adf4a23f58
- replace file reader code using TextFileReader and ValueTokenizer - replace traversing list of fixes with accessor functions - enable and apply clang-format - add examples for reading rigid bodies from file
329 lines
19 KiB
Groff
329 lines
19 KiB
Groff
LAMMPS (17 Feb 2022)
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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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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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Reading data file ...
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orthogonal box = (-12 -12 -12) to (12 12 12)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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81 atoms
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read_data CPU = 0.001 seconds
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velocity all create 100.0 4928459
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# 1 chain of connected bodies
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group clump1 id <> 1 9
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9 atoms in group clump1
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group clump2 id <> 9 18
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10 atoms in group clump2
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group clump3 id <> 18 27
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10 atoms in group clump3
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group clump4 id <> 27 36
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10 atoms in group clump4
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group clump5 id <> 36 45
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10 atoms in group clump5
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group clump6 id <> 45 54
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10 atoms in group clump6
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group clump7 id <> 54 63
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10 atoms in group clump7
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group clump8 id <> 63 72
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10 atoms in group clump8
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group clump9 id <> 72 81
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10 atoms in group clump9
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fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
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1 clusters, 9 bodies, 8 joints, 81 atoms
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems
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#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- fix poems command:
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@Article{Mukherjee08,
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author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
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title = {Substructured molecular dynamics using multibody dynamics algorithms},
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journal = {Intl.~J.~Non-linear Mechanics},
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year = 2008,
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volume = 43,
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pages = {1045--1055}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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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 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 18 18 18
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/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) = 3.514 | 3.545 | 3.639 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 217.7783 3430.3907 0 3466.6871 -2.7403788
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50 13679.637 1404.2468 0 3684.1863 12.446066
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100 16777.225 888.87665 0 3685.0808 -31.828677
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150 19595.365 418.45042 0 3684.3446 40.709078
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200 18524.188 596.47273 0 3683.8375 -0.8159371
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250 21015.789 180.96521 0 3683.5967 -10.042469
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300 20785.513 219.25314 0 3683.5053 2.6452719
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350 21072.46 171.2554 0 3683.3321 7.0609024
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400 19956.414 356.36381 0 3682.4328 19.320259
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450 20724.42 227.73284 0 3681.8028 8.1259249
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500 20152.578 322.71466 0 3681.4777 5.4929878
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550 20017.022 345.29701 0 3681.4673 5.4661666
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600 17897.743 698.72196 0 3681.6791 3.2854742
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650 17297.758 796.60256 0 3679.5623 15.191113
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700 18581.934 584.29715 0 3681.2861 5.1588289
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750 21774.158 52.821062 0 3681.8474 -10.775664
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800 21604.055 81.188546 0 3681.8644 -3.2045742
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850 17821.483 711.53827 0 3681.7854 7.4384281
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900 21033.292 175.98127 0 3681.5299 -16.345167
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950 20968.166 186.59847 0 3681.2929 -2.330456
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1000 20490.66 266.19374 0 3681.3037 11.787982
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1050 20222.396 310.94072 0 3681.34 -8.3459539
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1100 21321.687 127.61533 0 3681.2299 -1.2184716
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1150 20849.582 206.01696 0 3680.9472 -0.86699115
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1200 21815.003 45.317409 0 3681.1512 1.5988314
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1250 18655.437 572.41453 0 3681.654 10.064083
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1300 20780.781 217.36511 0 3680.8286 6.0538606
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1350 20558.971 254.36489 0 3680.8601 -3.6773868
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1400 21485.03 99.812843 0 3680.6511 -16.185479
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1450 21771.107 52.159652 0 3680.6775 -2.4756656
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1500 21520.949 93.503872 0 3680.3286 2.1023574
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1550 21351.419 121.68131 0 3680.2511 5.5159875
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1600 20778.804 216.92191 0 3680.0559 15.089203
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1650 21477.636 100.21877 0 3679.8247 -1.104524
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1700 18501.329 596.48084 0 3680.0357 -15.679806
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1750 18563.639 587.34841 0 3681.2882 33.532316
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1800 19110.174 494.82524 0 3679.8543 18.024079
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1850 21364.178 119.23767 0 3679.9339 2.5290075
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1900 20146.588 322.15506 0 3679.9197 5.7317368
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1950 20692.674 231.25288 0 3680.0319 4.2977982
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2000 20943.904 189.11229 0 3679.7629 -22.643749
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2050 19667.815 401.87016 0 3679.8394 3.6240972
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2100 20280.109 299.81759 0 3679.8357 7.4803647
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2150 19181.146 483.63975 0 3680.4974 22.634167
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2200 21301.194 130.53171 0 3680.7308 4.7072523
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2250 20484.79 266.99736 0 3681.1291 -8.6583002
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2300 18648.002 573.09962 0 3681.1 -5.2548835
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2350 21515.851 95.225745 0 3681.2009 -9.3875216
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2400 21462.37 104.21272 0 3681.2744 -29.459857
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2450 20108.034 330.94394 0 3682.2829 35.37058
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2500 20771.818 220.42545 0 3682.3951 -12.318936
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2550 20502.815 265.09577 0 3682.2316 -22.726822
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2600 21462.006 105.2733 0 3682.2744 -10.180394
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2650 21009.656 180.72738 0 3682.3367 4.9580828
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2700 18680.012 569.37179 0 3682.7071 21.114114
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2750 21256.19 139.42201 0 3682.1203 -7.4744399
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2800 21552.267 90.071446 0 3682.1159 -6.2906304
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2850 20879.958 202.00905 0 3682.0021 0.57990903
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2900 19018.645 512.35214 0 3682.1262 13.883084
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2950 19819.365 378.55747 0 3681.785 -0.7348943
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3000 20269.229 303.35149 0 3681.5563 6.3088075
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3050 19236.727 475.99457 0 3682.1158 -10.703575
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3100 18391.55 616.96976 0 3682.2281 9.850079
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3150 20258.563 305.82076 0 3682.248 7.1951283
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3200 20716.384 229.15502 0 3681.8856 2.9042294
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3250 18662.237 572.0784 0 3682.4512 9.2108597
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3300 19162.278 488.60646 0 3682.3195 3.3306562
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3350 21235.679 142.98279 0 3682.2626 0.29397483
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3400 17677.053 736.09247 0 3682.2679 32.75269
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3450 20852.392 206.65618 0 3682.0548 -4.8319056
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3500 21182.918 151.46754 0 3681.9539 -5.6330382
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3550 20589.85 250.40724 0 3682.049 12.582133
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3600 20973.659 186.28043 0 3681.8903 10.935266
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3650 17838.632 707.92145 0 3681.0268 -17.200926
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3700 21538.002 92.744409 0 3682.4114 -0.72124229
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3750 21390.294 117.90865 0 3682.9576 -7.8431786
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3800 17921.046 696.50311 0 3683.344 -9.4641531
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3850 20356.471 290.22624 0 3682.9715 2.4593463
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3900 20374.077 287.10249 0 3682.782 -1.9519082
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3950 20563.915 255.29993 0 3682.619 -6.124649
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4000 20991.467 184.76183 0 3683.3397 1.8954961
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4050 17805.623 716.24698 0 3683.8509 -20.454944
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4100 19916.389 363.86301 0 3683.2611 -0.27912557
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4150 19221.623 480.01232 0 3683.6161 -11.562492
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4200 20526.82 261.78571 0 3682.9224 -3.9522917
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4250 20922.813 196.1799 0 3683.3154 0.11947446
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4300 19956.66 357.78133 0 3683.8914 19.156093
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4350 19735.73 394.45981 0 3683.7482 14.865775
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4400 21702.656 67.099805 0 3684.2092 -13.502538
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4450 18163.055 656.97231 0 3684.1482 -0.6243111
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4500 17477.718 771.25976 0 3684.2127 -0.4664004
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4550 20676.507 238.19814 0 3684.2827 -19.444969
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4600 17322.922 796.77058 0 3683.9242 27.003966
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4650 11905.158 1704.9151 0 3689.1082 15.574169
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4700 18689.079 569.80982 0 3684.6563 -14.67311
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4750 19821.745 381.01914 0 3684.6433 5.0436795
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4800 20621.335 247.96269 0 3684.8518 -16.407263
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4850 21923.814 30.965964 0 3684.935 -13.418244
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4900 18840.555 544.41538 0 3684.5079 11.005357
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4950 15366.601 1124.2481 0 3685.3482 17.412375
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5000 18274.314 639.01311 0 3684.732 5.3261109
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5050 21173.687 155.83673 0 3684.7845 5.4056809
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5100 21738.219 61.75201 0 3684.7885 -2.631945
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5150 16597.949 918.84841 0 3685.1732 -10.124101
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5200 20752.758 225.95919 0 3684.7522 -5.2441372
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5250 17652.088 741.2645 0 3683.2793 2.0080739
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5300 19907.523 366.53115 0 3684.4516 8.4266792
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5350 20104.189 334.14522 0 3684.8433 17.21925
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5400 21499.848 101.71631 0 3685.0243 -6.1103541
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5450 21203.533 151.14574 0 3685.068 -5.9468503
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5500 21076.513 172.45652 0 3685.2088 5.1418181
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5550 20158.398 325.56609 0 3685.2992 -1.6486034
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5600 20787.836 221.19563 0 3685.835 -10.66805
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5650 19687.154 404.77204 0 3685.9644 -23.49128
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5700 20419.311 282.58328 0 3685.8017 -0.52808211
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5750 19738.522 395.95893 0 3685.7126 1.3889817
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5800 18300.025 635.66905 0 3685.6732 23.490447
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5850 20585.004 255.02032 0 3685.8543 -0.20699939
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5900 20373.839 290.15881 0 3685.7987 -7.9712187
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5950 18163.832 659.91192 0 3687.2173 5.4494586
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6000 21049.247 177.43029 0 3685.6382 2.9138342
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6050 21239.803 145.77613 0 3685.7433 -1.4927769
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6100 20686.361 237.86454 0 3685.5913 -0.95516297
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6150 20461.754 275.31546 0 3685.6079 -3.4166412
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6200 19264.208 474.73017 0 3685.4316 11.750757
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6250 21180.813 155.31746 0 3685.4529 2.8188219
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6300 21047.543 177.4394 0 3685.3632 1.8641486
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6350 20232.576 313.17716 0 3685.2731 2.8150209
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6400 20185.616 321.33454 0 3685.6038 -3.8697311
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6450 18969.632 523.95865 0 3685.5639 0.6725512
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6500 17592.574 753.49959 0 3685.5952 -1.2557393
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6550 21279.049 138.42524 0 3684.9335 -1.208945
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6600 21408.457 116.4143 0 3684.4904 -1.5332953
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6650 19758.218 391.17316 0 3684.2096 1.8511312
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6700 20766.943 223.44631 0 3684.6036 -2.3672623
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6750 20399.631 284.09914 0 3684.0377 -5.4089876
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6800 21296.628 135.14662 0 3684.5847 -3.8442549
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6850 20641.481 244.4451 0 3684.692 1.4020639
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6900 20852.81 209.23009 0 3684.6984 1.8512104
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6950 20940.555 194.66882 0 3684.7614 -6.554676
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7000 19496.988 435.28199 0 3684.78 -15.120269
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7050 19796.829 385.04227 0 3684.5138 -4.1068804
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7100 19945.264 360.42431 0 3684.635 -4.0629042
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7150 19431.123 446.12911 0 3684.6497 -6.8321751
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7200 16864.851 873.80043 0 3684.6089 14.309069
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7250 20438.75 277.85982 0 3684.3181 -11.41223
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7300 17688.684 734.01576 0 3682.1298 35.938373
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7350 21573.419 88.63421 0 3684.204 -3.9032749
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7400 21198.486 150.72249 0 3683.8034 -7.1477117
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7450 20586.708 252.93928 0 3684.0572 -7.6634645
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7500 21815.377 48.180377 0 3684.0765 0.97457507
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7550 17791.352 718.87564 0 3684.101 28.248235
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7600 21828.874 45.928597 0 3684.0742 -0.25814944
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7650 20827.961 212.35674 0 3683.6835 -3.4083384
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7700 21319.176 130.43547 0 3683.6315 -12.434856
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7750 20127.904 328.69643 0 3683.3471 -16.975711
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7800 21741.772 59.679206 0 3683.3078 3.6261863
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7850 19612.334 414.37418 0 3683.0964 1.3763274
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7900 20071.318 337.74624 0 3682.9658 -0.40982763
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7950 17925.664 695.29582 0 3682.9065 17.104439
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8000 19125.978 492.76383 0 3680.4268 10.807662
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8050 20233.848 310.42681 0 3682.7347 13.386237
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8100 20551.619 257.86699 0 3683.1368 -13.97515
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8150 21578.323 86.88362 0 3683.2708 -9.6811587
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8200 21154.833 157.72897 0 3683.5344 0.62312375
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8250 21321.143 129.83967 0 3683.3636 1.9536438
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8300 21041.696 176.04177 0 3682.9911 4.7475567
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8350 19883.39 369.32649 0 3683.2247 -7.0959328
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8400 21626.067 79.062992 0 3683.4075 -14.919059
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8450 21375.201 120.86836 0 3683.4019 -5.3461514
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8500 20281.059 303.10304 0 3683.2796 3.7975093
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8550 21170.533 154.48432 0 3682.9065 -1.1568561
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8600 17754.931 724.00158 0 3683.1568 14.15254
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8650 20685.478 235.65879 0 3683.2385 -5.2694179
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8700 21489.165 101.90509 0 3683.4326 -4.2510612
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8750 21106.682 165.41638 0 3683.1968 -3.9186708
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8800 19149.516 491.5843 0 3683.1702 -11.419849
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8850 21451.865 108.1814 0 3683.4923 -7.8256219
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8900 19567.4 421.81206 0 3683.0454 -0.71997056
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8950 20934.097 194.48033 0 3683.4965 -7.0106879
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9000 18531.559 595.25957 0 3683.8528 3.7449399
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9050 18868.821 537.22549 0 3682.029 9.9926092
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9100 19972.527 354.73119 0 3683.4858 -0.30871263
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9150 19641.651 409.18618 0 3682.7947 -1.3036238
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9200 20019.08 346.19657 0 3682.7099 6.7425386
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9250 19259.286 473.04973 0 3682.9308 -24.120659
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9300 21597.757 82.971857 0 3682.598 -13.748483
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9350 19348.379 457.23576 0 3681.9656 3.1571402
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9400 19129.588 493.35235 0 3681.617 8.6293783
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9450 20337.025 291.20959 0 3680.7138 6.8590795
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9500 20581.788 249.65891 0 3679.9569 -18.892836
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9550 19482.069 433.0077 0 3680.0192 23.029778
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9600 19182.794 482.96871 0 3680.101 -11.081731
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9650 20086.771 332.5311 0 3680.3263 -18.939681
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9700 20274.046 300.98818 0 3679.9959 6.7538762
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9750 18743.595 555.08045 0 3679.0129 8.2757138
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9800 19464.311 435.66288 0 3679.7148 7.0528759
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9850 21249.848 138.27382 0 3679.9152 -10.847402
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9900 21156.214 153.84621 0 3679.8819 -7.8359674
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9950 21643.134 72.547515 0 3679.7365 -10.507744
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10000 19587.948 414.64942 0 3679.3075 6.1173553
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Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms
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Performance: 36474.344 tau/day, 4221.568 timesteps/s
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99.2% CPU use with 4 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 | 0.005348 | 0.024925 | 0.056071 | 12.2 | 1.05
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Neigh | 0.0075012 | 0.022046 | 0.043933 | 9.3 | 0.93
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Comm | 0.13135 | 0.16461 | 0.1917 | 5.9 | 6.95
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Output | 0.0036298 | 0.004271 | 0.0056384 | 1.2 | 0.18
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Modify | 2.1147 | 2.1322 | 2.1418 | 0.7 | 90.01
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Other | | 0.02072 | | | 0.87
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Nlocal: 20.25 ave 81 max 0 min
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Histogram: 3 0 0 0 0 0 0 0 0 1
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Nghost: 41 ave 78 max 11 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 193.5 ave 774 max 0 min
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Histogram: 3 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 774
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Ave neighs/atom = 9.5555556
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Neighbor list builds = 989
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Dangerous builds = 915
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Total wall time: 0:00:02
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