#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3968 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1 fix 3 movable ave/time 200 1 200 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00254 0.762326 11904 2 97.5667 38.403 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.18 | 15.84 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 4467.2663 139006.3 1.4192018 417.33588 117.37395 708.83542 0 0 42503.293 14962.287 -396.67289 -379342.84 -321051.05 12355.398 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.41538e-06 11904 2 103.7 0.000106862 3968 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.16896e-06 11904 2 103.7 9.04833e-05 3968 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.10443e-06 11904 2 103.7 9.30589e-05 3968 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.1678e-06 11904 2 103.7 9.47816e-05 3968 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.21558e-06 11904 2 103.7 9.29426e-05 3968 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.39572e-06 11904 2 103.7 0.000107429 3968 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.35008e-06 11904 2 103.7 9.54441e-05 3968 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.55196e-06 11904 2 103.7 9.06503e-05 3968 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.21258e-06 11904 2 103.7 9.5682e-05 3968 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.35935e-06 11904 2 103.7 9.62893e-05 3968 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.23784e-06 11904 2 103.7 9.08947e-05 3968 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.25748e-06 11904 2 103.7 0.000101314 3968 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.29511e-06 11904 2 103.7 9.44434e-05 3968 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.35963e-06 11904 2 103.7 0.000104246 3968 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.41133e-06 11904 2 103.7 9.08201e-05 3968 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.55481e-06 11904 2 103.7 9.69317e-05 3968 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.04975e-06 11904 2 103.7 9.77678e-05 3968 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.10667e-06 11904 2 103.7 9.18275e-05 3968 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.36998e-06 11904 2 103.7 9.7093e-05 3968 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.35947e-06 11904 2 103.7 9.97255e-05 3968 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.43091e-06 11904 2 103.7 9.83006e-05 3968 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.26052e-06 11904 2 103.7 0.000100403 3968 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.25363e-06 11904 2 103.7 9.90321e-05 3968 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.19476e-06 11904 2 103.7 0.000103399 3968 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.22592e-06 11904 2 103.7 9.77973e-05 3968 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.45726e-06 11904 2 103.7 9.30982e-05 3968 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.14948e-06 11904 2 103.7 9.05441e-05 3968 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.2978e-06 11904 2 103.7 9.40845e-05 3968 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.1877e-06 11904 2 103.7 9.96938e-05 3968 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.65061e-06 11904 2 103.7 9.08475e-05 3968 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.56401e-06 11904 2 103.7 9.6813e-05 3968 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.21016e-06 11904 2 103.7 9.85601e-05 3968 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.57007e-06 11904 2 103.7 0.00012728 3968 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.1922e-06 11904 2 103.7 9.13882e-05 3968 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.57507e-06 11904 2 103.7 0.000108043 3968 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.27162e-06 11904 2 103.7 9.43844e-05 3968 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.25256e-06 11904 2 103.7 9.72211e-05 3968 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.21487e-06 11904 2 103.7 0.00011422 3968 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.3822e-06 11904 2 103.7 9.81968e-05 3968 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.73079e-06 11904 2 103.7 0.000115265 3968 2000000 2000000 -121.07271 139006.3 1.4192018 295.57401 343.75006 654.49337 0 0 37647.164 22777.629 -396.67289 -380037.19 -318614.15 8750.5883 Loop time of 43953.9 on 16 procs for 2000000 steps with 13901 atoms Performance: 3.931 ns/day, 6.105 hours/ns, 45.502 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22344 | 26523 | 33863 |2603.2 | 60.34 Bond | 9.8182 | 31.392 | 72.197 | 432.6 | 0.07 Kspace | 6078.9 | 13456 | 17664 |3677.6 | 30.61 Neigh | 1844.4 | 1845.7 | 1847.4 | 2.4 | 4.20 Comm | 821.32 | 856.97 | 892.26 | 72.7 | 1.95 Output | 0.021212 | 0.023792 | 0.026095 | 1.0 | 0.00 Modify | 1136.4 | 1159.6 | 1181.4 | 43.7 | 2.64 Other | | 80.6 | | | 0.18 Nlocal: 868.812 ave 1006 max 783 min Histogram: 3 4 2 3 0 0 0 0 0 4 Nghost: 10626 ave 11163 max 9860 min Histogram: 4 0 0 0 0 3 1 4 0 4 Neighs: 502235 ave 650091 max 409950 min Histogram: 2 3 7 0 0 0 0 0 0 4 Total # of neighbors = 8035756 Ave neighs/atom = 578.07035 Ave special neighs/atom = 2.0450327 Neighbor list builds = 99860 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.73079e-06 11904 2 103.7 0.000115265 3968 Per MPI rank memory allocation (min/avg/max) = 14.89 | 15.37 | 15.85 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 2000000 2000000 -119.88684 139006.3 1.4192018 295.57401 343.75006 654.49337 0 0 37647.164 22777.629 -396.67289 -380037.19 -318614.15 8750.5883 Loop time of 4.60419e-06 on 16 procs for 0 steps with 13901 atoms 122.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.604e-06 | | |100.00 Nlocal: 868.812 ave 1006 max 783 min Histogram: 3 4 2 3 0 0 0 0 0 4 Nghost: 10626 ave 11163 max 9860 min Histogram: 4 0 0 0 0 3 1 4 0 4 Neighs: 502235 ave 650091 max 409950 min Histogram: 2 3 7 0 0 0 0 0 0 4 Total # of neighbors = 8035756 Ave neighs/atom = 578.07035 Ave special neighs/atom = 2.0450327 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out