LAMMPS (9 Oct 2020) using 1 OpenMP thread(s) per MPI task # SPC/E water box benchmark units real atom_style full read_data data.spce Reading data file ... orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600) 2 by 2 by 1 MPI processor grid reading atoms ... 4500 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 3000 bonds reading angles ... 1500 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.0 0.0 0.0 special bond factors coul: 0.0 0.0 0.0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.001 seconds read_data CPU = 0.008 seconds replicate 2 4 1 Replicating atoms ... orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600) 1 by 4 by 1 MPI processor grid 36000 atoms 24000 bonds 12000 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.0 0.0 0.0 special bond factors coul: 0.0 0.0 0.0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds replicate CPU = 0.005 seconds pair_style lj/cut/coul/long 9.8 9.8 kspace_style pppm 1.0e-4 pair_coeff 1 1 0.15535 3.166 pair_coeff * 2 0.0000 0.0000 bond_style harmonic angle_style harmonic dihedral_style none improper_style none bond_coeff 1 1000.00 1.000 angle_coeff 1 100.0 109.47 special_bonds lj/coul 0.0 0.0 0.5 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.0 0.0 0.5 special bond factors coul: 0.0 0.0 0.5 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.004 seconds neighbor 2.0 bin neigh_modify every 1 delay 10 check yes fix 1 all shake 0.0001 20 0 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 12000 = # of frozen angles find clusters CPU = 0.003 seconds fix 2 all nvt temp 300.0 300.0 100.0 velocity all create 300 432567 dist uniform timestep 2.0 thermo_style one thermo 50 run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:328) G vector (1/distance) = 0.2688011 grid = 36 64 24 stencil order = 5 estimated absolute RMS force accuracy = 0.033101471 estimated relative force accuracy = 9.9684097e-05 using double precision KISS FFT 3d grid and FFT values/proc = 27993 13824 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.8 ghost atom cutoff = 11.8 binsize = 5.9, bins = 13 25 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 37.90 | 37.90 | 37.90 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -133281.51 0 -111820.57 516.17807 50 264.98553 -136986.74 0 -118030.61 -440.29255 100 274.45966 -136364.57 0 -116730.69 -128.61954 Loop time of 5.44355 on 4 procs for 100 steps with 36000 atoms Performance: 3.174 ns/day, 7.560 hours/ns, 18.370 timesteps/s 95.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.82 | 3.8744 | 3.9155 | 1.8 | 71.17 Bond | 7.8917e-05 | 8.6784e-05 | 9.4891e-05 | 0.0 | 0.00 Kspace | 0.79192 | 0.83671 | 0.88328 | 3.5 | 15.37 Neigh | 0.51754 | 0.5178 | 0.51789 | 0.0 | 9.51 Comm | 0.069774 | 0.078783 | 0.088247 | 2.3 | 1.45 Output | 9.0361e-05 | 0.00015712 | 0.00035048 | 0.0 | 0.00 Modify | 0.12822 | 0.13016 | 0.13486 | 0.8 | 2.39 Other | | 0.005435 | | | 0.10 Nlocal: 9000.00 ave 9002 max 8998 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 24134.2 ave 24184 max 24062 min Histogram: 1 0 0 0 0 0 1 1 0 1 Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 12462451 Ave neighs/atom = 346.17919 Ave special neighs/atom = 2.0000000 Neighbor list builds = 9 Dangerous builds = 6 Total wall time: 0:00:05