#------------------------------------------------------------------------------- # Stage 2.2: Compress Layer #------------------------------------------------------------------------------- min_style cg min_modify dmax 0.1 line fast reset_timestep 0 displace_atoms all move 0.0 0.0 0.16492029042014167 Displacing atoms ... # 1. Variable Indenter Stage, minimization to compress initial cell #------------------------------------------------------------------ variable lowz equal zlo print "INITIAL zlow=${lowz}" INITIAL zlow=0 variable highz equal zhi print "INITIAL zhigh=${highz}" INITIAL zhigh=45.28372 run 0 WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 15138 6348 generated 0 of 36 mixed pair_coeff terms from sixthpower 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/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) = 11.51 | 11.61 | 11.89 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 127307.31 92859.489 1.3074058 0 18011.105 3278.0917 0 0 93835.826 185002.19 -448.40969 -209994.06 90133.16 0 Loop time of 3.91744e-06 on 16 procs for 0 steps with 9101 atoms 105.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.917e-06 | | |100.00 Nlocal: 568.812 ave 608 max 532 min Histogram: 2 1 1 3 0 3 2 3 0 1 Nghost: 6420.25 ave 6468 max 6367 min Histogram: 2 0 2 1 1 2 4 1 1 2 Neighs: 177432 ave 196952 max 156843 min Histogram: 1 0 1 6 1 0 3 1 1 2 Total # of neighbors = 2838915 Ave neighs/atom = 311.9344 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 print "BEFORE MINIMIZE WITH VARIABLE INDENTER" BEFORE MINIMIZE WITH VARIABLE INDENTER print "zlow=${lowz}" zlow=0 print "zhigh=${highz}" zhigh=45.28372 # Minimization stage to push all atoms above max or below min inwards fix upper all indent 10.0 plane z 46.257883922420334 hi units box fix lower all indent 10.0 plane z -0.97416442152033467 lo units box thermo_style custom step fnorm vol v_sysdensity zlo zhi WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) thermo 50 minimize 0.0 1.0 5000 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 15138 6348 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Per MPI rank memory allocation (min/avg/max) = 12.63 | 12.74 | 13.01 Mbytes Step Fnorm Volume v_sysdensity Zlo Zhi 0 26884.737 92859.489 1.3074058 0 45.28372 50 1089.7749 92859.489 1.3074058 0 45.28372 62 13678.099 92859.489 1.3074058 0 45.28372 Loop time of 2.23884 on 16 procs for 62 steps with 9101 atoms 99.0% CPU use with 16 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 90133.1599028708 -151812.097674386 -152526.08493114 Force two-norm initial, final = 26884.737 13678.099 Force max component initial, final = 4476.0028 7376.6894 Final line search alpha, max atom move = 0.00019520954 1.4400002 Iterations, force evaluations = 62 304 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9988 | 1.1906 | 1.3284 | 8.4 | 53.18 Bond | 0.006354 | 0.0074127 | 0.0083653 | 0.6 | 0.33 Kspace | 0.71482 | 0.85374 | 1.0461 | 10.0 | 38.13 Neigh | 0.095265 | 0.095494 | 0.095687 | 0.0 | 4.27 Comm | 0.07612 | 0.077697 | 0.079729 | 0.4 | 3.47 Output | 5.3901e-05 | 5.5448e-05 | 6.7226e-05 | 0.0 | 0.00 Modify | 0.00069867 | 0.00093043 | 0.0012348 | 0.0 | 0.04 Other | | 0.01296 | | | 0.58 Nlocal: 568.812 ave 602 max 528 min Histogram: 1 1 2 2 1 0 3 3 1 2 Nghost: 6424.56 ave 6480 max 6380 min Histogram: 3 0 1 3 1 5 1 0 0 2 Neighs: 177442 ave 194422 max 154943 min Histogram: 1 0 0 3 4 1 2 2 0 3 Total # of neighbors = 2839070 Ave neighs/atom = 311.95143 Ave special neighs/atom = 1.8929788 Neighbor list builds = 18 Dangerous builds = 3 unfix upper unfix lower print "AFTER MINIMIZE WITH VARIABLE INDENTER..." AFTER MINIMIZE WITH VARIABLE INDENTER... print "zlow=${lowz}" zlow=0 print "zhigh=${highz}" zhigh=45.28372 # 2. Fixed Indenter Stage with NVT dynamics to compress initial cell #------------------------------------------------------------------- reset_timestep 0 velocity all create 298.2 72489 dist gaussian mom yes rot no # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.001 seconds variable zhigh equal "46.257883922420334 - elapsed * 0.000039741644" variable zlow equal "-0.97416442152033467 + elapsed * 0.000039741644" fix upper all indent 10.0 plane z v_zhigh hi units box fix lower all indent 10.0 plane z v_zlow lo units box thermo_style custom step v_time press vol v_sysdensity temp evdwl ecoul pe ke v_zlow v_zhigh zlo zhi thermo 1000 fix movable1 movable nve fix movable2 movable temp/rescale 20 298.2 298.2 10 1.0 timestep 1 run 100000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 15138 6348 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.994689 0.683452 8304 2 97.0853 26.0108 2768 Per MPI rank memory allocation (min/avg/max) = 12.38 | 12.5 | 12.76 Mbytes Step v_time Press Volume v_sysdensity Temp E_vdwl E_coul PotEng KinEng v_zlow v_zhigh Zlo Zhi 0 1e-06 7025.0344 92859.489 1.3074058 428.55654 23815.128 91911.053 -156885.45 8088.7858 -0.97416442 46.257884 0 45.28372 1000 1000 3813.3319 92859.489 1.3074058 298.2 22091.186 91974.219 -159459.18 5628.3727 -0.93442278 46.218142 0 45.28372 2000 2000 3531.7512 92859.489 1.3074058 302.89117 22393.54 90776.749 -160376.84 5716.9161 -0.89468113 46.178401 0 45.28372 3000 3000 3139.6459 92859.489 1.3074058 301.18019 22208.912 90794.617 -160570.76 5684.6222 -0.85493949 46.138659 0 45.28372 4000 4000 3359.9527 92859.489 1.3074058 298.37023 22432.21 90243.286 -160917.63 5631.5856 -0.81519785 46.098917 0 45.28372 5000 5000 3449.4853 92859.489 1.3074058 301.45682 22546.38 90072.285 -160975.78 5689.8435 -0.7754562 46.059176 0 45.28372 6000 6000 2989.8197 92859.489 1.3074058 304.39851 22222.502 90359.704 -161031.29 5745.3663 -0.73571456 46.019434 0 45.28372 7000 7000 3353.123 92859.489 1.3074058 300.75007 22463.912 89988.792 -161176.82 5676.504 -0.69597291 45.979692 0 45.28372 8000 8000 3197.8142 92859.489 1.3074058 302.56341 22495.515 89931.909 -161210.92 5710.7298 -0.65623127 45.939951 0 45.28372 9000 9000 2754.683 92859.489 1.3074058 299.24876 22262.122 90206.192 -161148.12 5648.1676 -0.61648963 45.900209 0 45.28372 10000 10000 3108.0165 92859.489 1.3074058 301.79159 22311.312 90100.302 -161196.34 5696.1621 -0.57674798 45.860467 0 45.28372 11000 11000 2800.4757 92859.489 1.3074058 302.11476 22186.529 90221.293 -161202.48 5702.2617 -0.53700634 45.820726 0 45.28372 12000 12000 3012.8283 92859.489 1.3074058 303.93849 22424.48 89965.339 -161237.21 5736.6838 -0.49726469 45.780984 0 45.28372 13000 13000 2867.7613 92859.489 1.3074058 300.2656 22179.433 90258.053 -161167.82 5667.3598 -0.45752305 45.741243 0 45.28372 14000 14000 2774.569 92859.489 1.3074058 296.43199 22291.168 90029.514 -161288.8 5595.0024 -0.41778141 45.701501 0 45.28372 15000 15000 3022.7224 92859.489 1.3074058 298.53799 22349.643 89935.821 -161328.82 5634.752 -0.37803976 45.661759 0 45.28372 16000 16000 3120.295 92859.489 1.3074058 299.31948 22489.484 89806.1 -161343.91 5649.5023 -0.33829812 45.622018 0 45.28372 17000 17000 2968.7288 92859.489 1.3074058 296.98259 22422.397 89925.203 -161300.18 5605.3946 -0.29855647 45.582276 0 45.28372 18000 18000 2991.2839 92859.489 1.3074058 299.12707 22378.994 89944.018 -161341.31 5645.8707 -0.25881483 45.542534 0 45.28372 19000 19000 3021.417 92859.489 1.3074058 302.14642 22314.276 89916.892 -161399.25 5702.8593 -0.21907319 45.502793 0 45.28372 20000 20000 3054.8886 92859.489 1.3074058 300.15328 22388.448 89847.962 -161364.66 5665.2399 -0.17933154 45.463051 0 45.28372 21000 21000 3032.1794 92859.489 1.3074058 299.64216 22334.132 89912.66 -161358.59 5655.5927 -0.1395899 45.423309 0 45.28372 22000 22000 3148.5201 92859.489 1.3074058 298.58292 22411.914 89904.233 -161343.7 5635.6 -0.099848254 45.383568 0 45.28372 23000 23000 2522.4426 92859.489 1.3074058 302.13506 22210.214 90060.344 -161418.75 5702.6449 -0.06010661 45.343826 0 45.28372 24000 24000 2543.1693 92859.489 1.3074058 300.09581 22188.323 90052.971 -161391.77 5664.1552 -0.020364966 45.304084 0 45.28372 25000 25000 2477.2569 92859.489 1.3074058 299.87978 22140.717 90101.094 -161407.96 5660.0777 0.019376678 45.264343 0 45.28372 26000 26000 2762.2506 92859.489 1.3074058 298.9729 22253.675 89963.853 -161420.03 5642.9608 0.059118322 45.224601 0 45.28372 27000 27000 2582.2452 92859.489 1.3074058 295.00774 22133.402 90128.986 -161388.7 5568.1203 0.098859966 45.18486 0 45.28372 28000 28000 2901.098 92859.489 1.3074058 298.90258 22300.24 89827.634 -161521.34 5641.6335 0.13860161 45.145118 0 45.28372 29000 29000 2679.7135 92859.489 1.3074058 295.29956 22276.486 89854.667 -161534.78 5573.6285 0.17834325 45.105376 0 45.28372 30000 30000 2721.0328 92859.489 1.3074058 294.51048 22384.76 89655.306 -161619.05 5558.735 0.2180849 45.065635 0 45.28372 31000 31000 2683.4382 92859.489 1.3074058 296.73962 22333.637 89760.893 -161585.69 5600.8088 0.25782654 45.025893 0 45.28372 32000 32000 2278.1655 92859.489 1.3074058 293.83241 22161.975 89791.801 -161672.08 5545.9367 0.29756819 44.986151 0 45.28372 33000 33000 2870.5768 92859.489 1.3074058 294.8548 22327.381 89686.887 -161654.6 5565.2338 0.33730983 44.94641 0 45.28372 34000 34000 2690.1744 92859.489 1.3074058 295.58954 22302.922 89703.912 -161644.39 5579.1015 0.37705147 44.906668 0 45.28372 35000 35000 2495.344 92859.489 1.3074058 289.3949 22279.075 89669.676 -161711.2 5462.181 0.41679312 44.866926 0 45.28372 36000 36000 1732.5416 92859.489 1.3074058 292.70267 21972.594 89934.052 -161734.83 5524.6133 0.45653476 44.827185 0 45.28372 37000 37000 2983.0905 92859.489 1.3074058 292.731 22491.636 89456.54 -161712.26 5525.148 0.49627641 44.787443 0 45.28372 38000 38000 2736.439 92859.489 1.3074058 289.92503 22375.225 89652.643 -161598.2 5472.1868 0.53601805 44.747701 0 45.28372 39000 39000 2524.1077 92859.489 1.3074058 292.70385 22232.203 89812.866 -161624.33 5524.6356 0.57575969 44.70796 0 45.28372 40000 40000 2561.5908 92859.489 1.3074058 292.10017 22265.27 89600.601 -161774.78 5513.2415 0.61550134 44.668218 0 45.28372 41000 41000 2597.1996 92859.489 1.3074058 291.37126 22331.025 89619.219 -161708.18 5499.4838 0.65524298 44.628477 0 45.28372 42000 42000 2759.7107 92859.489 1.3074058 295.6218 22342.139 89678.748 -161645.83 5579.7106 0.69498463 44.588735 0 45.28372 43000 43000 2823.2555 92859.489 1.3074058 293.05236 22374.493 89598.848 -161672.64 5531.2137 0.73472627 44.548993 0 45.28372 44000 44000 2205.3593 92859.489 1.3074058 296.15063 22076.325 89967.023 -161605.65 5589.6918 0.77446791 44.509252 0 45.28372 45000 45000 2586.848 92859.489 1.3074058 296.86983 22294.859 89717.165 -161649.02 5603.2664 0.81420956 44.46951 0 45.28372 46000 46000 2583.6555 92859.489 1.3074058 290.85961 22295.886 89798.376 -161557.17 5489.8265 0.8539512 44.429768 0 45.28372 47000 47000 2780.9205 92859.489 1.3074058 298.86407 22370.579 89739.314 -161534.12 5640.9066 0.89369285 44.390027 0 45.28372 48000 48000 2319.4418 92859.489 1.3074058 301.12032 22181.559 89903.249 -161576.04 5683.4923 0.93343449 44.350285 0 45.28372 49000 49000 2661.1394 92859.489 1.3074058 295.67337 22226.126 89962.779 -161484.96 5580.6839 0.97317613 44.310543 0 45.28372 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970001 0.00541658 8304 2 103.7 0.253926 2768 50000 50000 2860.8262 92859.489 1.3074058 301.4219 22415.668 89614.561 -161612.26 5689.1845 1.0129178 44.270802 0 45.28372 51000 51000 2759.0612 92859.489 1.3074058 300.24612 22317.342 89787.425 -161557.5 5666.9922 1.0526594 44.23106 0 45.28372 52000 52000 2679.7165 92859.489 1.3074058 297.65825 22254.305 89913.217 -161513.32 5618.1474 1.0924011 44.191318 0 45.28372 53000 53000 2661.3173 92859.489 1.3074058 297.4897 22253.94 89897.977 -161508.18 5614.9662 1.1321427 44.151577 0 45.28372 54000 54000 2614.0947 92859.489 1.3074058 300.85511 22320.9 89783.919 -161543.45 5678.4865 1.1718844 44.111835 0 45.28372 55000 55000 3010.1323 92859.489 1.3074058 295.38008 22344.762 89872.342 -161435.56 5575.1481 1.211626 44.072094 0 45.28372 56000 56000 2790.1072 92859.489 1.3074058 298.54815 22305.098 89848.477 -161468.12 5634.9438 1.2513676 44.032352 0 45.28372 57000 57000 2874.5158 92859.489 1.3074058 300.6796 22232.47 89940.972 -161498.84 5675.1739 1.2911093 43.99261 0 45.28372 58000 58000 2924.5106 92859.489 1.3074058 297.23597 22475.319 89741.855 -161427.97 5610.1771 1.3308509 43.952869 0 45.28372 59000 59000 2648.8951 92859.489 1.3074058 299.25176 22103.445 90094.705 -161428.42 5648.224 1.3705926 43.913127 0 45.28372 60000 60000 2801.8733 92859.489 1.3074058 298.982 22381.506 89850.606 -161423.67 5643.1326 1.4103342 43.873385 0 45.28372 61000 61000 2682.9767 92859.489 1.3074058 297.29849 22271.341 90002.75 -161379.24 5611.3572 1.4500759 43.833644 0 45.28372 62000 62000 3142.6589 92859.489 1.3074058 297.92783 22445.134 89848.879 -161353.82 5623.2355 1.4898175 43.793902 0 45.28372 63000 63000 3249.0615 92859.489 1.3074058 304.21636 22597.211 89613.666 -161447.3 5741.9284 1.5295592 43.75416 0 45.28372 64000 64000 3256.3033 92859.489 1.3074058 302.34277 22591.764 89686.332 -161383.48 5706.5654 1.5693008 43.714419 0 45.28372 65000 65000 2955.7814 92859.489 1.3074058 299.95873 22337.27 90004.095 -161308.61 5661.5679 1.6090424 43.674677 0 45.28372 66000 66000 2917.8357 92859.489 1.3074058 297.35909 22407.239 89799.057 -161437.72 5612.501 1.6487841 43.634935 0 45.28372 67000 67000 2602.9985 92859.489 1.3074058 294.93456 22283.739 89990.728 -161355.01 5566.7392 1.6885257 43.595194 0 45.28372 68000 68000 3006.1101 92859.489 1.3074058 294.21803 22419.878 89897.647 -161342.88 5553.215 1.7282674 43.555452 0 45.28372 69000 69000 2996.7581 92859.489 1.3074058 296.13335 22400.783 89884.634 -161347.72 5589.3657 1.768009 43.51571 0 45.28372 70000 70000 3055.564 92859.489 1.3074058 298.35168 22426.607 89851.929 -161344.06 5631.2356 1.8077507 43.475969 0 45.28372 71000 71000 3454.039 92859.489 1.3074058 297.68867 22692.161 89688.187 -161301.97 5618.7217 1.8474923 43.436227 0 45.28372 72000 72000 3315.1256 92859.489 1.3074058 302.51437 22601.056 89655.784 -161389.25 5709.8041 1.8872339 43.396486 0 45.28372 73000 73000 2977.4213 92859.489 1.3074058 300.70258 22425.66 89905.356 -161290.95 5675.6076 1.9269756 43.356744 0 45.28372 74000 74000 3517.4967 92859.489 1.3074058 297.72031 22647.918 89781.033 -161191.09 5619.3187 1.9667172 43.317002 0 45.28372 75000 75000 3679.2919 92859.489 1.3074058 301.37386 22729.968 89663.879 -161238.16 5688.2778 2.0064589 43.277261 0 45.28372 76000 76000 3908.4606 92859.489 1.3074058 294.12342 22860.06 89499.445 -161253.78 5551.4293 2.0462005 43.237519 0 45.28372 77000 77000 3670.2195 92859.489 1.3074058 297.44507 22811.525 89583.237 -161266.44 5614.1237 2.0859422 43.197777 0 45.28372 78000 78000 3786.3731 92859.489 1.3074058 301.68335 22794.884 89608.441 -161254.46 5694.1192 2.1256838 43.158036 0 45.28372 79000 79000 3900.66 92859.489 1.3074058 299.83438 22938.137 89513.969 -161183.96 5659.2208 2.1654255 43.118294 0 45.28372 80000 80000 4412.7064 92859.489 1.3074058 298.5269 23170.128 89159.631 -161285.23 5634.5427 2.2051671 43.078552 0 45.28372 81000 81000 4199.05 92859.489 1.3074058 296.53122 23104.152 89332.23 -161172.87 5596.8754 2.2449087 43.038811 0 45.28372 82000 82000 4609.5687 92859.489 1.3074058 294.75763 23212.476 89327.084 -161086.76 5563.3997 2.2846504 42.999069 0 45.28372 83000 83000 3686.71 92859.489 1.3074058 296.87937 22848.858 89670.294 -161076.28 5603.4464 2.324392 42.959327 0 45.28372 84000 84000 4586.5763 92859.489 1.3074058 302.10713 23178.419 89345.224 -161114.36 5702.1178 2.3641337 42.919586 0 45.28372 85000 85000 4386.9858 92859.489 1.3074058 301.37644 23040.279 89583.706 -160998.86 5688.3263 2.4038753 42.879844 0 45.28372 86000 86000 4988.8986 92859.489 1.3074058 298.22826 23300.171 89395.113 -160886.7 5628.9061 2.443617 42.840103 0 45.28372 87000 87000 5339.0972 92859.489 1.3074058 302.05268 23525.654 89195.946 -160892.83 5701.0901 2.4833586 42.800361 0 45.28372 88000 88000 5381.2057 92859.489 1.3074058 304.89697 23532.331 89153.783 -160921.42 5754.7747 2.5231003 42.760619 0 45.28372 89000 89000 5520.7721 92859.489 1.3074058 305.63958 23450.289 89296.323 -160872.72 5768.7909 2.5628419 42.720878 0 45.28372 90000 90000 6115.5238 92859.489 1.3074058 299.46068 23811.785 89123.47 -160667.78 5652.1673 2.6025835 42.681136 0 45.28372 91000 91000 5370.1601 92859.489 1.3074058 298.81622 23598.049 89182.002 -160816.62 5640.0035 2.6423252 42.641394 0 45.28372 92000 92000 5760.6687 92859.489 1.3074058 298.1438 23602.921 89214.156 -160800.91 5627.3119 2.6820668 42.601653 0 45.28372 93000 93000 6377.4792 92859.489 1.3074058 304.552 23926.128 88849.295 -160864.12 5748.2634 2.7218085 42.561911 0 45.28372 94000 94000 5630.9356 92859.489 1.3074058 303.29192 23575.741 89265.511 -160714.46 5724.4801 2.7615501 42.522169 0 45.28372 95000 95000 6404.1872 92859.489 1.3074058 298.05185 23932.184 88775.286 -160897.53 5625.5764 2.8012918 42.482428 0 45.28372 96000 96000 7092.9445 92859.489 1.3074058 305.32927 24180.868 88646.958 -160791.09 5762.934 2.8410334 42.442686 0 45.28372 97000 97000 6730.9029 92859.489 1.3074058 298.877 24041.203 88757.498 -160817.07 5641.1508 2.880775 42.402944 0 45.28372 98000 98000 6998.3251 92859.489 1.3074058 304.53652 24106.089 88727.354 -160755.92 5747.9713 2.9205167 42.363203 0 45.28372 99000 99000 7355.1727 92859.489 1.3074058 302.10401 24285.878 88667.176 -160633.77 5702.0589 2.9602583 42.323461 0 45.28372 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970072 0.0422513 8304 2 103.704 1.35624 2768 100000 100000 7433.4921 92859.489 1.3074058 298.93331 24332.205 88433.761 -160815.99 5642.2136 3 42.28372 0 45.28372 Loop time of 646.157 on 16 procs for 100000 steps with 9101 atoms Performance: 13.371 ns/day, 1.795 hours/ns, 154.761 timesteps/s 99.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 262.72 | 291.91 | 335.18 | 113.2 | 45.18 Bond | 0.12122 | 0.28988 | 0.39807 | 15.9 | 0.04 Kspace | 229.41 | 272.02 | 300.06 | 113.2 | 42.10 Neigh | 30.119 | 30.153 | 30.195 | 0.5 | 4.67 Comm | 24.054 | 26.019 | 27.005 | 14.6 | 4.03 Output | 0.0092554 | 0.0094086 | 0.010952 | 0.4 | 0.00 Modify | 20.016 | 21.032 | 22.839 | 15.6 | 3.25 Other | | 4.719 | | | 0.73 Nlocal: 568.812 ave 635 max 509 min Histogram: 3 3 2 0 0 0 0 4 2 2 Nghost: 6426.25 ave 6561 max 6269 min Histogram: 4 0 3 1 0 0 0 0 2 6 Neighs: 179251 ave 219776 max 130706 min Histogram: 2 2 0 2 2 0 0 2 3 3 Total # of neighbors = 2868020 Ave neighs/atom = 315.1324 Ave special neighs/atom = 1.8929788 Neighbor list builds = 4954 Dangerous builds = 0 restart 0 unfix movable1 unfix movable2 unfix upper unfix lower unfix shaken # 3. Minimization with wall potential in effect #--------------------------------------------------------------------- # Use wall potential lo and hi parameters equal to 0.0 and desired layer thickness, respectively reset_timestep 0 change_box all boundary p p f Changing box ... WARNING: Resetting image flags for non-periodic dimensions (../domain.cpp:1951) pair_style lj/class2/coul/cut 9.5 kspace_style none include parameters.dat bond_coeff 1 1.5325 277.56 -433.25 2922.8 # o1S- s4o- bond_coeff 2 0.97 563.28 -1428.2 1902.1 # h* o* angle_coeff 1 109.47 87.637 -98.528 174.89 # o1S- s4o- o1S- angle_coeff 2 103.7 49.84 -11.6 -8 # h* o* h* dihedral_coeff 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx xxx improper_coeff 1 0 0 # * s_ * * angle_coeff 1 bb 130.45 1.5325 1.5325 # o1S- s4o- o1S- angle_coeff 2 bb -9.5 0.97 0.97 # h* o* h* angle_coeff 1 ba 0.0 0.0 1.5325 1.5325 # o1S- s4o- o1S- angle_coeff 2 ba 22.35 22.35 0.97 0.97 # h* o* h* dihedral_coeff 1 mbt 0.0000 0.0000 0.0000 0.0 # xxx xxx xxx xxx dihedral_coeff 1 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 aat 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 bb13 0.0 0.0 0.0 # xxx xxx xxx xxx improper_coeff 1 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * s_ * * pair_coeff 1 1 0.05899 5.1728 # Cl - pair_coeff 2 2 0 1.098 # hw - pair_coeff 3 3 0.4691 3.292 # K+ - pair_coeff 4 4 0.3727 1.635 # Li+ - pair_coeff 5 5 0.2951 2.3959 # mg+ - pair_coeff 6 6 0.3828 2.494 # Na+ - pair_coeff 7 7 0.148 3.7824 # o* - pair_coeff 8 8 0.1436 3.6173 # o1S- - pair_coeff 9 9 0.24 4.08 # s4o- - fix upperW all wall/lj93 zhi 45.283719500899998 0.5 2.0 6.5 units box fix lowerW all wall/lj93 zlo 0.0 0.5 2.0 6.5 units box thermo_style custom step fnorm vol v_sysdensity evdwl pe zlo zhi thermo 50 dump sci all custom 5000 2.2.xyz id mol type q xs ys zs minimize 0.0 1.0 5000 10000 generated 0 of 36 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard ERROR on proc 0: Bond atom missing in image check (../domain.cpp:794) Last command: minimize 0.0 1.0 5000 10000