198 lines
15 KiB
Groff
198 lines
15 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 3
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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 0.99799183 -50.292972 -49.760479 16.176371 6.2763683e-07 15.879159 -0.0023935093
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200 0.99208279 -50.292959 -49.763618 16.157336 2.500618e-06 15.785139 -0.0047805057
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300 0.98260503 -50.292946 -49.768662 16.126279 5.5906177e-06 15.634338 -0.0071546335
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400 0.97006821 -50.292934 -49.775339 16.085102 9.8548762e-06 15.434863 -0.0095106986
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500 0.955104 -50.292922 -49.783311 16.036202 1.5241599e-05 15.196766 -0.011844212
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600 0.93840578 -50.292908 -49.792208 15.982141 2.1695575e-05 14.931079 -0.014152859
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700 0.92067359 -50.292894 -49.801655 15.925466 2.9163075e-05 14.64894 -0.016435757
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800 0.90257158 -50.292879 -49.811298 15.868564 3.7595562e-05 14.360917 -0.018694156
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900 0.88470062 -50.292862 -49.820817 15.813472 4.6952156e-05 14.07657 -0.020928907
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1000 0.8675856 -50.292845 -49.829932 15.761951 5.7201072e-05 13.804251 -0.02314186
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1100 0.85167476 -50.292826 -49.838402 15.715517 6.8320318e-05 13.551092 -0.025333843
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1200 0.83734746 -50.292806 -49.846027 15.675218 8.0297954e-05 13.323129 -0.027508552
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1300 0.8249274 -50.292785 -49.852632 15.642038 9.3132154e-05 13.125512 -0.0296698
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1400 0.81469844 -50.292762 -49.858068 15.616792 0.00010683122 12.962757 -0.031821941
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1500 0.80692178 -50.292739 -49.862194 15.600226 0.00012141373 12.839022 -0.033969494
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1600 0.80185336 -50.292715 -49.864874 15.593117 0.0001369088 12.758378 -0.03611606
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1700 0.79976156 -50.29269 -49.865965 15.596227 0.00015335664 12.725095 -0.038264652
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1800 0.80094541 -50.292664 -49.865307 15.610404 0.00017080942 12.743931 -0.040416801
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1900 0.80575383 -50.292637 -49.862715 15.636702 0.00018933238 12.820439 -0.042573524
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2000 0.81460711 -50.292611 -49.857965 15.67644 0.00020900552 12.961304 -0.044736822
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2100 0.82802133 -50.292583 -49.85078 15.731301 0.0002299256 13.174739 -0.046906382
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2200 0.84663738 -50.292556 -49.84082 15.80341 0.00025220879 13.470941 -0.049081478
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2300 0.87125571 -50.292527 -49.827656 15.895377 0.00027599404 13.862646 -0.051261652
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2400 0.90287869 -50.292499 -49.810754 16.010541 0.00030144708 14.365803 -0.053443791
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2500 0.94276179 -50.29247 -49.789446 16.15309 0.00032876555 15.000388 -0.055625674
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2600 0.99247509 -50.292441 -49.762891 16.328426 0.00035818508 15.791381 -0.05780423
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2700 1.0539754 -50.292412 -49.730048 16.543118 0.00038998665 16.76992 -0.059974442
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2800 1.1296876 -50.292383 -49.689621 16.805367 0.00042450539 17.974586 -0.062128128
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2900 1.2225906 -50.292352 -49.640021 17.125302 0.00046214072 19.452774 -0.064255792
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3000 1.3362969 -50.292321 -49.57932 17.515126 0.000503368 21.261968 -0.066348705
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3100 1.4751081 -50.292289 -49.505223 17.989435 0.0005487512 23.47061 -0.068394944
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3200 1.6440125 -50.292255 -49.415068 18.56525 0.00059895625 26.158066 -0.070379528
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3300 1.8485766 -50.292217 -49.305881 19.26156 0.00065476359 29.412908 -0.0722905
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3400 2.0946636 -50.292172 -49.174533 20.098518 0.0007170785 33.328425 -0.070298499
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3500 2.3878963 -50.292118 -49.01802 21.095116 0.00078693603 37.994084 -0.072718799
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3600 2.7327825 -50.29205 -48.833933 22.267046 0.00086549715 43.481606 -0.071117313
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3700 3.1314509 -50.291962 -48.621129 23.621508 0.00095403112 49.824863 -0.073902505
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3800 3.5820285 -50.29185 -48.380605 25.151938 0.0010538788 56.994053 -0.082019029
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3900 4.0768347 -50.291704 -48.116448 26.832847 0.0011663922 64.86697 -0.093365693
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4000 4.6007622 -50.291519 -47.836714 28.612446 0.0012928467 73.203239 -0.10732489
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4100 5.1304133 -50.29129 -47.553881 30.411364 0.0014343275 81.630577 -0.1197723
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4200 5.6346502 -50.291011 -47.284558 32.123915 0.0015915962 89.653545 -0.13080997
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4300 6.0770777 -50.290676 -47.04816 33.627475 0.0017649532 96.693059 -0.14165463
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4400 6.4205234 -50.29029 -46.864523 34.796349 0.0019541156 102.15766 -0.15242678
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4500 6.6328782 -50.28986 -46.750789 35.522716 0.0021581361 105.53646 -0.16280564
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4600 6.692974 -50.289399 -46.718262 35.736356 0.0023753855 106.49265 -0.17244062
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4700 6.5948627 -50.28892 -46.770133 35.418562 0.0026036121 104.93159 -0.18097864
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4800 6.3491738 -50.288443 -46.900746 34.606797 0.0028400768 101.02241 -0.18808564
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4900 5.981108 -50.287983 -47.096673 33.387033 0.0030817487 95.166073 -0.19348598
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5000 5.5256727 -50.287549 -47.339243 31.878041 0.0033255323 87.919593 -0.19697013
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5100 5.0215378 -50.287155 -47.607839 30.209726 0.0035684934 79.898246 -0.19841014
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5200 4.5051017 -50.286803 -47.883038 28.504102 0.0038080527 71.681174 -0.19776394
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5300 4.0060458 -50.286489 -48.149003 26.860164 0.0040421233 63.74064 -0.19507702
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5400 3.5450327 -50.286205 -48.394699 25.34642 0.0042691817 56.405409 -0.17980245
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5500 3.1335349 -50.28594 -48.613996 23.999815 0.0044882701 49.858022 -0.17499889
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5600 2.7752591 -50.28568 -48.804899 22.832197 0.0046989433 44.157456 -0.1804676
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5700 2.468384 -50.285415 -48.968371 21.836436 0.0049011768 39.274732 -0.17203381
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5800 2.2078676 -50.285131 -49.10709 20.994608 0.0050952576 35.129626 -0.17967923
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5900 1.9873283 -50.284819 -49.22445 20.285865 0.0052816779 31.620602 -0.18651596
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6000 1.8003086 -50.284474 -49.323892 19.687668 0.0054610429 28.64491 -0.19262321
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6100 1.640963 -50.284092 -49.408531 19.181029 0.0056340011 26.109545 -0.1982684
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6200 1.50433 -50.283675 -49.481017 18.749125 0.0058011964 23.935562 -0.19911595
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6300 1.3863531 -50.283219 -49.543509 18.379087 0.0059632392 22.058419 -0.20020649
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6400 1.2837837 -50.28273 -49.597748 18.059898 0.0061206908 20.426426 -0.20439271
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6500 1.1940433 -50.282206 -49.645106 17.783505 0.0062740588 18.998556 -0.19989782
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6600 1.1150882 -50.281655 -49.686683 17.543117 0.0064237975 17.742293 -0.20427813
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6700 1.0452925 -50.281076 -49.723345 17.333683 0.0065703119 16.631765 -0.20875566
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6800 0.98335363 -50.28048 -49.755796 17.150648 0.0067139628 15.646249 -0.21165511
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6900 0.92821916 -50.279858 -49.784593 16.991122 0.0068550735 14.768998 -0.21447191
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7000 0.87903062 -50.279219 -49.810199 16.85215 0.0069939349 13.986354 -0.21690274
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7100 0.83508106 -50.27857 -49.833 16.730809 0.0071308114 13.287068 -0.21879935
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7200 0.79578318 -50.277905 -49.853302 16.625931 0.007265945 12.661795 -0.24086146
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7300 0.76064516 -50.277227 -49.871373 16.535639 0.0073995599 12.10271 -0.24389998
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7400 0.72925259 -50.27654 -49.887437 16.458538 0.0075318653 11.603219 -0.24724178
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7500 0.70125479 -50.275848 -49.901683 16.39318 0.0076630586 11.157743 -0.24974257
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7600 0.67635448 -50.275145 -49.914266 16.338958 0.0077933274 10.761551 -0.26938357
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7700 0.65430014 -50.274434 -49.925322 16.294582 0.0079228516 10.410642 -0.27182741
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7800 0.63488023 -50.273717 -49.934967 16.259573 0.0080518043 10.10165 -0.27327965
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7900 0.61791898 -50.272993 -49.943293 16.233056 0.0081803536 9.8317776 -0.23270163
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8000 0.60327334 -50.272261 -49.950375 16.214226 0.0083086629 9.5987492 -0.21174158
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8100 0.59083054 -50.271521 -49.956274 16.203107 0.008436892 9.4007703 -0.20591477
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8200 0.580506 -50.270774 -49.961036 16.198733 0.0085651973 9.2364955 -0.20633623
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8300 0.57224102 -50.270016 -49.964688 16.201153 0.0086937323 9.1049904 -0.21200577
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8400 0.56599941 -50.26925 -49.967252 16.209734 0.0088226478 9.0056795 -0.21499276
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8500 0.56176264 -50.268474 -49.968737 16.224404 0.0089520921 8.9382678 -0.22565885
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8600 0.55952259 -50.267687 -49.969145 16.244765 0.0090822109 8.9026261 -0.23453558
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8700 0.55927158 -50.26689 -49.968482 16.270388 0.0092131476 8.8986323 -0.23126478
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8800 0.56098987 -50.266078 -49.966754 16.301455 0.009345043 8.9259722 -0.23759225
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8900 0.56463156 -50.265253 -49.963985 16.338219 0.0094780352 8.9839155 -0.25830691
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9000 0.57011105 -50.264414 -49.960222 16.379852 0.0096122592 9.0711003 -0.24455142
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9100 0.57729304 -50.263559 -49.955536 16.42695 0.0097478463 9.1853737 -0.25035816
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9200 0.5859895 -50.262689 -49.950026 16.479216 0.0098849239 9.3237441 -0.2560083
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9300 0.59596674 -50.261803 -49.943816 16.536984 0.010023615 9.482493 -0.26141076
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9400 0.60696386 -50.2609 -49.937045 16.600194 0.010164037 9.6574694 -0.26654733
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9500 0.61872142 -50.259982 -49.929854 16.669166 0.010306303 9.8445453 -0.2741745
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9600 0.63101587 -50.259043 -49.922355 16.744325 0.010450522 10.040164 -0.27940426
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9700 0.64369292 -50.258089 -49.914637 16.82549 0.010596798 10.24187 -0.28435931
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9800 0.65669202 -50.257118 -49.906731 16.913131 0.010745233 10.4487 -0.28904477
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9900 0.67005575 -50.256133 -49.898615 17.007446 0.01089593 10.661331 -0.29344272
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10000 0.68392108 -50.25513 -49.890213 17.108905 0.011048996 10.881944 -0.29755711
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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 | 2.8325 | 2.8325 | 2.8325 | 0.0 | 19.28
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Bond | 0.0010203 | 0.0010203 | 0.0010203 | 0.0 | 0.01
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Neigh | 6.5808 | 6.5808 | 6.5808 | 0.0 | 44.80
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Comm | 0.55003 | 0.55003 | 0.55003 | 0.0 | 3.74
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Output | 0.0030145 | 0.0030145 | 0.0030145 | 0.0 | 0.02
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Modify | 4.6599 | 4.6599 | 4.6599 | 0.0 | 31.72
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Other | | 0.06363 | | | 0.43
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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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