200 lines
15 KiB
Plaintext
200 lines
15 KiB
Plaintext
LAMMPS (8 Feb 2023)
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Processor partition = 0
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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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Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.0510430e-01 (kcal/mol/A^2)
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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 2.4190752e-312 4.331435e-14
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100 1.0017926 -50.292812 -49.758291 16.197861 4.265072e-05 0.99622709 -0.027624534
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200 1.0071966 -50.292414 -49.755009 16.235286 0.00017002327 1.0016011 -0.055248299
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300 1.0162913 -50.291757 -49.7495 16.297361 0.00038044032 1.0106453 -0.082873452
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400 1.0292116 -50.290849 -49.741697 16.38451 0.00067129747 1.0234938 -0.11047807
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500 1.046152 -50.289692 -49.731502 16.497053 0.0010393068 1.0403401 -0.13806207
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600 1.0673727 -50.288298 -49.718785 16.634959 0.0014807685 1.0614428 -0.16561253
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700 1.0932075 -50.286675 -49.703378 16.798983 0.0019918311 1.0871342 -0.19314289
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800 1.1240754 -50.284828 -49.68506 16.990234 0.0025687136 1.1178306 -0.22065895
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900 1.1604938 -50.28276 -49.663562 17.210179 0.0032078786 1.1540466 -0.24818038
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1000 1.2030968 -50.280481 -49.638551 17.460167 0.0039061562 1.196413 -0.27572028
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1100 1.2526583 -50.277991 -49.609616 17.742341 0.0046608267 1.2456991 -0.30331246
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1200 1.3101204 -50.275294 -49.576259 18.059364 0.0054696709 1.3028419 -0.33099732
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1300 1.3766308 -50.272386 -49.537864 18.415203 0.0063309999 1.3689828 -0.35880748
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1400 1.4535894 -50.269262 -49.493677 18.814095 0.007243672 1.4455139 -0.38678366
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1500 1.5427084 -50.265919 -49.442783 19.261431 0.0082071044 1.5341378 -0.41499269
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1600 1.6460882 -50.262344 -49.384049 19.763852 0.0092212862 1.6369433 -0.44348166
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1700 1.7663158 -50.25853 -49.316086 20.329991 0.010286796 1.756503 -0.47232409
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1800 1.9065905 -50.254461 -49.237171 20.96974 0.01140483 1.8959983 -0.50158483
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1900 2.0708856 -50.250115 -49.145163 21.696809 0.012577241 2.0593807 -0.53134846
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2000 2.2641571 -50.245477 -49.037402 22.525956 0.013806592 2.2515785 -0.5617101
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2100 2.4926123 -50.240516 -48.910546 23.477847 0.015096239 2.4787644 -0.59276642
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2200 2.7640541 -50.2352 -48.760398 24.577541 0.01645042 2.7486983 -0.62463764
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2300 3.088323 -50.229491 -48.58167 25.856282 0.017874391 3.0711656 -0.65745388
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2400 3.4778567 -50.223344 -48.367681 27.353194 0.01937458 3.4585353 -0.69135912
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2500 3.9483938 -50.216703 -48.109978 29.11873 0.020958791 3.9264583 -0.72652121
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2600 4.5198403 -50.209503 -47.797875 31.215234 0.02263645 4.4947301 -0.76313188
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2700 5.2173107 -50.201663 -47.417889 33.721815 0.024418904 5.1883257 -0.80140558
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2800 6.0723283 -50.193089 -46.953107 36.73757 0.026319777 6.0385931 -0.84159436
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2900 7.1241213 -50.183668 -46.382487 40.38551 0.028355393 7.0845429 -0.88396874
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3000 8.4208727 -50.173266 -45.680183 44.816478 0.030545255 8.3740901 -0.9288431
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3100 10.020649 -50.161717 -44.81505 50.212214 0.032912578 9.9649788 -0.97656436
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3200 11.991558 -50.148837 -43.750561 56.786471 0.035484852 11.924938 -1.0275116
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3300 14.410456 -50.134392 -42.445477 64.781319 0.038294377 14.330398 -1.0821007
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3400 17.359303 -50.11813 -40.855813 74.455919 0.041378722 17.262863 -1.14076
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3500 20.918126 -50.099744 -38.938564 86.068376 0.044780961 20.801915 -1.2039443
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3600 25.153676 -50.078895 -36.657774 99.840861 0.048549564 25.013933 -1.2720773
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3700 30.103431 -50.055212 -33.993075 115.91254 0.052737712 29.93619 -1.3455663
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3800 35.755845 -50.028299 -30.950232 134.28175 0.057401834 35.557201 -1.4247605
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3900 42.029581 -49.997746 -27.572232 154.74519 0.062599126 41.796084 -1.5098692
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4000 48.756702 -49.963159 -23.948289 176.84543 0.06838392 48.485832 -1.6010084
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4100 55.676392 -49.924188 -20.217214 199.84979 0.074802896 55.367079 -1.6980754
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4200 62.445716 -49.880563 -16.561714 222.7783 0.081889414 62.098795 -1.8007866
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4300 68.671023 -49.832118 -13.191664 244.49021 0.089657516 68.289518 -1.9086164
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4400 73.957826 -49.778843 -10.317535 263.82539 0.098096488 73.546949 -2.0208305
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4500 77.969954 -49.7209 -8.1188616 279.77238 0.10716704 77.536788 -2.1364913
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4600 80.483598 -49.658617 -6.7153862 291.6285 0.11680011 80.036467 -2.254524
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4700 81.421471 -49.592506 -6.1488596 299.10183 0.12689894 80.969129 -2.3737378
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4800 80.857888 -49.523204 -6.3802649 302.3328 0.13734453 80.408677 -2.492954
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4900 78.994781 -49.451459 -7.3026086 301.83334 0.14800388 78.555921 -2.6110228
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5000 76.117367 -49.378045 -8.7644823 298.36557 0.15873983 75.694493 -2.7269278
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5100 72.542745 -49.303735 -10.597466 292.79593 0.16942116 72.139729 -2.8398052
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5200 68.573953 -49.22923 -12.640569 285.96472 0.17993138 68.192987 -2.949009
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5300 64.467624 -49.155126 -14.757458 278.59037 0.19017535 64.10947 -3.0540851
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5400 60.41785 -49.081671 -16.844821 271.22804 0.20008281 60.082195 -3.1546148
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5500 56.554431 -49.009666 -18.834201 264.2355 0.20960898 56.24024 -3.250862
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5600 52.95111 -48.938861 -20.686002 257.84121 0.21873248 52.656937 -3.3428291
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5700 49.638794 -48.869827 -22.384304 252.12886 0.22745138 49.363023 -3.4305128
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5800 46.619514 -48.801888 -23.927347 247.13356 0.23577844 46.360517 -3.5141755
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5900 43.878389 -48.73593 -25.323958 242.80111 0.24373625 43.634621 -3.5942967
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6000 41.392437 -48.671406 -26.585851 239.09246 0.25135296 41.162479 -3.6710953
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6100 39.136252 -48.60798 -27.726246 235.9541 0.25865905 38.918828 -3.7449553
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6200 37.085195 -48.545774 -28.758412 233.32233 0.26568495 36.879167 -3.8159439
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6300 35.216896 -48.484909 -29.694407 231.1392 0.27245965 35.021246 -3.884503
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6400 33.511732 -48.42458 -30.543893 229.37842 0.2790099 33.325556 -3.9507385
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6500 31.952789 -48.365385 -31.316496 227.98228 0.2853599 31.775274 -4.0149897
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6600 30.525576 -48.307233 -32.019853 226.91697 0.29153132 30.35599 -4.0774486
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6700 29.217672 -48.24981 -32.660283 226.16022 0.29754342 29.055351 -4.1382338
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6800 28.018378 -48.192803 -33.243177 225.69366 0.30341329 27.862721 -4.1974677
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6900 26.918418 -48.136622 -33.773896 225.48194 0.30915615 26.768871 -4.2553485
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7000 25.909681 -48.08096 -34.256461 225.51257 0.31478562 25.765738 -4.311968
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7100 24.985015 -48.025534 -34.694405 225.77479 0.32031392 24.84621 -4.3675242
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7200 24.138072 -47.970746 -35.091516 226.24048 0.32575216 24.003972 -4.4219335
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7300 23.36317 -47.916089 -35.450319 226.90757 0.33111051 23.233375 -4.4754578
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7400 22.655198 -47.861976 -35.773956 227.75054 0.33639834 22.529336 -4.5280134
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7500 22.009532 -47.808135 -36.064618 228.76407 0.34162439 21.887257 -4.5797622
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7600 21.421974 -47.754508 -36.324492 229.93785 0.34679689 21.302963 -4.6307739
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7700 20.888691 -47.700827 -36.555352 231.26801 0.35192361 20.772643 -4.6812057
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7800 20.406177 -47.64705 -36.759028 232.73618 0.35701201 20.292809 -4.7306795
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7900 19.971205 -47.593833 -36.937897 234.33449 0.36206923 19.860254 -4.7798815
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8000 19.580795 -47.540435 -37.092808 236.06384 0.36710221 19.472013 -4.8285632
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8100 19.232176 -47.487281 -37.225665 237.90655 0.37211768 19.125331 -4.8768578
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8200 18.922755 -47.4341 -37.33758 239.86116 0.37712221 18.817628 -4.9247735
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8300 18.650078 -47.380856 -37.429827 241.92202 0.38212226 18.546466 -4.972363
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8400 18.4118 -47.327508 -37.503616 244.08393 0.38712418 18.309512 -5.0196756
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8500 18.205651 -47.273789 -37.559891 246.34742 0.3921342 18.104508 -5.06671
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8600 18.029398 -47.219424 -37.599568 248.71065 0.39715848 17.929235 -5.1133124
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8700 17.880815 -47.165549 -37.624972 251.14475 0.4022031 17.781477 -5.1600447
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8800 17.757645 -47.110958 -37.636101 253.66312 0.40727406 17.658991 -5.2066259
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8900 17.657573 -47.056554 -37.635091 256.25454 0.41237724 17.559475 -5.2531731
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9000 17.578197 -47.001835 -37.622724 258.91696 0.41751847 17.48054 -5.2996769
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9100 17.517006 -46.946535 -37.600073 261.64727 0.42270345 17.41969 -5.3462575
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9200 17.471368 -46.890625 -37.568515 264.44427 0.42793776 17.374305 -5.3925966
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9300 17.438519 -46.834765 -37.530181 267.28872 0.43322691 17.341639 -5.4391596
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9400 17.415579 -46.778464 -37.486121 270.18178 0.43857628 17.318826 -5.485798
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9500 17.399563 -46.721685 -37.437887 273.11812 0.44399119 17.302899 -5.5325337
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9600 17.387425 -46.664405 -37.387083 276.08982 0.44947693 17.290829 -5.5793912
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9700 17.376109 -46.606364 -37.335081 279.09236 0.45503878 17.279575 -5.6264788
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9800 17.362615 -46.547755 -37.283671 282.11747 0.46068208 17.266156 -5.6736623
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9900 17.344087 -46.488783 -37.234585 285.15699 0.46641232 17.247731 -5.7209993
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10000 17.317913 -46.42918 -37.188947 288.20641 0.4722352 17.221703 -5.7685405
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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, 680.689 timesteps/s, 122.524 katom-step/s
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96.5% 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 | 3.0453 | 3.0453 | 3.0453 | 0.0 | 20.73
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Bond | 0.00108 | 0.00108 | 0.00108 | 0.0 | 0.01
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Neigh | 6.6815 | 6.6815 | 6.6815 | 0.0 | 45.48
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Comm | 0.55477 | 0.55477 | 0.55477 | 0.0 | 3.78
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Output | 0.0028885 | 0.0028885 | 0.0028885 | 0.0 | 0.02
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Modify | 4.3341 | 4.3341 | 4.3341 | 0.0 | 29.50
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Other | | 0.07136 | | | 0.49
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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: 13729 ave 13729 max 13729 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 13729
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Ave neighs/atom = 76.272222
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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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