#------------------------------------------------------------------------------- # 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2812 = # 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) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.991932 0.808629 8436 2 97.0726 46.0985 2812 Per MPI rank memory allocation (min/avg/max) = 13.91 | 14.04 | 14.18 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 13941.586 93962.523 1.2789064 429.73544 29.024937 169.45257 0 0 22332.819 52597.326 -220.49494 -205873.42 -130744.8 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.30677e-06 8436 2 103.7 9.62874e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.36971e-06 8436 2 103.7 9.67518e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.66305e-06 8436 2 103.7 0.000101642 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.20072e-06 8436 2 103.7 0.000110947 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.33661e-06 8436 2 103.7 9.70642e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.21205e-06 8436 2 103.7 0.000117971 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.18037e-06 8436 2 103.7 0.000110775 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.25616e-06 8436 2 103.7 9.48523e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.27985e-06 8436 2 103.7 0.000103384 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.46011e-06 8436 2 103.7 0.000107429 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.84639e-06 8436 2 103.7 0.000123635 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.11633e-06 8436 2 103.7 0.00010724 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.17456e-06 8436 2 103.7 0.0001032 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.28157e-06 8436 2 103.7 0.000114882 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.08423e-06 8436 2 103.7 9.58789e-05 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13322e-06 8436 2 103.7 9.82739e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.31904e-06 8436 2 103.7 0.000120096 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.56869e-06 8436 2 103.7 0.000108475 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.4532e-06 8436 2 103.7 0.000114684 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.47564e-06 8436 2 103.7 0.000105125 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.48382e-06 8436 2 103.7 8.92572e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.31725e-06 8436 2 103.7 0.000103669 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28335e-06 8436 2 103.7 9.03593e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.22238e-06 8436 2 103.7 0.000101588 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.14713e-06 8436 2 103.7 9.49182e-05 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.4609e-06 8436 2 103.7 9.94989e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.16228e-06 8436 2 103.7 0.000105895 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.20194e-06 8436 2 103.7 9.79221e-05 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.60446e-06 8436 2 103.7 0.0001112 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.92658e-06 8436 2 103.7 0.000134516 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.1547e-06 8436 2 103.7 9.66996e-05 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.61481e-06 8436 2 103.7 0.000116344 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.15444e-06 8436 2 103.7 9.37091e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.36761e-06 8436 2 103.7 9.69212e-05 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.11631e-06 8436 2 103.7 9.91485e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.11537e-06 8436 2 103.7 8.69183e-05 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.15801e-06 8436 2 103.7 8.96951e-05 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.44659e-06 8436 2 103.7 9.32941e-05 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.16784e-06 8436 2 103.7 0.000103051 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.56847e-06 8436 2 103.7 0.00010615 2812 2000000 2000000 2154.0663 93962.523 1.2789064 294.4886 56.884749 87.973922 0 0 19495.231 46045.138 -220.49494 -206913.68 -141228.45 5596.0679 Loop time of 24536.7 on 16 procs for 2000000 steps with 9188 atoms Performance: 7.043 ns/day, 3.408 hours/ns, 81.510 timesteps/s 99.3% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16286 | 17007 | 17804 | 261.2 | 69.31 Bond | 4.3228 | 8.7689 | 13.21 | 84.9 | 0.04 Kspace | 3920.7 | 4731.8 | 5445.4 | 494.1 | 19.28 Neigh | 973.77 | 975.31 | 976.61 | 3.7 | 3.97 Comm | 773.31 | 792.93 | 809.44 | 37.3 | 3.23 Output | 0.014978 | 0.016838 | 0.018502 | 0.9 | 0.00 Modify | 959.06 | 963.69 | 969.26 | 9.8 | 3.93 Other | | 57.52 | | | 0.23 Nlocal: 574.25 ave 599 max 549 min Histogram: 1 1 2 1 1 3 4 1 0 2 Nghost: 9033.81 ave 9126 max 8897 min Histogram: 2 0 0 1 2 3 1 2 4 1 Neighs: 322509 ave 343911 max 307013 min Histogram: 2 2 3 0 4 0 3 0 1 1 Total # of neighbors = 5160140 Ave neighs/atom = 561.61733 Ave special neighs/atom = 1.9037875 Neighbor list builds = 98769 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) = 0.2557377 grid = 27 27 54 stencil order = 5 estimated absolute RMS force accuracy = 0.0032430487 estimated relative force accuracy = 9.7663448e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.56847e-06 8436 2 103.7 0.00010615 2812 Per MPI rank memory allocation (min/avg/max) = 13.91 | 14.12 | 14.19 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 2154.8125 93962.523 1.2789064 294.4886 56.884749 87.973922 0 0 19495.231 46045.138 -220.49494 -206913.68 -141228.45 5596.0679 Loop time of 4.13725e-06 on 16 procs for 0 steps with 9188 atoms 120.9% 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 | | 4.137e-06 | | |100.00 Nlocal: 574.25 ave 599 max 549 min Histogram: 1 1 2 1 1 3 4 1 0 2 Nghost: 9033.81 ave 9126 max 8897 min Histogram: 2 0 0 1 2 3 1 2 4 1 Neighs: 322509 ave 343911 max 307013 min Histogram: 2 2 3 0 4 0 3 0 1 1 Total # of neighbors = 5160140 Ave neighs/atom = 561.61733 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out