198 lines
15 KiB
Groff
198 lines
15 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 7
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 32 pad
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variable out_freq string 100
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variable job_name string H2
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units real
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atom_style full
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pair_style table linear 10000
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neighbor 2.0 bin
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neigh_modify every 1 delay 0 check no
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read_data H2.data
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Reading data file ...
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orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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180 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.002 seconds
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pair_coeff 1 * pair.table PAIR_H2
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WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
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WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
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timestep 0.001
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velocity all create 1.0 1985 rot yes dist gaussian
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fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
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thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
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thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
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thermo ${out_freq}
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thermo 100
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#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
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#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
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run 10000
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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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 = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11.55117
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ghost atom cutoff = 11.55117
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binsize = 5.775585, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair table, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
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Step Temp PotEng TotEng Pzz espring T_ring virial
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0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14
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100 0.99396717 -50.292908 -49.762562 16.16754 3.6546345e-06 31.630244 -0.01511026
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200 0.97647843 -50.292785 -49.77177 16.117482 1.4519126e-05 31.073714 -0.030258999
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300 0.94920978 -50.292584 -49.786119 16.040198 3.2307193e-05 30.205965 -0.045469889
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400 0.91451321 -50.292301 -49.804349 15.94486 5.6578376e-05 29.101843 -0.060775514
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500 0.87495051 -50.291935 -49.825092 15.839811 8.6783378e-05 27.84287 -0.07621024
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600 0.83290521 -50.291484 -49.847075 15.733867 0.00012231241 26.504895 -0.091795014
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700 0.79035049 -50.290943 -49.869239 15.633262 0.0001625386 25.150709 -0.10756384
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800 0.74877056 -50.29031 -49.890792 15.542706 0.00020685191 23.827543 -0.12353621
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900 0.70918842 -50.289582 -49.911184 15.465561 0.00025468227 22.567951 -0.13974782
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1000 0.67224667 -50.288756 -49.930069 15.403036 0.00030551305 21.392383 -0.15621567
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1100 0.63830199 -50.287828 -49.947252 15.356514 0.00035888685 20.312188 -0.17298512
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1200 0.60751172 -50.286791 -49.962644 15.325845 0.0004144061 19.332373 -0.19008041
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1300 0.57990404 -50.285641 -49.976225 15.311509 0.00047173031 18.453835 -0.20753645
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1400 0.5554312 -50.284374 -49.988015 15.313263 0.00053057146 17.675055 -0.22539174
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1500 0.53400813 -50.282975 -49.998047 15.33133 0.00059068877 16.993325 -0.24369544
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1600 0.51553984 -50.281444 -50.00637 15.365561 0.00065188331 16.405623 -0.26248285
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1700 0.49994085 -50.279767 -50.013016 15.416271 0.00071399304 15.909229 -0.28182209
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1800 0.48714931 -50.277932 -50.018006 15.48387 0.00077688833 15.502174 -0.30176215
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1900 0.47713797 -50.275928 -50.021344 15.569019 0.00084046832 15.183591 -0.32238808
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2000 0.46992375 -50.273735 -50.023 15.673314 0.00090465799 14.954018 -0.3437631
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2100 0.46557711 -50.271332 -50.022917 15.797801 0.00096940607 14.815698 -0.36598703
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2200 0.46423244 -50.2687 -50.021002 15.944553 0.0010346838 14.772908 -0.38915619
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2300 0.46610038 -50.26581 -50.017115 16.115839 0.0011004847 14.83235 -0.41338963
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2400 0.47148286 -50.262625 -50.011058 16.314677 0.0011668255 15.003632 -0.43882597
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2500 0.48079165 -50.259109 -50.002575 16.545079 0.0012337477 15.299859 -0.46562537
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2600 0.49457102 -50.255212 -49.991327 16.811386 0.0013013219 15.738349 -0.49395245
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2700 0.51352449 -50.250875 -49.976877 17.11979 0.0013696525 16.341491 -0.52401609
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2800 0.53854543 -50.246032 -49.958683 17.477089 0.0014388859 17.137712 -0.55604082
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2900 0.57074936 -50.240596 -49.936064 17.892199 0.0015092207 18.162513 -0.59030618
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3000 0.61150422 -50.234467 -49.90819 18.375616 0.001580922 19.459423 -0.62708735
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3100 0.66245096 -50.227523 -49.874062 18.939819 0.0016543394 21.080662 -0.66672955
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3200 0.72550205 -50.219616 -49.832514 19.60023 0.0017299293 23.087088 -0.70958417
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3300 0.80279929 -50.210579 -49.782233 20.37383 0.0018082826 25.546857 -0.75603924
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3400 0.89660476 -50.200203 -49.721806 21.28012 0.0018901552 28.531956 -0.80651501
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3500 1.0090938 -50.188252 -49.649835 22.340233 0.0019765002 32.111606 -0.86141363
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3600 1.1420183 -50.174459 -49.565118 23.57558 0.0020684981 36.34156 -0.92115194
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3700 1.2962221 -50.158518 -49.466899 25.006266 0.0021675754 41.248667 -0.98609175
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3800 1.4710194 -50.140107 -49.355223 26.648455 0.0022754045 46.811106 -1.0565325
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3900 1.6635051 -50.118886 -49.231298 28.511102 0.0023938687 52.936429 -1.1326688
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4000 1.8679372 -50.094526 -49.097861 30.592386 0.0025249809 59.441913 -1.214555
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4100 2.075405 -50.066723 -48.95936 32.878933 0.0026707445 66.044 -1.3020682
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4200 2.2740293 -50.035234 -48.821891 35.342354 0.0028329538 72.364666 -1.394874
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4300 2.449883 -49.999912 -48.69274 37.94169 0.0030129483 77.96072 -1.4924536
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4400 2.5886538 -49.960721 -48.579506 40.62924 0.0032113484 82.376716 -1.5940701
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4500 2.6778127 -49.917775 -48.488988 43.35421 0.0034278221 85.21395 -1.6987968
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4600 2.7088053 -49.871336 -48.426012 46.071925 0.0036609337 86.200203 -1.8055903
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4700 2.6786752 -49.821807 -48.39256 48.749456 0.0039081229 85.241397 -1.9133555
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4800 2.5906421 -49.769708 -48.387433 51.369043 0.0041658356 82.439989 -2.0209603
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4900 2.4534656 -49.71564 -48.406557 53.929171 0.0044297991 78.074727 -2.1273728
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5000 2.2797967 -49.660246 -48.443826 56.439389 0.0046953978 72.548196 -2.2316692
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5100 2.0839917 -49.60414 -48.492195 58.917167 0.0049580886 66.317246 -2.3330819
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5200 1.8799454 -49.547898 -48.544825 61.38072 0.0052137855 59.824039 -2.4310487
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5300 1.6794028 -49.492001 -48.59593 63.845702 0.0054591569 53.442329 -2.5251887
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5400 1.4910004 -49.436812 -48.641266 66.323664 0.0056917984 47.446947 -2.6153153
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5500 1.3200581 -49.382602 -48.678265 68.81759 0.0059102724 42.007182 -2.7013892
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5600 1.1689597 -49.32954 -48.705824 71.326608 0.0061140319 37.198896 -2.7834961
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5700 1.0378669 -49.277687 -48.723917 73.847293 0.0063032634 33.027232 -2.8618238
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5800 0.92551081 -49.227051 -48.733231 76.373912 0.0064786911 29.451811 -2.9366159
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5900 0.82988009 -49.177354 -48.734559 78.907054 0.0066413821 26.408629 -3.0079862
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6000 0.74872148 -49.128988 -48.729496 81.429069 0.0067925784 23.825981 -3.0765541
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6100 0.6798481 -49.081399 -48.718656 83.949013 0.0069335708 21.634277 -3.1425093
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6200 0.62129621 -49.034965 -48.703463 86.450184 0.0070656124 19.771026 -3.2059256
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6300 0.5713815 -48.989354 -48.684484 88.938306 0.0071898691 18.182629 -3.2671248
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6400 0.52869861 -48.944483 -48.662388 91.411964 0.0073073957 16.824365 -3.326325
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6500 0.49209369 -48.900284 -48.63772 93.869881 0.00741913 15.659515 -3.383704
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6600 0.4606278 -48.85645 -48.610675 96.319181 0.0075258972 14.6582 -3.4393879
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6700 0.4335401 -48.813153 -48.581831 98.754093 0.0076284202 13.796209 -3.4935699
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6800 0.41021495 -48.770575 -48.551698 101.16784 0.0077273325 13.053951 -3.546418
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6900 0.39015391 -48.728202 -48.520029 103.57385 0.0078231904 12.415565 -3.5980989
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7000 0.37295279 -48.686464 -48.487469 105.95986 0.0079164859 11.868187 -3.6485312
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7100 0.35828286 -48.645075 -48.453908 108.33347 0.008007657 11.401357 -3.6979091
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7200 0.34587564 -48.603786 -48.419239 110.70102 0.0080970974 11.006532 -3.7462688
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7300 0.33551045 -48.563011 -48.383994 113.05147 0.0081851643 10.676688 -3.7937749
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7400 0.32700405 -48.5225 -48.348023 115.39114 0.008272185 10.405996 -3.8404567
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7500 0.32020193 -48.481991 -48.311143 117.72756 0.0083584619 10.189537 -3.8863461
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7600 0.31497086 -48.441913 -48.273856 120.0495 0.008444277 10.023073 -3.9315862
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7700 0.31119256 -48.401778 -48.235736 122.37022 0.0085298943 9.9028389 -3.9761586
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7800 0.30875834 -48.362027 -48.197284 124.67777 0.0086155626 9.8253766 -4.020194
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7900 0.30756489 -48.322398 -48.158292 126.9798 0.0087015164 9.7873982 -4.0637137
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8000 0.30751134 -48.282865 -48.118788 129.27742 0.0087879767 9.7856943 -4.1067668
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8100 0.30849789 -48.243167 -48.078563 131.57737 0.0088751511 9.8170884 -4.1492332
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8200 0.31042593 -48.203515 -48.037882 133.87491 0.0089632335 9.8784428 -4.1915847
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8300 0.31319977 -48.163874 -47.996762 136.17056 0.0090524039 9.9667128 -4.2336145
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8400 0.3167294 -48.124228 -47.955232 138.46555 0.0091428273 10.079033 -4.2753558
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8500 0.32093339 -48.084773 -47.913534 140.75426 0.0092346543 10.212814 -4.3167737
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8600 0.32574097 -48.045251 -47.871447 143.04447 0.0093280205 10.365802 -4.3579897
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8700 0.33109202 -48.005633 -47.828974 145.33751 0.0094230472 10.536084 -4.3990428
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8800 0.33693414 -47.965895 -47.786118 147.63516 0.0095198428 10.721993 -4.4399711
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8900 0.34321684 -47.926004 -47.742875 149.9379 0.009618504 10.921922 -4.4808086
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9000 0.34988367 -47.885934 -47.699248 152.24678 0.0097191181 11.134076 -4.5215921
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9100 0.35686443 -47.845658 -47.655247 154.56358 0.0098217652 11.356219 -4.5623394
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9200 0.3640698 -47.805147 -47.610893 156.88915 0.0099265208 11.58551 -4.6030874
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9300 0.37139091 -47.764138 -47.565977 159.23099 0.010033457 11.818484 -4.6439479
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9400 0.37870543 -47.722844 -47.52078 161.5788 0.010142648 12.051248 -4.6846276
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9500 0.38588975 -47.68146 -47.475562 163.93728 0.010254165 12.279869 -4.7255143
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9600 0.39283543 -47.639735 -47.430132 166.30871 0.010368088 12.500896 -4.7664862
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9700 0.39946605 -47.597406 -47.384265 168.70114 0.010484497 12.711897 -4.8075181
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9800 0.40575037 -47.55491 -47.338416 171.10373 0.010603483 12.911878 -4.848721
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9900 0.41170816 -47.511756 -47.292083 173.53055 0.010725141 13.101469 -4.8900195
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10000 0.41740707 -47.468384 -47.245671 175.97095 0.010849577 13.282821 -4.9315123
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Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
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Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
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97.9% 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 | 2.9822 | 2.9822 | 2.9822 | 0.0 | 20.30
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Bond | 0.00090722 | 0.00090722 | 0.00090722 | 0.0 | 0.01
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Neigh | 6.5119 | 6.5119 | 6.5119 | 0.0 | 44.33
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Comm | 0.55377 | 0.55377 | 0.55377 | 0.0 | 3.77
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Output | 0.0024523 | 0.0024523 | 0.0024523 | 0.0 | 0.02
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Modify | 4.5713 | 4.5713 | 4.5713 | 0.0 | 31.12
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Other | | 0.06845 | | | 0.47
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Nlocal: 180 ave 180 max 180 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1510 ave 1510 max 1510 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 13712 ave 13712 max 13712 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 13712
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Ave neighs/atom = 76.177778
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Ave special neighs/atom = 0
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Neighbor list builds = 10000
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Dangerous builds not checked
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Total wall time: 0:00:14
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