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lammps/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4
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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 4 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) = 4.023 | 4.027 | 4.03 Mbytes
Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3]
0 0.8 5.1872229 -4.8361269 34 152.02869 34.711006 -0.72709593 34.71862
50 1.0819371 3.9250728 -5.2655842 34.02563 0.51385908 26.505979 0.2187864 26.506882
100 1.1182271 3.5397251 -5.3331401 34.100753 2.1059904 27.025883 -0.12127124 27.026156
150 1.1121434 3.7845571 -5.3440494 34.213993 1.7206575 26.894862 -1.3261751 26.927539
200 1.1446439 3.4114364 -5.4199119 34.358914 2.383615 27.054401 -1.4211151 27.091699
250 1.1115073 3.5603047 -5.3988013 34.517397 0.60819391 26.51404 -1.4089688 26.55145
300 1.0828478 3.7411116 -5.3842818 34.673948 0.73987465 26.528178 -2.062382 26.608225
350 1.0342597 3.9206217 -5.3384367 34.825105 0.99965014 26.657737 -1.6211152 26.706983
400 1.0064356 3.9929044 -5.324003 34.97579 0.41927007 26.402623 -1.7087432 26.457859
450 0.96799277 4.2764255 -5.2947175 35.133839 0.77739461 26.503753 -2.5217998 26.623456
500 0.94691076 4.1007962 -5.2922124 35.301893 0.17015805 26.212252 -2.0421698 26.291683
550 0.93675297 3.7404088 -5.3056917 35.474301 0.56247039 26.335926 -3.205722 26.530316
600 0.92707577 3.5439822 -5.3176094 35.641282 0.04054693 25.679461 -3.0301039 25.857615
650 0.91828226 3.1833648 -5.3278237 35.794766 0.8427054 26.4003 -3.6331211 26.649117
700 0.9084826 2.8374306 -5.3327944 35.928138 1.5635222 26.605971 -3.8575939 26.884173
750 0.91219559 2.46172 -5.3548299 36.039156 6.3772911 27.350725 -4.8971146 27.785678
800 0.90000337 2.2187716 -5.3499181 36.126451 4.9080838 27.085156 -5.1291678 27.566538
850 0.9003432 1.8634244 -5.3614648 36.189019 0.0081092188 25.497333 -5.4038153 26.063676
900 0.89741573 1.5697398 -5.3660799 36.226074 0.011155479 25.312724 -6.2574069 26.074684
950 0.88871454 1.4427205 -5.3604669 36.237407 0.3287078 25.659237 -6.232896 26.405406
1000 0.88606353 1.3088636 -5.3626576 36.226015 0.30068168 24.554896 -7.2832017 25.612262
1050 0.88527541 1.3194263 -5.3666773 36.19311 0.10646314 24.514921 -7.9419424 25.76928
1100 0.87522001 1.2852124 -5.3556811 36.143056 0.13675329 24.865981 -8.446822 26.261489
1150 0.8805978 1.246973 -5.3671716 36.0781 0.00043275463 24.187039 -9.4985495 25.98529
1200 0.85711495 1.376588 -5.3346243 36.002427 0.47623639 23.691349 -9.4648541 25.512026
1250 0.88116805 1.3562001 -5.3731036 35.919289 0.32797055 23.322103 -10.54448 25.595049
1300 0.87178482 1.5046564 -5.3610798 35.831278 0.17704849 24.190231 -10.314689 26.29753
1350 0.87022621 1.6830825 -5.3603618 35.743318 0.0052854997 23.731157 -10.747465 26.051408
1400 0.89019669 1.6144812 -5.3921986 35.659687 1.4152796 22.8393 -10.551347 25.158787
1450 0.88852819 1.7587964 -5.3918592 35.580319 0.63560961 23.599033 -12.195 26.563742
1500 0.89029085 1.8772498 -5.3966098 35.509232 0.20895386 23.055083 -12.703366 26.323229
1550 0.88639722 2.2284824 -5.3933288 35.449043 0.44413965 22.448774 -12.156068 25.528757
1600 0.88816451 2.2167704 -5.3994757 35.401661 0.12210235 23.108351 -12.44643 26.247085
1650 0.89154791 2.3397824 -5.4086923 35.365815 0.4820208 23.090699 -12.984179 26.490928
1700 0.88518032 2.5351236 -5.4041601 35.343757 0.080806002 22.749825 -12.99762 26.201005
1750 0.86848721 2.5527491 -5.3851928 35.336433 0.045102165 22.357111 -13.564328 26.15017
1800 0.88501061 2.5215825 -5.4169341 35.340849 0.27488483 22.086584 -14.408273 26.370732
1850 0.8716061 2.5809558 -5.4045854 35.355038 0.042909785 21.270956 -14.695278 25.853525
1900 0.85672517 2.4836326 -5.3902797 35.375469 0.72877764 21.639909 -15.474764 26.603646
1950 0.85133731 2.3141629 -5.3902573 35.398523 0.0016908803 21.106617 -15.132733 25.970924
2000 0.86152109 2.1562002 -5.4132601 35.419851 0.371016 21.325237 -15.614625 26.430706
2050 0.86243551 2.019931 -5.4220349 35.436069 0.017935421 20.4131 -16.255418 26.094698
2100 0.87417672 1.8083823 -5.4464117 35.445091 0.18429432 19.75625 -17.365705 26.303558
2150 0.85872128 1.7608768 -5.4293103 35.44341 0.91209166 20.149648 -17.480387 26.675312
2200 0.86615373 1.8372778 -5.4458315 35.430616 0.10151993 18.559234 -17.885469 25.7747
2250 0.85053605 1.7198437 -5.4272104 35.408688 0.96154548 17.200861 -18.562206 25.306622
2300 0.85400281 1.7939644 -5.4364682 35.377708 0.12283263 18.759325 -18.358539 26.247823
2350 0.85495278 1.5856029 -5.4417321 35.337987 0.20564329 18.967923 -18.248149 26.320658
2400 0.84606771 1.7782708 -5.4315646 35.287411 0.10063977 19.185527 -17.878215 26.224321
2450 0.85210051 1.8190391 -5.4432116 35.232321 0.69988647 19.268861 -18.325448 26.59156
2500 0.85304715 1.7466204 -5.4470889 35.175245 0.0048314937 18.09176 -18.74157 26.04915
2550 0.85401123 1.8601945 -5.4509309 35.115748 0.99467901 17.170045 -18.574587 25.294777
2600 0.85778606 1.974012 -5.4586742 35.058013 0.0026599702 17.438966 -19.333395 26.036469
2650 0.8521239 2.0606329 -5.4526006 35.003616 0.091056354 17.16363 -19.244738 25.786627
2700 0.85918482 2.0766792 -5.4658947 34.954171 0.89590606 15.77108 -19.822153 25.330707
2750 0.85786577 2.225549 -5.4667773 34.911468 0.26577575 15.769018 -21.128817 26.364538
2800 0.86764664 2.2325018 -5.4849414 34.877604 0.47167555 14.950515 -20.675229 25.514369
2850 0.85209564 2.3434319 -5.465734 34.852715 2.7350296 13.51553 -20.829996 24.830592
2900 0.85757283 2.3512971 -5.4786051 34.836138 0.14816492 14.06033 -21.545946 25.727819
2950 0.86098926 2.3480431 -5.4890615 34.826408 0.26401534 13.381395 -22.714827 26.363329
3000 0.85413421 2.3243973 -5.4844129 34.823242 0.024244334 12.739486 -22.538687 25.889899
3050 0.85015323 2.5479266 -5.4844303 34.825228 0.4463147 12.990582 -21.975063 25.527605
3100 0.8530523 2.3643505 -5.495343 34.834883 0.12144265 12.844293 -22.321989 25.753583
3150 0.85098478 2.2521299 -5.4990526 34.848419 0.33194916 12.747856 -23.126671 26.4074
3200 0.84391449 2.2650057 -5.495222 34.862626 0.031888328 12.788845 -22.782174 26.12627
3250 0.84807155 2.1715388 -5.5080873 34.877548 0.082426694 13.316219 -22.09441 25.796989
3300 0.83028242 2.242889 -5.4878846 34.89175 1.1334975 14.326678 -22.593363 26.752827
3350 0.82924001 2.0324002 -5.4924558 34.903232 0.35473989 14.354166 -22.181868 26.421153
3400 0.83032841 2.0003371 -5.4997142 34.908733 0.041677437 14.528378 -21.735998 26.144356
3450 0.82908891 1.8683902 -5.5029185 34.907936 0.02365857 15.069507 -21.053887 25.891237
3500 0.82842914 1.9165344 -5.5064218 34.898681 0.17663531 15.27043 -20.674834 25.702817
3550 0.82735822 1.98221 -5.5088197 34.88272 1.5607134 14.915228 -20.208431 25.116622
3600 0.82642915 1.8422766 -5.5110752 34.8611 1.1861112 15.312314 -20.051953 25.229899
3650 0.82556781 1.9351408 -5.5130349 34.833406 1.018872 16.152478 -19.454871 25.286252
3700 0.82360651 1.9791184 -5.5128431 34.802021 0.14080727 16.907104 -19.401616 25.734663
3750 0.83017793 1.9855734 -5.5253254 34.768644 0.15311334 16.969506 -19.331958 25.723311
3800 0.82362926 2.1029656 -5.5179624 34.734178 0.10807487 17.892584 -18.542426 25.76754
3850 0.82313508 2.0781681 -5.5196175 34.70093 0.13343085 19.072706 -17.28778 25.741707
3900 0.83643385 2.0570262 -5.5421224 34.669761 0.00022792038 19.551677 -17.1548 26.010675
3950 0.82346174 2.0842322 -5.5252757 34.640849 0.0093759386 20.892792 -15.590263 26.068469
4000 0.83485868 2.1196669 -5.5451736 34.612396 0.31198053 21.630258 -15.126984 26.394956
4050 0.82729429 2.2033274 -5.5365945 34.585721 0.53752252 21.283533 -14.011497 25.481578
4100 0.82040242 2.1757309 -5.5292269 34.562271 0.36031984 22.047609 -12.961927 25.575548
4150 0.81932521 2.285666 -5.5307807 34.542102 0.84343149 22.486289 -11.70555 25.350604
4200 0.83819319 2.231174 -5.5625532 34.526447 0.47190752 23.311855 -12.57189 26.485751
4250 0.82542274 2.1874789 -5.5472057 34.513795 0.70518398 23.411553 -12.614639 26.593795
4300 0.81971158 2.241167 -5.5424504 34.503969 0.26707612 23.089805 -12.727793 26.365429
4350 0.83255377 2.1295532 -5.5657895 34.496326 0.072548591 23.003138 -12.52181 26.190458
4400 0.8128474 2.3327845 -5.5402264 34.490126 0.0013023434 23.020811 -12.029795 25.974482
4450 0.82013491 2.3069915 -5.5554953 34.488039 0.041123896 23.632908 -11.178674 26.143394
4500 0.81411544 2.2247193 -5.5509183 34.488014 0.54440601 23.010678 -10.938506 25.478269
4550 0.82814624 2.1142779 -5.5763482 34.487885 0.1518945 23.696817 -11.351972 26.275585
4600 0.82929492 2.090881 -5.5823492 34.486698 0.0045520899 23.538527 -10.929741 25.952292
4650 0.81061417 1.9818043 -5.5584018 34.484038 0.012526806 23.993543 -10.219174 26.079142
4700 0.81816105 1.9605811 -5.5735005 34.476764 1.2079835 25.151166 -9.1888856 26.777169
4750 0.81657042 2.0064313 -5.5744795 34.465784 1.2045017 25.487486 -8.2063886 26.776048
4800 0.81789335 2.0838696 -5.5796632 34.451996 0.27642542 24.647157 -7.023095 25.62823
4850 0.80649339 1.9892413 -5.5654796 34.436067 0.024697945 25.09823 -6.3492244 25.888874
4900 0.81673441 2.0125635 -5.5835037 34.416236 0.0011188576 25.446818 -5.2182483 25.976348
4950 0.82250033 1.9770391 -5.5946082 34.394723 0.72696707 26.37002 -3.5122842 26.602896
5000 0.80762758 2.075517 -5.5746076 34.371696 0.12796344 26.102184 -2.8094827 26.252946
Loop time of 10.3394 on 4 procs for 5000 steps with 5120 atoms
Performance: 167127.370 tau/day, 483.586 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.029 | 6.0128 | 7.1918 | 35.0 | 58.15
Neigh | 0.65673 | 0.75825 | 0.88597 | 10.3 | 7.33
Comm | 0.43982 | 1.5284 | 2.4112 | 60.5 | 14.78
Output | 0.022835 | 0.023039 | 0.023453 | 0.2 | 0.22
Modify | 1.7294 | 1.9472 | 2.5687 | 25.7 | 18.83
Other | | 0.06978 | | | 0.67
Nlocal: 1280 ave 1404 max 1214 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 3521.25 ave 3581 max 3426 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 73872.2 ave 87973 max 64161 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 295489
Ave neighs/atom = 57.7127
Neighbor list builds = 278
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:10
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