LAMMPS (4 Jan 2019) using 1 OpenMP thread(s) per MPI task Reading data file ... orthogonal box = (-25 -25 -25) to (25 25 25) 2 by 2 by 4 MPI processor grid reading atoms ... 44 atoms reading velocities ... 44 velocities scanning bonds ... 9 = max bonds/atom scanning angles ... 21 = max angles/atom scanning dihedrals ... 29 = max dihedrals/atom scanning impropers ... 29 = max impropers/atom reading bonds ... 42 bonds reading angles ... 74 angles reading dihedrals ... 100 dihedrals reading impropers ... 44 impropers 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 6 = max # of 1-3 neighbors 12 = max # of 1-4 neighbors 41 = max # of special neighbors Read molecule mol1: 18 atoms with max type 8 16 bonds with max type 14 25 angles with max type 28 23 dihedrals with max type 36 14 impropers with max type 11 Read molecule mol2: 18 atoms with max type 9 17 bonds with max type 13 31 angles with max type 27 39 dihedrals with max type 33 20 impropers with max type 1 Read molecule mol3: 15 atoms with max type 9 14 bonds with max type 13 25 angles with max type 27 30 dihedrals with max type 33 16 impropers with max type 1 Read molecule mol4: 15 atoms with max type 11 13 bonds with max type 15 19 angles with max type 29 16 dihedrals with max type 32 10 impropers with max type 13 WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1674) WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1674) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.0534597 grid = 2 2 2 stencil order = 5 estimated absolute RMS force accuracy = 0.0402256 estimated relative force accuracy = 0.000121138 using single precision FFTs 3d grid and FFT values/proc = 216 2 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 10 10 10 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 WARNING: Inconsistent image flags (../domain.cpp:782) Per MPI rank memory allocation (min/avg/max) = 0.4459 | 25.28 | 34.42 Mbytes Step Temp Press Density f_myrxns[1] f_myrxns[2] 0 300 346.78165 0.0034851739 0 0 50 293.70542 -52.547388 0.0034851739 1 0 100 275.218 68.872729 0.0034851739 1 1 150 516.43828 15.040494 0.0034851739 1 1 200 365.28391 29.347223 0.0034851739 1 1 250 327.83476 58.164366 0.0034851739 1 1 300 300.43143 -45.977713 0.0034851739 1 1 350 292.88662 16.464939 0.0034851739 1 1 400 258.94249 53.745287 0.0034851739 1 1 450 252.61385 -3.9112672 0.0034851739 1 1 500 259.90979 -40.2941 0.0034851739 1 1 550 304.60292 -4.861455 0.0034851739 1 1 600 332.30258 9.6792788 0.0034851739 1 1 650 313.78638 52.301905 0.0034851739 1 1 700 313.60347 22.045775 0.0034851739 1 1 750 313.21912 7.5226537 0.0034851739 1 1 800 346.95414 7.1276807 0.0034851739 1 1 850 248.47686 -80.716954 0.0034851739 1 1 900 273.90311 -26.870573 0.0034851739 1 1 950 242.31345 70.463968 0.0034851739 1 1 1000 264.88861 9.5386586 0.0034851739 1 1 1050 231.42713 2.2642487 0.0034851739 1 1 1100 363.86197 7.6303794 0.0034851739 1 1 1150 336.43414 9.873602 0.0034851739 1 1 1200 331.61722 -53.593947 0.0034851739 1 1 1250 350.95793 -44.102876 0.0034851739 1 1 1300 303.48684 21.882017 0.0034851739 1 1 1350 296.11904 58.634679 0.0034851739 1 1 1400 288.25313 3.8879712 0.0034851739 1 1 1450 322.27345 -20.432291 0.0034851739 1 1 1500 318.73789 20.522016 0.0034851739 1 1 1550 285.46721 -18.927627 0.0034851739 1 1 1600 232.54747 0.91084408 0.0034851739 1 1 1650 201.32727 22.350034 0.0034851739 1 1 1700 202.73376 4.6611813 0.0034851739 1 1 1750 210.94442 -4.0247994 0.0034851739 1 1 1800 245.66274 32.614156 0.0034851739 1 1 1850 281.07154 40.27583 0.0034851739 1 1 1900 325.14045 -5.2576995 0.0034851739 1 1 1950 359.38783 -33.338869 0.0034851739 1 1 2000 303.32705 -7.1849518 0.0034851739 1 1 2050 321.3763 -15.695762 0.0034851739 1 1 2100 288.81624 -74.737082 0.0034851739 1 1 2150 303.59277 22.597705 0.0034851739 1 1 2200 263.06543 11.048839 0.0034851739 1 1 2250 279.32615 29.887123 0.0034851739 1 1 2300 310.90754 -6.8296647 0.0034851739 1 1 2350 362.71883 21.832349 0.0034851739 1 1 2400 318.98879 -15.439985 0.0034851739 1 1 2450 356.03665 -43.363045 0.0034851739 1 1 2500 298.42511 26.686089 0.0034851739 1 1 2550 263.68603 12.124022 0.0034851739 1 1 2600 292.75322 46.973721 0.0034851739 1 1 2650 284.12392 -53.426243 0.0034851739 1 1 2700 307.53146 6.5728747 0.0034851739 1 1 2750 253.09671 58.119089 0.0034851739 1 1 2800 269.96886 -22.814535 0.0034851739 1 1 2850 296.01876 -56.061641 0.0034851739 1 1 2900 312.62841 2.7986746 0.0034851739 1 1 2950 377.87905 12.674783 0.0034851739 1 1 3000 320.63802 10.647727 0.0034851739 1 1 3050 306.80672 -25.302106 0.0034851739 1 1 3100 300.76613 44.498218 0.0034851739 1 1 3150 249.91763 1.2063367 0.0034851739 1 1 3200 254.43602 -4.519904 0.0034851739 1 1 3250 201.63326 2.805658 0.0034851739 1 1 3300 258.40155 -23.643923 0.0034851739 1 1 3350 265.62382 -47.363137 0.0034851739 1 1 3400 296.56495 8.6752672 0.0034851739 1 1 3450 352.74428 26.386688 0.0034851739 1 1 3500 336.76362 -43.261034 0.0034851739 1 1 3550 292.43896 72.694963 0.0034851739 1 1 3600 312.00584 38.165632 0.0034851739 1 1 3650 321.84125 -42.244281 0.0034851739 1 1 3700 265.47894 -8.4921523 0.0034851739 1 1 3750 274.19465 -10.368274 0.0034851739 1 1 3800 266.52966 -15.343098 0.0034851739 1 1 3850 235.74949 -7.8021811 0.0034851739 1 1 3900 228.47265 -57.441259 0.0034851739 1 1 3950 263.61804 24.042377 0.0034851739 1 1 4000 321.04442 -19.552802 0.0034851739 1 1 4050 381.82478 39.515698 0.0034851739 1 1 4100 341.9375 -24.063572 0.0034851739 1 1 4150 340.72069 -54.786537 0.0034851739 1 1 4200 304.04169 36.67751 0.0034851739 1 1 4250 282.00872 5.2771007 0.0034851739 1 1 4300 291.10756 10.717423 0.0034851739 1 1 4350 280.3347 -25.257618 0.0034851739 1 1 4400 274.8628 11.161175 0.0034851739 1 1 4450 276.55102 20.510244 0.0034851739 1 1 4500 307.9366 -2.3124822 0.0034851739 1 1 4550 318.18619 -13.056889 0.0034851739 1 1 4600 356.39709 -43.817089 0.0034851739 1 1 4650 340.30645 8.6793656 0.0034851739 1 1 4700 313.40333 -33.027217 0.0034851739 1 1 4750 305.52084 24.490978 0.0034851739 1 1 4800 307.03937 -7.0011434 0.0034851739 1 1 4850 279.97258 -3.0952673 0.0034851739 1 1 4900 275.72785 2.2783183 0.0034851739 1 1 4950 302.58474 -15.9792 0.0034851739 1 1 5000 296.20838 1.9314011 0.0034851739 1 1 5050 270.26863 -6.597541 0.0034851739 1 1 5100 260.54728 -14.666277 0.0034851739 1 1 5150 259.78349 21.837638 0.0034851739 1 1 5200 277.83971 28.371226 0.0034851739 1 1 5250 257.32519 -3.9911026 0.0034851739 1 1 5300 306.37027 -29.913597 0.0034851739 1 1 5350 303.75802 54.177697 0.0034851739 1 1 5400 311.87659 44.652587 0.0034851739 1 1 5450 295.98228 -2.0302858 0.0034851739 1 1 5500 343.79102 -6.4542561 0.0034851739 1 1 5550 335.75475 11.796257 0.0034851739 1 1 5600 343.32573 7.8891976 0.0034851739 1 1 5650 296.76509 14.602137 0.0034851739 1 1 5700 304.1222 15.933875 0.0034851739 1 1 5750 328.59773 17.563065 0.0034851739 1 1 5800 290.9182 38.993554 0.0034851739 1 1 5850 280.25908 17.837635 0.0034851739 1 1 5900 288.40953 1.1346821 0.0034851739 1 1 5950 299.46539 8.434605 0.0034851739 1 1 6000 309.28935 -0.84810885 0.0034851739 1 1 6050 352.5355 20.333157 0.0034851739 1 1 6100 324.63076 -28.745403 0.0034851739 1 1 6150 319.07465 4.5658224 0.0034851739 1 1 6200 323.68778 1.3409484 0.0034851739 1 1 6250 304.6468 21.128144 0.0034851739 1 1 6300 265.01107 -7.5481756 0.0034851739 1 1 6350 246.15356 -12.201932 0.0034851739 1 1 6400 325.32089 -0.93975516 0.0034851739 1 1 6450 265.95946 19.089732 0.0034851739 1 1 6500 270.77472 21.050573 0.0034851739 1 1 6550 352.31133 1.3256144 0.0034851739 1 1 6600 395.14566 -1.7156978 0.0034851739 1 1 6650 300.35341 -12.188635 0.0034851739 1 1 6700 380.58773 13.916853 0.0034851739 1 1 6750 284.36959 17.015256 0.0034851739 1 1 6800 345.54678 -4.0559172 0.0034851739 1 1 6850 328.71411 -0.6559083 0.0034851739 1 1 6900 320.66401 -12.318462 0.0034851739 1 1 6950 328.99028 49.337957 0.0034851739 1 1 7000 287.98454 -15.209575 0.0034851739 1 1 7050 307.04983 4.2204588 0.0034851739 1 1 7100 246.15201 14.315822 0.0034851739 1 1 7150 253.71833 -6.6089739 0.0034851739 1 1 7200 318.9443 16.165436 0.0034851739 1 1 7250 287.53434 -32.241618 0.0034851739 1 1 7300 363.40822 31.239804 0.0034851739 1 1 7350 386.592 -53.38554 0.0034851739 1 1 7400 347.74837 44.878274 0.0034851739 1 1 7450 325.99672 -6.7238018 0.0034851739 1 1 7500 320.28124 -8.8181438 0.0034851739 1 1 7550 267.47462 -25.026575 0.0034851739 1 1 7600 291.0603 12.751329 0.0034851739 1 1 7650 264.21594 4.3432102 0.0034851739 1 1 7700 247.37803 13.364925 0.0034851739 1 1 7750 325.84649 64.927612 0.0034851739 1 1 7800 314.00501 -21.321935 0.0034851739 1 1 7850 366.5619 -16.996798 0.0034851739 1 1 7900 371.15791 2.418665 0.0034851739 1 1 7950 369.22285 15.227847 0.0034851739 1 1 8000 375.73681 -16.354888 0.0034851739 1 1 8050 298.27946 33.0001 0.0034851739 1 1 8100 321.37916 -29.746681 0.0034851739 1 1 8150 296.2973 1.6012546 0.0034851739 1 1 8200 308.31613 -9.0748628 0.0034851739 1 1 8250 294.55232 -2.8111201 0.0034851739 1 1 8300 284.41901 17.130131 0.0034851739 1 1 8350 297.49328 -16.171246 0.0034851739 1 1 8400 330.09169 15.051048 0.0034851739 1 1 8450 343.08307 -78.441056 0.0034851739 1 1 8500 369.9662 13.499807 0.0034851739 1 1 8550 304.90627 67.19005 0.0034851739 1 1 8600 316.78367 -51.600166 0.0034851739 1 1 8650 307.56465 42.576004 0.0034851739 1 1 8700 298.02768 -14.528248 0.0034851739 1 1 8750 293.34783 17.758225 0.0034851739 1 1 8800 298.5816 57.681169 0.0034851739 1 1 8850 303.97364 -10.517542 0.0034851739 1 1 8900 273.44698 27.162518 0.0034851739 1 1 8950 311.43729 -86.684887 0.0034851739 1 1 9000 293.07087 27.876376 0.0034851739 1 1 9050 382.07379 6.031161 0.0034851739 1 1 9100 406.6245 -26.536607 0.0034851739 1 1 9150 342.42132 80.977664 0.0034851739 1 1 9200 319.29278 47.358936 0.0034851739 1 1 9250 355.93003 -14.987329 0.0034851739 1 1 9300 260.30677 -43.753435 0.0034851739 1 1 9350 244.43785 22.573466 0.0034851739 1 1 9400 304.9854 -46.237432 0.0034851739 1 1 9450 282.34473 20.360435 0.0034851739 1 1 9500 313.56998 43.752753 0.0034851739 1 1 9550 304.33727 -12.787033 0.0034851739 1 1 9600 279.05711 29.109201 0.0034851739 1 1 9650 234.58178 -37.959846 0.0034851739 1 1 9700 242.9253 26.297334 0.0034851739 1 1 9750 268.12765 -28.13829 0.0034851739 1 1 9800 279.3347 -0.75967089 0.0034851739 1 1 9850 295.72903 -10.328113 0.0034851739 1 1 9900 286.55775 -13.974967 0.0034851739 1 1 9950 287.54629 18.386527 0.0034851739 1 1 10000 324.38897 -4.6659341 0.0034851739 1 1 Loop time of 2.76897 on 16 procs for 10000 steps with 44 atoms Performance: 312.029 ns/day, 0.077 hours/ns, 3611.448 timesteps/s 97.4% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.001585 | 0.019309 | 0.095998 | 20.2 | 0.70 Bond | 0.0053742 | 0.061604 | 0.24728 | 34.1 | 2.22 Kspace | 1.0855 | 1.3116 | 1.3745 | 8.3 | 47.37 Neigh | 0.36978 | 0.40013 | 0.42503 | 2.4 | 14.45 Comm | 0.22163 | 0.27124 | 0.32241 | 6.5 | 9.80 Output | 0.0045636 | 0.0046922 | 0.0059454 | 0.5 | 0.17 Modify | 0.60814 | 0.6714 | 0.71324 | 4.6 | 24.25 Other | | 0.02897 | | | 1.05 Nlocal: 2.75 ave 38 max 0 min Histogram: 15 0 0 0 0 0 0 0 0 1 Nghost: 26.625 ave 43 max 3 min Histogram: 5 0 0 0 0 0 0 4 2 5 Neighs: 46.375 ave 662 max 0 min Histogram: 14 1 0 0 0 0 0 0 0 1 Total # of neighbors = 742 Ave neighs/atom = 16.8636 Ave special neighs/atom = 9.77273 Neighbor list builds = 10000 Dangerous builds = 0 WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1674) WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1674) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 26996 RUNNING AT n3h3-2 = EXIT CODE: 11 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== Intel(R) MPI Library troubleshooting guide: https://software.intel.com/node/561764 ===================================================================================