LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # test of NB3B pair style with pair hybrid and KSpace solver units real atom_style full bond_style morse angle_style none dihedral_style none improper_style none read_data data.nb3b orthogonal box = (0 0 0) to (22.5907 22.359 23.4708) 2 by 1 by 2 MPI processor grid reading atoms ... 1400 atoms scanning bonds ... 1 = max bonds/atom reading bonds ... 560 bonds 1 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0 pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H Reading potential file MOH.nb3b.harmonic with DATE: 2016-07-29 pair_modify mix arithmetic pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869 pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978 pair_coeff 1 3 lj/cut/coul/long 0 2.632162934 pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088 pair_coeff 2 3 lj/cut/coul/long 0 1.582760044 pair_coeff 3 3 lj/cut/coul/long 0 0 kspace_style ewald/disp 0.0001 neighbor 2.0 bin neigh_modify delay 5 special_bonds lj/coul 0.0 0.0 1.0 1 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 1 = max # of special neighbors thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol timestep 1.0 run_style respa 2 2 pair 1 kspace 2 Respa levels: 1 = bond angle dihedral improper pair 2 = kspace thermo 50 ### Minimize forces in structure ### minimize 1.0e-06 1.0e-08 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) EwaldDisp initialization ... WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) G vector = 0.269426 accuracy = 0.0332064 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) 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 = 4 4 4 4 neighbor lists, perpetual/occasional/extra = 4 0 0 (1) pair nb3b/harmonic, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard (2) pair lj/cut/coul/long, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) pair nb3b/harmonic, perpetual, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) pair lj/cut/coul/long, perpetual, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none vectors: nbox = 6, nkvec = 478 Per MPI rank memory allocation (min/avg/max) = 20.64 | 21.18 | 22.02 Mbytes Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume 0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72822 22.5907 22.359 23.4708 0 0 0 11855.229 4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.43 22.5907 22.359 23.4708 0 0 0 11855.229 Loop time of 0.164255 on 4 procs for 4 steps with 1400 atoms 99.1% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -61505.9829 -61506.5882615 -61506.60415 Force two-norm initial, final = 17.893 3.40909 Force max component initial, final = 0.757547 0.131738 Final line search alpha, max atom move = 0.394559 0.0519786 Iterations, force evaluations = 4 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11101 | 0.12473 | 0.13747 | 3.3 | 75.93 Bond | 5.8889e-05 | 6.2823e-05 | 6.6757e-05 | 0.0 | 0.04 Kspace | 0.025273 | 0.036047 | 0.047969 | 5.3 | 21.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001081 | 0.0030527 | 0.0048478 | 2.8 | 1.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000367 | | | 0.22 Nlocal: 350 ave 399 max 305 min Histogram: 1 1 0 0 0 0 0 0 1 1 Nghost: 6602 ave 6647 max 6553 min Histogram: 1 1 0 0 0 0 0 0 1 1 Neighs: 149240 ave 170954 max 129384 min Histogram: 1 1 0 0 0 0 0 1 0 1 FullNghs: 298480 ave 340157 max 260160 min Histogram: 1 1 0 0 0 0 0 0 1 1 Total # of neighbors = 1193920 Ave neighs/atom = 852.8 Ave special neighs/atom = 0.8 Neighbor list builds = 0 Dangerous builds = 0 ### Run NVE to equilibrate velocities ### velocity all create 298.0 4928459 mom yes rot yes dist gaussian fix 1 all nve fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0 run 100 EwaldDisp initialization ... WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) G vector = 0.269426 accuracy = 0.0332064 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) Per MPI rank memory allocation (min/avg/max) = 20.26 | 20.8 | 21.65 Mbytes Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume 4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.1472 22.5907 22.359 23.4708 0 0 0 11855.229 50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229 100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229 104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229 Loop time of 3.0299 on 4 procs for 100 steps with 1400 atoms Performance: 2.852 ns/day, 8.416 hours/ns, 33.004 timesteps/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.424 | 2.5288 | 2.6552 | 6.3 | 83.46 Bond | 0.0011241 | 0.0011699 | 0.0011907 | 0.1 | 0.04 Kspace | 0.24584 | 0.25484 | 0.26259 | 1.5 | 8.41 Neigh | 0.031059 | 0.031067 | 0.031075 | 0.0 | 1.03 Comm | 0.070014 | 0.19745 | 0.30262 | 22.7 | 6.52 Output | 0.00011683 | 0.0002265 | 0.00050616 | 0.0 | 0.01 Modify | 0.0022085 | 0.0030763 | 0.0039916 | 1.3 | 0.10 Other | | 0.01331 | | | 0.44 Nlocal: 350 ave 357 max 340 min Histogram: 1 0 0 0 0 0 1 1 0 1 Nghost: 6639.25 ave 6657 max 6627 min Histogram: 1 1 0 0 0 1 0 0 0 1 Neighs: 148827 ave 152055 max 145212 min Histogram: 1 0 0 0 0 2 0 0 0 1 FullNghs: 297654 ave 303283 max 288784 min Histogram: 1 0 0 0 0 0 1 1 0 1 Total # of neighbors = 1190614 Ave neighs/atom = 850.439 Ave special neighs/atom = 0.8 Neighbor list builds = 2 Dangerous builds = 0 Total wall time: 0:00:03