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lammps/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1
Axel Kohlmeyer f07719e924 make fix rhok examples more consistent with LAMMPS conventions: 
- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility
2017-10-03 10:08:38 -04:00

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LAMMPS (22 Sep 2017)
using 1 OpenMP thread(s) per MPI task
units lj
dimension 3
boundary p p p
atom_style atomic
# truncated and shifted LJ potential
pair_style lj/cut 2.5
pair_modify shift yes
read_data data.halfhalf
orthogonal box = (0 0 0) to (12.8152 12.8152 34)
1 by 1 by 1 MPI processor grid
reading atoms ...
5120 atoms
reading velocities ...
5120 velocities
pair_coeff 1 1 1.0 1.0 2.5
mass 1 1.0
# simulation parameters
neighbor 0.6 bin
timestep 0.004
run_style verlet
velocity all create 0.8 1 mom yes rot yes
fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
fix 100 all momentum 100 linear 1 1 1
# harmonic rho_k bias-field
# nx ny nz k a
fix bias all rhok 16 0 0 4.0 26.00
# output U_bias rho_k_RE rho_k_IM |rho_k|
thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
thermo 50
dump dumpXYZ all xyz 500 traj.xyz
# NOTE: run reduced for demonstration purposes
# run 50000
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.723 | 5.723 | 5.723 Mbytes
Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3]
0 0.8 5.1566801 -4.8556711 34 179.52419 35.473155 -0.2832763 35.474286
50 1.072533 3.8158392 -5.2704532 34.024206 0.010596224 25.927135 -0.063106738 25.927212
100 1.1093231 3.6703116 -5.3380965 34.094814 1.8552612 26.958236 -0.51403326 26.963136
150 1.1080721 3.8202601 -5.3568368 34.207473 0.39188605 26.420755 -1.0759575 26.442655
200 1.1435287 3.3445987 -5.4365298 34.354119 3.0758718 27.239465 -0.19115251 27.240135
250 1.1203046 3.4669456 -5.4293867 34.511473 0.8543814 26.652785 -0.20818214 26.653598
300 1.1012709 3.4583154 -5.4281803 34.664509 2.4837156 27.097674 0.9518628 27.114387
350 1.0439632 3.8953869 -5.368619 34.810399 0.55385719 26.518391 0.64525272 26.52624
400 1.0083878 4.0523864 -5.3418278 34.957669 0.34806057 26.404011 0.83368604 26.417169
450 0.9675244 4.310087 -5.3089468 35.114208 0.7921285 26.607512 1.077889 26.629336
500 0.94605476 4.1050097 -5.3062273 35.284018 0.87757754 26.639125 1.1140858 26.662411
550 0.92662323 3.9299063 -5.3062927 35.458565 1.3746441 26.773494 1.7256603 26.829049
600 0.89723165 3.7683555 -5.289725 35.629881 0.46692943 26.372973 2.4135502 26.483182
650 0.90612566 3.1098837 -5.3267851 35.788537 0.032662126 25.918784 3.2982102 26.127793
700 0.9152508 2.6527976 -5.3597799 35.923343 0.014621588 25.834591 3.6093492 26.085503
750 0.90156356 2.3474851 -5.3545938 36.031813 0.75225637 26.307204 4.0247215 26.613293
800 0.89748513 1.9825103 -5.3610202 36.113888 0.33402511 26.261326 2.7858039 26.408672
850 0.89496343 1.8906342 -5.3673514 36.169424 0.85431557 26.534648 2.5150347 26.653573
900 0.89463983 1.5654217 -5.3753283 36.20181 1.5689239 26.764737 2.5474794 26.885699
950 0.88663832 1.4399476 -5.3703322 36.209971 0.044436903 25.818418 1.2963356 25.850941
1000 0.87407208 1.485718 -5.3572665 36.195386 1.4405611 26.828072 1.0520795 26.848693
1050 0.87580489 1.163155 -5.3647269 36.160279 0.15319559 26.234791 1.4845964 26.276763
1100 0.86978111 1.3743181 -5.3594907 36.104958 1.1313537 25.19895 1.5711793 25.247885
1150 0.86987861 1.3212927 -5.3628503 36.035486 0.039865678 25.841762 0.93898962 25.858816
1200 0.87142486 1.3293818 -5.3676854 35.954411 0.16827389 25.70952 -0.14639427 25.709936
1250 0.87582265 1.3203803 -5.3764058 35.86575 0.25946652 25.639682 0.082696867 25.639815
1300 0.87371627 1.4680294 -5.375151 35.772824 0.17697069 25.701417 0.2397926 25.702535
1350 0.88617453 1.5923057 -5.3954912 35.681046 0.00049155526 25.973634 -0.74521794 25.984323
1400 0.87809636 1.5821707 -5.3850722 35.594706 0.024050814 26.107395 -0.34393685 26.10966
1450 0.87912192 1.7820174 -5.3885842 35.514722 0.20999914 25.667238 -0.66933655 25.675964
1500 0.88293618 2.0295275 -5.3963602 35.443445 0.60232374 25.376395 -1.9501461 25.451218
1550 0.90012542 1.9476472 -5.4249456 35.382791 0.4488038 26.448928 -1.1452474 26.473711
1600 0.89155063 2.2462603 -5.4153432 35.332095 0.039621687 26.138157 -0.36825239 26.140751
1650 0.8942624 2.343747 -5.4233433 35.294954 0.0089980332 26.064277 0.38189192 26.067075
1700 0.90047841 2.451289 -5.4376312 35.27234 0.86985171 26.646438 0.83408084 26.659489
1750 0.87586052 2.6381221 -5.4067182 35.264564 6.346204 27.652722 2.6699692 27.78132
1800 0.87392582 2.6338176 -5.4109056 35.270073 0.046414129 26.016188 2.6651053 26.152339
1850 0.86540415 2.5434301 -5.4058587 35.285902 0.054615472 26.074279 2.1799787 26.165251
1900 0.87043082 2.5776772 -5.4216997 35.309062 0.68978148 26.38648 3.2614091 26.587274
1950 0.86281992 2.3107762 -5.4188978 35.338501 0.0072672577 25.736893 3.2375012 25.93972
2000 0.85905576 2.2894047 -5.4215995 35.36787 0.095633435 26.072085 2.7685848 26.21867
2050 0.85793751 2.2382039 -5.4279351 35.395213 0.13602344 25.598457 2.6881027 25.739209
2100 0.85585253 2.0765811 -5.4324511 35.418877 0.0059888115 25.754128 3.1436222 25.945279
2150 0.86701057 1.8449875 -5.4562208 35.436124 0.097328618 25.413697 4.3268293 25.7794
2200 0.85168154 1.9024923 -5.4395776 35.44246 0.20764576 25.094788 5.4406104 25.677784
2250 0.8429719 1.870335 -5.4320586 35.438363 0.34419961 24.998478 5.4475709 25.585151
2300 0.84176891 1.7100228 -5.4351472 35.422863 0.76036958 24.697018 5.8629967 25.383409
2350 0.84601588 1.8539039 -5.4456629 35.395979 0.38437531 25.647986 6.4163366 26.438392
2400 0.84637647 1.6299091 -5.4498948 35.36125 0.074236719 24.995872 7.8269968 26.192661
2450 0.85650449 1.6828907 -5.4683101 35.316669 0.3671827 25.280669 7.7040329 26.428476
2500 0.84963707 1.7305222 -5.4605394 35.265508 0.1406965 25.236741 7.2780025 26.265232
2550 0.84084365 1.8758368 -5.4497083 35.208725 0.33937687 24.544376 7.2334512 25.588067
2600 0.85317342 1.7781674 -5.4702734 35.149747 0.60378248 24.046307 8.3370138 25.450554
2650 0.85487644 2.0065374 -5.4747643 35.090431 0.22483651 24.937101 8.4669004 26.335288
2700 0.84550083 1.9363031 -5.4628401 35.034349 0.43442577 24.250196 7.9943738 25.533939
2750 0.85843419 2.0473138 -5.484528 34.980671 0.45959294 24.17438 8.179356 25.520629
2800 0.86047607 2.0754522 -5.4899966 34.932466 0.00038123477 24.619856 8.3153434 25.986194
2850 0.86375793 2.2751324 -5.4977459 34.892337 0.0016455263 24.927259 7.289789 25.971316
2900 0.84438986 2.3790377 -5.4721407 34.863512 1.2372354 25.819445 7.132603 26.786523
2950 0.8551438 2.2721926 -5.4925958 34.84473 1.5405388 25.956466 6.976385 26.87765
3000 0.83737707 2.4009609 -5.4707188 34.834171 0.28507766 25.643879 6.1778846 26.377543
3050 0.84923235 2.4187994 -5.4938573 34.830836 0.036512025 25.139252 7.1457857 26.135115
3100 0.83872396 2.3811576 -5.4838787 34.833673 0.246984 24.21358 8.4588719 25.648586
3150 0.83957817 2.3901421 -5.4913118 34.84163 0.20477984 24.309852 10.088243 26.319984
3200 0.84283033 2.17292 -5.5025459 34.853975 1.3367154 24.581685 10.72011 26.817531
3250 0.84002379 2.1247709 -5.5044955 34.866106 0.11434509 24.463842 9.4874246 26.239108
3300 0.83311101 2.1492058 -5.5000847 34.875625 0.0053284993 23.815298 10.560222 26.051616
3350 0.83216701 1.9587594 -5.5043446 34.881623 0.58985562 23.934253 11.475462 26.543073
3400 0.82396039 2.1914951 -5.4971506 34.881199 0.098206955 23.393402 10.82936 25.778407
3450 0.83483253 1.9783612 -5.5182844 34.877327 7.6571212e-05 23.675355 10.761012 26.006188
3500 0.82712062 1.9718522 -5.5111818 34.869214 0.014836125 23.314122 11.312845 25.913872
3550 0.8342927 1.9114357 -5.5259968 34.855179 1.4050442 22.442758 11.377192 25.161834
3600 0.82631637 1.9836457 -5.5176244 34.835738 0.084637609 23.413286 10.824194 25.794285
3650 0.82425697 1.9218541 -5.5178548 34.811901 0.11000071 22.788707 12.022258 25.765478
3700 0.82491437 1.9624493 -5.521738 34.782417 0.034984027 23.011433 12.384217 26.132257
3750 0.82758167 2.0856442 -5.5283493 34.748872 0.001362163 23.030662 12.122144 26.026098
3800 0.81891108 1.9858824 -5.5177774 34.714618 0.17075993 23.21344 12.345683 26.292199
3850 0.83392227 2.1631514 -5.5426333 34.681146 0.82106473 22.510204 11.678329 25.359272
3900 0.82230654 2.0017132 -5.5276756 34.650221 0.48735732 23.444809 12.339117 26.493638
3950 0.81929288 2.1749936 -5.5256673 34.61976 0.089219805 23.540062 11.527925 26.211211
4000 0.83415169 2.0446791 -5.5506187 34.591266 0.15593937 23.742282 11.26508 26.279231
4050 0.82362522 2.1998083 -5.5375157 34.563164 0.25405351 23.913834 11.081011 26.356408
4100 0.82589505 2.3074345 -5.543718 34.537763 0.080213125 24.03253 10.435108 26.200266
4150 0.83855297 2.2424199 -5.5658171 34.517758 0.62913338 23.974257 8.5079223 25.439138
4200 0.82522111 2.2622619 -5.5493275 34.502472 1.8756517 25.754617 7.9996898 26.968414
4250 0.82083124 2.4135193 -5.5464932 34.4919 1.1217436 25.8944 6.7070444 26.748914
4300 0.83059704 2.1375109 -5.5653245 34.487366 0.53623038 26.05979 4.9072346 26.517798
4350 0.82755047 2.1159821 -5.5650889 34.484506 0.10017723 25.405936 4.3532342 25.776195
4400 0.83192877 2.180851 -5.5759565 34.480909 0.053664012 25.993034 2.9844338 26.163805
4450 0.81860572 2.2333381 -5.5602138 34.477183 0.037864077 25.792233 1.9038859 25.862406
4500 0.82821762 2.1142023 -5.5788682 34.474784 0.088221344 26.20329 0.59417897 26.210025
4550 0.8205154 2.0896984 -5.5715531 34.472405 0.016076192 26.083166 -0.58187024 26.089655
4600 0.81294948 2.2274108 -5.5642678 34.469014 0.033774986 25.869616 0.14951307 25.870048
4650 0.80890532 2.1556346 -5.5622407 34.465277 0.67402048 25.413229 -0.56341819 25.419474
4700 0.82070227 1.9852605 -5.583747 34.460206 0.052623237 26.158394 -0.44673492 26.162209
4750 0.81451857 2.1097726 -5.5779782 34.451438 0.12221733 25.733718 -0.9911436 25.752798
4800 0.81300453 2.0211325 -5.5790076 34.439504 0.34536082 26.358606 -1.7335167 26.415548
4850 0.82035497 1.9489595 -5.5929886 34.424097 0.70899626 26.575865 -1.0191012 26.595397
4900 0.8127066 2.1312269 -5.584271 34.405998 0.087959314 26.185217 -1.1329105 26.209713
4950 0.81252621 2.1094866 -5.5866296 34.387869 0.79067667 26.564722 -1.8456354 26.628759
5000 0.80575936 2.1875995 -5.579054 34.370679 0.031787364 26.027557 -2.2666774 26.12607
Loop time of 32.2397 on 1 procs for 5000 steps with 5120 atoms
Performance: 53598.557 tau/day, 155.088 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.967 | 22.967 | 22.967 | 0.0 | 71.24
Neigh | 2.9914 | 2.9914 | 2.9914 | 0.0 | 9.28
Comm | 0.37485 | 0.37485 | 0.37485 | 0.0 | 1.16
Output | 0.064337 | 0.064337 | 0.064337 | 0.0 | 0.20
Modify | 5.7143 | 5.7143 | 5.7143 | 0.0 | 17.72
Other | | 0.1281 | | | 0.40
Nlocal: 5120 ave 5120 max 5120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7962 ave 7962 max 7962 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 296101 ave 296101 max 296101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 296101
Ave neighs/atom = 57.8322
Neighbor list builds = 283
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:32
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