LAMMPS (23 Jun 2022 - Update 3) WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:530) Reading data file ... orthogonal box = (0.2945 -2e-06 -2) to (114.2945 87.599996 100) 5 by 4 by 4 MPI processor grid reading atoms ... 83736 atoms scanning bonds ... 3 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 24 = max dihedrals/atom reading bonds ... 55398 bonds reading angles ... 46596 angles reading dihedrals ... 24018 dihedrals Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 11 = max # of 1-3 neighbors 22 = max # of 1-4 neighbors 26 = max # of special neighbors special bonds CPU = 0.145 seconds read_data CPU = 3.117 seconds 56136 atoms in group S 27600 atoms in group NS 66456 atoms in group A 17280 atoms in group B 7260 atoms in group P 54972 atoms in group W 52272 atoms in group WS WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:187) PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.000288 (../kspace.cpp:327) using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.20030612 grid = 60 50 128 stencil order = 5 estimated absolute RMS force accuracy = 0.0042382543 estimated relative force accuracy = 1.2763377e-05 using double precision KISS FFT 3d grid and FFT values/proc = 35378 14820 Generated 465 of 465 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 = 17 ghost atom cutoff = 17 binsize = 8.5, bins = 14 11 12 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 Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 21.26 | 31.07 | 45.82 Mbytes Step PotEng 0 1877696 1000 75356.198 2000 69863.844 3000 67545.053 4000 66273.022 5000 65548.485 6000 64942.223 7000 64586.682 8000 64272.153 9000 64017.232 10000 63848.167 11000 63681.777 12000 63516.424 13000 63357.212 14000 63269.292 15000 63178.063 16000 63119.292 16307 63106.963 Loop time of 2021.02 on 80 procs for 16307 steps with 83736 atoms 69.4% CPU use with 80 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 1877695.95118958 63106.9633807586 63106.9633807586 Force two-norm initial, final = 155108.8 5.9486986 Force max component initial, final = 13651.019 1.7852245 Final line search alpha, max atom move = 2.5418804e-10 4.5378271e-10 Iterations, force evaluations = 16307 32452 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 293.43 | 961.59 | 1652.5 |1080.0 | 47.58 Bond | 1.2462 | 3.2085 | 16.913 | 164.6 | 0.16 Kspace | 236.56 | 934.63 | 1604.5 |1098.2 | 46.25 Neigh | 6.2134 | 6.3219 | 6.5644 | 3.1 | 0.31 Comm | 38.145 | 84.703 | 116.64 | 274.6 | 4.19 Output | 0.0022964 | 0.0024066 | 0.0026754 | 0.2 | 0.00 Modify | 0.16486 | 0.27481 | 0.51212 | 16.8 | 0.01 Other | | 30.29 | | | 1.50 Nlocal: 1046.7 ave 1417 max 477 min Histogram: 2 0 2 10 14 12 15 5 10 10 Nghost: 13073.3 ave 17853 max 8591 min Histogram: 7 26 7 0 0 2 6 9 13 10 Neighs: 948723 ave 1.6025e+06 max 302965 min Histogram: 2 10 14 5 16 6 6 4 8 9 Total # of neighbors = 75897861 Ave neighs/atom = 906.39463 Ave special neighs/atom = 3.0097449 Neighbor list builds = 136 Dangerous builds = 0 Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 17424 = # of frozen angles find clusters CPU = 0.087 seconds PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.20030612 grid = 60 50 128 stencil order = 5 estimated absolute RMS force accuracy = 0.0042382543 estimated relative force accuracy = 1.2763377e-05 using double precision KISS FFT 3d grid and FFT values/proc = 35378 14820 Generated 465 of 465 mixed pair_coeff terms from geometric mixing rule Setting up Verlet run ... Unit style : real Current step : 16307 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 21.38 | 31.36 | 45.32 Mbytes Step PotEng 16307 61711.715 17000 93083.381 18000 99763.687 19000 98531.289 20000 97777.243 21000 97481.014 22000 97036.361 23000 97384.577 24000 97080.594 25000 97069.541 26000 97136.523 27000 96917.317 28000 96824.444 29000 96589.274 30000 96574.366 31000 96431.619 32000 96183.503 33000 96102.41 34000 96396.209 35000 96061.281 36000 95865.1 37000 95790.346 38000 96232.363 39000 95851.037 40000 95936.565 41000 95853.172 42000 95739.34 43000 95691.097 44000 95987.78 45000 95631.579 46000 95738.503 47000 95858.907 48000 95917.045 49000 95644.424 50000 96088.763 51000 95984.186 52000 95733.523 53000 96139.72 54000 95722.683 55000 95955.328 56000 95613.703 57000 95612.379 58000 95836.908 59000 95276.952 60000 95417.316 61000 95487.862 62000 95864.145 63000 95218.675 64000 95453.285 65000 95579.968 66000 95885.408 67000 95357.224 68000 95727.737 69000 95419.26 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94927.494 840000 94866.747 841000 95232.787 842000 95170.952 843000 95112.43 844000 95168.935 845000 94780.749 846000 95290.801 847000 95199.916 848000 95171.788 849000 94603.96 850000 95167.845 851000 95029.858 852000 94856.723 853000 94839.515 854000 95087.683 855000 95020.548 856000 94948.724 857000 94919.321 858000 95304.052 859000 95302.544 860000 95101.738 861000 94903.992 862000 94522.043 863000 94787.762 864000 95001.676 865000 94859.419 866000 95384.065 867000 94932.55 868000 94962.837 869000 95118.112 870000 95031.647 871000 95115.638 872000 95024.111 873000 95020.838 874000 95011.26 875000 94927.373 876000 95358.999 877000 94944.974 878000 94946.546 879000 95167.818 880000 95420.382 881000 95146.39 882000 95342.969 883000 95205.734 884000 94951.646 885000 95018.022 886000 94749.595 887000 94939.25 888000 95091.48 889000 94883.366 890000 94854.587 891000 95098.527 892000 95091.876 893000 95355.997 894000 94904.697 895000 94868.175 896000 95040.255 897000 94897.718 898000 94809.158 899000 94769.352 900000 94846.39 901000 95131.047 902000 94757.753 903000 94863.873 904000 95083.21 905000 95329.631 906000 95418.86 907000 95202.013 908000 95017.944 909000 94976.308 910000 95106.149 911000 95109.385 912000 95211.876 913000 94700.975 914000 94725.169 915000 94850.897 916000 95083.419 917000 95013.614 918000 94954.546 919000 94924.46 920000 94838.497 921000 95098.81 922000 94619.379 923000 95119.433 924000 94949.977 925000 94977.958 926000 95162.584 927000 95011.153 928000 94655.691 929000 95012.895 930000 95172.804 931000 94899.323 932000 95109.12 933000 94981.239 934000 94828.654 935000 95040.426 936000 94635.845 937000 95058.077 938000 94918.155 939000 95034.878 940000 95126.342 941000 94558.505 942000 94889.906 943000 95019.717 944000 94867.026 945000 94792.985 946000 94962.068 947000 95113.033 948000 94922.511 949000 95174.861 950000 94602.795 951000 94978.806 952000 94713.353 953000 94827.663 954000 95151.931 955000 95094.066 956000 95090.3 957000 95155.873 958000 95046.797 959000 95130.329 960000 94994.403 961000 95004.726 962000 95322.674 963000 94637.022 964000 94969.422 965000 94669.626 966000 94559.857 967000 94870.777 968000 95307.4 969000 94974.754 970000 94434.741 971000 94949.388 972000 95088.501 973000 95083.724 974000 94848.859 975000 94847.554 976000 94730.615 977000 94656.473 978000 95170.084 979000 94665.933 980000 95201.011 981000 95035.06 982000 94782.272 983000 94924.423 984000 94845.9 985000 95290.174 986000 95025.913 987000 94988.814 988000 95240.348 989000 94889.763 990000 95254.168 991000 95211.446 992000 94936.916 993000 95234.692 994000 95078.069 995000 94833.659 996000 94835.088 997000 94913.404 998000 94943.829 999000 95213.81 1000000 95363.944 1001000 95226.432 1002000 94968.339 1003000 94886.179 1004000 94659.535 1005000 94799.603 1006000 94704.752 1007000 94930.481 1008000 95030.752 1009000 95148.177 1010000 94881.775 1011000 94656.198 1012000 95180.748 1013000 95172.924 1014000 95184.27 1015000 94655.374 1016000 95110.8 1016307 95257.704 Loop time of 46953.3 on 80 procs for 1000000 steps with 83736 atoms Performance: 1.840 ns/day, 13.043 hours/ns, 21.298 timesteps/s 69.5% CPU use with 80 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7354.6 | 20824 | 31792 |5336.7 | 44.35 Bond | 0.89822 | 60.553 | 447.96 |1210.8 | 0.13 Kspace | 7072.8 | 18313 | 31661 |5645.5 | 39.00 Neigh | 3009.4 | 3049.3 | 3110.7 | 56.2 | 6.49 Comm | 1417.2 | 2331.3 | 3175.5 |1312.8 | 4.97 Output | 0.45547 | 0.4723 | 0.50826 | 1.1 | 0.00 Modify | 1710 | 2217 | 2708 | 825.2 | 4.72 Other | | 157.7 | | | 0.34 Nlocal: 1046.7 ave 1398 max 560 min Histogram: 4 16 0 0 0 0 25 26 5 4 Nghost: 13069.6 ave 17454 max 8387 min Histogram: 20 0 10 10 0 0 0 10 10 20 Neighs: 948596 ave 1.54047e+06 max 286210 min Histogram: 20 0 0 0 0 0 48 6 3 3 Total # of neighbors = 75887713 Ave neighs/atom = 906.27344 Ave special neighs/atom = 3.0097449 Neighbor list builds = 58450 Dangerous builds = 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.20030612 grid = 60 50 128 stencil order = 5 estimated absolute RMS force accuracy = 0.0042382543 estimated relative force accuracy = 1.2763377e-05 using double precision KISS FFT 3d grid and FFT values/proc = 35378 14820 Generated 465 of 465 mixed pair_coeff terms from geometric mixing rule Setting up cg style minimization ... Unit style : real Current step : 1016307 Per MPI rank memory allocation (min/avg/max) = 24.4 | 34.36 | 45.82 Mbytes Step PotEng 1016307 95257.704 1017000 40380.918 1018000 38782.972 1019000 38016.774 1020000 37638.941 1021000 37491.897 1022000 37388.781 1023000 37302.523 1024000 37258.133 1024943 37214.531 Loop time of 1039.69 on 80 procs for 8636 steps with 83736 atoms 69.7% CPU use with 80 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 95257.7042093785 37214.5310136777 37214.5310136777 Force two-norm initial, final = 7710.367 9.9169594 Force max component initial, final = 285.11319 4.235564 Final line search alpha, max atom move = 7.6048913e-11 3.2211004e-10 Iterations, force evaluations = 8636 17268 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 139.1 | 518.6 | 844.17 | 913.7 | 49.88 Bond | 0.43749 | 1.7257 | 9.3684 | 129.8 | 0.17 Kspace | 120.07 | 460.43 | 837.83 | 966.3 | 44.29 Neigh | 4.1201 | 4.2032 | 4.2902 | 2.1 | 0.40 Comm | 23.632 | 40.118 | 54.771 | 147.5 | 3.86 Output | 0.00074287 | 0.00090296 | 0.0011597 | 0.0 | 0.00 Modify | 0.051982 | 0.13933 | 0.30731 | 16.4 | 0.01 Other | | 14.48 | | | 1.39 Nlocal: 1046.7 ave 1437 max 468 min Histogram: 10 10 0 0 0 0 18 25 12 5 Nghost: 13122.3 ave 17944 max 8033 min Histogram: 20 0 0 20 0 0 0 18 2 20 Neighs: 977808 ave 1.63006e+06 max 216026 min Histogram: 20 0 0 0 0 0 36 18 3 3 Total # of neighbors = 78224618 Ave neighs/atom = 934.18145 Ave special neighs/atom = 3.0097449 Neighbor list builds = 77 Dangerous builds = 0 Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 18324 = # of frozen angles find clusters CPU = 0.170 seconds PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.20030612 grid = 60 50 128 stencil order = 5 estimated absolute RMS force accuracy = 0.0042382543 estimated relative force accuracy = 1.2763377e-05 using double precision KISS FFT 3d grid and FFT values/proc = 35378 14820 Generated 465 of 465 mixed pair_coeff terms from geometric mixing rule Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 25.24 | 35.06 | 46.37 Mbytes Step Time Temp PotEng KinEng TotEng Press 0 0 384.04091 35216.823 74879.439 110096.26 176210.03