LAMMPS (8 Feb 2023) Processor partition = 0 using 1 OpenMP thread(s) per MPI task # Example for an alchemical transformation of two water molecules into a hydronium and hydroxyl ion # WARNING: This input is intended for demonstrating the method only, # the force field parameters are mostly made up and NOT suitable for production simulations. # set up different names for two partitions variable name world twowater twoions units real atom_style full atom_modify map array region box block -5 5 -5 5 -5 5 boundary p p p create_box 2 box bond/types 2 angle/types 2 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3 Created orthogonal box = (-5 -5 -5) to (5 5 5) 1 by 1 by 2 MPI processor grid mass 1 15.9994 mass 2 1.008 pair_style lj/cut/coul/cut 10.0 pair_coeff 1 1 0.1553 3.166 pair_coeff 1 2 0.0 1.0 pair_coeff 2 2 0.0 1.0 bond_style harmonic bond_coeff * 1000.0 1.0 angle_style harmonic angle_coeff * 100.0 109.47 molecule water h2o.mol Read molecule template water: 1 molecules 0 fragments 3 atoms with max type 2 2 bonds with max type 1 1 angles with max type 1 0 dihedrals with max type 0 0 impropers with max type 0 # create the two molecules we want to transform ... create_atoms 0 single -2.0 0.0 0.0 mol water 453624 Created 3 atoms using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) create_atoms CPU = 0.003 seconds create_atoms 0 single 2.0 0.0 0.0 mol water 767353 Created 3 atoms using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) create_atoms CPU = 0.000 seconds # ... and put them in a group group transform id 1:6 6 atoms in group transform # now fill the rest of the box with more water create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33 Created 96 atoms using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) create_atoms CPU = 0.000 seconds # change topology and settings for the two states # we cannot simply create a different topology directly or # load a different data file because the order and position # of all atoms must be maintained across both replica # we first have to remove all topology data in the transform group delete_bonds transform bond 1 System init for delete_bonds ... 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 = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Deleting bonds ... 68 total bonds, 64 turned on, 4 turned off 34 total angles, 34 turned on, 0 turned off 0 total dihedrals, 0 turned on, 0 turned off 0 total impropers, 0 turned on, 0 turned off delete_bonds transform angle 1 remove System init for delete_bonds ... Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Deleting bonds ... 64 total bonds, 64 turned on, 0 turned off 32 total angles, 32 turned on, 0 turned off 0 total dihedrals, 0 turned on, 0 turned off 0 total impropers, 0 turned on, 0 turned off # then generate different topologies for the two partitions. select by name. if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775" create_bonds single/bond 2 1 2 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.000 seconds create_bonds single/bond 2 1 3 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.000 seconds create_bonds single/bond 2 4 5 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.000 seconds create_bonds single/bond 2 4 6 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.000 seconds create_bonds single/angle 2 2 1 3 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.000 seconds create_bonds single/angle 2 5 4 6 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 7 = max # of special neighbors special bonds CPU = 0.000 seconds velocity all create 300.0 5463576 timestep 0.2 # define ramp variable to combine the two different partitions if "${name} == twowater" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)" variable ramp equal ramp(1.0,0.0) # since the trajectory and forces are kept identical through fix alchemy, # we can do fix npt simulations, but we must use the "mixed" pressure fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 fix transform all alchemy v_ramp compute pressure all pressure/alchemy transform fix_modify integrate press pressure # only need to output a dump file from one partition # if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id" thermo_style custom step temp press etotal density pe ke f_transform f_transform[3] thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed thermo_modify press pressure thermo 100 run 20000 Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed 0 300 184631.17 -802.19609 1.0171193 -892.51464 90.318545 1 -892.51464 100 293.4335 -513.97927 189.09028 0.3029684 100.74865 88.341623 0.995 207.29243 200 320.81838 1513.3 111.09325 0.64509407 14.507087 96.586165 0.99 46.402434 300 261.53825 -3808.6942 -538.67351 0.88817871 -617.41269 78.739179 0.985 -614.76481 400 308.32444 1375.0327 -804.08042 0.97694485 -896.90513 92.824715 0.98 -897.24386 500 292.60623 -12843.384 -1141.5985 1.0140814 -1229.691 88.092563 0.975 -1221.948 600 326.16112 91608.645 2882.4855 1.0263567 2784.2908 98.194659 0.97 2786.0743 700 317.22811 -60420.408 -1517.0601 0.9919143 -1612.5654 95.505272 0.965 -1616.7677 800 309.94673 -56793.931 -1549.4612 1.0024958 -1642.7743 93.313126 0.96 -1640.8606 900 272.80718 -5076.2282 -1266.6775 1.0141078 -1348.8093 82.131824 0.955 -1357.1812 1000 346.52557 -16919.192 -1406.675 1.0170322 -1511.0006 104.32562 0.95 -1514.1398 1100 300.62984 -51826.972 -2469.2821 1.0063592 -2559.7903 90.508164 0.945 -2565.9668 1200 293.72767 45222.698 2039.1938 1.0272336 1950.7636 88.430186 0.94 1951.1683 1300 289.4971 94600.203 2184.5096 1.0298091 2097.3531 87.156524 0.935 2088.1011 1400 328.98666 35468.53 1816.723 1.0198467 1717.6777 99.045321 0.93 1716.9268 1500 392.9407 41220.21 1820.7312 1.0194044 1702.4317 118.29944 0.925 1690.6416 1600 284.90093 -37995.141 -2439.9256 1.0068497 -2525.6984 85.772791 0.92 -2529.5874 1700 267.67454 25275.255 1612.5912 1.0313556 1532.0046 80.586582 0.915 1520.9695 1800 247.16495 -68222.994 -2699.1903 1.0018048 -2773.6022 74.41193 0.91 -2788.9545 1900 328.41849 -51979.665 -2339.7432 1.0154952 -2438.6175 98.874268 0.905 -2461.3422 2000 313.8715 21726.003 1473.9594 1.018831 1379.4647 94.494725 0.9 1363.0739 2100 296.07341 66130.11 1379.1597 1.0224882 1290.0233 89.136398 0.895 1272.1884 2200 282.67889 51746.464 2376.377 1.0362683 2291.2732 85.103821 0.89 2276.1488 2300 281.04207 -71937.759 -2791.0867 1.0111968 -2875.6977 84.611035 0.885 -2892.2526 2400 321.00806 -51658.758 -2507.6376 1.0168161 -2604.2809 96.643269 0.88 -2622.9732 2500 288.95906 49645.753 2361.024 1.0355648 2274.0295 86.99454 0.875 2275.0348 2600 303.0064 -48470.216 -1973.9561 1.000439 -2065.1798 91.223657 0.87 -2082.5895 2700 361.7083 54973.584 1929.0772 1.0223169 1820.1806 108.89656 0.865 1817.1972 2800 289.27827 33564.017 1783.5154 1.0257088 1696.4248 87.090642 0.86 1682.9162 2900 283.94365 -47190.274 -2286.9529 1.0059224 -2372.4375 85.484591 0.855 -2395.9575 3000 337.10996 61988.686 2289.363 1.0258 2187.8721 101.49094 0.85 2168.1085 3100 305.28249 -50123.109 -1913.7375 1.0143567 -2005.6464 91.9089 0.845 -2040.3453 3200 270.19471 -18114.265 -1961.3048 1.0132413 -2042.6502 81.345309 0.84 -2076.9595 3300 263.39996 -109301.89 -2351.6647 0.99956867 -2430.9643 79.299671 0.835 -2471.0269 3400 249.01722 -37585.949 -2423.3849 1.0080932 -2498.3544 74.969576 0.83 -2537.734 3500 267.88868 65528.865 2164.3882 1.0390872 2083.7372 80.651054 0.825 2061.6421 3600 351.46458 -67583.574 -2861.4561 1.0059621 -2967.2687 105.81256 0.82 -3004.5028 3700 332.82565 -61204.843 -2275.2765 1.0053485 -2375.4776 100.20109 0.815 -2415.4435 3800 298.0279 61123.085 1951.1943 1.020672 1861.4695 89.724819 0.81 1831.9734 3900 317.04715 43210.045 1848.3875 1.0287838 1752.9367 95.450792 0.805 1721.1961 4000 261.75174 -111920.72 -3274.707 0.99457106 -3353.5105 78.803455 0.8 -3394.3528 4100 338.34245 89763.083 2115.4809 1.0318272 2013.6189 101.86199 0.795 1973.419 4200 288.52623 19989.792 1758.0617 1.0204119 1671.1975 86.86423 0.79 1633.1439 4300 322.05593 -33791.403 -2107.1643 1.0155065 -2204.1231 96.958741 0.785 -2246.4353 4400 280.59054 -27839.599 -1534.3265 1.0123506 -1618.8016 84.475096 0.78 -1672.1425 4500 296.08336 75206.112 2789.7494 1.0329133 2700.61 89.139393 0.775 2670.4908 4600 288.02094 -67445.101 -2983.5242 0.99579107 -3070.2363 86.712106 0.77 -3132.6352 4700 332.21641 -83964.647 -2746.0748 1.0053915 -2846.0925 100.01768 0.765 -2916.6652 4800 305.52557 -93111.682 -2354.6562 0.99824941 -2446.6383 91.982082 0.76 -2514.039 4900 272.82262 -53664.198 -2790.1342 0.99527907 -2872.2707 82.136472 0.755 -2947.2062 5000 288.96388 39846.089 1975.7895 1.0371205 1888.7935 86.99599 0.75 1833.3716 5100 293.25543 -71819.425 -2916.8817 0.99452016 -3005.1697 88.288011 0.745 -3069.7618 5200 296.16486 -64484.821 -2416.0381 1.0153125 -2505.2021 89.163931 0.74 -2589.6878 5300 342.07246 60255.985 1749.8984 1.0306374 1646.9134 102.98496 0.735 1608.5673 5400 295.53315 61421.189 1620.6432 1.0334762 1531.6695 88.973746 0.73 1492.0969 5500 285.1755 24845.113 1144.9009 1.0335035 1059.0454 85.855455 0.725 1014.0263 5600 276.79246 66244.072 1523.3405 1.0251134 1440.0089 83.331641 0.72 1390.9078 5700 288.43485 14629.129 1208.7278 1.02997 1121.8911 86.836719 0.715 1074.3779 5800 276.64233 59262.97 914.26981 1.0332305 830.98336 83.286443 0.71 763.27415 5900 358.25384 -111203.23 -3370.7104 1.006331 -3478.567 107.85655 0.705 -3561.6283 6000 327.82233 -62936.335 -1881.2426 1.0106476 -1979.9373 98.694786 0.7 -2062.107 6100 309.86553 -59110.381 -2698.4147 1.0076375 -2791.7034 93.28868 0.695 -2870.9566 6200 294.95752 -58011.845 -1819.201 1.0161986 -1908.0014 88.800448 0.69 -1971.2586 6300 307.27252 59016.127 1186.0709 1.0225343 1093.5629 92.508022 0.685 1032.9616 6400 292.21611 -118857.83 -2992.9227 1.0031304 -3080.8978 87.975114 0.68 -3175.9068 6500 332.21108 97132.547 2290.2726 1.0349752 2190.2565 100.01607 0.675 2121.4674 6600 321.93985 -50017.836 -2484.5919 1.0076385 -2581.5157 96.923796 0.67 -2673.6819 6700 299.07231 -98136.241 -3013.1584 1.0106261 -3103.1976 90.039252 0.665 -3194.0694 6800 285.33731 28487.407 455.68104 1.017186 369.77687 85.904169 0.66 294.02418 6900 296.41387 50054.533 2028.1018 1.0445934 1938.8629 89.238897 0.655 1851.1397 7000 318.34109 -71579.897 -3114.0324 1.007304 -3209.8728 95.840345 0.65 -3305.5715 7100 317.2192 12370.315 1139.7687 1.0177238 1044.2661 95.502589 0.645 961.68146 7200 289.91091 43944.333 1213.4685 1.0302599 1126.1874 87.281105 0.64 1039.3329 7300 324.81227 42859.173 1288.5297 1.0300698 1190.7411 97.788572 0.635 1083.5764 7400 305.72634 76516.72 2404.9462 1.0580673 2312.9036 92.042527 0.63 2218.3674 7500 283.77479 -87225.247 -3401.4354 0.9936609 -3486.8692 85.433754 0.625 -3581.9003 7600 318.72048 16084.995 1848.3396 1.0296163 1752.385 95.954566 0.62 1653.5125 7700 307.36895 74007.024 1754.8928 1.0363553 1662.3558 92.537054 0.615 1572.8568 7800 297.44704 28693.429 1261.5958 1.0206402 1172.0459 89.549946 0.61 1093.5903 7900 288.47173 -94644.76 -2455.4369 1.0095244 -2542.2847 86.847823 0.605 -2648.2974 8000 280.5001 63255.987 1584.7287 1.020587 1500.2808 84.44787 0.6 1418.7144 8100 320.23351 68383.584 2300.142 1.0419027 2203.7319 96.410082 0.595 2111.2616 8200 354.86765 50012.316 1350.3752 1.0292074 1243.5381 106.8371 0.59 1149.0631 8300 278.8859 24200.145 772.82478 1.0232468 688.86288 83.961894 0.585 569.83331 8400 295.95754 -12010.401 1078.6687 1.0200526 989.56716 89.101514 0.58 872.63254 8500 289.57525 -64114.236 -3017.5291 1.0062613 -3104.7091 87.18005 0.575 -3227.8592 8600 329.23192 15948.893 1427.4791 1.0271511 1328.3599 99.119161 0.57 1211.3868 8700 327.45998 39407.811 1697.908 1.0343756 1599.3223 98.585695 0.565 1480.9482 8800 296.99753 18017.036 871.11717 1.0178295 781.70256 89.414616 0.56 657.09357 8900 289.10016 79527.35 2536.8041 1.0462904 2449.7671 87.037018 0.555 2338.4742 9000 260.53308 -51430.717 -2680.1664 1.0040128 -2758.603 78.436561 0.55 -2894.7913 9100 314.17867 40043.249 2043.6144 1.0361707 1949.0272 94.5872 0.545 1836.5399 9200 362.21236 -55153.163 -2232.4614 1.0102652 -2341.5097 109.04831 0.54 -2497.8765 9300 266.62049 -72193.959 -2980.9254 1.0063615 -3061.1946 80.269248 0.535 -3225.2604 9400 259.59316 7674.9295 1378.2484 1.0326879 1300.0948 78.153588 0.53 1171.7119 9500 278.72962 -33127.835 -2581.8908 1.0163553 -2665.8057 83.914845 0.525 -2805.1711 9600 299.09039 24570.664 1839.3275 1.025317 1749.2828 90.044695 0.52 1631.8392 9700 336.65655 37767.059 1415.9074 1.0245842 1314.5529 101.35443 0.515 1218.4022 9800 279.68112 -55007.939 -2548.4947 1.0129837 -2632.696 84.201305 0.51 -2775.6909 9900 300.55694 14964.424 1332.287 1.0176315 1241.8008 90.486218 0.505 1127.7276 10000 276.77193 -75638.817 -3100.7483 1.0019055 -3184.0738 83.325459 0.5 -3341.663 10100 316.26926 61548.301 2406.8933 1.0427988 2311.6767 95.216598 0.495 2206.7159 10200 297.28171 56814.839 2073.2348 1.0270036 1983.7347 89.500171 0.49 1859.0176 10300 276.84774 83572.576 1920.2202 1.0322243 1836.8719 83.348283 0.485 1704.2233 10400 263.28687 -16549.994 1144.9186 1.0177296 1065.6529 79.265623 0.48 940.36339 10500 332.79252 47379.311 1538.8168 1.0223403 1438.6257 100.19112 0.475 1301.3762 10600 329.01105 39299.248 1330.9914 1.0230094 1231.9387 99.052663 0.47 1077.5639 10700 339.21335 -4217.0313 981.9193 1.0235915 879.79511 102.12419 0.465 741.87272 10800 297.11192 -80013.424 -3682.9794 1.0009566 -3772.4285 89.449054 0.46 -3958.8283 10900 299.63096 47783.864 1833.1832 1.0435283 1742.9757 90.207441 0.455 1620.9328 11000 363.58243 67370.65 1769.9236 1.0450565 1660.4628 109.46079 0.45 1543.803 11100 306.04664 50246.004 1323.7676 1.0341876 1231.6287 92.138957 0.445 1063.5345 11200 255.68488 43750.967 2205.2392 1.0530607 2128.2623 76.976955 0.44 1986.9636 11300 271.71957 -40289.299 -3083.4093 1.0168497 -3165.2137 81.804388 0.435 -3344.1558 11400 291.74007 -115249.24 -3319.2153 1.0067921 -3407.0471 87.831795 0.43 -3569.0256 11500 270.22077 28235.119 596.78348 1.0195886 515.43032 81.353155 0.425 373.78255 11600 297.08506 29790.701 1031.3514 1.0317561 941.91046 89.440969 0.42 803.92835 11700 295.33119 -101140.58 -3068.1166 1.0107252 -3157.0295 88.912943 0.415 -3348.5652 11800 308.77287 -120312.75 -3553.1266 0.99681611 -3646.0863 92.95972 0.41 -3835.4663 11900 293.86337 82287.969 1847.0953 1.0331446 1758.6242 88.47104 0.405 1625.4846 12000 279.9866 27919.689 2249.3175 1.0384909 2165.0242 84.293273 0.4 2028.6311 12100 292.19439 47035.018 1220.3593 1.0210948 1132.3908 87.968573 0.395 976.68113 12200 317.78325 46886.483 2039.3721 1.0310567 1943.6997 95.672401 0.39 1763.6359 12300 357.44038 51492.35 1898.3396 1.0414835 1790.7279 107.61165 0.385 1638.1905 12400 288.16042 -50528.478 -2837.5599 1.0130798 -2924.314 86.7541 0.38 -3115.1383 12500 300.37356 -114034.29 -3091.586 1.0130272 -3182.017 90.431009 0.375 -3364.511 12600 265.4402 73960.28 1297.3012 1.0343798 1217.3873 79.913907 0.37 1094.544 12700 287.07994 22722.337 1711.9055 1.0268893 1625.4767 86.428809 0.365 1490.443 12800 315.39745 46072.191 926.21362 1.0205906 831.25949 94.954129 0.36 662.83753 12900 307.48549 -120472.73 -3181.5418 1.005689 -3274.1139 92.57214 0.355 -3469.7834 13000 291.00577 -59154.878 -2652.0402 1.012821 -2739.6509 87.610727 0.35 -2966.2448 13100 318.37718 86703.775 2087.145 1.036209 1991.2938 95.851211 0.345 1819.7078 13200 280.41509 -107033.79 -2683.9682 1.0135499 -2768.3905 84.422277 0.34 -2953.8355 13300 275.01919 112086.85 2632.1169 1.0437945 2549.3192 82.797775 0.335 2394.6707 13400 299.46547 -111959.62 -3475.4354 0.98732074 -3565.593 90.157617 0.33 -3792.6798 13500 275.65631 17625.49 1762.6531 1.0255473 1679.6636 82.989588 0.325 1521.2745 13600 302.63525 122466.63 2853.8095 1.0438137 2762.6976 91.111917 0.32 2611.7188 13700 302.21323 -94399.663 -3003.7573 1.0068914 -3094.7422 90.984863 0.315 -3328.4539 13800 305.70483 30039.825 1792.3286 1.0225478 1700.2926 92.036052 0.31 1502.8476 13900 273.15564 -27822.597 -2346.6702 1.0131002 -2428.9069 82.236732 0.305 -2683.7804 14000 257.14635 -1821.0012 1378.2522 1.0172653 1300.8352 77.416947 0.3 1067.8821 14100 323.74174 -76139.363 -2747.4152 1.0139806 -2844.8814 97.466276 0.295 -3052.598 14200 274.99913 54440.943 983.27131 1.0186356 900.47957 82.791736 0.29 767.64274 14300 291.8774 1281.7286 1258.7881 1.0214356 1170.915 87.873139 0.285 1042.8585 14400 308.97245 -47961.551 -2680.7892 1.0155221 -2773.809 93.019806 0.28 -3007.3204 14500 311.05309 86026.739 2115.2413 1.0311818 2021.5951 93.646208 0.275 1830.5463 14600 269.27432 -12972.747 971.48792 1.0172239 890.41971 81.068214 0.27 711.81484 14700 262.20739 -77722.459 -3215.6796 1.0029421 -3294.6202 78.940634 0.265 -3537.1929 14800 300.33592 -107332.8 -2798.6664 1.0126785 -2889.086 90.419677 0.26 -3125.8439 14900 307.0173 -73204.94 -2652.7275 1.016875 -2745.1587 92.431185 0.255 -3016.0143 15000 334.08711 64440.709 1615.3385 1.0369481 1514.7576 100.58087 0.25 1323.9179 15100 293.46703 35179.395 2020.1996 1.0331703 1931.8479 88.351717 0.245 1768.9681 15200 307.80546 54006.291 1111.7619 1.0246134 1019.0935 92.668471 0.24 822.22754 15300 336.59792 33832.907 1282.8271 1.0242407 1181.4903 101.33678 0.235 956.25285 15400 285.46526 -99629.94 -2336.7535 1.0041261 -2422.6962 85.942688 0.23 -2730.1887 15500 269.15938 122546.45 3012.0792 1.0318941 2931.0456 81.033612 0.225 2695.4331 15600 294.50818 -104733.19 -1914.0242 1.0017241 -2002.6894 88.665166 0.22 -2281.5773 15700 321.05125 -40438.501 -1721.9536 1.0125007 -1818.6099 96.656271 0.215 -2084.0893 15800 303.22185 -42224.408 -2145.481 1.0090867 -2236.7695 91.288521 0.21 -2506.3355 15900 281.65025 78652.063 2791.9418 1.0460521 2707.1477 84.794136 0.205 2500.7128 16000 286.5056 63174.412 1725.0409 1.0185277 1638.785 86.255897 0.2 1442.2427 16100 271.74574 -75051.584 -2101.5778 1.0091727 -2183.3901 81.812265 0.195 -2447.1967 16200 266.40007 -64120.09 -2223.3693 1.0064388 -2303.5722 80.202888 0.19 -2525.4243 16300 330.67137 46204.124 1837.3168 1.0271037 1737.7643 99.552523 0.185 1529.8186 16400 310.94573 18510.676 1531.823 1.0188695 1438.2091 93.613887 0.18 1195.3041 16500 270.29191 79005.409 1989.9392 1.0354088 1908.5646 81.374574 0.175 1678.7342 16600 334.24108 17143.221 1644.1483 1.0230561 1543.521 100.62723 0.17 1379.3215 16700 292.28721 -78618.031 -2768.3997 0.99940789 -2856.3962 87.996518 0.165 -3087.379 16800 346.09157 -69398.937 -2647.1375 1.0153026 -2751.3325 104.19496 0.16 -3011.3476 16900 284.37042 39314.526 2287.7061 1.0343186 2202.093 85.613074 0.155 2045.8316 17000 281.69389 86032.163 1817.9125 1.0237583 1733.1052 84.807275 0.15 1528.8391 17100 297.2629 55128.393 2617.4156 1.0419182 2527.9211 89.494508 0.145 2369.0347 17200 328.81472 47063.86 1880.9768 1.0364627 1781.9832 98.993555 0.14 1526.7115 17300 313.41363 -46685.063 -2310.803 1.008117 -2405.1599 94.356878 0.135 -2685.8034 17400 288.17114 68721.523 2771.6788 1.0429105 2684.9215 86.757326 0.13 2490.5845 17500 260.01702 -23324.539 -1436.6738 1.0100415 -1514.955 78.281195 0.125 -1812.4813 17600 297.6633 72795.463 2635.741 1.0362827 2546.126 89.615054 0.12 2336.0152 17700 301.02937 93833.118 2690.518 1.0276466 2599.8896 90.628448 0.115 2364.8751 17800 238.92837 -78317.212 -2175.2589 1.0084077 -2247.1911 71.932208 0.11 -2579.4429 17900 299.27724 -65278.891 -2589.1173 1.0034773 -2679.2182 90.10095 0.105 -2987.498 18000 315.15753 -72437.481 -2338.6068 1.0136139 -2433.4887 94.881898 0.1 -2718.125 18100 268.39411 -42194.209 -2285.3824 1.0108104 -2366.1856 80.803219 0.095 -2656.3853 18200 284.91941 40905.162 2045.1299 1.0266185 1959.3515 85.778354 0.09 1723.6803 18300 329.41629 -56526.814 -2104.8386 1.0137784 -2204.0133 99.174667 0.085 -2540.6829 18400 293.16732 -22085.551 -1652.5444 1.0163557 -1740.8059 88.261484 0.08 -2052.7864 18500 276.28141 29367.359 2314.5497 1.0270087 2231.3719 83.177784 0.075 1971.9405 18600 331.18031 94669.124 2466.3928 1.0225403 2366.6871 99.705745 0.07 2081.8675 18700 265.4491 49872.536 2571.9864 1.0255308 2492.0698 79.916587 0.065 2260.4261 18800 314.51042 60758.629 2560.3258 1.0300818 2465.6387 94.687078 0.06 2219.6547 18900 317.70309 66345.835 1768.2041 1.0248229 1672.5558 95.648268 0.055 1410.3087 19000 291.39831 -96336.931 -2448.6251 1.0100498 -2536.354 87.728905 0.05 -2805.9396 19100 303.37353 -21421.495 -2012.0929 0.99771284 -2103.4271 91.334186 0.045 -2436.2173 19200 293.92948 36383.881 2042.0163 1.0251299 1953.5254 88.490944 0.04 1633.579 19300 287.24409 -46691.027 -2399.698 1.0112067 -2486.1762 86.478228 0.035 -2811.3506 19400 333.42205 21152.63 1524.8699 1.0189912 1424.4893 100.38065 0.03 1118.2463 19500 309.17989 60445.761 2298.6966 1.0338543 2205.6144 93.082259 0.025 1928.6181 19600 255.92246 -32795.547 -1724.7933 1.0157044 -1801.8418 77.04848 0.02 -2213.9484 19700 342.62332 33538.746 2439.138 1.0225905 2335.9872 103.1508 0.015 2081.9185 19800 295.68946 81474.342 2308.3249 1.0240743 2219.3041 89.020804 0.01 1910.5545 19900 306.4947 43488.052 2330.4958 1.0222707 2238.222 92.27385 0.005 1957.4368 20000 313.31679 -25133.284 -1161.6979 1.0163289 -1256.0256 94.327722 0 -1649.7551 Loop time of 8.92653 on 2 procs for 20000 steps with 102 atoms Performance: 38.716 ns/day, 0.620 hours/ns, 2240.513 timesteps/s, 228.532 katom-step/s 96.3% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7448 | 5.9908 | 7.2367 | 50.9 | 67.11 Bond | 0.036126 | 0.03641 | 0.036695 | 0.1 | 0.41 Neigh | 0.082247 | 0.082294 | 0.082342 | 0.0 | 0.92 Comm | 0.68467 | 1.9303 | 3.1759 | 89.7 | 21.62 Output | 0.0023377 | 0.0052347 | 0.0081317 | 4.0 | 0.06 Modify | 0.8194 | 0.82122 | 0.82303 | 0.2 | 9.20 Other | | 0.06029 | | | 0.68 Nlocal: 51 ave 51 max 51 min Histogram: 2 0 0 0 0 0 0 0 0 0 Nghost: 3317 ave 3317 max 3317 min Histogram: 2 0 0 0 0 0 0 0 0 0 Neighs: 18320 ave 21941 max 14699 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 36640 Ave neighs/atom = 359.21569 Ave special neighs/atom = 2 Neighbor list builds = 181 Dangerous builds = 0 Total wall time: 0:00:08