#------------------------------------------------------------------------------- # 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 6.3095199720659991 Displacing atoms ... # 1. Variable Indenter Stage, minimization to compress initial cell #------------------------------------------------------------------ variable lowz equal zlo print "INITIAL zlow=${lowz}" INITIAL zlow=40.380755767866 variable highz equal zhi print "INITIAL zhigh=${highz}" INITIAL zhigh=82.619244176266 run 0 WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) generated 0 of 1 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 = 6 6 7 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 WARNING: Inconsistent image flags (../domain.cpp:814) Per MPI rank memory allocation (min/avg/max) = 8.306 | 8.549 | 9.069 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 -17347.011 68987.965 0.95398425 0 12530.667 1679.0521 0 0 21611.208 -3675.2804 0 0 32145.647 0 Loop time of 4.1735e-06 on 8 procs for 0 steps with 6600 atoms 125.8% CPU use with 8 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 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 | | 4.173e-06 | | |100.00 Nlocal: 825 ave 862 max 786 min Histogram: 1 0 0 2 1 2 0 0 1 1 Nghost: 7153.62 ave 7252 max 7034 min Histogram: 1 0 1 0 2 0 2 0 0 2 Neighs: 411120 ave 497991 max 329359 min Histogram: 3 1 0 0 0 0 0 0 2 2 Total # of neighbors = 3288956 Ave neighs/atom = 498.32667 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 print "BEFORE MINIMIZE WITH VARIABLE INDENTER" BEFORE MINIMIZE WITH VARIABLE INDENTER print "zlow=${lowz}" zlow=40.380755767866 print "zhigh=${highz}" zhigh=82.619244176266 # Minimization stage to push all atoms above max or below min inwards fix upper all indent 10.0 plane z 82.61502093304199 hi units box fix lower all indent 10.0 plane z 40.384979066958003 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 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) Per MPI rank memory allocation (min/avg/max) = 9.431 | 9.674 | 10.19 Mbytes Step Fnorm Volume v_sysdensity Zlo Zhi 0 8753.1149 68987.965 0.95398425 40.380756 82.619244 50 589.69253 69237.3 0.95054878 40.461318 82.852464 100 291.12072 69832.69 0.94244445 40.187943 82.943622 150 176.65596 69687.012 0.9444146 40.350663 83.017149 200 129.32817 69554.25 0.94621725 40.424049 83.009251 250 105.45912 69554.25 0.94621725 40.424049 83.009251 300 90.864348 69554.25 0.94621725 40.424049 83.009251 350 87.609766 69554.25 0.94621725 40.424049 83.009251 400 86.542454 69554.25 0.94621725 40.424049 83.009251 450 86.029056 69739.847 0.9436991 40.348397 83.047232 500 79.829434 69739.847 0.9436991 40.348397 83.047232 550 71.023898 69739.847 0.9436991 40.348397 83.047232 600 71.391314 69739.847 0.9436991 40.348397 83.047232 650 73.464823 69739.847 0.9436991 40.348397 83.047232 700 72.598502 69739.847 0.9436991 40.348397 83.047232 750 69.794904 69739.847 0.9436991 40.348397 83.047232 800 68.468148 69739.847 0.9436991 40.348397 83.047232 850 68.616562 69739.847 0.9436991 40.348397 83.047232 900 68.453579 69739.847 0.9436991 40.348397 83.047232 950 68.864753 69739.847 0.9436991 40.348397 83.047232 1000 67.884587 69739.847 0.9436991 40.348397 83.047232 1050 67.619313 69739.847 0.9436991 40.348397 83.047232 1100 66.716985 69739.847 0.9436991 40.348397 83.047232 1150 68.44408 69739.847 0.9436991 40.348397 83.047232 1200 67.34904 69739.847 0.9436991 40.348397 83.047232 1250 67.057711 69739.847 0.9436991 40.348397 83.047232 1300 68.48278 69739.847 0.9436991 40.348397 83.047232 1350 68.302869 69739.847 0.9436991 40.348397 83.047232 1400 66.981454 69739.847 0.9436991 40.348397 83.047232 1450 65.247062 69739.847 0.9436991 40.348397 83.047232 1500 66.44595 69739.847 0.9436991 40.348397 83.047232 1550 66.307734 69739.847 0.9436991 40.348397 83.047232 1600 66.313371 69739.847 0.9436991 40.348397 83.047232 1650 65.228424 69739.847 0.9436991 40.348397 83.047232 1700 66.989545 69739.847 0.9436991 40.348397 83.047232 1750 66.325316 69739.847 0.9436991 40.348397 83.047232 1800 65.126388 69739.847 0.9436991 40.348397 83.047232 1850 67.881437 69739.847 0.9436991 40.348397 83.047232 1900 66.365857 69739.847 0.9436991 40.348397 83.047232 1950 67.200089 69739.847 0.9436991 40.348397 83.047232 2000 65.994501 69739.847 0.9436991 40.348397 83.047232 2050 65.504435 69739.847 0.9436991 40.348397 83.047232 2100 67.350981 69739.847 0.9436991 40.348397 83.047232 2150 66.253311 69739.847 0.9436991 40.348397 83.047232 2200 66.458336 69739.847 0.9436991 40.348397 83.047232 2250 66.962964 69739.847 0.9436991 40.348397 83.047232 2300 66.447378 69739.847 0.9436991 40.348397 83.047232 2350 66.984158 69739.847 0.9436991 40.348397 83.047232 2400 66.566879 69739.847 0.9436991 40.348397 83.047232 2450 66.687848 69739.847 0.9436991 40.348397 83.047232 2500 67.963909 69739.847 0.9436991 40.348397 83.047232 2550 66.723835 69739.847 0.9436991 40.348397 83.047232 2600 67.303808 69739.847 0.9436991 40.348397 83.047232 2650 67.25821 69739.847 0.9436991 40.348397 83.047232 2700 66.627204 69739.847 0.9436991 40.348397 83.047232 2750 67.697414 69739.847 0.9436991 40.348397 83.047232 2800 65.318313 69739.847 0.9436991 40.348397 83.047232 2850 67.727143 69739.847 0.9436991 40.348397 83.047232 2900 68.18059 69739.847 0.9436991 40.348397 83.047232 2950 65.867828 69739.847 0.9436991 40.348397 83.047232 3000 66.931844 69739.847 0.9436991 40.348397 83.047232 3050 66.517274 69739.847 0.9436991 40.348397 83.047232 3100 68.116305 69739.847 0.9436991 40.348397 83.047232 3150 67.86851 69739.847 0.9436991 40.348397 83.047232 3200 67.498619 69739.847 0.9436991 40.348397 83.047232 3250 67.974297 69739.847 0.9436991 40.348397 83.047232 3300 67.947742 69739.847 0.9436991 40.348397 83.047232 3350 68.003818 69739.847 0.9436991 40.348397 83.047232 3400 66.8821 69739.847 0.9436991 40.348397 83.047232 3450 67.617217 69739.847 0.9436991 40.348397 83.047232 3500 65.420658 69739.847 0.9436991 40.348397 83.047232 3550 67.081746 69739.847 0.9436991 40.348397 83.047232 3600 68.199751 69739.847 0.9436991 40.348397 83.047232 3650 68.021509 69739.847 0.9436991 40.348397 83.047232 3700 68.551078 69739.847 0.9436991 40.348397 83.047232 3750 67.134222 69739.847 0.9436991 40.348397 83.047232 3800 66.263713 69739.847 0.9436991 40.348397 83.047232 3850 67.986495 69739.847 0.9436991 40.348397 83.047232 3900 67.529492 69739.847 0.9436991 40.348397 83.047232 3950 68.541642 69739.847 0.9436991 40.348397 83.047232 4000 66.356232 69739.847 0.9436991 40.348397 83.047232 4050 67.541291 69739.847 0.9436991 40.348397 83.047232 4100 66.971679 69739.847 0.9436991 40.348397 83.047232 4150 66.809324 69739.847 0.9436991 40.348397 83.047232 4200 67.395117 69739.847 0.9436991 40.348397 83.047232 4250 68.060973 69739.847 0.9436991 40.348397 83.047232 4300 66.942855 69739.847 0.9436991 40.348397 83.047232 4350 66.023403 69739.847 0.9436991 40.348397 83.047232 4400 67.525158 69739.847 0.9436991 40.348397 83.047232 4450 66.185016 69739.847 0.9436991 40.348397 83.047232 4500 67.397639 69739.847 0.9436991 40.348397 83.047232 4550 67.333256 69739.847 0.9436991 40.348397 83.047232 4600 67.757848 69739.847 0.9436991 40.348397 83.047232 4650 67.161567 69739.847 0.9436991 40.348397 83.047232 4700 68.750858 69739.847 0.9436991 40.348397 83.047232 4750 67.438472 69739.847 0.9436991 40.348397 83.047232 4800 66.362141 69739.847 0.9436991 40.348397 83.047232 4850 66.55282 69739.847 0.9436991 40.348397 83.047232 4900 66.303908 69739.847 0.9436991 40.348397 83.047232 4950 66.344017 69739.847 0.9436991 40.348397 83.047232 5000 67.741721 69739.847 0.9436991 40.348397 83.047232 Loop time of 67.4562 on 8 procs for 5000 steps with 6600 atoms 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = 32145.6468689472 -17030.1716003276 -16954.1365465543 Force two-norm initial, final = 8753.1149 67.741721 Force max component initial, final = 2160.3568 4.2585007 Final line search alpha, max atom move = 2.798963e-08 1.1919386e-07 Iterations, force evaluations = 5000 5237 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.337 | 54.221 | 65.249 | 119.9 | 80.38 Bond | 0.20404 | 0.21627 | 0.22995 | 1.7 | 0.32 Neigh | 0.14625 | 0.14657 | 0.1469 | 0.1 | 0.22 Comm | 1.4502 | 12.488 | 23.373 | 250.1 | 18.51 Output | 0.0042958 | 0.0045278 | 0.0054849 | 0.6 | 0.01 Modify | 0.018224 | 0.019044 | 0.020688 | 0.6 | 0.03 Other | | 0.3607 | | | 0.53 Nlocal: 825 ave 866 max 777 min Histogram: 1 0 0 0 3 1 1 1 0 1 Nghost: 7150.25 ave 7294 max 6980 min Histogram: 1 0 0 2 1 0 2 0 1 1 Neighs: 412035 ave 502745 max 323141 min Histogram: 2 2 0 0 0 0 0 1 1 2 Total # of neighbors = 3296277 Ave neighs/atom = 499.43591 Ave special neighs/atom = 2 Neighbor list builds = 11 Dangerous builds = 1 unfix upper unfix lower print "AFTER MINIMIZE WITH VARIABLE INDENTER..." AFTER MINIMIZE WITH VARIABLE INDENTER... print "zlow=${lowz}" zlow=40.3483970308027 print "zhigh=${highz}" zhigh=83.0472321713023 # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # of frozen angles find clusters CPU = 0.001 seconds variable zhigh equal "82.61502093304199 - elapsed * -0.000037384979" variable zlow equal "40.384979066958003 + elapsed * -0.000037384979" 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 10000 fix movable1 movable nve fix movable2 movable temp/rescale 20 298.2 298.2 10 1.0 timestep 1 run 1000000 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.993478 0.0585143 6600 1 98.6505 13.2822 2200 Per MPI rank memory allocation (min/avg/max) = 9.181 | 9.472 | 9.95 Mbytes Step v_time Press Volume v_sysdensity Temp E_vdwl E_coul PotEng KinEng v_zlow v_zhigh Zlo Zhi 0 1e-06 2170.1665 69680.177 0.94450723 447.33389 6673.9933 -25922.58 -19248.587 5865.703 40.384979 82.615021 40.380359 83.042661 10000 10000 376.67513 71488.161 0.92062001 299.09444 5480.0851 -21968.7 -16488.615 3921.9007 40.011129 82.988871 39.672804 83.44206 20000 20000 -1052.9534 72495.049 0.90783346 296.96114 5594.8104 -27619.01 -22024.2 3893.9277 39.637279 83.362721 39.55051 83.936242 30000 30000 -2001.7353 71416.774 0.92154024 297.81938 5604.0029 -30447.601 -24843.598 3905.1814 39.26343 83.73657 40.016292 83.74184 40000 40000 -667.64549 71987.288 0.91423685 304.21321 5557.5779 -26020.716 -20463.138 3989.0211 38.88958 84.11042 39.886376 83.961227 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.25625e-06 6600 1 103.7 0.000100371 2200 50000 50000 -440.16855 71544.957 0.91988917 300.3089 5853.2601 -27399.296 -21546.036 3937.8255 38.51573 84.48427 39.43113 83.235159 60000 60000 -989.42313 71450.302 0.92110782 302.66969 5871.2475 -29677.762 -23806.515 3968.7816 38.14188 84.85812 39.848155 83.594231 70000 70000 -582.29973 73355.073 0.89718991 296.24191 5673.9212 -26941.048 -21267.127 3884.4968 37.768031 85.231969 38.858389 83.770678 80000 80000 244.69808 75084.33 0.87652686 301.31904 5787.3417 -25270.137 -19482.795 3951.0711 37.394181 85.605819 38.754194 84.725235 90000 90000 898.58794 72739.536 0.90478211 299.62718 5799.3441 -24043.657 -18244.313 3928.8863 37.020331 85.979669 39.343966 83.879387 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.34228e-06 6600 1 103.7 0.000103172 2200 100000 100000 -2391.5303 72425.115 0.90871006 298.28157 5809.4746 -33879.769 -28070.295 3911.242 36.646481 86.353519 39.277863 83.620778 110000 110000 -459.69042 74141.634 0.88767172 303.82783 5586.0941 -25955.829 -20369.735 3983.9678 36.272631 86.727369 38.207255 83.601122 120000 120000 -464.60052 73833.473 0.89137662 297.06538 5932.8606 -28710.189 -22777.328 3895.2946 35.898782 87.101218 37.836774 83.041967 130000 130000 -515.55404 71310.878 0.92290872 302.48645 6002.9988 -28969.531 -22966.532 3966.3788 35.524932 87.475068 39.159794 82.820507 140000 140000 -1053.0176 70671.538 0.93125795 297.94989 6060.0394 -31414.421 -25354.381 3906.8928 35.151082 87.848918 39.659163 82.928434 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.19703e-06 6600 1 103.7 0.000101422 2200 150000 150000 -494.18693 70741.545 0.93033635 301.28521 5991.3892 -29720.253 -23728.863 3950.6274 34.777232 88.222768 39.665048 82.977182 160000 160000 281.16984 71690.851 0.91801716 299.54911 6026.0849 -27232.661 -21206.576 3927.8627 34.403382 88.596618 39.519123 83.412477 170000 170000 -27.788774 71579.128 0.91945003 304.34198 5856.4999 -27200.697 -21344.197 3990.7096 34.029533 88.970467 38.76214 82.587091 180000 180000 943.62165 73084.045 0.90051708 302.11043 5952.9432 -24729.837 -18776.894 3961.4482 33.655683 89.344317 38.409718 83.156068 190000 190000 -1021.9794 72404.706 0.90896622 294.0862 5737.5135 -29464.802 -23727.289 3856.2298 33.281833 89.718167 38.446613 82.777031 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.61763e-06 6600 1 103.7 0.00013019 2200 200000 200000 -454.62088 71014.943 0.92675468 299.81395 5867.8417 -28139.432 -22271.59 3931.3354 32.907983 90.092017 39.079858 82.559382 210000 210000 -104.65906 71454.742 0.92105058 293.10506 5967.3643 -27657.06 -21689.695 3843.3646 32.534133 90.465867 39.149361 82.898156 220000 220000 -1370.4532 73920.546 0.89032664 302.52546 5863.8419 -31045.48 -25181.638 3966.8903 32.160284 90.839716 37.924699 83.183204 230000 230000 299.01212 73758.648 0.89228088 293.0036 6038.4846 -26882.795 -20844.311 3842.0341 31.786434 91.213566 36.845167 82.004549 240000 240000 -663.94858 72556.496 0.90706463 306.19288 5996.3881 -29907.441 -23911.052 4014.9797 31.412584 91.587416 37.263603 81.686956 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.33547e-06 6600 1 103.7 0.000113039 2200 250000 250000 -52.193902 71927.192 0.9150007 299.58545 5766.8437 -26382.631 -20615.787 3928.3392 31.038734 91.961266 38.125869 82.163926 260000 260000 825.28851 70293.554 0.93626553 298.23094 5933.6153 -25171.432 -19237.816 3910.5781 30.664885 92.335115 39.005036 82.042883 270000 270000 -890.10361 70563.11 0.93268893 302.28126 5835.9617 -29465.954 -23629.992 3963.6883 30.291035 92.708965 39.323791 82.526675 280000 280000 481.28215 69657.28 0.94481771 300.91007 5875.9256 -25561.749 -19685.823 3945.7084 29.917185 93.082815 39.146364 81.794647 290000 290000 684.38015 71591.61 0.91928972 302.68857 5954.2885 -25834.103 -19879.815 3969.0291 29.543335 93.456665 39.062705 82.895298 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.14069e-06 6600 1 103.7 9.89221e-05 2200 300000 300000 160.39699 71142.253 0.92509624 302.24864 5819.4597 -26023.407 -20203.947 3963.2606 29.169485 93.830515 38.643849 82.201319 310000 310000 -445.12337 74189.337 0.88710095 300.26039 5892.2801 -28713.357 -22821.076 3937.1894 28.795636 94.204364 38.391625 83.8147 320000 320000 -0.59427496 71876.093 0.91565121 303.84 5977.1287 -27610.085 -21632.956 3984.1274 28.421786 94.578214 38.679305 82.686076 330000 330000 -802.69758 71714.514 0.91771424 302.84571 5835.9187 -29512.009 -23676.091 3971.0896 28.047936 94.952064 38.406713 82.314555 340000 340000 -276.11517 71074.646 0.92597621 303.63837 5897.0011 -28248.839 -22351.838 3981.4834 27.674086 95.325914 38.351854 81.867932 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.30504e-06 6600 1 103.7 9.55637e-05 2200 350000 350000 -1943.4275 72675.568 0.90557849 304.37194 5830.9414 -32804.412 -26973.47 3991.1024 27.300236 95.699764 38.512867 83.009123 360000 360000 -1920.0842 72694.052 0.90534823 306.41372 5940.7294 -34006.985 -28066.256 4017.8754 26.926387 96.073613 38.224139 82.731712 370000 370000 1388.58 71780.035 0.91687656 300.00421 5762.9997 -21800.108 -16037.109 3933.8303 26.552537 96.447463 39.037878 82.985836 380000 380000 -1335.8031 72340.522 0.90977269 304.39222 5848.0581 -31448.803 -25600.745 3991.3684 26.178687 96.821313 38.419708 82.710829 390000 390000 -423.21407 71035.87 0.92648167 301.93269 5818.7754 -28495.375 -22676.6 3959.1175 25.804837 97.195163 38.676118 82.168455 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.33198e-06 6600 1 103.7 9.51065e-05 2200 400000 400000 129.70726 74265.875 0.88618671 301.25066 6007.6878 -28219.268 -22211.58 3950.1744 25.430987 97.569013 38.259391 83.729327 410000 410000 -2310.1582 71354.449 0.92234517 304.05719 5834.3084 -34540.984 -28706.675 3986.9753 25.057138 97.942862 38.44285 82.130239 420000 420000 -1541.3721 71588.652 0.91932771 303.42234 5664.3066 -30772.879 -25108.572 3978.6508 24.683288 98.316712 38.624974 82.455756 430000 430000 -295.3579 69409.831 0.94818602 295.18123 5933.6091 -29065.269 -23131.66 3870.5885 24.309438 98.690562 39.301801 81.798581 440000 440000 -37.839848 71728.752 0.91753208 305.80337 5865.3821 -27187.032 -21321.65 4009.8722 23.935588 99.064412 38.069416 81.985976 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.41666e-06 6600 1 103.7 9.74567e-05 2200 450000 450000 -2120.9059 71753.979 0.91720951 301.16052 5759.7373 -32725.444 -26965.707 3948.9924 23.561739 99.438261 38.519424 82.451429 460000 460000 -86.898114 72172.757 0.91188745 298.26996 5686.9096 -25442.499 -19755.589 3911.0897 23.187889 99.812111 37.73753 81.925935 470000 470000 -637.63781 70983.531 0.92716479 297.44915 5845.5774 -28743.783 -22898.205 3900.3268 22.814039 100.18596 38.337326 81.797618 480000 480000 -693.63042 72090.503 0.9129279 295.8139 5823.6167 -29186.707 -23363.09 3878.8844 22.440189 100.55981 37.882069 82.020114 490000 490000 -1747.7558 73362.206 0.89710268 307.71363 6013.5676 -34012.244 -27998.676 4034.9207 22.066339 100.93366 37.546337 82.462993 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.50363e-06 6600 1 103.7 0.000102823 2200 500000 500000 -1093.1324 71004.738 0.92688788 304.5173 5958.396 -31326.305 -25367.909 3993.0085 21.69249 101.30751 37.853908 81.327184 510000 510000 -830.43664 70505.907 0.93344564 302.26892 5828.3073 -29396.693 -23568.385 3963.5264 21.31864 101.68136 38.273352 81.441214 520000 520000 286.23295 73851.374 0.89116055 303.02241 6021.8218 -27731.26 -21709.438 3973.4067 20.94479 102.05521 37.710325 82.926478 530000 530000 -639.83141 71070.913 0.92602485 302.83038 5925.3541 -29712.407 -23787.053 3970.8886 20.57094 102.42906 38.425161 81.938953 540000 540000 -513.59836 72594.53 0.9065894 298.72315 5911.5863 -29026.098 -23114.512 3917.0322 20.19709 102.80291 38.622074 83.068714 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.0502e-06 6600 1 103.7 9.08785e-05 2200 550000 550000 -173.53386 73083.817 0.90051989 299.99264 5748.4059 -27253.548 -21505.142 3933.6785 19.823241 103.17676 37.41617 82.16238 560000 560000 -446.21935 70314.707 0.93598386 298.5661 5857.4514 -28285.853 -22428.401 3914.9729 19.449391 103.55061 38.817857 81.868655 570000 570000 -506.53989 71227.744 0.9239859 303.93477 5837.2783 -28574.441 -22737.163 3985.37 19.075541 103.92446 38.563111 82.172925 580000 580000 -791.66782 72419.98 0.9087745 296.79836 5785.9431 -28825.785 -23039.842 3891.7932 18.701691 104.29831 38.114842 82.454612 590000 590000 -431.2485 71693.083 0.91798858 303.60215 5737.5339 -27279.301 -21541.767 3981.0085 18.327841 104.67216 38.314876 82.209597 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.41107e-06 6600 1 103.7 9.27383e-05 2200 600000 600000 -856.65347 72154.098 0.91212326 298.70092 5866.8339 -29880.303 -24013.469 3916.7408 17.953992 105.04601 38.979194 83.156175 610000 610000 -1967.9475 73131.612 0.89993137 298.83668 5975.5882 -34436.306 -28460.718 3918.5208 17.580142 105.41986 38.443801 83.219274 620000 620000 -829.34719 73167.877 0.89948532 302.54286 5895.1774 -30316.209 -24421.032 3967.1185 17.206292 105.79371 38.114956 82.912632 630000 630000 -636.80422 74202.53 0.88694322 296.06374 5861.1814 -29298.397 -23437.215 3882.1604 16.832442 106.16756 38.612539 84.043691 640000 640000 -1323.6846 70734.557 0.93042827 306.59016 5863.0955 -31471.026 -25607.931 4020.189 16.458593 106.54141 38.479428 81.787283 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.27095e-06 6600 1 103.7 9.35794e-05 2200 650000 650000 -41.341947 71403.807 0.9217076 299.50191 5762.4343 -26800.461 -21038.026 3927.2437 16.084743 106.91526 38.516983 82.234593 660000 660000 -1000.8496 72945.647 0.90222562 298.2 5736.2978 -29355.859 -23619.561 3910.1724 15.710893 107.28911 38.527318 83.188933 670000 670000 -62.360822 70957.675 0.92750264 300.05712 5710.7147 -26845.393 -21134.679 3934.524 15.337043 107.66296 38.149057 81.593518 680000 680000 -1832.6836 72108.621 0.91269851 305.17167 5604.17 -31339.808 -25735.638 4001.589 14.963193 108.03681 38.206972 82.35611 690000 690000 -471.64326 71927.725 0.91499392 300.33161 5693.693 -27962.713 -22269.02 3938.1233 14.589344 108.41066 37.9751 82.013483 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.4831e-06 6600 1 103.7 0.000110058 2200 700000 700000 -1066.0529 71767.813 0.9170327 297.97873 6005.46 -31508.121 -25502.661 3907.271 14.215494 108.78451 38.383193 82.323668 710000 710000 509.03622 73904.341 0.89052187 300.92284 5910.343 -26211.714 -20301.371 3945.8758 13.841644 109.15836 37.254011 82.502593 720000 720000 -1543.2053 71877.196 0.91563715 299.72015 5880.8772 -32141.035 -26260.158 3930.1055 13.467794 109.53221 37.185367 81.192813 730000 730000 -68.117106 72959.52 0.90205406 297.28238 5877.6464 -28057.159 -22179.512 3898.1401 13.093944 109.90606 36.890541 81.560649 740000 740000 -844.86029 74896.953 0.87871974 298.252 5846.5304 -30422.725 -24576.195 3910.8542 12.720095 110.27991 36.290054 82.146373 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.21826e-06 6600 1 103.7 9.84262e-05 2200 750000 750000 1229.9411 70965.04 0.92740638 303.38419 6055.878 -25330.422 -19274.544 3978.1505 12.346245 110.65376 38.059715 81.508685 760000 760000 -191.72644 71554.035 0.91977247 304.23905 5918.3177 -28477.89 -22559.573 3989.3599 11.972395 111.0276 37.687366 81.496954 770000 770000 -966.73109 70631.527 0.93178548 300.61705 5800.8899 -29878.756 -24077.866 3941.8661 11.598545 111.40145 37.914573 81.159347 780000 780000 -1577.194 72983.221 0.90176112 299.34997 5904.0944 -32442.139 -26538.045 3925.2514 11.224695 111.7753 36.768075 81.452694 790000 790000 -2159.73 71263.531 0.9235219 296.46322 5929.7526 -34392.828 -28463.075 3887.3987 10.850846 112.14915 38.525175 82.156899 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.47177e-06 6600 1 103.7 0.00010307 2200 800000 800000 -1226.995 70673.692 0.93122956 304.299 5905.4781 -31551.871 -25646.392 3990.146 10.476996 112.523 38.395669 81.666259 810000 810000 1564.3905 70732.13 0.93046019 295.2938 5973.8109 -23809.946 -17836.135 3872.0646 10.103146 112.89685 37.836325 81.142694 820000 820000 -2129.5007 71747.16 0.91729667 298.02999 5850.3437 -34069.855 -28219.511 3907.9432 9.7292963 113.2707 38.625078 82.552908 830000 830000 -979.07006 70847.414 0.92894613 299.57268 5917.7359 -30561.35 -24643.614 3928.1718 9.3554465 113.64455 38.695515 82.072467 840000 840000 -843.52222 72935.952 0.90234554 297.19943 6010.2737 -31379.535 -25369.261 3897.0523 8.9815967 114.0184 37.085421 81.7411 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.17952e-06 6600 1 103.7 9.39758e-05 2200 850000 850000 -1632.359 71294.578 0.92311973 305.98107 6007.4817 -33779.28 -27771.799 4012.2023 8.6077469 114.39225 37.345157 80.99589 860000 860000 -1361.6229 69899.157 0.94154828 304.57242 5755.0068 -30855.917 -25100.911 3993.7313 8.2338971 114.7661 38.386329 81.182703 870000 870000 -410.8172 71448.1 0.9211362 300.71936 5827.9557 -28833.635 -23005.679 3943.2078 7.8600473 115.13995 37.730075 81.474803 880000 880000 -127.34517 72090.085 0.91293319 299.91715 6075.2198 -29591.088 -23515.868 3932.6887 7.4861975 115.5138 38.000634 82.138423 890000 890000 -821.37397 73315.906 0.89766921 299.57421 6029.9124 -31419.644 -25389.732 3928.1918 7.1123478 115.88765 37.737176 82.625484 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.34587e-06 6600 1 103.7 9.83301e-05 2200 900000 900000 -226.54113 71755.247 0.9171933 298.34153 5949.6595 -28348.02 -22398.36 3912.0282 6.738498 116.2615 38.103361 82.036143 910000 910000 599.83511 73136.46 0.89987171 302.83676 5880.6665 -25888.071 -20007.404 3970.9722 6.3646482 116.63535 37.565549 82.34399 920000 920000 -729.9911 70133.086 0.93840775 300.89003 5979.8119 -30395.536 -24415.724 3945.4456 5.9907984 117.0092 38.867894 81.807493 930000 930000 -1038.642 73583.355 0.8944065 304.47121 5966.2014 -31836.189 -25869.988 3992.4041 5.6169486 117.38305 38.186503 83.238559 940000 940000 -1770.2341 71288.749 0.92319521 301.48612 5905.5381 -33206.241 -27300.703 3953.2619 5.2430988 117.7569 38.699793 82.346957 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.16421e-06 6600 1 103.7 9.53583e-05 2200 950000 950000 -774.07944 72378.969 0.90928942 295.50686 6020.4299 -31493.165 -25472.735 3874.8583 4.869249 118.13075 38.040776 82.355437 960000 960000 519.34012 72211.124 0.91140295 299.07476 6063.6406 -27031.977 -20968.337 3921.6427 4.4953992 118.5046 37.960851 82.172747 970000 970000 -285.07272 71315.124 0.92285377 302.3448 6116.2203 -30150.594 -24034.374 3964.5215 4.1215494 118.87845 38.004761 81.668073 980000 980000 -1136.9175 69676.432 0.944558 299.88569 5971.121 -31573.939 -25602.818 3932.2762 3.7476996 119.2523 39.382287 82.042296 990000 990000 -1533.0992 70770.22 0.9299594 298.2 5968.9884 -32730.802 -26761.813 3910.1724 3.3738499 119.62615 39.095987 82.425678 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.16518e-06 6600 1 103.7 0.000106501 2200 1000000 1000000 -1488.8029 72890.034 0.90291399 301.36136 5935.247 -32358.264 -26423.017 3951.6259 3.0000001 120 37.646866 82.27443 Loop time of 10329 on 8 procs for 1000000 steps with 6600 atoms Performance: 8.365 ns/day, 2.869 hours/ns, 96.815 timesteps/s 98.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6164.6 | 7493.6 | 8874.3 |1346.7 | 72.55 Bond | 0.95681 | 1.0029 | 1.12 | 4.8 | 0.01 Neigh | 741.06 | 741.89 | 742.7 | 2.6 | 7.18 Comm | 438.01 | 1821.2 | 3152.5 |2739.1 | 17.63 Output | 0.0091922 | 0.0095031 | 0.010791 | 0.5 | 0.00 Modify | 232.57 | 236.26 | 241.13 | 22.6 | 2.29 Other | | 35.05 | | | 0.34 Nlocal: 825 ave 854 max 781 min Histogram: 1 0 0 1 1 1 1 0 1 2 Nghost: 7384.62 ave 7484 max 7270 min Histogram: 1 0 1 1 0 1 1 1 1 1 Neighs: 436559 ave 526128 max 347434 min Histogram: 1 3 0 0 0 0 0 1 1 2 Total # of neighbors = 3492472 Ave neighs/atom = 529.16242 Ave special neighs/atom = 2 Neighbor list builds = 49004 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 fix upperW all wall/lj93 zhi 123.0 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 1 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.37 | 11.89 Mbytes Step Fnorm Volume v_sysdensity E_vdwl PotEng Zlo Zhi 0 2450.6697 73270.024 0.89823133 5935.247 -26423.017 37.538831 82.399048 50 127.8901 73270.024 0.89823133 6297.4433 -18719.972 37.538831 82.399048 100 89.273984 72590.927 0.9066344 6361.4845 -18735.652 37.852273 82.296707 150 80.983732 72590.927 0.9066344 6378.3495 -16576.816 37.852273 82.296707 200 73.671884 72590.927 0.9066344 6385.4838 -17009.358 37.852273 82.296707 250 68.550442 72590.927 0.9066344 6388.9125 -16137.654 37.852273 82.296707 300 66.997195 72590.927 0.9066344 6390.6517 -16342.934 37.852273 82.296707 350 68.347091 72590.927 0.9066344 6391.8464 -16075.935 37.852273 82.296707 400 66.169753 72590.927 0.9066344 6392.4997 -16538.323 37.852273 82.296707 450 66.349737 72590.927 0.9066344 6392.6932 -15671.961 37.852273 82.296707 500 65.000575 72590.927 0.9066344 6392.8661 -16701.229 37.852273 82.296707 550 63.803489 72590.927 0.9066344 6392.9296 -15758.558 37.852273 82.296707 600 66.587277 72590.927 0.9066344 6392.9929 -16037.482 37.852273 82.296707 650 66.724756 72590.927 0.9066344 6393.0444 -15824.718 37.852273 82.296707 700 65.633843 72590.927 0.9066344 6393.1201 -16164.469 37.852273 82.296707 750 66.687946 72590.927 0.9066344 6393.1911 -16590.394 37.852273 82.296707 800 66.873646 72590.927 0.9066344 6393.2507 -16438.463 37.852273 82.296707 850 66.14073 72590.927 0.9066344 6393.3369 -16357.498 37.852273 82.296707 900 66.581814 72590.927 0.9066344 6393.4113 -16099.112 37.852273 82.296707 950 68.094701 72590.927 0.9066344 6393.485 -16540.234 37.852273 82.296707 1000 68.21528 72590.927 0.9066344 6393.5325 -15835.758 37.852273 82.296707 1050 66.204973 72590.927 0.9066344 6393.6049 -16281.937 37.852273 82.296707 1100 67.082936 72590.927 0.9066344 6393.6711 -16302.326 37.852273 82.296707 1150 68.143669 72590.927 0.9066344 6393.7293 -16287.217 37.852273 82.296707 1200 66.919542 72590.927 0.9066344 6393.7845 -16550.884 37.852273 82.296707 1250 66.888214 72590.927 0.9066344 6393.8148 -16028.841 37.852273 82.296707 1300 66.460238 72590.927 0.9066344 6393.8496 -15780.522 37.852273 82.296707 1350 67.600419 72590.927 0.9066344 6393.9059 -16627.103 37.852273 82.296707 1400 65.487395 72590.927 0.9066344 6393.9423 -16470.025 37.852273 82.296707 1450 67.474874 72590.927 0.9066344 6393.9851 -16672.845 37.852273 82.296707 1500 67.035927 72590.927 0.9066344 6394.0202 -16515.769 37.852273 82.296707 1550 67.175667 72590.927 0.9066344 6394.071 -16977.108 37.852273 82.296707 1600 69.073265 72590.927 0.9066344 6394.1058 -16749.065 37.852273 82.296707 1650 68.358763 72590.927 0.9066344 6394.1411 -16576.778 37.852273 82.296707 1700 64.668507 72590.927 0.9066344 6394.1827 -16911.385 37.852273 82.296707 1750 67.101302 72590.927 0.9066344 6394.1952 -16140.946 37.852273 82.296707 1800 67.330618 72590.927 0.9066344 6394.241 -17073.673 37.852273 82.296707 1850 68.032304 72590.927 0.9066344 6394.2514 -16668.201 37.852273 82.296707 1900 69.302175 72590.927 0.9066344 6394.2642 -16024.48 37.852273 82.296707 1950 66.715937 72590.927 0.9066344 6394.2802 -15811.608 37.852273 82.296707 2000 68.210491 72590.927 0.9066344 6394.278 -14924.571 37.852273 82.296707 2050 66.976173 72590.927 0.9066344 6394.3275 -16521.321 37.852273 82.296707 2100 67.25703 72590.927 0.9066344 6394.3552 -17018.103 37.852273 82.296707 2150 67.482913 72590.927 0.9066344 6394.3494 -16110.786 37.852273 82.296707 2200 66.654034 72590.927 0.9066344 6394.3805 -17043.489 37.852273 82.296707 2250 66.077722 72590.927 0.9066344 6394.3828 -16516.329 37.852273 82.296707 2300 66.409836 72590.927 0.9066344 6394.3872 -16257.826 37.852273 82.296707 2350 65.420365 72590.927 0.9066344 6394.3987 -16404.839 37.852273 82.296707 2400 66.650258 72590.927 0.9066344 6394.4115 -16754.612 37.852273 82.296707 2450 66.674141 72590.927 0.9066344 6394.4277 -17104.384 37.852273 82.296707 2500 68.755741 72590.927 0.9066344 6394.4267 -16592.429 37.852273 82.296707 2550 67.475872 72590.927 0.9066344 6394.424 -16278.169 37.852273 82.296707 2600 67.408359 72590.927 0.9066344 6394.4229 -15685.108 37.852273 82.296707 2650 66.016203 72590.927 0.9066344 6394.4454 -16364.359 37.852273 82.296707 2700 66.849201 72590.927 0.9066344 6394.4337 -15730.749 37.852273 82.296707 2750 66.455964 72590.927 0.9066344 6394.4278 -15446.898 37.852273 82.296707 2800 67.948169 72590.927 0.9066344 6394.4483 -16095.728 37.852273 82.296707 2850 65.670055 72590.927 0.9066344 6394.4507 -16070.391 37.852273 82.296707 2900 65.704524 72590.927 0.9066344 6394.4584 -16050.119 37.852273 82.296707 2950 67.059922 72590.927 0.9066344 6394.4763 -16572.224 37.852273 82.296707 3000 65.643815 72590.927 0.9066344 6394.4805 -16719.23 37.852273 82.296707 3050 68.489513 72590.927 0.9066344 6394.4735 -16242.751 37.852273 82.296707 3100 69.207498 72590.927 0.9066344 6394.4925 -16830.748 37.852273 82.296707 3150 66.844624 72590.927 0.9066344 6394.4676 -15583.788 37.852273 82.296707 3200 67.905802 72590.927 0.9066344 6394.4669 -15740.934 37.852273 82.296707 3250 65.952066 72590.927 0.9066344 6394.4898 -16769.935 37.852273 82.296707 3300 66.605162 72590.927 0.9066344 6394.4826 -16323.868 37.852273 82.296707 3350 66.619689 72590.927 0.9066344 6394.4933 -16769.938 37.852273 82.296707 3400 68.264947 72590.927 0.9066344 6394.506 -17155.177 37.852273 82.296707 3450 67.067932 72590.927 0.9066344 6394.5004 -17028.458 37.852273 82.296707 3500 66.82947 72590.927 0.9066344 6394.498 -16886.528 37.852273 82.296707 3550 68.334001 72590.927 0.9066344 6394.4886 -16582.394 37.852273 82.296707 3600 66.660668 72590.927 0.9066344 6394.512 -17586.046 37.852273 82.296707 3650 66.663599 72590.927 0.9066344 6394.4848 -16045.08 37.852273 82.296707 3700 66.931867 72590.927 0.9066344 6394.4911 -16749.674 37.852273 82.296707 3750 66.406212 72590.927 0.9066344 6394.4879 -16187.012 37.852273 82.296707 3800 65.722664 72590.927 0.9066344 6394.475 -15477.356 37.852273 82.296707 3850 64.94586 72590.927 0.9066344 6394.4833 -16009.6 37.852273 82.296707 3900 65.353326 72590.927 0.9066344 6394.4731 -15492.566 37.852273 82.296707 3950 66.539286 72590.927 0.9066344 6394.4673 -15462.158 37.852273 82.296707 4000 65.715969 72590.927 0.9066344 6394.481 -15984.258 37.852273 82.296707 4050 67.020294 72590.927 0.9066344 6394.491 -16541.845 37.852273 82.296707 4100 66.820435 72590.927 0.9066344 6394.4855 -16156.602 37.852273 82.296707 4150 67.791457 72590.927 0.9066344 6394.489 -16100.839 37.852273 82.296707 4200 67.408649 72590.927 0.9066344 6394.4921 -16536.776 37.852273 82.296707 4250 67.58581 72590.927 0.9066344 6394.4926 -16440.463 37.852273 82.296707 4300 66.747287 72590.927 0.9066344 6394.5016 -16856.117 37.852273 82.296707 4350 65.428628 72590.927 0.9066344 6394.4987 -16871.328 37.852273 82.296707 4400 67.508516 72590.927 0.9066344 6394.4672 -15193.499 37.852273 82.296707 4450 66.425775 72590.927 0.9066344 6394.4932 -16572.259 37.852273 82.296707 4500 65.310794 72590.927 0.9066344 6394.4886 -16176.876 37.852273 82.296707 4550 66.110355 72590.927 0.9066344 6394.4733 -15548.328 37.852273 82.296707 4600 68.947951 72590.927 0.9066344 6394.4874 -16187.016 37.852273 82.296707 4650 66.036895 72590.927 0.9066344 6394.5006 -16678.702 37.852273 82.296707 4700 67.079151 72590.927 0.9066344 6394.5164 -17525.22 37.852273 82.296707 4750 67.081898 72590.927 0.9066344 6394.4896 -16374.569 37.852273 82.296707 4800 68.158698 72590.927 0.9066344 6394.476 -15517.911 37.852273 82.296707 4850 67.63645 72590.927 0.9066344 6394.4926 -16095.768 37.852273 82.296707 4900 66.119718 72590.927 0.9066344 6394.4871 -16323.881 37.852273 82.296707 4950 67.156553 72590.927 0.9066344 6394.4896 -16334.017 37.852273 82.296707 5000 66.515727 72590.927 0.9066344 6394.4926 -16435.395 37.852273 82.296707 Loop time of 70.6825 on 8 procs for 5000 steps with 6600 atoms 99.1% CPU use with 8 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -26423.0165925016 -16268.1190235657 -16435.3951258122 Force two-norm initial, final = 2450.6697 66.515727 Force max component initial, final = 96.585311 3.7538004 Final line search alpha, max atom move = 1.2416169e-10 4.660782e-10 Iterations, force evaluations = 5000 5176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 45.641 | 57.544 | 68.875 | 119.2 | 81.41 Bond | 0.20632 | 0.21763 | 0.23027 | 1.5 | 0.31 Neigh | 0.014817 | 0.014837 | 0.014858 | 0.0 | 0.02 Comm | 1.1642 | 12.505 | 24.405 | 256.0 | 17.69 Output | 0.0064983 | 0.0066652 | 0.0076507 | 0.5 | 0.01 Modify | 0.021729 | 0.022342 | 0.023759 | 0.4 | 0.03 Other | | 0.3716 | | | 0.53 Nlocal: 825 ave 853 max 792 min Histogram: 2 0 0 0 1 1 1 1 1 1 Nghost: 7377.25 ave 7465 max 7289 min Histogram: 1 1 0 0 1 3 0 1 0 1 Neighs: 437651 ave 527973 max 343331 min Histogram: 1 3 0 0 0 0 0 1 1 2 Total # of neighbors = 3501211 Ave neighs/atom = 530.48652 Ave special neighs/atom = 2 Neighbor list builds = 1 Dangerous builds = 0 undump sci unfix upperW unfix lowerW print "AFTER MINIMIZE WITH WALL..." AFTER MINIMIZE WITH WALL... print "zlow=${lowz}" zlow=37.8522734927403 print "zhigh=${highz}" zhigh=82.2967071720229 Total wall time: 2:54:27