#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1928 = # 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.8193e-13 5784 2 103.7 8.87184e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.55 | 13.5 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 -338.05327 138406.7 0.6276451 296.67718 29.773861 41.191761 0 0 16247.018 11137.663 -76.429471 -152455.46 -124999.81 3942.3802 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.28869e-06 5784 2 103.7 8.8648e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.29799e-06 5784 2 103.7 9.90702e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.19542e-06 5784 2 103.7 0.000103012 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.39094e-06 5784 2 103.7 9.4246e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.3978e-06 5784 2 103.7 8.92087e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.19813e-06 5784 2 103.7 0.000100777 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.34668e-06 5784 2 103.7 0.00010892 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.13052e-06 5784 2 103.7 9.17287e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.10451e-06 5784 2 103.7 9.77187e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.2617e-06 5784 2 103.7 9.27301e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.49186e-06 5784 2 103.7 0.000108124 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.24423e-06 5784 2 103.7 9.94562e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.5602e-06 5784 2 103.7 0.000103484 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.47869e-06 5784 2 103.7 0.000105269 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.24073e-06 5784 2 103.7 9.24928e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.04808e-06 5784 2 103.7 9.43761e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.14506e-06 5784 2 103.7 9.76234e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.19453e-06 5784 2 103.7 9.714e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.90192e-06 5784 2 103.7 0.000151215 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.4199e-06 5784 2 103.7 0.000112474 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.00246e-06 5784 2 103.7 8.80066e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.84297e-06 5784 2 103.7 0.00011061 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.65975e-06 5784 2 103.7 0.000107952 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.11927e-06 5784 2 103.7 9.20836e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.4341e-06 5784 2 103.7 9.76435e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.30388e-06 5784 2 103.7 0.000101549 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.21834e-06 5784 2 103.7 9.19899e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.19186e-06 5784 2 103.7 9.99972e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.51809e-06 5784 2 103.7 0.000109032 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.08068e-06 5784 2 103.7 9.04296e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.07813e-06 5784 2 103.7 9.21063e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.34731e-06 5784 2 103.7 0.000103043 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.41324e-06 5784 2 103.7 8.68481e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.12765e-06 5784 2 103.7 0.000103187 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.31199e-06 5784 2 103.7 0.000102177 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.43316e-06 5784 2 103.7 0.000112655 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.09063e-06 5784 2 103.7 8.84731e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.25077e-06 5784 2 103.7 9.30304e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.51193e-06 5784 2 103.7 9.78086e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.06096e-06 5784 2 103.7 9.15473e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.43353e-06 5784 2 103.7 0.000105295 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.65018e-06 5784 2 103.7 0.000103585 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.19342e-06 5784 2 103.7 9.82691e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.08958e-06 5784 2 103.7 9.27417e-05 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.23691e-06 5784 2 103.7 0.000102809 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.24536e-06 5784 2 103.7 9.32623e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.14249e-06 5784 2 103.7 9.57894e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.13584e-06 5784 2 103.7 9.59224e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.31894e-06 5784 2 103.7 9.48405e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.27241e-06 5784 2 103.7 9.43309e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.08307e-06 5784 2 103.7 9.11351e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.07142e-06 5784 2 103.7 9.32974e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.3746e-06 5784 2 103.7 8.98064e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.41271e-06 5784 2 103.7 0.00011128 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.19011e-06 5784 2 103.7 9.14464e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.17293e-06 5784 2 103.7 9.3466e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.38557e-06 5784 2 103.7 0.000102755 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.0837e-06 5784 2 103.7 9.34104e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.24132e-06 5784 2 103.7 0.000116792 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.27061e-06 5784 2 103.7 9.30339e-05 1928 3000000 3000000 -228.4903 138406.7 0.6276451 299.15355 27.09362 40.819856 0 0 16330.4 11204.503 -76.429471 -152464.56 -124861.75 3975.2874 Loop time of 25168.8 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.298 ns/day, 2.330 hours/ns, 119.195 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.272 | 7660.2 | 18045 |8696.8 | 30.44 Bond | 2.527 | 5.8768 | 12.895 | 134.0 | 0.02 Kspace | 3944.4 | 14385 | 22125 |6380.1 | 57.15 Neigh | 1221.4 | 1227.6 | 1237.2 | 14.4 | 4.88 Comm | 333.52 | 660.67 | 867.39 | 779.0 | 2.62 Output | 0.010924 | 0.012609 | 0.014016 | 0.8 | 0.00 Modify | 1014.1 | 1170 | 1393.7 | 438.3 | 4.65 Other | | 59.63 | | | 0.24 Nlocal: 199.594 ave 410 max 0 min Histogram: 14 2 0 0 0 0 0 0 4 12 Nghost: 3933.5 ave 7263 max 554 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 90504.7 ave 226725 max 0 min Histogram: 16 0 0 0 0 2 2 2 8 2 Total # of neighbors = 2896151 Ave neighs/atom = 453.44465 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145137 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.27061e-06 5784 2 103.7 9.30339e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.55 | 13.51 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 -228.07829 138406.7 0.6276451 299.15355 27.09362 40.819856 0 0 16330.4 11204.503 -76.429471 -152464.56 -124861.75 3975.2874 Loop time of 7.4985e-06 on 32 procs for 0 steps with 6387 atoms 115.0% 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 | | 7.498e-06 | | |100.00 Nlocal: 199.594 ave 410 max 0 min Histogram: 14 2 0 0 0 0 0 0 4 12 Nghost: 3933.5 ave 7263 max 554 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 90504.7 ave 226725 max 0 min Histogram: 16 0 0 0 0 2 2 2 8 2 Total # of neighbors = 2896151 Ave neighs/atom = 453.44465 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 18:48:02