#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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 300000 300000 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 v_surfacetension file 2.5_averages.txt off 1 fix 3 movable ave/time 300 1 300 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 v_surfacetension file 2.5_instantaneous.txt restart 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24710655 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033650847 estimated relative force accuracy = 1.0133853e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 9.94316e-13 6000 1 103.7 9.0651e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.301 | 9.725 | 10.6 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 -236.42745 120435.32 0.49678445 299.8936 0 0 0 0 5047.8968 75576.711 -51.790667 -101689.99 -21065.383 3574.8095 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.31729e-06 6000 1 103.7 0.000119143 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.28558e-06 6000 1 103.7 9.67281e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.21278e-06 6000 1 103.7 0.000108305 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.1425e-06 6000 1 103.7 9.84076e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.21887e-06 6000 1 103.7 0.000107561 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.16147e-06 6000 1 103.7 0.000102425 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.33544e-06 6000 1 103.7 9.70357e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.19106e-06 6000 1 103.7 9.47842e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.60047e-06 6000 1 103.7 0.000121104 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.95484e-06 6000 1 103.7 0.000145208 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.66476e-06 6000 1 103.7 0.000117775 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.27521e-06 6000 1 103.7 9.91162e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.23472e-06 6000 1 103.7 9.55758e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.31932e-06 6000 1 103.7 8.96114e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.22436e-06 6000 1 103.7 9.57777e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.13567e-06 6000 1 103.7 9.72674e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.25634e-06 6000 1 103.7 9.48158e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.2353e-06 6000 1 103.7 9.24109e-05 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.73023e-06 6000 1 103.7 0.000124435 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.12133e-06 6000 1 103.7 0.000105842 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.54289e-06 6000 1 103.7 0.00010117 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.36963e-06 6000 1 103.7 0.000114644 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.29008e-06 6000 1 103.7 9.29026e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.50128e-06 6000 1 103.7 0.000110338 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.40293e-06 6000 1 103.7 0.000102193 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.644e-06 6000 1 103.7 0.000104998 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.24883e-06 6000 1 103.7 0.000100908 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.32294e-06 6000 1 103.7 0.000100875 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.36041e-06 6000 1 103.7 8.95189e-05 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.44242e-06 6000 1 103.7 0.000115426 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.10025e-06 6000 1 103.7 0.000109564 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.14395e-06 6000 1 103.7 9.28837e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.47873e-06 6000 1 103.7 0.000105908 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.21718e-06 6000 1 103.7 0.000108637 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.30497e-06 6000 1 103.7 9.36155e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.08236e-06 6000 1 103.7 9.07946e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.20573e-06 6000 1 103.7 9.54779e-05 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.2305e-06 6000 1 103.7 0.000105682 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.68891e-06 6000 1 103.7 0.000112083 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.23781e-06 6000 1 103.7 0.000124432 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.16206e-06 6000 1 103.7 0.000109119 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.61719e-06 6000 1 103.7 0.000102641 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.34896e-06 6000 1 103.7 0.0001063 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.06741e-06 6000 1 103.7 9.25669e-05 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.18623e-06 6000 1 103.7 0.000110985 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.24027e-06 6000 1 103.7 0.000101003 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.15167e-06 6000 1 103.7 9.93458e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.18501e-06 6000 1 103.7 9.29936e-05 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.47114e-06 6000 1 103.7 9.93019e-05 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.17748e-06 6000 1 103.7 9.1919e-05 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.29252e-06 6000 1 103.7 8.93031e-05 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.14237e-06 6000 1 103.7 0.000104041 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.79069e-06 6000 1 103.7 0.0001383 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.63686e-06 6000 1 103.7 0.000126344 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.24878e-06 6000 1 103.7 9.38668e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.30058e-06 6000 1 103.7 9.45718e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.92303e-06 6000 1 103.7 0.000148133 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.20885e-06 6000 1 103.7 9.31451e-05 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.24304e-06 6000 1 103.7 0.000113207 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.12382e-06 6000 1 103.7 9.99697e-05 2000 3000000 3000000 84.708589 120435.32 0.49678445 298.95292 0 0 0 0 5173.5281 75519.281 -51.790667 -101695.64 -21002.829 3563.5964 Loop time of 25006.4 on 32 procs for 3000000 steps with 6000 atoms Performance: 10.365 ns/day, 2.315 hours/ns, 119.969 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.852 | 7746.2 | 18358 |8670.1 | 30.98 Bond | 2.4005 | 3.5617 | 7.5038 | 57.3 | 0.01 Kspace | 3645.5 | 14320 | 22172 |6413.6 | 57.27 Neigh | 1123.9 | 1131.1 | 1141.9 | 17.6 | 4.52 Comm | 301.54 | 669.61 | 891.66 | 826.2 | 2.68 Output | 0.010347 | 0.012089 | 0.013706 | 0.9 | 0.00 Modify | 925.97 | 1086.5 | 1325.4 | 471.6 | 4.34 Other | | 49.08 | | | 0.20 Nlocal: 187.5 ave 396 max 0 min Histogram: 12 3 1 0 0 0 1 1 3 11 Nghost: 4066.62 ave 7677 max 458 min Histogram: 4 4 0 4 4 4 4 0 4 4 Neighs: 92919.4 ave 227810 max 0 min Histogram: 16 0 0 0 0 2 4 0 3 7 Total # of neighbors = 2973422 Ave neighs/atom = 495.57033 Ave special neighs/atom = 2 Neighbor list builds = 148938 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 2.5.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) = 0.24710655 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033650847 estimated relative force accuracy = 1.0133853e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.12382e-06 6000 1 103.7 9.99697e-05 2000 Per MPI rank memory allocation (min/avg/max) = 8.427 | 9.668 | 10.6 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 3000000 3000000 85.050042 120435.32 0.49678445 298.95292 0 0 0 0 5173.5281 75519.281 -51.790667 -101695.64 -21002.829 3563.5964 Loop time of 1.05295e-05 on 32 procs for 0 steps with 6000 atoms 108.6% CPU use with 32 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 | | 1.053e-05 | | |100.00 Nlocal: 187.5 ave 396 max 0 min Histogram: 12 3 1 0 0 0 1 1 3 11 Nghost: 4066.62 ave 7677 max 458 min Histogram: 4 4 0 4 4 4 4 0 4 4 Neighs: 92919.4 ave 227810 max 0 min Histogram: 16 0 0 0 0 2 4 0 3 7 Total # of neighbors = 2973422 Ave neighs/atom = 495.57033 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 13:51:55