198 lines
15 KiB
Groff
198 lines
15 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 6
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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 0.9951423 -50.292972 -49.761999 16.167254 3.663073e-06 27.030021 -0.0025950927
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200 0.98099313 -50.292958 -49.769535 16.121999 1.4652294e-05 26.645702 -0.0052104718
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300 0.95873287 -50.292945 -49.781399 16.050672 3.2966429e-05 26.041069 -0.0078660339
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400 0.93006021 -50.292932 -49.796684 15.959387 5.8599875e-05 25.262263 -0.010582044
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500 0.89689329 -50.292917 -49.814366 15.855074 9.1539141e-05 24.361385 -0.013380753
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600 0.86110024 -50.292898 -49.833445 15.744205 0.00013176059 23.389175 -0.016282487
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700 0.82431428 -50.292877 -49.853052 15.632253 0.00017923062 22.389996 -0.019305323
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800 0.78784526 -50.29285 -49.872483 15.523595 0.00023390859 21.399426 -0.022473781
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900 0.7526687 -50.292816 -49.891219 15.421094 0.00029575217 20.443961 -0.025805439
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1000 0.71946253 -50.292776 -49.908896 15.326586 0.0003647244 19.542016 -0.029318877
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1100 0.6886647 -50.292726 -49.925279 15.241234 0.00044080156 18.705487 -0.033035613
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1200 0.66053404 -50.292668 -49.94023 15.165485 0.00052398138 17.941403 -0.036980816
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1300 0.63520455 -50.292595 -49.953672 15.099745 0.00061429107 17.253404 -0.041183239
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1400 0.61273022 -50.292511 -49.965579 15.043883 0.00071179519 16.642957 -0.045662316
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1500 0.59312004 -50.29241 -49.975942 14.99787 0.00081660341 16.110306 -0.050440479
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1600 0.57636482 -50.292289 -49.984761 14.961722 0.00092887845 15.655202 -0.055550832
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1700 0.56245787 -50.292149 -49.992041 14.935319 0.0010488445 15.277461 -0.061027295
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1800 0.55141126 -50.291984 -49.99777 14.919091 0.0011767964 14.977414 -0.066900795
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1900 0.54326956 -50.291792 -50.001923 14.913094 0.0013131107 14.756269 -0.073216193
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2000 0.53812238 -50.29157 -50.004447 14.917947 0.0014582582 14.616462 -0.080017237
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2100 0.53611709 -50.291312 -50.005259 14.934473 0.0016128191 14.561994 -0.087363239
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2200 0.53747284 -50.291009 -50.004233 14.964038 0.0017775021 14.598819 -0.095297839
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2300 0.54249688 -50.290657 -50.001199 15.008081 0.0019531669 14.735282 -0.10390758
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2400 0.5516043 -50.290246 -49.995929 15.068555 0.0021408527 14.982657 -0.11326027
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2500 0.56534197 -50.289766 -49.988119 15.147769 0.0023418123 15.355799 -0.12345646
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2600 0.58441738 -50.289207 -49.977382 15.249155 0.0025575544 15.873925 -0.13459188
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2700 0.60973272 -50.28855 -49.963218 15.376625 0.0027898943 16.561539 -0.14680402
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2800 0.64242344 -50.287778 -49.945003 15.535379 0.0030410156 17.449483 -0.16021499
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2900 0.68389909 -50.286869 -49.921964 15.731194 0.003313542 18.576043 -0.1749965
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3000 0.73588147 -50.28579 -49.893149 15.972304 0.0036106211 19.987987 -0.19131687
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3100 0.80043087 -50.284508 -49.857426 16.267625 0.0039360184 21.741276 -0.20938994
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3200 0.87994497 -50.282984 -49.813476 16.627323 0.0042942181 23.901035 -0.229419
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3300 0.97710707 -50.281162 -49.759812 17.064318 0.0046905236 26.540149 -0.25165651
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3400 1.0947515 -50.278979 -49.694858 17.591402 0.0051311469 29.735603 -0.27634359
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3500 1.2356071 -50.276358 -49.617081 18.222808 0.0056232657 33.561517 -0.30373125
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3600 1.4018792 -50.273211 -49.525217 18.97057 0.0061750242 38.077795 -0.33406344
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3700 1.5946467 -50.269438 -49.41859 19.844391 0.0067954397 43.313738 -0.36756248
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3800 1.8130868 -50.264926 -49.297526 20.847335 0.0074941739 49.247003 -0.4044001
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3900 2.0536116 -50.259558 -49.163823 21.972799 0.0082811282 55.780127 -0.44468343
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4000 2.3090877 -50.253214 -49.021165 23.203274 0.0091658295 62.719362 -0.48844585
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4100 2.5684074 -50.245778 -48.875365 24.50535 0.010156603 69.762993 -0.53559997
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4200 2.8167153 -50.237155 -48.734254 25.832794 0.011259571 76.507524 -0.58595872
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4300 3.0365377 -50.22728 -48.607089 27.128084 0.012477576 82.478334 -0.63920669
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4400 3.2098494 -50.216129 -48.503465 28.32938 0.013809186 87.18582 -0.69492156
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4500 3.3207987 -50.203729 -48.431867 29.380289 0.015247971 90.19942 -0.75258375
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4600 3.3584946 -50.190151 -48.398176 30.239405 0.016782256 91.223315 -0.81162394
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4700 3.319109 -50.175529 -48.404569 30.887433 0.01839546 90.153525 -0.87142276
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4800 3.2066714 -50.160034 -48.449067 31.329923 0.020067061 87.099499 -0.93139568
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4900 3.0323121 -50.14386 -48.525924 31.596801 0.021774071 82.363558 -0.99098372
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5000 2.8121835 -50.127216 -48.626733 31.734704 0.02349282 76.384432 -1.04971
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5100 2.5646531 -50.11031 -48.741901 31.798135 0.025200765 69.661019 -1.1071803
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5200 2.3074925 -50.093317 -48.86212 31.840218 0.026878076 62.676032 -1.16309
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5300 2.0556744 -50.076391 -48.979555 31.905031 0.028508785 55.836159 -1.217247
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5400 1.820121 -50.059654 -49.088501 32.023732 0.030081384 49.438064 -1.2695269
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5500 1.6074407 -50.04318 -49.185506 32.214415 0.031588873 43.661248 -1.319891
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5600 1.4204416 -50.02701 -49.269112 32.484092 0.033028319 38.581985 -1.3683615
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5700 1.2590798 -50.011162 -49.339361 32.830285 0.034400107 34.199083 -1.4149934
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5800 1.1215045 -49.995631 -49.397236 33.245821 0.035707041 30.462267 -1.4598878
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5900 1.0049589 -49.980399 -49.444188 33.721747 0.03695346 27.29666 -1.5031416
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6000 0.90642926 -49.965438 -49.4818 34.248321 0.038144494 24.620401 -1.5448741
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6100 0.82303723 -49.950718 -49.511574 34.817039 0.039285497 22.355309 -1.585191
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6200 0.75223267 -49.936211 -49.534846 35.419814 0.040381668 20.432118 -1.6242074
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6300 0.69185501 -49.921889 -49.552739 36.050843 0.041437835 18.792142 -1.6620216
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6400 0.64012215 -49.907725 -49.566179 36.704661 0.042458347 17.386976 -1.6987306
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6500 0.59558646 -49.893699 -49.575915 37.378286 0.04344705 16.177299 -1.7344148
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6600 0.55708121 -49.879794 -49.582555 38.067181 0.044407312 15.131421 -1.7691453
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6700 0.52366875 -49.865988 -49.586576 38.769884 0.045342063 14.223873 -1.8030059
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6800 0.49459542 -49.852276 -49.588377 39.48355 0.046253857 13.434184 -1.8360506
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6900 0.46925412 -49.838637 -49.58826 40.206955 0.047144922 12.745864 -1.8683386
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7000 0.44715411 -49.825066 -49.58648 40.938794 0.048017218 12.145585 -1.8999205
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7100 0.427897 -49.811553 -49.583243 41.677982 0.048872484 11.622524 -1.9308529
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7200 0.4111577 -49.798086 -49.578707 42.423605 0.049712274 11.167851 -1.9611851
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7300 0.39666926 -49.784662 -49.573013 43.175155 0.050538 10.774317 -1.9909515
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7400 0.38421083 -49.771272 -49.56627 43.931762 0.051350953 10.435921 -2.0202015
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7500 0.37359789 -49.757907 -49.558568 44.69348 0.052152332 10.147653 -2.0489622
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7600 0.36467436 -49.744563 -49.549985 45.459725 0.052943262 9.9052723 -2.0772881
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7700 0.35730613 -49.731235 -49.540589 46.229921 0.053724811 9.7051368 -2.1052027
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7800 0.3513759 -49.717911 -49.530429 47.004627 0.054498005 9.54406 -2.1327445
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7900 0.34677906 -49.704589 -49.51956 47.78318 0.055263836 9.419201 -2.1599468
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8000 0.34342073 -49.691262 -49.508025 48.565675 0.056023277 9.327982 -2.1868375
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8100 0.34121371 -49.677922 -49.495862 49.351802 0.056777286 9.2680351 -2.2134444
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8200 0.34007764 -49.664566 -49.483112 50.141603 0.057526819 9.2371771 -2.2397997
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8300 0.33993883 -49.651181 -49.469802 50.935241 0.05827283 9.2334067 -2.2659331
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8400 0.34073085 -49.637766 -49.455963 51.732654 0.059016284 9.2549196 -2.2918688
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8500 0.34239516 -49.62431 -49.441619 52.534019 0.059758157 9.3001256 -2.317626
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8600 0.3448813 -49.610812 -49.426796 53.338612 0.060499441 9.367654 -2.3432261
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8700 0.34814597 -49.597265 -49.411506 54.147073 0.061241149 9.4563288 -2.3686991
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8800 0.35215054 -49.583658 -49.395763 54.959512 0.061984314 9.5651009 -2.3940587
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8900 0.35685687 -49.569985 -49.379579 55.776434 0.062729991 9.692934 -2.419329
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9000 0.36222181 -49.556241 -49.362972 56.597626 0.063479254 9.8386562 -2.4445253
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9100 0.36819143 -49.54242 -49.345966 57.423306 0.064233198 10.000803 -2.469667
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9200 0.37469636 -49.528518 -49.328593 58.253634 0.064992931 10.17749 -2.4947681
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9300 0.38164964 -49.514521 -49.310886 59.088869 0.065759574 10.366354 -2.5198522
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9400 0.38894823 -49.500427 -49.292898 59.929378 0.066534253 10.564598 -2.5449285
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9500 0.3964785 -49.486229 -49.274681 60.775174 0.067318101 10.769135 -2.5700196
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9600 0.4041249 -49.471917 -49.25629 61.626259 0.068112253 10.976827 -2.5951326
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9700 0.41178035 -49.457494 -49.237782 62.482132 0.06891785 11.184764 -2.6202815
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9800 0.41935645 -49.44294 -49.219186 63.343831 0.069736042 11.390545 -2.6454805
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9900 0.42679147 -49.428257 -49.200536 64.211037 0.070567996 11.592495 -2.670741
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10000 0.43405521 -49.413432 -49.181835 65.08463 0.071414903 11.789793 -2.6960774
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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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95.3% 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 | 3.1084 | 3.1084 | 3.1084 | 0.0 | 21.16
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Bond | 0.0010414 | 0.0010414 | 0.0010414 | 0.0 | 0.01
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Neigh | 6.6306 | 6.6306 | 6.6306 | 0.0 | 45.13
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Comm | 0.56093 | 0.56093 | 0.56093 | 0.0 | 3.82
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Output | 0.002951 | 0.002951 | 0.002951 | 0.0 | 0.02
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Modify | 4.3177 | 4.3177 | 4.3177 | 0.0 | 29.39
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Other | | 0.06942 | | | 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: 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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