LAMMPS (21 Nov 2023) # LAMMPS input file variable temp index 298 variable run string system01 variable lbox index 56 # ------------- Initializatiion units real atom_style full bond_style harmonic angle_style harmonic dihedral_style harmonic improper_style umbrella special_bonds dreiding pair_style soft 1.0 # ------------- read data read_data system.data Reading data file ... orthogonal box = (0 0 0) to (50 50 50) 1 by 2 by 2 MPI processor grid reading atoms ... 11130 atoms scanning bonds ... 3 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 12 = max dihedrals/atom scanning impropers ... 3 = max impropers/atom reading bonds ... 11970 bonds reading angles ... 19600 angles reading dihedrals ... 30450 dihedrals reading impropers ... 4830 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 4 = max # of 1-2 neighbors 7 = max # of 1-3 neighbors 11 = max # of special neighbors special bonds CPU = 0.041 seconds read_data CPU = 1.303 seconds include PARM.lammps pair_coeff 1 1 0.449657 2.412031 pair_coeff 2 2 0.0005 4.07 pair_coeff 3 3 0.0774 3.2625601957 pair_coeff 4 4 0.0152 2.84642140446 pair_coeff 5 5 0.0957 3.03315377578 pair_coeff 6 6 0.0951 3.47299047293 pair_coeff 7 7 0.0951 3.47299047293 pair_coeff 8 8 0.0957 3.03315377578 bond_coeff 1 350.0 1.43 bond_coeff 2 350.0 0.99 bond_coeff 3 350.0 0.98 bond_coeff 4 700.0 1.33 bond_coeff 5 350.0 0.935 bond_coeff 6 700.0 1.275 bond_coeff 7 350.0 1.09 bond_coeff 8 700.0 1.22 bond_coeff 9 350.0 1.375 bond_coeff 10 350.0 1.53 bond_coeff 11 350.0 1.42 bond_coeff 12 350.0 1.32 angle_coeff 1 50.0 120.0 angle_coeff 2 50.0 104.51 angle_coeff 3 50.0 109.471 angle_coeff 4 50.0 120.0 dihedral_coeff 1 5.625000 -1 2 dihedral_coeff 2 0.083333 -1 6 dihedral_coeff 3 0.111111 1 3 dihedral_coeff 4 0.166667 -1 2 dihedral_coeff 5 5.625000 -1 2 dihedral_coeff 6 0.083333 -1 6 dihedral_coeff 7 0.166667 1 3 dihedral_coeff 8 0.111111 1 3 dihedral_coeff 9 0.083333 -1 6 dihedral_coeff 10 0.166667 1 3 dihedral_coeff 11 0.083333 -1 6 improper_coeff 1 40.0 0.0 improper_coeff 2 40.0 0.0 # ------------- set output dump TRJ all custom 1000 ${run}.dump id xu yu zu dump TRJ all custom 1000 system01.dump id xu yu zu # ------------- soft neighbor 2 bin neigh_modify every 1 delay 0 check yes velocity all create ${temp} 12345 velocity all create 298 12345 timestep 1 thermo 1000 thermo_style custom step etotal evdwl ecoul elong ebond eangle edihed eimp pe ke temp press vol density fix 1 all nvt temp ${temp} ${temp} $(100*dt) drag 2 fix 1 all nvt temp 298 ${temp} $(100*dt) drag 2 fix 1 all nvt temp 298 298 $(100*dt) drag 2 fix 1 all nvt temp 298 298 100 drag 2 run 30000 Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.07 ghost atom cutoff = 6.07 binsize = 3.035, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair soft, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.91 | 13.94 | 13.98 Mbytes Step TotEng E_vdwl E_coul E_long E_bond E_angle E_dihed E_impro PotEng KinEng Temp Press Volume Density 0 88406.005 1172.876 0 0 53534.615 8134.3563 14397.202 1281.2713 78520.321 9885.6836 298 -217690.59 125000 1.4453379 1000 37411.194 1081.5115 0 0 5166.9669 8350.5392 6410.7262 934.46044 21944.204 15466.99 466.24625 2482.4317 125000 1.4453379 2000 27897.917 799.63593 0 0 3826.6134 6343.8779 5129.4453 666.78033 16766.353 11131.564 335.55656 -3415.0696 125000 1.4453379 3000 25507.584 696.25025 0 0 3305.8694 5806.9759 4889.2521 578.89295 15277.241 10230.343 308.38961 -1805.9171 125000 1.4453379 4000 25134.273 661.38297 0 0 3317.1677 5905.4262 4807.3609 573.17511 15264.513 9869.7597 297.51998 -165.20955 125000 1.4453379 5000 25017.332 644.24672 0 0 3308.1624 5827.6208 4804.7863 564.86195 15149.678 9867.6541 297.45651 596.63569 125000 1.4453379 6000 25045.88 651.94317 0 0 3296.749 5756.7462 4774.1527 583.90723 15063.498 9982.3819 300.91493 434.53577 125000 1.4453379 7000 24976.301 628.98651 0 0 3289.1699 5826.1842 4769.7225 562.19969 15076.263 9900.038 298.43271 558.71205 125000 1.4453379 8000 24997.276 664.06978 0 0 3395.9263 5771.8136 4717.5011 574.88032 15124.191 9873.0852 297.62022 -413.19805 125000 1.4453379 9000 25007.541 624.60526 0 0 3312.097 5742.9191 4770.0192 569.48973 15019.13 9988.4104 301.09666 -361.98434 125000 1.4453379 10000 24986.73 621.91607 0 0 3357.5037 5725.279 4754.6164 555.02966 15014.345 9972.3854 300.61359 1076.6104 125000 1.4453379 11000 25022.564 626.6852 0 0 3382.8941 5822.7229 4768.1719 573.43214 15173.906 9848.6583 296.88388 1256.8608 125000 1.4453379 12000 25015.652 627.63733 0 0 3389.3838 5802.8376 4742.6143 581.13821 15143.611 9872.0404 297.58873 804.80738 125000 1.4453379 13000 25041.644 637.12586 0 0 3397.34 5850.9097 4729.4911 563.09811 15177.965 9863.6788 297.33667 -1049.4075 125000 1.4453379 14000 25068.385 637.09748 0 0 3475.2525 5737.3381 4675.7187 583.11403 15108.521 9959.8641 300.23614 286.75334 125000 1.4453379 15000 25046.833 619.75534 0 0 3417.1225 5817.969 4731.7452 544.60024 15131.192 9915.6402 298.90303 -523.31138 125000 1.4453379 16000 24989.61 620.62039 0 0 3450.1804 5714.5838 4699.8075 574.4173 15059.609 9930.0008 299.33592 392.20109 125000 1.4453379 17000 25000.829 637.37727 0 0 3464.6096 5763.5302 4703.8842 569.87369 15139.275 9861.5539 297.27262 1012.1314 125000 1.4453379 18000 25005.991 612.51838 0 0 3488.2997 5852.9431 4674.8285 549.39035 15177.98 9828.0105 296.26147 -101.25911 125000 1.4453379 19000 25022.298 629.88037 0 0 3463.5458 5808.8264 4633.2867 552.66214 15088.201 9934.0963 299.45938 865.1879 125000 1.4453379 20000 25026.575 623.86067 0 0 3422.2947 5863.0767 4643.6427 558.85231 15111.727 9914.8476 298.87913 1342.685 125000 1.4453379 21000 25064.325 629.34915 0 0 3572.5745 5732.6935 4633.0567 563.58833 15131.262 9933.0629 299.42823 -407.82874 125000 1.4453379 22000 25046.887 626.97578 0 0 3587.2141 5803.4223 4638.2034 534.31293 15190.128 9856.7587 297.12807 -1222.3931 125000 1.4453379 23000 25025.746 630.70111 0 0 3534.8459 5793.1834 4673.4695 575.85175 15208.052 9817.6948 295.9505 756.80915 125000 1.4453379 24000 25059.273 636.34576 0 0 3459.7095 5762.8568 4659.0804 561.59731 15079.59 9979.6829 300.83357 -154.70879 125000 1.4453379 25000 25062.082 638.00841 0 0 3516.8421 5816.6433 4648.266 567.66728 15187.427 9874.6547 297.66754 948.22897 125000 1.4453379 26000 25032.294 619.63174 0 0 3569.0645 5756.5336 4670.9401 575.05452 15191.224 9841.07 296.65514 -3.9493407 125000 1.4453379 27000 25070.083 632.65485 0 0 3513.9423 5802.4651 4623.8276 552.46215 15125.352 9944.7308 299.77995 -7.2065209 125000 1.4453379 28000 25063.496 630.86013 0 0 3469.8313 5799.6954 4623.1875 566.82233 15090.397 9973.0996 300.63512 927.23312 125000 1.4453379 29000 25038.969 615.63705 0 0 3548.4975 5833.7783 4640.5014 559.97673 15198.391 9840.5782 296.64032 276.63075 125000 1.4453379 30000 25037.594 613.52884 0 0 3477.534 5762.6013 4625.2129 557.03258 15035.91 10001.685 301.49681 535.03651 125000 1.4453379 Loop time of 134.129 on 4 procs for 30000 steps with 11130 atoms Performance: 19.325 ns/day, 1.242 hours/ns, 223.665 timesteps/s, 2.489 Matom-step/s 88.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.658 | 35.439 | 40.24 | 48.1 | 26.42 Bond | 34.748 | 37.232 | 40.551 | 35.2 | 27.76 Neigh | 15.245 | 15.266 | 15.299 | 0.5 | 11.38 Comm | 30.912 | 38.619 | 43.586 | 75.5 | 28.79 Output | 0.19472 | 0.19939 | 0.20376 | 0.8 | 0.15 Modify | 4.4185 | 4.8185 | 5.101 | 13.2 | 3.59 Other | | 2.555 | | | 1.91 Nlocal: 2782.5 ave 2942 max 2619 min Histogram: 1 0 0 0 1 1 0 0 0 1 Nghost: 4836 ave 4930 max 4722 min Histogram: 1 0 0 0 0 1 1 0 0 1 Neighs: 68226.5 ave 77008 max 60920 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 272906 Ave neighs/atom = 24.519856 Ave special neighs/atom = 5.672956 Neighbor list builds = 1625 Dangerous builds = 0 # ------------- Lower the density variable scalex equal $(v_lbox/lx) variable scalex equal 1.1200000000000001066 fix 2 all deform 10 x scale ${scalex} y scale ${scalex} z scale ${scalex} fix 2 all deform 10 x scale 1.12 y scale ${scalex} z scale ${scalex} fix 2 all deform 10 x scale 1.12 y scale 1.12 z scale ${scalex} fix 2 all deform 10 x scale 1.12 y scale 1.12 z scale 1.12 run 30000 Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 15.26 | 15.39 | 15.68 Mbytes Step TotEng E_vdwl E_coul E_long E_bond E_angle E_dihed E_impro PotEng KinEng Temp Press Volume Density 30000 25037.594 613.52884 0 0 3477.534 5762.6013 4625.2129 557.03258 15035.91 10001.685 301.49681 535.03651 125000 1.4453379 31000 25091.268 616.21168 0 0 3556.6779 5871.9556 4618.9852 567.09481 15230.925 9860.3428 297.23611 328.12306 126506.01 1.4281317 32000 25072.876 592.04052 0 0 3513.1365 5798.3277 4648.2195 567.30741 15119.032 9953.8441 300.05467 -433.64674 128024.06 1.4111975 33000 25043.257 589.44322 0 0 3584.1449 5663.9073 4659.528 566.72687 15063.75 9979.5065 300.82825 943.72844 129554.22 1.39453 34000 25054.678 589.6075 0 0 3580.5642 5822.7548 4697.5423 564.50577 15254.975 9799.7037 295.40817 -1167.6415 131096.51 1.3781239 35000 25048.333 593.30184 0 0 3657.5905 5765.8898 4633.8252 572.40771 15223.015 9825.3176 296.18029 680.89718 132651 1.3619742 36000 25046.052 576.88766 0 0 3521.1581 5818.7075 4616.4925 549.34262 15082.588 9963.4634 300.34464 1008.1862 134217.73 1.3460758 37000 25023.649 546.51707 0 0 3600.5833 5877.8536 4584.7576 567.19764 15176.909 9846.7399 296.82606 417.4783 135796.74 1.3304239 38000 25024.853 556.39515 0 0 3606.7516 5786.5566 4605.8019 562.26303 15117.768 9907.0845 298.64512 777.52626 137388.1 1.3150138 39000 25013.031 549.9937 0 0 3583.5492 5743.1423 4668.7877 563.54101 15109.014 9904.0168 298.55265 -61.302197 138991.83 1.2998407 40000 24999.953 549.71665 0 0 3602.0433 5776.2276 4736.7973 571.95327 15236.738 9763.2151 294.30823 1025.5488 140608 1.2849001 41000 25009.644 519.40258 0 0 3480.4361 5730.0051 4704.7164 581.47217 15016.032 9993.6117 301.25345 113.94668 142236.65 1.2701877 42000 24996.884 532.73741 0 0 3609.2732 5798.3439 4619.2977 570.7022 15130.354 9866.5298 297.42261 430.3089 143877.82 1.255699 43000 25018.223 533.5637 0 0 3616.6796 5780.2857 4601.0368 560.10261 15091.668 9926.5547 299.23204 13.751084 145531.58 1.2414298 44000 25001.795 531.73524 0 0 3591.6254 5730.1653 4643.6879 567.57373 15064.787 9937.0076 299.54714 -84.703036 147197.95 1.227376 45000 24992.724 521.17354 0 0 3556.3663 5840.1551 4623.7191 569.48935 15110.903 9881.8206 297.88355 1102.9911 148877 1.2135336 46000 25006.918 504.89282 0 0 3601.0318 5792.385 4673.2311 576.82114 15148.362 9858.5562 297.18225 104.13578 150568.77 1.1998985 47000 25028.535 511.78684 0 0 3658.9585 5755.7494 4672.4528 568.55874 15167.506 9861.0286 297.25678 121.02608 152273.3 1.1864669 48000 25012.797 491.78072 0 0 3598.9192 5697.6968 4656.2035 569.46923 15014.069 9998.7273 301.40766 314.04167 153990.66 1.1732351 49000 24992.005 485.36701 0 0 3621.1723 5809.6347 4644.6046 581.61112 15142.39 9849.6155 296.91274 434.90557 155720.87 1.1601992 50000 24996.045 483.33804 0 0 3638.3014 5878.0962 4615.3662 555.87129 15170.973 9825.0717 296.17288 -442.60548 157464 1.1473558 51000 24979.084 477.49305 0 0 3549.4628 5701.6843 4702.0467 575.06425 15005.751 9973.3327 300.64215 331.08702 159220.09 1.1347013 52000 24989.676 488.43367 0 0 3599.4872 5786.6952 4679.1409 587.9127 15141.67 9848.0068 296.86425 -203.22015 160989.18 1.1222321 53000 24989.465 496.4738 0 0 3651.6059 5749.2216 4617.4023 573.73148 15088.435 9901.0301 298.46261 7.1696829 162771.34 1.109945 54000 24971.567 475.77588 0 0 3649.7135 5728.3093 4657.1489 573.93316 15084.881 9886.6863 298.03022 605.71414 164566.59 1.0978367 55000 24959.461 478.7211 0 0 3679.5228 5762.1445 4624.497 543.83188 15088.717 9870.7434 297.54963 407.60947 166375 1.0859038 56000 24966.828 456.3208 0 0 3687.7589 5807.1243 4586.0314 546.99099 15084.226 9882.6016 297.90709 684.10984 168196.61 1.0741432 57000 24982.768 458.49251 0 0 3727.4844 5736.5935 4609.4412 555.36324 15087.375 9895.3935 298.2927 -144.72834 170031.46 1.0625518 58000 24959.052 449.32191 0 0 3614.1737 5774.8572 4661.3103 578.3185 15077.982 9881.07 297.86092 914.66629 171879.62 1.0511266 59000 24937.494 454.76555 0 0 3713.667 5728.1813 4650.8179 572.11873 15119.551 9817.9436 295.958 237.62405 173741.11 1.0398646 60000 24937.941 455.37767 0 0 3671.6151 5726.9541 4602.3562 572.5632 15028.866 9909.0749 298.70512 351.98376 175616 1.028763 Loop time of 115.911 on 4 procs for 30000 steps with 11130 atoms Performance: 22.362 ns/day, 1.073 hours/ns, 258.819 timesteps/s, 2.881 Matom-step/s 89.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.888 | 30.181 | 32.989 | 33.8 | 26.04 Bond | 34.874 | 36.839 | 39.562 | 28.0 | 31.78 Neigh | 12.437 | 12.455 | 12.472 | 0.4 | 10.75 Comm | 24.688 | 29.988 | 34.002 | 62.1 | 25.87 Output | 0.2016 | 0.20644 | 0.21102 | 0.8 | 0.18 Modify | 3.4122 | 3.8649 | 4.289 | 20.3 | 3.33 Other | | 2.376 | | | 2.05 Nlocal: 2782.5 ave 2827 max 2759 min Histogram: 1 1 1 0 0 0 0 0 0 1 Nghost: 4215.5 ave 4418 max 4088 min Histogram: 1 1 0 1 0 0 0 0 0 1 Neighs: 51320.8 ave 52619 max 50554 min Histogram: 1 1 0 1 0 0 0 0 0 1 Total # of neighbors = 205283 Ave neighs/atom = 18.444115 Ave special neighs/atom = 5.672956 Neighbor list builds = 1537 Dangerous builds = 0 unfix 1 unfix 2 # ------------- Full potentential + minimisation. # ------------- It disentangles ions forming pairs. pair_style lj/cut/coul/long 12 kspace_style pppm 1.0e-4 include PARM.lammps pair_coeff 1 1 0.449657 2.412031 pair_coeff 2 2 0.0005 4.07 pair_coeff 3 3 0.0774 3.2625601957 pair_coeff 4 4 0.0152 2.84642140446 pair_coeff 5 5 0.0957 3.03315377578 pair_coeff 6 6 0.0951 3.47299047293 pair_coeff 7 7 0.0951 3.47299047293 pair_coeff 8 8 0.0957 3.03315377578 bond_coeff 1 350.0 1.43 bond_coeff 2 350.0 0.99 bond_coeff 3 350.0 0.98 bond_coeff 4 700.0 1.33 bond_coeff 5 350.0 0.935 bond_coeff 6 700.0 1.275 bond_coeff 7 350.0 1.09 bond_coeff 8 700.0 1.22 bond_coeff 9 350.0 1.375 bond_coeff 10 350.0 1.53 bond_coeff 11 350.0 1.42 bond_coeff 12 350.0 1.32 angle_coeff 1 50.0 120.0 angle_coeff 2 50.0 104.51 angle_coeff 3 50.0 109.471 angle_coeff 4 50.0 120.0 dihedral_coeff 1 5.625000 -1 2 dihedral_coeff 2 0.083333 -1 6 dihedral_coeff 3 0.111111 1 3 dihedral_coeff 4 0.166667 -1 2 dihedral_coeff 5 5.625000 -1 2 dihedral_coeff 6 0.083333 -1 6 dihedral_coeff 7 0.166667 1 3 dihedral_coeff 8 0.111111 1 3 dihedral_coeff 9 0.083333 -1 6 dihedral_coeff 10 0.166667 1 3 dihedral_coeff 11 0.083333 -1 6 improper_coeff 1 40.0 0.0 improper_coeff 2 40.0 0.0 dump TRJ2 all custom 1 ${run}.min id xu yu zu dump TRJ2 all custom 1 system01.min id xu yu zu minimize .01 .001 1000 100000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.19829927 grid = 18 18 18 stencil order = 5 estimated absolute RMS force accuracy = 0.024530488 estimated relative force accuracy = 7.3872835e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4508 1620 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 35.52 | 35.53 | 35.53 Mbytes Step TotEng E_vdwl E_coul E_long E_bond E_angle E_dihed E_impro PotEng KinEng Temp Press Volume Density 60000 1.5163874e+17 1.5163874e+17 34577.604 -24372.21 3672.3303 5726.9541 4602.3562 572.5632 1.5163874e+17 9909.0749 298.70512 2.3682644e+17 175616 1.028763 60100 49106.567 30055.296 18468.976 -33073.039 4744.9695 8523.9866 9737.3386 739.96514 39197.492 9909.0749 298.70512 32244.58 175616 1.028763 Loop time of 6.444 on 4 procs for 100 steps with 11130 atoms 94.5% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 1.51638737540558e+17 39424.4072416516 39197.4922386758 Force two-norm initial, final = 2.5106007e+19 1212.4651 Force max component initial, final = 1.2626802e+19 359.22766 Final line search alpha, max atom move = 0.0011093524 0.39851006 Iterations, force evaluations = 100 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0972 | 4.2521 | 4.6641 | 11.6 | 65.99 Bond | 0.18538 | 0.20104 | 0.22934 | 3.9 | 3.12 Kspace | 0.58658 | 1.032 | 1.1925 | 25.3 | 16.01 Neigh | 0.25854 | 0.26447 | 0.27041 | 1.2 | 4.10 Comm | 0.11618 | 0.11625 | 0.11632 | 0.0 | 1.80 Output | 0.46907 | 0.4929 | 0.51073 | 2.2 | 7.65 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08526 | | | 1.32 Nlocal: 2782.5 ave 2842 max 2759 min Histogram: 2 1 0 0 0 0 0 0 0 1 Nghost: 13830.5 ave 13854 max 13771 min Histogram: 1 0 0 0 0 0 0 0 1 2 Neighs: 1.02058e+06 ave 1.06119e+06 max 984715 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 4082322 Ave neighs/atom = 366.78544 Ave special neighs/atom = 5.672956 Neighbor list builds = 7 Dangerous builds = 0 undump TRJ2 # ------------- quick equilibration to dissipate the excess energy. velocity all create ${temp} 12345 velocity all create 298 12345 fix 1 all nvt temp ${temp} ${temp} $(100*dt) drag 2 fix 1 all nvt temp 298 ${temp} $(100*dt) drag 2 fix 1 all nvt temp 298 298 $(100*dt) drag 2 fix 1 all nvt temp 298 298 100 drag 2 run 40000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.19829927 grid = 18 18 18 stencil order = 5 estimated absolute RMS force accuracy = 0.024530488 estimated relative force accuracy = 7.3872835e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4508 1620 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 33.52 | 33.53 | 33.53 Mbytes Step TotEng E_vdwl E_coul E_long E_bond E_angle E_dihed E_impro PotEng KinEng Temp Press Volume Density 60100 49083.176 30055.296 18468.976 -33073.039 4744.9695 8523.9866 9737.3386 739.96514 39197.492 9885.6836 298 32238.491 175616 1.028763 61000 27884.464 22153.97 3343.8786 -41419.463 7749.4993 10123.102 9614.837 812.61098 12378.435 15506.028 467.42305 1400.3371 175616 1.028763 62000 17890.819 21560.22 635.90559 -41912.038 7559.6162 9402.2974 8237.6111 670.84522 6154.4574 11736.362 353.78796 -1038.529 175616 1.028763 63000 14082.536 21511.979 -558.20895 -42052.746 7239.9311 9102.6524 7717.4283 627.98459 3589.0202 10493.515 316.32285 609.98539 175616 1.028763 64000 12765.848 21294.461 -1200.7841 -42097.03 7404.6563 8958.4892 7738.5056 612.59439 2710.8924 10054.956 303.10264 -168.59324 175616 1.028763 65000 12113.087 21217.278 -1492.615 -42166.661 7580.8057 8811.456 7614.4671 606.9928 2171.724 9941.3628 299.67843 -814.86821 175616 1.028763 66000 11786.293 21019.479 -1736.3427 -42187.29 7676.397 8986.2291 7438.0742 592.48113 1789.0275 9997.2655 301.36359 -547.33976 175616 1.028763 67000 11572.857 20898.86 -1961.2737 -42189.557 7923.196 8822.3962 7492.6022 621.44876 1607.6723 9965.1847 300.39653 -1544.9334 175616 1.028763 68000 11434.487 21065.998 -2049.934 -42216.6 7841.9007 8862.6339 7322.0692 638.84946 1464.9176 9969.5696 300.52871 -401.11028 175616 1.028763 69000 11342.904 20849.288 -2113.767 -42221.322 8026.2442 8889.5621 7244.8947 642.8531 1317.7531 10025.151 302.2042 -1378.0025 175616 1.028763 70000 11232.987 20684.439 -2233.3403 -42224.909 8079.8125 9033.8707 7304.3001 647.36494 1291.5379 9941.4488 299.68102 -1416.3405 175616 1.028763 71000 11149.483 20923.281 -2428.8576 -42236.272 8149.2045 8995.1147 7269.26 617.06484 1288.7955 9860.6873 297.2465 -841.01275 175616 1.028763 72000 11116.498 20759.517 -2441.5447 -42231.93 8378.5954 8912.7804 7231.8443 628.8942 1238.1563 9878.3417 297.77868 -1689.0872 175616 1.028763 73000 11049.962 21025.094 -2412.4114 -42249.972 8094.7405 8821.7261 7143.1417 628.2456 1050.5647 9999.3976 301.42786 287.29794 175616 1.028763 74000 10975.046 20621.124 -2487.5395 -42218.953 8333.6653 8975.1822 7190.5218 645.40852 1059.4092 9915.6366 298.90292 -1692.4573 175616 1.028763 75000 10975.16 20592.812 -2513.8866 -42271.89 8406.9163 8884.6691 7219.0019 654.29625 971.91948 10003.241 301.54371 -1624.0102 175616 1.028763 76000 10912.077 20832.714 -2722.2589 -42263.685 8401.2898 8889.9782 7260.4768 662.54356 1061.0583 9851.0183 296.95503 -1214.6157 175616 1.028763 77000 10823.836 20665.514 -2740.9225 -42259.542 8510.471 8947.2065 7195.7805 631.36499 949.87275 9873.9636 297.6467 -1544.7777 175616 1.028763 78000 10797.569 20725.106 -2668.2039 -42264.273 8434.4692 8895.5913 7173.5099 644.14753 940.34717 9857.222 297.14204 -964.95617 175616 1.028763 79000 10775.658 20710.753 -2761.6493 -42257.237 8398.5646 8916.5439 7239.4869 646.46272 892.92464 9882.7337 297.91107 -813.27607 175616 1.028763 80000 10744.985 20457.138 -2654.9059 -42255.644 8556.4192 8959.158 7190.066 611.84584 864.07638 9880.9087 297.85606 -2317.9007 175616 1.028763 81000 10753.235 20551.248 -2825.7929 -42250.58 8513.4963 9022.8583 7186.0618 644.03886 841.33017 9911.9051 298.79043 -1846.6079 175616 1.028763 82000 10691.067 20628.344 -2817.2479 -42263.55 8550.0149 8922.5262 7181.8308 640.47608 842.3944 9848.6723 296.88431 -1760.0367 175616 1.028763 83000 10659.247 20642.668 -2814.5725 -42271.514 8406.4521 8911.9647 7230.6741 649.92209 755.59455 9903.6524 298.54166 -831.06751 175616 1.028763 84000 10614.685 20660.234 -2823.9652 -42270.172 8437.8147 8891.4399 7187.6501 631.95311 714.95422 9899.7307 298.42344 -795.63385 175616 1.028763 85000 10558.383 20641.689 -2956.0403 -42277.934 8434.3265 8934.9982 7189.2557 650.7885 617.08363 9941.2991 299.67651 -825.54335 175616 1.028763 86000 10565.492 20883.724 -2967.3444 -42264.882 8324.9841 8826.0771 7157.009 626.41916 585.9866 9979.5057 300.82823 -249.43135 175616 1.028763 87000 10538.036 20595.211 -2774.0033 -42283.092 8384.8566 8990.4273 7108.6209 646.08674 668.10679 9869.9289 297.52508 -1144.6067 175616 1.028763 88000 10515.541 20588.594 -2903.6806 -42298.785 8458.4756 9018.1995 7156.798 653.46599 673.0675 9842.4731 296.69743 -1687.5409 175616 1.028763 89000 10498.63 20766.143 -3030.5006 -42281.154 8459.0366 8824.1595 7194.3739 648.18209 580.2409 9918.3889 298.98589 -679.43277 175616 1.028763 90000 10500.239 20720.019 -3049.7988 -42283.375 8509.4736 8869.3775 7163.3191 626.84272 555.85794 9944.3813 299.76942 -807.71588 175616 1.028763 91000 10504.224 20539.747 -2875.0147 -42283.041 8597.6202 8906.6038 7114.6875 654.95242 655.55531 9848.6683 296.88419 -1406.2368 175616 1.028763 92000 10503.417 20578.266 -2986.2848 -42286.621 8578.5455 8849.9662 7187.9063 639.6324 561.4098 9942.0074 299.69786 -1851.5249 175616 1.028763 93000 10468.324 20406.921 -2891.9207 -42279.986 8568.4545 8913.3597 7184.7393 686.97182 588.54006 9879.7839 297.82215 -2400.5523 175616 1.028763 94000 10490.566 20467.513 -2926.1327 -42274.07 8451.534 8906.0477 7234.7609 650.268 509.92087 9980.6449 300.86257 -1147.8649 175616 1.028763 95000 10457.144 20650.696 -2952.3384 -42296.722 8453.2914 8924.8791 7179.7551 644.52454 604.08586 9853.0579 297.01651 -773.44418 175616 1.028763 96000 10455.454 20674.929 -3038.9169 -42278.783 8418.6114 9043.6506 7104.334 649.77512 573.60041 9881.8539 297.88455 -979.29173 175616 1.028763 97000 10468.304 20530.171 -2948.5097 -42280.341 8589.555 8907.0328 7120.3629 673.18403 591.45569 9876.8482 297.73366 -1849.2866 175616 1.028763 98000 10448.157 20553.153 -2895.8068 -42277.558 8451.8483 8873.7089 7180.8978 659.30937 545.55213 9902.6048 298.51008 -1014.0818 175616 1.028763 99000 10426.12 20429.438 -2947.4222 -42273.341 8567.4494 8896.846 7199.2782 639.80561 512.05371 9914.066 298.85558 -1438.75 175616 1.028763 100000 10433.95 20493.196 -2946.7939 -42286.272 8615.4004 8922.0799 7162.7275 632.96455 593.30248 9840.648 296.64242 -1847.9207 175616 1.028763 100100 10429.875 20530.518 -3041.9507 -42289.157 8528.3797 8966.8452 7273.294 620.44224 588.37099 9841.5042 296.66823 -1342.3307 175616 1.028763 Loop time of 1378.39 on 4 procs for 40000 steps with 11130 atoms Performance: 2.507 ns/day, 9.572 hours/ns, 29.019 timesteps/s, 322.986 katom-step/s 91.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 779.1 | 859.06 | 928.37 | 196.3 | 62.32 Bond | 47.375 | 49.659 | 51.887 | 29.1 | 3.60 Kspace | 261.89 | 332.44 | 412.87 | 320.3 | 24.12 Neigh | 78.278 | 78.289 | 78.306 | 0.1 | 5.68 Comm | 46.1 | 46.577 | 47.607 | 9.0 | 3.38 Output | 0.31571 | 0.32211 | 0.328 | 0.8 | 0.02 Modify | 4.3626 | 5.526 | 6.2701 | 33.5 | 0.40 Other | | 6.518 | | | 0.47 Nlocal: 2782.5 ave 2869 max 2611 min Histogram: 1 0 0 0 0 0 0 1 0 2 Nghost: 13888.5 ave 14060 max 13802 min Histogram: 2 0 1 0 0 0 0 0 0 1 Neighs: 1.02689e+06 ave 1.12682e+06 max 882738 min Histogram: 1 0 0 0 0 0 1 1 0 1 Total # of neighbors = 4107547 Ave neighs/atom = 369.05184 Ave special neighs/atom = 5.672956 Neighbor list builds = 1915 Dangerous builds = 0 unfix 1 # ------------- NPT simulation fix 1 all npt temp ${temp} ${temp} $(100*dt) iso 1 1 $(1000*dt) drag 2 fix 1 all npt temp 298 ${temp} $(100*dt) iso 1 1 $(1000*dt) drag 2 fix 1 all npt temp 298 298 $(100*dt) iso 1 1 $(1000*dt) drag 2 fix 1 all npt temp 298 298 100 iso 1 1 $(1000*dt) drag 2 fix 1 all npt temp 298 298 100 iso 1 1 1000 drag 2 run 50000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.19829927 grid = 18 18 18 stencil order = 5 estimated absolute RMS force accuracy = 0.024530488 estimated relative force accuracy = 7.3872835e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4508 1620 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 33.53 | 33.82 | 33.92 Mbytes Step TotEng E_vdwl E_coul E_long E_bond E_angle E_dihed E_impro PotEng KinEng Temp Press Volume Density 100100 10429.875 20530.518 -3041.9507 -42289.157 8528.3797 8966.8452 7273.294 620.44224 588.37099 9841.5042 296.66823 -1342.3307 175616 1.028763 101000 10247.149 20442.866 -3008.9639 -42302.398 8380.9403 8848.4408 7261.6932 662.69109 285.26959 9961.8798 300.2969 -245.92447 167316.73 1.0797918 102000 10198.494 20450.27 -2978.0418 -42302.649 8398.8023 8872.48 7247.0494 635.98607 323.89633 9874.5981 297.66583 -235.31764 164160.72 1.100551 103000 10146.555 20437.929 -3155.7148 -42307.327 8499.5487 8906.7518 7263.5053 659.81061 304.50368 9842.0515 296.68473 -180.16912 163501.27 1.1049898 104000 10113.636 20404.907 -3148.3614 -42296.07 8479.8229 8839.3569 7316.6125 676.1072 272.37498 9841.2607 296.66089 137.26347 163807.3 1.1029254 105000 10113.724 20409.84 -3301.3618 -42309.661 8486.0193 8906.3674 7343.5686 653.858 188.63034 9925.0935 299.18799 -997.5291 163799.28 1.1029794 106000 10058.428 20445.339 -3134.8037 -42304.806 8468.5946 8896.78 7300.1776 629.64756 300.92876 9757.4996 294.13594 18.81698 162391.56 1.1125408 107000 10025.631 20509.53 -3291.0115 -42314.37 8497.9085 8894.888 7243.5007 650.88395 191.33014 9834.3005 296.45108 -152.75144 162700.38 1.1104291 108000 10013.991 20254.069 -3125.801 -42313.135 8446.459 8853.1239 7344.2265 643.89452 102.8368 9911.1542 298.7678 -482.85414 162908.96 1.1090073 109000 10008.729 20405.776 -3331.2941 -42306.152 8452.6192 8885.0561 7306.2542 658.48049 70.740733 9937.9884 299.5767 -38.375906 162900.57 1.1090645 110000 10005.226 20292.712 -3361.6718 -42303.574 8523.9343 8894.1091 7329.0977 652.91509 27.52235 9977.7032 300.77389 -774.70336 163011.41 1.1083104 111000 9976.2331 20377.357 -3257.0102 -42297.814 8377.0926 8878.7351 7347.6302 658.94732 84.937491 9891.2957 298.16917 -236.22135 162369.83 1.1126897 112000 9951.0355 20524.679 -3343.1473 -42313.963 8282.7465 8789.1412 7390.3792 645.06476 -25.100541 9976.136 300.72665 656.93321 162479.51 1.1119386 113000 9960.628 20488.547 -3336.6697 -42298.101 8433.0914 8825.8243 7250.795 665.9071 29.394034 9931.234 299.3731 -107.06885 162212.54 1.1137686 114000 9954.8058 20493.613 -3297.4059 -42308.381 8441.3001 8756.4287 7300.9718 665.05359 51.579915 9903.2259 298.5288 -112.0932 162410.16 1.1124134 115000 9931.9408 20160.891 -3264.636 -42302.88 8565.1867 8855.7998 7341.5849 647.70582 3.6514215 9928.2894 299.28433 -1003.3907 162286.45 1.1132614 116000 9948.392 20359.92 -3202.3258 -42295.162 8355.204 8821.9331 7353.0792 660.68645 53.334921 9895.0571 298.28256 99.740558 162349.46 1.1128293 117000 9931.2201 20335.333 -3221.4424 -42300.631 8432.9407 8889.1526 7334.0478 641.61525 111.01569 9820.2044 296.02615 -106.77097 161355.57 1.1196839 118000 9933.0584 20518.105 -3380.9692 -42322.205 8460.0514 8765.124 7398.8588 674.75826 113.72263 9819.3357 295.99997 940.51669 161585.48 1.1180908 119000 9921.2528 20271.89 -3187.7518 -42305.271 8433.1319 8853.8612 7251.603 660.35976 -22.177107 9943.43 299.74074 -181.26204 162079.07 1.1146858 120000 9934.777 20635.277 -3276.0505 -42304.706 8418.109 8674.5538 7234.0214 651.26512 32.469094 9902.3079 298.50113 885.35987 161155.37 1.1210749 121000 9914.5401 20326.206 -3179.4565 -42313.95 8397.7428 8777.4963 7319.4355 646.34505 -26.180805 9940.7209 299.65907 776.0635 160744.42 1.123941 122000 9912.0163 20460.815 -3302.5126 -42301.879 8479.012 8809.6577 7258.7522 645.12396 48.969683 9863.0466 297.31762 647.27624 161510.78 1.1186079 123000 9913.5538 20350.378 -3221.1053 -42300.945 8402.0521 8837.4971 7322.9488 630.29639 21.12165 9892.4321 298.20343 -192.29487 161883.68 1.1160312 124000 9904.9121 20347.769 -3214.8146 -42317.29 8394.5701 8911.8621 7342.9904 658.31805 123.40473 9781.5074 294.85965 767.58243 160899.2 1.1228598 125000 9917.6913 20361.617 -3328.2208 -42323.349 8499.6149 8844.4803 7317.6888 647.51303 19.34427 9898.347 298.38173 100.88086 161947.85 1.115589 126000 9893.2425 20274.199 -3327.3802 -42318.892 8508.8474 8808.0577 7388.0838 643.21338 -23.871484 9917.114 298.94745 -403.23679 161408.27 1.1193183 127000 9890.5965 20481.986 -3333.6125 -42321.32 8371.668 8804.9126 7332.2771 651.23248 -12.855902 9903.4524 298.53563 103.40355 161893.4 1.1159642 128000 9906.832 20509.009 -3270.8697 -42311.031 8464.1814 8811.9336 7312.8202 652.94766 168.99109 9737.8409 293.54334 324.67729 161732.24 1.1170762 129000 9893.2602 20292.063 -3199.9148 -42329.933 8378.8926 8868.4429 7330.2011 672.77222 12.523948 9880.7362 297.85086 -48.381932 161374.76 1.1195507 130000 9881.5053 20253.197 -3237.0685 -42319.019 8437.238 8821.4971 7276.9511 670.10405 -97.101198 9978.6065 300.80112 -1044.3553 161250.92 1.1204106 131000 9891.2503 20487.314 -3339.0393 -42320.056 8400.3366 8760.1857 7283.5301 664.34684 -63.381473 9954.6318 300.07841 398.014 160519.68 1.1255146 132000 9890.0734 20444.561 -3287.8768 -42340.241 8471.8478 8803.8459 7238.1609 682.07639 12.374386 9877.699 297.75931 121.58801 161837.19 1.1163518 133000 9893.3659 20267.25 -3294.4657 -42318.383 8527.8945 8854.1224 7329.4379 698.70842 64.564439 9828.8014 296.28531 -636.31672 161752 1.1169398 134000 9903.4219 20327.265 -3286.9577 -42305.496 8566.1509 8746.0101 7308.5378 664.30708 19.817024 9883.6049 297.93734 -133.96341 161235.1 1.1205205 135000 9889.5634 20371.401 -3377.419 -42324.415 8538.0063 8755.6241 7405.7588 662.32847 31.284924 9858.2784 297.17388 47.547571 161194.95 1.1207996 136000 9884.4326 20496.781 -3326.8049 -42321.78 8306.4208 8964.0421 7234.5155 666.70225 19.875881 9864.5567 297.36314 897.20435 161765.92 1.1168437 137000 9880.6711 20390.143 -3226.1783 -42300.92 8349.7216 8705.1047 7444.2774 649.40535 11.553467 9869.1177 297.50063 -19.617906 161455.66 1.1189898 138000 9883.5481 20435.32 -3374.0707 -42310.902 8492.0693 8854.9249 7202.3654 631.12244 -69.170263 9952.7183 300.02073 -344.59125 161264.73 1.1203147 139000 9885.4159 20451.915 -3279.3281 -42325.381 8483.9104 8680.912 7222.9337 636.69056 -128.34765 10013.764 301.86092 321.93217 161643.02 1.1176928 140000 9873.301 20321.737 -3213.1748 -42320.101 8344.2139 8807.1553 7343.7204 649.56306 -66.886718 9940.1877 299.643 328.62826 160960.51 1.1224321 141000 9885.0114 20366.752 -3244.337 -42312.564 8502.7913 8838.4793 7222.334 638.57899 12.034224 9872.9771 297.61697 -186.70969 160870.86 1.1230576 142000 9880.2069 20425.185 -3278.3516 -42311.637 8389.5513 8924.0631 7255.3198 650.73564 54.866099 9825.3408 296.18099 532.76427 161053.15 1.1217864 143000 9877.9088 20448.9 -3333.5516 -42323.696 8491.649 8927.2475 7206.2902 670.95779 87.796808 9790.112 295.11903 720.91214 161561.19 1.1182589 144000 9879.8459 20435.87 -3367.2996 -42310.647 8562.987 8778.708 7207.7096 632.87212 -59.799598 9939.6455 299.62666 -423.85686 161338.46 1.1198026 145000 9908.1 20487.632 -3303.1503 -42314.456 8514.2508 8847.2547 7209.2378 662.24074 103.00959 9805.0904 295.57055 -229.33239 161600.4 1.1179876 146000 9902.0164 20450.96 -3339.1332 -42328.803 8472.7136 8862.2011 7242.5719 639.76725 0.27842795 9901.7379 298.48395 541.15476 161170.29 1.1209711 147000 9890.499 20343.128 -3216.1007 -42311.271 8488.415 8870.3547 7249.2098 674.41043 98.14591 9792.3531 295.18659 -363.88293 161413.97 1.1192788 148000 9896.2448 20398.192 -3305.4584 -42303.187 8433.5665 8933.3631 7379.1379 680.4467 216.06161 9680.1832 291.80527 117.70103 161100.45 1.1214571 149000 9886.2079 20394.469 -3169.6793 -42325.125 8468.6387 8760.8996 7257.5494 662.9475 49.700048 9836.5078 296.51762 -256.89043 161579.81 1.11813 150000 9880.6428 20524.397 -3303.9277 -42323.064 8341.8458 8790.9879 7304.6343 664.36414 -0.76209113 9881.4049 297.87102 468.29938 162149.95 1.1141985 150100 9890.8522 20382.678 -3264.3465 -42324.382 8451.8095 8855.5056 7274.5261 675.2278 51.019129 9839.833 296.61785 -137.74784 162101.04 1.1145347 Loop time of 1869.27 on 4 procs for 50000 steps with 11130 atoms Performance: 2.311 ns/day, 10.385 hours/ns, 26.748 timesteps/s, 297.711 katom-step/s 92.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1067.8 | 1175 | 1275.9 | 240.1 | 62.86 Bond | 71.011 | 75.004 | 78.378 | 32.2 | 4.01 Kspace | 313.86 | 418.58 | 529.22 | 416.0 | 22.39 Neigh | 108.47 | 108.54 | 108.61 | 0.5 | 5.81 Comm | 49.905 | 50.853 | 51.453 | 9.1 | 2.72 Output | 0.31236 | 0.32463 | 0.33347 | 1.4 | 0.02 Modify | 24.786 | 27.209 | 29.552 | 44.9 | 1.46 Other | | 13.8 | | | 0.74 Nlocal: 2782.5 ave 2912 max 2616 min Histogram: 1 0 0 0 1 0 0 0 1 1 Nghost: 14479.2 ave 14693 max 14343 min Histogram: 1 1 0 1 0 0 0 0 0 1 Neighs: 1.10742e+06 ave 1.1863e+06 max 1.00636e+06 min Histogram: 1 0 1 0 0 0 0 0 0 2 Total # of neighbors = 4429676 Ave neighs/atom = 397.99425 Ave special neighs/atom = 5.672956 Neighbor list builds = 2171 Dangerous builds = 0 unfix 1 write_data ${run}.final write_data system01.final System init for write_data ... PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.20032204 grid = 18 18 18 stencil order = 5 estimated absolute RMS force accuracy = 0.022733654 estimated relative force accuracy = 6.8461724e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4508 1620 Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule Total wall time: 0:58:25