forked from lijiext/lammps
387 lines
19 KiB
Plaintext
387 lines
19 KiB
Plaintext
LAMMPS (10 Sep 2013)
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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 0.5999999999999999778
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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 = 2.07097 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 1.0384034 -1.6029204 0 -0.56581499 0.82862864
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8000 1.03126 -1.5776603 0 -0.54768937 1.122187
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10000 1.0159313 -1.6063811 0 -0.59171973 0.9961884
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Loop time of 1.89357 on 1 procs for 10000 steps with 800 atoms
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Pair time (%) = 1.05965 (55.9602)
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Neigh time (%) = 0.227317 (12.0047)
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Comm time (%) = 0.0356276 (1.88151)
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Outpt time (%) = 5.60284e-05 (0.00295888)
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Other time (%) = 0.570923 (30.1506)
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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: 264 ave 264 max 264 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5614 ave 5614 max 5614 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5614
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Ave neighs/atom = 7.0175
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Neighbor list builds = 1103
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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])*33.333333333333328596
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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 = 2.07097 Mbytes
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Step Temp Press Pxy v11
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0 1 0.98664157 0.1056765 0.18612539
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2000 0.95291404 1.199872 0.16190354 6.3622865
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4000 0.97035474 0.95019583 -0.028108952 -0.019331326
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6000 0.99784792 1.0066466 0.0085549073 -0.12148778
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8000 0.99816414 0.90521139 0.00095639386 0.0098644997
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10000 0.9951641 0.96718253 0.090881095 0.50006024
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12000 0.93744355 1.2391514 0.014185646 1.4928658
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14000 1.000559 0.97734913 -0.096964014 1.3899184
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16000 1.002721 1.1185539 0.026144411 1.0983068
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18000 0.96861294 1.0439439 0.090245855 1.4107497
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20000 0.98664185 0.97686008 -0.27549912 1.3394189
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22000 0.97569716 1.0845656 -0.0734503 1.2870138
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24000 0.98609865 1.0625182 -0.01142576 1.0253871
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26000 0.988828 0.99456937 -0.019918137 0.9418664
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28000 0.98671933 0.94373279 -0.21675597 0.94445052
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30000 0.98778176 0.8446134 0.15106071 0.9681741
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32000 0.97606274 1.0297113 -0.15539564 0.91574182
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34000 1.0018246 0.96354339 0.0040827444 0.86638522
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36000 1.0106496 0.78936538 -0.075881707 0.85472064
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38000 1.002101 0.84613466 0.096875042 0.79935874
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40000 0.99674744 1.0228324 0.068840647 0.75555879
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42000 0.98994908 0.96088667 -0.067028764 0.89587645
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44000 0.96432917 1.0396458 -0.14766862 0.98252655
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46000 0.9857594 1.0493731 -0.16618989 0.92998032
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48000 0.99435908 1.0474288 -0.099147004 0.96068255
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50000 0.98424778 1.0498745 -0.02093585 0.91727045
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52000 1.0087964 1.0044041 -0.17322 0.85023294
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54000 0.98865025 0.96826791 -0.0040697022 0.78082036
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56000 0.99830593 0.85271022 -0.0095598719 0.76991826
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58000 1.0067449 0.83099437 -0.0088816687 0.73064231
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60000 0.99157769 0.97115433 0.054722168 0.68728526
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62000 0.98221722 1.0180359 -0.019303097 0.6924154
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64000 1.0107737 0.8729291 0.14432752 0.67840745
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66000 0.98057736 1.147233 -0.15209863 0.6829561
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68000 0.99861459 1.013 0.096201469 0.64354984
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70000 0.99465851 0.99448469 -0.15043327 0.65410181
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72000 0.96494888 1.0879386 0.10533378 0.59884711
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74000 0.98295883 1.0364372 -0.15043121 0.89748148
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76000 1.0006934 1.0423573 -0.019296985 0.96967781
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78000 0.97007774 0.89100292 0.082518797 1.0416848
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80000 0.9673494 1.0862372 0.0059477626 1.0154864
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82000 1.00901 0.91118297 0.11024238 1.0445278
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84000 0.99091853 1.029323 0.064448536 1.0177414
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86000 0.99769204 1.0031789 0.049276808 1.012145
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88000 1.0043966 0.87571549 0.0098902782 1.0258499
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90000 0.98664263 0.95754039 -0.078411226 1.0183036
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92000 0.97082418 1.0007131 -0.16528157 1.0313541
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94000 0.9718415 1.134436 0.13053227 1.0133067
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96000 0.97769459 1.1823894 -0.034238523 0.98394844
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98000 1.0212676 1.0322511 0.019298484 0.98987481
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100000 0.98939854 0.94010891 -0.14270608 0.93622435
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102000 0.99029022 1.032313 -0.084354688 0.9349947
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104000 0.97710114 0.93914663 -0.061639137 0.95912515
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106000 1.0015283 0.94261993 -0.065425987 0.98677831
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108000 1.0277867 0.90869174 0.012240704 0.93883613
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110000 0.99627564 0.96468532 0.016729662 0.92041863
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112000 1.0053403 0.89703815 0.053013062 0.90792399
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114000 1.0061962 0.88630948 0.074929857 0.89048522
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116000 0.95237809 1.0422611 0.03659581 0.90269348
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118000 0.99935668 0.95007176 0.17759824 0.91222275
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120000 0.96695648 1.0439211 0.034405839 0.97878534
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122000 0.97945456 0.99746187 0.0068417 0.97320581
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124000 1.0205146 0.94768233 -0.0059643466 0.97517978
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126000 0.99066371 1.1996852 -0.014932912 0.98986369
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128000 0.98292228 1.0610561 0.045677014 0.99324967
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130000 0.97938306 1.056683 -0.070425405 1.0229877
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132000 0.98907671 1.1401504 0.017589327 1.0266663
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134000 0.97298779 1.0372376 -0.053985765 1.0140165
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136000 1.006034 0.95903957 0.02253597 0.99236069
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138000 0.99107129 0.93393363 0.12735171 0.97191787
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140000 0.97467096 1.1824765 -0.037275252 0.95115537
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142000 0.99599019 0.93770801 -0.0063475745 0.91527534
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144000 0.98928711 1.0100989 -0.14030583 0.92830561
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146000 1.0252234 0.86035265 -0.10246737 0.93782417
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148000 1.014654 0.79624898 0.016043825 0.91183296
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150000 1.0025365 0.94434929 0.061147641 0.91181019
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152000 0.98239056 0.96273739 -0.06423689 0.91302568
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154000 0.99242128 1.0133692 0.054121583 0.90943966
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156000 0.9565225 1.1188086 0.14095454 0.90748691
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158000 0.98447114 1.0678162 0.029354999 0.95922918
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160000 0.99401344 0.88196818 0.035219872 0.95995359
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162000 0.99157731 0.98581187 0.092655892 1.0460888
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164000 0.98700844 1.0628065 -0.097600946 1.0021877
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166000 0.99653656 1.0967715 -0.13363058 1.0272155
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168000 0.97631159 1.0234334 -0.085606659 1.0452207
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170000 1.0037365 0.87168897 -0.05818739 1.1534091
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172000 0.99599564 0.9223394 -0.021708101 1.1079595
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174000 0.95487975 1.1632417 0.07399437 1.0992262
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176000 0.99699032 1.0259118 -0.069297394 1.086451
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178000 0.99794248 0.92978817 -0.036423033 1.0850363
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180000 0.97147417 1.0886532 -0.10560093 1.0831337
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182000 0.9875809 1.1116588 0.074972498 1.1130653
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184000 0.97900449 0.93659533 -0.039279882 1.1189945
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186000 0.9679462 1.2538405 -0.015579462 1.099796
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188000 1.0074452 0.87991578 -0.20476294 1.1007234
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190000 0.97473004 0.98106665 -0.072522838 1.0894785
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192000 0.98717919 0.9718274 0.059062062 1.086273
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194000 1.0030985 0.94066352 0.15646304 1.1914576
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196000 0.98500284 0.96429266 0.11204948 1.1594863
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198000 0.9840631 0.90903459 -0.0053663326 1.1502972
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200000 0.97458345 1.0019506 0.00027337741 1.1410582
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202000 0.98772368 1.0082562 0.0069097265 1.2104792
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204000 0.99875662 0.90609936 -0.024992308 1.2337143
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206000 0.98028117 0.92135146 0.015407324 1.2200096
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208000 0.98909505 0.89346463 -0.13505415 1.2282618
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210000 0.99264762 1.0637228 0.15772329 1.2298716
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212000 1.001344 0.92015447 -0.022356905 1.2175726
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214000 1.0199747 0.92259571 0.012763156 1.2046812
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216000 0.95599898 1.0739248 -0.075513344 1.1935807
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218000 0.99797077 1.0673568 0.049840078 1.1801809
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220000 0.9905579 0.97950128 0.058186552 1.2027082
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222000 0.99177609 1.028659 -0.076396538 1.1782589
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224000 1.0105632 1.0136738 0.039008755 1.1848006
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226000 1.0023731 0.8427875 -0.10734019 1.177471
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228000 0.98752126 0.90957923 -0.050531743 1.3182698
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230000 0.9810267 1.0784386 0.08508881 1.3092904
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232000 1.0021266 0.93921109 -0.18635777 1.2973489
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234000 0.99533025 0.91807335 0.16664865 1.2848923
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236000 0.98011149 0.92896398 0.020234263 1.2941781
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238000 1.0080589 1.0422206 0.080342493 1.2756861
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240000 1.013769 0.91271642 0.10024033 1.2720643
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242000 1.0084395 0.8645878 -0.014896263 1.2473047
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244000 0.96637824 1.0817071 -0.16165169 1.2490751
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246000 0.97629725 1.0768466 0.062453669 1.2348816
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248000 0.97081168 0.95332682 0.09584424 1.2232201
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250000 1.001316 0.90207588 -0.045980098 1.2179401
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252000 1.0107243 0.97832107 -0.14601722 1.2134106
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254000 0.98659744 1.0943909 -0.088294528 1.2333875
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256000 1.0123386 0.99162386 -0.039344985 1.2164364
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258000 0.95762302 1.0676734 0.012199759 1.2076414
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260000 0.99842463 0.99944454 -0.060917216 1.1988621
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262000 0.97766994 1.0286325 -0.10141058 1.2395609
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264000 0.97615582 0.90531751 0.18512981 1.2044769
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266000 0.96241019 1.0566036 0.078113491 1.2005364
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268000 1.0168176 0.81665569 -0.030349244 1.2025997
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270000 0.99827104 1.0749573 -0.056801916 1.1962529
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272000 0.9968558 0.94529972 0.028725191 1.1828897
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274000 0.97566641 0.91457261 0.015049168 1.1902579
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276000 0.99070015 0.94576384 0.025755724 1.1896323
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278000 0.96895102 1.0397797 0.080651494 1.1763571
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280000 1.0072996 0.89570696 -0.15542961 1.1652696
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282000 1.0144016 0.77288242 -0.029784437 1.1582708
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284000 1.0181351 0.7694665 -0.054640099 1.1544617
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286000 0.98291392 0.9938831 -0.0062479011 1.1596522
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288000 0.97279582 1.0358224 -0.13401081 1.1505486
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290000 0.99909636 1.0213079 -0.0012162009 1.1399725
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292000 0.98460352 0.94742548 -0.031343507 1.1581955
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294000 0.99038521 0.98665849 0.051955637 1.1524198
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296000 0.99556533 0.86180797 0.055142099 1.1523058
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298000 0.97636077 0.98781403 0.013204553 1.129189
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300000 0.97032776 1.0678134 0.11879155 1.1176141
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302000 1.0003067 0.87686391 0.023979249 1.1210971
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304000 1.0209877 0.82384059 -0.019162225 1.1201332
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306000 0.98495148 0.97853853 0.0067884582 1.1146556
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308000 1.0080456 0.89962394 -0.039014939 1.1072495
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310000 0.98760314 1.0580182 -0.0084950963 1.1128641
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312000 1.0163132 0.743878 -0.13381063 1.1072529
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314000 0.97482482 0.93981262 0.1188583 1.1113744
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316000 0.99642196 0.92559157 -0.076386258 1.1180406
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318000 0.98668334 0.9960588 0.051851225 1.1282305
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320000 1.018361 0.82279734 -0.033370883 1.1306313
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322000 1.0101361 0.79697655 -0.0097104031 1.1269227
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324000 0.98374012 0.89538164 0.072387631 1.1184602
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326000 1.0005728 0.81698596 -0.097827025 1.1067008
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328000 0.98296796 1.0888354 -0.00019150727 1.1026196
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330000 0.97244323 1.1015085 0.047308269 1.0967215
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332000 0.99301221 1.0908167 -0.12434045 1.0911357
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334000 0.99279827 1.0192878 -0.030977699 1.0804029
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336000 0.98580679 1.055276 0.11288823 1.0750277
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338000 0.98757346 1.0072102 0.10201237 1.0933627
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340000 1.0067327 0.87701361 0.067382458 1.0850067
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342000 1.0154351 0.94291159 0.070059816 1.0801363
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344000 0.9743083 1.1059353 0.066961003 1.1524185
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346000 0.99814584 1.0356474 -0.016510209 1.1432772
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348000 0.97641572 1.1686199 0.046528576 1.1496039
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350000 0.99518846 1.0517486 0.13448583 1.1381818
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352000 0.98588655 0.98536282 -0.060862396 1.1294455
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354000 0.96615995 1.1110151 0.083719861 1.1256268
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356000 1.0078606 0.78439358 -0.10603102 1.1362455
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358000 0.99367549 1.0489552 0.07500459 1.1427616
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360000 0.98811261 1.0329632 0.02037644 1.1456498
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362000 0.99543973 0.89319851 0.071618522 1.1516636
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364000 0.98165417 0.88412777 0.01496297 1.1479466
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366000 0.97321522 1.1989343 0.12226461 1.1407247
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368000 0.98226259 0.98513508 -0.032773905 1.145514
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370000 0.98523554 0.99191598 0.048321875 1.1454723
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372000 0.99757543 1.0704533 -0.044499362 1.1397563
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374000 0.96826544 1.0155716 0.10537727 1.1380956
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376000 0.97764036 0.91461704 -0.0071326471 1.1311759
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378000 0.96197183 1.2654546 0.063772824 1.1342523
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380000 0.9563135 0.92013089 0.14946354 1.122797
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382000 0.99157671 1.1416454 -0.0020281283 1.1146792
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384000 0.99439496 1.0461009 -0.095485509 1.1101174
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386000 0.9964491 0.96726205 -0.096570092 1.1043801
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388000 0.98660387 0.92002862 -0.050238768 1.1028544
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390000 0.97619357 0.95568771 -0.0093958893 1.0994103
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392000 0.97043698 1.1278757 0.078765507 1.1095933
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394000 0.97478556 0.93908482 0.010033169 1.0896552
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|
396000 0.98483138 0.88172231 -0.0092943479 1.0731932
|
|
398000 0.99224177 0.84195437 -0.0059744644 1.0682901
|
|
400000 1.0140238 0.88969569 -0.14294787 1.0626823
|
|
402000 0.98939257 0.91691411 0.0064466276 1.0892164
|
|
404000 0.9930004 0.91196344 -0.15724573 1.0852194
|
|
406000 0.98184881 0.93556127 -0.030604809 1.0779626
|
|
408000 1.0097979 0.97009028 -0.011737511 1.0779471
|
|
410000 0.9913927 0.9406984 0.00091540813 1.0902918
|
|
412000 0.95799086 1.1298786 -0.03512312 1.1138864
|
|
414000 1.0089501 0.84475916 0.13645298 1.1142398
|
|
416000 0.9897256 0.98316262 0.010485716 1.1164657
|
|
418000 1.0133333 0.86050241 0.055260598 1.1048567
|
|
420000 0.97407581 0.97216618 0.098782939 1.1125666
|
|
422000 1.0009494 0.88470049 0.038139624 1.1163397
|
|
424000 0.97321563 1.1466493 -0.086272829 1.1173945
|
|
426000 0.96442304 1.0810966 -0.061944411 1.1068751
|
|
428000 0.9982547 0.87602547 0.081196445 1.1070854
|
|
430000 0.97915448 1.1485682 -0.065531916 1.1259179
|
|
432000 0.96422041 1.1298461 -0.0082763069 1.1175144
|
|
434000 0.99510123 1.0224406 -0.11423626 1.1160931
|
|
436000 1.0240236 0.88695443 0.0075708194 1.1085978
|
|
438000 0.99001944 1.0244717 0.075879487 1.1212094
|
|
440000 1.0116423 0.89412767 -0.11768379 1.1190682
|
|
442000 0.98993631 0.92631483 0.067324168 1.111235
|
|
444000 0.95107091 1.1508927 0.0019160629 1.1098578
|
|
446000 0.98621381 0.91043895 -0.061521131 1.1148618
|
|
448000 0.97695569 1.177126 -0.05322695 1.1104409
|
|
450000 0.99066051 0.99745105 0.080431605 1.1058023
|
|
452000 1.0146071 0.95227428 0.007801217 1.1249178
|
|
454000 0.99162513 0.96925579 -0.036153968 1.1100001
|
|
456000 1.0215781 0.88427275 -0.050979723 1.1071667
|
|
458000 0.98021089 0.84902388 0.08620799 1.1003492
|
|
460000 0.98981752 1.0990911 0.047765387 1.1091971
|
|
462000 0.97418524 1.023144 -0.11243577 1.101482
|
|
464000 0.98172755 1.0676962 0.065603574 1.0966983
|
|
466000 0.99352242 0.88377489 0.11849997 1.0934089
|
|
468000 0.9916114 0.9404547 0.041191002 1.0843991
|
|
470000 0.9675487 1.0416201 0.038992075 1.0909162
|
|
472000 0.97960188 1.0249638 0.1102279 1.087763
|
|
474000 0.97114134 1.1160983 0.046857123 1.0919439
|
|
476000 0.99567674 0.93675154 -0.06832563 1.0879316
|
|
478000 0.9784867 1.0660872 0.0030176417 1.0834439
|
|
480000 0.99936399 0.97607692 0.096835801 1.0780983
|
|
482000 1.0274496 0.87081314 0.054818419 1.0724507
|
|
484000 0.97139265 1.0730706 -0.12345378 1.0754362
|
|
486000 0.97408298 0.99765268 -0.0064488819 1.0691212
|
|
488000 0.9873109 1.0488011 0.001679366 1.0680362
|
|
490000 1.0289514 0.77625996 -0.090952895 1.0799008
|
|
492000 0.98122494 0.97560083 0.068756789 1.0746541
|
|
494000 1.0009648 1.0046735 0.013556863 1.074882
|
|
496000 0.96262432 0.94043431 -0.1359217 1.078487
|
|
498000 1.00248 1.1101056 -0.065062628 1.0774483
|
|
500000 0.964375 1.1119972 0.062483884 1.0744491
|
|
Loop time of 78.4755 on 1 procs for 500000 steps with 800 atoms
|
|
|
|
Pair time (%) = 54.1325 (68.9801)
|
|
Neigh time (%) = 12.1352 (15.4637)
|
|
Comm time (%) = 1.85499 (2.36378)
|
|
Outpt time (%) = 0.00424814 (0.00541334)
|
|
Other time (%) = 10.3486 (13.1871)
|
|
|
|
Nlocal: 800 ave 800 max 800 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 267 ave 267 max 267 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 5583 ave 5583 max 5583 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 5583
|
|
Ave neighs/atom = 6.97875
|
|
Neighbor list builds = 58699
|
|
Dangerous builds = 0
|
|
|
|
variable eta equal v_v11
|
|
print "running average viscosity: ${eta}"
|
|
running average viscosity: 1.0744491378557243788
|