LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom) units real atom_style full read_data data.spce orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) 1 by 1 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 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors pair_style lj/cut/coul/long 12.0 12.0 pair_coeff * * 0.0 1.0 pair_coeff 1 1 0.15535 3.166 kspace_style pppm 1.0e-6 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 # need to set bond/angle inclusion to > 0.0 # so that intramolecular pairs are included in neighbor lists (required for second ADF) special_bonds lj/coul 1.0e-100 1.0e-100 1.0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 2 = max # of special neighbors neighbor 2.0 bin timestep 2.0 neigh_modify every 1 delay 2 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 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 velocity all create 300.0 6244325 thermo 100 run 500 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.000394674 estimated relative force accuracy = 1.18855e-06 using double precision FFTs 3d grid and FFT values/proc = 103823 64000 Neighbor list info ... update every 1 steps, delay 2 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 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) = 35.36 | 35.36 | 35.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -16692.369 0 -14010.534 -112.83562 100 283.44729 -17008.717 0 -14474.854 -162.06378 200 298.75279 -16765.543 0 -14094.858 428.7917 300 296.65014 -16589.155 0 -13937.267 547.40796 400 303.82963 -16625.011 0 -13908.942 237.93694 500 298.00057 -16716.887 0 -14052.926 231.55014 Loop time of 38.2796 on 1 procs for 500 steps with 4500 atoms Performance: 2.257 ns/day, 10.633 hours/ns, 13.062 timesteps/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.428 | 28.428 | 28.428 | 0.0 | 74.26 Bond | 0.00056672 | 0.00056672 | 0.00056672 | 0.0 | 0.00 Kspace | 5.3161 | 5.3161 | 5.3161 | 0.0 | 13.89 Neigh | 4.1185 | 4.1185 | 4.1185 | 0.0 | 10.76 Comm | 0.12788 | 0.12788 | 0.12788 | 0.0 | 0.33 Output | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00 Modify | 0.26748 | 0.26748 | 0.26748 | 0.0 | 0.70 Other | | 0.02102 | | | 0.05 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21248 ave 21248 max 21248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60146e+06 ave 2.60146e+06 max 2.60146e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2601459 Ave neighs/atom = 578.102 Ave special neighs/atom = 2 Neighbor list builds = 45 Dangerous builds = 0 reset_timestep 0 compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector run 1000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.000394674 estimated relative force accuracy = 1.18855e-06 using double precision FFTs 3d grid and FFT values/proc = 103823 64000 Neighbor list info ... update every 1 steps, delay 2 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (3) compute adf, occasional attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 36.67 | 36.67 | 36.67 Mbytes Step Temp E_pair E_mol TotEng Press 0 298.00057 -16716.887 0 -14052.926 231.6595 100 307.31045 -16761.022 0 -14013.835 449.26027 200 299.52847 -16679.165 0 -14001.546 148.44719 300 293.68499 -16583.548 0 -13958.166 140.79069 400 306.76266 -16658.573 0 -13916.284 481.26934 500 294.75648 -16640.446 0 -14005.485 585.05479 600 303.19282 -16629.985 0 -13919.608 328.23667 700 300.28233 -16590.155 0 -13905.797 -176.71076 800 292.36899 -16620.826 0 -14007.208 -194.83408 900 304.92802 -16633.331 0 -13907.443 479.49808 1000 300.64529 -16598.233 0 -13910.63 904.96137 Loop time of 107.579 on 1 procs for 1000 steps with 4500 atoms Performance: 1.606 ns/day, 14.942 hours/ns, 9.295 timesteps/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58.928 | 58.928 | 58.928 | 0.0 | 54.78 Bond | 0.0012271 | 0.0012271 | 0.0012271 | 0.0 | 0.00 Kspace | 10.698 | 10.698 | 10.698 | 0.0 | 9.94 Neigh | 8.7649 | 8.7649 | 8.7649 | 0.0 | 8.15 Comm | 0.2608 | 0.2608 | 0.2608 | 0.0 | 0.24 Output | 0.00043702 | 0.00043702 | 0.00043702 | 0.0 | 0.00 Modify | 28.883 | 28.883 | 28.883 | 0.0 | 26.85 Other | | 0.04301 | | | 0.04 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21275 ave 21275 max 21275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60217e+06 ave 2.60217e+06 max 2.60217e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5.20478e+06 ave 5.20478e+06 max 5.20478e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5204784 Ave neighs/atom = 1156.62 Ave special neighs/atom = 2 Neighbor list builds = 94 Dangerous builds = 0 Total wall time: 0:02:26