LAMMPS (27 Jun 2024) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task variable sname index ch4 units electron newton on boundary f f f atom_style electron read_data data.${sname} read_data data.ch4 Reading data file ... orthogonal box = (-500 -500 -500) to (500 500 500) 1 by 1 by 1 MPI processor grid reading atoms ... 15 atoms read_data CPU = 0.000 seconds pair_style eff/cut 100.0 pair_coeff * * comm_modify vel yes # Minimize min_style cg compute 1 all property/atom spin eradius dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z min_modify line quadratic dmax 0.1 minimize 0 1.0e-6 1000 10000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - EFF package: doi:10.1002/jcc.21637 @Article{Jaramillo-Botero11, author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.}, title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments}, journal = {J.~Comp.\ Chem.}, year = 2011, volume = 32, number = 3, pages = {497--512} } - Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 @Article{Gissinger24, author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor}, title = {Type Label Framework for Bonded Force Fields in LAMMPS}, journal = {J. Phys. Chem. B}, year = 2024, volume = 128, number = 13, pages = {3282–-3297} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 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 = 102 ghost atom cutoff = 102 binsize = 51, bins = 20 20 20 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair eff/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.405 | 5.405 | 5.405 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27.314082 0 -27.314082 -56588.53 1000 0 -34.07448 0 -34.07448 1.3464499 Loop time of 0.0308104 on 1 procs for 1000 steps with 15 atoms 88.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -27.3140820331247 -34.0744796893375 -34.0744796893447 Force two-norm initial, final = 10.728716 0.00017815706 Force max component initial, final = 6.1727999 8.2675815e-05 Final line search alpha, max atom move = 1 8.2675815e-05 Iterations, force evaluations = 1000 1943 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012522 | 0.012522 | 0.012522 | 0.0 | 40.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012209 | 0.00012209 | 0.00012209 | 0.0 | 0.40 Output | 0.016563 | 0.016563 | 0.016563 | 0.0 | 53.76 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001604 | | | 5.20 Nlocal: 15 ave 15 max 15 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105 Ave neighs/atom = 7 Neighbor list builds = 0 Dangerous builds = 0 # Dynamics compute effTemp all temp/eff thermo 1000 thermo_style custom step pe temp press thermo_modify temp effTemp velocity all create 300.0 4928459 dist gaussian rot yes mom yes timestep 0.005 fix 1 all nve/eff # the custom dump includes the radii dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z dump 3 all xyz 1000 ${sname}.nve.xyz dump 3 all xyz 1000 ch4.nve.xyz run 100000 Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 5.406 | 5.406 | 5.406 Mbytes Step PotEng Temp Press 1000 -34.07448 1050 392.66426 2000 -34.065618 583.71716 -618.55027 3000 -34.063563 475.54605 661.95076 4000 -34.06119 350.76183 -449.64687 5000 -34.0652 561.71223 -131.2575 6000 -34.065798 593.21728 754.38406 7000 -34.067408 677.86019 -409.21139 8000 -34.065663 586.03411 446.32573 9000 -34.06294 442.71136 414.41408 10000 -34.060101 293.33406 -1203.0131 11000 -34.064946 548.39598 345.29601 12000 -34.067323 673.49043 444.55927 13000 -34.063275 460.43973 -854.83884 14000 -34.064666 533.57265 1542.0127 15000 -34.063343 463.97449 -778.73252 16000 -34.064462 522.77625 -1.5339614 17000 -34.061203 351.37068 -148.19163 18000 -34.066534 631.87837 -237.0746 19000 -34.065169 560.16772 1360.7348 20000 -34.063042 448.13104 -664.72128 21000 -34.060696 324.68723 -167.83333 22000 -34.065376 570.90279 -831.73853 23000 -34.063127 452.61143 766.59984 24000 -34.064572 528.62282 -107.80755 25000 -34.06584 595.42175 610.33075 26000 -34.066886 650.43579 -894.20521 27000 -34.062035 395.20224 1754.7666 28000 -34.060696 324.66878 -2622.013 29000 -34.066777 644.66282 1551.3147 30000 -34.066421 625.94614 -507.44173 31000 -34.066163 612.36658 610.11907 32000 -34.063109 451.70185 -47.463209 33000 -34.062833 437.16794 -607.25848 34000 -34.061657 375.30056 -158.28097 35000 -34.064937 547.86519 272.75585 36000 -34.067509 683.23088 359.91072 37000 -34.067582 686.96461 -384.97405 38000 -34.063213 457.13191 411.86349 39000 -34.06272 431.13187 -594.23723 40000 -34.062286 408.41212 456.09079 41000 -34.064078 502.64096 -1149.8496 42000 -34.066408 625.33334 1403.4937 43000 -34.065948 601.03876 -773.40678 44000 -34.064113 504.49498 179.93456 45000 -34.060573 318.11433 223.38679 46000 -34.063614 478.24588 -409.99081 47000 -34.064814 541.38544 614.25246 48000 -34.065602 582.87984 -743.92184 49000 -34.063923 494.52673 474.88127 50000 -34.064616 530.94533 288.81199 51000 -34.062038 395.2991 -480.07513 52000 -34.06497 549.5123 -305.53764 53000 -34.065578 581.59919 964.80956 54000 -34.06766 691.12707 -437.99603 55000 -34.064707 535.85658 1058.6734 56000 -34.062481 418.58003 -1011.5341 57000 -34.064997 551.06731 -32.91724 58000 -34.064281 513.25358 374.91628 59000 -34.066177 613.1188 -464.85124 60000 -34.064718 536.29803 1011.6698 61000 -34.065746 590.46955 -1057.9241 62000 -34.063253 459.23293 1526.2698 63000 -34.062261 407.08636 -1743.6652 64000 -34.063835 489.88286 761.60266 65000 -34.069569 791.614 323.26812 66000 -34.065557 580.45685 874.52459 67000 -34.064917 546.77223 -1349.3606 68000 -34.062963 443.96697 1178.4319 69000 -34.063063 449.26418 -1660.686 70000 -34.063597 477.39716 1323.13 71000 -34.065424 573.47914 -131.55428 72000 -34.065211 562.31067 -415.56361 73000 -34.06339 466.38097 724.92885 74000 -34.062286 408.34027 -1094.3845 75000 -34.065545 579.79767 587.58121 76000 -34.066774 644.61685 -357.22241 77000 -34.064479 523.74831 1545.6628 78000 -34.065506 577.88405 -1013.2409 79000 -34.062874 439.24856 240.66725 80000 -34.06306 449.09678 -799.14252 81000 -34.063338 463.66067 1528.3351 82000 -34.066812 646.52985 -1351.1758 83000 -34.064724 536.65114 1338.595 84000 -34.063774 486.67172 -876.0475 85000 -34.06156 370.19256 617.89915 86000 -34.063628 478.95398 -134.40164 87000 -34.065141 558.60424 -758.03942 88000 -34.066732 642.27865 1159.5992 89000 -34.067349 674.83453 -301.45201 90000 -34.063623 478.69626 386.87752 91000 -34.061885 387.30728 -774.32296 92000 -34.061363 359.77745 500.06117 93000 -34.065724 589.32209 -469.10399 94000 -34.065006 551.42796 818.92294 95000 -34.06541 572.75191 -677.20865 96000 -34.062331 410.64868 1383.8935 97000 -34.061499 366.95753 -1715.2058 98000 -34.061153 348.68703 353.63545 99000 -34.066217 615.27816 193.79593 100000 -34.067739 695.36238 205.35389 101000 -34.067314 672.94727 929.41223 Loop time of 2.23163 on 1 procs for 100000 steps with 15 atoms Performance: 19358038.198 fs/day, 0.000 hours/fs, 44810.274 timesteps/s, 672.154 katom-step/s 85.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59187 | 0.59187 | 0.59187 | 0.0 | 26.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061524 | 0.0061524 | 0.0061524 | 0.0 | 0.28 Output | 1.5983 | 1.5983 | 1.5983 | 0.0 | 71.62 Modify | 0.017759 | 0.017759 | 0.017759 | 0.0 | 0.80 Other | | 0.01755 | | | 0.79 Nlocal: 15 ave 15 max 15 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105 Ave neighs/atom = 7 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:02