 1.1212088 -0.04261016 1.0843387
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282000 1.0210332 0.93982023 -0.11219324 1.0790461
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284000 1.0157606 1.0203143 0.0002164565 1.0721431
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286000 1.0062366 1.0025507 -0.16786234 1.0720064
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288000 0.98467873 1.2326624 -0.081203997 1.0660396
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290000 1.0099975 0.88882236 -0.031064103 1.0590327
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292000 1.0122416 1.0611548 -0.022475529 1.0519549
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294000 1.0104116 1.0266518 -0.10512697 1.0414083
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296000 1.0034132 1.0427754 -0.014337433 1.0415291
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298000 1.0171588 0.92899734 0.10623709 1.0432266
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300000 1.0280222 1.0524269 0.079178549 1.0534846
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|
302000 1.035771 0.87031074 0.029223556 1.0548035
|
||
|
|
304000 0.99817826 0.96586889 -0.092577945 1.051271
|
||
|
|
306000 0.99961879 1.1082249 -0.079054344 1.0495721
|
||
|
|
308000 1.0136108 1.0992365 -0.11696242 1.0384906
|
||
|
|
310000 0.99316114 1.0758087 0.067733542 1.0276102
|
||
|
|
312000 1.0106481 0.99751609 0.096323719 1.0260196
|
||
|
|
314000 1.0069421 1.0474061 -0.0071188531 1.0257001
|
||
|
|
316000 1.0401836 0.81939716 -0.088499972 1.0302389
|
||
|
|
318000 1.0095707 1.1018438 -0.0069997734 1.0318989
|
||
|
|
320000 1.0316135 1.003588 0.010687649 1.0262453
|
||
|
|
322000 1.009186 0.93116391 0.02270494 1.0207195
|
||
|
|
324000 1.0186856 1.0207355 -0.049273034 1.0315045
|
||
|
|
326000 1.0496148 0.9479271 -0.019377803 1.0186608
|
||
|
|
328000 1.0280164 0.83246382 -0.067199824 1.0121899
|
||
|
|
330000 1.0292958 0.96946051 -0.0067323294 1.0106087
|
||
|
|
332000 1.0118055 0.94580297 -0.1158678 0.99982007
|
||
|
|
334000 1.0090884 1.1414243 -0.082638749 0.98931612
|
||
|
|
336000 0.96668553 1.2041384 0.0042176058 0.98213644
|
||
|
|
338000 1.0292409 0.91712359 -0.10674714 1.0014886
|
||
|
|
340000 1.0056353 1.0054878 -0.067790602 0.97639404
|
||
|
|
342000 1.0105034 1.1000009 -0.065106486 0.98781851
|
||
|
|
344000 1.0296097 0.97446628 -0.11031518 0.98121512
|
||
|
|
346000 1.022878 1.0302285 -0.092796664 1.0040982
|
||
|
|
348000 1.0200294 0.84461432 0.001340607 1.0143357
|
||
|
|
350000 0.9942428 1.0974217 0.032976965 1.0066948
|
||
|
|
352000 1.0038173 1.1777572 -0.02105487 0.99841101
|
||
|
|
354000 1.0363725 1.0742789 -0.068095272 0.99311679
|
||
|
|
356000 1.0142211 0.93380261 0.011873553 0.98531527
|
||
|
|
358000 0.99346289 1.2559305 -0.1027067 0.98126142
|
||
|
|
360000 0.99957906 1.0307272 -0.052751638 1.0043971
|
||
|
|
362000 1.0196151 1.1349776 -0.09260849 1.0011441
|
||
|
|
364000 1.0371154 0.88342615 0.12450793 0.99706262
|
||
|
|
366000 1.014625 1.0304514 -0.027977229 0.9921965
|
||
|
|
368000 1.0584324 0.83998131 -0.07933342 0.99525213
|
||
|
|
370000 1.0480268 0.83980605 -0.089536871 0.99539504
|
||
|
|
372000 1.0124627 1.060244 0.14069432 0.99714731
|
||
|
|
374000 1.0319035 0.80898054 0.13773298 0.99196179
|
||
|
|
376000 1.0175987 0.86095756 -0.022196463 0.99034665
|
||
|
|
378000 1.024277 0.96855584 -0.082372168 0.98711506
|
||
|
|
380000 1.0309973 0.91266594 -0.0038718874 1.0004437
|
||
|
|
382000 1.0195474 0.84949163 -0.090011652 0.97877658
|
||
|
|
384000 1.0127199 0.92573997 -0.047436984 0.99568293
|
||
|
|
386000 1.0155482 1.0260345 0.058825776 1.0032397
|
||
|
|
388000 1.0341266 1.0684283 0.042324727 0.9962933
|
||
|
|
390000 1.015419 1.2043476 -0.065809399 0.98978792
|
||
|
|
392000 0.99510423 1.0679104 0.1194931 0.98198405
|
||
|
|
394000 0.99275686 1.1827413 0.064956819 1.0203304
|
||
|
|
396000 1.0004565 1.1524019 -0.12851079 1.0328568
|
||
|
|
398000 1.0230487 1.1653679 0.066552948 1.0356753
|
||
|
|
400000 1.0246668 1.0378562 -0.014987589 1.0388305
|
||
|
|
402000 0.99713302 0.98996019 -0.12440697 1.0369703
|
||
|
|
404000 1.0078626 1.0678616 -0.0361031 1.0292353
|
||
|
|
406000 1.0264278 0.91482461 0.1001659 1.0269674
|
||
|
|
408000 0.99866487 1.1801482 -0.062540579 1.021615
|
||
|
|
410000 0.97734309 1.1861242 0.05416943 1.014162
|
||
|
|
412000 1.0157071 0.9442541 0.22262556 1.0141824
|
||
|
|
414000 0.98254015 1.2581149 0.015246929 1.0085563
|
||
|
|
416000 1.0325598 0.90098178 0.041081387 1.0044668
|
||
|
|
418000 1.0285532 0.82679005 -0.10105529 1.0017654
|
||
|
|
420000 1.0324223 0.95868597 0.024808094 0.99789922
|
||
|
|
422000 1.0056928 1.0690554 -0.024850455 1.0197904
|
||
|
|
424000 0.99482351 1.1228662 0.049501791 1.0272213
|
||
|
|
426000 1.0222594 0.97941801 -0.11968536 1.0186344
|
||
|
|
428000 1.0111263 1.1141009 0.1437415 1.0130656
|
||
|
|
430000 0.98139004 1.0366378 0.067956814 1.0108714
|
||
|
|
432000 0.98613642 1.0119979 0.041509654 1.0033766
|
||
|
|
434000 1.0230324 0.86869314 0.055734923 1.0020727
|
||
|
|
436000 1.0212417 0.8436869 -0.022905431 0.9985587
|
||
|
|
438000 1.0093302 0.97821341 0.023100883 0.99687144
|
||
|
|
440000 1.0419272 0.87856473 -0.020071536 0.99762884
|
||
|
|
442000 1.0172555 0.90164932 0.19704935 0.99904268
|
||
|
|
444000 1.0399087 1.0051297 -0.022213498 0.99616218
|
||
|
|
446000 1.0281756 1.0867446 -0.048363674 0.99230925
|
||
|
|
448000 0.98980118 1.1266212 0.16193455 0.99381525
|
||
|
|
450000 1.0397066 1.0216642 -0.017946472 1.0119634
|
||
|
|
452000 1.0148816 1.0709423 -0.072255226 1.0011103
|
||
|
|
454000 0.97505657 1.1553955 -0.019747328 0.9952685
|
||
|
|
456000 1.0423127 0.93927199 0.1031593 1.0160711
|
||
|
|
458000 1.0185738 0.9317795 -0.14238875 1.0212947
|
||
|
|
460000 1.0254941 0.94237321 0.17279884 1.0176267
|
||
|
|
462000 1.0331624 0.90556647 -0.17064389 1.0197747
|
||
|
|
464000 1.0170281 0.98452898 -0.17212408 1.006159
|
||
|
|
466000 1.0201836 1.0477978 0.0063101913 0.99741201
|
||
|
|
468000 0.99055758 1.19768 -0.04304958 0.99395064
|
||
|
|
470000 1.0140337 1.1042576 0.06483947 1.0006513
|
||
|
|
472000 1.0369845 0.82562513 -0.06621037 1.0320218
|
||
|
|
474000 1.0149565 0.86550007 0.060011486 1.0723558
|
||
|
|
476000 1.0056806 0.99384495 -0.069441814 1.0623019
|
||
|
|
478000 1.0333144 0.91193908 0.0045431056 1.0625281
|
||
|
|
480000 1.0176402 0.90416174 -0.065787627 1.0534142
|
||
|
|
482000 0.99406615 1.1281258 0.15969853 1.0526461
|
||
|
|
484000 1.0119737 1.0284268 -0.020359549 1.0710582
|
||
|
|
486000 0.98481179 1.08347 0.049797547 1.0738962
|
||
|
|
488000 1.0444857 0.87660853 0.0011127729 1.0730464
|
||
|
|
490000 1.0253141 0.92405109 0.070770655 1.0712017
|
||
|
|
492000 1.0167975 0.88249423 0.12097353 1.0689941
|
||
|
|
494000 0.96051412 1.3166559 -0.034841104 1.0721439
|
||
|
|
496000 1.0284614 1.0149666 -0.0055275607 1.0641449
|
||
|
|
498000 1.0107367 1.0406533 -0.030980028 1.0623882
|
||
|
|
500000 0.9902026 1.2232023 -0.038731213 1.0606073
|
||
|
|
Loop time of 70.5579 on 1 procs for 500000 steps with 800 atoms
|
||
|
|
|
||
|
|
Pair time (%) = 47.4863 (67.3012)
|
||
|
|
Neigh time (%) = 11.1177 (15.7568)
|
||
|
|
Comm time (%) = 1.90226 (2.69603)
|
||
|
|
Outpt time (%) = 0.00377345 (0.00534802)
|
||
|
|
Other time (%) = 10.0479 (14.2406)
|
||
|
|
|
||
|
|
Nlocal: 800 ave 800 max 800 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 260 ave 260 max 260 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 5611 ave 5611 max 5611 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 5611
|
||
|
|
Ave neighs/atom = 7.01375
|
||
|
|
Neighbor list builds = 59311
|
||
|
|
Dangerous builds = 0
|
||
|
|
|
||
|
|
variable eta equal v_v11
|
||
|
|
print "running average viscosity: ${eta}"
|
||
|
|
running average viscosity: 1.06060731864499
|