Lmod Warning: USER-SPACK/0.18.x is deprecated and will be removed in the future. Consider using a newer version. While processing the following module(s): Module fullname Module Filename --------------- --------------- USER-SPACK/0.18.1 /cluster/modulefiles/non-hierarchical/USER-SPACK/0.18.1.lua INFO: Please use 'spack install' only on login nodes INFO: By default no module files are generated for the system compiler (gcc@8.5.0) INFO: Please specify another compiler (ex: spack install %gcc@12.1.0) if you want to generate module files INFO: Refresh upstream modules with: spack module lmod refresh --delete-tree --upstream-modules -y ib_umad 28672 4 ib_core 405504 13 beegfs,rdma_cm,ib_ipoib,rpcrdma,ib_srpt,iw_cm,ib_iser,ib_umad,ib_isert,rdma_ucm,ib_uverbs,mlx5_ib,ib_cm Currently Loaded Modules: 1) USER-SPACK/0.18.1 2) gcc/12.1.0 3) intel-oneapi-mpi/2021.6.0 LAMMPS (7 Jan 2022) using 1 OpenMP thread(s) per MPI task nitrogen_molecules_in_1Ang3: 2.43e-05 nitrogen_upper: 2470 nitrogen_tip: 106 nitrogen_lower: 2470 nitrogen_right: 0 nitrogen_left: 0 nitrogen: 5046 New timer settings: style=full mode=sync timeout=off Lattice spacing in x,y,z = 5.43 5.43 5.43 Created orthogonal box = (0 0 0) to (1357.5 689.61 276.93) 32 by 18 by 8 MPI processor grid Created 2890647 atoms using lattice units in orthogonal box = (0 0 0) to (1357.5 689.61 276.93) create_atoms CPU = 0.008 seconds 2890647 atoms in group solid 15621 atoms in group cantilever_towall 2875026 atoms in group cantilever 28067 atoms in group results Created 5046 atoms using lattice units in orthogonal box = (0 0 0) to (1357.5 689.61 276.93) create_atoms CPU = 0.001 seconds 5046 atoms in group gas num_atoms_in_tip: 28067 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 20000, page size: 1000000 master list distance cutoff = 9.9325 ghost atom cutoff = 9.9325 binsize = 4.96625, bins = 274 139 56 4 neighbor lists, perpetual/occasional/extra = 4 0 0 (1) pair tersoff, perpetual, skip from (3) attributes: full, newton on pair build: skip stencil: none bin: none (2) pair lj/cut, perpetual, skip from (4) attributes: half, newton on pair build: skip stencil: none bin: none (3) neighbor class addition, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (4) neighbor class addition, perpetual, half/full from (3) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 23.7 | 24.51 | 24.71 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 3.9730235e+09 0 3.9731358e+09 98540014 1000 299.99992 -13123386 0 -13011097 689.94171 Loop time of 19.1839 on 4608 procs for 1000 steps with 2895692 atoms 99.7% CPU use with 4608 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = 3973023486.89593 -13123385.6782459 -13123385.8485237 Force two-norm initial, final = 1.3730157e+11 1.7012134 Force max component initial, final = 8.4868785e+10 0.064184152 Final line search alpha, max atom move = 0.17004792 0.010914382 Iterations, force evaluations = 1000 1957 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %CPU | %total ----------------------------------------------------------------------- Pair | 0.0010547 | 2.4199 | 12.644 | 279.6 | 99.9 | 12.61 Neigh | 0.00096078 | 0.59382 | 3.3453 | 137.8 | 99.8 | 3.10 Comm | 0.038327 | 0.23917 | 0.50625 | 27.8 | 99.3 | 1.25 Output | 8.0193e-05 | 8.9048e-05 | 0.00010834 | 0.0 | 100.0 | 0.00 Modify | 0.00066955 | 0.0015839 | 0.007645 | 3.9 | 100.0 | 0.01 Sync | 3.1265 | 15.629 | 18.846 | 140.0 | 99.7 | 81.47 Other | | 15.93 | | | | 83.03 Nlocal: 628.405 ave 3016 max 0 min Histogram: 3528 0 0 0 0 0 30 267 285 498 Nghost: 1523.27 ave 5700 max 0 min Histogram: 2448 540 36 504 0 18 36 18 504 504 Neighs: 0 ave 0 max 0 min Histogram: 4608 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 425 Dangerous builds = 1 Setting up Verlet run ... Unit style : metal Current step : 1000 Time step : 0.005 Per MPI rank memory allocation (min/avg/max) = 22.57 | 23.38 | 23.58 Mbytes Step Temp E_pair E_mol TotEng Press 1000 300.00003 -13123386 0 -13011097 689.94171 5000 296.16656 -13010606 0 -12899752 29.160043 10000 302.84405 -13012527 0 -12899173 695.4017 15000 307.27893 -13013597 0 -12898583 -85.251653 20000 308.32831 -13017269 0 -12901863 653.34002 25000 307.27991 -13020165 0 -12905151 -121.64477 30000 308.08248 -13023786 0 -12908471 538.39124 35000 306.59856 -13026528 0 -12911769 -45.838758 40000 306.49448 -13029808 0 -12915088 509.41725 45000 305.04285 -13032619 0 -12918442 -71.033981 50000 309.29864 -13033815 0 -12918045 489.24434 51000 300.00584 -13034017 0 -12921726 402.51801 Loop time of 587.733 on 4608 procs for 50000 steps with 2895692 atoms Performance: 36.751 ns/day, 0.653 hours/ns, 85.073 timesteps/s 99.7% CPU use with 4608 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %CPU | %total ----------------------------------------------------------------------- Pair | 0.028735 | 62.79 | 302.97 |1421.0 | 99.9 | 10.68 Neigh | 0.063284 | 39.895 | 195.06 |1127.0 | 99.9 | 6.79 Comm | 1.4198 | 8.1198 | 15.711 | 146.5 | 99.4 | 1.38 Output | 0.00079726 | 0.00081401 | 0.0010409 | 0.0 | 100.0 | 0.00 Modify | 0.085779 | 0.51509 | 2.1374 | 104.2 | 99.8 | 0.09 Sync | 80.68 | 475.42 | 585.26 | 862.3 | 99.7 | 80.89 Other | | 476.4 | | | | 81.06 Nlocal: 628.405 ave 2948 max 0 min Histogram: 3528 0 0 0 0 0 0 18 540 522 Nghost: 1527.15 ave 5681 max 0 min Histogram: 2448 540 36 504 0 18 36 18 504 504 Neighs: 0 ave 0 max 0 min Histogram: 4608 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 25905 Dangerous builds = 1847 Iyy: 1648491213.34137 Fz: -7.04922146829835e-05 num_atoms_in_group: 28067 Setting up Verlet run ... Unit style : metal Current step : 51000 Time step : 0.005 Per MPI rank memory allocation (min/avg/max) = 22.7 | 23.4 | 23.58 Mbytes Step Temp E_pair E_mol TotEng Press 51000 300.00584 -13034017 0 -12921726 402.51801 55000 307.18367 -13036421 0 -12921443 -23.178888 60000 306.23798 -13039560 0 -12924936 476.70861 65000 308.72116 -13040086 0 -12924532 -3.0233718 70000 307.05647 -13043022 0 -12928092 391.13172 75000 309.57738 -13043594 0 -12927720 69.202481 80000 307.58343 -13046350 0 -12931222 341.12179 85000 305.13952 -13048902 0 -12934689 83.142371 90000 307.85475 -13049615 0 -12934386 307.0073 95000 305.0026 -13052039 0 -12937878 104.65867 100000 307.3932 -13052699 0 -12937643 297.1254 105000 309.12079 -13053058 0 -12937355 125.71367 110000 306.55709 -13055647 0 -12940904 268.8877 115000 308.41648 -13056083 0 -12940643 135.24731 120000 305.44123 -13058558 0 -12944232 200.07804 125000 307.03518 -13058951 0 -12944029 216.35792 130000 308.33136 -13059256 0 -12943848 157.89781 135000 305.24192 -13061720 0 -12947469 235.53054 140000 306.50334 -13062036 0 -12947312 159.97623 145000 307.8712 -13062390 0 -12947155 219.6353 150000 309.09379 -13062675 0 -12946982 174.01087 155000 305.4837 -13064970 0 -12950628 234.2282 160000 306.3176 -13065162 0 -12950509 145.38862 165000 307.38167 -13065450 0 -12950398 255.70018 170000 308.17269 -13065603 0 -12950255 121.63552 175000 309.34844 -13065895 0 -12950107 277.64772 180000 305.22965 -13067976 0 -12953730 91.12372 185000 306.36979 -13068298 0 -12953624 312.99992 190000 306.83812 -13068366 0 -12953517 78.947028 195000 307.72508 -13068625 0 -12953444 309.66286 200000 308.40023 -13068757 0 -12953324 85.833695 205000 309.15726 -13068959 0 -12953242 295.51739 210000 305.021 -13071096 0 -12956928 102.07719 215000 305.90986 -13071359 0 -12956858 275.22663 220000 306.15829 -13071374 0 -12956780 120.61902 225000 306.66414 -13071489 0 -12956706 270.57497 230000 307.15139 -13071618 0 -12956652 113.08398 235000 307.81855 -13071792 0 -12956576 252.39666 240000 308.33383 -13071925 0 -12956517 139.09823 245000 308.67801 -13071995 0 -12956458 224.19569 250000 309.23083 -13072142 0 -12956398 151.5814 255000 309.77608 -13072279 0 -12956330 215.74523 260000 305.34208 -13074365 0 -12960076 137.65706 265000 305.65936 -13074422 0 -12960014 223.19999 270000 305.99766 -13074492 0 -12959958 155.88235 275000 306.52327 -13074640 0 -12959909 198.31508 280000 306.64077 -13074639 0 -12959864 177.24362 285000 307.1576 -13074788 0 -12959820 185.3174 290000 307.38738 -13074811 0 -12959756 161.50429 295000 307.58965 -13074828 0 -12959698 212.08688 300000 307.87939 -13074875 0 -12959637 162.81853 305000 308.17075 -13074931 0 -12959583 194.56838 310000 308.50413 -13074997 0 -12959524 174.53022 315000 308.79805 -13075061 0 -12959479 211.60892 320000 308.83734 -13075018 0 -12959421 132.23841 325000 309.16606 -13075093 0 -12959373 246.25935 330000 309.04907 -13075021 0 -12959345 176.67236 335000 309.02503 -13074976 0 -12959309 187.39374 340000 309.63493 -13075187 0 -12959292 205.33551 345000 309.37307 -13075058 0 -12959261 175.29838 350000 309.46072 -13075056 0 -12959225 121.8156 355000 304.98956 -13077187 0 -12963031 250.98507 360000 304.9038 -13077137 0 -12963012 167.84766 365000 305.4539 -13077307 0 -12962976 148.76995 370000 305.57631 -13077324 0 -12962948 219.11586 375000 305.70534 -13077352 0 -12962927 157.60278 380000 305.64725 -13077310 0 -12962907 143.41362 385000 305.66505 -13077310 0 -12962900 213.53928 390000 306.01199 -13077435 0 -12962896 186.62214 395000 305.84584 -13077362 0 -12962885 124.42026 400000 306.1999 -13077493 0 -12962884 246.59774 405000 306.33571 -13077526 0 -12962865 177.3658 410000 306.20847 -13077470 0 -12962857 147.26829 415000 306.39306 -13077530 0 -12962847 207.90652 420000 306.54819 -13077579 0 -12962839 209.17624 425000 306.43952 -13077535 0 -12962835 116.31656 430000 306.61707 -13077597 0 -12962831 241.92982 435000 306.46936 -13077530 0 -12962819 188.7275 440000 306.73055 -13077619 0 -12962810 142.87772 445000 306.92627 -13077684 0 -12962802 207.3402 450000 306.87782 -13077651 0 -12962788 194.82302 455000 306.97726 -13077680 0 -12962780 142.63455 460000 307.21386 -13077753 0 -12962763 209.59804 465000 306.96878 -13077646 0 -12962748 188.0768 470000 307.12556 -13077692 0 -12962736 151.41227 475000 307.10893 -13077669 0 -12962719 181.51733 480000 307.3033 -13077717 0 -12962694 215.24986 483099 307.30562 -13077700 0 -12962676 179.72515 Loop time of 5192.47 on 4608 procs for 432099 steps with 2895692 atoms Performance: 35.950 ns/day, 0.668 hours/ns, 83.216 timesteps/s 99.7% CPU use with 4608 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %CPU | %total ----------------------------------------------------------------------- Pair | 0.25374 | 546.57 | 2557.8 |2955.5 | 99.8 | 10.53 Neigh | 0.53874 | 346.25 | 1613.1 |2368.3 | 99.8 | 6.67 Comm | 12.1 | 68.592 | 131.21 | 352.3 | 99.4 | 1.32 Output | 3.5976 | 3.5977 | 3.599 | 0.0 | 100.0 | 0.07 Modify | 21.976 | 26.561 | 39.989 | 93.2 | 99.5 | 0.51 Sync | 892.87 | 4192 | 5145.5 |1794.8 | 99.7 | 80.73 Other | | 4201 | | | | 80.90 Nlocal: 628.405 ave 2974 max 0 min Histogram: 3168 126 90 108 94 118 104 134 139 527 Nghost: 1555.06 ave 7097 max 0 min Histogram: 2808 162 216 215 181 241 260 126 142 257 Neighs: 0 ave 0 max 0 min Histogram: 4608 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 Neighbor list builds = 217279 Dangerous builds = 2459 WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/src/output.cpp:888) Setting up Verlet run ... Unit style : metal Current step : 483099 Time step : 0.005 Per MPI rank memory allocation (min/avg/max) = 23.2 | 23.93 | 24.1 Mbytes Step v_avg_disp_z 483099 -0.048218535 485000 -0.052720642 490000 -0.060469156 495000 -0.069952853 500000 -0.073892431 505000 -0.075889246 510000 -0.082567031 515000 -0.079937648 520000 -0.077112938 525000 -0.075367088 530000 -0.069966739 535000 -0.071657151 540000 -0.072787625 545000 -0.075462442 550000 -0.07853109 555000 -0.080602909 560000 -0.081688111 565000 -0.079448806 570000 -0.076978491 575000 -0.070144795 580000 -0.063398276 585000 -0.053665282 590000 -0.041719139 595000 -0.034879371 600000 -0.0271751 605000 -0.021020916 610000 -0.015482006 615000 -0.0077064198 620000 -0.005077386 625000 -0.0025437378 630000 -0.0013213668 635000 0.0034345516 640000 0.00939428 645000 0.018048077 650000 0.024781614 655000 0.031248005 660000 0.040773127 665000 0.049207671 670000 0.059141647 675000 0.065926084 680000 0.067981979 685000 0.072013268 690000 0.0726984 695000 0.075044043 700000 0.075369868 705000 0.072997009 710000 0.072154595 715000 0.072632462 720000 0.076203935 725000 0.079563305 730000 0.083089736 735000 0.082913866 740000 0.08526428 745000 0.086355197 750000 0.083488537 755000 0.081918169 760000 0.07425258 765000 0.066717612 770000 0.060474519 775000 0.051570121 780000 0.047711536 785000 0.042122368 790000 0.036090592 795000 0.031661337