198 lines
15 KiB
Groff
198 lines
15 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 1
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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 = 0.003 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 1.0008585 -50.292908 -49.758885 16.189586 7.3078196e-06 4.6642574 -0.013945396
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200 1.0034473 -50.292787 -49.757382 16.20341 2.9015288e-05 4.6763219 -0.027851725
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300 1.0078065 -50.292593 -49.754863 16.225711 6.4500006e-05 4.6966366 -0.041662754
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400 1.0140035 -50.29233 -49.751293 16.257176 0.00011280318 4.7255165 -0.055352542
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500 1.022135 -50.292004 -49.746629 16.297097 0.000172727 4.7634112 -0.068879202
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600 1.0323282 -50.291621 -49.740807 16.346105 0.00024293886 4.810914 -0.082221014
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700 1.044744 -50.291188 -49.733749 16.404167 0.00032206529 4.8687751 -0.095360512
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800 1.0595808 -50.290712 -49.725357 16.471712 0.00040876559 4.9379182 -0.10826526
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900 1.0770788 -50.290199 -49.715507 16.549069 0.00050178229 5.0194635 -0.1209272
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1000 1.0975268 -50.289655 -49.704053 16.636751 0.00059997025 5.1147563 -0.13335203
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1100 1.1212697 -50.289087 -49.690817 16.735749 0.00070230922 5.2254045 -0.14552504
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1200 1.1487191 -50.288499 -49.675582 16.846901 0.00080790454 5.3533259 -0.15745048
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1300 1.1803661 -50.287894 -49.658092 16.971484 0.00091598038 5.5008089 -0.16912662
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1400 1.2167975 -50.287272 -49.638032 17.111786 0.001025869 5.6705884 -0.18056175
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1500 1.2587169 -50.286644 -49.615037 17.26922 0.0011369979 5.8659438 -0.19176702
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1600 1.3069713 -50.286008 -49.588654 17.446637 0.0012488773 6.0908216 -0.20274823
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1700 1.3625842 -50.285365 -49.558338 17.646978 0.0013610874 6.349992 -0.21351296
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1800 1.4267987 -50.284719 -49.523429 17.874056 0.0014732674 6.6492481 -0.2240754
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1900 1.5011316 -50.284073 -49.483122 18.132347 0.0015851058 6.9956586 -0.23443788
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2000 1.5874426 -50.283426 -49.436422 18.428012 0.0016963317 7.3978897 -0.24461477
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2100 1.6880217 -50.282783 -49.382113 18.767914 0.0018067084 7.866614 -0.25461336
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2200 1.805701 -50.282144 -49.318685 19.160875 0.0019160281 8.4150298 -0.26443254
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2300 1.9439951 -50.281509 -49.244262 19.617751 0.0020241086 9.0595157 -0.27408815
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2400 2.1072772 -50.280879 -49.15651 20.152728 0.0021307926 9.8204522 -0.28357876
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2500 2.3009976 -50.28026 -49.052528 20.78256 0.0022359485 10.723239 -0.29290505
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2600 2.5319494 -50.279651 -48.928691 21.528586 0.0023394759 11.799534 -0.30206821
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2700 2.8085834 -50.279048 -48.780486 22.417919 0.0024413142 13.088719 -0.31106836
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2800 3.1413661 -50.278457 -48.602334 23.483643 0.0025414581 14.639572 -0.31990395
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2900 3.5431594 -50.277876 -48.38737 24.766603 0.0026399801 16.512032 -0.32855403
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3000 4.029577 -50.277305 -48.127264 26.316279 0.0027370628 18.778862 -0.33702346
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3100 4.6192292 -50.276739 -47.81208 28.192254 0.0028330445 21.526793 -0.3452905
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3200 5.333716 -50.276174 -47.43029 30.464107 0.0029284791 24.856485 -0.35332773
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3300 6.1971481 -50.275605 -46.969024 33.208128 0.0030242128 28.8803 -0.36114465
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3400 7.2349012 -50.27502 -46.41473 36.506582 0.0031214781 33.716495 -0.36868512
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3500 8.4712457 -50.274401 -45.754441 40.437918 0.0032219998 39.478178 -0.37595678
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3600 9.9255066 -50.273728 -44.977825 45.065017 0.0033281047 46.255407 -0.38292345
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3700 11.606561 -50.27297 -44.080116 50.41841 0.0034428151 54.089554 -0.38955061
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3800 13.505865 -50.272095 -43.065838 56.472981 0.0035698989 62.940797 -0.39583139
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3900 15.589837 -50.271059 -41.952868 63.125206 0.0037138374 72.652639 -0.40173444
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4000 17.793286 -50.26982 -40.775945 70.171007 0.0038796665 82.921278 -0.40724146
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4100 20.016352 -50.26833 -39.588305 77.297059 0.0040726574 93.281337 -0.350557
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4200 22.127692 -50.266548 -38.459986 84.091411 0.0042978175 103.12072 -0.42427987
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4300 23.975875 -50.264442 -37.471754 90.07826 0.0045592402 111.73373 -0.44332019
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4400 25.408871 -50.262001 -36.704717 94.780152 0.0048593802 118.41186 -0.4712594
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4500 26.298516 -50.259233 -36.227265 97.796601 0.0051983826 122.55783 -0.48751932
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4600 26.564146 -50.256176 -36.082477 98.874143 0.0055736202 123.79574 -0.50751557
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4700 26.188683 -50.252888 -36.279523 97.96053 0.0059795748 122.04598 -0.53463961
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4800 25.22218 -50.249455 -36.791783 95.211762 0.0064081371 117.54183 -0.56057187
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4900 23.771743 -50.245971 -37.562201 90.960801 0.0068493041 110.78242 -0.58649549
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5000 21.981009 -50.242542 -38.514245 85.651619 0.0072921623 102.43714 -0.58569676
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5100 20.005118 -50.239262 -39.565231 79.762203 0.0077259803 93.228984 -0.58814947
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5200 17.987555 -50.236217 -40.638687 73.732022 0.0081412203 83.826622 -0.64456631
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5300 16.043551 -50.23346 -41.673183 67.91308 0.0085303062 74.767062 -0.66253179
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5400 14.252123 -50.231042 -42.626609 62.542995 0.0088880521 66.418547 -0.67647833
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5500 12.656267 -50.228973 -43.476032 57.750687 0.0092117291 58.981452 -0.69035428
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5600 11.269006 -50.227253 -44.214506 53.573237 0.0095008225 52.516458 -0.70182381
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5700 10.082247 -50.225863 -44.846329 49.983875 0.0097565822 46.985857 -0.71107461
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5800 9.075711 -50.224777 -45.382295 46.920816 0.0099814848 42.295142 -0.72796918
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5900 8.2241323 -50.223954 -45.835845 44.308503 0.010178713 38.326566 -0.7341011
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6000 7.5020778 -50.223364 -46.220518 42.071534 0.010351726 34.961607 -0.73860614
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6100 6.8865776 -50.222972 -46.548535 40.142111 0.010503944 32.093218 -0.74169302
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6200 6.3581625 -50.222743 -46.83025 38.464555 0.010638555 29.630669 -0.74355815
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6300 5.9009471 -50.222651 -47.074112 36.993223 0.010758413 27.499927 -0.72351831
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6400 5.5022478 -50.222668 -47.286861 35.692229 0.010866003 25.641886 -0.72491142
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6500 5.1520445 -50.222775 -47.473825 34.533075 0.010963451 24.009849 -0.72550196
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6600 4.842444 -50.222956 -47.639197 33.493966 0.011052555 22.567032 -0.72539576
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6700 4.5672154 -50.223194 -47.786287 32.557859 0.011134828 21.284396 -0.72468094
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6800 4.3214112 -50.22348 -47.917726 31.710288 0.011211542 20.138885 -0.69977477
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6900 4.1010719 -50.223805 -48.035616 30.941022 0.011283771 19.112047 -0.6977173
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7000 3.9029992 -50.224161 -48.141657 30.240625 0.011352422 18.188977 -0.69521625
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7100 3.7245829 -50.22454 -48.237233 29.602229 0.011418274 17.357512 -0.69232721
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7200 3.5636708 -50.224941 -48.323491 29.019374 0.011482 16.60762 -0.68909561
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7300 3.4184697 -50.225359 -48.401383 28.487117 0.011544187 15.930946 -0.68553322
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7400 3.2874703 -50.225791 -48.471712 28.00136 0.011605358 15.320455 -0.68167743
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7500 3.1693898 -50.226236 -48.53516 27.5579 0.01166598 14.77017 -0.67389187
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7600 3.0631284 -50.226689 -48.592311 27.15399 0.011726479 14.274964 -0.66987688
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7700 2.9677349 -50.227151 -48.643671 26.786563 0.011787244 13.830406 -0.66561073
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7800 2.8823804 -50.227616 -48.689679 26.453373 0.011848631 13.432632 -0.66110134
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7900 2.8063371 -50.228091 -48.730728 26.151709 0.011910973 13.078251 -0.65637083
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8000 2.7389612 -50.228567 -48.767153 25.879876 0.011974573 12.764262 -0.65142182
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8100 2.6796793 -50.229048 -48.799265 25.636155 0.01203971 12.487993 -0.64626697
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8200 2.6279769 -50.229528 -48.827332 25.418653 0.012106636 12.247046 -0.64092634
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8300 2.583388 -50.230009 -48.851603 25.225967 0.012175578 12.039251 -0.63576886
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8400 2.5454874 -50.230488 -48.872305 25.056681 0.012246734 11.862624 -0.63004687
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8500 2.5138825 -50.230965 -48.889645 24.909342 0.012320275 11.715337 -0.62413585
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8600 2.4882074 -50.231439 -48.903818 24.782526 0.012396346 11.595685 -0.65229004
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8700 2.468117 -50.231904 -48.915003 24.674923 0.012475068 11.502059 -0.64624002
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8800 2.4532823 -50.232364 -48.923378 24.585268 0.012556541 11.432925 -0.6399876
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8900 2.4433865 -50.232811 -48.929106 24.512562 0.012640854 11.386808 -0.63354
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9000 2.4381226 -50.233249 -48.932352 24.45498 0.012728083 11.362277 -0.62690844
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9100 2.4371917 -50.233668 -48.933268 24.411953 0.012818306 11.357939 -0.62009589
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9200 2.4403031 -50.234074 -48.932014 24.381442 0.012911605 11.372438 -0.61311776
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9300 2.4471754 -50.234458 -48.928731 24.362769 0.013008072 11.404465 -0.60599097
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9400 2.4575396 -50.234822 -48.923565 24.354135 0.013107819 11.452765 -0.60061336
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9500 2.4711435 -50.235157 -48.916642 24.354998 0.013210974 11.516163 -0.59323525
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9600 2.4877569 -50.235465 -48.908085 24.363855 0.013317688 11.593585 -0.58576008
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9700 2.5071778 -50.235743 -48.898 24.380012 0.013428136 11.684092 -0.57821051
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9800 2.5292388 -50.235983 -48.886469 24.402788 0.013542514 11.786902 -0.57061067
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9900 2.5538131 -50.236185 -48.873559 24.431609 0.013661041 11.901424 -0.56299206
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10000 2.5808184 -50.236346 -48.859312 24.466316 0.013783954 12.027276 -0.55538687
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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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98.6% 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 | 2.8924 | 2.8924 | 2.8924 | 0.0 | 19.69
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Bond | 0.00092288 | 0.00092288 | 0.00092288 | 0.0 | 0.01
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Neigh | 6.5718 | 6.5718 | 6.5718 | 0.0 | 44.73
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Comm | 0.55162 | 0.55162 | 0.55162 | 0.0 | 3.75
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Output | 0.0029431 | 0.0029431 | 0.0029431 | 0.0 | 0.02
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Modify | 4.6104 | 4.6104 | 4.6104 | 0.0 | 31.38
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Other | | 0.06102 | | | 0.42
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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: 13680 ave 13680 max 13680 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 13680
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Ave neighs/atom = 76
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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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