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) 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 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 = 34263 16000 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) = 13.1 | 13.1 | 13.1 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 -14094.858 428.79175 300 296.65013 -16589.155 0 -13937.267 547.40809 400 303.82993 -16625.014 0 -13908.942 237.957 500 298.00206 -16716.893 0 -14052.919 231.33112 Loop time of 12.5516 on 4 procs for 500 steps with 4500 atoms Performance: 6.884 ns/day, 3.487 hours/ns, 39.836 timesteps/s 94.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.739 | 7.9051 | 8.2663 | 7.5 | 62.98 Bond | 0.00061631 | 0.00064486 | 0.00070524 | 0.0 | 0.01 Kspace | 2.7001 | 3.0573 | 3.2239 | 11.9 | 24.36 Neigh | 1.1736 | 1.174 | 1.1743 | 0.0 | 9.35 Comm | 0.18222 | 0.1869 | 0.19248 | 0.8 | 1.49 Output | 0.00017595 | 0.00032246 | 0.00076079 | 0.0 | 0.00 Modify | 0.20354 | 0.20467 | 0.20652 | 0.2 | 1.63 Other | | 0.02259 | | | 0.18 Nlocal: 1125 ave 1132 max 1114 min Histogram: 1 0 0 0 0 0 1 1 0 1 Nghost: 12241 ave 12298 max 12196 min Histogram: 2 0 0 0 0 0 0 1 0 1 Neighs: 650366 ave 671163 max 631441 min Histogram: 1 0 0 1 0 1 0 0 0 1 Total # of neighbors = 2601464 Ave neighs/atom = 578.103 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 = 34263 16000 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) = 13.96 | 13.96 | 13.96 Mbytes Step Temp E_pair E_mol TotEng Press 0 298.00206 -16716.893 0 -14052.919 231.44272 100 307.28155 -16760.647 0 -14013.72 452.38436 200 299.05168 -16674.695 0 -14001.338 177.44237 300 292.7564 -16573.946 0 -13956.865 122.27796 400 299.2644 -16578.318 0 -13903.059 482.03304 500 296.04028 -16623.179 0 -13976.742 89.968145 600 300.30911 -16664.206 0 -13979.608 132.70079 700 292.39517 -16703.749 0 -14089.897 825.267 800 298.75851 -16661.684 0 -13990.948 468.68671 900 301.55689 -16644.846 0 -13949.093 -72.16965 1000 298.2852 -16682.077 0 -14015.572 0.69725342 Loop time of 32.3106 on 4 procs for 1000 steps with 4500 atoms Performance: 5.348 ns/day, 4.488 hours/ns, 30.950 timesteps/s 96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.647 | 15.876 | 16.119 | 4.3 | 49.13 Bond | 0.0011718 | 0.0012704 | 0.001348 | 0.2 | 0.00 Kspace | 5.286 | 5.5364 | 5.7729 | 7.5 | 17.13 Neigh | 2.3892 | 2.3962 | 2.3991 | 0.3 | 7.42 Comm | 0.34641 | 0.35514 | 0.35988 | 0.9 | 1.10 Output | 0.00047851 | 0.00069892 | 0.0013568 | 0.0 | 0.00 Modify | 8.0882 | 8.0963 | 8.1047 | 0.3 | 25.06 Other | | 0.04887 | | | 0.15 Nlocal: 1125 ave 1137 max 1114 min Histogram: 1 1 0 0 0 0 0 1 0 1 Nghost: 12206.2 ave 12239 max 12169 min Histogram: 1 0 1 0 0 0 0 0 1 1 Neighs: 650464 ave 655962 max 641444 min Histogram: 1 0 0 0 0 0 0 2 0 1 FullNghs: 1.30095e+06 ave 1.31925e+06 max 1.28413e+06 min Histogram: 1 0 1 0 0 0 1 0 0 1 Total # of neighbors = 5203786 Ave neighs/atom = 1156.4 Ave special neighs/atom = 2 Neighbor list builds = 94 Dangerous builds = 0 Total wall time: 0:00:45