LAMMPS (23 Jun 2022 - Update 1) units metal dimension 3 box tilt large atom_style full boundary p p p read_data output3_final_cropped_in_a_b_direct.data Reading data file ... triclinic box = (0 0 0) to (278.29694 118.46718 25) with tilt (68.397048 0 0) 4 by 1 by 1 MPI processor grid reading atoms ... 25766 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.044 seconds mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate group layer1 molecule 1 12895 atoms in group layer1 group layer2 molecule 2 12871 atoms in group layer2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/z 15.0 ################################################################### pair_coeff * * rebo CH.rebo C C # chemical Reading rebo potential file CH.rebo with DATE: 2018-7-3 pair_coeff 1 2 kolmogorov/crespi/z CH.KC C C # long range Reading kolmogorov/crespi/z potential file CH.KC with DATE: 2018-09-12 #pair_modify neigh/trim no #################################################################### #fix freeze_all layer1 setforce 0.0 0.0 0.0 # Neighbor update settings neighbor 2.0 bin neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes # Initial temperature velocity all create 0.1 88 mom yes rot yes dist uniform # Equilibration settings timestep 0.0001 fix 1 all nvt temp 0.1 100.0 1 #fix freeze_all layer1 setforce 0.0 0.0 0.0 thermo 100 thermo_style custom step temp pe ke etotal press run 10000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 binsize = 8.5, bins = 41 14 3 3 neighbor lists, perpetual/occasional/extra = 3 0 0 (1) pair rebo, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) pair kolmogorov/crespi/z, perpetual, skip from (3) attributes: half, newton on pair build: skip stencil: none bin: none (3) neighbor class addition, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard Per MPI rank memory allocation (min/avg/max) = 38.16 | 38.16 | 38.17 Mbytes Step Temp PotEng KinEng TotEng Press 0 0.1 -82994.054 0.33303876 -82993.721 192684.59 100 0.66594193 -190050.77 2.2178448 -190048.55 29946.412 200 0.24432222 -190207.67 0.81368769 -190206.85 30064.019 300 0.13663134 -190278.02 0.45503532 -190277.56 29951.162 400 0.088738237 -190321.05 0.29553273 -190320.76 29894.225 500 0.062154133 -190350.01 0.20699735 -190349.8 29885.025 600 0.047333736 -190371.12 0.15763969 -190370.96 29861.795 700 0.039281196 -190387.9 0.13082161 -190387.77 29797.92 800 0.034103804 -190402.2 0.11357889 -190402.09 29723.325 900 0.030204248 -190414.76 0.10059185 -190414.65 29657.695 1000 0.027110167 -190425.95 0.090287366 -190425.86 29599.256 1100 0.024562781 -190436.05 0.081803583 -190435.97 29546.557 1200 0.022406983 -190445.23 0.07462394 -190445.16 29498.609 1300 0.020539403 -190453.63 0.068404174 -190453.56 29454.859 1400 0.018903646 -190461.34 0.062956469 -190461.28 29414.65 1500 0.017460289 -190468.46 0.05814953 -190468.4 29377.46 1600 0.016181988 -190475.04 0.053892293 -190474.98 29342.926 1700 0.015044517 -190481.15 0.050104072 -190481.1 29310.749 1800 0.014027063 -190486.83 0.046715556 -190486.79 29280.681 1900 0.013112826 -190492.14 0.043670793 -190492.1 29252.51 2000 0.012288091 -190497.11 0.040924107 -190497.07 29226.051 2100 0.011541546 -190501.78 0.038437821 -190501.74 29201.148 2200 0.010863789 -190506.16 0.036180628 -190506.12 29177.66 2300 0.010246588 -190510.29 0.03412511 -190510.26 29155.467 2400 0.0096831531 -190514.19 0.032248653 -190514.16 29134.462 2500 0.0091686733 -190517.88 0.030535236 -190517.85 29114.549 2600 0.0086974546 -190521.38 0.028965895 -190521.35 29095.644 2700 0.008264368 -190524.7 0.027523549 -190524.67 29077.671 2800 0.0078650654 -190527.86 0.026193716 -190527.83 29060.564 2900 0.0074958278 -190530.86 0.024964012 -190530.84 29044.261 3000 0.0071534905 -190533.73 0.023823896 -190533.71 29028.706 3100 0.0068353199 -190536.47 0.022764265 -190536.45 29013.85 3200 0.0065389444 -190539.09 0.02177722 -190539.06 28999.647 3300 0.0062622981 -190541.59 0.02085588 -190541.57 28986.056 3400 0.0060035749 -190543.99 0.019994232 -190543.97 28973.039 3500 0.0057611891 -190546.3 0.019186993 -190546.28 28960.561 3600 0.0055337401 -190548.51 0.0184295 -190548.49 28948.59 3700 0.0053199915 -190550.63 0.017717634 -190550.61 28937.096 3800 0.0051188454 -190552.68 0.01704774 -190552.66 28926.052 3900 0.0049293225 -190554.64 0.016416555 -190554.63 28915.431 4000 0.0047505448 -190556.54 0.015821156 -190556.52 28905.211 4100 0.0045817263 -190558.37 0.015258925 -190558.35 28895.37 4200 0.0044221551 -190560.13 0.014727491 -190560.11 28885.885 4300 0.0042711816 -190561.83 0.01422469 -190561.82 28876.739 4400 0.0041282155 -190563.48 0.013748558 -190563.46 28867.913 4500 0.0039927179 -190565.07 0.013297298 -190565.05 28859.389 4600 0.0038641953 -190566.6 0.012869268 -190566.59 28851.153 4700 0.0037421942 -190568.09 0.012462957 -190568.08 28843.189 4800 0.0036262964 -190569.54 0.012076973 -190569.52 28835.483 4900 0.0035161827 -190570.93 0.011710251 -190570.92 28828.077 5000 0.003411554 -190572.29 0.011361797 -190572.28 28820.939 5100 0.003312023 -190573.61 0.01103032 -190573.6 28814.023 5200 0.0032172609 -190574.89 0.010714726 -190574.87 28807.318 5300 0.003126969 -190576.13 0.010414019 -190576.12 28800.814 5400 0.0030408735 -190577.34 0.010127288 -190577.33 28794.501 5500 0.0029587219 -190578.51 0.0098536907 -190578.5 28788.368 5600 0.0028802801 -190579.65 0.0095924492 -190579.64 28782.408 5700 0.0028053309 -190580.77 0.0093428395 -190580.76 28776.611 5800 0.002733672 -190581.85 0.0091041876 -190581.84 28770.971 5900 0.002665115 -190582.91 0.0088758662 -190582.9 28765.48 6000 0.0025994842 -190583.94 0.0086572902 -190583.93 28760.131 6100 0.0025366155 -190584.95 0.0084479129 -190584.94 28754.917 6200 0.0024763553 -190585.93 0.0082472231 -190585.92 28749.832 6300 0.0024185602 -190586.89 0.0080547431 -190586.88 28744.871 6400 0.0023630886 -190587.82 0.0078700011 -190587.81 28740.029 6500 0.0023098103 -190588.74 0.0076925637 -190588.73 28735.299 6600 0.0022586095 -190589.63 0.007522045 -190589.62 28730.678 6700 0.0022093775 -190590.51 0.0073580833 -190590.5 28726.161 6800 0.0021620123 -190591.36 0.0072003391 -190591.36 28721.743 6900 0.0021164183 -190592.2 0.0070484934 -190592.19 28717.42 7000 0.0020725054 -190593.02 0.0069022464 -190593.01 28713.189 7100 0.0020301892 -190593.82 0.0067613169 -190593.82 28709.046 7200 0.0019893904 -190594.61 0.0066254411 -190594.6 28704.987 7300 0.0019500344 -190595.38 0.0064943705 -190595.38 28701.01 7400 0.0019120511 -190596.14 0.0063678712 -190596.13 28697.11 7500 0.0018753742 -190596.88 0.0062457229 -190596.87 28693.286 7600 0.0018399415 -190597.61 0.0061277184 -190597.6 28689.534 7700 0.0018056944 -190598.32 0.0060136622 -190598.32 28685.851 7800 0.0017725774 -190599.02 0.0059033699 -190599.02 28682.236 7900 0.0017405385 -190599.71 0.005796668 -190599.7 28678.685 8000 0.0017095247 -190600.39 0.00569338 -190600.38 28675.198 8100 0.0016794619 -190601.05 0.0055932591 -190601.04 28671.786 8200 0.0016503453 -190601.7 0.0054962897 -190601.7 28668.432 8300 0.0016221307 -190602.34 0.0054023239 -190602.34 28665.134 8400 0.001594777 -190602.97 0.0053112256 -190602.97 28661.89 8500 0.0015682465 -190603.59 0.0052228688 -190603.59 28658.698 8600 0.0015425035 -190604.2 0.0051371347 -190604.2 28655.557 8700 0.0015175144 -190604.8 0.0050539112 -190604.8 28652.464 8800 0.0014932472 -190605.39 0.0049730919 -190605.39 28649.419 8900 0.0014696719 -190605.97 0.004894577 -190605.97 28646.419 9000 0.0014467602 -190606.54 0.0048182722 -190606.54 28643.463 9100 0.0014244853 -190607.1 0.0047440882 -190607.1 28640.55 9200 0.0014028216 -190607.66 0.0046719397 -190607.65 28637.678 9300 0.0013817449 -190608.2 0.0046017461 -190608.2 28634.847 9400 0.0013612326 -190608.74 0.0045334321 -190608.74 28632.054 9500 0.0013412631 -190609.27 0.0044669262 -190609.26 28629.299 9600 0.0013218163 -190609.79 0.0044021606 -190609.79 28626.581 9700 0.0013028727 -190610.3 0.004339071 -190610.3 28623.898 9800 0.0012844139 -190610.81 0.0042775961 -190610.81 28621.25 9900 0.0012664227 -190611.31 0.0042176784 -190611.31 28618.634 10000 0.0012488827 -190611.8 0.0041592633 -190611.8 28616.052 Loop time of 872.118 on 4 procs for 10000 steps with 25766 atoms Performance: 0.099 ns/day, 242.255 hours/ns, 11.466 timesteps/s 98.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 808.43 | 812.94 | 819.41 | 14.1 | 93.21 Bond | 0.0025611 | 0.0026651 | 0.0028841 | 0.2 | 0.00 Neigh | 2.7616 | 2.8141 | 2.9129 | 3.6 | 0.32 Comm | 30.221 | 37.667 | 44.085 | 85.8 | 4.32 Output | 0.0048431 | 0.0052808 | 0.0064636 | 0.9 | 0.00 Modify | 14.224 | 16.892 | 20.375 | 59.5 | 1.94 Other | | 1.798 | | | 0.21 Nlocal: 6441.5 ave 6449 max 6422 min Histogram: 1 0 0 0 0 0 0 0 0 3 Nghost: 19490 ave 19514 max 19457 min Histogram: 1 0 0 0 0 1 0 1 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 2.70158e+06 ave 2.7068e+06 max 2.69219e+06 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 10806336 Ave neighs/atom = 419.40293 Ave special neighs/atom = 0 Neighbor list builds = 7 Dangerous builds = 6 write_data temp_output_0_100K_.data System init for write_data ... Total wall time: 0:14:32